bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying contact patterns: development and characteristics of the British Columbia COVID-19 population mixing patterns survey (BC-Mix)
Authors: Adu Prince A. , Binka Mawuena , Mahmood Bushra , Jeong Dahn , Buller-Taylor Terri , Damascene Makuza Jean , Iyaniwura Sarafa , Ringa Notice , Velásquez García Héctor A. , Wong Stanley , Yu Amanda , Bartlett Sofia , Wilton James , Irvine Mike A. , Otterstatter Michael , Janjua Naveed Z.
Published: August 2021

Introduction

Several non-pharmaceutical interventions such as physical distancing, hand washing, self-isolation, and schools and business closures, were implemented in British Columbia (BC) following the first laboratory-confirmed case of coronavirus disease 2019 (COVID-19) on January 26, 2020, to minimize in-person contacts that could spread infections. The BC COVID-19 Population Mixing Patterns survey (BC-Mix) was established as a surveillance system to measure behaviour and contact patterns in BC over time to inform the timing of the easing/re-imposition of control measures. In this paper, we describe the BC-Mix survey design and the demographic characteristics of respondents.

Methods

The ongoing repeated online survey was launched in September 2020. Participants are mainly recruited through social media platforms (including Instagram, Facebook, YouTube, WhatsApp). A follow up survey is sent to participants two to four weeks after completing the baseline survey. Survey responses are weighted to BC’s population by age, sex, geography, and ethnicity to obtain generalizable estimates. Additional indices such as the material and social deprivation index, residential instability, economic dependency, and others are generated using census and location data.

Results

As of July 26, 2021, over 61,000 baseline survey responses were received of which 41,375 were eligible for analysis. Of the eligible participants, about 60% consented to follow up and about 27% provided their personal health numbers for linkage with healthcare databases. Approximately 50% of respondents were female, 39% were 55 years or older, 65% identified as white and 50% had at least a university degree.

Conclusion

The pandemic response is best informed by surveillance systems capable of timely assessment of behaviour patterns. BC-Mix survey respondents represent a large cohort of British Columbians providing near real-time information on behavioural and contact patterns in BC. Data from the BC-Mix survey would inform provincial COVID-19-related control measures.
SCL28 promotes cell expansion and endoreplication in Arabidopsis by activatingSIAMESE-RELATEDcyclin-dependent kinase inhibitors
Authors: Goldy Camila , Barrera Virginia , Taylor Isaiah , Buchensky Celeste , Vena Rodrigo , Benfey Philip N. , De Veylder Lieven , Rodriguez Ramiro E.
Published: August 2021

The processes that contribute to plant organ morphogenesis are spatial-temporally organized. Within the meristem the mitotic cell cycle produces new cells that subsequently engage in specific cell expansion and differentiation programs once they exit the division competent zone. The latter is frequently accompanied by endoreplication, being an alternative cell cycle that replicates the DNA without nuclear division, causing a stepwise increase in somatic ploidy. We have previously shown that the Arabidopsis SCL28 transcription factor promotes progression through G2/M and modulates division plane orientation. Here, we demonstrate thatSCL28co-express and regulates genes specific to cell elongation and differentiation, including genes related to cell wall and cytoskeleton assembly. Consistently, this correlates with defects in post-mitotic cell expansion in ascl28mutant. Strikingly, SCL28 controls expression of 6 members of theSIAMESE/SIAMESE-RELATED(SIM/SMR) family, encoding cyclin-dependent kinase inhibitors with a role in promoting mitotic cell cycle exit and endoreplication onset, both in response to developmental and environmental cues. Consistent with this role,scl28mutants displayed reduced endoreplication, both in roots and leaves. Altogether, these results suggest thatSCL28controls cell expansion and differentiation by promoting endoreplication onset and by modulating aspects of the biogenesis, assembly and remodeling of the cytoskeleton and cell wall.
Assessment of 3D MINFLUX data for quantitative structural biology in cells
Authors: Prakash Kirti , Curd Alistair P.
Published: August 2021

MINFLUX is a promising new development in single-molecule localization microscopy, claiming a resolution of 1-3 nm in living and fixed biological specimens. While MINFLUX can achieve very high localisation precision, quantitative analysis of reported results leads us to dispute the resolution claim and question reliability for imaging sub-100-nm structural features, in its current state.
Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing
Authors: Peterka Martin , Akrap Nina , Li Songyuan , Wimberger Sandra , Hsieh Pei-Pei , Degtev Dmitrii , Bestas Burcu , Barr Jack , van de Plassche Stijn , Mendoza-Garcia Patricia , Šviković Saša , Sienski Grzegorz , Firth Mike , Maresca Marcello
Published: August 2021

Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two novel strategies that install precise genomic insertions using an SpCas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing lead to increased levels of by-products, it rescued pegRNAs that performed poorly with a nickase-based prime editor. We also present a small molecule approach that yielded increased product purity of PEn editing. Next, we developed a homology-independent PEn editing strategy by engineering a single primed insertion gRNA (springRNA) which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells.
Rationalizing generation of broad spectrum antibiotics with the addition of a primary amine
Authors: Haloi Nandan , Vasan Archit Kumar , Geddes Emily , Prasanna Arjun , Wen Po-Chao , Metcalf William W. , Hergenrother Paul , Tajkhorshid Emad
Published: August 2021

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and while forming favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.
MYCN mediates cysteine addiction and sensitizes to ferroptosis
Authors: Alborzinia Hamed , Flórez Andrés F. , Gogolin Sina , Brückner Lena M. , Shao Chunxuan , Gartlgruber Moritz , Nadler-Holly Michal , Ziehm Matthias , Paul Franziska , Steinhauser Sebastian , Bell Emma , Shaikhkarami Marjan , Hartlieb Sabine , Dreidax Daniel , Hess Elisa M. , Kreth Jochen , Poschet Gernot , Büttner Michael , Nicke Barbara , Stresemann Carlo , Reiling Jan H. , Fischer Matthias , Amit Ido , Selbach Matthias , Herrmann Carl , Wölfl Stefan , Henrich Kai-Oliver , Höfer Thomas , Westermann Frank
Published: August 2021

Aberrant expression of MYC family members predicts poor clinical outcome in many human cancers. Oncogenic MYC profoundly alters metabolism and mediates an antioxidant response to maintain redox balance. Here we show that MYC induces massive lipid peroxidation upon depletion of cysteine, the rate-limiting amino acid for glutathione biosynthesis and sensitizes cells to ferroptosis, an oxidative, non-apoptotic and irondependent type of cell death. In MYCN-amplified childhood neuroblastoma, MYCN mediates resistance to ferroptosis by activating transsulfuration of methionine to cysteine. MYCN may contribute to spontaneous tumor regression in low-risk neuroblastomas by promoting ferroptosis in cells with epigenetically silenced cystathionine-beta-synthase, the rate-limiting enzyme for transsulfuration. We identified enzymes and antiporter proteins crucial to ferroptotic escape, providing multiple previously unknown sites that may be acted on therapeutically.
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq
Authors: Missarova Alsu , Jain Jaison , Butler Andrew , Ghazanfar Shila , Stuart Tim , Brusko Maigan , Wasserfall Clive , Nick Harry , Brusko Todd , Atkinson Mark , Satija Rahul , Marioni John
Published: August 2021

The problem of selecting targeted gene panels that capture maximum variability encoded in scRNA-sequencing data has become of great practical importance. scRNA-seq datasets are increasingly being used to identify gene panels that can be probed using alternative molecular technologies, such as spatial transcriptomics. In this context, the number of genes that can be probed is an important limiting factor, so choosing the best subset of genes is vital. Existing methods for this task are limited by either a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cell types. We resolve this by introducing an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. We demonstrate, using a variety of metrics and diverse datasets, that our approach outperforms existing strategies, and can not only resolve cell types but also more subtle cell state differences. Our approach is available as an open source, easy-to-use, documented R package (https://github.com/MarioniLab/geneBasisR).
Development of motor neurons and motor activity in zebrafish requires F-actin nucleation by Fmn2b
Authors: Nagar Dhriti , Carrington Blake , Burgess Shawn M , Ghose Aurnab
Published: August 2021

Background

Cytoskeletal remodelling plays a pivotal role in the establishment of neuronal connectivity during development and in plasticity in adults. Mutations in the cytoskeleton regulatory protein Formin-2 (Fmn2) are associated with neurodevelopmental disorders like intellectual disability, though its function in neuronal morphogenesis has not been characterisedin vivo.

Results

Here we develop a loss-of-function model forfmn2b, the zebrafish orthologue of Fmn2, using CRISPR/Cas9-mediated gene editing.fmn2bmutants display motor deficits starting from the earliest motor responses in the embryo. We find thatfmn2bis expressed in spinal motor neurons and its loss reduces motor neuron innervation of the axial muscles without affecting myotome integrity. The translocation of caudal primary (CaP) motor neuron outgrowth is compromised infmn2bmutants, while rostral primary (RoP) motor neurons have missing soma or stall at the horizontal myoseptum. Strikingly, axon collateral branching of the motor neurons is severely compromised and results in reduced synaptic coverage of the myotome. Rescue experiments identify the requirement for Fmn2-mediated actin nucleation for motor neuron outgrowth and arborisation.

