bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of the net energy value of barley for finishing beef steers1
Authors: Bowman Jan G P , Boss Darrin L , Surber Lisa M M , Blake Tom K 
Published: August 2019

Abstract
The objective of this study was to identify barley grain characteristics measured by laboratory procedures that could be used to predict barley energy content for finishing beef steers. Twenty-eight different barley genotypes were evaluated including 18 cultivars and 10 experimental lines. Laboratory analysis of barley samples included bulk density, particle size, N, ADF, starch, and ISDMD (in situ DM disappearance after 3 h of ruminal incubation). Animal performance data (BW, DMI, ADG, steer NEm, and NEg requirements) were collected from 26 feedlot experiments conducted in Montana and Idaho during a 10-yr period and were used to estimate barley NEm and NEg content. A total of 80 experimental units were available with each experimental unit being a diet mean from an individual feedlot experiment. Fifty-eight of the 80 experimental units were randomly selected and used in the development data set and the remaining 22 experimental units were used in the validation data set. Forward, backward, and stepwise selection methods were used to identify variables to be included in regression equations for NEm using PROC REG of SAS. Barley samples in the model development data set represented a wide range in concentrations (DM basis): N (1.6% to 2.8%), ISDMD (25.7% to 58.7%), ADF (3.6% to 8.0%), starch (44.1% to 62.4%), particle size (1,100 to 2,814 µm), and bulk density (50.8 to 69.4 kg/hL). The barley grain characteristics of particle size, ISDMD, starch, and ADF were the most important variables in six successful models (R2 = 0.48 to 0.60; P = 0.001). The six prediction equations gave mean predicted values for NEm ranging from 1.99 to 2.05 Mcal/kg (average 2.04 Mcal/kg; 0.45% CV). The mean actual NEm values from animal performance trials ranged from 1.75 to 2.48 Mcal/kg (average 2.03 Mcal/kg; 6.5% CV). The mean bias or difference in predicted vs. actual values ranged from −0.001 to 0.005 Mcal/kg. Barley NEg values calculated from animal performance ranged from 1.13 to 1.78 Mcal/kg (average 1.39 Mcal/kg; 8.4% CV). Average predicted barley NEm and NEg were 0.02 and 0.01 Mcal/kg less, respectively, than the 2.06 Mcal/kg NEm and 1.40 Mcal/kg NEg reported by NRC. Barley NE can be predicted from simple laboratory procedures which will aid plant breeders developing new feed varieties and nutritionists formulating finishing rations for beef cattle.
Blood lactate and rectal temperature can predict exit velocity of beef feedlot steers
Authors: Williams Andrew F , Boles Jane A , Herrygers Melissa R , Berardinelli James G , Meyers Michael C , Thomson Jennifer M 
Published: August 2019

