bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Reproducibility of High-throughput Experiments in the Case of Missing Data
Authors: Singh Roopali , Zhang Feipeng , Li Qunhua 
Published: July 2021

AbstractHigh-throughput experiments are an essential part of modern biological and biomedical research. The outcomes of high-throughput biological experiments often have a lot of missing observations due to signals below detection levels. For example, most single-cell RNA-seq (scRNA-seq) protocols experience high levels of dropout due to the small amount of starting material, leading to a majority of reported expression levels being zero. Though missing data contain information about reproducibility, they are often excluded in the reproducibility assessment, potentially generating misleading assessments.In this paper, we develop a regression model to assess how the reproducibility of high-throughput experiments is affected by the choices of operational factors (e.g., platform or sequencing depth) when a large number of measurements are missing. Using a latent variable approach, we extend correspondence curve regression (CCR), a recently proposed method for assessing the effects of operational factors to reproducibility, to incorporate missing values. Using simulations, we show that our method is more accurate in detecting differences in reproducibility than existing measures of reproducibility. We illustrate the usefulness of our method using a single-cell RNA-seq dataset collected on HCT116 cells. We compare the reproducibility of different library preparation platforms and study the effect of sequencing depth on reproducibility, thereby determining the cost-effective sequencing depth that is required to achieve sufficient reproducibility.
Inferring the demographic history of tetraploid species from genomic data
Authors: Roux Camille , Vekemans Xavier , Pannell John 
Published: July 2021

AbstractGenomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems and demographic history. The latter is characterised by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution, but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidisation, the mode of inheritance and different scenarios of gene flow between subgenomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.
Scalable full-transcript coverage single cell RNA sequencing with Smart-seq3xpress
Authors: Hagemann-Jensen Michael , Ziegenhain Christoph , Sandberg Rickard 
Published: July 2021

AbstractPlate-based single-cell RNA-sequencing methods with full-transcript coverage typically excel at sensitivity but are more costly and time-consuming. Here, we miniaturized and streamlined the Smart-seq3 protocol for drastically reduced cost and increased throughput. Applying Smart-seq3xpress to 16,349 human peripheral blood mononuclear cells revealed a highly granular atlas complete with both common and rare cell types whose identification previously relied on additional protein measurements or the integration with a reference atlas.
Structural basis for carbapenamC-alkylation by TokK, a B12-dependent radical SAM enzyme
Authors: Knox Hayley L. , Sinner Erica K. , Townsend Craig A. , Boal Amie K. , Booker Squire J. 
Published: July 2021

AbstractCobalamin- or B12-dependent radicalS-adenosylmethionine (SAM) enzymes acting during carbapenem antibiotic biosynthesis carry out radical-mediated methyl transfers that underlie the therapeutic usefulness of these essential medicines. Here we present x-ray crystal structures of TokK, which are representative of this functional class, containing its two metallocofactors and determined in the presence and absence of carbapenam substrate. The structures give the first visualization of a cobalamin-dependent radical SAM methylase that employs the radical mechanism shared by a vast majority of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggests that substrate positioning governs the rate of each methylation event.One Sentence SummaryStructural insight into a cobalamin-dependent radical SAM methylase that performs three sequential radical-mediated methylations to install the C6 side chain of a carbapenem antibiotic.
Enhancing Precision in Bioprinting Utilizing Fuzzy Systems
Authors: Sedigh Ashkan , DiPiero Dayna , Shine Kristy M. , Tomlinson Ryan E. 
Published: July 2021

ABSTRACTBioprinting facilitates the generation of complex, three-dimensional (3D), cell-based constructs for a variety of applications. Although multiple bioprinting technologies have been developed, extrusion-based systems have become the dominant technology due to the diversity of substrate materials (bioinks) that can be accommodated, either individually or in combination. However, each bioink has unique material properties and extrusion characteristics that limit bioprinting precision, particularly when generating constructs from different bioinks. Here, we aimed to achieve high precision (i.e. repeatability) across samples by generating bioink-specific printing parameters using a systematic approach. We hypothesized that a fuzzy system could be used as a “black box” method to tackle the inherent vagueness and imprecision in 3D bioprinting data and uncover the optimal printing parameters for a specific bioink that would result in high accuracy and precision. Our fuzzy model was used to approximate and quantify the precision and ease of printability for two common bioinks - type I collagen and Pluronic F127, with or without dilution in αMEM culture media. The model consisted of three inputs (pressure, speed, and dilution percent of bioink) and a single output (layer width). Using this system, we introduce the Bioink Precision Index (BPI), a metric that can be used to quantify and compare the precision of any bioink. Here, we show that printing with parameters optimized using BPI increases the precision for collagen (+15%) and Pluronic F127 (+29%) as compared to the manufacturer’s recommended printing parameters.
A dynamic 1/f noise protocol to assess visual attention without biasing perceptual processing
Authors: Hanning Nina M. , Deubel Heiner 
Published: July 2021