Conclusions

The zebrafish loss-of-function model of Fmn2 reveals the specific requirement of F-actin polymerisation by Fmn2 in neuromuscular development. It also underscores the role of Fmn2 in motor neuropathies, especially as a proportion of individuals harbouring mutations in Fmn2 present with hypotonia.
Estimating Intraclonal Heterogeneity and Subpopulation Changes from Perturbational Bulk Gene Expression Profiles in LINCS L1000 CMap by Premnas
Authors: Hsieh Chiao-Yu , Tu Ching-Chih , Hung Jui-Hung
Published: August 2021

Background

The connectivity among signatures upon perturbations curated in the CMap library provides a valuable resource for understanding therapeutic pathways and biological processes associated with the drugs and diseases.

Motivation

However, due to the nature of bulk-level expression profiling by the L1000 assay, intraclonal heterogeneity and subpopulation compositional change that could contribute to the responses to perturbations are largely neglected, hampering the interpretability and reproducibility of the connections.

Results

In this work, we proposed a computational framework, Premnas, to estimate the abundance of undetermined subpopulations from L1000 profiles in CMap directly according to an ad hoc subpopulation representation learned from a well-normalized batch of single-cell RNA-seq datasets by the archetypal analysis. By recovering the information of subpopulation changes upon perturbation, the potentials of searching for drug cocktails and drug-resistant/susceptible subpopulations with CMap L1000 were further explored and examined.

Conclusions

The proposed framework enables a new perspective to understand the connectivity among cellular signatures and expands the scope of the CMAP and other similar perturbation datasets limited by the bulk profiling technology. The executable and source code of Premnas is freely available athttps://github.com/jhhung/Premnas.

Highlights

A computational framework (i.e., Premnas) for learning subpopulation characteristics by the archetypal analysis and deconvoluting bulk expression profiles using the digital cytometry into subpopulation composition was proposed and validated.

Intraclonal heterogeneity and subpopulation changes upon different perturbagen treatments in LINCS CMap L1000 datasets were estimated by Premnas.

With Premnas, we introduced a new strategy of finding effective drug cocktails and further linked the drug-resistant subpopulation found in CMap L1000 to a known drug-resistant clone (i.e., the pre-adapted [PA] cell).

To our best knowledge, this work is the first attempt to provide a new subpopulation perspective to CMap database.

We believe Premnas can be applied to all the perturbation datasets, of which intraclonal/intratumoral heterogeneity was concealed by the bulk profiling and hereafter provides a new dimension of interpreting the connectivity.
CD155 and EndoA1 mediate growth and tissue invasion downstream of MAP4K4 in medulloblastoma cells
Authors: Capdeville Charles , Russo Linda , Penton David , Migliavacca Jessica , Zecevic Milica , Gries Alexandre , Neuhauss Stephan C.F. , Grotzer Michael A. , Baumgartner Martin
Published: August 2021

The composition of the plasma membrane (PM)-associated proteome of tumor cells determines cell-cell and cell-matrix interactions and the response to environmental cues. Whether the PM-associated proteome impacts the phenotype of Medulloblastoma (MB) tumor cells and how it adapts in response to growth factor cues is poorly understood. Using a spatial proteomics approach, we observed that hepatocyte growth factor (HGF)-induced activation of the receptor tyrosine kinase c-MET in MB cells changes the abundance of transmembrane and membrane-associated proteins. The depletion of MAP4K4, a pro-migratory effector kinase downstream of c-MET, leads to a specific decrease of the adhesion and immunomodulatory receptor CD155 and of components of the fast-endophilin-mediated endocytosis (FEME) machinery in the PM-associated proteome of HGF-activated MB cells. The decreased surface expression of CD155 or of the FEME effector Endophilin A1 reduces growth and invasiveness of MB tumor cells in the tissue context. These data thus describe a novel function of MAP4K4 in the control of the PM-associated proteome of tumor cells and identified two downstream effector mechanisms controlling proliferation and invasiveness of MB cells.

Graphical abstract

c-MET activation upon HGF stimulation induces c-MET internalization and induces downstream MAP4K4 activity. (1) MAP4K4 is required downstream of activated c-MET for the maintenance of surface presentation of CD155 in activated cells. CD155 expression is required for MB cell migration, invasion and proliferation in the tissue context. (2) MAP4K4 is required downstream of activated c-MET to maintain membrane depolarization, possibly by regulating the surface localization of several ion channels and transporters. (3) MAP4K4 is required downstream of activated c-MET cause PM-proximal localization of FEME effector CIP4, FBP17 and CIN85. The FEME effector endophilin A is necessary for MB cell migration, invasion and dissemination.
Echolocating whales use ultra-fast echo-kinetic responses to track evasive prey
Authors: Vance Heather Margaret , Madsen Peter Teglberg , Aguilar de Soto Natacha , Wisniewska Danuta Maria , Ladegaard Michael , Hooker Sascha Kate , Johnson Mark
Published: August 2021

