bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of the two flagellar stators in swimming motility ofPseudomonas putida
Authors: Pfeifer Veronika , Beier Sönke , Alirezaeizanjani Zahra , Beta Carsten 
Published: August 2022

ABSTRACTIn the soil bacteriumPseudomonas putida, the motor torque for flagellar rotation is generated by the two stators MotAB and MotCD. Here, we construct mutant strains, in which one or both stators are knocked out and investigate their swimming motility in fluids of different viscosity and in heterogeneous structured environments (semisolid agar). Besides bright-field imaging of single cell trajectories and spreading cultures, dual color fluorescence microscopy allows us to quantify the role of the stators in formingP. putida’sthree different swimming modes, where the flagellar bundle pushes, pulls, or wraps around the cell body. The MotAB stator is essential for swimming motility in liquids, while spreading in semisolid agar is not affected. Moreover, if the MotAB stator is knocked out, wrapped mode formation under low viscosity conditions is strongly impaired and only partly restored for increased viscosity and in semisolid agar. In contrast, when the MotCD stator is missing, cells are indistinguishable from the wild-type in fluid experiments, but spread much slower in semisolid agar. Analysis of the microscopic trajectories reveals that the MotCD knockout strain forms sessile clusters thereby reducing the number of motile cells, while the swimming speed is unaffected. Together, both stators ensure a robust wild-type that swims efficiently under different environmental conditions.IMPORTANCEBecause of its heterogeneous habitat, the soil bacteriumPseudomonas putidaneeds to swim efficiently under very different environmental conditions. In this paper, we knocked out the stators MotAB and MotCD to investigate their impact on swimming motility ofP. putida. While the MotAB stator is crucial for swimming in fluids, in semisolid agar both stators are sufficient to sustain a fast swimming phenotype and increased frequencies of the wrapped mode, which is know to be beneficial for escaping mechanical traps. However, in contrast to the MotAB knock-out, a culture of MotCD knock-out cells spreads much slower in the agar as it forms non-motile clusters that reduce the amount of motile cells.
Who is pregnant? defining real-world data-based pregnancy episodes in the National COVID Cohort Collaborative (N3C)
Authors: Jones Sara , Bradwell Katie R. , Chan Lauren E. , Olson-Chen Courtney , Tarleton Jessica , Wilkins Kenneth J. , Qin Qiuyuan , Faherty Emily Groene , Lau Yan Kwan , Xie Catherine , Kao Yu-Han , Liebman Michael N. , Mariona Federico , Challa Anup , Li Li , Ratcliffe Sarah J. , McMurry Julie A. , Haendel Melissa A. , Patel Rena C. , Hill Elaine L. 
Published: August 2022

ABSTRACTObjectiveTo define pregnancy episodes and estimate gestational aging within electronic health record (EHR) data from the National COVID Cohort Collaborative (N3C).Materials and MethodsWe developed a comprehensive approach, named Hierarchy and rule-based pregnancy episode Inference integrated with Pregnancy Progression Signatures (HIPPS) and applied it to EHR data in the N3C from 1 January 2018 to 7 April 2022. HIPPS combines: 1) an extension of a previously published pregnancy episode algorithm, 2) a novel algorithm to detect gestational aging-specific signatures of a progressing pregnancy for further episode support, and 3) pregnancy start date inference. Clinicians performed validation of HIPPS on a subset of episodes. We then generated three types of pregnancy cohorts based on the level of precision for gestational aging and pregnancy outcomes for comparison of COVID-19 and other characteristics.ResultsWe identified 628,165 pregnant persons with 816,471 pregnancy episodes, of which 52.3% were live births, 24.4% were other outcomes (stillbirth, ectopic pregnancy, spontaneous abortions), and 23.3% had unknown outcomes. We were able to estimate start dates within one week of precision for 431,173 (52.8%) episodes. 66,019 (8.1%) episodes had incident COVID-19 during pregnancy. Across varying COVID-19 cohorts, patient characteristics were generally similar though pregnancy outcomes differed.DiscussionHIPPS provides support for pregnancy-related variables based on EHR data for researchers to define pregnancy cohorts. Our approach performed well based on clinician validation.ConclusionWe have developed a novel and robust approach for inferring pregnancy episodes and gestational aging that addresses data inconsistency and missingness in EHR data.
Nanoblades allow high-level genome editing in organoids
Authors: Tirolle Victor , Krug Adrien , Bokobza Emma , Bulcaen Mattijs , Ensinck Marjolein M. , Geurts Maarten H. , Hendriks Delilah , Vermeulen François , Larbret Frédéric , Gutierrez-Guerrero Alejandra , Medaer Louise , Gijsbers Rik , Mangeot Philippe E. , Clevers Hans , Carlon Marianne S. , Bost Frederic , Verhoeyen Els 
Published: August 2022

