The 1994-1995 National Health Interview Survey on Disability (NHIS-D): A Bibliography of 20 Years of Research

The 1994-1995 National Health Interview Survey on Disability (NHIS-D) has been one of the most unique and important data sources for studying disability, impairment, and health in the United States. In celebration of the NHIS-D’s twenty-year anniversary, we created an extensive bibliography (n=212) of research that has used these data

Correcting motion induced fluorescence artifacts in two-channel neural imaging

Imaging neural activity in a behaving animal presents unique challenges in part because motion from an animal's movement creates artifacts in fluorescence intensity time-series that are difficult to distinguish from neural signals of interest. One approach to mitigating these artifacts is to image two channels; one that captures an activity-dependent fluorophore, such as GCaMP, and another that captures an activity-independent fluorophore such as RFP. Because the activity-independent channel contains the same motion artifacts as the activity-dependent channel, but no neural signals, the two together can be used to remove the artifacts. Existing approaches for this correction, such as taking the ratio of the two channels, do not account for channel independent noise in the measured fluorescence. Moreover, no systematic comparison has been made of existing approaches that use two-channel signals. Here, we present Two-channel Motion Artifact Correction (TMAC), a method which seeks to remove artifacts by specifying a generative model of the fluorescence of the two channels as a function of motion artifact, neural activity, and noise. We further present a novel method for evaluating ground-truth performance of motion correction algorithms by comparing the decodability of behavior from two types of neural recordings; a recording that had both an activity-dependent fluorophore (GCaMP and RFP) and a recording where both fluorophores were activity-independent (GFP and RFP). A successful motion-correction method should decode behavior from the first type of recording, but not the second. We use this metric to systematically compare five methods for removing motion artifacts from fluorescent time traces. We decode locomotion from a GCaMP expressing animal 15x more accurately on average than from control when using TMAC inferred activity and outperform all other methods of motion correction tested.Comment: 11 pages, 3 figure

Organic and conventional tomato cropping systems.

Among several alternative agricultural systems have been developed, organic agriculture has deserved increasing interest from. The objective of this paper was comparing both organic (OS) and conventional (CS) tomato cropping systems for varieties Débora and Santa Clara, through an interdisciplinary study. The experiment was set up in a randomized blocks design with six replicates, in a dystrophic Ultisol plots measuring 25 ´ 17 m. Cropping procedures followed by either local conventional or organic growers practices recommendations. Fertilization in the OS was done with organic compost, single superphosphate, dolomitic limes (5L, 60 g, and 60 g per pit), and sprayed twice a week with biofertilizer. Fertilization in the CS was done with 200 g 4-14-8 (NPK) per pit and, after planting, 30 g N, 33 g K and 10.5 g P per pit; from 52 days after planting forth, plants were sprayed once a week with foliar fertilizer. In the CS, a blend of insecticides, fungicides and miticides was sprayed twice a week, after planting. In the OS, extracts of black pepper, garlic, and Eucalyptus; Bordeaux mixture, and biofertilizer, were applied twice a week to control diseases and pests. Tomato spotted wilt was the most important disease in the OS, resulting in smaller plant development, number of flower clusters and yield. In the CS, the disease was kept under control, and the population of thrips, the virus vector, occurred at lower levels than in the OS. Variety Santa Clara presented greater incidence of the viral disease, and for this reason had a poorer performance than 'Débora', especially in the OS. Occurrence of Liriomyza spp. was significantly smaller in the OS, possibly because of the greater frequency of Chrysoperla. The CS had smaller incidence of leaf spots caused by Septoria lycopersici and Xanthomonas vesicatoria. However, early blight and fruit rot caused by Alternaria solani occurred in larger numbers. No differences were observed with regard to the communities of fungi and bacteria in the phylloplane, and to the occurrence of weeds

Graphical representation of the partition function for a 1-D delta-function Bose gas

