Enabling Factor Analysis on Thousand-Subject Neuroimaging Datasets

The scale of functional magnetic resonance image data is rapidly increasing as large multi-subject datasets are becoming widely available and high-resolution scanners are adopted. The inherent low-dimensionality of the information in this data has led neuroscientists to consider factor analysis methods to extract and analyze the underlying brain activity. In this work, we consider two recent multi-subject factor analysis methods: the Shared Response Model and Hierarchical Topographic Factor Analysis. We perform analytical, algorithmic, and code optimization to enable multi-node parallel implementations to scale. Single-node improvements result in 99x and 1812x speedups on these two methods, and enables the processing of larger datasets. Our distributed implementations show strong scaling of 3.3x and 5.5x respectively with 20 nodes on real datasets. We also demonstrate weak scaling on a synthetic dataset with 1024 subjects, on up to 1024 nodes and 32,768 cores

Truthmakers and modality

This paper attempts to locate, within an actualist ontology, truthmakers for modal truths: truths of the form or . In section 1 I motivate the demand for substantial truthmakers for modal truths. In section 2 I criticise Armstrong’s account of truthmakers for modal truths. In section 3 I examine essentialism and defend an account of what makes essentialist attributions true, but I argue that this does not solve the problem of modal truth in general. In section 4 I discuss, and dismiss, a theistic account of the source of modal truth proposed by Alexander Pruss. In section 5 I offer a means of (dis)solving the problem

Effect of three-particle correlations in low dimensional Hubbard models

A simple approximation which captures some non-perturbative aspects of the one electron Green function of strongly interacting Fermion systems is developed. It provides a way to go one step beyond the usual dilute limit since particle-particle as well as particle-hole scattering are treated on the same footing. Intermediate states are constrained to contain only one particle-hole excitation besides the incoming particle. The Faddeev equations resulting from an exact treatment of this three-body problem are investigated. In one dimension the method is able to show spin and charge decoupling, but does not reproduce the exact nature of power-law singularities. Hey dudes, check out the analytical solution in section III!Comment: 21 pages plus six figures (appended as postscript files) in RevTeX v.

LIMITED ANTIBODY EVIDENCE OF EXPOSURE TO MYCOBACTERIUM BOVIS IN FERAL SWINE (\u3ci\u3eSUS SCROFA\u3c/i\u3e) IN THE USA

Bovine tuberculosis is a chronic disease of cattle (Bos taurus) caused by the bacterium Mycobacterium bovis. Efforts have been made in the US to eradicate the disease in cattle, but spillover into wildlife and subsequent spillback have impeded progress in some states. In particular, infection in white-tailed deer (Odocoileus virginianus) has been followed by infection in cattle in some Midwestern states. Infection has also been documented in feral swine (Sus scrofa) on the Hawaiian island of Molokai and in various European countries, but no large-scale survey of antibody exposure to the bacteria has been conducted in feral swine in the US. We tested 488 sera from feral swine collected near previously documented outbreaks of bovine tuberculosis in cattle and captive cervids, in addition to 2,237 feral swine sera collected across the US from 1 October 2013 to 30 September 2014. While all but one of the samples were antibody negative, the results are important for establishing baseline negative data since feral swine are capable reservoirs and could be implicated in future outbreaks of the disease

Equine Arteritis Virus Uses Equine CXCL16 as an Entry Receptor

Previous studies in our laboratory have identified equine CXCL16 (EqCXCL16) to be a candidate molecule and possible cell entry receptor for equine arteritis virus (EAV). In horses, the CXCL16 gene is located on equine chromosome 11 (ECA11) and encodes a glycosylated, type I transmembrane protein with 247 amino acids. Stable transfection of HEK-293T cells with plasmid DNA carrying EqCXCL16 (HEK-EqCXCL16 cells) increased the proportion of the cell population permissive to EAV infection from \u3c 3% to almost 100%. The increase in permissiveness was blocked either by transfection of HEK-EqCXCL16 cells with small interfering RNAs (siRNAs) directed against EqCXCL16 or by pretreatment with guinea pig polyclonal antibody against EqCXCL16 protein (Gp anti-EqCXCL16 pAb). Furthermore, using a virus overlay protein-binding assay (VOPBA) in combination with far-Western blotting, gradient-purified EAV particles were shown to bind directly to the EqCXCL16 protein in vitro. The binding of biotinylated virulent EAV strain Bucyrus at 4°C was significantly higher in HEK-EqCXCL16 cells than nontransfected HEK-293T cells. Finally, the results demonstrated that EAV preferentially infects subpopulations of horse CD14+ monocytes expressing EqCXCL16 and that infection of these cells is significantly reduced by pretreatment with Gp anti-EqCXCL16 pAb. The collective data from this study provide confirmatory evidence that the transmembrane form of EqCXCL16 likely plays a major role in EAV host cell entry processes, possibly acting as a primary receptor molecule for this virus