AbstractGenome engineering has become more accessible thanks to the RNA programmable endonucleases such as the CRISPR/Cas9 system. However, using this editing technology in synthetic organs called ‘organoids’ is still very inefficient. This is due to the delivery methods used for the CRISPR-Cas9 machinery, which include electroporation of CRISPR/Cas9 DNA, mRNA or ribonucleoproteins (RNPs) containing the CAS9-gRNA complex. However, these procedures are toxic to some extent for the organoids. Here we describe the use of the ‘Nanoblade’ technology, which outperformed by far knock-out (KO) levels achieved to date by gene editing in murine and human tissue derived organoids. We reached up to 80% of gene KO in organoids after treatment with nanoblades. Indeed, high-level nanoblade-mediated KO for the androgen receptor (AR) encoding gene and the cystic fibrosis transmembrane conductance regulator (CFTR) gene was achieved with single gRNA or dual gRNA containing nanoblades in murine prostate and colon organoids. Likewise, nanoblades achieved high levels of gene editing in human organoids ranging between 20% and 50%.Most importantly, in contrast to other gene editing methods, this was obtained without toxicity for the organoids. Only four weeks are required to obtain stable gene KO in organoids and nanoblades simplify and allow rapid genome editing in organoids with little to no side-effects such as possible unwanted INDELS in off-target sites.
Factors influencing the effectiveness of nature–based Interventions (NBIs) aimed at improving mental health and wellbeing: Protocol of an umbrella review
Authors: Shrestha Topaz , Chi Cheryl Voon Yi , Cassarino Marica , Foley Sarah , Di Blasi Zelda 
Published: August 2022

AbstractSeveral systematic reviews support the use of nature–based interventions (NBIs) as a mechanism of enhancing mental health and wellbeing. However, the available evidence for the effectiveness of these interventions is fragmentary and mixed. The heterogeneity of existing evidence and significant fragmentation of knowledge within the field make it difficult to draw firm conclusions regarding the effectiveness of NBIs. The aim of this mixed method umbrella review is to synthesise evidence on the effectiveness of nature–based interventions through a summative review of existing published systematic reviews and meta-analyses. A systematic search in PsycINFO, PubMed, Greenfile, Web of Science, Embase, Scopus, Academic Search Complete (EBSCO), Environment Complete (EBSCO), Cochrane Library, CINAHL, Health Policy Reference Center and Google Scholar will be performed from inception to May 2022. The search strategy will aim to find published systematic reviews of nature–based interventions (NBIs) where improving health and wellbeing is an explicit goal. This is a mixed method review and systematic reviews with both quantitative and qualitative data synthesis will be considered. Two authors will independently perform the literature search, record screening, data extraction, and quality assessment of each included systematic review and meta-analysis. The individual qualitative and quantitative syntheses will be conducted in parallel and then combined in an overarching narrative synthesis. The quantitative evidence will be used to assess the strength and direction of effect of nature–based interventions on mental health and wellbeing outcomes. Evidence drawn from qualitative studies will be analysed and synthesised to understand the various pathways to engagement, process of involvement and experiential factors which may mediate experiences. The risk of bias of the systematic reviews will be assessed using a 16-item Assessment of Multiple Systematic Reviews 2 (AMSTAR2) checklist. This review is registered on PROSPERO (CRD42022329179).
Modulation of cannabinoid receptor signaling by endocannabinoids
Authors: Kumar Kaavya Krishna , Robertson Michael J. , Thadhani Elina , Wang Haoqing , Suomivuori Carl-Mikael , Powers Alexander S. , Ji Lipin , Nikas Spyros P. , Gerasi Maria , Vemuri Kiran , Dror Ron O. , Inoue Asuka , Makriyannis Alexandros , Skiniotis Georgios , Kobilka Brian 
Published: August 2022

