Making the farm pay

"We have chosen as the title of the present publication 'Making the Farm Pay'. We choose to interpret this title rather broadly. Farm labor must be properly compensated in dollars for capital invested and labor expended. The farm must, at the same time, offer other compensations which, in many cases, dollars cannot buy. The farm must pay in terms of satisfactory living conditions for the farm family. The farm must pay in terms of a progressive environment in which boys and girls may grow to manhood and womanhood. The farm must pay in terms of communities which satisfy that in born desire of human beings everywhere to mingle with their kind in work, in play, and in giving expression to their community, state, and national patriotism. To make the farm pay from each and all of these angles is the purpose of the Agricultural Extension Service. The following pages may reveal the extent to which that purpose is being accomplished. This report, if it may be so designated, comprises two divisions. The first of these is a general statement by the Director of Extension covering matters of immediate administrative concern. The second division has been prepared for publication by the agricultural editor. Division two is not a report, but rather an analysis of reports by one intent upon the purpose of interpreting for farmer readers agricultural facts and figures."--Page 3 and 4

Magnetic Switching of Phase-Slip Dissipation in NbSe2 Nanobelts

The stability of the superconducting dissipationless and resistive states in single-crystalline NbSe2 nanobelts is characterized by transport measurements in an external magnetic field (H). Current-driven electrical measurements show voltage steps, indicating the nucleation of phase-slip structures. Well below the critical temperature, the position of the voltage steps exhibits a sharp, periodic dependence as a function of H. This phenomenon is discussed in the context of two possible mechanisms: the interference of the order parameter and the periodic rearrangement of the vortex lattice within the nanobelt.Comment: 4 figure

Ordinal Probit Functional Regression Models with Application to Computer-Use Behavior in Rhesus Monkeys

Research in functional regression has made great strides in expanding to non-Gaussian functional outcomes, however the exploration of ordinal functional outcomes remains limited. Motivated by a study of computer-use behavior in rhesus macaques (\emph{Macaca mulatta}), we introduce the Ordinal Probit Functional Regression Model or OPFRM to perform ordinal function-on-scalar regression. The OPFRM is flexibly formulated to allow for the choice of different basis functions including penalized B-splines, wavelets, and O'Sullivan splines. We demonstrate the operating characteristics of the model in simulation using a variety of underlying covariance patterns showing the model performs reasonably well in estimation under multiple basis functions. We also present and compare two approaches for conducting posterior inference showing that joint credible intervals tend to out perform point-wise credible. Finally, in application, we determine demographic factors associated with the monkeys' computer use over the course of a year and provide a brief analysis of the findings

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Bayesian Function-on-Function Regression for Multilevel Functional Data

Medical and public health research increasingly involves the collection of complex and high dimensional data. In particular, functional data—where the unit of observation is a curve or set of curves that are finely sampled over a grid—is frequently obtained. Moreover, researchers often sample multiple curves per person resulting in repeated functional measures. A common question is how to analyze the relationship between two functional variables. We propose a general function-on-function regression model for repeatedly sampled functional data on a fine grid, presenting a simple model as well as a more extensive mixed model framework, and introducing various functional Bayesian inferential procedures that account for multiple testing. We examine these models via simulation and a data analysis with data from a study that used event-related potentials to examine how the brain processes various types of images

Examining the Links Between Challenging Behaviors in Youth with ASD and Parental Stress, Mental Health, and Involvement: Applying an Adaptation of the Family Stress Model to Families of Youth with ASD

Raising a child with autism spectrum disorder (ASD) poses unique challenges that may impact parents’ mental health and parenting experiences. The current study analyzed self-report data from 77 parents of youth with ASD. A serial multiple mediation model revealed that parenting stress (SIPA) and parental mental health (BAI and BDI-II) appears to be impacted by challenging adolescent behaviors (SSIS-PBs) and, in turn, affect parental involvement (PRQ), controlling for social skills (SSIS-SSs). Further, the study explored the malleability of parents’ mental health over the course of a social skills intervention, and provides modest evidence that parent depressive symptoms decline across intervention. This study illustrates the importance of considering the entire family system in research on youth with ASD

Epithelial laminin α5 is necessary for distal epithelial cell maturation, VEGF production, and alveolization in the developing murine lung

