bluuebunny/crossref_metadata_2025_split huggingface dataset:
DirectMS1Quant: ultrafast quantitative proteomics with MS/MS-free mass spectrometry
Authors: Ivanov Mark V. , Bubis Julia A. , Gorshkov Vladimir , Tarasova Irina A. , Levitsky Lev I. , Solovyeva Elizaveta M. , Lipatova Anastasiya V. , Kjeldsen Frank , Gorshkov Mikhail V. 
Published: May 2022

AbstractRecently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at 1% false discovery rate (FDR) when using 5-min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000 to 5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue we performed one-by-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free quantification (LFQ), tandem mass tag (TMT), both based on data dependent acquisition (DDA), and data independent acquisition (DIA). For the comparison we performed a series of proteome-wide analysis of well-characterized (ground truth) and biological relevant samples, including a mix of UPS1 proteins spiked at different concentrations into E. coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods utilizing 10 to 20-fold longer instrumentation time.
Miro GTPase domains regulate assembly of the mitochondrial motor-adaptor complex
Authors: Davis Kayla , Basu Himanish , Shurberg Ethan , Schwarz Thomas L. 
Published: May 2022

AbstractMitochondrial transport relies on a motor-adaptor complex containing Miro1, a mitochondrial outer membrane protein with two GTPase domains, as well as TRAK1/2, kinesin-1, and dynein. Using a peroxisome-directed Miro1, we quantified the ability of GTPase mutations to influence peroxisomal recruitment of complex components. Miro1 whose N-GTPase is locked in the GDP-state doesn’t recruit TRAK1/2, kinesin or P135 to peroxisomes whereas the GTP-state does. Miro1 C-GTPase mutations have little influence on complex recruitment. Though Miro2 is thought to support mitochondrial motility, peroxisome-directed Miro2 did not recruit the other complex components regardless of the state of its GTPase domains. Neurons expressing peroxisomal Miro1 with the GTP-state form of the N-GTPase had markedly increased peroxisomal transport to growth cones while the GDP-state caused their retention in the soma. Thus, the N-GTPase of Miro1 is critical for regulating Miro1’s interaction with the other components of the motor-adaptor complex and thereby for regulating mitochondrial motility.SummaryA Miro-containing complex mediates mitochondrial motility. Relocalizing Miro1 and 2 to peroxisomes and systematically manipulating each GTPase domain of Miro revealed the importance of the N-terminal GTPase domain of Miro1 for governing interaction with TRAK proteins, motors, and transport.
Changes of oscillatory and aperiodic neuronal activity in working memory following anaesthesia: a prospective observational study
Authors: Lendner Janna D. , Harler Ulrich , Daume Jonathan , Engel Andreas K. , Zöllner Christian , Schneider Till R. , Fischer Marlene 
Published: May 2022

AbstractBackgroundAnaesthesia and surgery can lead to cognitive decline, especially in the elderly. However, to date, the neurophysiological underpinnings of perioperative cognitive decline remain unknown.MethodsWe included male patients, who were 60 years or older scheduled for elective radical prostatectomy under general anaesthesia. We obtained neuropsychological (NP) tests as well as a visual match-to-sample working memory (WM) task with concomitant 62-channel scalp electroencephalography (EEG) before and after surgery.ResultsA total number of 26 patients completed neuropsychological assessments and EEG pre- and postoperatively. Behavioural performance declined in the neuropsychological assessment after anaesthesia (total recall; t-tests: t25 = -3.25, Bonferroni-corrected p = 0.015 d = -0.902), while WM performance showed a dissociation between match and mis-match accuracy (rmANOVA: match*session F1,25 = 3.866, p = 0.060). Distinct EEG signatures tracked behavioural performance: Better performance in the NP assessment was correlated with an increase of non-oscillatory (aperiodic) activity, reflecting increased cortical activity (cluster permutation tests: total recall r = 0.66, p = 0.029, learning slope r = 0.66, p = 0.015), while WM accuracy was tracked by distinct temporally-structured oscillatory theta/alpha (7 – 9 Hz), low beta (14 – 18 Hz) and high beta/gamma (34 – 38 Hz) activity (cluster permutation tests: matches: p < 0.001, mis-matches: p = 0.022).ConclusionsOscillatory and non-oscillatory (aperiodic) activity in perioperative scalp EEG recordings track distinct features of perioperative cognition. Aperiodic activity provides a novel electrophysiological biomarker to identify patients at risk for developing perioperative neurocognitive decline.
Impact of different mutations on Kelch13 protein levels, ART resistance and fitness cost inPlasmodium falciparumparasites
Authors: Behrens Hannah M. , Schmidt Sabine , Peigney Domitille , Sabitzki Ricarda , Henshall Isabelle , May Jürgen , Maïga-Ascofaré Oumou , Spielmann Tobias 
Published: May 2022

