bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas
Authors: Kalcioglu M. Tayyar , Guldemir Dilek , Unaldi Ozlem , Egilmez Oguz Kadir , Celebi Bekir , Durmaz Riza 
Published: April 2018

ObjectiveChronic otitis media can cause cholesteatomas or tympanosclerosis; however, the pathophysiology of such conditions is not completely known. The aim was to identify a bacterial genome that might be present in tympanosclerotic plaques and cholesteatomas using sequence analysis of the gene responsible for the transcription of 16 ribosomal RNA (rRNA).Study DesignMetagenomics analysis of the samples.SettingSamples were collected and evaluated at tertiary care centers.Subjects and MethodsSixty‐five tympanosclerotic plaques and 37 cholesteatomas were evaluated. The polymerase chain reaction (PCR) was performed using primers designed for the amplification of the gene responsible for the transcription of bacterial 16 rRNA. The PCR‐positive samples were sequenced via Sanger method, and 46 selected samples were analyzed with next‐generation sequencing (NGS).ResultsSanger sequencing revealed the presence of bacterial genomes in a total of 18 of the 102 samples tested. Sequencing of these genomes indicated the presence of Alloiococcus otitis, Staphylococcus aureus, Achromobacter xylosoxidans, Escherichia coli, Staphylococcus sciuri, Staphylococcus caprae, Parvimonas spp., and Bacillus sp. in the tested samples. The NGS showed 1 or more different bacterial genomes in 44 (95.7%) of the 46 samples tested. Predominately, genome of Clostridiales (27 samples), Staphylococcaceae (24 samples), Peptoniphilaceae (12 samples), and Turicella otitidis (9 samples) were identified.ConclusionThe middle ear is inhabited by a diverse microbial community than that previously known. With the use of molecular biology, it has become easier to identify the bacterial genomes and improve our understanding of the role of middle ear microbiota in the pathogenesis of chronic inflammatory ear diseases.
Randomized Controlled Trial Examining the Effects of Balloon Catheter Dilation on “Sinus Pressure” / Barometric Headaches
Authors: Laury Adrienne M. , Chen Philip G. , McMains Kevin C. 
Published: April 2018

ObjectiveTo determine if balloon catheter dilation of sinus ostia affects the severity or frequency of headache among patients who have barometric pressure–related “sinus” headache.Study DesignProspective single‐blinded randomized controlled trial.SettingTertiary care medical center.Subjects and MethodsSubjects with a diagnosis of sinus pressure headache without evidence of mucosal thickening on computed tomography were recruited. Subjects were blinded and randomized to undergo balloon dilation of affected sinus ostia (active treatment) or balloon dilation in the nasal cavity (placebo). Two balloon devices were utilized (Acclarent and Entellus) and outcomes compared. Subjects were followed with pre‐ and postprocedure SNOT‐22 scores (Sinonasal Outcome Test–22), HIT‐6 scores (Headache Impact Test–6), and medication utilization logs for 6 months.ResultsThere was no statistically significant difference in SNOT‐22 or HIT‐6 scores between the arms at any time point. However, both arms experienced statistically and clinically significant decreases in SNOT‐22 and HIT‐6 scores from preprocedure to 6 months postprocedure. There was no statistically significant difference in SNOT‐22 or HIT‐6 score reductions between the Entellus and Acclarent devices. There was no statistically significant difference in medication utilization between the groups at any time point.ConclusionsSubjects with sinus pressure headache without evidence of mucosal thickening on computed tomography had no significant difference in outcomes between active treatment (balloon dilation of sinus ostia) and placebo (nasal dilation). Further study on the etiology and effective treatment of barometric pressure / “sinus” headache is needed.
Elevated Levels of BRAFV600 Mutant Circulating Tumor DNA and Circulating Hepatocyte Growth Factor Are Associated With Poor Prognosis in Patients With Metastatic Melanoma
Authors: Lu William , Burton Luciana , Larkin James , Chapman Paul B. , Ascierto Paolo A. , Ribas Antoni , Robert Caroline , Sosman Jeffrey A. , McArthur Grant A. , Chang Ilsung , Caro Ivor , Penuel Elicia , Yan Yibing , Wongchenko Matthew J. 
Published: April 2018

