bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting effects of the onset of spring on reproductive success of Arctic-nesting geese
Authors: Nolet Bart A , Schreven Kees H T , Boom Michiel P , Lameris Thomas K
Published: November 2019

Breeding output of geese, measured as the proportion of juveniles in autumn or winter flocks, is lower in years with a late onset of spring in some species, but higher in at least one other species. Here we argue that this is because the timing of spring affects different stages of the reproductive cycle differently in different species. Because the effects on 2 different stages are opposite, the combined effects can result in either a positive or a negative overall effect. These stages are the pre-laying, laying, and nesting phase on the one hand; and the hatchling, fledgling, and juvenile phase on the other hand. The first phase is predominantly positively affected by an early snowmelt, with higher breeding propensity, clutch size, and nest success. The second phase in contrast is negatively affected by early snowmelt because of a mismatch with a nutrient food peak, leading to slow gosling growth and reduced survival. We argue that recognition of this chain of events is crucial when one wants to predict goose productivity and eventually goose population dynamics. In a rapidly warming Arctic, the negative effects of a mismatch might become increasingly important.
Quantifying functional impact of non-coding variants with multi-task Bayesian neural network
Authors: Xu Chencheng , Liu Qiao , Zhou Jianyu , Xie Minzhu , Feng Jianxing , Jiang Tao
Published: November 2019

Motivation

Advances in high-throughput genotyping and sequencing technologies during recent years have revealed essential roles of non-coding regions in gene regulation. Genome-wide association studies (GWAS) suggested that a large proportion of risk variants are located in non-coding regions and remain unexplained by current expression quantitative trait loci catalogs. Interpreting the causal effects of these genetic modifications is crucial but difficult owing to our limited knowledge of how regulatory elements function. Although several computational methods have been designed to prioritize regulatory variants that substantially impact human phenotypes, few of them achieve consistently high performance even when large-scale multi-omic data are integrated.

Results

We propose a novel multi-task framework based on Bayesian deep neural networks, MtBNN, to quantify the deleterious impact of single nucleotide polymorphisms in non-coding genomic regions. With the high-efficiency provided by the multi-task Bayesian framework to integrate information from different sources, MtBNN is capable of extracting features from genomic sequences of large-scale chromatin-profiling data, such as chromatin accessibility and transcript factor binding affinities, and calculating the distribution of the probability that a non-coding variant disrupts regulatory activities. A series of comprehensive experiments show that MtBNN quantifies the functional impact of cis-regulatory variations with high accuracy, including expression quantitative trait locus, DNase I sensitivity quantitative trait locus and functional genetic variants located within ATAC-peaks that affect the accessibility of the corresponding peak and achieves significantly better performance than the existing methods. Moreover, MtBNN has applications in the discovery of potentially causal disease-associated single-nucleotide polymorphisms (SNPs), thus helping fine-map the GWAS SNPs.

Availability and implementation

Code can be downloaded from https://github.com/Zoesgithub/MtBNN.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Chiral Bioconversion and Pharmacokinetic Analysis of Trelagliptin in Beagle Dog Plasma by LC–MS/MS
Authors: Zhou Li , Xi Wang , Zhang Hui , Sun Lili , Yu Jinlong , Zou Qiaogen
Published: November 2019

A simple and enantioselective method was developed and validated for the simultaneous determination of (R)- and (S)-trelagliptin in beagle dog plasma by chiral liquid chromatography tandem mass spectrometry. Trelagliptin enantiomers and (R)-rabeprazole (as internal standard, IS) were extracted from plasma samples by liquid–liquid extraction and separated on a CHIRALCEL OX-3R column using acetonitrile-5 ammonium bicarbonate as the mobile phase in gradient elution mode. The multiple reactions monitoring transitions of m/z 358.1→341.2 and 359.9→150.1 were used to quantify trelagliptin enantiomers and IS, respectively. This method was validated for sensitivity, specificity, linearity, precision, accuracy and stability of specific analytes under various conditions. And it was successfully applied to evaluating the pharmacokinetic profile of trelagliptin enantiomers in beagle dogs after single intravenous administration of (R)-trelagliptin injection (at 1 mg/kg) and oral administration (at 6.7 mg/kg). In this study, no chiral bioconversion of (R)-trelagliptin to (S)-trelagliptin in beagle dog plasma was observed. The absolute bioavailability of (R)-trelagliptin was identified to be 128.2%.
Acrylamide-Modified 3-Aminopropyltriethoxysilanes Hybrid Monomer for Highly Selective Imprinting Recognition of Theophylline
Authors: Lv Yaying , Qu Qi , Li Caiwen , Zhu Tao
Published: November 2019

The hybrid monomer synthesized with 3-aminopropyltriethoxysilanes and acrylamide was applied for synthesis of molecularly imprinting polymers, and the obtained polymers were used as sorbent in solid-phase extraction for purification of theophylline (THP) in green tea. The static adsorption curves showed better molecular recognition ability and binding capability of the polymers for the target. On the optimized condition, a method was developed for increasing extraction of THP with satisfactory recovery of 93.7%. Good calibration linearity obtained in a range of 5–500 μg·mL−1. The recoveries at three spiked levels ranged from 86.7% to 100.7% with relative standard deviations ≤6.6% (n = 3). The result showed that the obtained polymers exhibited highly selective imprinting recognition to the analyte, and the number of templates was an important factor affecting the selective recognition ability of polymers. The proposed method with hybrid monomer imprinting polymers was successfully applied for purification of THP in green tea.
Simultaneous Quantification of DPPG, DEPC and Cholesterol in Propofol Liposome by HPLC-ELSD Using Alkaline Hydrolysis
Authors: Shen Jie , Chen Zili , Yue Feng , Li Yanfei , Xu Zhiqin , Xu Xinjun
Published: November 2019

