bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens
Authors: Dixit Atray , Kuksenko Olena , Feldman David , Regev Aviv 
Published: December 2019

AbstractGenetic interactions, defined as the non-additive phenotypic impact of combinations of genes, are a hallmark of the mapping from genotype to phenotype. However, genetic interactions remain challenging to systematically test given the massive number of possible combinations. In particular, while large-scale screening efforts in yeast have quantified pairwise interactions that affect cell viability, or synthetic lethality, between all pairs of genes as well as for a limited number of three-way interactions, it has previously been intractable to perform the large screens needed to comprehensively assess interactions in a mammalian genome. Here, we develop Shuffle-Seq, a scalable method to assay genetic interactions. Shuffle-Seq leverages the co-inheritance of genetically encoded barcodes in dividing cells and can scale in proportion to sequencing throughput. We demonstrate the technical validity of Shuffle-Seq and apply it to screening for mechanisms underlying drug resistance in a melanoma model. Shuffle-Seq should allow screens of hundreds of millions of combinatorial perturbations and facilitate the understanding of genetic dependencies and drug sensitivities.
Cluster Analysis Based on Fasting and Postprandial Plasma Glucose and Insulin Concentrations
Authors: Altuve Miguel , Severeyn Erika 
Published: December 2019

AbstractPlasma glucose and insulin concentrations are clinical markers used in the diagnosis of metabolic diseases, particularly prediabetes and diabetes. In this paper, we carried out a cluster analysis using plasma glucose and insulin data in fasting and two-hour postprandial. Different clustering experiments were performed by changing the attributes, from one (fasting glucose) to four (fasting and postprandial glucose and insulin) attribute input to a k-means clustering algorithm. Based on the elbow and silhouette methods, three clusters were chosen to carry out the clustering experiments. The Pearson correlation coefficient was used to assess the dependence between the glucose and insulin levels for each cluster created. Results show that one cluster contained prediabetics, another cluster contained diabetics, and subjects without prediabetes and diabetes were assigned to another cluster. Although age was not used as an attribute, we have found that subjects in the three clusters have a different age range. Finally, significant correlations were found between insulin levels in fasting and postprandial and between glucose levels in fasting and postprandial. These associations were stronger in the cluster containing diabetics, where insulin production or action is compromised.
Modeling Resistance and Recurrence Patterns of Combined Targeted-Chemoradiotherapy Predicts Benefit of Shorter Induction Period
Authors: McClatchy David M. , Willers Henning , Hata Aaron N. , Piotrowska Zofia , Sequist Lecia V , Paganetti Harald , Grassberger Clemens 
Published: December 2019

AbstractThe optimal integration of molecularly targeted therapies with concurrent chemotherapy and radiation (CRT) to improve cures in genotype-defined cancers is unknown. Here, we develop a bio-mathematical framework to simulate patterns of local versus distant recurrences in a heterogeneous lung cancer population receiving combined targeted therapy and CRT. Our validated model predicts that targeted induction before CRT, an approach currently being tested in clinical trials, may render adjuvant targeted therapy less effective due to proliferation of drug-resistant cancer cells when using very long induction periods. Furthermore, our simulations not only demonstrate the competing effects of drug-resistant cell expansion versus overall tumor regression as a function of induction length, but can also directly estimate the probability of observing an improvement in progression-free survival at a given cohort size. We thus demonstrate that such stochastic biological simulations have the potential to quantitatively inform the design of multimodality clinical trials in genotype-defined cancers.
Decoupling of Dopamine Release and Neural Activity in Major Depressive Disorder during Reward Processing Assessed by Simultaneous fPET-fMRI
Authors: Zhang Xue , Wang Fuyixue , Hamilton J. Paul , Sacchet Matthew D. , Chen Jingyuan , Khalighi Mehdi , Gotlib Ian H. , Glover Gary H. 
Published: December 2019

