bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of compact transcriptional effectors using high-throughput measurements in diverse contexts
Authors: Tycko Josh , Van Mike V. , Aradhana  , DelRosso Nicole , Yao David , Xu Xiaoshu , Ludwig Connor , Spees Kaitlyn , Liu Katherine , Hess Gaelen T , Gu Mingxin , Mukund Adi Xiyal , Suzuki Peter H. , Kamber Roarke A. , Qi Lei S. , Bintu Lacramioara , Bassik Michael C.
Published: May 2023

Human nuclear proteins contain >1000 transcriptional effector domains that can activate or repress transcription of target genes. We lack a systematic understanding of which effector domains regulate transcription robustly across genomic, cell-type, and DNA-binding domain (DBD) contexts. Here, we developed dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous targets, and tested effector function for a library containing 5092 nuclear protein Pfam domains across varied contexts. We find many effectors depend on target and DBD contexts, such as HLH domains that can act as either activators or repressors. We then confirm these findings and further map context dependencies of effectors drawn from unannotated protein regions using a larger library containing 114,288 sequences tiling chromatin regulators and transcription factors. To enable efficient perturbations, we select effectors that are potent in diverse contexts, and engineer (1) improved ZNF705 KRAB CRISPRi tools to silence promoters and enhancers, and (2) a compact human activator combination NFZ for better CRISPRa and inducible circuit delivery. Together, this effector-by-context functional map reveals context-dependence across human effectors and guides effector selection for robustly manipulating transcription.
Cryo-electron tomography reveals postsynaptic nanoblocks in excitatory synapses
Authors: Sun Rong , Allen James P , Wilson Liana , Haider Mariam , Alten Baris , Zhou Zimeng , Wang Xinyi , Zhou Qiangjun
Published: May 2023

The nanoscale organization of proteins within synapses is critical for maintaining and regulating synaptic transmission and plasticity. Here, we use cryogenic electron tomography to directly visualize the three-dimensional architecture and supramolecular organization of pre-cleft-postsynaptic components in their near-native cellular context in both synaptosomes from rat hippocampi and synapses from rat primary cultured neurons. High-resolution electron microscopy and quantitative analyses revealed that postsynaptic density (PSD) is composed of membrane-associated nanoblocks of various sizes, which are in close relationship with potential presynaptic release sites through adhesion molecules spanning the synaptic cleft, as well as with post-synaptic receptors. Subtomogram averaging from synaptosomes showed two distinct types of postsynaptic membrane proteins at resolutions of 24 Å and 26 Å respectively. Furthermore, our data reveal that majority of potential release sites and ∼50% subtomogram averaged receptor-like particles are located within the boundary of PSD nanoblocks, while PSD nanoblocks might be redundant for neurotransmission. The results of this study provide a more comprehensive understanding of synaptic ultrastructure and suggest that PSD is composed of clustering of various nanoblocks, which likely underlies the dynamic nature of PSD to modulate synaptic strength.
Systematic evaluation of protein-small molecule hybrids on the yeast surface
Authors: Huang Manjie , Rueda-Garcia Marina , Harthorn Abbigael , Hackel Benjamin J. , Van Deventer James A.
Published: May 2023

Protein-small molecule hybrids are structures that have the potential to combine the inhibitory properties of small molecules and the specificities of binding proteins. However, achieving such synergies is a substantial engineering challenge, with fundamental principles yet to be elucidated. Recent work has demonstrated the power of yeast display-based discovery of hybrids using a combination of fibronectin binding domains and thiol-mediated conjugations to introduce small molecule warheads. Here, we systematically study the effects of expanding the chemical diversity of these hybrids on the yeast surface, investigating a combinatorial set of fibronectins, noncanonical amino acid (ncAA) substitutions, and small molecule pharmacophores. Our results show that previously discovered thiol-fibronectin hybrids are generally tolerant of a range of ncAA substitutions and retain binding to carbonic anhydrases following click chemistry-mediated assembly of hybrids with diverse linker structures. Most surprisingly, we identified several cases where replacement of a potent acetazolamide warhead with a substantially weaker benzenesulfonamide warhead still resulted in the assembly of functional hybrids. In addition to these unexpected findings, we expanded the throughput of our system by validating a 96-well plate-based format to produce yeast-displayed hybrid conjugates in parallel. These efficient explorations of hybrid chemical diversity demonstrate that there are abundant opportunities to expand the functions of protein-small molecule hybrids and elucidate principles that dictate their efficient discovery and design.
The impact of host heterogeneity on pathogen evolution depends on spatial structure
Authors: Visher Elisa , Ali Anisha , Barajas Jonathan , Masud Sehar , McBride Annika , Ramos Edwin , Sui Melissa , Villalobos-Heredia Cristina , Walzer Natalie , White P. Signe , Boots Mike
Published: May 2023

