bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct ‘pattern of autofluorescence’ of acute ischemic stroke patients’ skin and fingernails: A novel diagnostic biomarker for acute ischemic stroke
Authors: Wu Danhong , Zhang Mingchao , Tao Yue , Yu Haibo , Li Yujia , Zhang Shufan , Chu Tianqing , Zou Xiaofeng , Chen Xin , Ying Weihai 
Published: April 2018

AbstractEarly and economical diagnosis of acute ischemic stroke (AIS) is pivotal for therapeutic efficacy, particularly for the settings where medical imaging resource is deficient. We have obtained evidence supporting our hypothesis that collective properties of the green autofluorescence (AF) of the fingernails and certain skin’s positions may be a novel diagnostic biomarker for AIS: Both the green AF intensity and AF asymmetry of the AIS patients in their Index Fingernails and most examined skin’s positions were significantly higher than that of the healthy subjects and the Non-AIS subjects. ROC analyses and machine learning-based analyses on the AF properties showed that AUC was 0.93 and 0.87, respectively, for differentiating the AIS patients from the healthy subjects and for differentiating the AIS patients from the Non-AIS subjects. The AIS patients had significantly higher AF intensity and AF asymmetry at several examined positions, compared to those of the patients of Parkinson’s disease, pulmonary infection and transient ischemic attack. The AUC was 0.79 – 0.88 for differentiating AIS patients from each of these diseases. There was evidence suggesting that the AF originates from keratins. Collectively, our study has indicated that the characteristic AIS’s ‘Pattern of AF’ is a novel diagnostic biomarker for the disease. The ‘Pattern of AF Technology’ holds excellent potential to become a new non-invasive, label-free and economical diagnostic approach for AIS, which is particularly valuable when MRI or CT imaging resource is deficient.
Optical alignment device for two-photon microscopy
Authors: Galiñanes Gregorio L. , Marchand Paul J. , Turcotte Raphaёl , Pellat Sebastien , Ji Na , Huber Daniel 
Published: May 2018

AbstractTwo-photon excitation fluorescence microscopy has revolutionized our understanding of brain structure and function through the high resolution and large penetration depth it offers. Investigating neural structures in vivo requires gaining optical access to the brain, which is typically achieved by replacing a part of the skull with one or several layers of cover glass windows. To compensate for the spherical aberrations caused by the presence of these layers of glass, collar-correction objectives are typically used. However, the efficiency of this correction has been shown to depend significantly on the tilt angle between the glass window surface and the optical axis of the imaging system. Here we expand these observations and characterize the effect of the tilt angle on the collected fluorescence signal with thicker windows (double cover glass) and compare these results with an objective devoid of collar-correction. Finally, we present a simple optical alignment device designed to rapidly minimize the tilt angle in vivo and align the optical axis of the microscope perpendicularly to the glass window, thereby significantly improving the imaging quality. The performance of the device is demonstrated in an in vivo setting and a tilt-correction procedure is described, enabling the accurate alignment (<0.2°) of the cover glass with the imaging plane in only few iterations.
Minor sequence modifications in temporin B cause drastic changes in antibacterial potency and selectivity by fundamentally altering membrane activity
Authors: Manzo Giorgia , Ferguson Philip M. , Gustilo V. Benjamin , Bui Tam T. , Drake Alex F. , Atkinson R. Andrew , Batoni Giovanna , Lorenz Christian D. , Phoenix David A. , Mason A. James 
Published: May 2018

ABSTRACTAntimicrobial peptides (AMPs) are a potential source of new molecules to counter the increase in antimicrobial resistant infections but a better understanding of their properties is required to understand their native function and for effective translation as therapeutics. Details of the mechanism of their interaction with the bacterial plasma membrane are desired since damage or penetration of this structure is considered essential for AMP activity. Relatively modest modifications to AMP primary sequence can induce substantial changes in potency and/or spectrum of activity but, hitherto, have not been predicted to substantially alter the mechanism of interaction with the bacterial plasma membrane. Here we use a combination of molecular dynamics simulations, circular dichroism, solid-state NMR and patch clamp to investigate the extent to which temporin B and its analogues can be distinguished both in vitro and in silico on the basis of their interactions with model membranes. Enhancing the hydrophobicity of the N-terminus and cationicity of the C-terminus in temporin B improves its membrane activity and potency against both Gram-negative and Gram-positive bacteria. In contrast, enhancing the cationicity of the N-terminus abrogates its ability to trigger channel conductance and renders it ineffective against Staphylococcus aureus while nevertheless enhancing its potency against Escherichia coli. Our findings suggest even closely related AMPs may target the same bacterium with fundamentally differing mechanisms of action.
PLK4 is a microtubule-associated protein that self assembles promoting de novo MTOC formation
Authors: Gouveia Susana Montenegro , Zitouni Sihem , Kong Dong , Duarte Paulo , Gomes Beatriz Ferreira , Sousa Ana Laura , Tranfield Erin M. , Hyman Antony , Loncarek Jadranka , Bettencourt-Dias Monica 
Published: May 2018

