Miracle-dz/UniFAR-FTUs huggingface dataset:
Matlab code for "Numerically stable and accurate stochastic simulation approaches for solving dynamic economic models"

We develop numerically stable and accurate stochastic simulation approaches for solving dynamic economic models. First, instead of standard least-squares methods, we examine a variety of alternatives, including least-squares methods using singular value decomposition and Tikhonov regularization, least-absolute deviations methods, and principal component regression method, all of which are numerically stable and can handle ill-conditioned problems. Second, instead of conventional Monte Carlo integration, we use accurate quadrature and monomial integration. We test our generalized stochastic simulation algorithm (GSSA) in three applications: the standard representative agent neoclassical growth model, a model with rare disasters and a multi-country models with hundreds of state variables. GSSA is simple to program, and MATLAB codes are provided.
Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.
March tests for word-oriented memories

Most memory test algorithms are optimized tests for a particular memory technology, and a particular set of fault models, under the assumption that the memory is bit-oriented; i.e., read and write operations affect only a single bit in the memory. Traditionally, word-oriented memories have been tested by repeated application of a test for bit-oriented memories whereby a different data background (which depends on the used intra-word fault model) is used during each iteration. This results in rime inefficiencies and limited fault coverage. A new approach for testing word-oriented memories is presented, distinguishing between inter-word and intra-word faults and allowing for a systematic way of converting tests for bit-oriented memories to rests for word-oriented memories. The conversion consists of concatenating the bit-oriented test for inter-word faults with a test for intra-word faults. This approach results in more efficient tests with complete coverage of the targeted faults. Because most memories have an external data path which is wider than one bit, word-oriented memory tests are very important.
Sphingosine 1-phosphate signalling

Sphingosine 1-phosphate (S1P) is a lipid mediator formed by the metabolism of sphingomyelin. In vertebrates, S1P is secreted into the extracellular environment and signals via G protein-coupled S1P receptors to regulate cell-cell and cell-matrix adhesion, and thereby influence cell migration, differentiation and survival. The expression and localization of S1P receptors is dynamically regulated and controls vascular development, vessel stability and immune cell trafficking. In addition, crucial events during embryogenesis, such as angiogenesis, cardiogenesis, limb development and neurogenesis, are regulated by S1P signalling. Here, and in the accompanying poster, we provide an overview of S1P signalling in development and in disease.
Identifying fallers with Parkinson's disease using home‐based tests: Who is at risk?

The objective of this work is to determine risk factors for falling in patients with Parkinson's disease (PD) using home‐based assessments and develop a prediction model. Data on falls, balance, gait‐related activities, and nonmotor symptoms were obtained from 153 PD patients (Hoehn‐Yahr 2–4) in their home. Fifty‐one candidate determinants for falling were independently tested using bivariate logistic regression analysis. A multivariate logistic regression model was developed to identify patients susceptible to falls. Sixty‐six subjects (43%) were classified as fallers. Eighteen determinants for falling were selected. The final multivariate model showed an accuracy of 74% and included: (1) Freezing of Gait Questionnaire, (2) Timed Get Up and Go (TGUG) score, (3) disease duration, (4) item 15 of the Unified Parkinson's Disease Rating Scale. Based on disease duration, freezing symptoms, walking problems, and a prolonged TGUG duration, assessed in the home situation, it was possible to accurately identify 74% of PD patients as fallers. © 2008 Movement Disorder Society
Self-monitoring & Metatraits Self-monitoring and the Metatraits

Authors Note Michael P. Wilmot and Colin G. DeYoung, Department of Psychology, University of Minnesota; David Stillwell and Michal Kosinski, The Psychometrics Centre, University of Cambridge, Cambridge, United Kingdom. Portions of this article were presented at the 28 th annual conference of the Society for Industrial and Organizational Psychology, April 2013, Houston, Texas. We thank Mark Snyder for helpful conversations about the nature and history of self-monitoring, and Lew Goldberg for making available data from the Eugene-Springfield community sample. Correspondence concerning this article should be addressed to Michael P. Wilmot, Psychology Department, University of Minnesota, Twin Cities, 75 East River Road, Minneapolis, MN 55455. E-mail: wilmo040@umn.edu
Spatial and temporal characteristics and removal methodology of suspended particulate matter speckles from Geostationary Ocean Color Imager data