AbstractThe interaction of the midbrain dopaminergic system and the striatum is implicated in reward processing; it is still unknown, however, how this interaction is altered in Major Depressive Disorder (MDD). In the current study, we related the dopamine release/binding inferred by [11C] Raclopride functional Positron Emission Tomography (fPET) to neural activity monitored by blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI) in adults diagnosed with MDD and healthy controls (CTL). Participants completed a monetary incentive delay (MID) task during simultaneous [11C] Raclopride fPET and fMRI. Instead of the usual kinetic modeling method for analyzing dynamic PET time activity curves (TACs), we used a simpler general linear model (GLM) approach, which includes introducing a fPET dopamine activation response function to model changes in the TAC associated with the MID task. In addition, using simulations, we show that the GLM approach has several advantages over kinetic modeling. This is achieved without invoking erroneous steady-state assumptions or selecting a suitable reference region. Our results include the observation of both decreased fMRI activation and dopamine release/binding in the striatum in the MDD cohort, implying a reduced reward processing capacity in MDD. Furthermore, in the MDD group, individuals with lower fMRI activations in the right middle putamen and ventral medial prefrontal cortex (vmPFC) had higher reflection rumination scores, and individuals with lower dopamine release/binding in the left putamen and the right nucleus accumbens (NAcc) also had higher reflection rumination scores. Significant cross-modal inter-subject and intra-subject correlations of dopamine release/binding and fMRI activation were observed in the CTL group, but not in the MDD group. The intra-subject correlation of the two modalities was negatively associated with reflection rumination scores in the CTL group, indicating that decoupling of the dopaminergic system and striatum may be important in the pathophysiology of MDD.
Construction and Integration of Three De Novo Japanese Human Genome Assemblies toward a Population-Specific Reference
Authors: Takayama Jun , Tadaka Shu , Yano Kenji , Katsuoka Fumiki , Gocho Chinatsu , Funayama Takamitsu , Makino Satoshi , Okamura Yasunobu , Kikuchi Atsuo , Kawashima Junko , Otsuki Akihito , Yasuda Jun , Kure Shigeo , Kinoshita Kengo , Yamamoto Masayuki , Tamiya Gen 
Published: December 2019

ABSTRACTThe complete sequence of the human genome is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the international human reference genome (e.g., GRCh37), especially Asian populations, due to a strong bias toward European and African ancestries in a single mosaic haploid genome consisting chiefly of a single donor. Here, we performed de novo assembly of the genomes from three Japanese male individuals using >100× PacBio long reads and Bionano optical maps per sample. We integrated the genomes using the major allele for consensus, and anchored the scaffolds using sequence-tagged site markers from conventional genetic and radiation hybrid maps to reconstruct each chromosome sequence. The resulting genome sequence, designated JG1, is highly contiguous, accurate, and carries the major allele in the majority of single nucleotide variant sites for a Japanese population. We adopted JG1 as the reference for confirmatory exome re-analyses of seven Japanese families with rare diseases and found that re-analysis using JG1 reduced false-positive variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genome assemblies from a single ethnic population can aid next-generation sequencing analyses of individuals originated from the population.
Spatial suppression in visual motion perception is driven by inhibition: evidence from MEG gamma oscillations
Authors: Orekhova E.V. , Rostovtseva E.N. , Manyukhina V.O. , Prokofiev A.O. , Obukhova T.S. , Nikolaeva A.Yu. , Schneiderman J.F. , Stroganova T.A. 
Published: December 2019