Summary statementPLK4 binds to microtubules and self assembles into supramolecular assemblies that recruit tubulin and trigger de novo MTOC formation in Xenopus laevis extracts.AbstractThe centrosome is an important microtubule-organizing center (MTOCs) in animal cells and it consists of two barrel-shaped structures (centrioles), surrounded by the pericentriolar material (PCM), which nucleates microtubules. PCM components form condensates, supramolecular assemblies that concentrate microtubule nucleators. Centrosomes can form close to an existing structure (canonical duplication) or de novo. How centrosomes form de novo is not known. PLK4 is a master driver of centrosome biogenesis, which is critical to recruit several centriole components. Here, we investigate the beginning of centrosome biogenesis, taking advantage of Xenopus egg extracts, where we and others have shown that PLK4 can induce de novo MTOC formation (Eckerdt et al., 2011; Zitouni et al., 2016). Surprisingly, we observe that in vitro, PLK4 can self-assemble into supramolecular assemblies that recruit α/β-tubulin. In Xenopus extracts, PLK4 supramolecular assemblies additionally recruit the PLK4 substrate STIL and the microtubule nucleator, γ-tubulin, and form acentriolar MTOCs de novo. The assembly of these robust microtubule asters is independent of dynein, similarly to centrosomes. We suggest a new mechanism of action for PLK4, where it forms a self-organizing catalytic scaffold that recruits centriole components, PCM factors and α/β-tubulin, leading to MTOC formation.
Hotspot mutations and ColE1 plasmids contribute to the fitness ofSalmonellaHeidelberg in poultry litter
Authors: Oladeinde Adelumola , Cook Kimberly , Orlek Alex , Zock Greg , Herrington Kyler , Cox Nelson , Lawrence Jodie Plumblee , Hall Carolina 
Published: May 2018

ABSTRACTSalmonella entericasubsp.entericaserovar Heidelberg (S.Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specificS.Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.
Adaptation after vastus lateralis denervation in rats suggests neural regulation of joint stresses and strains
Authors: Alessando Cristiano , Rellinger Benjamin A. , Barroso Filipe O. , Tresch Matthew C. 
Published: May 2018

AbstractIn order to produce movements, muscles must act through joints. The translation from muscle force to limb movement is mediated by internal joint structures that permit movement in some directions but constrain it in others. Although muscle forces acting against constrained directions will not affect limb movements, such forces can cause excess stresses and strains in joint structures, leading to pain or injury. In this study, we hypothesized that the central nervous system (CNS) chooses muscle activations to avoid excess joint stresses and strains. We evaluated this hypothesis by examining adaptation strategies after selective paralysis of a muscle acting at the rat knee. We show that the CNS compromises between restoration of task performance and regulation of joint stresses and strains. These results have significant implications to our understanding of the neural control of movements, suggesting that common theories emphasizing task performance are insufficient to explain muscle activations during behaviors.
Enterococcus faecalisCRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine
Authors: Price Valerie J. , McBride Sara W. , Hullahalli Karthik , Chatterjee Anushila , Duerkop Breck A. , Palmer Kelli L. 
Published: May 2018

AbstractCRISPR-Cas systems are barriers to horizontal gene transfer (HGT) in bacteria. Little is known about CRISPR-Cas interactions with conjugative plasmids, and studies investigating CRISPR-Cas/plasmid interactions inin vivomodels relevant to infectious disease are lacking. These are significant gaps in knowledge because conjugative plasmids disseminate antibiotic resistance genes among pathogensin vivo, and it is essential to identify strategies to reduce the spread of these elements. We use enterococci as models to understand the interactions of CRISPR-Cas with conjugative plasmids.Enterococcus faecalisis a native colonizer of the mammalian intestine and harbors pheromone-responsive plasmids (PRPs). PRPs mediate inter- and intraspecies transfer of antibiotic resistance genes. We assessedE. faecalisCRISPR-Cas anti-PRP activity in the mouse intestine and under varyingin vitroconditions. We observed striking differences in CRISPR-Cas efficiencyin vitroversusin vivo. With few exceptions, CRISPR-Cas blocked intestinal PRP dissemination, whilein vitro, the PRP frequently escaped CRISPR-Cas defense. Our results further the understanding of CRISPR-Cas biology by demonstrating that standardin vitroexperiments do not adequately model thein vivoanti-plasmid activity of CRISPR-Cas. Additionally, our work identifies several variables that impact the apparentin vitroanti-plasmid activity of CRISPR-Cas, including planktonic versus biofilm settings, different donor/recipient ratios, production of a plasmid-encoded bacteriocin, and the time point at which matings are sampled. Our results are clinically significant because they demonstrate that barriers to HGT encoded by normal human microbiota can have significant impacts onin vivoantibiotic resistance dissemination.ImportanceCRISPR-Cas is a type of immune system encoded by bacteria that is hypothesized to be a natural impediment to the spread of antibiotic resistance genes. In this study, we directly assessed the impact of CRISPR-Cas on antibiotic resistance dissemination in the mammalian intestine and under varyingin vitroconditions. We observed a robust effect of CRISPR-Cas onin vivobut notin vitrodissemination of antibiotic resistance plasmids in the native mammalian intestinal colonizerEnterococcus faecalis. We conclude that standard laboratory experiments currently do not appropriately model thein vivoconditions where antibiotic resistance dissemination occurs betweenE. faecalisstrains. Moreover, our results demonstrate that CRISPR-Cas encoded by native members of the mammalian intestinal microbiota can block the spread of antibiotic resistance plasmids.
The molecular basis of antigenic variation among A(H9N2) avian influenza viruses
Authors: Peacock Thomas P. , Harvey William T. , Sadeyen Jean-Remy , Reeve Richard , Iqbal Munir 
Published: May 2018

