bluuebunny/crossref_metadata_2025 huggingface dataset:
Heterogeneous disease-propagating stem cells in juvenile myelomonocytic leukemia
Authors: Louka Eleni , Povinelli Benjamin , Meira Alba Rodriguez , Buck Gemma , Ashley Neil , Hamblin Angela , Booth Christopher A.G. , Sousos Nikolaos , Roy Anindita , Elliott Natalina , Iskander Deena , de la Fuente Josu , Fordham Nicholas , O’Byrne Sorcha , Inglott Sarah , Rao Anupama , Roberts Irene , Mead Adam J.
Published: May 2019

Juvenile Myelomonocytic Leukemia (JMML) is a poor prognosis childhood leukemia usually caused by germline or somatic RAS-activating mutations. The cellular hierarchy in JMML is poorly characterized, including the identity of leukemia stem cells (LSCs). FACS and single-cell RNA-sequencing reveal marked heterogeneity of JMML hematopoietic stem/progenitor cells (HSPCs), including an aberrant Lin-CD34+CD38-CD90+CD45RA+ population. Single-cell HSPC index-sorting and clonogenic assays show that (1) all somatic mutations can be backtracked to the phenotypic HSC compartment with RAS-activating mutations as a “first hit”, (2) mutations are acquired with both linear and branching patterns of clonal evolution and (3) mutant HSPCs are present after allogeneic HSC transplant before molecular/clinical evidence of relapse. Stem cell assays reveal inter-patient heterogeneity of JMML-LSCs which are present in, but not confined to, the phenotypic HSC compartment. RNA-sequencing of JMML-LSCs reveals upregulation of stem cell and fetal genes (HLF, MEIS1, CNN3, VNN2, HMGA2) and candidate therapeutic targets/biomarkers (MTOR, SLC2A1, CD96) paving the way for LSC-directed disease monitoring and therapy in this disease.
Quantitative insights into age-associated DNA-repair inefficiency in single cells
Authors: Young Thomas Z. , Liu Ping , Acar Murat
Published: May 2019

The double strand break (DSB) is a highly toxic form of DNA damage that is thought to be both a driver and consequence of age-related dysfunction. Although DSB repair is essential for a cell’s survival, little is known about how DSB repair mechanisms are affected by cellular age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a repair mechanism for DSBs occurring between direct repeats. Using a single-cell reporter of SSA repair, we measure SSA repair efficiency in young and old cells, and report a 23.4% decline in repair efficiency. This decline is not due to increased usage of non-homologous end joining (NHEJ). Instead, we identify increased G1-phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. We further explore how SSA repair efficiency is affected by sequence heterology and find that heteroduplex rejection remains high in old cells. Our work provides novel quantitative insights into the links between cellular aging and DSB repair efficiency at single-cell resolution in replicatively aging cells.
Protein and Lipid Mass Concentration Measurement in Tissues by Stimulated Raman Scattering Microscopy
Authors: Oh Seungeun , Lee ChangHee , Yang Wenlong , Li Ang , Mukherjee Avik , Basan Markus , Ran Chongzhao , Yin Wei , Tabin Clifford J. , Fu Dan , Sunney Xie X. , Kirschner Marc W.
Published: May 2019

Cell mass and its chemical composition are important aggregate cellular variables for physiological processes including growth control and tissue homeostasis. Despite their central importance, it has been difficult to quantitatively measure these quantities from single cells in intact tissue. Here, we introduce Normalized Raman Imaging (NoRI), a Stimulated Raman Scattering (SRS) microscopy method that provides the local concentrations of protein, lipid and water from live or fixed tissue samples with high spatial resolution. Using NoRI, we demonstrate that single cell protein, lipid and water concentrations are maintained in a tight range in cells under same physiological conditions and are altered in different physiological states such as cell cycle stages, attachment to substrates of different stiffness, or by entering senescence. In animal tissues, protein and lipid concentration varies with cell types, yet an unexpected cell-to-cell heterogeneity was found in cerebellar Purkinje cells. Protein and lipid concentration profile provides a new means to quantitatively compare disease-related pathology as demonstrated using models of Alzheimer’s disease. Our demonstration shows that NoRI is a broadly applicable tool for probing the biological regulation of protein mass, lipid mass and water in cellular and tissue growth, homeostasis, and disease.
Force-independent interactions of talin and vinculin govern integrin-mediated mechanotransduction
Authors: Atherton Paul , Lausecker Franziska , Carisey Alexandre , Gilmore Andrew , Critchley David , Barsukov Igor , Ballestrem Christoph
Published: May 2019