Visual predators rely on fast-acting optokinetic reflexes to track and capture agile prey. Most toothed whales, however, rely on echolocation for hunting and have converged on biosonar clicking rates reaching 500/s during prey pursuits. If echoes are processed on a click-by-click basis, as assumed, neural responses 100x faster than those in vision are required to keep pace with this information flow. Using high-resolution bio-logging of wild predator-prey interactions we show that toothed whales adjust clicking rates to track prey movement within 50-200ms of prey escape responses. Hypothesising that these stereotyped biosonar adjustments are elicited by sudden prey accelerations, we measured echo-kinetic responses from trained harbour porpoises to a moving target and found similar latencies. High biosonar sampling rates are, therefore, not supported by extreme speeds of neural processing and muscular responses. Instead, the neuro-kinetic response times in echolocation are similar to those of tracking reflexes in vision, suggesting a common neural underpinning.
Retinoids rescue ceruloplasmin secretion and alleviate oxidative stress in Wilson’s disease-specific hepatocytes
Authors: Song Dan , Takahashi Gou , Zheng Yun-Wen , Matsuo-Takasaki Mami , Li Jingyue , Takami Miho , An Yuri , Hemmi Yasuko , Miharada Natsumi , Fujioka Tsuyoshi , Noguchi Michiya , Nakajima Takashi , Saito Megumu K. , Nakamura Yukio , Oda Tatsuya , Miyaoka Yuichiro , Hayashi Yohei
Published: August 2021

Wilson’s disease (WD) is a copper metabolic disorder, which is caused by defective ATP7B function. Here, we have generated induced pluripotent stem cells (iPSCs) from WD patients carrying compound heterozygous mutations on ATP7B. ATP7B loss- and gain-of-functions were further manifested with ATP7B-deficient iPSCs and heterozygously-corrected R778L WD patient-derived iPSCs using CRISPR-Cas9-based gene editing. Transcriptome analysis identified abnormalities of retinoid signaling pathway and lipid metabolism in WD-specific hepatocytes. Although the expression level of ATP7B protein was variable among WD-specific hepatocytes, the expression and secretion of ceruloplasmin (Cp), which is a downstream copper carrier in plasma, were consistently decreased. Cp secretion-based drug screening identified all-trans retinoic acid (ATRA) as promising candidates for rescuing Cp secretion. ATRA also alleviated reactive oxygen species (ROS) production induced by lipid accumulation in WD-specific hepatocytes. Our patient-derived iPSC-based hepatic models provide potential therapeutics for liver steatosis in WD and other fatty liver diseases.
pOPIN-GG: A resource for modular assembly in protein expression vectors
Authors: Bentham Adam R. , Youles Mark , Mendel Melanie N. , Varden Freya A. , Concepcion Juan Carlos De la , Banfield Mark J.
Published: August 2021

The ability to recombinantly produce target proteins is essential to many biochemical, structural, and biophysical assays that allow for interrogation of molecular mechanisms behind protein function. Purification and solubility tags are routinely used to maximise the yield and ease of protein expression and purification from E. coli. A major hurdle in high-throughput protein expression trials is the cloning required to produce multiple constructs with different solubility tags. Here we report a modification of the well-established pOPIN expression vector suite to be compatible with modular cloning via Type IIS restriction enzymes. This allows users to rapidly generate multiple constructs with any desired tag, introducing modularity in the system and delivering compatibility with other modular cloning vector systems, for example streamlining the process of moving between expression hosts. We demonstrate these constructs maintain the expression capability of the original pOPIN vector suite and can also be used to efficiently express and purify protein complexes, making these vectors an excellent resource for high-throughput protein expression trials.

Highlights

pOPIN-GG expression vectors allow for modular cloning enabling rapid screening of purification and solubility tags at no loss of expression compared to previous vectors.

Cloning into the pOPIN-GG vectors can be performed from PCR products or from level 0 vectors containing the required parts.

Several vectors with different resistances and origins of replication have been generated allowing the effective co-expression and purification of protein complexes.