AbstractPsychophysical paradigms measure visual attention via localized test items to which observers must react or whose features have to be discriminated. These items, however, potentially interfere with the intended measurement as they bias observers’ spatial and temporal attention to their location and presentation time. Furthermore, visual sensitivity for conventional test items naturally decreases with retinal eccentricity, which prevents direct comparison of central and peripheral attention assessments. We developed a stimulus that overcomes these limitations. A brief oriented discrimination signal is seamlessly embedded into a continuously changing 1/f noise field, such that observers cannot anticipate potential test locations or times. Using our new protocol, we demonstrate that local orientation discrimination accuracy for 1/f filtered signals is largely independent of retinal eccentricity. Moreover, we show that items present in the visual field indeed shape the distribution of visual attention, suggesting that classical studies investigating the spatiotemporal dynamics of visual attention via localized test items may have obtained a biased measure. We recommend our protocol as an efficient method to evaluate the behavioral and neurophysiological correlates of attentional orienting across space and time.Significance statementWhere (and when) we pay attention can be experimentally quantified via visual sensitivity: Attending to a certain visual signal results in better detection and feature discrimination performance. This approach is widely used, but poses an unrecognized dilemma: The test signal itself, typically a grating or letter stimulus, biases observers’ perception and expectations – and thus also the attention measurement. We developed a stimulus that manages without test items. The signal to measure attention is seamlessly embedded in a dynamic 1/f noise field, so that neither spatial nor temporal information about signal presentation is conveyed. Unlike with conventional approaches, perception and expectations in this new protocol remain unbiased, and the undistorted spatial and temporal spread of visual attention can be measured.
Effects of Frontoparietal Theta tACS on Verbal Working Memory: Behavioral and Neurophysiological Analysis
Authors: Hu Zhenhong , Samuel Immanuel B.H. , Meyyappan Sreenivasan , Rana Ke Bo Chandni , Ding Mingzhou 
Published: July 2021

AbstractLeft-lateralized frontoparietal theta oscillations are thought to play an important role in verbal working memory. We causally tested this idea by stimulating the frontoparietal theta network at individual theta frequencies (4 to 8 Hz) during verbal working memory and observing the subsequent behavioral and neurophysiological effects. Weak electric currents were delivered via two 4×1 HD electrode arrays centered at F3 and P3. Three stimulation configurations, including in-phase, anti-phase, or sham, were tested on three different days in a cross-over design. On each test day, the subject underwent three experimental sessions: pre-, during- and post-stimulation sessions. In all sessions, the subject performed a Sternberg verbal working memory task with three levels of memory load (load 2, 4 and 6), imposing three levels of cognitive demand. Analyzing behavioral, EEG, and pupillometry data from the post-stimulation sessions, we report three results. First, in-phase stimulation improved task performance only in subjects with higher working memory capacity (WMC) and under higher memory load (load 6). Second, in-phase stimulation enhanced frontoparietal theta synchrony during working memory retention only in subjects with higher WMC under higher memory loads (load 4 and load 6), and the enhanced frontoparietal theta synchronization is mainly driven by enhanced frontal→parietal theta Granger causality. Third, the pupil diameter was not different irrespective of whether the preceding stimulation was in-phase, anti-phase, or sham. These findings suggest that theta tACS effects on verbal working memory were load- and subject-dependent, rooted in tACS-induced changes in frontoparietal network interactions, and not driven by changes in arousal levels.
Regulation of positive and negative selection and TCR signaling during thymic T cell development by capicua
Authors: Kim Soeun , Park Guk-Yeol , Park Jong Seok , Park Jiho , Hong Hyebeen , Lee Yoontae 
Published: July 2021