Purpose We performed a retrospective exploratory analysis to evaluate the prognostic and predictive effect of two circulating biomarkers, BRAFV600 mutant circulating tumor DNA (ctDNA) and circulating hepatocyte growth factor (cHGF), in metastatic melanoma. Materials and Methods This study evaluated patients from BRIM-3, a phase III trial comparing vemurafenib and dacarbazine in 675 patients with BRAFV600 mutated advanced melanoma. ctDNA was measured using droplet digital polymerase chain reaction, and cHGF was measured by enzyme-linked immunosorbent assay. Overall survival (OS) was estimated using the Kaplan-Meier method, and hazard ratios (HRs) were estimated using Cox proportional hazards modeling. Partitioning analysis was used to group patients into risk categories. Results Patients with elevated levels of baseline BRAFV600 ctDNA had significantly shorter median OS than those with undetectable levels of ctDNA (vemurafenib arm, 9.9 v 21.4 months, respectively, and dacarbazine arm: 6.1 v 21.0 months, respectively). Median OS was also shorter in patients with high levels of cHGF compared with those with low cHGF (vemurafenib arm, 11.9 v 17.3 months, respectively, and dacarbazine arm, 6.1 v 14.4 months, respectively). In a multivariable proportional hazards model with adjustment for lactate dehydrogenase, Eastern Cooperative Oncology Group status, disease stage, and treatment, ctDNA and cHGF were both independent prognostic factors for OS, (HR, 1.75; 95% CI, 1.35 to 2.28 for high v undetectable ctDNA; HR, 1.24; 95% CI, 1.00 to 1.53 for high v low cHGF). Using partitioning analysis, we found that patients with elevated ctDNA combined with elevated cHGF constituted the highest risk group with significantly shorter OS. Conclusion Here, we report that BRIM-3 patients with high levels of ctDNA and cHGF have worse OS regardless of treatment and that these factors are independent prognostic markers for metastatic melanoma.
Carnitine Acetyltransferase in AgRP Neurons Is Required for the Homeostatic Adaptation to Restricted Feeding in Male Mice
Authors: Reichenbach Alex , Mequinion Mathieu , Bayliss Jacqueline A , Lockie Sarah H , Lemus Moyra B , Mynatt Randall L , Stark Romana , Andrews Zane B 
Published: April 2018

Abstract
Behavioral adaptation to periods of varying food availability is crucial for survival, and agouti-related protein (AgRP) neurons have been associated with entrainment to temporal restricted feeding. We have shown that carnitine acetyltransferase (Crat) in AgRP neurons enables metabolic flexibility and appropriate nutrient partitioning. In this study, by restricting food availability to 3 h/d during the light phase, we examined whether Crat is a component of a food-entrainable oscillator (FEO) that helps link behavior to food availability. AgRP Crat knockout (KO) mice consumed less food and regained less body weight but maintained blood glucose levels during the 25-day restricted feeding protocol. Importantly, we observed no difference in meal latency, food anticipatory activity (FAA), or brown adipose tissue temperature during the first 13 days of restricted feeding. However, as the restricted feeding paradigm progressed, we noticed an increased FAA in AgRP Crat KO mice. The delayed increase in FAA, which developed during the last 12 days of restricted feeding, corresponded with elevated plasma levels of corticosterone and nonesterified fatty acids, indicating it resulted from greater energy debt incurred by KO mice over the course of the experiment. These experiments highlight the importance of Crat in AgRP neurons in regulating feeding behavior and body weight gain during restricted feeding but not in synchronizing behavior to food availability. Thus, Crat within AgRP neurons forms a component of the homeostatic response to restricted feeding but is not likely to be a molecular component of FEO.
Suppression of epithelial folding at actomyosin-enriched compartment boundaries downstream of Wingless signalling in Drosophila
Authors: Urbano Jose M. , Naylor Huw W. , Scarpa Elena , Muresan Leila , Sanson Bénédicte 
Published: April 2018

