Hysteresis, Avalanches, and Noise: Numerical Methods

In studying the avalanches and noise in a model of hysteresis loops we have developed two relatively straightforward algorithms which have allowed us to study large systems efficiently. Our model is the random-field Ising model at zero temperature, with deterministic albeit random dynamics. The first algorithm, implemented using sorted lists, scales in computer time as O(N log N), and asymptotically uses N (sizeof(double)+ sizeof(int)) bits of memory. The second algorithm, which never generates the random fields, scales in time as O(N \log N) and asymptotically needs storage of only one bit per spin, about 96 times less memory than the first algorithm. We present results for system sizes of up to a billion spins, which can be run on a workstation with 128MB of RAM in a few hours. We also show that important physical questions were resolved only with the largest of these simulations

Effect of Absent Tactile Sensation on Multi-digit Coordination Underlying Hand Control

We investigated the effect of anesthesia, causing absent tactile sensation feedback, on multi-digit coordination underlying hand control. The purpose of the study is to expand our understanding on the essential role of tactile sensation feedback in the sensorimotor integration process by examining the motor coordination patterns during multi-digit forces production tasks. We hypothesized that absent tactile sensation feedback would interrupt the force sharing pattern at local and non-local digits. Twelve participants were utilized for data collection and statistical analysis (25.6 ± 4.1 years old, 6 males and 6 females), right-handed (according to their preferred hand use for writing and eating) and had no significant hand injury within the last five years. All participants performed a maximal voluntary contraction (MVC), ramp, and step task, pre- and post-anesthesia. In general, participants presented lower maximal force production in all MVC conditions after anesthesia, total MVC force was not distributed evenly among individual digits, and when sensory function of the MVC involved digits are uniformly absent or intact, force sharing pattern across the individual digits would be maintained. When the instructed finger (master finger) was index, other fingers (enslaved fingers) barely produced force. However, other enslaved fingers showed relatively higher forces when the master finger was ring or little finger. When required force level increased, performance error was increased accordingly. The findings from the current study confirmed our hypothesis that absent tactile sensation feedback (somatosensory feedback) will not only affect force production at local digits, but also at non-local digits as well

Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann’s area 32 and area 21

Published in final edited form as: Brain Struct Funct. 2019 January ; 224(1): 351–362. doi:10.1007/s00429-018-1777-z.Optical coherence tomography is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles. Optical coherence microscopy (OCM) is higher resolution (i.e., 1.25 µm) and is capable of detecting neurons. In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II. In the current method-oriented study, we aimed to determine the colocalization success rate between OCM and Nissl in other brain cortical areas with different laminar arrangements and cell packing density. We focused on two additional cortical areas: medial prefrontal, pre-genual Brodmann area (BA) 32 and lateral temporal BA 21. We present the data as colocalization matrices and as quantitative percentages. The overall average colocalization in OCM compared to Nissl was 67% for BA 32 (47% for Nissl colocalization) and 60% for BA 21 (52% for Nissl colocalization), but with a large variability across cases and layers. One source of variability and confounds could be ascribed to an obscuring effect from large and dense intracortical fiber bundles. Other technical challenges, including obstacles inherent to human brain tissue, are discussed. Despite limitations, OCM is a promising semi-high throughput tool for demonstrating detail at the neuronal level, and, with further development, has distinct potential for the automatic acquisition of large databases as are required for the human brain.Accepted manuscrip

Influence of management and precipitation on carbon fluxes in Great Plains grasslands

Suitable management and sufficient precipitation on grasslands can provide carbon sinks. The net carbon accumulation of a site from the atmosphere, modeled as the Net Ecosystem Productivity (NEP), is a useful means to gauge carbon balance. Previous research has developed methods to integrate flux tower data with satellite biophysical datasets to estimate NEP across large regions. A related method uses the Ecosystem Performance Anomaly (EPA) as a satellite-derived indicator of disturbance intensity (e.g., livestock stocking rate, fire, and insect damage). To better understand the interactions among management, climate, and carbon dynamics, we evaluated the relationship between EPA and NEP data at the 250 m scale for grasslands in the Central Great Plains, USA (ranging from semi-arid to mesic). We also used weekly estimates of NEP to evaluate the phenology of carbon dynamics, classified by EPA (i.e., by level of disturbance impact). Results show that the cumulative carbon balance over these grasslands from 2000 to 2008 was a weak net sink of 13.7 g C m−2 yr−1. Overall, NEP increased with precipitation (R2 = 0.39, P \u3c 0.05) from west to east. Disturbance influenced NEP phenology; however, climate and biophysical conditions were usually more important. The NEP response to disturbance varies by ecoregion, and more generally by grassland type, where the shortgrass prairie NEP is most sensitive to disturbance, the mixed-grass prairie displays a moderate response, and tallgrass prairie is the least impacted by disturbance (as measured by EPA). Sustainable management practices in the tallgrass and mixed-grass prairie may potentially induce a period of average net carbon sink until a new equilibrium soil organic carbon is achieved. In the shortgrass prairie, management should be considered sustainable if carbon stocks are simply maintained. The consideration of site carbon balance adds to the already difficult task of managing grasslands appropriately to site conditions. Results clarify the seasonal and interannual dynamics of NEP, specifically the influence of disturbance and moisture availability