Host diversity and spatial structure both separately impact parasite evolution and may also interact when space structures host heterogeneity and populations must adapt to both selection pressures. Here, we experimentally evolve granulosis virus in microcosms of itsPlodia interpunctella(Indian meal moth) host that vary in spatial structure and host genetic diversity. We do this by manipulating food viscosity (spatial structure) and adding either one (homogeneous) or two (heterogeneous) host genotypes to the microcosm. Spatial structure therefore bot generally structures of infectious contacts and decreases the rate of contact between genotypes. We preserve spatial structure across passages and assay virus from different positions on the two host genotypes. We find that virus evolves specific interactions with its locally familiar host genotype, but that the impact of specialization on evolved phenotypes depends on the spatial structure. In spatially structured treatments, exploitation rates are higher on the familiar host, while, in well-mixed treatments, they are lower. We also find that virus can specialize to their locally familiar host in heterogeneous microcosms when spatial structure lowers contact rates between hosts. These results demonstrate that host genetic diversity and spatial structure can interact to reshape the evolution of pathogen host range. [197/200]
Defining Mitochondrial Cristae Morphology Changes Induced by Aging in Brown Adipose Tissue
Authors: Crabtree Amber , Neikirk Kit , Marshall Andrea G. , Vang Larry , Whiteside Aaron J. , Williams Qiana , Altamura Christopher T. , Owens Trinity Celeste , Stephens Dominique , Shao Bryanna , Koh Alice , Killion Mason , Lopez Edgar Garza , Lam Jacob , Rodriguez Ben , Mungai Margaret , Stanley Jade , Dean E. Danielle , Koh Ho-Jin , Gaddy Jennifer A. , Scudese Estevão , Sweetwyne Mariya , Davis Jamaine , Zaganjor Elma , Murray Sandra A. , Katti Prasanna , Damo Steven M. , Vue Zer , Hinton Antentor
Published: May 2023

Mitochondria are required for energy production and even give brown adipose tissue (BAT) its characteristic color due to their high iron content and abundance. The physiological function and bioenergetic capacity of mitochondria are connected to the structure, folding, and organization of its inner-membrane cristae. During the aging process, mitochondrial dysfunction is observed, and the regulatory balance of mitochondrial dynamics is often disrupted, leading to increased mitochondrial fragmentation in aging cells. Therefore, we hypothesized that significant morphological changes in BAT mitochondria and cristae would be present with aging. We developed a quantitative three-dimensional (3D) electron microscopy approach to map cristae network organization in mouse BAT to test this hypothesis. Using this methodology, we investigated the 3D morphology of mitochondrial cristae in adult (3-month) and aged (2-year) murine BAT tissue via serial block face-scanning electron microscopy (SBF-SEM) and 3D reconstruction software for manual segmentation, analysis, and quantification. Upon investigation, we found increases in mitochondrial volume, surface area, and complexity and decreased sphericity in aged BAT, alongside significant decreases in cristae volume, area, perimeter, and score. Overall, these data define the nature of the mitochondrial structure in murine BAT across aging.

Abstract Figure

Graphical Abstract:

Overview of serial block facing-scanning electron microscopy (SBF-SEM) workflow, data segmentation, and 3D analysis of mitochondria using Amira software for murine interscapular BAT.
Regulation of shelterin proteins TERF2IP and TRF2 by H3K4me3-p65 axis drives hyperglycemia dependent endothelial senescence
Authors: Thakar Sumukh , Bhattacharya Ritobrata , Katakia Yash T , Chakraborty Srinjoy , Ramakrishnan S , Thakkar Niyati Pandya , Dey Smita , Chowdhury Shibasish , Majumder Syamantak
Published: May 2023

Background

Endothelial senescence has been linked to several cardiovascular diseases. Dysregulation of proteins of the shelterin complex including TRF2 and TERF2IP causes senescence as it hampers DNA repair and cell proliferation. However, whether exposure to hyperglycemia interplays with proteins of the shelterin complex thus further dictates the senescent phenotype of endothelial cells (EC) remain to be explored.

Approach and Results

In this study, we observed elevated levels of p21 and p53 in endothelial cells upon exposure to intermittent hyperglycemia. We also noted hyperglycemia exposure increased the levels of TERF2IP and TRF2, part of the shelterin complex. No change in the level of TRF1 and TPP1 were detected. Furthermore, a robust induction was detected in p65 level upon intermittent hyperglycemia challenge. ChIP-qPCR analysis revealed enhanced H3K4me3 enrichment in the promoter regions of p65, TERF2IP and TRF2. Inhibition of catalysis of H3K4me3 either by pharmacological inhibitor or siRNA-mediated knockdown of MLL2 attenuated increase in p65, TERF2IP and TRF2 levels including reversal of senescence markers p53 and p21. Interestingly, pharmacological inhibition of NF-κB signaling also diminished abrupt increase in TERF2IP and TRF2 levels thus further reversed intermittent hyperglycemia-induced p53 and p21 levels. More importantly, co-immunoprecipitation and co-localization analysis revealed an interaction between nuclear p65 and MLL2 in EC stimulated with hyperglycemia. Further knockdown of either TERF2IP or TRF2 impaired intermittent hyperglycemia-induced p53 and p21 expression and associated endothelial senescence.

