Proximity Interactions in a Permanently Housed Dairy Herd: Network Structure, Consistency, and Individual Differences

Understanding the herd structure of housed dairy cows has the potential to reveal preferential interactions, detect changes in behavior indicative of illness, and optimize farm management regimes. This study investigated the structure and consistency of the proximity interaction network of a permanently housed commercial dairy herd throughout October 2014, using data collected from a wireless local positioning system. Herd-level networks were determined from sustained proximity interactions (pairs of cows continuously within three meters for 60 s or longer), and assessed for social differentiation, temporal stability, and the influence of individual-level characteristics such as lameness, parity, and days in milk. We determined the level of inter-individual variation in proximity interactions across the full barn housing, and for specific functional zones within it (feeding, non-feeding). The observed networks were highly connected and temporally varied, with significant preferential assortment, and inter-individual variation in daily interactions in the non-feeding zone. We found no clear social assortment by lameness, parity, or days in milk. Our study demonstrates the potential benefits of automated tracking technology to monitor the proximity interactions of individual animals within large, commercially relevant groups of livestock

Reconstructing the Inflaton Potential---in Principle and in Practice

Generalizing the original work by Hodges and Blumenthal, we outline a formalism which allows one, in principle, to reconstruct the potential of the inflaton field from knowledge of the tensor gravitational wave spectrum or the scalar density fluctuation spectrum, with special emphasis on the importance of the tensor spectrum. We provide some illustrative examples of such reconstruction. We then discuss in some detail the question of whether one can use real observations to carry out this procedure. We conclude that in practice, a full reconstruction of the functional form of the potential will not be possible within the foreseeable future. However, with a knowledge of the dark matter components, it should soon be possible to combine intermediate-scale data with measurements of large-scale cosmic microwave background anisotropies to yield useful information regarding the potential.Comment: 39 pages plus 2 figures (upon request:[email protected]), LaTeX, FNAL--PUB--93/029-A; SUSSEX-AST 93/3-

Bunching behaviour in housed dairy cows at higher ambient temperatures.

Bunching behavior in cattle may occur for several reasons including enabling social interactions, a response to stress or danger, or due to shared interest in resources such as feeding or watering areas. There is evidence in pasture grazed cattle that bunching may occur more frequently at higher ambient temperatures, possibly due to sharing of fly-load or to seek shade from the direct sun under heat stress conditions. Here we demonstrate how bunching behavior is associated with higher ambient temperatures in a barn-housed UK dairy herd. A real-time local positioning system (RTLS) was used, as part of a precision livestock farming (PLF) approach, to track the spatial position and activity of a commercial dairy herd (c100 cows) in a freestall barn continuously at high temporal resolution for 4 mo between August and November 2014. Bunching was determined using 4 different spatial measures determined on an hourly basis: herd full and core range size, mean herd inter-cow distance (ICD), and mean herd nearest neighbor distance (NND). For hourly mean ambient temperatures above 20°C, the herd showed higher bunching behavior with increasing ambient temperature (i.e., reduced full and core range size, ICD, and NND). Aggregated space-use intensity was found to positively correlate with localized variations in temperature across the barn (as measured by animal mounted sensors), but the level of correlation decreased at higher ambient barn temperatures. Bunching behavior may increase localized temperatures experienced by individuals and hence may be a maladaptive behavioral response in housed dairy cattle, which are known to suffer heat stress at higher temperatures. Our study is the first to use high-resolution positional data to provide evidence of associations between bunching behavior and higher ambient temperatures for a barn-housed dairy herd in a temperate region (UK). Further studies are needed to explore the exact mechanisms for this response to inform both welfare and production management

Statistical Analysis of Molecular Signal Recording

A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.United States. Defense Advanced Research Projects Agency. Living Foundries ProgramGoogle (Firm)New York Stem Cell Foundation. Robertson Neuroscience Investigator AwardNational Institutes of Health (U.S.) (EUREKA Award 1R01NS075421)National Institutes of Health (U.S.) (Transformative R01 1R01GM104948)National Institutes of Health (U.S.) (Single Cell Grant 1 R01 EY023173)National Institutes of Health (U.S.) (Grant 1R01DA029639)National Institutes of Health (U.S.) (Grant 1R01NS067199)National Science Foundation (U.S.) (CAREER Award CBET 1053233)National Science Foundation (U.S.) (Grant EFRI0835878)National Science Foundation (U.S.) (Grant DMS1042134)Paul G. Allen Family Foundation (Distinguished Investigator in Neuroscience Award