Talin, vinculin and paxillin are core components of the dynamic link between integrins and actomyosin. Here we study the mechanisms that mediate their activation and association using a mitochondrial-targeting assay, structure-based mutants, and advanced microscopy. As expected, full-length vinculin and talin are auto-inhibited and do not interact with each other in this state. Contrary to previous models that propose a critical role for forces driving talin-vinculin association, our data show that force-independent relief of auto-inhibition is sufficient to mediate their tight interaction. Interestingly, paxillin can bind to both talin and vinculin when either is inactive. Further experiments demonstrate that adhesions containing paxillin and vinculin can form without talin following integrin activation. However, these are largely deficient in exerting traction forces to the matrix. Our observations lead to a model whereby paxillin contributes to talin and vinculin recruitment into nascent adhesions. Activation of the talin-vinculin axis subsequently leads to the engagement with the traction force-machinery and focal adhesion maturation.
Neural correlates of cardiac interoceptive accuracy across development: implications for social symptoms in autism spectrum disorders
Authors: Failla Michelle D. , Bryant Lauren K. , Heflin Brynna H. , Mash Lisa E. , Schauder Kim , Davis Samona , Gerdes Madison B. , Weitlauf Amy , Rogers Baxter P. , Cascio Carissa J.
Published: May 2019

Background

Interoception involves the processing of sensory information relevant to physiological functioning and is integral to building self-awareness, emotional states, and modulating social behaviors. With the role of interoception in emotional processing and social functioning, there is growing interest in characterizing interoception in autism spectrum disorder (ASD), yet, there are mixed results regarding cardiac interoceptive accuracy in ASD.

Methods

In this study, we explored the neural basis of cardiac interoception using an fMRI heartbeat counting task in order to assess neural correlates of primary interoception. We predicted that interoceptive-specific response in the insula, a “hub” for interoception, would be related to ASD symptomatology. We investigated the relationship of insula responses during cardiac interoceptive accuracy and a self/caregiver-reported autism-related symptom scale (Social Responsiveness Scale-2 (SRS)). Participants included 46 individuals with autism spectrum disorder (ASD) (age 8-54, mean= 19.43±10.68 years) and 54 individuals with typical development for comparison (TC, age 8-53, mean= 21.43±10.41 years).

Results

We found no significant difference in cardiac interoceptive accuracy or neural response to cardiac interoception in ASD. Several insula sudivisons had a curvilinear relationship to age, peaking in early adulthood. Interoceptive-specific insula response was associated with adult self-report SRS scores; this association differed by diagnostic group and self/other report.

Conclusions

This work suggests that 1) there is no global deficit in interoception in ASD, but that integrating interoceptive cues with social information may distinguish individuals with ASD, and 2) there is a developmental trajectory for interoceptive processing in the insula that may be relevant for socio-emotional health.
Basis for discrimination by engineered CRISPR/Cas9 enzymes
Authors: Liu Mu-Sen , Gong Shanzhong , Yu Helen-Hong , Jung Kyungseok , Johnson Kenneth A. , Taylor David W.
Published: May 2019

CRISPR/Cas9 is a programmable genome editing tool that has been widely used for biological applications. While engineered Cas9s have been reported to increase discrimination against off-target cleavage compared with wild type Streptococcus pyogenes (SpCas9) in vivo, the mechanism for enhanced specificity has not been extensively characterized. To understand the basis for improved discrimination against off-target DNA containing important mismatches at the distal end of the guide RNA, we performed kinetic analyses on the high-fidelity (Cas9-HF1) and hyper-accurate (HypaCas9) engineered Cas9 variants. While DNA unwinding is the rate-limiting step for on-target cleavage by SpCas9, we show that chemistry is seriously impaired by more than 100-fold for the high-fidelity variants. The high-fidelity variants improve discrimination by slowing the rate of chemistry without increasing the rate of DNA rewinding—the kinetic partitioning favors release rather than cleavage of a bound off-target substrate because chemistry is slow. Further improvement in discrimination may require engineering increased rates of dissociation of off-target DNA.
A Temporal Transcriptional Map of Human Natural Killer Cell Differentiation
Authors: Pfefferle Aline , Netskar Herman , Ask Eivind Heggernes , Lorenz Susanne , Goodridge Jodie P. , Sohlberg Ebba , Clancy Trevor , Malmberg Karl-Johan
Published: May 2019

Natural killer cell repertoires are functionally diversified as a result of differentiation, homeostatic receptor-ligand interactions and adaptive responses to viral infections. However, the regulatory gene-circuits that define the manifold cell states and drive NK cell differentiation have not been clearly resolved. Here, we performed single-cell RNA sequencing of 26,506 cells derived from sorted phenotypically-defined human NK cell subsets to delineate a tightly coordinated differentiation process from a small population of CD56brightprecursors to adaptive NKG2C+CD56dimNK cells. RNA velocity analysis identified a clear directionality in the transition from CD56brightto CD56dimNK cells, which was dominated by genes involved in transcription and translation as well as acquisition of NK cell effector function. Gene expression trends mapped to pseudotime, defined by increasing entropy, identified three distinct transcriptional checkpoints, reflecting important changes in regulatory gene-circuits. The CD56brightNK cell population dominated pseudotime with two distinct checkpoints separating precursors from intermediate states that gradually took on transcriptional signatures similar to CD56dimNK cells. The final checkpoint occurred during late terminal differentiation of CD56dimNK cells and was associated with unique divergent gene-expression trends. Furthermore, we utilized this single-cell RNA sequencing resource to decipher the regulation of genes involved in lysosomal biogenesis and found a coordinated gradual increase in theRAB4andBLOC1Sgene families with differentiation into CD56dimNK cells. These results identify important gene programs driving functional diversification and specialization during NK cell differentiation and hold potential to guide new strategies for NK cell-based cancer immunotherapy.
Clustering of the structures by using “snakes-&-dragons” approach, or correlation matrix as a signal
Authors: Andreev Victor P. , Liu Gang , Zee Jarcy , Henn Lisa , Flores Gilberto E. , Merion Robert M.
Published: May 2019