ABSTRACT Reviewing six years of Geostationary Ocean Color Imager (GOCI) suspended particulate matter (SPM) concentration images from 2011 to 2016 revealed unexpected and some enormously high or low values. These speckles are randomly scattered throughout the entire study area or congregated at a certain part, which has strongly restricted the scientific applications of GOCI data thus far. They can be classified into four types: isolated, near-cloud, patch-type, and slot-related speckles, based on spatial distribution and potential causes. These types are investigated. The speckles are induced by a moving-cloud during a complete observation of 8 bands for each slot of GOCI, partly by an incomplete cloud masking procedure near cloud edges, by relatively low reflectance of pixels corresponding to a cloud shadow, by imperfect atmospheric corrections related to water vapor after cloud passage, or by sensor-related troubles related to the effects of stray light. Spatial and temporal variabilities of the identified speckles are investigated and used to develop a methodology for their removal. The SPM concentration values of the error-free pixels, passing through the post-processing of the speckle removal procedure, are compared to those previously with speckles. As a result, the enormously large values of SPM, occupying 6.06% of the pixel numbers, are all eliminated. Typical seasonality of SPM, unrevealed using the speckled images, is clearly presented through the removal procedure. This study addresses the importance of preprocessing for speckle error in SPM concentrations from GOCI data and implies more reliable SPM data without speckles can be used in scientific application research.
Shear-Sensitive Regulation of Neutrophil Flow Behavior and Its Potential Impact on Microvascular Blood Flow Dysregulation in Hypercholesterolemia

Objective— Shear stress–induced pseudopod retraction is an anti-inflammatory measure that minimizes neutrophil activity and is regulated by membrane cholesterol. We tested the hypothesis that a hypercholesterolemic impairment of shear mechanotransduction alters the neutrophil flow behavior leading to microvascular dysfunction. Approach and Results— We examined the shear effects on the flow behavior of human leukocytes. When subjected to shearing during cone-plate viscometry, leukocyte suspensions exhibited parallel time-dependent reductions in viscosity and pseudopod activity. Shear-induced reductions in suspension viscosity were attenuated by membrane cholesterol enrichment. We also showed that enhanced pseudopod activity of leukocyte suspensions in 10% hematocrit significantly (P<0.05) raised the flow resistance of microvascular mimics. These results implicate an impaired neutrophil pseudopod retraction response to shear in hypercholesterolemic microvascular dysfunction. We confirmed this using near-infrared diffuse correlation spectroscopy to assess skeletal muscle blood flow regulation in the hindlimbs of mice subjected to reactive hyperemia. Using a custom protocol for the mouse, we extrapolated an adjusted peak flow and time to adjusted peak flow to quantify the early phase of the blood flow recovery response during reactive hyperemia when shear mechanobiology likely has a maximal impact. Compared with mice on normal diet, hypercholesterolemic mice exhibited significantly (P<0.05) reduced adjusted peak flow and prolonged time to adjusted peak flow which correlated (r=0.4 and r=−0.3, respectively) with neutrophil shear responsiveness and were abrogated by neutropenia. Conclusions— These results provide the first evidence that the neutrophils contribute to tissue blood flow autoregulation. Moreover, a deficit in the neutrophil responsiveness to shear may be a feature of hypercholesterolemia-related microvascular dysfunction.
A Fast PC Algorithm for High Dimensional Causal Discovery with Multi-Core PCs

Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC algorithm, in the worst-case, is exponential to the number of nodes (variables), and thus it is inefficient when being applied to high dimensional data, e.g., gene expression datasets. On another note, the advancement of computer hardware in the last decade has resulted in the widespread availability of multi-core personal computers. There is a significant motivation for designing a parallelized PC algorithm that is suitable for personal computers and does not require end users’ parallel computing knowledge beyond their competency in using the PC algorithm. In this paper, we develop parallel-PC, a fast and memory efficient PC algorithm using the parallel computing technique. We apply our method to a range of synthetic and real-world high dimensional datasets. Experimental results on a dataset from the DREAM 5 challenge show that the original PC algorithm could not produce any results after running more than 24 hours; meanwhile, our parallel-PC algorithm managed to finish within around 12 hours with a 4-core CPU computer, and less than six hours with a 8-core CPU computer. Furthermore, we integrate parallel-PC into a causal inference method for inferring miRNA-mRNA regulatory relationships. The experimental results show that parallel-PC helps improve both the efficiency and accuracy of the causal inference algorithm.
Interests in high-functioning autism are more intense, interfering, and idiosyncratic than those in neurotypical development