AbstractReduced susceptibility to ART, the first-line treatment against malaria, is common in South East Asia (SEA). It is caused by point mutations, mostly inkelch13(k13) but also in other genes, likeupb1. K13 and its compartment neighbors (KICs), including UBP1, are involved in endocytosis of host cell cytosol. We tested 135 mutations in KICs but none conferred ART resistance. Double mutations ofk13C580Y withk13R539T ork13C580Y withubp1R3138H, did also not increase resistance. In contrast,k13C580Y parasites subjected to consecutive RSAs did, but thek13sequence was not altered. Using isogenic parasites with differentk13mutations, we found correlations between K13 protein amount, resistance and fitness cost. Titration of K13 and KIC7 indicated that the cellular levels of these proteins determined resistance through the rate of endocytosis. While fitness cost ofk13mutations correlated with ART resistance,ubp1R3138H caused a disproportionately higher fitness cost.SignificanceART resistance is only a partial resistance with a proportion of ring stages surviving physiological ART levels. The correlation of resistance with fitness cost in isogenic lines indicates that fitness cost likely prevents resistance levels permitting survival of all ring stages under physiological ART concentrations. We also found no indication that double mutations ink13, including the two most common resistance mutations in SEA, or with non-k13genes, are a threat to lead to higher resistance. However, repeated ART exposure increased resistance by mechanisms not alteringk13gene sequence, indicating changes in the background of these parasites. The disproportionally high fitness cost ofubp1R3138H may explain whykicmutations affecting resistance are rare and highlights the unique property of K13 to influence endocytosis only in ring stages.
Integrating opportunistic and structured non-invasive surveys with spatial capture-recapture models to map connectivity of the Pyrenean brown bear population
Authors: Kervellec Maëlis , Milleret Cyril , Vanpé Cécile , Quenette Pierre-Yves , Sentilles Jérôme , Palazón Santiago , Jordana Ivan Afonso , Jato Ramón , Elósegui Irurtia Miguel Mari , Gimenez Olivier 
Published: May 2022

AbstractConnectivity, in the sense of the persistence of movements between habitat patches, is key to maintain endangered populations and has to be evaluated in management plans. In practice, connectivity is difficult to quantify especially for rare and elusive species. Here, we use spatial capture-recapture (SCR) models with an ecological detection distance to identify barriers to movement. We focused on the transnational critically endangered Pyrenean brown bear (Ursus arctos) population, which is distributed over Spain, France and Andorra and is divided into two main cores areas following translocations. We integrate structured monitoring from camera traps and hair snags with opportunistic data gathered after depredation events. While structured monitoring focuses on areas of regular bear presence, the integration of opportunistic data allows us to obtain information in a wider range of habitat, which is especially important for ecological inference. By estimating a resistance parameter from encounter data, we show that the road network impedes movements, leading to smaller home ranges with increasing road density. Although the quantitative effect of roads is context-dependent (i.e. varying according to landscape configuration), our model predicts that a brown bear with a home range located in an area with relatively high road density (8.29km/km2) has a home range size reduced by 1.4-fold for males and 1.6-fold for females compared to a brown bear with a home range located in an area with low road density (1.38km/km2). When assessing connectivity, spatial capture-recapture modeling offers an alternative to the use of experts’ opinion when telemetry data are not available.
Single particle tracking with compressive sensing using progressive refinement method on sparse recovery (spt-PRIS)
Authors: Yi Xiyu , Shrestha Rebika , McDonald Torin , Chen De , Bhatia Harsh , Pascucci Valerio , Turbyville Thomas , Bremer Peer-Timo 
Published: May 2022