Conclusion

Overall, the present study describes an interplay of epigenetics in defining NF-κB signaling and shelterin proteins’ expression which further govern the biochemical and functional state of endothelial senescence in hyperglycemic milieu.
Novel metrics reveal new structure and unappreciated heterogeneity in C. elegans development
Authors: Natesan Gunalan , Hamilton Timothy , Deeds Eric J. , Shah Pavak K.
Published: May 2023

High throughput experimental approaches are increasingly allowing for the quantitative description of cellular and organismal phenotypes. Distilling these large volumes of complex data into meaningful measures that can drive biological insight remains a central challenge. In the quantitative study of development, for instance, one can resolve phenotypic measures for single cells onto their lineage history, enabling joint consideration of heritable signals and cell fate decisions. Most attempts to analyze this type of data, however, discard much of the information content contained within lineage trees. In this work we introduce a generalized metric, which we term the branch distance, that allows us to compare any two embryos based on phenotypic measurements in individual cells. This approach aligns those phenotypic measurements to the underlying lineage tree, providing a flexible and intuitive framework for quantitative comparisons between, for instance, Wild-Type (WT) and mutant developmental programs. We apply this novel metric to data on cell-cycle timing from over 1300 WT and RNAi-treatedCaenorhabditis elegansembryos. Our new metric revealed surprising heterogeneity within this data set, including subtle batch effects in WT embryos and dramatic variability in RNAi-induced developmental phenotypes, all of which had been missed in previous analyses. Further investigation of these results suggests a novel, quantitative link between pathways that govern cell fate decisions and pathways that pattern cell cycle timing in the early embryo. Our work demonstrates that the branch distance we propose, and similar metrics like it, have the potential to revolutionize our quantitative understanding of organismal phenotype.
In Silico Investigations of Adaptive Therapy Using Two Cytotoxic or Two Cytostatic Drugs
Authors: Saha Daniel K. , Anderson Alexander R. A. , Cisneros Luis , Maley Carlo C.
Published: May 2023

While the dose modulation (DM) protocols (DM Cocktail Tandem, DM Ping-Pong Alternate Every Cycle, DM Ping-Pong on Progression) involves adjusting drug dosages when the tumor burden changes, the fixed-dose (FD) protocols involves administering a specific, constant dosage of the drug only when the tumor is growing (Dose-Skipping) or when the absolute tumor burden is above the baseline level until it reduces to a certain percentage of the baseline (Intermittent). Moreover, two different drugs can be administered simultaneously (cocktail), or the drugs can be switched such that only one drug is applied at a given time (ping-pong), either every cycle (ping-pong alternate every cycle) or when the tumor grows (ping-pong on progression). The dose modulation protocols work well when treated with two cytotoxic drugs, however, the ping-pong protocols (DM Ping-Pong Alternate Every Cycle, DM Ping-Pong on Progression, FD Ping-Pong Intermittent) work well when treated with two cytostatic drugs. In general, adaptive therapy, using either two cytotoxic or two cytostatic drugs works best under conditions of high competition, such as high fitness cost, high replacement rates, and high turnover, although treatment using two cytostatic drugs works best under low turnover in many cases. Adaptive therapy works best when drug dosages are changed as soon as a change in tumor burden is detected, and it is best to pause treatment sooner rather than later when the tumor is shrinking. Adaptive therapy works best when an intermediate level of drug dosage is used, and both treatment with too little or too much drug leads to poor survival outcome.
Frequency and Phase Correction of GABA-Edited Magnetic Resonance Spectroscopy using Complex-Valued Convolutional Neural Networks
Authors: Bugler Hanna , Berto Rodrigo Pommot , Souza Roberto , Harris Ashley D.
Published: May 2023

Purpose

To determine the significance of complex-valued inputs and complex-valued convolutions compared to real-valued inputs and real-valued convolutions in Convolutional Neural Networks (CNNs) for frequency and phase correction (FPC) of GABA-edited Magnetic Resonance Spectroscopy (MRS) data.

Methods

An ablation study was performed to determine the most effective input (real or complex) and convolution type (real or complex) to predict frequency and phase shifts in GABA-edited MEGA-PRESS data using CNNs. The best CNN model was subsequently compared to two recently proposed deep learning (DL) methods for FPC of GABA-edited MRS. All methods were trained using the same experimental setup and evaluated using GABA’s signal-to-noise ratio and linewidth, Choline artifact, and by analyzing the reconstructed final difference spectrum. Statistical significance and effect size were assessed using the Wilcoxon signed rank test and Cohen’s d respectively.

