Function-based Intersubject Alignment of Human Cortical Anatomy

Making conclusions about the functional neuroanatomical organization of the human brain requires methods for relating the functional anatomy of an individual's brain to population variability. We have developed a method for aligning the functional neuroanatomy of individual brains based on the patterns of neural activity that are elicited by viewing a movie. Instead of basing alignment on functionally defined areas, whose location is defined as the center of mass or the local maximum response, the alignment is based on patterns of response as they are distributed spatially both within and across cortical areas. The method is implemented in the two-dimensional manifold of an inflated, spherical cortical surface. The method, although developed using movie data, generalizes successfully to data obtained with another cognitive activation paradigm—viewing static images of objects and faces—and improves group statistics in that experiment as measured by a standard general linear model (GLM) analysis

Altitude dependence of atmospheric temperature trends: Climate models versus observation

As a consequence of greenhouse forcing, all state of the art general circulation models predict a positive temperature trend that is greater for the troposphere than the surface. This predicted positive trend increases in value with altitude until it reaches a maximum ratio with respect to the surface of as much as 1.5 to 2.0 at about 200 to 400 hPa. However, the temperature trends from several independent observational data sets show decreasing as well as mostly negative values. This disparity indicates that the three models examined here fail to account for the effects of greenhouse forcings.Comment: 9 pages, 3 figure

Astronomical and Tectonic Influences on Climate and Deposition Revealed Through Radioisotopic Geochronology and Bayesian Age-Depth Modeling of the Early Eocene Green River Formation, Wyoming, USA

The Wilkins Peak Member (WPM) of the Green River Formation in Wyoming, USA, comprises alternating lacustrine and alluvial strata that preserve a record of terrestrial climate during the early Eocene climatic optimum. We use a Bayesian framework to develop age-depth models for three sites, based on new 40Ar/39Ar sanidine and 206Pb/238U zircon ages from seven tuffs. The new models provide two- to ten-fold increases in temporal resolution compared to previous radioisotopic age models, confirming eccentricity-scale pacing of WPM facies, and permitting their direct comparison to astronomical solutions. Starting at ca. 51 Ma, the median ages for basin-wide flooding surfaces atop six successive alluvial marker beds coincide with short eccentricity maxima in the astronomical solutions. These eccentricity maxima have been associated with hyperthermal events recorded in marine strata during the early Eocene. WPM strata older than ca. 51 Ma do not exhibit a clear relationship to the eccentricity solutions, but accumulated 31%–35% more rapidly, suggesting that the influence of astronomical forcing on sedimentation was modulated by basin tectonics. Additional high-precision radioisotopic ages are needed to reduce the uncertainty of the Bayesian model, but this approach shows promise for unambiguous evaluation of the phase relationship between alluvial marker beds and theoretical eccentricity solutions

A negative feedback loop mediated by the Bcl6-cullin 3 complex limits Tfh cell differentiation

Induction of Bcl6 (B cell lymphoma 6) is essential for T follicular helper (Tfh) cell differentiation of antigen-stimulated CD4(+) T cells. Intriguingly, we found that Bcl6 was also highly and transiently expressed during the CD4(+)CD8(+) (double positive [DP]) stage of T cell development, in association with the E3 ligase cullin 3 (Cul3), a novel binding partner of Bcl6 which ubiquitinates histone proteins. DP stage-specific deletion of the E3 ligase Cul3, or of Bcl6, induced the derepression of the Bcl6 target genes Batf (basic leucine zipper transcription factor, ATF-like) and Bcl6, in part through epigenetic modifications of CD4(+) single-positive thymocytes. Although they maintained an apparently normal phenotype after emigration, they expressed increased amounts of Batf and Bcl6 at basal state and produced explosive and prolonged Tfh responses upon subsequent antigen encounter. Ablation of Cul3 in mature CD4(+) splenocytes also resulted in dramatically exaggerated Tfh responses. Thus, although previous studies have emphasized the essential role of Bcl6 in inducing Tfh responses, our findings reveal that Bcl6-Cul3 complexes also provide essential negative feedback regulation during both thymocyte development and T cell activation to restrain excessive Tfh responses

Early Adoption of Dabigatran and Its Dosing in US Patients With Atrial Fibrillation: Results From the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation

Background: Dabigatran is a novel oral anticoagulant approved for thromboprophylaxis in atrial fibrillation. Adoption patterns of this new agent in community practice are unknown. Methods and Results: We studied patterns of dabigatran use among patients enrolled in the Outcomes Registry for Better Informed Treatment of Atrial Fibrillation (ORBIT‐AF) Registry between June 2010 and August 2011 and followed for 12 months. Among 9974 atrial fibrillation patients included, 1217 (12%) were treated with dabigatran during the study. Overall, patients receiving dabigatran were younger (median age 72 versus 75 years, P<0.0001), more likely to be white (92% versus 89%, P=0.005), more likely to have private insurance (33% versus 25%, P<0.0001), and less likely to have prior cardiovascular disease (4% versus 33%, P<0.0001). They had more new‐onset atrial fibrillation (8.8% versus 4.1%, P<0.0001), lower CHADS2 scores (estimated risk based on the presence of congestive heart failure, hypertension, aged ≥75 years, diabetes mellitus, and prior stroke or transient ischemic attack; mean 2.0 versus 2.3, P<0.0001), and lower Anticoagulation and Risk Factors in Atrial Fibrillation scores (mean 2.4 versus 2.8, P<0.0001). More than half (n=14/25, 56%) of patients with severe kidney disease were not prescribed reduced dosing, whereas 10% (n=91/920) with preserved renal function received lower dosing. Among patients not on dabigatran at baseline, 8% had dabigatran initiated during follow‐up. Patient education was significantly associated with switching from warfarin to dabigatran (adjusted odds ratio for postgraduate 1.73, P=0.007), whereas antiarrhythmic drug use significantly correlated with de novo adoption of dabigatran (adjusted odds ratio 2.4, P<0.0001). Conclusions: Patients receiving dabigatran were younger and at a lower risk of stroke and bleeding. Patients appeared to drive switching from warfarin, whereas clinical characteristics influenced de novo start of dabigatran. These data suggest cautious early uptake of dabigatran, and more careful attention to dosing adjustments is warranted. Clinical Trial Registration URL: Clinicaltrials.gov. Unique identifier: NCT01165710

Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting

We present an analytical method to quantify clustering in super-resolution localization images of static surfaces in two dimensions. The method also describes how over-counting of labeled molecules contributes to apparent self-clustering and how the effective lateral resolution of an image can be determined. This treatment applies to clustering of proteins and lipids in membranes, where there is significant interest in using super-resolution localization techniques to probe membrane heterogeneity. When images are quantified using pair correlation functions, the magnitude of apparent clustering due to over-counting will vary inversely with the surface density of labeled molecules and does not depend on the number of times an average molecule is counted. Over-counting does not yield apparent co-clustering in double label experiments when pair cross-correlation functions are measured. We apply our analytical method to quantify the distribution of the IgE receptor (Fc{\epsilon}RI) on the plasma membranes of chemically fixed RBL-2H3 mast cells from images acquired using stochastic optical reconstruction microscopy (STORM) and scanning electron microscopy (SEM). We find that apparent clustering of labeled IgE bound to Fc{\epsilon}RI detected with both methods arises from over-counting of individual complexes. Thus our results indicate that these receptors are randomly distributed within the resolution and sensitivity limits of these experiments.Comment: 22 pages, 5 figure

Technology dictates algorithms: Recent developments in read alignment

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of genomic data in the form of nucleotide sequences or reads. Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines. Aligned reads are essential for answering important biological questions, such as detecting mutations driving various human diseases and complex traits as well as identifying species present in metagenomic samples. The read alignment problem is extremely challenging due to the large size of analyzed datasets and numerous technological limitations of sequencing platforms, and researchers have developed novel bioinformatics algorithms to tackle these difficulties. Importantly, computational algorithms have evolved and diversified in accordance with technological advances, leading to todays diverse array of bioinformatics tools. Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads. We provide rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read aligners. We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques. We also discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology, including whole transcriptome, adaptive immune repertoire, and human microbiome studies

Evaluating Evidence for Association of Human Bladder Cancer with Drinking-Water Chlorination Disinfection By-Products

Exposure to chlorination disinfection by-products (CxDBPs) is prevalent in populations using chlorination-based methods to disinfect public water supplies. Multifaceted research has been directed for decades to identify, characterize, and understand the toxicology of these compounds, control and minimize their formation, and conduct epidemiologic studies related to exposure. Urinary bladder cancer has been the health risk most consistently associated with CxDBPs in epidemiologic studies. An international workshop was held to (1) discuss the qualitative strengths and limitations that inform the association between bladder cancer and CxDBPs in the context of possible causation, (2) identify knowledge gaps for this topic in relation to chlorine/chloramine-based disinfection practice(s) in the United States, and (3) assess the evidence for informing risk management. Epidemiological evidence linking exposures to CxDBPs in drinking water to human bladder cancer risk provides insight into causality. However, because of imprecise, inaccurate, or incomplete estimation of CxDBPs levels in epidemiologic studies, translation from hazard identification directly to risk management and regulatory policy for CxDBPs can be challenging. Quantitative risk estimates derived from toxicological risk assessment for CxDBPs currently cannot be reconciled with those from epidemiologic studies, notwithstanding the complexities involved, making regulatory interpretation difficult. Evidence presented here has both strengths and limitations that require additional studies to resolve and improve the understanding of exposure response relationships. Replication of epidemiologic findings in independent populations with further elaboration of exposure assessment is needed to strengthen the knowledge base needed to better inform effective regulatory approaches