AbstractSingle particle tracking (SPT) is an indispensable tool for scientific studies. However, SPT for datasets with a high density of particles is still challenging, especially for the study of particle interactions where the point spread functions (PSFs) are overlapping. In this study, we present spt-PRIS, a new SPT solution where we apply compressive sensing to SPT by integrating the progressive refinement method on sparse recovery (PRIS) into the framework of the state-of-the-art SPT algorithm (uTrack). We systematically characterized and validated spt-PRIS performance using simulations, applied it to the experimental data of membrane-bound KRAS4b proteins in either 2-lipid or 8-lipid membrane supported lipid bilayers (SLB), and compared the results to the conventional method (uTrack). Our results show that spt-PRIS is effective for SPT when the data contains overlapping PSFs and provides unprecedented information about KRAS4b subpopulations. spt-PRIS is helpful for a broad range of scientific studies where precise and fast high-density localization is beneficial. spt-PRIS is also flexible for extensions for multi-species, multi-multi-channel, and multi-dimensional SPT methods with the generalization of PRIS reconstruction schemes.
Distinct population and single-neuron selectivity for executive and episodic processing in human dorsal posterior cingulate
Authors: Aponik-Gremillion Lyndsey , Chen Yvonne Y. , Bartoli Eleonora , Koslov Seth R. , Rey Hernan G. , Weiner Kevin S. , Yoshor Daniel , Hayden Benjamin Y. , Sheth Sameer A. , Foster Brett L. 
Published: May 2022

AbstractPosterior cingulate cortex (PCC) is an enigmatic region implicated in psychiatric and neurological disease, yet its role in cognition remains unclear. Human studies link PCC to episodic memory and default mode network (DMN), while findings from the non-human primate emphasize executive processes more associated with the cognitive control network (CCN) in humans. We hypothesized this difference reflects an important functional division between dorsal (executive) and ventral (episodic) PCC. To test this, we utilized human intracranial recordings of population and single unit activity targeting dorsal PCC during an alternated executive/episodic processing task. Dorsal PCC population responses were significantly enhanced for executive, compared to episodic, task conditions, consistent with the CCN. Single unit recordings, however, revealed four distinct functional types with unique executive (CCN) or episodic (DMN) response profiles. Our findings provide critical electrophysiological data from human PCC, bridging incongruent views within and across species, furthering our understanding of PCC function.
Exogenous DNA upregulates DUOX2 expression and function in human pancreatic cancer cells by activating the cGAS-STING signaling pathway
Authors: Wang Stephen L. , Wu Yongzhong , Konaté Mariam , Lu Jiamo , Antony Smitha , Meitzler Jennifer L. , Jiang Guojian , Dahan Iris , Juhasz Agnes , Diebold Becky , Roy Krishnendu , Doroshow James H. 
Published: May 2022