Abstract:
Interest in beef cattle temperament has increased due to growing consumer awareness of animal welfare and increased concern for handler safety. Temperament measures are based on behavioral responses to a perceived stressor. Subjective chute scoring has been used to give a numeric value to temperament; however, the subjectivity and variability among observers have been questioned. To deal with the perceived subjectivity and variability, other researchers have used exit velocity. Researchers have related faster exit velocities to increased cortisol and plasma lactate. The objectives of this study were to compare temperament between feedlot steers and heifers and to confirm chute side measures of temperament relationship to physiological responses to stress. Body temperature, blood and plasma lactate, serum glucose, salivary and serum cortisol concentrations were measured on Bos taurus commercial crossbred feedlot cattle (n = 197). Fast, medium, and slow classifications were developed from exit velocities. Plasma lactate was significantly different between all exit velocity classes. Exit velocity and physiological measures indicated that heifers were more excitable (faster exit velocities (P = 0.003), higher plasma lactate concentrations (P = 0.03), and cortisol concentrations (P = 0.001)). Simple correlations among these variables indicated body temperature (heifers r = 0.44, P &lt; 0.0001; steers r = 0.45, P &lt; .0001), plasma lactate (heifers r = 0.52, P &lt; 0.0001; steers r = 0.63, P &lt; 0.0001), blood lactate (heifers r = 0.53, P &lt; 0.001; steers r = 0.59, P &lt; 0.001), and glucose (heifers r = 0.54, P &lt; 0.001; steers r = 0.32, P &lt;0.003) were all related to exit velocity. Cortisol measures were not correlated to exit velocity in steers but were in heifers. Linear models constructed and evaluated using the Akaike information criterion indicated that blood lactate in combination with rectal temperature were strong candidates to predict exit velocity. Using the discriminate function analysis, the model correctly categorized fast and slow classifications 69.23% and 61.54%, respectively, indicating that in combination measures of body temperature and blood lactate can potentially increase accuracy of temperament identification or replace exit velocity as a measure of temperament. The plasma lactate and rectal temperature have the potential to become strong objective measures to augment or replace exit velocity.
Enhanced mindfulness based stress reduction (MBSR+) in episodic migraine: a randomized clinical trial with MRI outcomes
Authors: Seminowicz David A. , Burrowes Shana AB , Kearson Alexandra , Zhang Jing , Krimmel Samuel R , Samawi Luma , Furman Andrew J , Keaser Michael L , Gould Neda F. , Magyari Trish , White Linda , Goloubeva Olga , Goyal Madhav , Peterlin B. Lee , Haythornthwaite Jennifer A. 
Published: August 2019

AbstractWe aimed to evaluate the efficacy of an enhanced mindfulness based stress reduction (MBSR+) versus stress management for headache (SMH). We performed a randomized, assessor-blind, clinical trial of 98 adults with episodic migraine recruited at a single academic center comparing MBSR+ (n=50) to SMH (n=48). MBSR+ and SMH were delivered weekly by group for 8 weeks, then bi-weekly for another 8 weeks. The primary clinical outcome was reduction in headache days from baseline to 20 weeks. MRI outcomes included activity of left dorsolateral prefrontal cortex (DLPFC) and cognitive task network during cognitive challenge, resting state connectivity of right dorsal anterior insula (daINS) to DLPFC and cognitive task network, and gray matter volume of DLPFC, daINS, and anterior midcingulate. Secondary outcomes were headache-related disability, pain severity, response to treatment, migraine days, and MRI whole-brain analyses. Reduction in headache days from baseline to 20 weeks was greater for MBSR+ (7.8 [95%CI, 6.9-8.8] to 4.6 [95%CI, 3.7-5.6]) than for SMH (7.7 [95%CI 6.7-8.7] to 6.0 [95%CI, 4.9-7.0]) (P=0.04). 52% of the MBSR+ group showed a response to treatment (50% reduction in headache days) compared with 23% in the SMH group (P=0.004). Reduction in headache-related disability was greater for MBSR+ (59.6 [95%CI, 57.9-61.3] to 54.6 [95%CI, 52.9-56.4]) than SMH (59.6 [95%CI, 57.7-61.5] to 57.5 [95%CI, 55.5-59.4])(P=0.02). There were no differences in clinical outcomes at 52 weeks or MRI outcomes at 20 weeks, although changes related to cognitive networks with MBSR+ were observed. MBSR+ is an effective treatment option for episodic migraine.
Map3k2-Regulated Intestinal Stromal Cells (MRISC) Define a Distinct Sub-cryptic Stem Cell Niche for Damage Induced Wnt Agonist R-spondin1 Production
Authors: Wu Ningbo , Sun Hongxiang , Zhao Xiaoyun , Chen Lei , Qi Yuanyuan , Han Yuheng , Liu Xianan , Gao Caixia , Wang Qun , He Lingjuan , Niu Xiaoyin , Liu Zhiduo , Li Hua-Bing , Zeng Yi Arial , Roulis Manolis , Liu Dou , Yang Zhengfeng , Zhou Bin , Flavell Richard A. , Su Bing 
Published: August 2019