All pOPIN-GG vectors generated here are available on Addgene, as well as level 0 acceptors and tags.
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences
Authors: O’Toole Áine , Pybus Oliver G. , Abram Michael E. , Kelly Elizabeth J. , Rambaut Andrew
Published: August 2021

More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status. Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a “lineage set”, which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.
Trial by trial, machine learning approach identifies temporally discrete Aδ- and C-fibre mediated laser evoked potentials that predict pain behaviour in rats
Authors: Sales A.C. , Blockeel A.J. , Huxter J.R. , Dunham J.P. , Drake R.A.R. , Truini A. , Mouraux A. , Treede RD. , Phillips K.G. , Pickering A.E.
Published: August 2021

Laser evoked potentials (LEPs) – the EEG response to temporally-discrete thermal stimuli – are commonly used in experimental pain studies in humans. Such stimuli selectively activate nociceptors and produce EEG features which correlate with pain intensity. The rodent LEP has been proposed to be a translational biomarker of nociception and pain, however its validity has been questioned because of reported differences in the classes of nociceptive fibres mediating the response. Here we use a machine learning, trial by trial analysis approach on wavelet-denoised LEPs generated by stimulation of the plantar hindpaw of rats. The LEP amplitude was more strongly related to behavioural response than to laser stimulus energy. A simple decision tree classifier using LEP features was able to predict behavioural responses with 73% accuracy. An examination of the features used by the classifier showed that mutually exclusive short and long latency LEP peaks were clearly seen in single-trial data, yet were not evident in grand average data pooled from multiple trials. This bimodal distribution of LEP latencies was mirrored in the paw withdrawal latencies which were preceded and predicted by the LEP responses. The proportion of short latency events was increased after intradermal application of high dose capsaicin (to defunctionalise TRPV1 expressing nociceptors), suggesting they were mediated by Aδ-fibres (specifically AMH-I). These findings demonstrate that both C- and Aδ-fibres contribute to rodent LEPs and concomitant behavioural responses, providing a real-time assay of specific fibre function in conscious animals. Single-trial analysis approaches can improve the utility of LEPs as a translatable biomarker of pain.
Clonal reconstruction from co-occurrence of vector integration sites allows accurate quantification of expanding clones in vivo
Authors: Wagner Sebastian , Baldow Christoph , Calabria Andrea , Rudilosso Laura , Gallina Pierangela , Montini Eugenio , Cesana Daniela , Glauche Ingmar
Published: August 2021

High transduction rates of viral vectors in gene therapies (GT) and experimental hematopoiesis ensure a high frequency of gene delivery, although multiple integration events can occur in the same cell. Therefore, tracing of integration sites (IS) leads to misquantification of the true clonal spectrum and limits safety considerations in GT.

Hence, we use correlations between repeated measurements of IS abundances to estimate their mutual similarity and identify clusters of co-occurring IS, for which we assume a clonal origin. We evaluate the performance, robustness and specificity of our methodology using clonal simulations. The reconstruction methods, implemented and provided as an R-package, are further applied to experimental clonal mixes and to a preclinical model of hematopoietic GT.

Our results demonstrate that clonal reconstruction from IS data allows to overcome systematic biases in the clonal quantification as an essential prerequisite for the assessment of safety and long-term efficacy of GT involving integrative vectors.
Three-level Sleep Stage Classification Based on Wrist-worn Accelerometry Data Alone
Authors: Hu Jian , Shou Haochang
Published: August 2021

Objective

The use of wearable sensor devices on daily basis to track real-time movements during wake and sleep has provided opportunities for automatic sleep quantification using such data. Existing algorithms for classifying sleep stages often require large training data and multiple input signals including heart rate and respiratory data. We aimed to examine the capability of classifying sleep stages using sensible features directly from accelerometers only with the aid of advanced recurrent neural networks.

Materials and Methods

We analyzed a publicly available dataset with accelerometry data in 5s epoch length and polysomnography assessments. We developed long short-term memory (LSTM) models that take the 3-axis accelerations, angles, and temperatures from concurrent and historic observation windows to predict wake, REM and non-REM sleep. Leave-one-subject-out experiments were conducted to compare and evaluate the model performance with conventional nonsequential machine learning models using metrics such as multiclass training and testing accuracy, weighted precision, F1 score and area-under-the-curve (AUC).

Results

Our sequential analysis framework outperforms traditional non-sequential models in all aspects of model evaluation metrics. We achieved an average of 65% and a maximum of 81% validation accuracy for classifying three sleep labels even with a relatively small training sample of clinical visitors. The presence of two additional derived variables, local variability and range, have shown to strongly improve the model performance.