Results

The ablation study showed that using complex values for the input represented by real and imaginary channels in our model input tensor, with real (conventional) convolutions was most effective for FPC. For the comparative study, the simulated data test set showed that our CNN model that received complex-valued inputs with real convolutions outperformed models it was compared against with a lower mean absolute error (p<0.05). For the in vivo data test set, our model performed similarly to other DL FPC models.

Conclusion

Our results indicate that the optimal CNN configuration for GABA-edited MRS FPC uses a complex-valued input and real-valued convolutions. This model outperformed existing DL models on simulated data and performed similarly on in vivo data.
Considering Zeros in Single Cell Sequencing Data Correlation Analysis
Authors: Cai Guoshuai , Yu Xuanxuan , Xiao Feifei
Published: May 2023

Single-cell sequencing technology has enabled correlation analysis of genomic features at the cellular level. However, high levels of noise and sparsity in single-cell sequencing data make accurate assessment of correlations challenging. This study provides a toolkit, SCSC (https://github.com/thecailab/SCSC), for the estimation of correlation coefficients in single-cell sequencing data. It comprehensively assessed four strategies (classical, non-zero, dropout-weighted, imputation) and the impact of data features in various simulated scenarios. The study found that filtering zeros significantly improves estimation accuracy, and further improvement can be achieved by considering the drop-out probability. In addition, the study also identified data features including expression level, library size, and biological variations that affect correlation estimation.
AnnoPRO: an Innovative Strategy for Protein Function Annotation based on Image-like Protein Representation and Multimodal Deep Learning
Authors: Zheng Lingyan , Shi Shuiyang , Fang Pan , Zhang Hongning , Pan Ziqi , Huang Shijie , Xia Weiqi , Li Honglin , Zeng Zhenyu , Zhang Shun , Chen Yuzong , Lu Mingkun , Li Zhaorong , Zhu Feng
Published: May 2023

Protein function annotation has been one of the longstanding issues, which is key for discovering drug targets and understanding physiological or pathological process. A variety of computational methods have therefore been constructed to facilitate the research developments in this particular direction. However, the annotation of protein function based on computational methods has been suffering from the serious “long-tail problem”, and it remains extremely challenging for existing methods to improve the prediction accuracies for protein families intail label levels. In this study, an innovative strategy, entitled ‘AnnoPRO’, for protein function annotation was thus constructed.First, a novel method enabling image-like protein representations was proposed. This method is unique in capturing the intrinsic correlations among protein features, which can greatly favor the application of thestate-of-the-artdeep learning methods popular in image classification.Second, a multimodal framework integrating multichannel convolutional neural network and long short-term memory neural network was constructed to realize a deep learning-based protein functional annotation. Since this framework was inspired by a reputable method used in image classification for dealing with its ‘long-tail problem’, ourAnnoPROwas expected to significantly improve the annotation performance of the protein families intail label level. Multiple case studies based on benchmark were also conducted, which confirmed the superior performance ofAnnoPROamong the existing methods. All source codes and models ofAnnoPROwere freely available to all users athttps://github.com/idrblab/AnnoPRO, and would be essential complement to existing methods.
Models to Estimate Genetic Gain of Soybean Seed Yield from Annual Multi-Environment Field Trials
Authors: Krause Matheus D. , Piepho Hans-Peter , Dias Kaio O. G. , Singh Asheesh K. , Beavis William D.
Published: May 2023

1

Genetic improvements of discrete characteristics such as flower color, the genetic improvements are obvious and easy to demonstrate; however, for characteristics that are measured on continuous scales, the genetic contributions are incremental and less obvious. Reliable and accurate methods are required to disentangle the confounding genetic and non-genetic components of quantitative traits. Stochastic simulations of soybean (Glycine max (L.) Merr.) breeding programs were performed to evaluate models to estimate the realized genetic gain (RGG) from 30 years of multi-environment trials (MET). True breeding values were simulated under an infinitesimal model to represent the genetic contributions to soybean seed yield under various MET conditions. Estimators were evaluated using objective criteria of bias and linearity. Results indicated all estimation models were biased. Covariance modeling as well as direct versus indirect estimation resulted in substantial differences in RGG estimation. Although there were no unbiased models, the three best-performing models resulted in an average bias of ±7.41 kg/ha−1/yr−1(±0.11 bu/ac−1/yr−1). Rather than relying on a single model to estimate RGG, we recommend the application of multiple models and consider the range of the estimated values. Further, based on our simulations parameters, we do not think it is appropriate to use any single models to compare breeding programs or quantify the efficiency of proposed new breeding strategies. Lastly, for public soybean programs breeding for maturity groups II and III in North America from 1989 to 2019, the range of estimated RGG values was from 18.16 to 39.68 kg/ha−1/yr−1(0.27 to 0.59 bu/ac−1/yr−1).
DNA damage primes hematopoietic stem cells for direct megakaryopoiesis
Authors: Garyn Corey M. , Bover Oriol , Murray John W. , Jing Ma , Salas-Briceno Karen , Ross Susan R , Snoeck Hans-Willem
Published: May 2023