Correlations of behavioral deficits with brain pathology assessed through longitudinal MRI and histopathology in the R6/1 mouse model of huntington's disease

Huntington's disease (HD) is caused by the expansion of a CAG repeat in the huntingtin (HTT) gene. The R6 mouse models of HD express a mutant version of exon 1 HTT and typically develop motor and cognitive impairments, a widespread huntingtin (HTT) aggregate pathology and brain atrophy. Unlike the more commonly used R6/2 mouse line, R6/1 mice have fewer CAG repeats and, subsequently, a less rapid pathological decline. Compared to the R6/2 line, fewer descriptions of the progressive pathologies exhibited by R6/1 mice exist. The association between the molecular and cellular neuropathology with brain atrophy, and with the development of behavioral phenotypes remains poorly understood in many models of HD. In attempt to link these factors in the R6/1 mouse line, we have performed detailed assessments of behavior and of regional brain abnormalities determined through longitudinal, in vivo magnetic resonance imaging (MRI), as well as an end-stage, ex vivo MRI study and histological assessment. We found progressive decline in both motor and non-motor related behavioral tasks in R6/1 mice, first evident at 11 weeks of age. Regional brain volumes were generally unaffected at 9 weeks, but by 17 weeks there was significant grey matter atrophy. This age-related brain volume loss was validated using a more precise, semi-automated Tensor Based morphometry assessment. As well as these clear progressive phenotypes, mutant HTT (mHTT) protein, the hallmark of HD molecular pathology, was widely distributed throughout the R6/1 brain and was accompanied by neuronal loss. Despite these seemingly concomitant, robust pathological phenotypes, there appeared to be little correlation between the three main outcome measures: behavioral performance, MRI-detected brain atrophy and histopathology. In conclusion, R6/1 mice exhibit many features of HD, but the underlying mechanisms driving these clear behavioral disturbances and the brain volume loss, still remain unclear. © 2013 Rattray et al

Transcriptional Activation of OsDERF1 in OsERF3 and OsAP2-39 Negatively Modulates Ethylene Synthesis and Drought Tolerance in Rice

The phytohormone ethylene is a key signaling molecule that regulates a variety of developmental processes and stress responses in plants. Transcriptional modulation is a pivotal process controlling ethylene synthesis, which further triggers the expression of stress-related genes and plant adaptation to stresses; however, it is unclear how this process is transcriptionally modulated in rice. In the present research, we report the transcriptional regulation of a novel rice ethylene response factor (ERF) in ethylene synthesis and drought tolerance. Through analysis of transcriptional data, one of the drought-responsive ERF genes, OsDERF1, was identified for its activation in response to drought, ethylene and abscisic acid. Transgenic plants overexpressing OsDERF1 (OE) led to reduced tolerance to drought stress in rice at seedling stage, while knockdown of OsDERF1 (RI) expression conferred enhanced tolerance at seedling and tillering stages. This regulation was supported by negative modulation in osmotic adjustment response. To elucidate the molecular basis of drought tolerance, we identified the target genes of OsDERF1 using the Affymetrix GeneChip, including the activation of cluster stress-related negative regulators such as ERF repressors. Biochemical and molecular approaches showed that OsDERF1 at least directly interacted with the GCC box in the promoters of ERF repressors OsERF3 and OsAP2-39. Further investigations showed that OE seedlings had reduced expression (while RI lines showed enhanced expression) of ethylene synthesis genes, thereby resulting in changes in ethylene production. Moreover, overexpression of OsERF3/OsAP2-39 suppressed ethylene synthesis. In addition, application of ACC recovered the drought-sensitive phenotype in the lines overexpressing OsERF3, showing that ethylene production contributed to drought response in rice. Thus our data reveal that a novel ERF transcriptional cascade modulates drought response through controlling the ethylene synthesis, deepening our understanding of the regulation of ERF proteins in ethylene related drought response