Paul Nizan: conspiracy and the contemplation of crime

Paul Nizan (1905-1940) is also known in France as the ‘impossible communist’, for his long-term allegiance to the Party and the abrupt cancellation of his membership, in the late 1930s, following the Nazi-Soviet pact. This paper discusses a number of his writings, focusing particularly on his best known novel, The Conspiracy, where a revolutionary cell plans illegal political action. Conflict, nihilism, suicide and betrayal are among the topics stemming from the novel, which will be examined from a criminological perspective. The analysis will primarily address ‘cultural’ aspects of crime and refer to notions such as ‘thrill’ and ‘seductions of crime’ among others. These notions, it will be argued, require some revision in the face of the imagined or actual criminality described in the novel

Therapeutic exercise attenuates neutrophilic lung injury and skeletal muscle wasting

Early mobilization of critically ill patients with the acute respiratory distress syndrome (ARDS) has emerged as a therapeutic strategy that improves patient outcomes, such as the duration of mechanical ventilation and muscle strength. Despite the apparent efficacy of early mobility programs, their use in clinical practice is limited outside of specialized centers and clinical trials. To evaluate the mechanisms underlying mobility therapy, we exercised acute lung injury (ALI) mice for 2 days after the instillation of lipopolysaccharides into their lungs. We found that a short duration of moderate intensity exercise in ALI mice attenuated muscle ring finger 1 (MuRF1)?mediated atrophy of the limb and respiratory muscles and improved limb muscle force generation. Exercise also limited the influx of neutrophils into the alveolar space through modulation of a coordinated systemic neutrophil chemokine response. Granulocyte colony-stimulating factor (G-CSF) concentrations were systemically reduced by exercise in ALI mice, and in vivo blockade of the G-CSF receptor recapitulated the lung exercise phenotype in ALI mice. Additionally, plasma G-CSF concentrations in humans with acute respiratory failure (ARF) undergoing early mobility therapy showed greater decrements over time compared to control ARF patients. Together, these data provide a mechanism whereby early mobility therapy attenuates muscle wasting and limits ongoing alveolar neutrophilia through modulation of systemic neutrophil chemokines in lung-injured mice and humans.Fil: Files, D. Clark. School Of Medicine; Estados UnidosFil: Liu, Chun. School Of Medicine; Estados UnidosFil: Pereyra, Andrea Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner". Universidad Nacional de la Plata. Facultad de Ciencias Médicas. Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner"; ArgentinaFil: Wang, Zhong Min. University Wake Forest; Estados Unidos. School Of Medicine; Estados UnidosFil: Aggarwal, Neil. Johns Hopkins Asthma And Allergy Center; Estados UnidosFil: D´Alessio, Franco. Johns Hopkins Asthma And Allergy Center; Estados UnidosFil: Garibaldi, Brian T.. Johns Hopkins Asthma and Allergy Center; Estados UnidosFil: Mock, Jason R.. Johns Hopkins Asthma and Allergy Center; Estados UnidosFil: Singer, Benjamin D.. Johns Hopkins Asthma and Allergy Center; Estados UnidosFil: Feng, Xin. Wake Forest School of Medicine; Estados UnidosFil: Yammani, Raghunatha R.. Wake Forest School of Medicine; Estados UnidosFil: Zhang, Tan. Wake Forest School of Medicine; Estados UnidosFil: Lee, Amy L.. Wake Forest School of Medicine; Estados UnidosFil: Philpott, Sydney. Wake Forest School of Medicine; Estados UnidosFil: Lussier, Stephanie. Wake Forest School of Medicine; Estados UnidosFil: Purcell, Lina. Wake Forest School of Medicine; Estados UnidosFil: Chou, Jeff. Wake Forest School of Medicine; Estados UnidosFil: Seeds, Michael. Wake Forest School of Medicine; Estados UnidosFil: King, Landon S.. Johns Hopkins Asthma and Allergy Center; Estados UnidosFil: Morris, Peter E.. Wake Forest School of Medicine; Estados UnidosFil: Delbono, Osvaldo. School Of Medicine; Estados Unido