Hematopoietic stem cells (HSCs) reside in the bone marrow (BM), can self-renew, and generate all cells of the hematopoietic system.1Most hematopoietic lineages arise through successive, increasingly lineage-committed progenitors. In contrast, megakaryocytes (MKs), hyperploid cells that generate platelets essential to hemostasis, can derive rapidly and directly from HSCs.2The underlying mechanism is unknown however. Here we show that DNA damage and subsequent arrest in the G2 phase of the cell cycle rapidly induce MK commitment specifically in HSCs, but not in progenitors, through an initially predominantly post-transcriptional mechanism. Cycling HSCs show extensive replication-induced DNA damage associated with uracil misincorporationin vivoandin vitro. Consistent with this notion, thymidine attenuated DNA damage, rescued HSC maintenance and reduced the generation of CD41+MK-committed HSCsin vitro. Similarly, overexpression of the dUTP-scavenging enzyme, dUTPase, enhancedin vitromaintenance of HSCs. We conclude that a DNA damage response drives direct megakaryopoiesis and that replication stress-induced direct megakaryopoiesis, at least in part caused by uracil misincorporation, is a barrier to HSC maintenancein vitro. DNA damage-induced direct megakaryopoiesis may allow rapid generation of a lineage essential to immediate organismal survival, while simultaneously removing damaged HSCs and potentially avoiding malignant transformation of self-renewing stem cells.
A combined lipidomic and proteomic profiling ofArabidopsis thalianaplasma membrane
Authors: Bahammou Delphine , Recorbet Ghislaine , Cassim Adiilah Mamode , Robert Franck , Balliau Thierry , Delft Pierre Van , Haddad Youcef , Mongrand Sébastien , Fouillen Laetitia , Simon-Plas Françoise
Published: May 2023

The plant plasma membrane (PM) plays a key role in nutrition, cell homeostasis, perception of environmental signals, and set-up of appropriate adaptive responses. An exhaustive and quantitative description of the whole set of lipids and proteins constituting the PM is thus necessary to understand how the way these components, are organized and interact together, allow to fulfill such essential physiological functions. Here we provide by state-of-the-art approaches the first combined reference of the plant PM lipidome and proteome fromArabidopsis thalianasuspension cell culture. We identified a reproducible core set of 2,165 proteins (406 of which had not been shown associated to PM previously), which is by far the largest set of available data concerning the plant PM proteome. Using the same samples, we combined lipidomic approaches, allowing the identification and quantification of an unprecedented repertoire of 405 molecular species of lipids. We showed that the different classes of lipids (sterols, phospholipids, and sphingolipids) are present in similar proportions in the plant PM. Within each lipid class, the precise amount of each lipid family and the relative proportion of each molecular species were further determined, allowing us to establish the complete lipidome of Arabidopsis PM, and highlighting specific characteristics of the different molecular species of lipids (for instance fatty acyl chain length and saturation according to the polar head). Results obtained are consistent with the plant PM being an ordered mosaic of domains and point to a finely tuned adjustment of the molecular characteristics of lipids and proteins. More than a hundred proteins related to lipid metabolism, transport or signaling have been identified and put in perspective of the lipids with which they are associated. All these results provide an overall view of both the organization and the functioning of the PM.
Post-training sleep modulates motor adaptation and task-related beta oscillations
Authors: Ameen Mohamed S. , Petzka Marit , Peigneux Philippe , Hoedlmoser Kerstin
Published: May 2023

Motor adaptation reflects the ability of the brain’s sensorimotor system to flexibly deal with environmental changes to generate effective motor behaviour. Whether sleep contributes to the consolidation of motor adaptation remains controversial. In this study, we investigated the impact of sleep on motor adaptation and its neurophysiological correlates in a novel motor adaptation task that leverages a highly automatized motor skill, i.e., typing. We hypothesized that sleep-associated memory consolidation would benefit motor adaptation and induce modulations in task-related beta band (13-30Hz) activity during adaptation. Healthy young male experts in typing on the regular computer keyboard were trained to type on a vertically mirrored keyboard while brain activity was recorded using electroencephalography (EEG). Typing performance was assessed either after a full night of sleep with polysomnography or a similar period of daytime wakefulness. Results showed improved motor adaptation performance after nocturnal sleep but not after daytime wakefulness, and decreased beta power (a) during mirrored typing as compared to regular typing, and (b) in the post-sleep vs. the pre-sleep mirrored typing sessions. Furthermore, the slope of the EEG signal, a measure of aperiodic brain activity, decreased during mirrored as compared to regular typing. Changes in the EEG spectral slope from pre- to post-sleep mirrored typing sessions were correlated with changes in task performance. Finally, increased fast sleep spindle density (13-15Hz) during the night following motor adaptation training was predictive of successful motor adaptation. These findings suggest that post-training sleep modulates neural activity mechanisms supporting adaptive motor functions.
Synaptic and dendritic architecture of different types of hippocampal somatostatin interneurons
Authors: Takács Virág , Bardóczi Zsuzsanna , Orosz Áron , Major Abel , Tar Luca , Berki Péter , Papp Péter , Mayer Márton I. , Sebők Hunor , Zsolt Luca , Sos Katalin E. , Káli Szabolcs , Freund Tamás F. , Nyiri Gábor
Published: May 2023

