bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographically Biased Composition of NetMHCpan Training Datasets and Evaluation of MHC-Peptide Binding Prediction Accuracy on Novel Alleles
Authors: Atkins Thomas Karl , Solanki Arnav , Vasmatzis George , Cornette James , Riedel Marc 
Published: September 2023

AbstractBias in neural network model training datasets has been observed to decrease prediction accuracy for groups underrepresented in training data. Thus, investigating the composition of training datasets used in machine learning models with health-care applications is vital to ensure equity. Two such machine learning models are NetMHCpan-4.1 and NetMHCIIpan-4.0, used to predict antigen binding scores to major histocompatibility complex class I and II molecules, respectively. As antigen presentation is a critical step in mounting the adaptive immune response, previous work has used these or similar predictions models in a broad array of applications, from explaining asymptomatic viral infection to cancer neoantigen prediction. However, these models have also been shown to be biased toward hydrophobic peptides, suggesting the network could also contain other sources of bias. Here, we report the composition of the networks’ training datasets are heavily biased toward European Caucasian individuals and against Asian and Pacific Islander individuals. We test the ability of NetMHCpan-4.1 and NetMHCpan-4.0 to distinguish true binders from randomly generated peptides on alleles not included in the training datasets. Unexpectedly, we fail to find evidence that the disparities in training data lead to a meaningful difference in prediction quality for alleles not present in the training data. We attempt to explain this result by mapping the HLA sequence space to determine the sequence diversity of the training dataset. Furthermore, we link the residues which have the greatest impact on NetMHCpan predictions to structural features for three alleles (HLA-A*34:01, HLA-C*04:03, HLA-DRB1*12:02).
Recurrent circuits encode visual center-surround computations in the mouse superior colliculus
Authors: Cui Peng , Song Kuisong , Mariatos-Metaxas Dimitris , Isla Arturo G. , Femenia Teresa , Lazaridis Iakovos , Meletis Konstantinos , Kumar Arvind , Kardamakis Andreas A. 
Published: September 2023

AbstractCenter-surround interactions are fundamental to visual saliency computation, but debate continues over whether and how subcortical visual circuits actively contribute. To address this, we developed an optogenetic approach to delineate the visual center and surround zones of individual neurons in the superficial layer of the superior colliculus (SCs) using only retinal ganglion cell input. Using whole-cell recordings, we demonstrate that surround network activation suppresses center excitability, indicating that SCs circuitry is self-sufficient in driving center-surround dynamics. Through cell-type-specific trans-synaptic tracing and large-scale modeling, we identified an SCs-based circuit with two key motifs driving surround modulation: recurrent excitation and feedback inhibition. We propose that subcortical visual circuits in the SCs have evolved to perform surround suppression alongside retinal and cortical suppression, facilitating the distribution of parallel saliency computations across different levels.Significance statementThis study questions the notion that the superior colliculus (SC) merely acts as a passive recipient of saliency information from upstream circuits. We demonstrate that the SC can independently generate center-surround interactions that could contribute to visual saliency through local circuits without top-down input. This ability represents a computation that has been conserved since the dawn of vertebrate evolution. By mapping these interactions, we reveal that the mouse SC actively induces visual surround suppression. These findings suggest that phylogenetically older circuits in the SC may play a more independent role in active vision than previously acknowledged, prompting a reevaluation of visual saliency processing across subcortical brain regions.
MCT4 and CD147 co-localize with MMP14 in invadopodia and autolysosomes and collectively stimulate breast cancer cell invasion by increasing extracellular matrix degradation
Authors: Meng Signe , Sørensen Ester E. , Ponniah Muthulakshmi , Thorlacius-Ussing Jeppe , Crouigneau Roxane , Borre Magnus T. , Willumsen Nicholas , Flinck Mette , Pedersen Stine F. 
Published: September 2023