Demonstration of a Thermally Coupled Row-Column SNSPD Imaging Array

While single-pixel superconducting nanowire single photon detectors (SNSPDs) have demonstrated remarkable efficiency and timing performance from the UV to near-IR, scaling these devices to large imaging arrays remains challenging. Here, we propose a new SNSPD multiplexing system using thermal coupling and detection correlations between two photosensitive layers of an array. Using this architecture with the channels of one layer oriented in rows and the second layer in columns, we demonstrate imaging capability in 16-pixel arrays with accurate spot tracking at the few-photon level. We also explore the performance trade-offs of orienting the top layer nanowires parallel and perpendicular to the bottom layer. The thermally coupled row-column scheme is readily able to scale to the kilopixel size with existing readout systems and, when combined with other multiplexing architectures, has the potential to enable megapixel scale SNSPD imaging arrays

Intersubject Regularity in the Intrinsic Shape of Human V1

Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 μm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results

Bcl11b—A Critical Neurodevelopmental Transcription Factor—Roles in Health and Disease

B cell leukemia 11b (Bcl11b) is a zinc finger protein transcription factor with a multiplicity of functions. It works as both a genetic suppressor and activator, acting directly, attaching to promoter regions, as well as indirectly, attaching to promoter-bound transcription factors. Bcl11b is a fundamental transcription factor in fetal development, with important roles for the differentiation and development of various neuronal subtypes in the central nervous system (CNS). It has been used as a specific marker of layer V subcerebral projection neurons as well as striatal interneurons. Bcl11b also has critical developmental functions in the immune, integumentary and cardiac systems, to the extent that Bcl11b knockout mice are incompatible with extra-uterine life. Bcl11b has been implicated in a number of disease states including Huntington’s disease, Alzheimer’s disease, HIV and T-Cell malignancy, amongst others. Bcl11b is a fascinating protein whose critical roles in the CNS and other parts of the body are yet to be fully explicated. This review summarizes the current literature on Bcl11b and its functions in development, health, and disease as well as future directions for research

Aligning ecology and markets in the forest carbon cycle

A forest carbon (C) offset is a quantifiable unit of C that is commonly developed at the local or regional project scale and is designed to counterbalance anthropogenic C emissions by sequestering C in trees. In cap-and-trade programs, forest offsets have market value if the sequestered C is additional (more than would have occurred in the absence of the project) and permanent (sequestered within the project boundary for a specified period of time). Local management and ecological context determine the rate of C sequestration, risk of loss, and hence the market value. An understanding of global C dynamics can inform policy but may not be able to effectively price an ecosystem service, such as C sequestration. Appropriate pricing requires the assistance of ecologists to assess C stock abundance and stability over spatial and temporal scales appropriate for the regional market. We use the risk that sequestered C will be emitted as a result of wildfire (reversal risk) to show how ecological context can influence market valuation in offset programs

Planar Cell Polarity Enables Posterior Localization of Nodal Cilia and Left-Right Axis Determination during Mouse and Xenopus Embryogenesis

Left-right asymmetry in vertebrates is initiated in an early embryonic structure called the ventral node in human and mouse, and the gastrocoel roof plate (GRP) in the frog. Within these structures, each epithelial cell bears a single motile cilium, and the concerted beating of these cilia produces a leftward fluid flow that is required to initiate left-right asymmetric gene expression. The leftward fluid flow is thought to result from the posterior tilt of the cilia, which protrude from near the posterior portion of each cell's apical surface. The cells, therefore, display a morphological planar polarization. Planar cell polarity (PCP) is manifested as the coordinated, polarized orientation of cells within epithelial sheets, or as directional cell migration and intercalation during convergent extension. A set of evolutionarily conserved proteins regulates PCP. Here, we provide evidence that vertebrate PCP proteins regulate planar polarity in the mouse ventral node and in the Xenopus gastrocoel roof plate. Asymmetric anterior localization of VANGL1 and PRICKLE2 (PK2) in mouse ventral node cells indicates that these cells are planar polarized by a conserved molecular mechanism. A weakly penetrant Vangl1 mutant phenotype suggests that compromised Vangl1 function may be associated with left-right laterality defects. Stronger functional evidence comes from the Xenopus GRP, where we show that perturbation of VANGL2 protein function disrupts the posterior localization of motile cilia that is required for leftward fluid flow, and causes aberrant expression of the left side-specific gene Nodal. The observation of anterior-posterior PCP in the mouse and in Xenopus embryonic organizers reflects a strong evolutionary conservation of this mechanism that is important for body plan determination