Discussion

Results indicate that it is crucial to account for deep temporal dependency and assess local variability of the features. The post-hoc analysis of individual model performances on subjects’ demographic characteristics also suggest the need of including pathological samples in the training data in order to develop robust machine learning models that are capable of capturing normal and anomaly sleep patterns in the population.
High Leaf Respiration Rates May Limit the Success of White Spruce Saplings growing in The Kampfzone at the Arctic Treeline
Authors: Griffin Kevin L , Schmeige Stephanie C , Bruner Sarah G , Boelman Natalie T , Vierling Lee A , Eitel Jan U.H.
Published: August 2021

Arctic Treeline is the transition from the boreal forest to the treeless tundra and may be determined by growing season temperatures. The physiological mechanisms involved in determining the relationship between the physical and biological environment and the location of treeline are not fully understood. In Northern Alaska we studied the relationship between temperature and leaf respiration in 36 white spruce (Picea glauca) trees, sampling both the upper and lower canopy, to test two research hypotheses (H0). The first H01 is that canopy position will not influence leaf respiration. The associated alternative hypothesis (HA) is that the upper canopy leaves which are more directly coupled to the atmosphere will experience more challenging environmental conditions and thus have higher respiration rates to facilitate metabolic function. The second H02 is that tree size will not influence leaf respiration. The associated HA is that saplings (stems that are 5-10 cm DBH (diameter at breast height)) will have higher respiration rates than trees (stems ≥ 10 cm DBH) since saplings represent the transition from seedlings growing in the more favorable aerodynamic boundary layer, to trees which are fully coupled to the atmosphere but of sufficient size to persist. Respiration did not change with canopy position, however respiration at 25°C was 42% higher in saplings compared to trees (3.43 ± 0.19 vs. 2.41 ± 0.14 μmol m-2s-1). Furthermore, there were significant differences in the temperature response of respiration, and seedlings reached their maximum respiration rates at 59°C, more than two degrees higher than trees. Our results demonstrate that the respiratory characteristics of white spruce saplings at treeline are extreme, imposing a significant carbon cost that may contribute to their lack of perseverance beyond treeline. In the absence of thermal acclimation, the rate of leaf respiration could increase by 57% by the end of the century, posing further challenges to the ecology of this massive ecotone.
Light-sheet photonic force optical coherence elastography for high-throughput quantitative 3D micromechanical imaging
Authors: Lin Yuechuan , Leartprapun Nichaluk , Luo Justin C. , Adie Steven G.
Published: August 2021

Microscale mechanical properties of the extracellular matrix (ECM) and dynamic cell-ECM interactions play an important role in physiological processes and disease. However, it remains a challenge for current mechanical characterization methods to combine quantitative 3D imaging of ECM mechanics with cellular-scale resolution and dynamic monitoring of cell-mediated changes to pericellular viscoelasticity. Here, we present light-sheet photonic force optical coherence elastography (LS-pfOCE) to address these challenges by leveraging a light-sheet for parallelized, non-invasive, and localized mechanical loading. We demonstrate the capabilities of LS-pfOCE by imaging the micromechanical heterogeneity of fibrous 3D collagen matrices and perform a live-cell study to image micromechanical heterogeneity induced by NIH-3T3 cells seeded in 3D fibrin constructs. We also show that LS-pfOCE is able to quantify temporal variations in pericellular viscoelasticity in response to altered cellular activity. By providing access to the spatiotemporal variations in the micromechanical properties of 3D complex biopolymer constructs and engineered cellular systems, LS-pfOCE has the potential to drive new discoveries in the rapidly growing field of mechanobiology.
LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data
Authors: Ma Wenjing , Sharma Sumeet , Jin Peng , Gourley Shannon L. , Qin Zhaohui
Published: August 2021

Given most tissues are consist of abundant and diverse sub cell-types, an important yet unaddressed problem in bulk RNA-seq analysis is to identify at which sub cell-type(s) the differential expression occur. Single-cell RNA-sequencing (scRNA-seq) technologies can answer the question, but they are often labor-intensive and cost-prohibitive. Here, we present LRcell, a computational method aiming to identify specific sub-cell type(s) that drives the changes observed in a bulk RNA-seq experiment. In addition, LRcell provides pre-embedded marker genes computed from putative single-cell RNA-seq experiments as options to execute the analyses. Using three different real datasets, we show that LRcell successfully identifies known cell types involved in psychiatric disorders and LRcell is more sensitive than even the leading deconvolution methods.
Neural network-based predictions of antimicrobial resistance inSalmonellaspp. using k-mers counting from whole-genome sequences
Authors: Barros Cristian C.
Published: August 2021

