bluuebunny/crossref_metadata_2025 huggingface dataset:
ImmuNet: A Segmentation-Free Machine Learning Pipeline for Immune Landscape Phenotyping in Tumors by Muliplex Imaging
Authors: Sultan Shabaz , Gorris Mark A. J. , Martynova Evgenia , van der Woude Lieke L. , Buytenhuijs Franka , van Wilpe Sandra , Verrijp Kiek , Figdor Carl G. , de Vries I. Jolanda M. , Textor Johannes
Published: October 2021

Tissue specimens taken from primary tumors or metastases contain important information for diagnosis and treat-ment of cancer patients. Multiplex imaging allowsin situvisualization of heterogeneous cell populations, such as immune cells, in tissue samples. Most image processing pipelines first segment cell boundaries and then measure marker expression to assign cell phenotypes. In dense tissue environments, this segmentation-first approach can be inaccurate due to segmentation errors or overlapping cells. Here we introduce the machine learning pipeline “ImmuNet” that identifies positions and phenotypes of cells without segmenting them. ImmuNet is easy to train: human annotators only need to click on an immune cell and score its expression of each marker. This approach al-lowed us to annotate 34,458 cells. We show that ImmuNet consistently outperforms a state-of-the-art segmentation-based pipeline for multiplex immunohistochemistry analysis across tissue types, cell types and tissue densities, achieving error rates below 5-10% on challenging detection and phenotyping tasks. We externally validate Im-muNet results by comparing them to flow cytometric measurements from the same tissue. In summary, ImmuNet is an effective, simpler alternative to segmentation-based approaches when only cell positions and phenotypes, but not their shapes, are required for downstream analyses. Thus, ImmuNet helps researchers to analyze multiplex tissue images more easily and accurately.
Two structurally different oomycete lipophilic MAMPs induce distinctive plant immune responses
Authors: Monjil Mohammad Shahjahan , Kato Hiroaki , Ota Satomi , Matsuda Kentaro , Suzuki Natsumi , Tenhiro Shiho , Tatsumi Ayane , Pring Sreynich , Miura Atsushi , Camagna Maurizio , Suzuki Takamasa , Tanaka Aiko , Terauchi Ryohei , Sato Ikuo , Chiba Sotaro , Kawakita Kazuhito , Ojika Makoto , Takemoto Daigo
Published: October 2021

Plants recognize a variety of external signals and induce appropriate mechanisms to increase their tolerance to biotic and abiotic stresses. Precise recognition of attacking pathogens and induction of effective resistance mechanisms are critical functions for plant survival. Some molecular patterns unique to a certain group of microbes, microbe-associated molecular patterns (MAMPs), are sensed by plant cells as non-self molecules via pattern recognition receptors. While MAMPs of bacterial and fungal origin have been identified, reports on oomycete MAMPs are relatively limited. This study aimed to identify MAMPs from an oomycete pathogenPhytophthora infestans, the causal agent of potato late blight. Using reactive oxygen species (ROS) production and phytoalexin production in potato as markers, two structurally different groups of elicitors, namely ceramides and diacylglycerols were identified.P. infestansceramides (Pi-Cer A, B and D) induced ROS production, while diacylglycerol (Pi-DAG A and B), containing eicosapentaenoic acid (EPA) as a substructure, induced phytoalexins production in potato. The molecular patterns in Pi-Cers and Pi-DAGs essential for defense induction were identified as 9-methyl-4,8-sphingadienine (9Me-Spd) and 5,8,11,14-tetraene-type fatty acid (5,8,11,14-TEFA), respectively. These structures are not found in plants, but in oomycetes and fungi, indicating that they are microbe molecular patterns recognized by plants. When Arabidopsis was treated with Pi-Cer D and EPA, partially overlapping but different sets of genes were induced. Furthermore, expression of some genes is upregulated only after the simultaneous treatment with Pi-Cer D and EPA, indicating that plants combine the signals from simultaneously recognized MAMPs to adapt the defense response to pathogens.
Distribution of multi-unit pitch responses recorded intracranially from human auditory cortex
Authors: Berger Joel I , Gander Phillip E , Kikuchi Yukiko , Kumar Sukhbinder , Kovach Christopher , Oya Hiroyuki , Kawasaki Hiroto , Howard Matthew A , Griffiths Timothy D
Published: October 2021

The perception of pitch requires the abstraction of stimulus properties related to the spectrotemporal structure of sound. Previous studies utilizing both animal electrophysiology and human imaging have indicated the presence of a center for pitch representation in the auditory cortex. Recent data from our own group - examining local field potentials (LFPs) in humans - indicate more widely distributed pitch-associated responses within the auditory cortex (Gander et al., 2019). To probe this with greater spatial resolution, we examined multi-unit activity related to three different auditory stimuli, in seven epilepsy patients who were implanted with high-impedance electrodes in auditory cortex for the clinical purpose of localizing seizures. The stimuli were regular-interval noise (RIN) with a pitch strength that is related to the temporal regularity, and pitch value determined by repetition rate, and harmonic complexes with missing fundamentals. We demonstrated increases in spiking activity in 69 of 104 (66%) responsive multiunit activity in auditory cortex due to pitch-associated stimuli. Importantly, these responses were distributed across the entire extent of Heschl’s gyrus (HG), in both primary and non-primary areas, rather than isolated to a specific region, and this finding was evident regardless of the stimulus presented. These findings are the first multi-unit pitch responses recorded from humans, and align with a recent study in macaques (Kikuchi et al., 2019) demonstrating that both local field potential and unit responses to pitch-inducing stimuli are distributed throughout auditory cortex.