AbstractEndocannabinoids (eCBs) are endogenous lipid molecules that activate the cannabinoid receptor 1 (CB1), a G protein coupled receptor (GPCR) that signals primarily through the Gi/o family of G proteins to regulate neurotransmitter release. Consequently, CB1 is an important therapeutic target for several neurological disorders. How eCBs interact with CB1 is not known and the downstream signaling they activate is not well understood. In this study we show that eCBs do not activate Gi1 as much as synthetic cannabinoids. To characterize activation of CB1 by eCB, we formed an eCB analogue-bound (AMG315) CB1-Gi signaling complex for structural studies. The structure reveals differences in the orthosteric ligand binding pocket not seen in the previous CB1 structures, providing insights into the structural determinants of ligand efficacy. In combination with signaling and simulation data, this study provides mechanistic insights into CB1 activation by different classes of ligands, and sheds light on the G protein preferences between endogenous and exogenous ligands.
A Universal Language for Finding Mass Spectrometry Data Patterns
Authors: Jarmusch Alan K. , Aron Allegra T. , Petras Daniel , Phelan Vanessa V. , Bittremieux Wout , Acharya Deepa D. , Ahmed Mohammed M. A. , Bauermeister Anelize , Bertin Matthew J. , Boudreau Paul D. , Borges Ricardo M. , Bowen Benjamin P. , Brown Christopher J. , Chagas Fernanda O. , Clevenger Kenneth D. , Correia Mario S. P. , Crandall William J. , Crüsemann Max , Damiani Tito , Fiehn Oliver , Garg Neha , Gerwick William H , Gilbert Jeffrey R. , Globisch Daniel , Gomes Paulo Wender P. , Heuckeroth Steffen , James C. Andrew , Jarmusch Scott A. , Kakhkhorov Sarvar A. , Kang Kyo Bin , Kersten Roland D , Kim Hyunwoo , Kirk Riley D. , Kohlbacher Oliver , Kontou Eftychia E. , Liu Ken , Lizama-Chamu Itzel , Luu Gordon T. , Knaan Tal Luzzatto , Marty Michael T. , McAvoy Andrew C. , McCall Laura-Isobel , Mohamed Osama G. , Nahor Omri , Niedermeyer Timo H.J. , Northen Trent R. , Overdahl Kirsten E. , Pluskal Tomáš , Rainer Johannes , Reher Raphael , Rodriguez Elys , Sachsenberg Timo T. , Sanchez Laura M. , Schmid Robin , Stevens Cole , Tian Zhenyu , Tripathi Ashootosh , Tsugawa Hiroshi , Nishida Kozo , Matsuzawa Yuki , van der Hooft Justin J.J. , Vicini Andrea , Walter Axel , Weber Tilmann , Xiong Quanbo , Xu Tao , Zhao Haoqi Nina , Dorrestein Pieter C. , Wang Mingxun 
Published: August 2022

AbstractEven though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.
“Multiphoton holographic photostimulation induces potassium-dependent spike silencing in label-free mouse cortex in vivo”
Authors: Papaioannou Stylianos , Zakrisson Johan , Kuznetsova Tatiana , Medini Paolo 
Published: August 2022