AbstractThe lactate-proton cotransporter MCT4 and its chaperone CD147 are upregulated in breast cancers, correlating with decreased patient survival. Here, we test the hypothesis that MCT4 and CD147 favor breast cancer invasion through interdependent effects on extracellular matrix (ECM) degradation. MCT4 and CD147 expression and membrane localization were strongly reciprocally interdependent in MDA-MB-231 invasive breast cancer cells. Knockdown (KD) and overexpression (OE) of MCT4 and/or CD174 in- and decreased, respectively, migration, invasion, and fluorescent gelatin degradation. OE of both proteins increased gelatin degradation and appearance of the matrix metalloprotease (MMP)-generated collagen-I cleavage product reC1M more than each protein alone, suggesting a concerted role in ECM degradation. MCT4 and CD147 co-localized strongly with invadopodia markers at the plasma membrane and with MMP14, the lysosomal marker LAMP-1, and in some cases the autophagosome marker LC3, in F-actin-decorated, large intracellular vesicles.We conclude that MCT4 and CD147 reciprocally regulate each other and support migration and invasiveness of MDA-MB-231 breast cancer cells in an interdependent manner. Mechanistically, this involves the MCT4-CD147-dependent stimulation of ECM degradation and specifically of MMP-mediated collagen-I degradation. We suggest that the MCT4-CD147 complex is co-delivered to invadopodia with MMP14.
Mettl1-dependent m7G tRNA modification is essential for maintaining spermatogenesis and fertility inDrosophila melanogaster
Authors: Kaneko Shunya , Miyoshi Keita , Tomuro Kotaro , Terauchi Makoto , Kondo Shu , Tani Naoki , Ishiguro Kei-Ichiro , Toyoda Atsushi , Noguchi Hideki , Iwasaki Shintaro , Saito Kuniaki 
Published: September 2023

AbstractN7-methylguanosine (m7G) in the variable loop region of tRNA is catalyzed by METTL1/WDR4 heterodimer and stabilizes target tRNA. Here, we reveal essential functions of Mettl1 inDrosophilafertility. Knockout of Mettl1 (Mettl1-KO) lost the elongated spermatids and mature sperm, which was fully rescued by a Mettl1-transgene expression, but not a catalytic-dead Mettl1 transgene. This demonstrates that Mettl1-dependent m7G is required for spermatogenesis. Mettl1-KO resulted in a loss of m7G modification on a subset of tRNAs and a decreased level of tRNA expression. Strikingly, overexpression of the translational elongation factor, EF1α1, which can compete with the rapid tRNA decay (RTD) pathway inS. cerevisiae, significantly counteracted the sterility of Mettl1-KO males, supporting a critical role of m7G modification of tRNAs in spermatogenesis. Ribosome profiling showed that Mettl1-KO led to the ribosome stalling at codons decoded by tRNAs that were reduced in expression. Mettl1-KO also significantly reduced the translation efficiency of genes involved in elongated spermatid formation and sperm stability. These findings reveal a developmental role for m7G tRNA modifications and indicate that m7G modification-dependent tRNA stability differs among tissues.
Twisted plywood-like tissue formationin vitro. Does curvature do the twist?
Authors: Schamberger Barbara , Ehrig Sebastian , Dechat Thomas , Spitzer Silvia , Bidan Cécile M. , Fratzl Peter , Dunlop John W. C. , Roschger Andreas 
Published: September 2023