Significance Statement

The perception of pitch is a fundamental acoustic attribute that is mediated by the auditory system. Despite its importance, there is still debate as to the precise areas responsible for its encoding, which may be due to differences in the recording measures and choices of stimuli used in previous studies. Here, we present the first study to measure multi-unit pitch responses in the auditory cortices of intracranially-implanted humans. Importantly, we demonstrate reliable responses to three different pitch-inducing paradigms that are distributed throughout Heschl’s gyrus, rather than being localized to a particular region. These data provide a bridge across animal and human studies, and aid in our understanding of the processing of a critical attribute of acoustic stimuli.
Generating accurate 3D gaze vectors using synchronized eye tracking and motion capture
Authors: Stone Scott A. , Boser Quinn A. , Dawson T. Riley , Vette Albert H. , Hebert Jacqueline S. , Pilarski Patrick M. , Chapman Craig S.
Published: October 2021

Assessing gaze behaviour during real-world tasks is difficult; dynamic bodies moving through dynamic worlds make gaze analysis difficult. Current approaches involve laborious coding of pupil positions. In settings where motion capture and mobile eye tracking are used concurrently in naturalistic tasks, it is critical that data collection be simple, efficient, and systematic. One solution is to combine eye tracking with motion capture to generate 3D gaze vectors. When combined with tracked or known object locations, 3D gaze vector generation can be automated. Here we use combined eye and motion capture and explore how linear regression models generate accurate 3D gaze vectors. We compare spatial accuracy of models derived from four short calibration routines across three pupil data inputs: the efficacy of calibration routines were assessed, a validation task requiring short fixations on taskrelevant locations, and a naturalistic object interaction task to bridge the gap between laboratory and “in the wild” studies. Further, we generated and compared models using spherical and cartesian coordinate systems and monocular (Left or Right) or binocular data. All calibration routines performed similarly, with the best performance (i.e., sub-centimetre errors) coming from the naturalistic task trials when the participant is looking at an object in front of them. We found that spherical coordinate systems generate the most accurate gaze vectors with no differences in accuracy when using monocular or binocular data. Overall, we recommend one-minute calibration routines using binocular pupil data combined with a spherical world coordinate system to produce the highest quality gaze vectors.
In-vitro cellular reprogramming to model gonad development and its disorders
Authors: Gonen Nitzan , Eozenou Caroline , Mitter Richard , Bernardo Andreia , Chervova Almira , Frachon Emmanuel , Commère Pierre-Henri , Mazen Inas , Gobaa Samy , McElreavey Kenneth , Lovell-Badge Robin , Bashamboo Anu
Published: October 2021

During embryonic development, mutually antagonistic signaling cascades determine the fate of the bipotential gonad towards a testicular or ovarian identity. Errors in this process result in human Disorders of Sex Development (DSDs), where there is discordance between chromosomal, gonadal, and anatomical sex. The absence of an appropriate, accessible in-vitro system is a major obstacle in understanding mechanisms of sex-determination/DSDs. Here, we describe protocols for differentiation of mouse and human pluripotent cells towards gonadal progenitors. Transcriptomic analysis reveals that the in-vitro-derived murine gonadal cells are equivalent to E11.5 in-vivo progenitors. Using similar conditions, Sertoli-like cells derived from 46,XY human induced pluripotent stem cells (hiPSCs) exhibit sustained expression of testis-specific genes, secrete AMH, migrate and form tubular structures. The cells derived from a 46,XY DSD female hiPSCs, carrying a NR5A1 variant, show aberrant gene expression and absence of tubule formation. CRISPR/Cas9-mediated correction of the variant rescued the phenotype. This is a robust tool to understand mechanisms of sex-determination and model DSDs.
Structural basis of malaria transmission blockade by a monoclonal antibody to gamete fusogen HAP2
Authors: Feng Juan , Dong Xianchi , DeCosta Adam , Su Yang , Angrisano Fiona , Sala Katarzyna A. , Blagborough Andrew M. , Lu Chafen , Springer Timothy A.
Published: October 2021

HAP2 is a transmembrane gamete fusogen found in multiple eukaryotic kingdoms and is structurally homologous to viral class II fusogens. Studies in Plasmodium have suggested that HAP2 is an attractive target for vaccines that block transmission of malaria. HAP2 has three extracellular domains, arranged in the order D2, D1, and D3. Here, we report monoclonal antibodies against the D3 fragment of Plasmodium berghei HAP2 and crystal structures of D3 in complex with Fab fragments of two of these antibodies, one of which blocks fertilization of Plasmodium berghei in vitro and transmission of malaria in mosquitos. We also show how this Fab binds the complete HAP2 ectodomain with electron microscopy. The two antibodies cross-react with HAP2 among multiple plasmodial species. Our characterization of the Plasmodium D3 structure, HAP2 ectodomain architecture, and mechanism of inhibition provide insights for the development of a vaccine to block malaria transmission.
Modelling Eurasian lynx populations in Western Europe: What prospects for the next 50 years?
Authors: Sarah Bauduin , Estelle Germain , Fridolin Zimmermann , Sylvia Idelberger , Micha Herdtfelder , Marco Heurich , Stephanie Kramer-Schadt , Christophe Duchamp , Nolwenn Drouet-Hoguet , Alain Morand , Laetitia Blanc , Anaïs Charbonnel , Olivier Gimenez
Published: October 2021