Biological, ecological, social, and technological systems are complex structures with multiple interacting parts, often represented by networks. Correlation matrices describing interdependency of the variables in such structures provide key information for comparison and classification of such systems. Classification based on correlation matrices could supplement or improve classification based on variable values, since the former reveals similarities in system structures, while the latter relies on the similarities in system states. Importantly, this approach of clustering correlation matrices is different from clustering elements of the correlation matrices, because our goal is to compare and cluster multiple networks – not the nodes within the networks. A novel approach for clustering correlation matrices, named “snakes-&-dragons,” is introduced and illustrated by examples from neuroscience, human microbiome, and macroeconomics.
Reconciling Base-Pair Resolution 5-methylcytosine and 5-hydroxymethylcytosine Data in Neuroepigenetics
Authors: Kochmanski Joseph , Savonen Candace , Bernstein Alison I.
Published: May 2019

Epigenetic marks operate at multiple chromosomal levels to regulate gene expression, from direct covalent modification of DNA to 3D chromosomal structure. Research has shown that 5-methylcytosine (5-mC) and its oxidized form, 5-hydroxymethylcytosine (5-hmC), are stable epigenetic marks with distinct genomic distributions and separate regulatory functions. In addition, recent data indicate that 5-hmC plays a critical regulatory role in the mammalian brain, emphasizing the importance of considering this alternative DNA modification in the context of neuroepigenetics. Traditional bisulfite (BS) treatment-based methods to measure the methylome are not able to distinguish between 5-mC and 5-hmC, meaning much of the existing literature does not differentiate these two DNA modifications. Recently developed methods, including Tet-assisted bisulfite (TAB) treatment and oxidative bisulfite (oxBS) treatment, allow for differentiation of 5-hmC and/or 5-mC levels at base-pair resolution when combined with next-generation sequencing or methylation arrays. Despite these technological advances, there remains a lack of clarity regarding the appropriate statistical methods for integration of 5-mC and 5-hmC data. As a result, it can be difficult to determine the effects of an experimental treatment on 5-mC and 5-hmC dynamics. Here, we propose a statistical approach involving mixed effects to simultaneously model paired 5-mC and 5-hmC data as repeated measures. Using this approach, it will be possible to determine the effects of an experimental treatment on both 5-mC and 5-hmC at the base-pair level.
High-throughput isolation and culture of human gut bacteria with droplet microfluidics
Authors: Villa Max M , Bloom Rachael J , Silverman Justin D , Durand Heather K , Jiang Sharon , Wu Anchi , Huang Shuqiang , You Lingchong , David Lawrence A
Published: May 2019

Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for isolating and assaying microbiota members in picoliter droplets (MicDrop). MicDrop can be used to create millions of distinct bacterial colonies in a single experiment while using off-the-shelf parts compact enough to fit in an anaerobic chamber. In proof-of-concept experiments, we used the platform to characterize inter-individual metabolic variation among hundreds of polysaccharide-degrading gut bacteria from nine stool donors. We also used MicDrop to test the hypothesis that growth kinetics of individual gut bacterial taxa are associated with longterm community dynamics in an artificial gut. These demonstrations suggest the MicDrop platform could support future diagnostic efforts to personalize microbiota-directed therapies, as well as to provide comprehensive new insights into the ecology of human gut microbiota.
Superloser: a plasmid shuffling vector forSaccharomyces cerevisiaewith exceedingly low background
Authors: Haase Max A. B. , Truong David M. , Boeke Jef D.
Published: May 2019

Here we report a new plasmid shuffle vector for forcing budding yeast (Saccharomyces cerevisiae) to incorporate a new genetic pathway in place of a native pathway – even essential ones – while maintaining low false positive rates (less than 1 in 108per cell). This plasmid, dubbed “Superloser”, was designed with reduced sequence similarity to commonly used yeast plasmids (i.e. pRS400 series) to limit recombination, a process that in our experience leads to retention of the yeast gene(s) instead of the desired gene(s). In addition, Superloser utilizes two orthogonal copies of the counter-selectable markerURA3to reduce spontaneous 5-fluoroorotic acid resistance. Finally, the CEN/ARS sequence is fused to theGAL1-10promoter, which disrupts plasmid segregation in the presence of the sugar galactose, causing Superloser to rapidly be removed from a population of cells. We show one proof of concept shuffling experiment: swapping yeast’s core histones out for their human counterparts. Superloser is especially useful for forcing yeast to use highly unfavorable genes, such as human histones, as it enables plating a large number of cells (1.4×109) on a single 10 cm petri dish while maintaining a very low background. Therefore, Superloser is a useful tool for yeast geneticists to effectively shuffle low viability genes and/or pathways in yeast that may arise in as low as 1 in 108cells.
Loss of dominant caterpillar genera in a protected tropical forest
Authors: Salcido Danielle M. , Forister Matthew L. , Lopez Humberto Garcia , Dyer Lee A.
Published: May 2019