AbstractMultiphoton microscopy allows measurement of network activity as well as the manipulation of cell type specific or functionally identified neuronal subpopulations with optogenetic holographic stimulation. When neurons co-express an activity reporter (e.g. calcium or voltage-sensitive indicators) and an (excitatory or inhibitory) opsin, such “all optical” interrogation approaches in vivo allows to draw causal links between function of cell-type specific microcircuits and behaviour. However, the net effects of near-infrared stimulation on network activity per se remain to be adequately investigated in vivo. Here we show that multicell holographic photostimulation with near-infrared radiation with total powers to sample used in current literature halves the spike rate of the non-illuminated neurons in label-free mouse cortex in vivo. The effect is not mediated by GABA release, but depends on NIR-dependent gating of potassium channels as it is absent when neurons are intracellularly perfused with the broad potassium channel blocker cesium ions, and are possibly mediated by heating. The phenomenon may contribute to set an upper limit to holographic photostimulation efficacy, calls for the need to control the effects of holographic stimulation protocols per se in label free preparations, and might be of relevance to interpret the therapeutical effects on infrared stimulation in psychiatry and neurology.Highlights- Holographic multi-cell, infrared illumination halves spike rates of no-target neurons- The effect happens with total powers to sample used in “all-optical” literature- Infrared-driven spike killing is GABA-independent but depends on potassium channels
Object representation in a gravitational reference frame
Authors: Emonds Alexandriya M.X. , Srinath Ramanujan , Nielsen Kristina J. , Connor Charles E. 
Published: August 2022

ABSTRACTWhen your head tilts laterally, as in sports, reaching, and resting, your eyes counterrotate less than 20%, and thus eye images rotate, over a total range of about 180°. Yet, the world appears stable and vision remains normal. We discovered a neural strategy for rotational stability in anterior inferotemporal cortex (IT), the final stage of object vision in primates. We measured object orientation tuning of IT neurons in macaque monkeys tilted +25 and –25° laterally, producing ∼40° difference in retinal image orientation. Among IT neurons with consistent object orientation tuning, 63% remained stable with respect to gravity across tilts. Gravitational tuning depended on vestibular/somatosensory but also visual cues, consistent with previous evidence that IT processes scene cues for gravity’s orientation. In addition to stability across image rotations, an internal gravitational reference frame is important for physical understanding of a world where object position, posture, structure, shape, movement, and behavior interact critically with gravity.
Pupil dynamics-derived sleep stage classification of a head-fixed mouse using a recurrent neural network
Authors: Kobayashi Goh , Tanaka Kenji F. , Takata Norio 
Published: August 2022

SummaryThe standard method for sleep state classification is thresholding amplitudes of electroencephalography (EEG) and electromyography (EMG), followed by an expert’s manual correction. Although popular, the method entails some shortcomings: 1) the time-consuming manual correction by human experts is sometimes a bottleneck hindering sleep studies; 2) EEG electrodes on the skull interfere with wide-field imaging of the cortical activity of a head-fixed mouse under a microscope; 3) invasive surgery to fix the electrodes on the thin skull of a mouse risks brain tissue injury; and 4) metal electrodes for EEG and EMG are difficult to apply to some experiment apparatus such as that for functional magnetic resonance imaging. To overcome these shortcomings, we propose a pupil dynamics-based vigilance state classification for a head-fixed mouse using a long short-term memory (LSTM) model, a variant of recurrent neural networks, for multi-class labeling of NREM, REM, and WAKE states. For supervisory hypnography, EEG and EMG recording were performed for a head-fixed mouse, combined with left eye pupillometry using a USB camera and a markerless tracking toolbox, DeepLabCut. Our open-source LSTM model with feature inputs of pupil diameter, location, velocity, and eyelid opening for 10 s at a 10 Hz sampling rate achieved vigilance state estimation with a higher classification performance (macro F1 score, 0.77; accuracy, 86%) than a feed forward neural network. Findings from diverse pupillary dynamics implied subdivision of a vigilance state defined by EEG and EMG. Pupil dynamics-based hypnography can expand the scope of alternatives for sleep stage scoring of head fixed mice.
Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir
Authors: Iketani Sho , Mohri Hiroshi , Culbertson Bruce , Hong Seo Jung , Duan Yinkai , Luck Maria I. , Annavajhala Medini K. , Guo Yicheng , Sheng Zizhang , Uhlemann Anne-Catrin , Goff Stephen P. , Sabo Yosef , Yang Haitao , Chavez Alejandro , Ho David D. 
Published: August 2022