Persistence of populations may be uncertain for large carnivore species, especially for those established in human-dominated landscapes. Here, we studied the Eurasian lynx in Western Europe established in the Upper Rhine meta-population (i.e., Jura, Vosges-Palatinian and Black Forest populations) and in the Alpine population. These populations are currently considered as endangered or critically endangered due to high anthropogenic mortality, small population size and low genetic diversity, and isolation. We assessed lynx persistence over a 50-year time horizon by implementing a spatially-explicit individual-based model, while accounting for road mortality and habitat selection. Forecasts showed a steady growth rapidly reaching a more stable phase for the Alpine and Jura populations, and a more heterogeneous positive growth with less precision for the Vosges-Palatinian and Black Forest populations. Exchanges of individuals between populations were limited, the Jura population playing the role of a crossroad. Finally, persistence of lynx in Western Europe seems likely on a large scale over the next 50 years. Indeed, simulations showed high female occupancy as well as average lynx density over the whole core areas of the four studied populations. Nevertheless, these results should be interpreted bearing in mind the model limitations concerning the absence of movement barriers and inbreeding depression.
Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection
Authors: Cecilia Hélène , Vriens Roosmarie , Kortekaas Jeroen , Schreur Paul J. Wichgers , de Wit Mariken , Métras Raphaëlle , Ezanno Pauline , ten Bosch Quirine A.
Published: October 2021

Rift Valley fever (RVF) is a viral, vector-borne, zoonotic disease. The relative contributions of livestock species to RVFV transmission has not been previously quantified. To estimate their potential to transmit the virus over the course of their infection, we 1) fitted a within-host model to viral RNA and infectious virus measures, obtained daily from infected lambs, calves, and young goats, 2) estimated the relationship between vertebrate host infectious titers and probability to infect mosquitoes, and 3) estimated the net infectiousness of each host species over the duration of their infectious periods, taking into account different survival outcomes for lambs. Our results indicate that the efficiency of viral replication, along with the lifespan of infectious particles, could be sources of heterogeneity between hosts. For similar infectious titers, we found that infection rates in Aedes spp. vectors were significantly higher than in Culex spp. vectors. Consequently, for Aedes infections, we estimated the net infectiousness of lambs to be 2.93 (median) and 3.65 times higher than that of calves and goats, respectively. Among lambs, individuals which eventually died from the infection were 1.93 times more infectious than lambs recovering. Beyond infectiousness, the relative contributions of host species to transmission depend on local ecological factors, including relative abundances and vector host-feeding preferences. Quantifying these contributions will ultimately help design efficient, targeted, surveillance and vaccination strategies.
Geographic distribution and future expansion ofAedes albopictusin the Democratic Republic of the Congo
Authors: Vulu Fabien , Bobanga Thierry Lengu , Sunahara Toshihiko , Futami Kyoko , Jinping Hu , Minakawa Noboru
Published: October 2021

Aedes albopictuswith an Asian origin has been reported from central African countries. The establishment of this mosquito species poses a serious threat as the vector of various infectious diseases. Since information aboutAe. albopictusin Democratic Republic of the Congo (DRC) is scarce, we investigated the current distribution of this mosquito species. Based on the factors affecting the distribution, we predicted future distribution. We conduced entomological surveys in Kinshasa and three neighboring cities from May 2017 to September 2019. The survey was extended to seven inland cities. A total of 19 environmental variables were examined using the maximum entropy method to identify areas suitable forAe. albopictusto establish a population. We foundAe. albopictusat 21 of 23 sites in Kinshasa and three neighboring cities. For the first timeAe. albopictuswas also found from three of seven inland cities, while it was not found in four cities located in the eastern and southeastern parts of DRC. A maximum entropy model revealed that the occurrence ofAe. albopictuswas positively associated with maximum temperature of the warmest month, and negatively associated with wider mean diurnal temperature range and enhanced vegetation index. The model predicted that most parts of DRC are suitable for the establishment of the mosquito. The unsuitable areas were the eastern and southeastern highlands, which have low temperatures and long dry seasons. We confirmed thatAe. albopictusis well established in Kinshasa and its neighboring cities. The expansion ofAe. albopictusto the inland is ongoing, and in the future the mosquito may establish in most parts of DRC.
Circadian programming of the ellipsoid body sleep homeostat in Drosophila
Authors: Andreani Tomas , Rosensweig Clark , Sisobhan Shiju , Ogunlana Emmanuel , Kath William , Allada Ravi
Published: October 2021