ABSTRACTCentral tolerance is achieved through positive and negative selection of thymocytes mediated by T cell receptor (TCR) signaling strength. Thus, the dysregulation of the thymic selection process often leads to autoimmunity. Here, we show that capicua (CIC), a transcriptional repressor that suppresses autoimmunity, controls the thymic selection process. Loss of CIC prior to T-cell lineage commitment impaired both positive and negative selection of thymocytes. CIC deficiency attenuated TCR signaling in CD4+CD8+double-positive (DP) cells, as evidenced by a decrease in CD5 and phospho-ERK levels and calcium flux. We identifiedSpry4,Dusp4,Dusp6,andSpred1as CIC target genes that could inhibit TCR signaling in DP cells. Furthermore, impaired positive selection and TCR signaling were partially rescued inCicandSpry4double mutant mice. Our findings indicate that CIC is a transcription factor required for thymic T cell development and suggest that CIC acts at multiple stages of T cell development and differentiation to prevent autoimmunity.
Altered costimulatory signals and hypoxia support chromatin landscapes limiting the functional potential of exhausted T cells in cancer
Authors: Ford B. Rhodes , Rittenhouse Natalie L. , Scharping Nicole E. , Vignali Paolo D. A. , Frisch Andrew T. , Peralta Ronal , Delgoffe Greg M. , Poholek Amanda C. 
Published: July 2021

AbstractImmunotherapy has changed cancer treatment with major clinical successes, but response rates remain low due in part to elevated prevalence of dysfunctional, terminally exhausted T cells. However, the mechanisms promoting progression to terminal exhaustion remain undefined. We profiled the histone modification landscape of tumor-infiltrating CD8 T cells throughout differentiation, finding terminally exhausted T cells possessed chromatin features limiting their transcriptional potential. Active enhancers enriched for bZIP/AP-1 transcription factor motifs lacked correlated gene expression, which were restored by immunotherapeutic costimulatory signaling. Epigenetic repression was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Our study is the first to profile the precise epigenetic changes during intratumoral differentiation to exhaustion, highlighting their altered function is driven by both improper costimulatory signals and environmental factors. These data suggest even terminally exhausted T cells remain poised for transcription in settings of increased costimulatory signaling and reduced hypoxia.
Genetic slippage after sex maintains diversity for parasite resistance in a natural host population
Authors: Ameline Camille , Vögtli Felix , Andras Jason , Dexter Eric , Engelstädter Jan , Ebert Dieter 
Published: July 2021

AbstractAlthough parasite-mediated selection is thought to be a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored a large population of the planktonic crustaceanDaphnia magnaover eight years, as it underwent yearly epidemics of the bacterial pathogenPasteuria ramosa. We observed a cyclical pattern of resistance evolution: resistant phenotypes increased in frequency throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages, a phenomenon described as genetic slippage in response to sex. Collecting and hatchingD. magnaresting stages across multiple seasons showed that largely resistant host populations can produce susceptible offspring through recombination. Resting stages produced throughout the planktonic season accurately represent the hatching population cohort of the following spring. A genetic model of resistance developed for this host–parasite system, based on multiple loci and strong epistasis, is in partial agreement with these findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction has the potential to maintain genetic diversity of host resistance.
Evolutionary footprints of a cold relic in a rapidly warming world
Authors: Wolf Eva M. , Gaquerel Emmanuel , Scharmann Mathias , Yant Levi , Koch Marcus A. 
Published: July 2021

AbstractWith accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genusCochlearia(Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene.Cochleariarapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This rapid change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed ancestral central carbon metabolism responses to cold in diverse ecotypes, likely due to continuous connections to cold habitats that we hypothesize facilitated widespread parallel adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.
Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness
Authors: Ke Ruian , Martinez Pamela P. , Smith Rebecca L. , Gibson Laura L. , Mirza Agha , Conte Madison , Gallagher Nicholas , Luo Chun Huai , Jarrett Junko , Conte Abigail , Liu Tongyu , Farjo Mireille , Walden Kimberly K.O. , Rendon Gloria , Fields Christopher J. , Wang Leyi , Fredrickson Richard , Edmonson Darci C. , Baughman Melinda E. , Chiu Karen K. , Choi Hannah , Scardina Kevin R. , Bradley Shannon , Gloss Stacy L. , Reinhart Crystal , Yedetore Jagadeesh , Quicksall Jessica , Owens Alyssa N. , Broach John , Barton Bruce , Lazar Peter , Heetderks William J. , Robinson Matthew L. , Mostafa Heba H. , Manabe Yukari C. , Pekosz Andrew , McManus David D. , Brooke Christopher B. 
Published: July 2021