AbstractLittle is known about the contribution of 3D surface geometry on the development of multi-layered tissues containing fibrous extracellular matrix components such as those found in bone. Here we elucidate the role of curvature in the formation of chiral, twisted plywood-like structures. Tissues consisting of murine pre-osteoblast cells (MC3T3-E1) were grown on 3D scaffolds with constant mean curvature and negative Gaussian curvature for up to 32 days. Using 3D fluorescence microscopy, the influence of surface curvature on actin stress-fiber alignment and chirality was investigated. To gain mechanistic insights, also MC3T3-E1 cells deficient in nuclear A-type lamins or treated with drugs targeting cytoskeleton proteins were used in our study. We find that wild type cells grow multilayered tissue with fibers predominantly aligned along directions of negative curvature, but where subsequent layers twist in orientation with respect to older tissues with time. Fiber orientation is conserved below the tissue surface thus creating a twisted plywood like material. We further show that this directional organization strongly depends on structural components of the cells (A-type lamins, actin and myosin). Our data indicate the importance of substrate curvature in the formation of 3D tissues and provides new insights into the emergence of chirality.Significance StatementBiological tissues (like compact bone) often consist of multiple fibrous layers which are staggered with a twisting angle relative to each other, thereby improving mechanical performance. The underlying principles of how such tissues are formed and what determines the fiber direction are still debated. Here we report the formation of a twisted plywood-like tissue grownin vitroon constant mean and negative Gaussian curvature substrates and present evidence that for tissue consisting of pre-osteoblast like cells, surface curvature is a main determinant for fiber orientation.
Neuronal FOS reports synchronized activity of presynaptic neurons
Authors: Anisimova Margarita , Lamothe-Molina Paul J. , Franzelin Andreas , Aberra Aman S. , Hoppa Michael B. , Gee Christine E. , Oertner Thomas G. 
Published: September 2023

AbstractThe immediate early gene FOS is frequently used as a marker for highly active neurons. Implicit in this use is the assumption that there is a correlation between neuronal spiking and FOS expression. Here we use optogenetic stimulation of hippocampal neurons to investigate the relation between spike frequency and FOS expression, and report several surprising observations. First, FOS expression is cell-type specific, spiking CA2 pyramidal neurons rarely express FOS. Second, FOS has a U-shaped dependence on frequency: Spiking at 0.1 Hz is more effective than high frequency spiking (50 Hz) while intermediate frequencies do not induce FOS. Third, the pathway from spiking to FOS is not cell-autonomous. Instead, transmitter release and metabotropic glutamate receptor (mGluR) activation are required and, at 0.1 Hz, FOS is induced independently of CREB/calcineurin/MEK pathways. We propose that FOS does not primarily encode a neuron’s own spike frequency but indicates repeated participation in highly synchronized activity, e.g. sharp wave ripples.
Serial colonization shapes genetic variation and defines conservation units in Asian elephants
Authors: Khan Anubhab , Sil Maitreya , Thekaekara Tarsh , Garg Kritika M. , Sinha Ishani , Khurana Rupsy , Sukumar Raman , Ramakrishnan Uma 
Published: September 2023

AbstractAsian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analysed 34 whole genomes (between 11X - 32X) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern) India, Central India and three in Southern India. Our genetic data reveal signatures of serial colonisation, and a dilution of genetic diversity from north to south of India. The Northern populations diverged from other populations more than 70,000 years ago, have higher genetic diversity, and low inbreeding/high effective size (Pi = 0.0016±0.0001; FROH>1MB= 0.09±0.03). Two of three populations in Southern India (South of Palghat Gap: SPG, and South of Shencottah Gap:SSG) have low diversity and are inbred, with very low effective population sizes compared to current census sizes (Pi = 0.0014±0.00009 and 0.0015±0.0001; FROH>1MB= 0.25±0.09 and 0.17±0.02). Analyses of genetic load reveals purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the Southern populations and potential dilution of all deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity make these populations (SPG and SSG) high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to geographic signatures of serial founding events, even in large, highly mobile, endangered mammals.
Linking serotonergic median raphe input to dorsal CA1 with mnemonic functions
Authors: Gerdey Jill , Masseck Olivia Andrea 
Published: September 2023

AbstractThe role of serotonergic signaling within the hippocampus and its role in mnemonic function is still not well understood. We used optogenetics to specifically alter median raphe serotonin input to the dorsal CA1 subfield to investigate its role in hippocampus-dependent behavior. Unexpectedly, neither activation nor inhibition of serotonin release at dCA1 fiber terminals significantly modulated object recognition, spatial memory, or anxiety behavior. Nevertehless, we observed opposite effects of increased and decreased serotonergic input on spatial learning, and a marked reduction in the use of a direct search strategy in spatial navigation following activation of serotonergic terminals in dCA1, i.e. release of serotonin.Furthermore, since the 5-HT1Areceptor is one of the most abundant serotonergic receptors in CA1, we also optogenetically activated 5-HT1Apathways specifically in pyrdamidal neurons of dCA1. Activation of 5-HT1Asignaling significantly improved spatial memory without affecting object recognition or avoidance behavior. In conclusion, our data reveal modulatory effects of serotonin specifically on the acquisition of spatial memory.
Experimental nerve block study on painful withdrawal reflex responses in humans
Authors: Thorell Oumie , Mahns David A. , Otto Jan , Liljencrantz Jaquette , Svantesson Mats , Olausson Håkan , Nagi Saad S. 
Published: September 2023