SummaryIntestinal stem cell propagation and differentiation are essential for rapid repair of tissue damage in the gut. While intestinal stromal cells were recently identified as key mediators of this process, the cellular and molecular mechanisms by which this diverse population induces tissue repair remains poorly understood. Here we show that Map3k2 has a colon stromal cell specific function critically required for maintenance of Lgr5+ intestinal stem cells and protection against acute intestinal damage. This Map3k2-specific function is mediated by enhancing Wnt agonist R-spondin1 production. We further reveal a unique novel cell population, named Map3k2-regulated intestinal stromal cells (MRISC), as the primary cellular source of R-spondin1 following intestinal injury. Together, our data identify a novel intestinal stem cell niche organized by MRISC, which specifically dependent on the Map3k2-signaling pathway to augment the production of Wnt agonist R-spondin1 and promote regeneration of the acutely damaged intestine.HighlightsMap3k2 protects mice from DSS-induced colitis by promoting intestinal stem cell regeneration.Map3k2-MAPK pathway cross-talks with Wnt signaling pathway via upregulation of R-spondin1.Map3k2-Regulated Intestinal Stromal Cells (MRISC) marked by co-expression of CD90, CD34 and CD81 defines a novel colonic stem cell niche.
The interaction between elapsed time and decision accuracy differs between humans and rats
Authors: Shevinsky Carly A , Reinagel Pamela 
Published: August 2019

AbstractA stochastic visual motion discrimination task is widely used to study rapid decision-making in humans and animals. Among trials of the same sensory difficulty within a block of fixed decision strategy, humans and monkeys are widely reported to make more errors in the individual trials with longer reaction times. This finding has posed a challenge for the drift-diffusion model of sensory decision-making, which in its basic form predicts that errors and correct responses should have the same reaction time distributions. We previously reported that rats also violate this model prediction, but in the opposite direction: for rats, motion discrimination accuracy was highest in the trials with the longest reaction times. To rule out task differences as the cause of our divergent finding in rats, the present study tested humans and rats using the same task and analyzed their data identically. We confirmed that rats’ accuracy increased with reaction time, whereas humans’ accuracy decreased with reaction time in the same task. These results were further verified using a new temporally-local analysis method, ruling out that the observed trend was an artifact of non-stationarity in the data of either species. The main effect was found whether the signal strength (motion coherence) was varied in randomly interleaved trials or held constant within a block. The magnitude of the effects increased with motion coherence. These results provide new constraints useful for refining and discriminating among the many alternative mathematical theories of decision-making.
Mutation of Ebola virus VP35 Ser129 uncouples interferon antagonist and replication functions
Authors: Morwitzer MJ , Corona A , Zinzula L , Fanunza E , Nigri C , Distinto S , Vornholt C , Kumar V , Tramontano E , Reid SP 
Published: August 2019

AbstractEbolaviruses are non-segmented, negative-sense RNA viruses (NNSVs) within the orderMononegaviralesthat possess the multifunctional virion protein 35 (VP35), a major determinant of virulence and pathogenesis that is indispensable for viral replication and host innate immune evasion. VP35 is functionally equivalent to the phosphoprotein (P) of other mononegaviruses such as rhabdoviruses and paramyxoviruses. Phosphorylation of the P protein is universally regarded as functionally important however, a regulatory role(s) of phosphorylation on VP35 function remains unexplored. Here, we identified a highly conserved Ser129 residue near the homo-oligomerization coiled coil motif, which is essential for VP35 functions. Affinity-purification MS followed by post-translational modification (PTM) analysis predicted phosphorylation of Ser129. Co-immunoprecipitation, cross-linking, and biochemical characterization studies revealed a moderately decreased capacity of VP35-S129A to oligomerize. Functional analysis showed that Ser-to-Ala substitution of Ebola virus (EBOV) VP35 did not affect IFN inhibitory activity but nearly abolished EBOV minigenome activity. Further coimmunoprecipitation studies demonstrated a lost interaction between VP35-S129A and the amino terminus of the viral polymerase but not between viral nucleoprotein (NP) or VP35-WT. Taken together, our findings provide evidence that phosphorylation modulates VP35 function, supporting VP35 as a NNSV P protein and providing a potentially valuable therapeutic target.ImportanceEbola virus (EBOV) can cause severe disease in humans. The 2013-2016 West African epidemic and the two recent outbreaks in the Democratic Republic of the Congo underscore the urgent need for effective countermeasures, which remain lacking. A better understanding of EBOV biology and the modulation of multifunctional viral proteins is desperately needed to develop improved therapeutics. We provide evidence here that function of virion protein 35 (VP35) is modulated by phosphorylation of Ser129, a conserved residue among other ebolavirus species. These findings shed light on EBOV biology and present a potential target for broad acting anti-ebolavirus therapeutics.
SMART: An open source extension of WholeBrain for iDISCO+ LSFM intact mouse brain registration and segmentation
Authors: Jin Michelle , Nguyen Joseph D. , Weber Sophia J. , Mejias-Aponte Carlos A. , Madangopal Rajtarun , Golden Sam A. 
Published: August 2019