GABAergic inhibitory neurons fundamentally shape the activity and plasticity of cortical circuits. A major subset of these neurons contains somatostatin (SOM); these cells play crucial roles in neuroplasticity, learning and memory in many brain areas including the hippocampus, and are implicated in several neuropsychiatric diseases and neurodegenerative disorders. Two main types of SOM-containing cells in area CA1 of the hippocampus are oriens-lacunosum-moleculare (OLM) cells and hippocampo-septal (HS) cells. These cell types show many similarities in their soma-dendritic architecture, but they have different axonal targets, display different activity patternsin vivoand are thought to have distinct network functions. However, a complete understanding of the functional roles of these interneurons requires a precise description of their intrinsic computational properties and their synaptic interactions. In the current study we generated, analyzed and make available several key datasets that enable a quantitative comparison of various anatomical and physiological properties of OLM and HS cells in mouse. The dataset includes detailed scanning electron microscopy-based 3-dimensional reconstructions of OLM and HS cells along with their excitatory and inhibitory synaptic inputs. Combining this core dataset with other anatomical data, patch-clamp electrophysiology and compartmental modeling, we examined the precise morphological structure, inputs, outputs, and basic physiological properties of these cells. Our results highlight key differences between OLM and HS cells, particularly regarding the density and distribution of their synaptic inputs and mitochondria. For instance, we estimated that an OLM cell receives about 8400, whereas an HS cell about 15600 synaptic inputs, about 16% of which are GABAergic. Our data and models provide insight into the possible basis of the different functionality of OLM and HS cell types and supply essential information for more detailed functional models of these neurons and the hippocampal network.
Comparing manual and automatic artifact detection in sleep EEG recordings
Authors: Péter Ujma P. , Dresler Martin , Bódizs Róbert
Published: May 2023

All sleep EEG recordings can be contaminated by artifacts. Both visual and automatic methods have been developed to mark such erroneous segments of EEG data. Here we systematically explore the effect of artifacts on the sleep EEG power spectrum density (PSD), and we compare gold-standard visual detections to a simple automatic detector using Hjorth parameters to identify artifacts. We find that most distortions in the all-night average PSD occur because of a small minority of highly anomalous artifacts, which mainly affect the beta and gamma frequency ranges and NREM delta. Visual and automatic detections only show moderate agreement in which data segments are artefactual. However, the resulting all-night average PSD is highly similar across all methods, and PSDs calculated with all methods successfully recover the known correlations of PSD with age and sex. No parameter settings of the automatic detector clearly outperformed others. Additionally, we show that accurate average PSD estimates can be recovered from just a fraction of available data epochs. Our results suggest that artifacts represent a minor and easily solvable problem in sleep EEG recordings. Most visually identified artifacts do not seriously distort estimates of mid-frequency activity in the sleep EEG spectrum, and distortions to low and high frequencies can be eliminated using a simple automatic detection method nearly as well as with visual detections. These findings show that the visual inspection of EEG data is not necessary to eliminate the effects of artifacts, which is encouraging for the expected performance of automatic preprocessing in large sleep EEG databases.
STimage:robust, confident and interpretable models for predicting gene markers from cancer histopathological images
Authors: Tan Xiao , Mulay Onkar , MacDonald Samual , Kim Taehyun , Werry Jason , Simpson Peter T , Roosta Fred , Trzaskowski Maciej , Nguyen Quan
Published: May 2023

Spatial transcriptomic (ST) data enables us to link tissue morphological features with thousands of unseen gene expression values, opening a horizon for breakthroughs in digital pathology. Models to predict the presence/absence, high/low, or continuous expression of a gene using images as the only input have a huge potential clinical applications, but such models require improvements in accuracy, interpretability, and robustness. We developed STimage models to estimate parameters of gene expression as distributions rather than fixed data points, thereby allowing for the essential quantification of uncertainty in the predicted results. We assessed aleatoric and epistemic uncertainty of the models across a diverse range of test cases and proposed an ensemble approach to improve the model performance and trust. STimage can train prediction models for one gene marker or a panel of markers and provides important interpretability analyses at a single-cell level, and in the histopathological annotation context. Through a comprehensive benchmarking with existing models, we found that STimage is more robust to technical variation in platforms, data types, and sample types. Using images from the cancer genome atlas, we showed that STimage can be applied to non-spatial omics data. STimage also performs better than other models when only a small training dataset is available. Overall, STimage contributes an important methodological advance needed for the potential application of spatial technology in cancer digital pathology.
Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
Authors: Catalinas Celia Alda , Ibarra-Soria Ximena , Flouri Christina , Gordillo Jorge Esparza , Cousminer Diana , Hutchinson Anna , Krejci Adam , Cortes Adrian , Acevedo Alison , Malla Sunir , Fishwick Carl , Drewes Gerard , Rapiteanu Radu
Published: May 2023