Effect of spinal manipulation on sensorimotor functions in back pain patients: study protocol for a randomised controlled trial

<p>Abstract</p> <p>Background</p> <p>Low back pain (LBP) is a recognized public health problem, impacting up to 80% of US adults at some point in their lives. Patients with LBP are utilizing integrative health care such as spinal manipulation (SM). SM is the therapeutic application of a load to specific body tissues or structures and can be divided into two broad categories: SM with a high-velocity low-amplitude load, or an impulse "thrust", (HVLA-SM) and SM with a low-velocity variable-amplitude load (LVVA-SM). There is evidence that sensorimotor function in people with LBP is altered. This study evaluates the sensorimotor function in the lumbopelvic region, as measured by postural sway, response to sudden load and repositioning accuracy, following SM to the lumbar and pelvic region when compared to a sham treatment.</p> <p>Methods/Design</p> <p>A total of 219 participants with acute, subacute or chronic low back pain are being recruited from the Quad Cities area located in Iowa and Illinois. They are allocated through a minimization algorithm in a 1:1:1 ratio to receive either 13 HVLA-SM treatments over 6 weeks, 13 LVVA-SM treatments over 6 weeks or 2 weeks of a sham treatment followed by 4 weeks of full spine "doctor's choice" SM. Sensorimotor function tests are performed before and immediately after treatment at baseline, week 2 and week 6. Self-report outcome assessments are also collected. The primary aims of this study are to 1) determine immediate pre to post changes in sensorimotor function as measured by postural sway following delivery of a single HVLA-SM or LVVA-SM treatment when compared to a sham treatment and 2) to determine changes from baseline to 2 weeks (4 treatments) of HVLA-SM or LVVA-SM compared to a sham treatment. Secondary aims include changes in response to sudden loads and lumbar repositioning accuracy at these endpoints, estimating sensorimotor function in the SM groups after 6 weeks of treatment, and exploring if changes in sensorimotor function are associated with changes in self-report outcome assessments.</p> <p>Discussion</p> <p>This study may provide clues to the sensorimotor mechanisms that explain observed functional deficits associated with LBP, as well as the mechanism of action of SM.</p> <p>Trial registration</p> <p>This trial is registered in ClinicalTrials.gov, with the ID number of <a href="http://www.clinicaltrials.gov/ct2/show/NCT00830596">NCT00830596</a>, registered on January 27, 2009. The first participant was allocated on 30 January 2009 and the final participant was allocated on 17 March 2011.</p

Reconstructing the Inflaton Potential --- an Overview

We review the relation between the inflationary potential and the spectra of density (scalar) perturbations and gravitational waves (tensor perturbations) produced, with particular emphasis on the possibility of reconstructing the inflaton potential from observations. The spectra provide a potentially powerful test of the inflationary hypothesis; they are not independent but instead are linked by consistency relations reflecting their origin from a single inflationary potential. To lowest-order in a perturbation expansion there is a single, now familiar, relation between the tensor spectral index and the relative amplitude of the spectra. We demonstrate that there is an infinite hierarchy of such consistency equations, though observational difficulties suggest only the first is ever likely to be useful. We also note that since observations are expected to yield much better information on the scalars than on the tensors, it is likely to be the next-order version of this consistency equation which will be appropriate, not the lowest-order one. If inflation passes the consistency test, one can then confidently use the remaining observational information to constrain the inflationary potential, and we survey the general perturbative scheme for carrying out this procedure. Explicit expressions valid to next-lowest order in the expansion are presented. We then briefly assess the prospects for future observations reaching the quality required, and consider a simulated data set that is motivated by this outlook.Comment: 69 pages standard LaTeX plus 4 postscript figures. Postscript version of text in landscape format (35 pages) available at http://star-www.maps.susx.ac.uk/papers/infcos_papers.html Modifications are a variety of updates to discussion and reference