AbstractSpatial suppression (SS) is a visual perceptual phenomenon that is manifest in a reduction of directional sensitivity for drifting high-contrast gratings whose size exceeds the center of the visual field. Gratings moving at faster velocities induce stronger SS. The neural processes that give rise to such size- and velocity-dependent reductions in directional sensitivity are currently unknown, and the role of surround inhibition is unclear. In magnetoencephalogram (MEG), large high-contrast drifting gratings induce a strong gamma response (GR), which also attenuates with an increase in the gratings’ velocity. It has been suggested that the slope of this GR attenuation is mediated by inhibitory interactions in the primary visual cortex. Herein, we investigate whether SS is related to this inhibitory-based MEG measure. We evaluated SS and GR in two independent samples of participants: school-age boys and adult women. The slope of GR attenuation predicted inter-individual differences in SS in both samples. Test-retest reliability of the neuro-behavioral correlation was assessed in the adults, and was high between two sessions separated by several days or weeks. Neither frequencies nor absolute amplitudes of the GRs correlated with SS, which highlights the functional relevance of velocity-related changes in GR magnitude caused by augmentation of incoming input. Our findings provide evidence that links the psychophysical phenomenon of SS to inhibitory-based neural responses in the human primary visual cortex. This supports the role of inhibitory interactions as an important underlying mechanism for spatial suppression.HighlightsThe role of surround inhibition in perceptual spatial suppression (SS) is debatedGR attenuation with increasing grating’s velocity may reflect surround inhibitionPeople with greater GR attenuation exhibit stronger SSThe neuro-behavioral correlation is replicated in school-age boys and adult womenThe surround inhibition in the V1 is an important mechanism underlying SS
Impute.me: an open source, non-profit tool for using data from DTC genetic testing to calculate and interpret polygenic risk scores
Authors: Folkersen Lasse , Pain Oliver , Ingasson Andres , Werge Thomas , Lewis Cathryn M. , Austin Jehannine 
Published: December 2019

AbstractTo date, interpretation of genomic information has focused on single variants conferring disease risk, but most disorders of major public concern have a polygenic architecture. Polygenic risk scores (PRS) give a single measure of disease liability by summarising disease risk across hundreds of thousands of genetic variants. They can be calculated in any genome-wide genotype data-source, using a prediction model based on genome-wide summary statistics from external studies.As genome-wide association studies increase in power, the predictive ability for disease risk will also increase. While PRS are unlikely ever to be fully diagnostic, they may give valuable medical information for risk stratification, prognosis, or treatment response prediction.Public engagement is therefore becoming important on the potential use and acceptability of PRS. However, the current public perception of genetics is that it provides ‘Yes/No’ answers about the presence/absence of a condition, or the potential for developing a condition, which in not the case for common, complex disorders with of polygenic architecture.Meanwhile, unregulated third-party applications are being developed to satisfy consumer demand for information on the impact of lower risk variants on common diseases that are highly polygenic. Often applications report results from single SNPs and disregard effect size, which is highly inappropriate for common, complex disorders where everybody carries risk variants.Tools are therefore needed to communicate our understanding of genetic predisposition as a continuous trait, where a genetic liability confers risk for disease. Impute.me is one such a tool, whose focus is on education and information on common, complex disorders with polygenetic architecture. Its research-focused open-source website allows users to upload consumer genetics data to obtain PRS, with results reported on a population-level normal distribution. Diseases can only be browsed by ICD10-chapter-location or alphabetically, thus prompting the user to consider genetic risk scores in a medical context of relevance to the individual.Here we present an overview of the implementation of the impute.me site, along with analysis of typical usage-patterns, which may advance public perception of genomic risk and precision medicine.
Swimming performance traits of twenty-one Australian fish species: a fish passage management tool for use in modified freshwater systems
Authors: Watson Jabin R. , Goodrich Harriet R. , Cramp Rebecca L. , Gordos Matthew A. , Yan Yulian , Ward Patrick J. , Franklin Craig E. 
Published: December 2019