Homeostatic and circadian processes collaborate to appropriately time and consolidate sleep and wake. To understand how these processes are integrated, we scheduled brief sleep deprivation at different times of day in Drosophila and find elevated morning rebound compared to evening. These effects depend on discrete morning and evening clock neurons, independent of their roles in circadian locomotor activity. In the R5 ellipsoid body sleep homeostat, we identified elevated morning expression of activity dependent and presynaptic gene expression as well as the presynaptic protein BRUCHPILOT consistent with regulation by clock circuits. These neurons also display elevated calcium levels in response to sleep loss in the morning, but not the evening consistent with the observed time-dependent sleep rebound. These studies reveal the circuit and molecular mechanisms by which discrete circadian clock neurons program a homeostatic sleep center.
Green notes: The rhythms of cyanobacteria exoelectrogenesis as de-composed by the Hilbert-Huang transform
Authors: Okedi Tonny , Yunus Kamran , Fisher Adrian
Published: October 2021

1

Electrons from cyanobacteria photosynthetic and respiratory systems are implicated in current generated in biophotovoltaic (BPV) devices. However, the pathway that electrons follow to electrodes remains largely unknown, limiting progress of applied research. Here we use Hilbert-Huang transforms to decomposeSynechococcus elongatussp. PCC7942 BPV current density profiles into physically meaningful oscillatory components, and compute their instantaneous frequencies. We develop hypotheses for the genesis of the oscillationsviarepeat experiments with iron-depleted and 20% CO2enriched biofilms. The oscillations exhibit rhythms that are consistent with the state of the art cyanobacteria circadian model, and putative exoelectrogenic pathways. In particular, we observe oscillations consistent with: rhythmic D1:1 (photosystem II core) expression; circadian-controlled glycogen accumulation; circadian phase shifts under modified intracellular %ATP; and circadian period shortening in the absence of the iron-sulphur protein LdpA. We suggest that the extracted oscillations may be used to reverse-identify proteins and/or metabolites responsible for cyanobacteria exoelectrogenesis.
Sexual identity of enterocytes regulates rapamycin-mediated intestinal homeostasis and lifespan extension
Authors: Regan Jennifer C , Lu Yu-Xuan , Ureña Enric , Meilenbrock Ralf , Catterson James H , Kißler Disna , Partridge Linda
Published: October 2021

Pharmacological attenuation of mTOR by rapamycin and other compounds presents a promising route for delay of ageing-related pathologies, including intestinal cancers. Here, we show that rapamycin treatment in Drosophila extends lifespan in females but not in males. Female-specific, age-related gut pathology and impaired intestinal barrier function are both markedly slowed by rapamycin treatment, mediated by increased autophagy. Upon rapamycin treatment, female intestinal enterocytes increase autophagy, via the H3/H4 histone-Bchs axis, while male enterocytes show high basal levels of autophagy that do not increase further upon rapamycin treatment. Sexual identity of enterocytes alone, determined by the expression of transformerFemale, dictates sexually dimorphic cell size, H3/H4-Bchs expression, basal rates of autophagy, fecundity, intestinal homeostasis and extension of lifespan in response to rapamycin. This study highlights that tissue sex determines regulation of metabolic processes by mTOR and the efficacy of mTOR-targeted, anti-ageing drug treatments.
Early epigenetic influence on EGR1, KLF2 and KLF4 transcriptional network associates with alteration of HSCs quiescence
Authors: Pelletier Alexandre , Carrier Arnaud , Zhao Yong Mei , Canouil Mickaël , Derhourhi Mehdi , Durand Emmanuelle , Berberian-Ferrato Lionel , Greally John , Hughes Francine , Froguel Philippe , Bonnefond Amélie , Delahaye Fabien
Published: October 2021

Excessive fetal growth is associated with DNA methylation alterations in human hematopoietic stem and progenitor cells (HSPC), but their functional impact remains elusive. We implemented an integrative analysis combining single-cell epigenomics, single-cell transcriptomics, and in vitro analyses to functionally link DNA methylation changes to putative alterations of HSPC functions. We showed in hematopoietic stem cells (HSC) from large for gestational age neonates that both DNA hypermethylation and chromatin rearrangement target a specific network of transcription factors known to sustain stem cell quiescence. In parallel, we found a decrease expression of key genes regulating HSC differentiation including EGR1, KLF2, SOCS3, and JUNB. Our functional analyses showed that this epigenetic programming was associated with a decreased ability for HSCs to stay quiescent. Taken together, our multimodal approach using single-cell (epi)genomics showed that human fetal overgrowth affects hematopoietic stem cells quiescence maintenance via epigenetic programming.
Altered collective mitochondrial dynamics in an Arabidopsis msh1 mutant compromising organelle DNA maintenance
Authors: Chustecki Joanna M. , Etherington Ross D. , Gibbs Daniel J. , Johnston Iain G.
Published: October 2021

Mitochondria form highly dynamic populations in the cells of plants (and all eukaryotes). The characteristics of this collective behaviour, and how it is influenced by nuclear features, remain to be fully elucidated. Here, we use a recently-developed quantitative approach to reveal and analyse the physical and collective “social” dynamics of mitochondria in an Arabidopsis msh1 mutant where organelle DNA maintenance machinery is compromised. We use a newly-created line combining the msh1 mutant with mitochondrially-targeted GFP, and characterise mitochondrial dynamics with a combination of single-cell timelapse microscopy, computational tracking and network analysis. The collective physical behaviour of msh1 mitochondria is altered from wildtype in several ways: mitochondria become less evenly spread, and networks of inter-mitochondrial encounters become more connected with greater potential efficiency for inter-organelle exchange. We find that these changes are similar to those observed in friendly, where mitochondrial dynamics are altered by a physical perturbation, suggesting that this shift to higher connectivity may reflect a general response to mitochondrial challenges.
Tickle contagion in the somatosensory cortex
Authors: Kaufmann Lena V. , Brecht Michael , Ishiyama Shimpei
Published: October 2021