Reports of biodiversity loss have increasingly focused on the abundance and diversity of insects, but it is still unclear if substantive insect diversity losses are occurring in intact low-latitude forests. We collected 22 years of plant-caterpillar-parasitoid data in a protected tropical forest and found reductions in diversity and density of these insects that appear to be partly driven by a changing climate and weather anomalies. The decline in parasitism represents a reduction in an important ecosystem service: enemy control of primary consumers. The consequences of these changes are in many cases irreversible and are likely to be mirrored in nearby forests; overall declines in the region will have negative consequences for surrounding agriculture. The decline of important tropical taxa and associated ecosystem function illuminates the consequences of numerous threats to global insect diversity and provides additional impetus for research on tropical diversity.
Postpartum breast cancer progression is driven by semaphorin 7a mediated invasion and survival
Authors: Tarullo Sarah E , Hill Ryan C , Hansen Kirk , Behbod Fariba , Borges Virginia F , Nelson Andrew C , Lyons Traci R
Published: May 2019

Young women diagnosed with breast cancer (BC) have poor prognosis due to increased rates of metastasis. Additionally, women within 10 years of most recent childbirth at diagnosis are ∼3 times more likely to develop metastasis than age and stage matched nulliparous women. We define these cases as postpartum BC (PPBC) and propose that the unique biology of the postpartum mammary gland drives tumor progression. Our published results revealed roles for SEMA7A in breast tumor cell growth, motility, invasion, and tumor associated-lymphangiogenesis, all of which are also increased in pre-clinical models of PPBC. However, whether SEMA7A drives progression in PPBC remains largely unexplored. Our results presented herein show that silencing of SEMA7A decreases tumor growth in a model of PPBC while overexpression is sufficient to increase growth in nulliparous hosts. Further, we show that SEMA7A promotes multiple known drivers of PPBC progression including tumor associated COX-2 expression and fibroblast-mediated collagen deposition in the tumor microenvironment. Additionally, we show for the first time that SEMA7A expressing cells deposit fibronectin to promote tumor cell survival. Finally, we show that co-expression of SEMA7A/COX-2/FN predicts for poor prognosis in breast cancer patient cohorts. These studies suggest SEMA7A as a key mediator of BC progression and that targeting SEMA7A may open avenues for novel therapeutic strategies.
Nearly unbiased estimator of contemporary effective population size using within-cohort sibling pairs incorporating parental and non-parental reproductive variations
Authors: Akita Tetsuya
Published: May 2019

In this study, we developed a nearly unbiased estimator of contemporary effective mother size in a population, which is based on a known maternal half-sibling relationship found within the same cohort. Our method allows for variance of the average number of offspring per mother (i.e., parental variation, such as age-specific fecundity) and variance of the number of offspring among mothers with identical reproductive potential (i.e., non-parental variation, such as family-correlated survivorship). We also developed estimators of the variance and coefficient variation of contemporary effective mother size and qualitatively evaluated the performance of the estimators by running an individual-based model. Our results provide guidance for (i) a sample size to ensure the required accuracy and precision when the order of effective mother size is available and (ii) a degree of uncertainty regarding the estimated effective mother size when information about the size is unavailable. To the best of our knowledge, this is the first report to demonstrate the derivation of a nearly unbiased estimator of effective population size; however, its current application is limited to effective mother size and situations in which the sample size is not particularly small and maternal half-sibling relationships can be detected without error. The results of this study demonstrate the usefulness of a sibship assignment method for estimating effective population size; in addition, they have the potential to greatly widen the scope of genetic monitoring.
Bagremycin Antibiotics and Ferroverdin iron-chelators are synthetized by the Same Gene Cluster
Authors: Martinet Loïc , Naômé Aymeric , Deflandre Benoit , Maciejewska Marta , Tellatin Déborah , Tenconi Elodie , Smargiasso Nicolas , de Pauw Edwin , van Wezel Gilles P. , Rigali Sébastien
Published: May 2019

Biosynthetic gene clusters (BGCs) are organized groups of genes involved in the production of specialized metabolites. Typically, one BGC is responsible for the production of one or several similar compounds with bioactivities that usually only vary in terms of strength and/or specificity. Here we show that the previously described ferroverdins and bagremycins, which are families of metabolites with different bioactivities, are produced from the same BGC, whereby the fate of the biosynthetic pathway depends on iron availability. Under conditions of iron depletion, the monomeric bagremycins are formed, which are amino-aromatic antibiotics resulting from the condensation of 3-amino-4-hydroxybenzoic acid with p-vinylphenol. Conversely, when iron is abundantly available, the biosynthetic pathway additionally produces a molecule based on p-vinylphenyl-3-nitroso-4-hydroxybenzoate, which complexes iron to form the trimeric ferroverdins that have anticholesterol activity. Thus our work challenges the concept that BGCs should produce a single family of molecules with one type of bioactivity, the occurrence of the different metabolites being triggered by the environmental conditions.
Galacto-oligosaccharides modulate the juvenile gut microbiome and innate immunity to improve broiler chicken performance
Authors: Richards Philip J. , Flaujac Lafontaine Geraldine M. , Connerton Phillippa L. , Liang Lu , Asiani Karishma , Fish Neville M. , Connerton Ian F.
Published: May 2019