AbstractThe nociceptive withdrawal reflex (NWR) is a protective limb withdrawal response triggered by painful stimuli, used to assess spinal nociceptive excitability. Conventionally, the NWR is understood as having two reflex responses: a short-latency Aβ-mediated response, considered tactile, and a longer-latency Aδ-mediated response, considered nociceptive. However, nociceptors with conduction velocities similar to Aβ tactile afferents have been identified in human skin. In this study, we investigated the effect of a preferential conduction block of Aβ fibers on pain perception and NWR signaling evoked by intradermal electrical stimulation in healthy participants. We recorded a total of 198 NWR responses in the intact condition, and no dual reflex responses occurred within our latency bandwidth (50-150 ms). The current intensity required to evoke the NWR was magnitude higher than the perceptual pain threshold, indicating that NWR did not occur before pain was felt. In the block condition, when the Aβ-mediated tuning fork sensation was lost while Aδ-mediated nonpainful cooling was still detectable (albeit reduced), we observed that the reflex was abolished. Further, short-latency electrical pain intensity at pre-block thresholds was greatly reduced, with any residual pain sensation having a longer latency. Although electrical pain was unaffected at suprathreshold current intensities, the reflex could not be evoked despite a two-fold increase in the pre-block current intensity and a five-fold increase in the pre-block pulse duration. These observations lend support to the possible involvement of Aβ-fiber inputs in pain and reflex signaling.
Reliability of the TMS-evoked potential in dorsolateral prefrontal cortex
Authors: Gogulski Juha , Cline Christopher C. , Ross Jessica M. , Parmigiani Sara , Keller Corey J. 
Published: September 2023

AbstractBackgroundWe currently lack a robust and reliable method to probe cortical excitability noninvasively from the human dorsolateral prefrontal cortex (dlPFC), a region heavily implicated in psychiatric disorders. We recently found that the strength ofearlyandlocaldlPFC single pulse transcranial magnetic stimulation (TMS)-evoked potentials (EL-TEPs) varied widely depending on the anatomical subregion probed, with more medial regions eliciting stronger responses than anterolateral sites. Despite these differences inamplitudeof response, thereliabilityat each target is not known.ObjectiveTo evaluate the reliability of EL-TEPs across the dlPFC.MethodsIn 15 healthy subjects, we quantified within-session reliability of dlPFC EL-TEPs after single pulse TMS to six dlPFC subregions. We evaluated the concordance correlation coefficient (CCC) across targets and analytical parameters including time window, quantification method, region of interest, sensor-vs. source-space, and number of trials.ResultsAt least one target in the anterior and posterior dlPFC produced reliable EL-TEPs (CCC>0.7). The medial target was most reliable (CCC = 0.78) and the most anterior target was least reliable (CCC = 0.24). ROI size and type (sensor vs. source space) did not affect reliability. Longer (20-60 ms, CCC = 0.62) and later (30-60 ms, CCC = 0.61) time windows resulted in higher reliability compared to earlier and shorter (20-40 ms, CCC 0.43; 20-50 ms, CCC = 0.55) time windows. Peak-to-peak quantification resulted in higher reliability than the mean of the absolute amplitude. Reliable EL-TEPs (CCC up to 0.86) were observed using only 25 TMS trials for a medial dlPFC target.ConclusionsMedial TMS location, wider time window (20-60ms), and peak-to-peak quantification improved reliability. Highly reliable EL-TEPs can be extracted from dlPFC after only a small number of trials.HighlightsMedial dlPFC target improved EL-TEP reliability compared to anterior targets.After optimizing analytical parameters, at least one anterior and one posterior target was reliable (CCC>0.7).Longer (20-60 ms) and later (30-60 ms) time windows were more reliable than earlier and shorter (20-40 ms or 20-50 ms) latencies.Peak-to-peak quantification resulted in higher reliability compared to the mean of the absolute amplitude.As low as 25 trials can yield reliable EL-TEPs from the dlPFC.
Microbially-conjugated Bile Salts Found in Human Bile Activate the Bile Salt Receptors TGR5 and FXR
Authors: Ay Ümran , Leníček Martin , Haider Raphael S. , Classen Arno , van Eijk Hans , Koelfat Kiran V.K. , van der Kroft Gregory , Neumann Ulf. P. , Hoffmann Carsten , Bolm Carsten , Olde Damink Steven W.M. , Schaap Frank G. 
Published: September 2023