The cellular mechanisms of emotional contagion are unknown. We investigated tickle contagion and the underlying neuronal representations in rats. We recorded trunk somatosensory cortex activity of observer rats while they received tickling, audio-visual playback of tickling footage, and while they witnessed tickling of demonstrator rats. Observers vocalized, and showed “Freudensprünge” (“joy jumps”) during witnessing live tickling, while they showed little behavioral responses to playbacks. A fraction of trunk somatosensory neurons responded to both direct and witnessed tickling in action-specific manner. The correlation between direct and witnessed tickling responses increased towards deeper cortical layers. Tickle-mirror neurons but not non-mirror neurons discharged prior to and during vocalizations and hence might drive contagious ‘laughter’. We conclude that trunk somatosensory cortex represents mirrored ticklishness.
TransferGWAS: GWAS of images using deep transfer learning
Authors: Kirchler Matthias , Konigorski Stefan , Norden Matthias , Meltendorf Christian , Kloft Marius , Schurmann Claudia , Lippert Christoph
Published: October 2021

Abstract

Motivation

Medical images can provide rich information about diseases and their biology. However, investigating their association with genetic variation requires non-standard methods. We propose transferGWAS, a novel approach to perform genome-wide association studies directly on full medical images. First, we learn semantically meaningful representations of the images based on a transfer learning task, during which a deep neural network is trained on independent but similar data. Then, we perform genetic association tests with these representations.

Results

We validate the type I error rates and power of transferGWAS in simulation studies of synthetic images. Then we apply transferGWAS in a genome-wide association study of retinal fundus images from the UK Biobank. This first-of-a-kind GWAS of full imaging data yielded 60 genomic regions associated with retinal fundus images, of which 7 are novel candidate loci for eye-related traits and diseases.

Contact

matthias.kirchler@hpi.de, christoph.lippert@hpi.de

Supplementary information

Our method is implemented in Python and available at https://github.com/mkirchler/transferGWAS/
Longitudinal single-cell transcriptional dynamics throughout neurodegeneration in SCA1
Authors: Tejwani Leon , Ravindra Neal G , Nguyen Billy , Luttik Kimberly , Lee Changwoo , Gionco John , Kim Kristen , Yoon Jennifer , Haidery Fatema , Ro Hannah , Ni Luhan , Orr Harry T , Ranum Laura PW , Shakkottai Vikram G , Faust Phyllis L , van Dijk David , Lim Janghoo
Published: October 2021

Neurodegeneration is a protracted process involving progressive changes in myriad cell types that ultimately result in neuronal death. Changes in vulnerable neuronal populations are highly influenced by concomitant changes in surrounding cells, complicating experimental approaches to interrogate the simultaneous events that underlie neurodegeneration. To dissect how individual cell types within a heterogeneous tissue contribute to the pathogenesis and progression of a neurodegenerative disorder, we performed longitudinal single-nucleus RNA sequencing of the mouse and human spinocerebellar ataxia type 1 (SCA1) cerebellum, establishing continuous dynamic trajectories of each population. Furthermore, we defined the precise transcriptional changes that precede loss of Purkinje cells and identified early oligodendroglial impairments that can profoundly impact cerebellar function. Finally, we applied a deep learning method to accurately predict disease state and identify drivers of disease. Together, this work uncovers new roles for diverse cerebellar cell types in SCA1 and provides a generalizable analysis framework for studying neurodegeneration.
Hierarchical Bayesian Modeling of the Relationship between Task Related Hemodynamic Responses and Cortical Excitability
Authors: Cai Zhengchen , Pellegrino Giovanni , Lina Jean-Marc , Benali Habib , Grova Christophe
Published: October 2021

Background

Investigating the relationship between task-related hemodynamic responses and cortical excitability is challenging because it requires simultaneous measurement of hemodynamic responses while applying non-invasive brain stimulation. Moreover, cortical excitability and task-related hemodynamic responses are both associated with inter-/intra-subject variability. To reliably assess such a relationship, we applied hierarchical Bayesian modeling.

Methods

This study involved 16 healthy subjects who underwent simultaneous Paired Associative Stimulation (PAS10, PAS25, Sham) while monitoring brain activity using functional Near-Infrared Spectroscopy (fNIRS), targeting the primary motor cortex (M1). Cortical excitability was measured by Motor Evoked Potentials (MEPs), and the motor task-related hemodynamic responses were measured using fNIRS 3D reconstructions. We constructed three models to investigate: 1) PAS effects on the M1 excitability; 2) PAS effects on fNIRS hemodynamic responses to a finger tapping task, and 3) the correlation between PAS effects on M1 excitability and PAS effects on task-related hemodynamic responses.