Improvements in growth performance and health are key goals in broiler chicken production. Inclusion of prebiotic galacto-oligosaccharides in broiler feed enhanced the growth rate and feed conversion of chickens relative to a calorie-matched control diet. Comparison of the cecal microbiota identified key differences in abundance ofLactobacillusspp. Increased levels ofL. johnsoniiin GOS-fed juvenile birds at the expense ofL. crispatuswas linked to improved performance (growth rate and market weight). Investigation of the innate immune responses highlighted increases of ileal and cecal IL-17A gene expression counterposed to a decrease in IL-10 and IL-17F. Quantification of the autochthonousLactobacillusssp. revealed a correlation between bird performance andL. johnsoniiabundance. Shifts in the cecal populations of keyLactobacillusspp. of juvenile birds primed intestinal innate immunity without harmful pathogen challenge.

IMPORTANCE

Improvements in the growth rate of broiler chickens can be achieved through dietary manipulation of the naturally occurring bacterial populations whilst mitigating the withdrawal of antibiotic growth promoters. Prebiotic galacto-oligosaccharides (GOS) are manufactured as a by-product of dairy cheese production, which can be incorporated in the diets of juvenile chickens to improve their health and performance. This study investigates the key mechanisms behind this progression and pin pointsL. johnsoniias a key species that facilitates the enhancements in growth rate and gut health. It also relates the role of the innate immune system in the response to the GOS diet.
Cyclic di-GMP Increases Catalase Production and Hydrogen Peroxide Tolerance inVibrio cholerae
Authors: Fernandez Nicolas L. , Waters Christopher M.
Published: May 2019

Vibrio choleraeis a Gram-negative bacterial pathogen that causes the disease cholera, which affects nearly 1 million people each year. In between outbreaks,V. choleraeresides in fresh and salt water environments where it is able to persist through changes in temperature, oxygen, and salinity. One key characteristic that promotes environmental persistence ofV. choleraeis the ability to form multicellular communities, called biofilms, that often adhere to biotic and abiotic sources. Biofilm formation inV. choleraeis positively regulated by the dinucleotide second messenger cyclic dimeric guanosine monophosphate (c-di-GMP). While most research on the c-di-GMP regulon has focused on biofilm formation or motility, we hypothesized the c-di-GMP signaling network encompassed a larger set of effector functions than reported. We found that high intracellular c-di-GMP increased catalase activity approximately 4-fold relative to strains with unaltered c-di-GMP. Genetic studies demonstrated that c-di-GMP mediated catalase activity was due to increased expression of the catalase encoding genekatB. Moreover, c-di-GMP mediated regulation of catalase activity andkatBexpression required the c-di-GMP dependent transcription factors VpsT and VpsR. Lastly, we found that high c-di-GMP increased survival after H2O2challenge in akatB, vpsR, andvpsTdependent manner. Our results indicate antioxidant production is regulated by c-di-GMP inV. choleraeuncovering a new node in the growing VpsT and VpsR c-di-GMP signaling network.

Importance

As a result of infection withV. cholerae, patients become dehydrated leading to death if not properly treated. The marine environment is the natural reservoir forV. choleraewhere it can survive alterations in temperature, salinity, and oxygen. The second messenger molecule c-di-GMP is an important signal regulating host and marine environmental persistence because it controls whetherV. choleraewill form a biofilm or disperse through flagellar motility. In this work, we demonstrate another function of c-di-GMP inV. choleraebiology: promoting tolerance to the reactive oxygen species H2O2through differential regulation of catalase expression. Our results suggest a mechanism where c-di-GMP simultaneously controls biofilm formation and antioxidant production, which could promote persistence in human and marine environments.
Directional DBS Leads Show Large Deviations from their Intended Implantation Orientation
Authors: Dembek TA , Hoevels M , Hellerbach A , Horn A , Petry-Schmelzer JN , Borggrefe J , Wirths J , Dafsari HS , Barbe MT , Visser-Vandewalle V , Treuer H
Published: May 2019

Objective

Lead orientation is a new degree of freedom with directional deep brain stimulation (DBS) leads. We investigated how prevalent deviations from the intended implantation direction are in a large patient cohort.

Methods

The Directional Orientation Detection (DiODe) algorithm to determine lead orientation from postoperative CT scans was implemented into the open-source Lead-DBS toolbox. Lead orientation was analysed in 100 consecutive patients (198 leads). Different anatomical targets and intraoperative setups were compared.

Results

Deviations of up to 90° from the intended implantation direction were observed. Deviations of more than 30° were seen in 42 % of the leads and deviations of more than 60° in about 11 % of the leads. Deviations were independent from the neuroanatomical target and the stereotactic frame but increased depending on which microdrive was used.

Discussion

Our results indicate that large deviations from the intended implantation direction are a common phenomenon in directional leads. Postoperative determination of lead orientation is thus mandatory for investigating directional DBS.

Full Disclosures

Till A. Dembek reports speaker honoraria from Medtronic and Boston Scientific.

Mauritius Hoevels has nothing to disclose.

Alexandra Hellerbach has nothing to disclose.

Andreas Horn reports speaker honoraria from Medtronic.