Abstract Although circumscribed interests are pathognomonic with autism, much about these interests remains unknown. Using the Interests Scale (IS), this study compares interests between 76 neurotypical (NT) individuals and 109 individuals with high-functioning autism spectrum disorder (HF-ASD) matched groupwise on age, IQ, and gender ratio. Participants and their parents/caregivers completed diagnostic measures (the Autism Diagnostic Interview—Revised and the Autism Diagnostic Observation Schedule; HF-ASD only), cognitive tests (Wechsler IQ Scales), and questionnaires (the Repetitive Behavior Scale—Revised, the Behavior Rating Inventory of Executive Function, and the Social Responsiveness Scale), in addition to the IS. Consistent with previous research, HF-ASD and NT individuals did not differ in number of interest areas, but the types of interests and intensity of those interests differed considerably. Using only the IS intensity score, 81% of individuals were correctly classified (NT or HF-ASD) in a logistic regression analysis. Among individuals with HF-ASD, Interests Scale scores were significantly related to Autism Diagnostic Observation Schedule, Behavior Rating Inventory of Executive Function, Repetitive Behavior Scale—Revised, and Social Responsiveness Scale scores, but they were not related to Autism Diagnostic Interview—Revised scores, IQ, gender, age, or psychotropic medication use. The type and intensity, but not the number, of interests distinguish high-functioning individuals with ASD from NT individuals.
Characterization of Intestinal and Pancreatic Dysfunction in VPAC1-Null Mutant Mouse

Objectives: These studies examined the effect of homozygous deletion of vasoactive intestinal peptide receptor type 1 (VPAC1) on development and function of intestines and pancreas. Methods: Genetically engineered VPAC1-null mutant mice were monitored for growth, development, and glucose homeostasis. Expression of VPAC1 was examined during embryonic development using VPAC1 promoter-driven &bgr;-galactosidase transgenic mice. Results: Homozygous deletion of VPAC1 resulted in fetal, neonatal, and postweaning death owing to failure to thrive, intestinal obstruction, and hypoglycemia. Histological findings demonstrated disorganized hyperproliferation of intestinal epithelial cells with mucus deposition and bowel wall thickening. The pancreas demonstrated small dysmorphic islets of Langerhans containing &agr;, &bgr;, and &dgr; cells. Expression of a VPAC1 promoter-driven transgene was observed in E12.5 and E14.5 intestinal epithelial and pancreatic endocrine cells. Vasoactive intestinal peptide receptor type 1-null mutant animals had lower baseline blood glucose levels compared to both heterozygous and wild-type littermates. Vasoactive intestinal peptide receptor type 1-deficient mice responded to oral glucose challenge with normal rise in blood glucose followed by rapid hypoglycemia and failure to restore baseline glucose levels. Insulin challenge resulted in profound hypoglycemia and inadequate glucose homeostasis in VPAC1-null mutant animals. Conclusions: These observations support a role for VPAC1 during embryonic and neonatal development of intestines and endocrine pancreas.
Altitude , exercise and immune function Altitude , exercise and immune function

Little is known with regard to how acute and chronic high altitude exposure effects immune function. Hypoxia is an environmental stressor that is known to elicit alterations in both the autonomic nervous system and endocrine function. Alterations in these systems can have an immediate as well as a longer lasting impact on immune function. Studies from the summit of Pikes Peak (4300 m) have indicated a strong α& β-adrenergic component in the regulation of immune function at altitude that can persist weeks after initial exposure. Specifically, interleukin (IL)-6 is elevated with acute altitude exposure primarily mediated via β-adrenergic stimulation and remains elevated for several weeks as a result of αadrenergic activation. When the added stress of physical exercise is combined with that of hypoxia, a more pronounced impact on immune function is observed compared to that of either exercise or hypoxia alone. A popular training paradigm currently employed by endurance athletes to enhance performance involves living at high altitude while training at low altitude. The concept entails incorporating the physiologic and metabolic adaptations associated with chronic high altitude exposure (increase in RBC, mitochondrial oxidative capacity, capillary density, etc) while training at a lower altitude allowing for the maintenance of a high absolute training intensity. Others have demonstrated that a short-term application (18 days) of the live high-train low paradigm results in suppression of the mucosal immune system as indicated by a cumulative decline in salivary IgA levels. Taken together, the majority of evidence suggests a potential additive effect of combined hypoxia and exercise in transiently suppressing immune function, at least in the short-term. Implications for the athletes and training are addressed.
THE FINE STRUCTURE OF MEISSNER's TOUCH CORPUSCLES OF HUMAN FINGERS