ABSTRACT
Epithelial folding shapes embryos and tissues during development. Here, we investigate the coupling between epithelial folding and actomyosin-enriched compartmental boundaries. The mechanistic relationship between the two is unclear, because actomyosin-enriched boundaries are not necessarily associated with folds. Also, some cases of epithelial folding occur independently of actomyosin contractility. We investigated the shallow folds called parasegment grooves that form at boundaries between anterior and posterior compartments in the early Drosophila embryo. We demonstrate that formation of these folds requires the presence of an actomyosin enrichment along the boundary cell-cell contacts. These enrichments, which require Wingless signalling, increase interfacial tension not only at the level of the adherens junctions but also along the lateral surfaces. We find that epithelial folding is normally under inhibitory control because different genetic manipulations, including depletion of the Myosin II phosphatase Flapwing, increase the depth of folds at boundaries. Fold depth correlates with the levels of Bazooka (Baz), the Par-3 homologue, along the boundary cell-cell contacts. Moreover, Wingless and Hedgehog signalling have opposite effects on fold depth at the boundary that correlate with changes in Baz planar polarity.
Field Comparison of TSI DustTrak versus TEOM in Two Poultry Houses
Authors: Yang Xufei , Zhang Chen , Li Hong 
Published: April 2018

Abstract. The TSI DustTrak monitor has been used for particulate matter (PM) monitoring at various animal facilities. The instrument determines PM concentrations based on the principle of light scattering. Several assumptions (e.g., particle size, refractive index, and density) are imposed during the calibration process; however, they may not apply to PM emanating from agricultural settings. In this study, PM10 monitoring was conducted at a broiler house and a layer breeding house with four collocated instruments: three DustTrak monitors and one tapered element oscillating microbalance (TEOM). Being a federal equivalent method (FEM) for PM10 monitoring, TEOM was selected here as a transfer standard for assessing the field performance of DustTrak. Results revealed a good linearity between DustTrak and TEOM PM10 readings (R2 =0.92 and 0.85 in the broiler and layer breeding houses, respectively). However, DustTrak significantly underestimated PM10 concentrations in both houses. To correct for the monitoring bias by DustTrak, an average correction factor was derived from correlation analysis that characterized the ratio of DustTrak’s PM10 response to TEOM’s. The factor was calculated as 0.267 for the broiler house and 0.244 for the layer breeding house. Mie scattering simulation was performed to further verify the derived correction factors. A factor of 0.204 was estimated from the simulation, and it accorded well with experimental results. A dependence of the correction factor on PM10 concentration was noted in both poultry houses, indicating the feasibility of developing a concentration-dependent correction factor for future monitoring efforts. Such a relationship could also be explained by Mie scattering. This study is expected to facilitate a better understanding of the limitations and perspectives of the TSI DustTrak and other light scattering PM monitors for agricultural air quality research. Keywords: DustTrak, Mass concentration, Mie scattering, PM10, Poultry, TEOM.
Speciation and Geochemical Implications of Carcass Burial Leachate
Authors: Pratt Dyan L. , Fonstad Terrance A. 
Published: April 2018