Jan Niklas Petry-Schmelzer reports travel grants from Boston Scientific.

Jan Borggrefe has nothing to disclose.

Jochen Wirths reports travel grants from Boston Scientific.

Haidar Salimi-Dafsari reports honoraria from Medtronic and Boston Scientific.

Michael T. Barbe reports grants from Medtronic and Boston Scientific.

Veerle Visser-Vandewalle is a member of the advisory boards and reports consultancies for Medtronic, Boston Scientific and St Jude Medical. She received a grant from SAPIENS Steering Brain Stimulation. Harald Treuer has nothing to disclose.
Systems-wide analysis unravels the new roles of CCM signal complex (CSC)
Authors: Abou-Fadel Johnathan , Vasquez Mariana , Grajeda Brian , Ellis Cameron , Zhang Jun
Published: May 2019

Cerebral cavernous malformations (CCMs) are characterized by abnormally dilated intracranial capillaries that result in increased susceptibility to stroke. Three genes have been identified as causes of CCMs; KRIT1 (CCM1), MGC4607 (CCM2) and PDCD10 (CCM3); one of them is disrupted in most CCM cases. It was demonstrated that both CCM1 and CCM3 bind to CCM2 to form a CCM signaling complex (CSC) to modulate angiogenesis. In this report, we deployed both RNA-seq and proteomic analysis of perturbed CSC after depletion of one of three CCM genes to generate interactomes for system-wide studies. Our results demonstrated a unique portrait detailing alterations in angiogenesis and vascular integrity. Interestingly, only in-direct overlapped alterations between RNA and protein levels were detected, supporting the existence of multiple layers of regulation in CSC cascades. Notably, this is the first report identifying that both β4 integrin and CAV1 signaling are downstream of CSC, conveying the angiogenic signaling. Our results provide a global view of signal transduction modulated by the CSC, identifies novel regulatory signaling networks and key cellular factors associated with CSC.
Spatial Confidence Sets for Raw Effect Size Images
Authors: Bowring Alexander , Telschow Fabian , Schwartzman Armin , Nichols Thomas E.
Published: May 2019

The mass-univariate approach for functional magnetic resonance imagery (fMRI) analysis remains a widely used and fundamental statistical tool within neuroimaging. However, this method suffers from at least two fundamental limitations: First, with sample sizes growing to 4, 5 or even 6 digits, the entire approach is undermined by the null hypothesis fallacy, i.e. with sufficient sample size, there is high enough statistical power to reject the null hypothesis everywhere, making it difficult if not impossible to localize effects of interest. Second, with any sample size, when cluster-size inference is used a significantp-value only indicates that a cluster is larger than chance, and no notion of spatial uncertainty is provided. Therefore, no perception of confidence is available to express the size or location of a cluster that could be expected with repeated sampling from the population.

In this work, we address these issues by extending on a method proposed bySommerfeld, Sain, and Schwartzman (2018)to develop spatial Confidence Sets (CSs) on clusters found in thresholded raw effect size maps. While hypothesis testing indicates where the null, i.e. a raw effect size of zero, can be rejected, the CSs give statements on the locations where raw effect sizes exceed, and fall short of, anon-zerothreshold, providing both an upper and lower CS.

While the method can be applied to any parameter in a mass-univariate General Linear Model, we motivate the method in the context of BOLD fMRI contrast maps for inference on percentage BOLD change raw effects. We propose several theoretical and practical implementation advancements to the original method in order to deliver an improved performance in small-sample settings. We validate the method with 3D Monte Carlo simulations that resemble fMRI data. Finally, we compute CSs for the Human Connectome Project working memory task contrast images, illustrating the brain regions that show a reliable %BOLD change for a given %BOLD threshold.
Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype
Authors: Hesse Raphael , Hurtado Maica Llavero , Jackson Rosemary J. , Eaton Samantha L. , Herrmann Abigail G , Colom-Cadena Marti , King Declan , Rose Jamie , Tulloch Jane , McKenzie Chris-Anne , Smith Colin , Henstridge Christopher , Lamont Douglas , Wishart Thomas M. , Spires-Jones Tara L.
Published: May 2019

Degeneration of synapses in Alzheimer’s disease (AD) strongly correlates with cognitive decline, and synaptic pathology contributes to disease pathophysiology. We recently discovered that the strongest genetic risk factor for sporadic AD, apolipoprotein E epsilon 4 (APOE4), exacerbates synapse loss and synaptic accumulation of oligomeric amyloid beta in human AD brain. To begin to understand the molecular cascades involved in synapse loss in AD and how this is mediated byAPOE, and to generate a resource of knowledge of changes in the synaptic proteome in AD, we conducted a proteomic screen and systematicin-silicoanalysis of synaptoneurosome preparations from temporal and occipital cortices of human AD and control subjects with knownAPOEgene status. Our analysis identified over 5,500 proteins in human synaptoneurosomes and highlighted disease, brain region, and APOE-associated changes in multiple molecular pathways including a decreased abundance in AD of proteins important for synaptic and mitochondrial function and an increased abundance of proteins involved in neuroimmune interactions and intracellular signaling.

Highlights

Proteomic analysis of synapses isolated from Alzheimer’s disease and control subject brains identifies over 5,500 proteins in human synapses.