Drug targets with human genetic evidence are expected to increase clinical success by at least two-fold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge of early drug discovery. A key issue is that, currently, the vast majority of complex disease associations cannot be cleanly mapped to a gene. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes and thus the molecular programs modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+T cells. Our pipeline enables the interrogation of transcriptomic changes induced by the perturbation of regulatory elements at scale. We first optimised a highly efficient CRISPRi protocol in primary human CD4+T cells via CROPseq vectors. Subsequently, we performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites and profiled approximately 250,000 CD4+T cell single-cell transcriptomes. We developed a bespoke analytical pipeline for element-to-gene (E2G) mapping and demonstrate that our method can identify both previously annotated and novel E2G links. Lastly, we integrated genetic association data for immune-related traits and demonstrate how our platform can aid in the identification of effector genes for GWAS loci.
Modeling of enzyme-mediated glucose release to facilitate continuous feed in miniaturized cultivations
Authors: Kemmer Annina , Cai Linda , Born Stefan , Cruz Bournazou M. Nicolas , Neubauer Peter
Published: May 2023

When striving for maximal throughput at minimal volumes while cultivating close to industrial conditions, simple and robust feeding strategies offer important advantages. Enzyme-mediated glucose cleavage from dextrin is an easy way of imitating continuous fed-batch in the small scale, with no complex equipment required. While the release rate – and thus the feed rate – can be controlled by adapting the enzyme concentration, it strongly depends on the concentration of the involved substances and the environmental conditions. Thus, it is a challenge to use the technology for controlling the specific growth rate, as it is commonly done with feed pumps. For solving this problem, we present here a mathematical model that extends simple Michaelis-Menten kinetics by considering different substrate fractions and can be applied to control the glucose release rate even in high throughput experiments. The fitted model was used during automated microbial cultivations to control the growth rate in quasi-continuous fed-batch processes and to realize different exponential growth rates by intermittent additions of enzyme and dextrin by a liquid handling robot system. We thus present an approach for defined biocatalytically controlled glucose supply of small-scale systems, where – if at all – continuous feeding was only possible with low accuracy or high technical efforts until now.
Shared Genetic Architecture between Muscle and Bone: Identification and Functional Implications ofEPDR1,PKDCC, andSPTBN1
Authors: Jung Jongyun , Wu Qing
Published: May 2023

Recent studies suggest a shared genetic architecture between muscle and bone, yet the underlying molecular mechanisms remain elusive. This study aims to identify the functionally annotated genes with shared genetic architecture between muscle and bone using the most up-to-date genome-wide association study (GWAS) summary statistics from bone mineral density (BMD) and fracture-related genetic variants. We employed an advanced statistical functional mapping method to investigate shared genetic architecture between muscle and bone, focusing on genes highly expressed in muscle tissue. Our analysis identified three genes,EPDR1, PKDCC, andSPTBN1, highly expressed in muscle tissue and previously unlinked to bone metabolism. About 90% and 85% of filtered Single-Nucleotide Polymorphisms were located in the intronic and intergenic regions for the threshold atP≤ 5 × 10−8andP≤ 5 × 10−100, respectively.EPDR1was highly expressed in multiple tissues, including muscle, adrenal gland, blood vessels, and thyroid.SPTBN1was highly expressed in all 30 tissue types except blood, whilePKDCCwas highly expressed in all 30 tissue types except the brain, pancreas, and skin. Our study provides a framework for using GWAS findings to highlight functional evidence of crosstalk between multiple tissues based on shared genetic architecture between muscle and bone. Further research should focus on functional validation, multi-omics data integration, gene-environment interactions, and clinical relevance in musculoskeletal disorders.