AbstractBackground & AimsBile salts of hepatic and microbial origin mediate inter-organ crosstalk in the gut-liver axis. Here, we assessed whether the newly discovered class of microbial bile salt conjugates (MBSCs), activate the main host bile salt receptors (TGR5 and FXR) and enter the human systemic and enterohepatic circulation.Approach & ResultsN-amidates of (chenodeoxy)cholic acid and leucine, tyrosine and phenylalanine were synthesized. Receptor activation was studied in cell-free and cell-based assays. MBSCs were quantified in mesenteric and portal blood and bile of patients undergoing pancreatic surgery. MBSCs were activating ligands of TGR5 as evidenced by recruitment of Gsαprotein, activation of a cAMP-driven reporter, and diminution of LPS-induced cytokine release from macrophages. Intestine- and liver-enriched FXR isoforms were both activated by MBSCs, provided that a bile salt importer was present. Affinity of MBSCs for TGR5 and FXR was not superior to host-derived bile salt conjugates. Individual MBSCs were generally not detected (i.e. <2.5 nmol/L) in human mesenteric or portal blood, but Leu- and Phe-variants were readily measurable in bile, where MBSCs comprised up to 213 ppm of biliary bile salts.ConclusionsMBSCs activate the cell surface receptor TGR5 and the transcription factor FXR, and are substrates for intestinal (ASBT) and hepatic (NTCP) transporters. Their entry into the human circulation is, however, non-substantial. Given low systemic levels and surplus of other equipotent bile salt species, the studied MBSCs are unlikely to have an impact on enterohepatic TGR5/FXR signaling in humans. Origin and function of biliary MBSCs remain to be determined.Graphical AbstractCreated withBioRender.com
Ring Array Illumination Microscopy: Combination of Super-Resolution with Large Field of View Imaging and long Working Distances
Authors: von Hase Johann , Birk Udo , Humbel Bruno M. , Liu Xiaomin , Failla Antonio V. , Cremer Christoph 
Published: September 2023

AbstractHere we present a novel fluorescence microscopy concept which enables a direct integration of Super-Resolution Microscopy (SRM) approaches (SIM/Nanosizing, STED, SMLM, MINFLUX, SIMFLUX) into microscopy systems with working distances (WD) up to the multicentimeter range while still allowing nanometer scale resolution at selected sites. This becomes possible by a “synthetic aperture” illumination mode with multiple, constructively interfering excitation beams positioned in a “Ring-Array” arrangement around a beam free interior zone containing instrumentation involved in complementary imaging modes. The feasibility of such a direct correlative microscopy method is validated by extensive numerical simulations; on the basis of these calculations, experimental implementation options are discussed. Such “Ring Array” illumination modes may be useful for various correlative microscopy methods, such as a direct combination of correlative light and electron microscopy in the same device (dCLEM); or a direct combination of low NA/large field-of-view widefield microscopy and super-resolution of selected sites in the same device (direct Correlative Opical Microscopy/dCOLM). Ring-Array supported correlative microscopy modes will open novel imaging perspectives in a variety of disciplines, from material sciences to biomedical applications.