In silico analysis reveals region-specific decreases in proteins involved in synaptic and mitochondrial function and increases in proteins involved in neuroimmune signaling and intracellular signaling in AD.

The apolipoprotein E4 risk gene is associated with exacerbated changes in synaptic proteins in AD.
Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure
Authors: Waldl Maria , Will Sebastian , Wolfinger Michael T. , Hofacker Ivo L. , Stadler Peter F.
Published: May 2019

RNA molecules may experience independent selection pressures on their sequence and (secondary) structure. Structural features then may be preserved without maintaining their exact position along the sequence. In such cases, corresponding base pairs are no longer formed by homologous bases, leading to the incongruent evolutionary conservation of sequence and structure. In order to model this phenomenon, we introduce bi-alignments as a superposition of two alignments: one modeling sequence homology; the other, structural homology. We show that under natural assumptions on the scoring functions, bi-alignments form a special case of 4-way alignments, in which the incongruencies are measured as indels in the pairwise alignment of the two alignment copies. A preliminary survey of the Rfam database suggests that incongruent evolution of RNAs is not a very rare phenomenon.

Availability

Our software is freely available at https://github.com/s-will/BiAlign
Effect of structure in ionized albumin – based nanoparticle: Characterisation, Emodin interaction, and in vitro cytotoxicity
Authors: Siri Macarena , Ruocco Maria Julieta Fernandez , Achilli Estefanía , Pizzuto Malvina , Delgado Juan F. , Ruysschaert Jean-Marie , Grasselli Mariano , Alonso Silvia del V.
Published: May 2019

A γ–irradiated bovine albumin serum based nanoparticle was characterised structurally, and functionally. The nanoparticle was characterised by A.F.M, D.L.S, zeta potential, T.E.M., gel-electrophoresis, spectroscopy (UV-Vis, Fluorescence, FT-IR, and CD). Its stability was studied under adverse experimental conditions: pH values, chaotropic agents, and ionic strength and stability studies against time were mainly carried out by fluorescence spectroscopy following the changes in the tryptophan environment in the nanoparticle. Its function was studied by the interaction of the NP with the hydrophobic drug Emodin was studied. The binding and kinetic properties of the obtained complex were tested by biophysical methods as well as its toxicity in tumour cells.

According to its biophysics, the nanoparticle is a spherical nanosized vehicle with a hydrodynamic diameter of 70 nm. Data obtained describe the nanoparticle alone as nontoxic for cancer cell lines. When combined with Emodin, the bioconjugate proved to be more active on MCF-7 and PC-3 cancer cell lines than the nanoparticle alone. No haemolytic activity was found when tested against ex vivo red blood cells. The stability of the albumin nanoparticle is based on a competition between short-range attraction forces and long-range repulsion forces. The nanoparticle showed similar behaviour as albumin against pH while improving its stability in urea and tween 80. It was stable up to 15 days and presented no protein degradation in solutions up to 2 M salt concentration. Significantly, the albumin aggregate preserves the main activity-function of albumin and improved characteristics as an excellent carrier of molecules.

Graphical Abstract
Simulation-based comparison of Biopharmaceutics Classification System and drug structure
Authors: Chen Tianyu , Wu Tianqiang , Li Ningxi , Yin Huanli , Wu Min
Published: May 2019

Background

The Biopharmaceutics Classification System (BCS), which classifies bioactive molecules based on solubility and permeability, is widely used to guide new drug development and drug formulation, as well as predict pharmacokinetics. Here we performed computer simulations to study correlations between a molecule’s structure and its BCS classification.

Methods

A total of 411 small molecules were assigned to BCS categories based on published drug data, and their Pybel-FP4 fingerprints were extrapolated. The information gain(IG) of each fingerprint was calculated and its characteristic structure analyzed. IG was calculated using multiple thresholds, and results were verified using support vector machine prediction, while taking into account the dose coefficient(0-0.1, 0.1-1, or>1). Structural functional features common to fingerprints of compounds in each type of BCS class were determined using computer simulations.

Results

BCS classes III and IV appear to share several structural and functional characteristics, including Secondary aliphaticamine, Michael_acceptor, Isothiourea, and Sulfonamide Sulfonic_derivatives.

Conclusion

We demonstrate that our approach can correlate characteristic fingerprints of small-molecule drugs with BCS classifications, which may help guide the development and optimization of new drugs.
The state of preparation in performance climbing
Authors: Trifu Simona , Trifu Antonia Ioana
Published: May 2019

This research has been carried out among climbing performers in Romania (a group of 60 climbers), starting from the desire to induce a state of preparation by watching a motivational short movie before performing a high difficulty route. The concept of preparation was related to the emotional impact of tonic or sensitive type (depending on the content of the movie) and the personality structure of the athletes, the conclusions drawn being in the area of optimization of performance by inducing an optimal state of preparation.

Performance climbers can have two main attitudes to impact with emotional stimuli in the competitive environment: tonic versus sensitivity. We propose the study of the correlations between the personality structure of the athletes, the emotional impact on stimulation, respectively the quality of the prepared state of state, as the active regulatory status.