AbstractNirmatrelvir, an oral antiviral targeting the 3CL protease of SARS-CoV-2, has been demonstrated to be clinically useful in reducing hospitalization or death due to COVID-191,2. However, as SARS-CoV-2 has evolved to become resistant to other therapeutic modalities3–9, there is a concern that the same could occur for nirmatrelvir. Here, we have examined this possibility by in vitro passaging of SARS-CoV-2 in increasing concentrations of nirmatrelvir using two independent approaches, including one on a large scale in 480 wells. Indeed, highly resistant viruses emerged from both, and their sequences revealed a multitude of 3CL protease mutations. In the experiment done at a larger scale with many replicates, 53 independent viral lineages were selected with mutations observed at 23 different residues of the enzyme. Yet, several common mutational pathways to nirmatrelvir resistance were preferred, with a majority of the viruses descending from T21I, P252L, or T304I as precursor mutations. Construction and analysis of 13 recombinant SARS-CoV-2 clones, each containing a unique mutation or a combination of mutations showed that the above precursor mutations only mediated low-level resistance, whereas greater resistance required accumulation of additional mutations. E166V mutation conferred the strongest resistance (~100-fold), but this mutation resulted in a loss of viral replicative fitness that was restored by compensatory changes such as L50F and T21I. Structural explanations are discussed for some of the mutations that are proximal to the drug-binding site, as well as cross-resistance or lack thereof to ensitrelvir, another clinically important 3CL protease inhibitor. Our findings indicate that SARS-CoV-2 resistance to nirmatrelvir does readily arise via multiple pathways in vitro, and the specific mutations observed herein form a strong foundation from which to study the mechanism of resistance in detail and to inform the design of next generation protease inhibitors.
A benchmark study of protein folding algorithms on nanobodies
Authors: Liang Shibo , Liang Ziquan , Wu Zecheng , Huang Feijuan , Wang Xu , Tan Zihao , He Rui , Lu Zeyi , Cai Yuanzhe , Huang Bingding , Wang Xin 
Published: August 2022

AbstractNanobodies, also known as single domain or VHH antibodies, are the artificial recombinant variable domains of heavy-chain-only antibodies. Nanobodies have many unique properties, including small size, good solubility, superior stability, rapid clearance from blood, and deep tissue penetration. Therefore, nanobodies have emerged as promising tools for diagnosing and treating diseases. In recent years, many deep-learning-based protein structure prediction methods have emerged that require only protein sequences as input to obtain highly-credible 3D protein structures. Among them, AlphaFold2, RoseTTAFold, DeepAb, NanoNet, and tFold performed excellently in protein prediction or antibody/nanobody prediction. In this study, we selected 60 nanobody samples with known experimental 3D structures in the Protein Data Bank (PDB). Next, we predicted their 3D structures using these five prediction algorithms from only their 2D amino acid sequences. Then, we individually compared the predicted and experimental structures. Finally, the results are analyzed and discussed.
Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers
Authors: Mobley Robert J. , Myers Jacquelyn A. , Wills Kendall M. , Malone Hayden A. , Manzano Trishabelle I. , Partridge Janet F. , Roberts Charles W. M. 
Published: August 2022

AbstractGenes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are mutated in >20% of cancers. SWI/SNF complexes exist in three distinct families that each contribute to regulation of transcription, although the functional interactions between the families are not well understood. Rhabdoid tumors constitute an informative model system as these highly aggressive cancers are driven by inactivation of a single SWI/SNF subunit, SMARCB1, which is present in two SWI/SNF families (cBAF and PBAF) but not in the third (GBAF/ncBAF). We and others have shown that BRD9, a therapeutically targetable member of ncBAF, is essential specifically in SMARCB1-deficient cancers, suggesting key functional relationships between SMARCB1-containing complexes and BRD9/ncBAF. However, the mechanistic underpinnings of these relationships are poorly understood. Here, we demonstrate that genomic binding of BRD9 is largely dependent upon SMARCB1 such that the absence of SMARCB1 results in significantly reduced BRD9 binding. At select sites, however, we show that SMARCB1-loss results in gain of BRD9 binding and BRD9-dependent accessibility. We find that this gain is associated with expression of genes promoting cell migration. Our results define relationships between SWI/SNF complex families, elucidate mechanisms by which SMARCB1 loss drives oncogenesis, and provide mechanistic insight into the synthetic-lethal relationship between SMARCB1 and BRD9.