AbstractLaminin α5 is prominent in the basement membrane of alveolar walls, airways, and pleura in developing and adult lung. Targeted deletion of laminin α5 in mice causes developmental defects in multiple organs, but embryonic lethality has precluded examination of the latter stages of lung development. To identify roles for laminin α5 in lung development, we have generated an inducible lung epithelial cell-specific Lama5 null (SP-CLama5fl/−) mouse through use of the Cre/loxP system, the human surfactant protein C promoter, and the reverse tetracycline transactivator. SP-CLama5fl/− embryos exposed to doxycycline from E6.5 died a few hours after birth. Compared to control littermates, SP-CLama5fl/− lungs had dilated, enlarged distal airspaces, but basement membrane ultrastructure was preserved. Distal epithelial cell differentiation was perturbed, with a marked reduction of alveolar type II cells and a virtual absence of type I cells. Cell proliferation was reduced and apoptosis was increased. Capillary density was diminished, and this was associated with a decrease in total lung VEGF production. Overall, these findings indicate that epithelial laminin α5, independent of its structural function, is necessary for murine lung development, and suggest a role for laminin α5 in signaling pathways that promote alveolar epithelial cell differentiation and VEGF expression

An Optical Precursor to the Recent X-ray Outburst of the Black Hole Binary GRO J1655-40

The All Sky Monitor on the Rossi X-ray Timing Explorer detected an X-ray (2-12 keV) outburst from the black hole binary GRO J1655-40 beginning near April 25, 1996. Optical photometry obtained April 20-24, 1996 shows a steady brightening of the source in B, V, R, and I beginning about six days before the start of the X-ray outburst. The onset of the optical brightening was earliest in I and latest in B. However, the rate of the optical brightening was fastest in B and slowest in I. The order of the increases in the different optical filters suggests that the event was an "outside-in" disturbance of the accretion disk. The substantial delay between the optical rise and the rise of the X-rays may provide indirect support for the advection-dominated accretion flow model of the inner regions of the accretion disk.Comment: 8 pages, 2 figures, Latex (uses the standard AAS style file aas2pp4.sty), accepted for publication in the ApJ Letter

Impact of collimator leaf width and treatment technique on stereotactic radiosurgery and radiotherapy plans for intra- and extracranial lesions

<p>Abstract</p> <p>Background</p> <p>This study evaluated the dosimetric impact of various treatment techniques as well as collimator leaf width (2.5 vs 5 mm) for three groups of tumors – spine tumors, brain tumors abutting the brainstem, and liver tumors. These lesions often present challenges in maximizing dose to target volumes without exceeding critical organ tolerance. Specifically, this study evaluated the dosimetric benefits of various techniques and collimator leaf sizes as a function of lesion size and shape.</p> <p>Methods</p> <p>Fifteen cases (5 for each site) were studied retrospectively. All lesions either abutted or were an integral part of critical structures (brainstem, liver or spinal cord). For brain and liver lesions, treatment plans using a 3D-conformal static technique (3D), dynamic conformal arcs (DARC) or intensity modulation (IMRT) were designed with a conventional linear accelerator with standard 5 mm leaf width multi-leaf collimator, and a linear accelerator dedicated for radiosurgery and hypofractionated therapy with a 2.5 mm leaf width collimator. For the concave spine lesions, intensity modulation was required to provide adequate conformality; hence, only IMRT plans were evaluated using either the standard or small leaf-width collimators.</p> <p>A total of 70 treatment plans were generated and each plan was individually optimized according to the technique employed. The Generalized Estimating Equation (GEE) was used to separate the impact of treatment technique from the MLC system on plan outcome, and t-tests were performed to evaluate statistical differences in target coverage and organ sparing between plans.</p> <p>Results</p> <p>The lesions ranged in size from 2.6 to 12.5 cc, 17.5 to 153 cc, and 20.9 to 87.7 cc for the brain, liver, and spine groups, respectively. As a group, brain lesions were smaller than spine and liver lesions. While brain and liver lesions were primarily ellipsoidal, spine lesions were more complex in shape, as they were all concave. Therefore, the brain and the liver groups were compared for volume effect, and the liver and spine groups were compared for shape. For the brain and liver groups, both the radiosurgery MLC and the IMRT technique contributed to the dose sparing of organs-at-risk(OARs), as dose in the high-dose regions of these OARs was reduced up to 15%, compared to the non-IMRT techniques employing a 5 mm leaf-width collimator. Also, the dose reduction contributed by the fine leaf-width MLC decreased, as dose savings at all levels diminished from 4 – 11% for the brain group to 1 – 5% for the liver group, as the target structures decreased in volume. The fine leaf-width collimator significantly improved spinal cord sparing, with dose reductions of 14 – 19% in high to middle dose regions, compared to the 5 mm leaf width collimator.</p> <p>Conclusion</p> <p>The fine leaf-width MLC in combination with the IMRT technique can yield dosimetric benefits in radiosurgery and hypofractionated radiotherapy. Treatment of small lesions in cases involving complex target/OAR geometry will especially benefit from use of a fine leaf-width MLC and the use of IMRT.</p