AbstractPro-inflammatory cytokines upregulate the expression of the H2O2-producing NADPH oxidase dual oxidase 2 (DUOX2) which, when elevated, adversely affects survival from pancreatic ductal adenocarcinoma (PDAC). Because the cGAS-STING pathway is known to initiate pro-inflammatory cytokine expression following uptake of exogenous DNA, we examined whether activation of cGAS-STING could play a role in the generation of reactive oxygen species by PDAC cells. Here, we found that a variety of exogenous DNA species markedly increased the production of cGAMP, the phosphorylation of TBK1 and IRF3, and the translocation of phosphorylated IRF3 into the nucleus, leading to a significant, IRF3-dependent enhancement of DUOX2 expression, and a significant flux of H2O2 in PDAC cells. However, unlike the canonical cGAS-STING pathway, DNA-related DUOX2 upregulation was not mediated by NF-κB; and although exogenous IFN-β significantly increased Stat1/2-associated DUOX2 expression, intracellular IFN-β signaling that followed cGAMP or DNA exposure did not itself increase DUOX2 levels. Finally, DUOX2 upregulation subsequent to cGAS-STING activation was accompanied by the enhanced, normoxic expression of HIF-1α as well as DNA double strand cleavage, suggesting that cGAS-STING signaling may support the development of an oxidative, pro-angiogenic microenvironment that could contribute to the inflammation-related genetic instability of pancreatic cancer.
Bioengineering multifunctional extracellular vesicles for targeted delivery of biologics to T cells
Authors: Stranford Devin M. , Simons Lacy M. , Berman Katherine E. , Cheng Luyi , Lucks Julius B. , Hultquist Judd F. , Leonard Joshua N. 
Published: May 2022

AbstractGenetically modifying T cells can enable applications ranging from cancer immunotherapy to HIV treatment, yet delivery of T cell-targeted therapeutics remains challenging. Extracellular vesicles (EVs) are nanoscale particles secreted by all cells that naturally encapsulate and transfer proteins and nucleic acids, making them an attractive and clinically-relevant platform for engineering biocompatible delivery vehicles. We report a suite of technologies for genetically engineering cells to produce multifunctional EV vehicles—without employing chemical modifications that complicate biomanufacturing. We display high affinity targeting domains on the EV surface to achieve specific, efficient binding to T cells, identify a protein tag to confer active cargo loading into EVs, and display fusogenic glycoproteins to increase EV uptake and fusion with recipient cells. We demonstrate integration of these technologies by delivering Cas9-sgRNA complexes to edit primary human T cells. These approaches could enable targeting vesicles to a range of cells for the efficient delivery of cargo.
The history and organization of the Workshop on Population and Speciation Genomics
Authors: Barth Julia MI , Handley Scott , Kintzl Daniel , Leonard Guy , Malinsky Milan , Matschiner Michael , Meyer Britta S , Salzburger Walter , Stefka Jan , Trucchi Emiliano 
Published: May 2022

AbstractWith the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of work-shops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of Český Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, and describe the routine for workshop organization that we have optimized over the years. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.
TGFβ treatment alters the scleral fibroblast migratory response to cyclic strain in an ERK-dependent manner
Authors: Mozzer Ann , Pitha Ian 
Published: May 2022

AbstractPurposeMyofibroblasts are associated with scleral remodeling in myopia and glaucoma. We showed reduced myofibroblast alignment with topographic cues in sclera can be modeled by cyclic strain exposure of aligned myofibroblasts in vitro. Here, we characterize the scleral myofibroblast response to cyclic mechanical strain.MethodsHuman peripapillary scleral (PPS) fibroblasts were cultured on topographically aligned grooves to promote cell alignment, exposed to TGFβ (2 ng/ml) in the presence of vehicle or kinase inhibitors, and exposed to uniaxial strain (1 Hz, 5%, 12-24 hours). Alignment with grooves was determined at baseline, immediately following strain, and 24 hours after strain cessation with 0° being completely aligned and 90° being perpendicular to grooves. A wound healing assay was developed to investigate further fibroblast migration across topographic cues. Transcriptional profiling of myofibroblasts with or without strain was performed by RT-PCR and pERK, pSMAD2, and pSMAD3 levels were measured by immunoblot.ResultsPre-strain alignment (6.2±1.5°) was reduced after strain (21.7±5.3°, p<0.0001) and restored 24 hours after cessation (9.5±2.6°). ERK, FAK, and ALK5 inhibition preserved alignment following strain; however, alignment reduction was not inhibited by ROCK, YAP, or SMAD3 inhibition. TGFβ-induced myofibroblast markers were reduced by strain. While TGFβ-induced phosphorylation of ERK and SMAD2 was unaffected by strain, SMAD3 phosphorylation was reduced (p=0.0004). Wound healing across grooves was enhanced by ROCK and SMAD3 inhibition but not ERK or TGFβR1 inhibition.ConclusionsStrain-induced myofibroblast migration across topographic confinement is ERK dependent and associated with pSMAD3 inhibition. These results provide insight into potential mechanisms of pathologic scleral remodeling.PrecisGlaucomatous scleral remodeling is driven by cellular activity. Here we find that scleral myofibroblasts have an exaggerated response to mechanical strain that is ERK dependent, associated with pSMAD3 inhibition and mitigated TGFβ signaling.
Time series transcriptome analysis uncovers regulatory networks and a role for the circadian clock in theDrosophila melanogasterfemale’s response to Sex Peptide
Authors: Delbare Sofie Y.N. , Venkatraman Sara , Scuderi Kate , Wells Martin T. , Wolfner Mariana F. , Basu Sumanta , Clark Andrew G. 
Published: May 2022