Results

Significant increase in cortical excitability was found following PAS25, whereas a small reduction of the cortical excitability was shown after PAS10 and a subtle increase occurred after sham. Both HbO and HbR absolute amplitudes increased after PAS25 and decreased after PAS10. The probability of the positive correlation between modulation of cortical excitability and hemodynamic activity was 0.77 for HbO and 0.79 for HbR.

Conclusion

We demonstrated that PAS stimulation modulates task-related cortical hemodynamic responses in addition to M1 excitability. Moreover, the positive correlation between PAS modulations of excitability and hemodynamics brought insight into understanding the fundamental properties of cortical function and cortical excitability.
Dynamic Cell Imaging: application to the diatom Phaeodactylum tricornutum under environmental stresses
Authors: Bey Houda , Charton Florent , de Carvalho Helena Cruz , Liu Shun , Dorrell Richard G. , Bowler Chris , Boccara Claude , Boccara Martine
Published: October 2021

The dynamic movement of cell organelles is an important and poorly understood component of cellular organisation and metabolism. In this work we present a non-invasive non-destructive method (Dynamic Cell Imaging, DCI) based on light scattering and interferometry to monitor dynamic events within photosynthetic cells using the diatom Phaeodactylum tricornutum as a model system. For this monitoring we acquire few seconds movies of the signals that are related to the motion of dynamic structures within the cell (denoted scatterers), followed by a statistical analysis of each pixel time series. Illuminating P.tricornutum with LEDs of different wavelengths associated to short pulsed or continuous-wave modes of illumination revealed that dynamic movements depend on chloroplast activity, in agreement with the reduction in the number of pixels with dynamic behaviour after addition of photosystemII inhibitors. We studied P. tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. The major dynamic sites were located within lipid droplets and chloroplast envelope membranes. By comparing standard deviation and cumulative sum analysis of the time series, we showed that within the droplets two types of scatterer movement could be observed: random motions (Brownian type) but also anomalous movements corresponding to a drift which may relate to molecular fluxes within a cell. The method appears valuable for studying the effects of various environments on a large variety of microalgae in the laboratory as well as in natural aquatic environments.

HIGHLIGHTs

Light scattering an alternative to fluorescence to rapidly evidence dynamic processes.

Lipid droplets the major metabolic active sites under stress

A non-destructive visualisation method for laboratory microalgae and aquatic samples..

SIGNIFICANCE STATEMENT

Light scattering could be an alternative to fluorescence techniques to study dynamic processes within photosynthetic cells. We used a method combining light scattering and interferometry to analyse movements of intracellular scatterers in the marine diatom Phaedactylum tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. Lipid droplets were the major active sites under stress. The method which is rapid and non destructive can be broadly expanded to study other microalgae and their stress responses, in the laboratory and in aquatic environments.
Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET
Authors: Pandey Kushagra , Zafar Hamim
Published: October 2021

Despite recent advances in inferring cellular dynamics using single-cell RNA-seq data, existing trajectory inference (TI) methods face difficulty in accurately reconstructing cell-state manifold and inferring trajectory and cell fate plasticity for complex topologies. We present MARGARET, a novel TI method that utilizes a deep unsupervised metric learning-based approach for inferring the cellular embeddings and employs a novel measure of connectivity between cell clusters and a graph-partitioning approach to reconstruct complex trajectory topologies. MARGARET utilizes the inferred trajectory for determining terminal states and inferring cell-fate plasticity using a scalable absorbing Markov Chain model. On a diverse simulated benchmark, MARGARET out-performed state-of-the-art methods in recovering global topology and cell pseudotime ordering. When applied to experimental datasets from hematopoiesis, embryogenesis, and colon differentiation, MARGARET reconstructed major lineages and associated gene expression trends, better characterized key branching events and transitional cell types, and identified novel cell types, and branching events that were previously uncharacterized.
Oral administration of bacterial Beta cell expansion factor A (BefA) alleviates diabetes in mice with Type 1 and Type 2 diabetes
Authors: Wang Huan , Wei Jing , Hu Hong , Le Fuyin , Wu Heng , Wei Hong , Luo Jie , Chen Tingtao
Published: October 2021

Diabetes mellitus (DM) is a group of metabolic diseases, which is of urgent need to develop new therapeutic DM oral drugs with less side effects and sound therapeutic efficacy. In this study, a Beta cell expansion factor A (BefA) production strain of Escherichia Coli BL21-pet 28C-BefA was constructed, and the anti-diabetes effect of BefA was evaluated using type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM) mice models. The T1DM mice results indicated that BefA significantly reduced the blood glucose level, exerted protective function of islet β cell morphology, down-regulated the TLR-4, p-NFκB/NFκB, Bax/Bcl-2 expressions and the secretion level of IL-1β, TNF-α, increased the expression of PDX-1 protein and insulin secretion in a concentration-dependent manner, and restored the disturbed microbial diversity to normal level. Similar with the T1DM mice, BefA obviously increased islet β cells, reduced inflammatory reaction and apoptosis in T2DM mice, and also improved liver lipid metabolism by down-regulating the expression of CEBP-α, ACC, Fasn and inhibiting the synthesis of triglyceride and induce Cpt-1, Hmgcs2, Pparα in a concentration-dependent manner. In the present study, we verified therapeutic effect and potential mechanisms of BefA in mammal for the first time, providing basic data for its clinical application.
Predominance of clonal propagationconceals extinction risks of the highly endangered floodplain herbCnidium dubium
Authors: Leyer Ilona , Ziegenhagen Birgit , Mengel Christina , Mosner Eva , Liepelt Sascha
Published: October 2021