Abstract. In the event of a mass livestock mortality situation, disposal routes such as burial are commonly chosen. The impact of burial on the environment could be substantial, but the composition of the leachate arising from a burial site has not been well documented. This study was performed to determine the chemical composition of leachate arising from animal mortalities in a burial setting. Three species of livestock were used: bovine, swine, and poultry. Leachate collected from lined burial pits over two years of decomposition was analyzed for major and minor ions. Analysis indicated that livestock mortality leachate contains, on average, concentrations of 46,000 mg L-1 of alkalinity (as bicarbonate), 12,600 mg L-1 of ammonium-N, 2600 mg L-1 of chloride, 3600 mg L-1 of sulfate, 2300 mg L-1 of potassium, 1800 mg L-1 of sodium, and 1500 mg L-1 of phosphorus, along with lesser amounts of iron, calcium, and magnesium. Select samples had maximum concentrations of ammonium-N and bicarbonate up to 50% higher than these average values. In comparison to earthen swine manure storages and landfills, the ionic strength of the leachate was 2 to 4 times higher, and therefore its impact on water resources could be greater. Following the study of the chemical composition of livestock mortality leachate, the potential impacts of this leachate on the soil/water systems below a burial site were investigated. The ionic strength of the leachate presents its own set of challenges. Basic modeling of ion activity using the five most common activity coefficient equations (Debye-Hückel, extended Debye-Hückel, Truesdell-Jones, Davies, and Pitzer) were considered to assess the sensitivity of these methods for calculated ion activity as impacted by the ionic strength of the leachate. This was completed to further enhance the modeling and speciation efforts. Based on the results and the applicability of the Truesdell-Jones equation, PHREEQC was used to assess the chemical speciation of the leachate. The speciation of this leachate provides evidence of phosphate and sulfate compounds available for potential unattenuated transport. Understanding the geochemical implications of livestock mortality burial will give scientists and regulators more information for performing future risk analyses when considering mortality burial as a management option, either routinely or during a mass mortality event. Keywords: Ion activity coefficient, Ionic strength, Leachate chemical composition, Livestock burial leachate, Speciation.
Greenhouse Gas Emissions from Beef Feedlot Surface Materials as Affected by Diet, Moisture, Temperature, and Time
Authors: Woodbury Bryan L. , Gilley John E. , Parker David B. , Stromer Bobbi S. 
Published: April 2018

Abstract. A laboratory study was conducted to measure the effects of diet, moisture, temperature, and time on greenhouse gas (GHG) emissions from feedlot surface materials (FSM). The FSM were collected from open-lot pens where beef cattle were fed either a dry-rolled corn (DRC) diet containing no wet distillers grains with solubles (WDGS) or a DRC diet containing 35% WDGS. The FSM were collected, air-dried or mixed with 3.0 L of water to represent dry or wet conditions, and then incubated at temperatures of 5°C, 15°C, 25°C, or 35°C. Static flux chambers were used to quantify GHG emissions over a 14-day period. Flux data for each diet × moisture combination were analyzed using repeated measures in time. The largest GHG emissions occurred under wet conditions at temperatures of 25°C and 35°C. Flux values for these conditions typically were significantly greater than measurements obtained on the same day at 5°C and 15°C. Mean emissions under wet conditions for CO2, CH4, and N2O were 35, 121, and 278 times greater, respectively, than emissions from dry FSM. The 0% WDGS diet produced mean CO2 and N2O flux measurements that were 1.8 and 1.5 times greater, respectively, than those obtained for the 35% WDGS diet. The 35% WDGS diet, in contrast, produced a mean CH4 emission rate that was 6 times greater than the 0% WDGS diet. Management for GHG mitigation should include design and/or maintenance of pen drainage to speed drying as well as the use of modified animal diets. Keywords: Air quality, Carbon dioxide, Confined animal feeding operations, Drainage, Emission rates, Feedlot, Greenhouse gas, Methane, Nitrous oxide, Pen design.
Assessment of Perennial Grass Inventories Predicted in the Billion-Ton Studies
Authors: Jones Daniela  Sofia , Searcy Stephen   W. , Eaton Laurence   M. 
Published: April 2018

Abstract. The U.S. Department of Energy (DOE) has estimated herbaceous biomass availability through simulations with the Policy Analysis System (POLYSYS) agricultural modeling framework. An operational assumption for POLYSYS limited conversion of pastureland to perennial grass crops to counties east of the 100th meridian as a proxy for precipitation sufficient for economically viable yield, but allowed cropland conversion regardless of location. Knowledge of local conditions raised questions about predicted biomass quantities for Texas counties in the 2011 assessment. POLYSYS was rerun with different assumptions, specifically replacing the 100th meridian boundary with annual average precipitation data and limiting cropland conversion in low-rainfall counties. Perennial grass production was found to be overestimated by 8% and 87% in the U.S. and Texas, respectively (at $66.14 DMg-1), when limiting all land conversion to regions with &gt;635 mm precipitation. Total herbaceous biomass predicted was approximately the same as in the BT2, but the biomass geographical location changed across the nation. Texas’ biomass contribution decreased from 6% to 1% at $66.14 DMg-1 and from 16% to 11% at $88.18 DMg-1. Subsequent to this research being conducted, the DOE released the 2016 biomass inventory assessment, and these results are compared to those newest estimates. Keywords: Billion-Ton Study, Biomass, Perennial grass, Precipitation, Switchgrass.
Spatial Variability of Soil Particle-Size Distribution Heterogeneity in Farmland
Authors: Liu Jilong , Zhang Lingling , Fu Qiang , Ren Gaoqi , Liu Lu , Yu Peng , Tan Siyuan 
Published: April 2018