Author Summary

Osteoporotic fractures in the aging population pose a significant health concern. They are often attributed to decreased bone strength and muscle loss. However, the underlying molecular connections between bone and muscle are not well understood. This lack of knowledge persists despite recent genetic discoveries linking certain genetic variants to bone mineral density and fracture risk. Our study aimed to uncover genes that share genetic architecture between muscle and bone. We utilized state-of-the-art statistical methods and the most recent genetic data related to bone mineral density and fractures. Our focus was on genes that are highly active in muscle tissue. Our investigation identified three new genes -EPDR1, PKDCC, andSPTBN1- which are highly active in muscle tissue and influence bone health. These discoveries offer fresh insights into the interconnected genetic makeup of bone and muscle. Our work not only uncovers potential targets for therapeutic strategies to enhance bone and muscle strength but also provides a blueprint for identifying shared genetic structures across multiple tissues. This research represents a crucial step forward in our understanding of the interplay between our muscles and bones at a genetic level.
Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1
Authors: Glunčić Matko , Vlahović Ines , Rosandić Marija , Paar Vladimir
Published: May 2023

It is known that the ∼1.6 kb NBPF repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ∼50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo and collaborators, comparing it to the results obtained for human hg38 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga and collaborators, identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.
Effect of annealing on the magnetic microstructure of high-pressure torsion iron: the relevance of higher-order contributions to the magnetic small-angle neutron scattering cross section
Authors: Bersweiler Mathias , Sato Hirokazu , Adachi Nozomu , Todaka Yoshikazu , Peral Inma , Kohlbrecher Joachim , Zaporozhets Vladislav D. , Metlov Konstantin L. , Michels Andreas , Oba Yojiro
Published: May 2023

The development of higher-order micromagnetic small-angle neutron scattering theory in nanocrystalline materials is still in its infancy. One key challenge remaining in this field is understanding the role played by the microstructure on the magnitude and sign of the higher-order scattering contribution recently observed in nanocrystalline materials prepared by high-pressure torsion. By combining structural and magnetic characterization techniques, namely X-ray diffraction, electron backscattered diffraction and magnetometry with magnetic small-angle neutron scattering, this work discusses the relevance of higher-order terms in the magnetic small-angle neutron scattering cross section of pure iron prepared by high-pressure torsion associated with a post-annealing process. The structural analysis confirms: (i) the preparation of ultra-fine-grained pure iron with a crystallite size below 100 nm and (ii) rapid grain growth with increasing annealing temperature. The analysis of neutron data based on the micromagnetic small-angle neutron scattering theory extended to textured ferromagnets yields uniaxial magnetic anisotropy values that are larger than the magnetocrystalline value reported for bulk iron, supporting the existence of induced magnetoelastic anisotropy in the mechanically deformed samples. Furthermore, the neutron data analysis revealed unambiguously the presence of non-negligible higher-order scattering contributions in high-pressure torsion iron. Though the sign of the higher-order contribution might be related to the amplitude of the anisotropy inhomogeneities, its magnitude appears to be clearly correlated to the changes in the microstructure (density and/or shape of the defects) induced by combining high-pressure torsion and a post-annealing treatment.
Application of the method for visualization of noncovalent interactions in conformational polymorphs of four organic acids
Authors: Pirozhkov Pavel A. , Uhanov Andrei S. , Savchenkov Anton V.
Published: May 2023

A method for the visualization of noncovalent interactions using examples of the conformational polymorphs of four organic compounds: 2-(phenylamino)nicotinic, 2-(3-chloro-2-methylphenylamino)nicotinic, N-(3-chloro-2-methylphenyl)anthranilic and 2-(methylphenylamino)nicotinic acids is examined. The changes in noncovalent contacts are plotted against the angle between the planes of aromatic rings allowing a visual representation of conformational adjustment of molecules as well as packing features of crystal structures. According to the k–Φ criterion, the studied structures represent conformational polymorphs. Different types of hydrogen bonding are discussed within the framework of the method of visualization and molecular Voronoi–Dirichlet polyhedra. Good correlations are found between calculated and experimental data for several cases, such as the agreement between π stacking and polymorphic transition temperatures as well as between the area of a contact and the energy of conjugation. Also, an attempt has been made to assess the relative contributions of conformational and packing polymorphism in the formation of polymorphs.
The composition of the remuneration committee and the vertical pay gap: the role of proprietary directors in Spain
Authors: Acero Isabel , Alcalde Nuria
Published: May 2023

Purpose

This study investigates whether the proportion of proprietary directors (blockholders or their representatives) on the board's remuneration committee influences vertical pay inequality in Spanish listed companies and whether this relationship can be conditioned by the concentration of ownership.

Design/methodology/approach

The sample contains information on the individual compensation of 1048 directors of 57 Spanish listed firms during the period 2013–2018 making up an unbalanced panel with 3565 observations. Panel data regressions are used to study how the presence of proprietary directors on the remuneration committee influences the remuneration of directors, focusing not on their absolute remuneration levels, but rather on their relationship to the average remuneration of the organization's employees (as a measure of vertical pay inequality within the company). The authors also investigate whether this relationship is conditioned by firm ownership concentration.

Findings

The results indicate that the presence of proprietary directors on the remuneration committee acts as a mechanism to reduce vertical pay inequality, even in the context of high ownership concentration.

Originality/value

Unlike the majority of previous research dedicated to the independence of the remuneration committee, this study focuses on the role played by proprietary directors. The results help elucidate the importance of proprietary directors to properly monitor and restrain directors' compensation in contexts of high ownership concentration.