One-dimensional repulsive delta-function bose system is studied. By only using the Bethe ansatz equation, n-particle partition functions are exactly calculated. From this expression for the n-particle partition function, the n-particle cluster integral is derived. The results completely agree with those of the thermal Bethe ansatz (TBA). This directly proves the validity of the TBA. The theory of partitions and graphs is used to simplify the discussion.Comment: 15 page

Technical report: Modeling nitrate leaching risk from specialty crop fields during on-farm managed floodwater recharge in the Kings Groundwater Basin and the potential for its management

This project has focused on better understanding the potential impact of On-Farm Flood Capture and Recharge (OFFCR) on groundwater quality pertaining to salts and nitrate and on assessing potential management opportunities. To achieve these goals, we used a combination of field and modeling studies. For the field study, soil cores were taken to a depth of 30 feet in replicate across fields with three different specialty crops identified as important to the San Joaquin Valley (tomatoes, almonds, vineyards) and with potential suitability for OFFCR. A prime goal of the field study was to provide data for parameterizing two models developed to assess nitrate, salt and water transport through the vadose zone, prior to percolating into the groundwater aquifer. However, the field study also resulted in key findings that show its value as a stand-alone study: 1) Nitrate concentrations are highest in the upper vadose zone and affected by texture. Those effects are not evident in the deeper vadose zone. 2) Vadose zone nitrate concentrations are affected by the crop grown. These results suggest an opportunity for lower legacy mass transport for grapes and higher legacy mass transport for both tomatoes and almonds. 3) Variability in individual farmers’ past and present fertilizer and water management practices contributes to different legacy salt and nitrate loads in the vadose zone. Data from the field study and other related and concurrent OFFCR field efforts were used during model development. The overall modeling approach was designed to model nitrate and salt transport for lands under OFFCR operation for different crop types, vadose zone characteristics and groundwater characteristics. The defined goals of this design and modeling approach were to: 1) model nitrate and salt movement through the vadose zone and into groundwater; 2) test the model against scenarios that consider different recharge rates, cultural practices, soil types, and depths to groundwater, assessing the timing and magnitude of loading through the vadose zone and the effects on underlying groundwater; and 3) recommend management practices to mitigate potential groundwater impacts. To achieve these goals, two models were integrated to simulate nitrate and salt transport through the vadose zone to groundwater under different scenarios: a 1D Hydrus model and an analytical groundwater model (AGM)

Swainsonine Biosynthesis Genes in Diverse Symbiotic and Pathogenic Fungi

Swainsonine—a cytotoxic fungal alkaloid and a potential cancer therapy drug—is produced by the insect pathogen and plant symbiont Metarhizium robertsii, the clover pathogen Slafractonia leguminicola, locoweed symbionts belonging to Alternaria sect. Undifilum, and a recently discovered morning glory symbiont belonging to order Chaetothyriales. Genome sequence analyses revealed that these fungi share orthologous gene clusters, designated “SWN,” which included a multifunctional swnKgene comprising predicted adenylylation and acyltransferase domains with their associated thiolation domains, a β-ketoacyl synthase domain, and two reductase domains. The role of swnK was demonstrated by inactivating it in M. robertsii through homologous gene replacement to give a ∆swnK mutant that produced no detectable swainsonine, then complementing the mutant with the wild-type gene to restore swainsonine biosynthesis. Other SWN cluster genes were predicted to encode two putative hydroxylases and two reductases, as expected to complete biosynthesis of swainsonine from the predicted SwnK product. SWN gene clusters were identified in six out of seven sequenced genomes of Metarhzium species, and in all 15 sequenced genomes of Arthrodermataceae, a family of fungi that cause athlete’s foot and ringworm diseases in humans and other mammals. Representative isolates of all of these species were cultured, and all Metarhizium spp. with SWN clusters, as well as all but one of the Arthrodermataceae, produced swainsonine. These results suggest a new biosynthetic hypothesis for this alkaloid, extending the known taxonomic breadth of swainsonine producers to at least four orders of Ascomycota, and suggest that swainsonine has roles in mutualistic symbioses and diseases of plants and animals