AbstractSex Peptide, a seminal fluid protein ofD. melanogastermales, has been described as driving a virgin-to-mated switch in females, through eliciting an array of responses, including increased egg laying, activity and food intake and a decreased re-mating rate. While it is known that Sex Peptide achieves this, at least in part, by altering neuronal signaling in females, the identity of key molecular regulators that act downstream of Sex Peptide is not known. Here, we used a high-resolution time series RNA-sequencing dataset of female heads at 10 time points within the first 24 hours after mating to investigate the genetic architecture, at the gene- and exon-level, of the female’s response to Sex Peptide. We find that Sex Peptide is not essential to trigger a virgin-to-mated transcriptional switch, which involves changes in a metabolic gene regulatory network. However, Sex Peptide is needed to maintain and diversify metabolic changes and to trigger changes in a neuronal gene regulatory network. We further find that Sex Peptide might interact with the female’s circadian clock to orchestrate transcriptional changes across different regulatory networks. That a male seminal fluid protein can alter a female’s rhythmic gene expression has implications for our understanding of both reproductive and circadian behaviors.
HIV-phyloTSI: Subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data
Authors: Golubchik Tanya , Abeler-Dörner Lucie , Hall Matthew , Wymant Chris , Bonsall David , Macintyre-Cockett George , Thomson Laura , Baeten Jared M. , Celum Connie L , Galiwango Ronald M. , Kosloff Barry , Limbada Mohammed , Mujugira Andrew , Mugo Nelly R , Gall Astrid , Blanquart François , Bakker Margreet , Bezemer Daniela , Ong Swee Hoe , Albert Jan , Bannert Norbert , Fellay Jacques , Gunsenheimer-Bartmeyer Barbara , Günthard Huldrych F. , Kivelä Pia , Kouyos Roger D. , Meyer Laurence , Porter Kholoud , van Sighem Ard , van der Valk Mark , Berkhout Ben , Kellam Paul , Cornelissen Marion , Reiss Peter , Ayles Helen , Burns David N. , Fidler Sarah , Grabowski Mary Kate , Hayes Richard , Herbeck Joshua T , Kagaayi Joseph , Kaleebu Pontiano , Lingappa Jairam R , Ssemwanga Deogratius , Eshleman Susan H , Cohen Myron S , Ratmann Oliver , Laeyendecker Oliver , Fraser Christophe ,   the BEEHIVE collaboration and the PANGEA consortium
Published: May 2022

AbstractEstimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining duration of infection classify samples into recent and non-recent and are unable to give more granular TSI estimates. These binary classifications have a limited recency time window of several months, therefore requiring large sample sizes, and cannot assess the cumulative impact of an intervention. We developed a Random Forest Regression model, HIV-phyloTSI, that combines measures of within-host diversity and divergence to generate TSI estimates from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9 years, with a mean absolute error of less than 12 months overall and less than 5 months for infections with a TSI of up to a year. It performed equally well for all major HIV subtypes based on data from African and European cohorts. We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.