Abstract

Artificial intelligence-based predictions have emerged as a friendly and reliable tool for the surveillance of the antimicrobial resistance (AMR) worldwide. In this regard, genome databases typically include whole-genome sequencing (WGS) data containing AMR meta-data that can be used to train machine learning (ML) models, in order to predict phenotype features from genome samples. In this study, using a Neural Network (NN) architecture and the SGD-ADAM algorithm, we build ML antibiotic resistance models that can predict Minimum Inhibitory Concentrations (MICs) and antimicrobial susceptibility profiles ofSalmonellaspp. Data analysis was based on 7,268 genomes publicly available in PATRIC database, containing about 75,000 AMR annotations. ML models were built using reference-freek-mer analysis of whole-genome sequences, MIC measurements and susceptibility categories, obtaining robust and accurate results for 9 antibiotics belonging to beta-lactam, fluoroquinolone, phenicol, aminoglycoside, tetracycline and sulphonamide classes. Al-though the accuracy of predicting the actual MIC reaches modest levels, the within ± 1 2-fold dilution accuracy per antibiotic reaches significant levels with values that varies from 85% to 95%, with narrow 95% CIs of about 5% and individual accuracies per MIC ≳ 80%. For differentiation between “susceptible” and “resistant” values, by measuring the accuracy and error of model’s susceptibility predictions to different antibiotics, the accuracy is the same as before and ranges from 85% to 95%, with 95% CIs of about 5%, the recall extends from 75% to 85%, the precision from 60% to 90%, whereas the very major error is ≲ 20%. In summary, these results show that NN-based models are able to learn and predict the AMR phenotype from bacterial genomes based on a gene-freek-mer analysis.
Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers
Authors: Li Qiuye , Jaroniec Christopher P. , Surewicz Witold K.
Published: August 2021

One of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with Y145Stop mutation that is associated with a familial prion disease. This structural insight allows us not only to explain previous biochemical findings, but also provides direct support for the conformational adaptability model of prion transmissibility barriers.
Incompatibility of DFHBI based fluorescent RNA aptamers with particular commercial cell-free expression systems
Authors: Speakman Alexander J. , Dunn Katherine E.
Published: August 2021

Fluorescent RNA aptamers are an increasingly used tool for quantifying transcription and for visualising RNA interactions, bothin vitroandin vivo. However when tested in the commercially available,E. coliextract based Expressway™ cell-free expression system, no fluorescence is detected. The same experimental setup is shown to successfully produce fluorescent RNA aptamers when tested in another buffer designed forin vitrotranscription, and RNA purification of the Expressway™ reaction products show that transcription does occur, but does not result in a fluorescent product. In this paper we demonstrate the incompatibility of a narrow selection of RNA aptamers in one particular cell-free expression system, and consider that similar issues may arise with other cell-free expression systems, RNA aptamers, and their corresponding fluorophores.
Typhoid toxin sorting and exocytic transport fromSalmonellaTyphi infected cells
Authors: Chang Shu-Jung , Lin Yen-Yi , Lara-Tejero Maria , Galán Jorge E.
Published: August 2021

Typhoid toxin is an essential virulence factor forSalmonellaTyphi, the cause of typhoid fever in humans. This toxin has an unusual biology in that it is produced bySalmonellaTyphi only when located within host cells. Once synthesized, the toxin is secreted to the lumen of theSalmonella-containing vacuole from where it is transported to the extracellular space by vesicle carrier intermediates. Here we report the identification of the typhoid toxin sorting receptor and the cellular machinery that packages the toxin into vesicle carriers, and exports it to the extracellular space. We found that the cation- independent mannose-6-phosphate receptor serves as typhoid toxin sorting receptor and that the coat protein COPII and the GTPase Sar1 mediate its packaging into vesicle carriers. Formation of the typhoid toxin carriers requires the specific environment of theSalmonellaTyphi-containing vacuole, which is determined by the activities of specific effectors of its type III protein secretion systems. We also found that Rab11B and its interacting protein Rip11 control the intracellular transport of the typhoid toxin carriers, and the SNARE proteins VAMP7, SNAP23, and Syntaxin 4 their fusion to the plasma membrane. Typhoid toxin’s cooption of specific cellular machinery for its transport to the extracellular space illustrates the remarkable adaptation of an exotoxin to exert its function in the context of an intracellular pathogen.
Caveats and nuances of model-based and model-free representational connectivity analysis
Authors: Karimi-Rouzbahani Hamid , Woolgar Alexandra , Henson Richard , Nili Hamed
Published: August 2021

Brain connectivity analyses have conventionally relied on statistical relationship between one-dimensional summaries of activation in different brain areas. However, summarising activation patterns within each area to a single dimension ignores the potential statistical dependencies between their multi-dimensional activity patterns. Representational Connectivity Analyses (RCA) is a method that quantifies the relationship between multi-dimensional patterns of activity without reducing the dimensionality of the data. We consider two variants of RCA. In model-free RCA, the goal is to quantify the shared information for two brain regions. In model-based RCA, one tests whether two regions have shared information about a specific aspect of the stimuli/task, as defined by a model. However, this is a new approach and the potential caveats of model-free and model-based RCA are still understudied. We first explain how model-based RCA detects connectivity through the lens of models, and then present three scenarios where model-based and model-free RCA give discrepant results. These conflicting results complicate the interpretation of functional connectivity. We highlight the challenges in three scenarios: complex intermediate models, common patterns across regions and transformation of representational structure across brain regions. The paper is accompanied by scripts that reproduce the results. In each case, we suggest potential ways to mitigate the difficulties caused by inconsistent results. The results of this study shed light on some understudied aspects of RCA, and allow researchers to use the method more effectively.
Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties
Authors: Walcott S. , Warshaw D. M.
Published: August 2021

Myosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350nm vs. 1,750nm) transport by myoVa motors. 5,000 simulated liposomes transported within each network adopted one of three states: transport, tug of war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug of wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, Nc. Nc, is a geometric property of the actin network that depends only on the position and polarity of the actin filaments and the liposome diameter, as evidenced by a five-fold increase in liposome diameter resulting in a five-fold decrease in Nc. Thus, in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell’s physiological demands.
Anterior Cingulate Cortex Signals the Need to Control Intrusive Thoughts During Motivated Forgetting
Authors: García Maité Crespo , Wang Yulin , Jiang Mojun , Anderson Michael C. , Lei Xu
Published: August 2021

How do people limit awareness of unwanted memories? Evidence suggests that when unwelcome memories intrude, a retrieval stopping process engages the right dorsolateral prefrontal cortex (rDLPFC; Anderson et al., 2004) to inhibit hippocampal activity (Benoit and Anderson, 2012; Benoit et al., 2015; Gagnepain et al., 2017) and disrupt retrieval. It remains unknown how and when the need to engage prefrontal control is detected, and whether control operates proactively to prevent an unwelcome memory from being retrieved, or must respond reactively, to counteract its intrusion. We hypothesized that dorsal anterior cingulate cortex (dACC) achieves this function by detecting signals indicating that an unwanted trace is emerging in awareness, and transmitting the need for inhibitory control to right DLPFC (Alexander and Brown, 2011; Botvinick et al., 2001). During a memory suppression task, we measured trial-by-trial variations in dACC’s theta power and N2 amplitude, two electroencephalographic (EEG) markers of the need for enhanced control (Cavanagh and Frank, 2014). With simultaneous EEG-fMRI recordings, we tracked dynamic interactions between the dACC, rDLPFC and hippocampus during suppression. EEG analyses revealed a clear role of dACC in detecting the need for memory control, and in upregulating prefrontal inhibition. Importantly, we identified dACC contributions before episodic retrieval could have occurred (500 ms) and afterwards, indicating distinct proactive and reactive control signalling. Stronger proactive control by the dACC led to reduced hippocampal activity and diminished overall blood-oxygen-level-dependent (BOLD) signal in dACC and rDLPFC, suggesting that pre-empting retrieval early reduced overall control demands. However, when dACC activity followed the likely onset of recollection, retrieval was cancelled reactively: effective connectivity analyses revealed robust communication from dACC to rDLPFC and from rDLPFC to hippocampus, tied to successful forgetting. Together, our findings support a model in which dACC detects the emergence of unwanted content, triggering top-down inhibitory control, and in which rDLPFC countermands intruding thoughts that penetrate awareness.
Artemisinin-independent inhibitory activity ofArtemisiasp. infusions against differentPlasmodiumstages including relapse-causing hypnozoites
Authors: Ashraf Kutub , Tajeri Shahin , Arnold Christophe-Sébastien , Amanzougaghene Nadia , Franetich Jean-François , Vantaux Amélie , Soulard Valérie , Bordessoulles Mallaury , Cazals Guillaume , Bousema Teun , van Gemert Geert-Jan , Grand Roger Le , Dereuddre-Bosquet Nathalie , Barale Jean-Christophe , Witkowski Benoit , Snounou Georges , Duval Romain , Botté Cyrille Y. , Mazier Dominique
Published: August 2021

Artemisinin-based combination therapies (ACT) are the frontline treatments against malaria worldwide. Recently the use of traditional infusions fromArtemisia annua(from which artemisinin is obtained) orA. afra(lacking artemisinin) has been controversially advocated. Such unregulated plant-based remedies are strongly discouraged as they might constitute sub-optimal therapies and promote drug resistance. Here, we conducted the first comparative study of the anti-malarial effects of both plant infusionsin vitroagainst the asexual erythrocytic stages ofP. falciparumand the pre-erythrocytic (i. e., liver) stages of variousPlasmodiumspecies. Low concentrations of either infusion accounted for significant inhibitory activities across every parasite species and stage studied. We show that these antiplasmodial effects were essentially artemisinin-independent and were additionally monitored by observations of the parasite apicoplast and mitochondrion. In particular, the infusions significantly incapacitated sporozoites, and forP. vivaxandP. cynomolgi,disrupted the hypnozoites. This provides the first indication that compounds other than 8-aminoquinolines could be effective antimalarials against relapsing parasites. These observations advocate for further screening to uncover urgently needed novel antimalarial lead compounds.