AbstractFreshwater ecosystems have been severely fragmented by artificial in-stream structures designed to manage water for human use. Significant efforts have been made to reconnect freshwater systems for fish movement, through the design and installation of dedicated fish passage structures (fishways) and by incorporating fish-sensitive design features into conventional infrastructure (e.g. culverts). Key to the success of these structures is making sure that the water velocities within them do not exceed the swimming capacities of the local fish species. Swimming performance data is scarce for Australian fish, which have a reduced swimming capacity when compared to many North American and European species. To help close this knowledge gap and assist fisheries management and civil engineering, we report the swimming performance capacities of twenty-one small-bodied fish and juveniles (< 10 cm) of large bodied species native to Australia as measured by critical swimming speed (Ucrit) and burst swimming speed (Usprint) in a recirculating flume. This data is complemented by endurance swim trials in a 12-meter hydraulic flume channel, and by measures of flume traverse success. Building on the utility of this dataset, we used a panel of morphological, behavioural and ecological traits to first assess their relative contributions to the observed swimming performance data, and second, to determine if they could be used to predict swimming performance capacity – a useful tool to assist in the management of species of conservation concern where access to swimming performance data may be limited. We found that body length combined with depth station (benthic, pelagic or surface) explained most of the interspecific variation in observed swimming performance data, followed by body shape and tail shape. These three traits were the most effective at predicting swimming performance in a model/unknown fish. This data will assist civil engineers and fisheries managers in Australia to mitigate the impact of in-stream structures on local fish populations.
Role of centromere sites in activation of ParB proteins for partition complex assembly
Authors: Audibert Sylvain , Tanguy-Le Gac Nicolas , Rech Jérôme , Turlan Catherine , Bouet Jean-Yves , Bystricky Kerstin , Lane David 
Published: December 2019

AbstractThe ParB-parSpartition complexes that bacterial replicons use to ensure their faithful inheritance also find employment in visualization of DNA loci, as less intrusive alternatives to fluorescent repressor-operator systems. The ability of ParB molecules to interact via their N-terminal domains and to bind to non-specific DNA enables expansion of the initial complex to a size both functional in partition and, via fusion to fluorescent peptides, visible by light microscopy. We have investigated whether it is possible to dispense with the need to insertparSin the genomic locus of interest, by determining whether ParB fused to proteins that bind specifically to natural DNA sequences can still assemble visible complexes. In yeast cells, coproduction of fusions of ParB to a fluorescent peptide and to a TALE protein targeting an endogenous sequence did not yield visible foci; nor did any of several variants of these components. InE.coli, coproduction of fusions of SopB (F plasmid ParB) to fluorescent peptide, and to dCas9 together with specific guide RNAs, likewise yielded no foci. The result of coproducing analogous fusions of SopB proteins with distinct binding specificities was also negative. We conclude that in order to assemble higher order partition complexes, ParB proteins need specific activation through binding to their cognateparSsites.
TopicNet: a framework for measuring transcriptional regulatory network change
Authors: Lou Shaoke , Li Tianxiao , Kong Xiangmeng , Zhang Jing , Liu Jason , Lee Donghoon , Gerstein Mark 
Published: December 2019

SummaryNext generation sequencing data highlights comprehensive and dynamic changes in the human gene regulatory network. Moreover, changes in regulatory network connectivity (network “rewiring”) manifest different regulatory programs in multiple cellular states. However, due to the dense and noisy nature of the connectivity in regulatory networks, directly comparing the gains and losses of targets of key TFs is not that informative. Thus, here, we seek a abstracted lower-dimensional representation to understand the main features of network change. In particular, we propose a method called TopicNet that applies latent Dirichlet allocation (LDA) to extract meaningful functional topics for a collection of genes regulated by a TF. We then define a rewiring score to quantify the large-scale changes in the regulatory network in terms of topic change for a TF. Using this framework, we can pinpoint particular TFs that change greatly in network connectivity between different cellular states. This is particularly relevant in oncogenesis. Also, incorporating gene-expression data, we define a topic activity score that gives the degree that a topic is active in a particular cellular state. Furthermore, we show how activity differences can highlight differential survival in certain cancers.
High-force magnetic tweezers with hysteresis-free force feedback
Authors: Kah D. , Dürrbeck C. , Schneider W. , Fabry B. , Gerum R. C. 
Published: December 2019