AbstractAvian influenza A(H9N2) viruses are an increasing threat to global poultry production and, through zoonotic infection, to human health where they are considered viruses with pandemic potential. Vaccination of poultry is a key element of disease control in endemic countries, but vaccine effectiveness is persistently challenged by the emergence of antigenic variants. Here we employed a combination of techniques to investigate the genetic basis of H9N2 antigenic variability and evaluate the role of different molecular mechanisms of immune escape. We systematically tested the influence of published H9N2 monoclonal antibody escape mutants on chicken antisera binding, determining that many have no significant effect. Substitutions introducing additional glycosylation sites were a notable exception, though these are relatively rare among circulating viruses. To identify substitutions responsible for antigenic variation in circulating viruses, we performed an integrated meta-analysis of all published H9 haemagglutinin sequences and antigenic data. We validated this statistical analysis experimentally and allocated several new residues to H9N2 antigenic sites providing molecular markers that will help explain vaccine breakdown in the field and inform vaccine selection decisions. We find evidence for the importance of alternative mechanisms of immune escape, beyond simple modulation of epitope structure, with substitutions increasing glycosylation or receptor-binding avidity exhibiting the largest impacts on chicken antisera binding. Of these, meta-analysis indicates avidity regulation to be more relevant to the evolution of circulating viruses, suggesting that a specific focus on avidity regulation is required to fully understand the molecular basis of immune escape by influenza, and potentially other viruses.
Assessing distinct patterns of cognitive aging using tissue-specific brain age prediction based on diffusion tensor imaging and brain morphometry
Authors: Richard Geneviève , Kolskår Knut , Sanders Anne-Marthe , Kaufmann Tobias , Petersen Anders , Doan Nhat Trung , Sánchez Jennifer Monereo , Alnæs Dag , Ulrichsen Kristine M. , Dørum Erlend S. , Andreassen Ole A. , Nordvik Jan Egil , Westlye Lars T. 
Published: May 2018

AbstractMultimodal imaging enables sensitive measures of the architecture and integrity of the human brain, but the high-dimensional nature of advanced brain imaging features poses inherent challenges for the analyses and interpretations. Multivariate age prediction reduces the dimensionality to one biologically informative summary measure with potential for assessing deviations from normal lifespan trajectories. A number of studies documented remarkably accurate age prediction, but the differential age trajectories and the cognitive sensitivity of distinct brain tissue classes have to a lesser extent been characterized.Exploring differential brain age models driven by tissue-specific classifiers provides a hitherto unexplored opportunity to disentangle independent sources of heterogeneity in brain biology. We trained machine-learning models to estimate brain age using various combinations of FreeSurfer based morphometry and diffusion tensor imaging based indices of white matter microstructure in 612 healthy controls aged 18–87 years. To compare the tissue- specific brain ages and their cognitive sensitivity we applied each of the 11 models in an independent and cognitively well-characterized sample (n=265, 20–88 years). Correlations between true and estimated age in our test sample were highest for the most comprehensive brain morphometry (r=0.83, CI:0.78–0.86) and white matter microstructure (r=0.79, CI:0.74–0.83) models, confirming sensitivity and generalizability. The deviance from the chronological age were sensitive to performance on several cognitive tests for various models, including spatial Stroop and symbol coding, indicating poorer performance in individuals with an over-estimated age. Tissue-specific brain age models provide sensitive measures of brain integrity, with implications for the study of a range of brain disorders.
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity
Authors: DeWitt William S , Smith Anajane , Schoch Gary , Hansen John A , Matsen Frederick A , Bradley Philip 
Published: May 2018