Habitat loss and degradation due to human-induced landscape alterations are considered to be a major threat to biodiversity. The decline of biodiversity may occur with a time delay leading to a so called extinction debt. Therefore, determining extinction risks and conservation status is not always straightforward. Several life history traits might play a role for the accumulation of an extinction debt. Thus, perennial plant species capable of vegetative propagation might be able to persist temporarily in degraded habitats even though sexual and evolutionary processes are effectively halted.

We studiedCnidium dubium, which occurs in scattered patches along river corridors in Central Europe and is critically endangered in Germany. It is a perennial species which is able to propagate clonally. Our aims were to reconstruct demographic processes regarding clonal propagation and gene flow along 400 km of river stretch and with respect to the position in the flooplain, i.e. before or behind dykes. We also wanted to determine whether there is evidence for an extinction debt inC. dubiumand to use our insights for conservation recommendations.

For this, we used nuclear microsatellites and maternally inherited chloroplast DNA markers and applied a systematic grid based sampling strategy for small scale geographic structures.

We observed a high level of clonal propagation. In 935 analysed plants we observed only 121 different genotypes and of 50 studied patches ofC. dubiumthe majority (31 patches) consisted of one single genotype each. Patch size and position were correlated with clonal diversity. Large patches and patches behind dykes exhibited higher clonal diversity. There was no evidence for a large scale genetic substructuring of the study area and no differences in overall genetic diversity between upstream and downstream patches as well as between patches before and behind the dykes. High levels of heterozygosity and a high number of 18 chloroplast DNA haplotypes togetherwith a slightly elevated inbreeding coefficient (Fis) point toward a high level of ancestral polymorphism in an out of equilibrium population due to high levels of clonal propagation and low levels of gene flow and recombination. Therefore, we assume that an extinction debt is present in C. dubium. As a management strategy, we propose to transplant ramets between multiple patches to increase the number of mating partners and therefore restore sexual reproduction.
Shared hotspot mutations in spontaneously arising cancers position dog as an unparalleled comparative model for precision therapeutics
Authors: Rodrigues Lucas , Watson Joshua , Feng Yuan , Lewis Benjamin , Harvey Garrett , Post Gerald , Megquier Kate , Lambert Lindsay , Miller Aubrey , Lopes Christina , Zhao Shaying
Published: October 2021

Naturally occurring canine cancers have remarkable similarities to their human counterparts. In order to determine whether these similarities occur at the molecular level, we investigated hotspot mutations in a variety of spontaneously arising canine cancers and found high concordance in oncogenic drivers between cancers in both species. These findings suggest that canines may present a powerful and complementary model for preclinical investigations for targeted cancer therapeutics. Through analysis of 708 client-owned dogs from 96 breeds (plus mixed breeds) with 23 common tumor types, we discovered mutations in 50 well-established oncogenes and tumor suppressors, and compared them to those reported in human cancers. TP53 is the most commonly mutated gene, detected in 30.81% of canine tumors overall and >40% in hemangiosarcoma and osteosarcoma. Canine tumors share mutational hotspots with human tumors in oncogenes including PIK3CA, KRAS, NRAS, BRAF, KIT and EGFR. Hotspot mutations with significant (P<0.0001) association to tumor type include NRAS G61R and PIK3CA H1047R in hemangiosarcoma, ERBB2 V659E in pulmonary carcinoma, and BRAF V588E in urothelial carcinoma. This work positions canines as excellent spontaneous models of human cancers that can help to investigate a wide spectrum of targeted therapies.
An Unsupervised Machine Learning Paradigm for Artifact Removal from Electrodermal Activity in an Uncontrolled Clinical Setting
Authors: Subramanian Sandya , Tseng Bryan , Barbieri Riccardo , Brown Emery N.
Published: October 2021

Objective

Electrodermal activity (EDA) reflects sympathetic nervous system activity through sweating-related changes in skin conductance. To enable EDA data to be used robustly in clinical settings, we need to develop artifact detection and removal frameworks that can handle the types of interference experienced in clinical settings.

Methods

We collected EDA data from 69 subjects while they were undergoing surgery in the operating room. We then built an artifact removal framework using unsupervised learning methods and informed features to remove the heavy artifact that resulted from the use of surgical electrocautery during the surgery and compared it to other existing methods for artifact removal from EDA data.

Results

Our framework was able to remove the vast majority of artifact from the EDA data across all subjects with high sensitivity (94%) and specificity (90%). In contrast, existing methods used for comparison struggled to be sufficiently sensitive and specific, and none effectively removed artifact even if it was identifiable. In addition, the use of unsupervised learning methods in our framework removes the need for manually labeled datasets for training.

Conclusion

Our framework allows for robust removal of heavy artifact from EDA data in clinical settings such as surgery. Since this framework only relies on a small set of informed features, it can be expanded to other modalities such as ECG and EEG.