Abstract. The objective of this research was to reveal the spatial variability of soil particle-size distribution heterogeneity. The farmland (48 m × 48 m) used in this study is located in the black soil region of northeast China and was divided into sixty-four 6 m × 6 m squares for sampling. The soil particle-size distribution was measured with a Mastersizer 2000. Soil particle-size distribution heterogeneity, the spatial variability of soil particle-size distribution heterogeneity, and the relationships between soil particle-size distribution heterogeneity and the clay, silt, and sand contents were studied by applying multifractal, geostatistical, and joint multifractal methods, respectively. The soil particle-size distribution had multifractal characteristics. Local information causing soil particle-size distribution heterogeneities were mainly low values of soil particle-size distribution; heterogeneities from the low-value side of the particle-size distribution were larger than those from the high-value side of the particle-size distribution. In the different soil layers, the degree of variation in soil particle-size distribution heterogeneities was moderate, with spatial correlation ranges of 37.82 m and moderate spatial dependences. At the single scale and multi-scale, the impacts of the clay, silt, and sand contents on the soil particle-size distribution heterogeneity changed with soil layer depth. The clay, silt, and sand contents had different degrees of influence on the spatial variability of soil particle-size distribution heterogeneity at the single scale and multi-scale. Multi-scale analysis could better reveal the degrees of influence of the above soil properties on the spatial variability of soil particle-size distribution heterogeneity. The results of this study enrich the knowledge of the spatial variability of soil properties and provide a reference and additional information for the quantitative characterization of soil particle-size distribution heterogeneity and soil management in this research area. Keywords: Geostatistics, Multifractal analysis, Relationship, Soil property.
Quantification of Odorants in Animal Feeds at Commercial Swine and Poultry Operations
Authors: Yang Xufei , Lorjaroenphon Yaowapa , Li Hong , Cadwallader Keith .  R , Wang Xinlei , Zhang Yuanhui 
Published: April 2018

Abstract. Odorants in animal feeds may come from various processes, such as fermentation and decay of feed ingredients, contamination by fecal materials, and sorption of volatiles in the air of animal houses. Those odorants may affect feed flavor and may serve as indicators of feed quality. The objective of this study was to examine the composition and concentration of odorants in animal feeds and to explore the variability of those odorants with animal operation type and season. Thirty-seven feed samples were collected from 14 swine and poultry operations in the U.S. Midwest and were submitted for gas chromatography-mass spectrometry (GC-MS) analysis. A total of 55 organic odorants were quantitated, including fatty acids, alcohols, aldehydes, ketones, phenols, and nitrogen-containing compounds. Those compounds together accounted for 0.46% ±0.20% of fresh feed mass, with the highest percentage (0.54% ±0.19%) found at layer hen houses and the lowest percentage (0.38% ±0.14%) at swine farrowing houses. Acetic acid and ethanol were most abundant, accounting for 0.22% ±0.13% and 0.13% ±0.07% of fresh feed mass, respectively. Fecal indicators, including indole and skatole, were &lt;5 ppm by mass. Principal component analysis (PCA) revealed that the variability in odorant composition was largely ascribed to two loading factors that were dominated by acetic acid and ethanol, respectively. The odorant composition of feed samples showed no significant effect by animal operation type, while a gradual seasonal change was noted. This study is expected to improve the understanding of the causes of odorants in animal feeds and their implications for animal health and production performance. Keywords: Animal feed, Animal operation, GC-MS, Odorant, Principal component analysis.