The methodology included a batch of 60 climbers divided into two equal subgroups, before making a difficult route being allowed to view a movie with a tonic impact, or a sensitive impact. Personality was evaluated through five scales (Intelligence, Emotional Stability, Sensitivity, Imagination, and Perspicacity) while administering a Preparatory and Motivation Questionnaire.

People with a high level of intelligence, imagination and perspicacity can more easily create attitudes, habits and habitual contests, as well as conduct appropriate to the concrete conditions of the competitive situation, while people with low emotional stability and sensitivity are more inclined towards a sensitive, labile, sensitive approach to the competitive situation. The research implies the necessity of organizing the mental operators with the purpose of suitability to the performance poor, in accordance with the tactical training of the athlete and with the personality traits.

Emotional stimulation leads to affective participation, reception and awareness of favoring issues, stimulation of will, self-regulation of activity according to aspirations and strategies.
Scaling of inertial delays in terrestrial mammals
Authors: Mohamed Thangal Sayed Naseel , Donelan J. Maxwell
Published: May 2019

As part of its response to a perturbation, an animal often needs to reposition its body. Inertia acts to oppose motion, delaying the completion of the movement—we refer to this additional elapsed time as inertial delay. As animal size increases, muscle moment arms also increase, but muscles are proportionally weaker, and limb inertia is proportionally larger. Consequently, the scaling of inertial delays is complex. Here, we quantify it using two biomechanical models representing common scenarios in animal locomotion: a distributed mass pendulum approximating swing limb repositioning (swing task), and an inverted pendulum approximating whole body posture recovery (posture task). We parameterized the anatomical, muscular, and inertial properties of these models using literature scaling relationships, then determined inertial delay for each task across a large range of movement magnitudes and the full range of terrestrial mammal sizes. We found that inertial delays scaled with an average ofM0.28in the swing task andM0.35in the posture task across movement magnitudes—larger animals require more absolute time to perform the same movement as small animals. The time available to complete a movement also increases with animal size, but less steeply. Consequently, inertial delays comprise a greater fraction of swing duration and other characteristic movement times in larger animals. We also compared inertial delays to the other component delays within the stimulus-response pathway. As movement magnitude increased, inertial delays exceeded these sensorimotor delays, and this occurred for smaller movements in larger animals. Inertial delays appear to be a challenge for motor control, particularly for bigger movements in larger animals.
Cell-autonomous regulation of epithelial cell quiescence by calcium channel Trpv6
Authors: Xin Yi , Malick Allison , Hu Meiqin , Liu Chengdong , Batah Heya , Xu Haoxing , Duan Cunming
Published: May 2019

Epithelial homeostasis and regeneration require a pool of quiescent cells. How the quiescent cells are established and maintained is poorly understood. Here we report that Trpv6, a cation channel responsible for epithelial Ca2+ absorption, functions as a key regulator of cellular quiescence. Genetic deletion and pharmacological blockade of Trpv6 promoted zebrafish epithelial cells to exit from quiescence and re-enter the cell cycle. Reintroducing Trpv6, but not its channel dead mutant, restored the quiescent state. Ca2+ imaging showed that Trpv6 is constitutively open in vivo. Mechanistically, Trpv6-mediated Ca2+ influx maintained the quiescent state by suppressing insulin-like growth factor (IGF)-mediated Akt and Tor signaling. In zebrafish epithelia and human colon cancer cells, Trpv6/TRPV6 elevated intracellular Ca2+ levels and activated PP2A, which down-regulated IGF signaling and promoted the quiescent state. Our findings suggest that Trpv6 mediates constitutive Ca2+ influx into epithelial cells to continuously suppress growth factor signaling and maintain the quiescent state.
Predicting longitudinal traits derived from high-throughput phenomics in contrasting environments using genomic Legendre polynomials and B-splines
Authors: Momen Mehdi , Campbell Malachy T. , Walia Harkamal , Morota Gota
Published: May 2019

Recent advancements in phenomics coupled with increased output from sequencing technologies can create the platform needed to rapidly increase abiotic stress tolerance of crops, which increasingly face productivity challenges due to climate change. In particular, the high-throughput phenotyping (HTP) enables researchers to generate large-scale data with temporal resolution. Recently, a random regression model (RRM) was used to model a longitudinal rice projected shoot area (PSA) dataset in an optimal growth environment. However, the utility of RRM is still unknown for phenotypic trajectories obtained from stress environments. Here, we sought to apply RRM to forecast the rice PSA in control and water-limited conditions under various longitudinal cross-validation scenarios. To this end, genomic Legendre polynomials and B-spline basis functions were used to capture PSA trajectories. Prediction accuracy declined slightly for the water-limited plants compared to control plants. Overall, RRM delivered reasonable prediction performance and yielded better prediction than the baseline multi-trait model. The difference between the results obtained using Legendre polynomials and that using B-splines was small; however, the former yielded a higher prediction accuracy. Prediction accuracy for forecasting the last five time points was highest when the entire trajectory from earlier growth stages was used to train the basis functions. Our results suggested that it was possible to decrease phenotyping frequency by only phenotyping every other day in order to reduce costs while minimizing the loss of prediction accuracy. This is the first study showing that RRM could be used to model changes in growth over time under abiotic stress conditions.