AbstractMapping immediate early gene (IEG) expression across intact brains is becoming a popular approach for identifying the brain-wide activity patterns underlying behavior. Registering whole brains to an anatomical atlas presents a technical challenge that has predominantly been tackled using automated voxel-based registration methods; however, these methods may fail when brains are damaged or only partially imaged, can be challenging to correct, and require substantial computational power. Here we present an open source package in R called SMART (semi-manual alignment to reference templates) as an extension to the WholeBrain framework for automated segmentation and semi-automated registration of experimental images to vectorized atlas plates from the Allen Brain Institute Mouse Common Coordinate Framework (CCF).The SMART package was created with the novice programmer in mind and introduces a streamlined pipeline for aligning, registering, and segmenting large LSFM volumetric datasets with the CCF across the anterior-posterior axis, using a simple ‘choice game’ and interactive user-friendly menus. SMART further provides the flexibility to register partial brains or discrete user-chosen experimental images across the CCF, making it compatible with analysis of traditionally sectioned coronal brain slices. In addition to SMART, we introduce a modified tissue clearing protocol based on the iDISCO+ procedure that is optimized for uniform Fos antibody labeling and tissue clearing across whole intact mouse brains. Here we demonstrate the utility of the SMART-WholeBrain pipeline, in conjunction with the modified iDISCO+ Fos procedure, by providing example datasets alongside a full user tutorial. Finally, we present a subset of these data online in an interactive web applet. The complete SMART package is available for download on GitHub.
A Dual-sensing DNA Nanostructure with an Ultra-broad Detection Range
Authors: Kang Byunghwa , Park Soyeon V. , Soh H. Tom , Oh Seung Soo 
Published: August 2019

AbstractDespite considerable interest in the development of biosensors that can measure analyte concentrations with a dynamic range spanning many orders of magnitude, this goal has proven difficult to achieve. We describe here a modular biosensor architecture that integrates two different readout mechanisms into a single-molecule construct that can achieve target detection across an extraordinarily broad dynamic range. Our dual-mode readout DNA biosensor (DMRD) combines an aptamer and a DNAzyme to quantify ATP with two different mechanisms, which respond to low (micromolar) and high (millimolar) concentrations by generating distinct readouts based on changes in fluorescence and absorbance, respectively. Importantly, we have also devised regulatory strategies to finely tune the target detection range of each sensor module by controlling the target-sensitivity of each readout mechanism. Using this strategy, we report the detection of ATP at a dynamic range spanning 1–500,000 μM—more than five orders of magnitude, representing the largest dynamic range reported to date with a single biosensor construct.
Drp1-mediated mitochondrial fission regulates calcium and F-actin dynamics during wound healing
Authors: Ponte Susana , Carvalho Lara , Gagliardi Maria , Campos Isabel , Oliveira Paulo J. , Jacinto António 
Published: August 2019