ABSTRACTThe dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimate viral reproduction and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome load often peaked days earlier in saliva than in nasal swabs, indicating strong compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of B.1.1.7 and non-B.1.1.7 viruses in nasal swabs were indistinguishable, however B.1.1.7 exhibited a significantly slower pre-peak growth rate in saliva. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
The co-evolution of the genome and epigenome in colorectal cancer
Authors: Heide Timon , Househam Jacob , Cresswell George D , Spiteri Inmaculada , Lynn Claire , Mossner Max , Kimberley Chris , Fernandez-Mateos Javier , Chen Bingjie , Zapata Luis , James Chela , Barozzi Iros , Chkhaidze Ketevan , Nichol Daniel , Berner Alison , Schmidt Melissa , Lakatos Eszter , Baker Ann-Marie , Costa Helena , Mitchinson Miriam , Jansen Marnix , Caravagna Giulio , Ramazzotti Daniele , Shibata Darryl , Bridgewater John , Rodriguez-Justo Manuel , Magnani Luca , Graham Trevor A , Sottoriva Andrea 
Published: July 2021

AbstractColorectal malignancies are a leading cause of cancer death. Despite large-scale genomic efforts, DNA mutations do not fully explain malignant evolution. Here we study the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,373 samples from 30 primary cancers and 9 concomitant adenomas and generated 1,212 chromatin accessibility profiles, 527 whole-genomes and 297 whole-transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent chromatin changes in regulatory regions of cancer drivers with otherwise no mutation. Genome-wide alterations in transcription factor binding accessibility involvedCTCF, downregulation of interferon, and increased accessibility forSOXandHOX, indicating developmental genes reactivation. Epigenetic aberrations were heritable, distinguishing adenomas from cancers. Mutational signature analysis showed the epigenome influencing DNA mutation accumulation. This study provides a map of (epi)genetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
Serotonin GPCR-based biosensing modalities in yeast
Authors: Lengger Bettina , Hoch-Schneider Emma E. , Jensen Christina N. , Jakočiūnas Tadas , Jensen Emil D. , Jensen Michael K. 
Published: July 2021

SummarySerotonin is a key neurotransmitter involved in numerous physiological processes and serves as an important precursor for manufacturing bioactive indoleamines and alkaloids used in the treatment of human pathologies. In humans, serotonin sensing and signaling can occur by 12 G protein-coupled receptors (GPCRs) coupled to G proteins. To systematically assess serotonin GPCR signaling, we characterized reporter gene expression of a 144-sized library encoding all 12 human serotonin GPCRs in combination with 12 different Gα proteins in yeast exposed to serotonin. For the 5-HT4 receptor, we observe 25- and 64-fold changes in EC50 values and dynamic reporter gene outputs, respectively. Furthermore, we show that optimal biosensing designs enable high-resolution sensing of serotonin produced in yeast, as well as provide a platform for characterization of 19 serotonin GPCR polymorphisms found in human populations. Taken together, our study highlights serotonin biosensing modalities of relevance to both biotechnological and human health applications.HighlightsHuman serotonin G protein-coupled receptors display promiscuous Gα coupling in yeastGα-coupled serotonin receptors display up to 64-fold changes in reporter expression outputDifferences in Gα protein evokes 25- and 2-fold difference in EC50 and sensitivity, respectivelySerotonin receptor 5-HT4 and human SNP variants display physiologically relevant EC50 values in yeast5-HT4 can be applied for high-resolution biosensing of serotonin produced from yeast
The mediating role of social informal learning in the relationship between learning climate and employability
Authors: Crans Samantha , Gerken Maike , Beausaert Simon , Segers Mien 
Published: July 2021

PurposeThis study examines whether learning climate relates to employability competences through social informal learning (i.e. feedback, help and information seeking).Design/methodology/approachMultiple regression analyses and structural equation modeling were used to test direct and indirect effects in a sample of 372 employees working in two Dutch governmental institutes.FindingsThe analyses confirmed that learning climate has an indirect effect on employability competences through feedback, help and information seeking. More specifically, the findings suggest that learning climate is important for employees' engagement in proactive social informal learning activities. Engaging in these learning activities, in turn, relates to a higher level of employability.Originality/valueThis study employs an integrative approach to understanding employability by including the organization's learning climate and employees' social informal learning behavior. It contributes to the extant literature on professional development by unraveling how proactive social informal learning relates to employability competences. It also provides new insights on learning climate as a determinant for social informal learning and employability.