Significance

Robust artifact removal from EDA data is the first step to enable clinical integration of EDA as part of standard monitoring in settings such as the operating room.
Symmetric Inheritance of Histones H3 in Drosophila Male Germline Stem Cell Divisions
Authors: Ray Julie , Maggert Keith A.
Published: October 2021

Mitotically-stable “epigenetic” memory requires a mechanism for the maintenance of gene-regulatory information through the cell division cycle. Typically DNA-protein contacts are disrupted by DNA replication, but in some cases locus-specific association between DNA and overlying histones may appear to be maintained, providing a plausible mechanism for the transmission of histone-associated gene-regulatory information to daughter cells. Male Drosophila melanogaster testis germ stem cell divisions seem a clear example of such inheritance, as previously chromatin-bound Histone H3.2 proteins (presumably with their post-translational modifications intact) have been reported to be retained in the germ stem cell nuclei, while newly synthesized histones are incorporated into daughter spermatogonial chromosomes. To investigate the rate of errors in this selective partitioning that may lead to defects in the epigenetic identity of germ stem cells, we employed a photoswitchable Dendra2 moiety as a C-terminal fusion on Histones H3 (Histone H3.2 and Histone H3.3); we could thereby discriminate histones translated before photoswitching and those translated after. We found instead that male germ line stem cell divisions show no evidence of asymmetric histone partitioning, even after a single division, and thus no evidence for locus-specific retention of either Histone H3.2 or Histone H3.3. We considered alternative hypotheses for the appearance of asymmetry and find that previous reports of asymmetric histone distribution in male germ stem cells can be satisfactorily explained by asynchrony between subsequent sister stem cell and spermatogonial divisions.
Bioactive constituents ofVerbena officinalisalleviate inflammation and enhance killing efficiency of natural killer cells
Authors: Dai Xiangdong , Zhou Xiangda , Shao Rui , Zhao Renping , Yanamandra Archana K. , Xing Zhimei , Ding Mingyu , Wang Junhong , Zhang Han , Wang Yi , Zheng Qi , Zhang Peng , Qu Bin , Wang Yu
Published: October 2021

Natural killer (NK) cells play a key role in eliminating pathogen-infected cells.Verbena officinalis(V. officinalis) has been used as a medical plant in traditional and modern medicine, exhibiting anti-tumor and anti-inflammation activities, but its roles in immune responses still remains largely elusive. In this work, investigated the regulation of inflammation and NK functionsby V. officinalisextract (VO-extract). In an influenza virus infection mouse model, oral administration of VO-extract alleviated lung injury, promoted maturation and activation of NK cells residing in the lung, and decreased the levels of inflammatory cytokines (IL-6, TNF-α and IL-1β) in the serum. We further analyzed the impact of five bioactive components of VO-extract on NK killing functions. Among them, Verbenalin enhanced NK killing efficiency significantly as determined by real-time killing assays based on plate-reader or high-throughput live-cell imaging in 3D using primary human NK cells. Further investigation showed that treatment of Verbenalin accelerated killing processes by reducing the contact time of NK cells with their target cells without affecting NK proliferation, expression of cytotoxic proteins, or lytic granule degranulation. Together, our findings reveal that low doses ofV. officinaliscan achieve a satisfactory anti-inflammation effect against viral infectionin vivo, andV. officinalisregulates activation, maturation and killing functions of NK cells. NK killing efficiency is enhanced by Verbenalin fromV. officinalis, suggesting a promising potential of verbenalin to fight viral infection.
Regulation of Neuroendocrine Plasticity by the RNA-Binding Protein ZFP36L1
Authors: Chen Hsiao-Yun , Durmaz Yavuz T. , Li Yixiang , Sabet Amin H. , Vajdi Amir , Denize Thomas , Walton Emily , Doench John G. , Mahadevan Navin R. , Losman Julie-Aurore , Barbie David A. , Tolstorukov Michael Y. , Rudin Charles M. , Sen Triparna , Signoretti Sabina , Oser Matthew G.
Published: October 2021

Some small cell lung cancers (SCLCs) are highly sensitive to inhibitors of the histone demethylase LSD1. LSD1 inhibitors are thought to induce their anti-proliferative effects by blocking neuroendocrine differentiation, but the mechanisms by which LSD1 controls the SCLC neuroendocrine phenotype are not well understood. To identify genes required for LSD1 inhibitor sensitivity in SCLC, we performed a positive selection genome-wide CRISPR/Cas9 loss of function screen and found that ZFP36L1, an mRNA-binding protein that destabilizes mRNAs, is required for LSD1 inhibitor sensitivity. LSD1 binds and represses ZFP36L1 and upon LSD1 inhibition, ZFP36L1 expression is restored, which is sufficient to block the SCLC neuroendocrine differentiation phenotype and induce a non-neuroendocrine “inflammatory” phenotype. Mechanistically, ZFP36L1 binds and destabilizes SOX2 and INSM1 mRNAs, two transcription factors that are required for SCLC neuroendocrine differentiation. This work identifies ZFP36L1 as an LSD1 target gene that controls the SCLC neuroendocrine phenotype and demonstrates that modulating mRNA stability of lineage transcription factors controls neuroendocrine to non-neuroendocrine plasticity.