ABSTRACTMagnetic tweezers based on solenoids with iron alloy cores are widely used to apply large forces (~100 nN) onto micron-sized (~5 μm) superparamagnetic particles for mechanical manipulation or microrheological measurements at the cellular and molecular level. The precision of magnetic tweezers, however, is limited by the magnetic hysteresis of the core material, especially for time-varying force protocols. Here, we eliminate magnetic hysteresis by a feedback control of the magnetic induction, which we measure with a Hall sensor mounted to the distal end of the solenoid core. We find that the generated force depends on the induction according to a power-law relationship, and on the bead-tip distance according to a stretched exponential relationship. Together, both relationships allow for an accurate force calibration and precise force feedback with only 3 calibration parameters. We apply our method to measure the force-dependence of the viscoelastic and plastic properties of fibroblasts using a protocol with stepwise increasing and decreasing forces. We find that soft cells show an increasing stiffness but decreasing plasticity at higher forces, indicating a pronounced stress stiffening of the cytoskeleton. By contrast, stiff cells show no stress stiffening but an increasing plasticity at higher forces. These findings indicate profound differences between soft and stiff cells regarding their protection mechanisms against external mechanical stress. In summary, our method increases the precision, simplifies the handling and extends the applicability of magnetic tweezers.SIGNIFICANCEMagnetic tweezers are widely used, versatile tools to investigate the mechanical behavior of cells or to measure the strength of receptor-ligand bonds. A limitation of existing high-force magnetic tweezer setups, however, is caused by the magnetic hysteresis of the tweezer core material. This magnetic hysteresis requires that the tweezer core must be de-magnetized (de-Gaussed) prior to each measurement, and that flexible force protocols with decreasing forces are not possible. We describe how these limitations can be overcome with a force feedback though direct magnetic field measurement. We demonstrate the applicability of our setup by investigating the visco-elastic and plastic deformations of fibroblasts to forces of different amplitudes.
Cryogenic OrbiSIMS Localizes Semi-Volatile Molecules in Biological Tissues
Authors: Newell Clare L. , Vorng Jean-Luc , MacRae James I. , Gilmore Ian S. , Gould Alex P. 
Published: December 2019

AbstractOrbiSIMS is a recently developed instrument for label-free imaging of chemicals with micron spatial resolution and high mass resolution. Here we report a cryogenic workflow for OrbiSIMS (Cryo-OrbiSIMS) that improves chemical detection of lipids and other biomolecules in tissues. Cryo-OrbiSIMS decreases ion-beam induced fragmentation, allowing large molecules such as triglycerides to be more reliably identified. It also increases chemical coverage to include biomolecules with intermediate or high vapor pressures, such as free fatty acids and semi-volatile organic compounds (SVOCs). We find that Cryo-OrbiSIMS reveals the hitherto unknown localization patterns of SVOCs with high spatial and chemical resolution in diverse plant, animal and human tissues. We also show that Cryo-OrbiSIMS can be combined with genetic analysis to identify enzymes regulating SVOC metabolism. Cryo-OrbiSIMS is applicable to high resolution imaging of a wide variety of non-volatile and semi-volatile molecules across many areas of biomedicine.
Genetic Underpinnings of Risky Behaviour Relate to Altered Neuroanatomy
Authors: Aydogan Gökhan , Daviet Remi , Linnér Richard Karlsson , Hare Todd A. , Kable Joseph W. , Kranzler Henry R. , Wetherill Reagan R. , Ruff Christian C. , Koellinger Philipp D. , Nave Gideon 
Published: December 2019

AbstractPrevious research points to the heritability of risk-taking behaviour. However, evidence on how genetic dispositions are translated into risky behaviour is scarce. Here, we report a genetically-informed neuroimaging study of real-world risky behaviour across the domains of drinking, smoking, driving, and sexual behaviour, in a European sample from the UK Biobank (N= 12,675). We find negative associations between risky behaviour and grey matter volume (GMV) in distinct brain regions, including amygdala, ventral striatum, hypothalamus, and dorsolateral prefrontal cortex (dlPFC). These effects replicate in an independent sample recruited from the same population (N=13,004). Polygenic risk scores for risky behaviour, derived from a genome-wide association study in an independent sample (N=297,025), are inversely associated with GMV in dlPFC, putamen, and hypothalamus. This relation mediates ~2.2% of the association between genes and behaviour. Our results highlight distinct heritable neuroanatomical features as manifestations of the genetic propensity for risk taking.One Sentence SummaryRisky behaviour and its genetic associations are linked to less grey matter volume in distinct brain regions.