AbstractThe T cell receptor (TCR) repertoire encodes immune exposure history through the dynamic formation of immunological memory. Statistical analysis of repertoire sequencing data has the potential to decode disease associations from large cohorts with measured phenotypes. However, the repertoire perturbation induced by a given immunological challenge is conditioned on genetic background via major histocompatibility complex (MHC) polymorphism. We explore associations between MHC alleles, immune exposures, and shared TCRs in a large human cohort. Using a previously published repertoire sequencing dataset augmented with high-resolution MHC genotyping, our analysis reveals rich structure: striking imprints of common pathogens, clusters of co-occurring TCRs that may represent markers of shared immune exposures, and substantial variations in TCR-MHC association strength across MHC loci. Guided by atomic contacts in solved TCR:peptide-MHC structures, we identify sequence covariation between TCR and MHC. These insights and our analysis framework lay the groundwork for further explorations into TCR diversity.
CHASMplus reveals the scope of somatic missense mutations driving human cancers
Authors: Tokheim Collin , Karchin Rachel 
Published: May 2018

SummaryLarge-scale cancer sequencing studies of patient cohorts have statistically implicated many genes driving cancer growth and progression, and their identification has yielded substantial translational impact. However, a remaining challenge is to increase the resolution of driver prediction from the gene level to the mutation level, because mutation-level predictions are more closely aligned with the goal of precision cancer medicine. Here we present CHASMplus, a computational method, that is uniquely capable of identifying driver missense mutations, including those specific to a cancer type, as evidenced by significantly superior performance on diverse benchmarks. Applied to 8,657 tumor samples across 32 cancer types in The Cancer Genome Atlas, CHASMplus identifies over 4,000 unique driver missense mutations in 240 genes, supporting a prominent role for rare driver mutations. We show which TCGA cancer types are likely to yield discovery of new driver missense mutations by additional sequencing, which has important implications for public policy.SignificanceMissense mutations are the most frequent mutation type in cancers and the most difficult to interpret. While many computational methods have been developed to predict whether genes are cancer drivers or whether missense mutations are generally deleterious or pathogenic, there has not previously been a method to score the oncogenic impact of a missense mutation specifically by cancer type, limiting adoption of computational missense mutation predictors in the clinic. Cancer patients are routinely sequenced with targeted panels of cancer driver genes, but such genes contain a mixture of driver and passenger missense mutations which differ by cancer type. A patient’s therapeutic response to drugs and optimal assignment to a clinical trial depends on both the specific mutation in the gene of interest and cancer type. We present a new machine learning method honed for each TCGA cancer type, and a resource for fast lookup of the cancer-specific driver propensity of every possible missense mutation in the human exome.
White Matter Network Architecture Guides Direct Electrical Stimulation Through Optimal State Transitions
Authors: Stiso Jennifer , Khambhati Ankit N. , Menara Tommaso , Kahn Ari E. , Stein Joel M. , Das Sandihitsu R. , Gorniak Richard , Tracy Joseph , Litt Brian , Davis Kathryn A. , Pasqualetti Fabio , Lucas Timothy , Bassett Danielle S. 
Published: May 2018

AbstractElectrical brain stimulation is currently being investigated as a potential therapy for neurological disease. However, opportunities to optimize and personalize such therapies are challenged by the fact that the beneficial impact (and potential side effects) of focal stimulation on both neighboring and distant regions is not well understood. Here, we use network control theory to build a formal model of brain network function that makes explicit predictions about how stimulation spreads through the brain’s white matter network and influences large-scale dynamics. We test these predictions using combined electrocorticography (ECoG) and diffusion weighted imaging (DWI) data from patients with medically refractory epilepsy undergoing evaluation for resective surgery, and who volunteered to participate in an extensive stimulation regimen. We posit a specific model-based manner in which white matter tracts constrain stimulation, defining its capacity to drive the brain to new states, including states associated with successful memory encoding. In a first validation of our model, we find that the true pattern of white matter tracts can be used to more accurately predict the state transitions induced by direct electrical stimulation than the artificial patterns of a topological or spatial network null model. We then use a targeted optimal control framework to solve for the optimal energy required to drive the brain to a given state. We show that, intuitively, our model predicts larger energy requirements when starting from states that are farther away from a target memory state. We then suggest testable hypotheses about which structural properties will lead to efficient stimulation for improving memory based on energy requirements. We show that the strength and homogeneity of edges between controlled and uncontrolled nodes, as well as the persistent modal controllability of the stimulated region, predict energy requirements. Our work demonstrates that individual white matter architecture plays a vital role in guiding the dynamics of direct electrical stimulation, more generally offering empirical support for the utility of network control theoretic models of brain response to stimulation.