AbstractMitochondria adapt to cellular needs by changes in morphology through fusion and fission events, referred to as mitochondrial dynamics. Mitochondrial function and morphology are intimately connected and the dysregulation of mitochondrial dynamics is linked to several human diseases. In this work, we investigated the role of mitochondrial dynamics in wound healing in theDrosophilaembryonic epidermis. Mutants for mitochondrial fusion and fission proteins fail to close their wounds, indicating that the regulation of mitochondrial dynamics is required for wound healing. By live-imaging, we found that loss of function of the mitochondrial fission protein Dynamin-related protein 1 (Drp1) compromises the increase of cytosolic and mitochondrial calcium upon wounding and leads to F-actin defects at the wound edge, culminating in wound healing impairment. Our results highlight a new role for mitochondrial dynamics in the regulation of calcium and F-actin during epithelial repair.SummaryWe show that mitochondrial dynamics proteins are required for epithelial repair. In particular, Drp1 loss-of-function leads to defects in the dynamics of cytosolic and mitochondrial calcium and F-actin upon wounding.
Markov modelling of run length and velocity for molecular motors
Authors: Buchanan James L , Gilbert Robert P 
Published: August 2019

AbstractMolecular motors are nanometer scale proteins involved in various in-tracellular processes such as cargo transport, muscle contraction and cell division. The steps in the chemo-mechanical cycle that use ATP hydrolysis to generate motion along the cytoskeletal tracks can be characterized by stepping rates depending only on the current state, permitting modeling of the cycle as a Markov process. To learn more about the nature of motor mo-tion, cell researchers have conducted in vitro experiments in which molecular motors pull beads along filaments attached to glass slides and their veloc-ity and run length until detachment from the microtubule are recorded. In this article a formula is derived for distance traveled until detachment. Combining this with a standard result for time to absorption for Markov processes gives a formula for velocity. Two kinesins, and two variants of myosin VI, for which there are run length and velocity measurements in the literature are considered. In each case the derived formulas for run length and velocity have a generalized Michaelis-Menten form as functions of ATP concentration. The degrees of the numerator and denominator polynomials increase with the complexity of chemo-mechanical cycle. The degrees of the Michaelis-Menten form determine the maximum number of of reaction rates that can be determined from experimental data on run length and velocity, however consistency conditions may reduce this number and restrict which rates can be determined.
Twister3: a simple and fast microwire twister
Authors: Newman Jonathan P. , Voigts Jakob , Borius Maxim , Karlsson Mattias , Harnett Mark T. , Wilson Matthew A. 
Published: August 2019

AbstractWe present Twister3, a microwire twisting machine. This device greatly increases the speed and repeatability of constructing twisted microwire neural probes (e.g. stereotrodes and tetrodes) compared to existing options. It is cheap, well documented, and all associated designs and source code are open-source. Twister3 is of interest to any lab performing twisted microwire neural recordings, for example, using tetrode drives.
On the evolution of sexual receptivity in female primates
Authors: Rooker Kelly , Gavrilets Sergey 
Published: August 2019

AbstractThere has been much interest in the evolutionary forces responsible for, and underlying the diversity in, female primate reproductive cycles. Some primate species are like humans, sexually receptive to mating throughout their entire estrus cycle, while other species are the opposite, receptive for mere hours out of their several-week cycles. Why is there such prominent variation in sexual receptivity length among primate species? Here we examine the evolutionary trade-offs associated with sexual receptivity length using mathematical modeling. We investigate how various factors, including having ovulation signs present vs. concealed ovulation, female physiological costs, and group size, each influence the length of females’ receptive periods. We find that both continuous receptivity and very short lengths of receptivity are able to evolve. Our model predicts that increasing the impacts of infanticide will increase the length of the female receptive period, emphasizing the possible importance of paternity confusion. Similar effects can also be achieved by increasing the non-genetic benefits provided by males. Overall, our work offers a theoretical framework for understanding the evolution and diversity of mating traits in female primates.