Thin slices of the finger pads of six individuals were fixed in buffered 1 per cent osmic acid, embedded in deaerated, nitrogenated methacrylate, and cut into thin sections for electron microscopic study. Before embedding, the slices were trimmed so as to include several digital tactile corpuscles. Some thin sections were stained in 10 per cent aqueous phosphotungstic acid solution. The principal part of Meissner's corpuscle is made up of flattened laminar cells stretching across the corpuscle in irregular layers. The perinuclear cytoplasm of these cells contains numerous small mitochondria, a sparse granular endoplasmic reticulum, and a large number of small vesicles. Nerve fibers enter the side or base of the corpuscle, lose their myelin sheaths, and follow a meandering course between the laminar cell plates. The nerve endings enter into a close appositional relationship with the flattened portions of the laminar cells. In some areas the apposed axolemma and cell membranes are slightly thickened with small vesicles located along the cell membrane or on both surfaces. These regions are interpreted as synapses. The most prominent feature of the nerve endings is an extraordinary accumulation of small mitochondria which vary in size and internal density. The nerve endings also contain vacuoles, groups of dense concentric membranes, and small dense vesicles of irregular distribution. The laminar cells are separated from one another by a dense intercellular substance of uniform thickness which also envelops the entire corpuscle. This material contains randomly oriented collagen fibers and fine fibrils bound together by a dense material at nodal points recurring at regular intervals of approximately 120 mmicro. These findings are discussed in relation to the problems of the function of Meissner's corpuscle, neural material loss and replacement, and the presence of synapses.
Population coding in mouse visual cortex: response reliability and dissociability of stimulus tuning and noise correlation

The primary visual cortex is an excellent model system for investigating how neuronal populations encode information, because of well-documented relationships between stimulus characteristics and neuronal activation patterns. We used two-photon calcium imaging data to relate the performance of different methods for studying population coding (population vectors, template matching, and Bayesian decoding algorithms) to their underlying assumptions. We show that the variability of neuronal responses may hamper the decoding of population activity, and that a normalization to correct for this variability may be of critical importance for correct decoding of population activity. Second, by comparing noise correlations and stimulus tuning we find that these properties have dissociated anatomical correlates, even though noise correlations have been previously hypothesized to reflect common synaptic input. We hypothesize that noise correlations arise from large non-specific increases in spiking activity acting on many weak synapses simultaneously, while neuronal stimulus response properties are dependent on more reliable connections. Finally, this paper provides practical guidelines for further research on population coding and shows that population coding cannot be approximated by a simple summation of inputs, but is heavily influenced by factors such as input reliability and noise correlation structure.
Individualized and Clinically Derived Stimuli Activate Limbic Structures in Depression: An fMRI Study

Objectives In the search for neurobiological correlates of depression, a major finding is hyperactivity in limbic-paralimbic regions. However, results so far have been inconsistent, and the stimuli used are often unspecific to depression. This study explored hemodynamic responses of the brain in patients with depression while processing individualized and clinically derived stimuli. Methods Eighteen unmedicated patients with recurrent major depressive disorder and 17 never-depressed control subjects took part in standardized clinical interviews from which individualized formulations of core interpersonal dysfunction were derived. In the patient group such formulations reflected core themes relating to the onset and maintenance of depression. In controls, formulations reflected a major source of distress. This material was thereafter presented to subjects during functional magnetic resonance imaging (fMRI) assessment. Results Increased hemodynamic responses in the anterior cingulate cortex, medial frontal gyrus, fusiform gyrus and occipital lobe were observed in both patients and controls when viewing individualized stimuli. Relative to control subjects, patients with depression showed increased hemodynamic responses in limbic-paralimbic and subcortical regions (e.g. amygdala and basal ganglia) but no signal decrease in prefrontal regions. Conclusions This study provides the first evidence that individualized stimuli derived from standardized clinical interviewing can lead to hemodynamic responses in regions associated with self-referential and emotional processing in both groups and limbic-paralimbic and subcortical structures in individuals with depression. Although the regions with increased responses in patients have been previously reported, this study enhances the ecological value of fMRI findings by applying stimuli that are of personal relevance to each individual's depression.