Expert Consensus Guidelines for Stocking of Antidotes in Hospitals That Provide Emergency Care

We provide recommendations for stocking of antidotes used in emergency departments (EDs). An expert panel representing diverse perspectives (clinical pharmacology, medical toxicology, critical care medicine, hematology/oncology, hospital pharmacy, emergency medicine, emergency medical services, pediatric emergency medicine, pediatric critical care medicine, poison centers, hospital administration, and public health) was formed to create recommendations for antidote stocking. Using a standardized summary of the medical literature, the primary reviewer for each antidote proposed guidelines for antidote stocking to the full panel. The panel used a formal iterative process to reach their recommendation for both the quantity of antidote that should be stocked and the acceptable timeframe for its delivery. The panel recommended consideration of 45 antidotes; 44 were recommended for stocking, of which 23 should be immediately available. In most hospitals, this timeframe requires that the antidote be stocked in a location that allows immediate availability. Another 14 antidotes were recommended for availability within 1 hour of the decision to administer, allowing the antidote to be stocked in the hospital pharmacy if the hospital has a mechanism for prompt delivery of antidotes. The panel recommended that each hospital perform a formal antidote hazard vulnerability assessment to determine its specific need for antidote stocking. Antidote administration is an important part of emergency care. These expert recommendations provide a tool for hospitals that offer emergency care to provide appropriate care of poisoned patients

Host Feeding Patterns of Culex Mosquitoes and West Nile Virus Transmission, Northeastern United States

Culex salinarius is a bridge vector to humans, while Cx. pipiens and Cx. restuans are more efficient enzootic vectors

scMRI Reveals Large-Scale Brain Network Abnormalities in Autism

Autism is a complex neurological condition characterized by childhood onset of dysfunction in multiple cognitive domains including socio-emotional function, speech and language, and processing of internally versus externally directed stimuli. Although gross brain anatomic differences in autism are well established, recent studies investigating regional differences in brain structure and function have yielded divergent and seemingly contradictory results. How regional abnormalities relate to the autistic phenotype remains unclear. We hypothesized that autism exhibits distinct perturbations in network-level brain architecture, and that cognitive dysfunction may be reflected by abnormal network structure. Network-level anatomic abnormalities in autism have not been previously described. We used structural covariance MRI to investigate network-level differences in gray matter structure within two large-scale networks strongly implicated in autism, the salience network and the default mode network, in autistic subjects and age-, gender-, and IQ-matched controls. We report specific perturbations in brain network architecture in the salience and default-mode networks consistent with clinical manifestations of autism. Extent and distribution of the salience network, involved in social-emotional regulation of environmental stimuli, is restricted in autism. In contrast, posterior elements of the default mode network have increased spatial distribution, suggesting a ‘posteriorization’ of this network. These findings are consistent with a network-based model of autism, and suggest a unifying interpretation of previous work. Moreover, we provide evidence of specific abnormalities in brain network architecture underlying autism that are quantifiable using standard clinical MRI

A large CRISPR-induced bystander mutation causes immune dysregulation.

A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic bystander mutations that escape detection by routine targeted genotyping assays

How do farmers learn from extension services? Evidence from Malawi

Though extension services have long since proved their value to agricultural production and farmer prosperity, their record in sub‐Saharan Africa has been mixed. To study the impact of such programs on farmers' learning about agricultural technologies, we implemented a quasi‐randomized controlled trial and collected detailed panel data among Malawian farmers. Based on those findings, we develop a two‐stage learning framework, in which farmers formulate yield expectations before deciding on how much effort to invest in learning about these processes. Using data centered on farmer beliefs, knowledge, and constraints, we find evidence that beliefs about potential yields hinge on first‐hand and local experience, and that these beliefs significantly impact learning efforts. Consistent with this, we find that farmers who participated in season‐long, farmer‐led demonstration plot cultivation plan to adopt more components of new multi‐component technology, compared to farmers who were invited to attend only field‐day events