A high-performance liquid chromatography method with evaporative light-scattering detection (ELSD) was performed for simultaneous determination of dipalmitoyl phosphatidylglycerol (DPPG), dierucoyl phosphatidylcholine (DEPC) and cholesterol in propofol liposome by the pretreatment of alkaline hydrolysis (temperature, concentration of KOH anhydrous ethanol solution and reaction time were 90°C, 1 mol · L−1 and 10 min, respectively). The analysis was carried out on an Agilent TC-C18 column (4.6 mm × 250 mm, 5 μm) with isocratic elution of methanol and 0.1% acetic acid aqueous solution (95:5, v/v) at a flow rate of 1.0 mL · min−1. The column temperature was 30°C. The drift tube temperature of the ELSD system was set at 30°C, and the pressure of carrier gas was 350 KPa. The regression equation revealed a good linear relationship (r = 0.9990–0.9993) during the test ranges. The RSD of stability and repeatability (n = 6) was found to be less than 1.96 and 1.46%, respectively. The average recoveries ranged from 97.90 to 101.00%. The proposed method was validated and showed good precision, stability, repeatability and recovery, which indicated that the method could be readily utilized as a quality evaluation method for the determination of DPPG, DEPC and cholesterol in propofol liposome.
Anti-Müllerian hormone concentrations in women with chronic kidney disease
Authors: Wiles Kate , Anckaert Ellen , Holden Francesca , Grace Jan , Nelson-Piercy Catherine , Lightstone Liz , Chappell Lucy C , Bramham Kate
Published: November 2019

Background

Serum anti-Müllerian hormone (AMH) is a biomarker of ovarian reserve. There are limited data to guide the clinical interpretation of AMH in women with chronic kidney disease (CKD). The purpose of this study was to examine AMH concentrations in women with CKD compared with women without CKD.

Methods

We conducted a prospective cohort study of serum AMH concentrations in 163 non-pregnant women with CKD. Serum AMH concentrations were compared with age-specific AMH centiles from 887 healthy female controls.

Results

Participants included 30 women with Stage 1 CKD, 37 women with Stage 2 CKD, 26 women with Stage 3a CKD, 31 women with Stage 3b CKD and 39 women with Stages 4 and 5 CKD. The median estimated glomerular filtration rate (eGFR) was 51 (interquartile range 31–80) mL/min/1.73 m2. Serum AMH concentrations were lower in all CKD stages compared with women without CKD. Women ages 20–24 years with CKD had comparable serum AMH concentrations (median 1.959 ng/mL) to women ages 35–39 years without CKD (median 1.995 ng/mL). There was no evidence that eGFR was an independent modifier of serum AMH concentrations. More than half of women with CKD (58%) were predicted to have a low response to gonadotrophin stimulation.

Conclusions

Women with CKD have a lower ovarian reserve and are predicted to have a lower ovarian response to gonadotrophin stimulation compared with women without CKD of a similar age. Women with CKD who fail to conceive within 6 months of regular unprotected intercourse should be considered for fertility assessment and intervention.
A case report of heart transplant for ischaemic cardiomyopathy from lupus coronary vasculitis
Authors: Nandkeolyar Shuktika , Kim Hyungjin B , Doctorian Tanya , Stoletniy Liset N , Sandhu Vaneet K , Yu Micah , Zuppan Craig W , Razzouk Anees , Hilliard Anthony , Parwani Purvi
Published: November 2019

Background 

Coronary vasculitis is a rare, life-threatening complication of systemic lupus erythematosus (SLE).

Case summary

A 23-year-old woman with SLE presented with typical angina and worsening dyspnoea on exertion. Coronary angiography revealed severe triple vessel disease with a ‘string of beads’ appearance classic for coronary vasculitis. Transthoracic echocardiogram revealed ejection fraction of 25–30% with a severely hypokinetic distal septum and distal anterior wall and an akinetic apical wall. Despite vasculitis treatment with cyclophosphamide and pulse-dose steroids, her coronary vasculitis did not improve. She was refractory to anti-anginal and guideline-directed medical therapy for heart failure and successfully underwent orthotopic heart transplant (OHT).

Discussion 

This is the first reported case of OHT in the case of SLE coronary vasculitis. Chronic SLE coronary vasculitis is caused by lymphocyic infiltration leading to inflammation and fibrosis of the major epicardial coronary arteries but can be successfully managed with OHT when refractory to medical SLE and heart failure therapies. It can affect patients of all ages with SLE, emphasizing the importance of thorough history taking and clinical evaluation in young patients presenting with cardiac symptoms to establish an appropriate diagnosis and treatment plan.
Environmental control of Vibrio spp. abundance and community structure in tropical waters
Authors: Wong Yi You , Lee Choon Weng , Bong Chui Wei , Lim Joon Hai , Narayanan Kumaran , Sim Edmund Ui Hang
Published: November 2019

We measured Vibrio spp. distribution and community profile in the tropical estuary of Port Klang and coastal water of Port Dickson, Malaysia. Vibrio spp. abundance ranged from 15 to 2395 colony forming units mL−1, and was driven by salinity and chlorophyll a (Chl a) concentration. However, the effect of salinity was pronounced only when salinity was <20 ppt. A total of 27 Vibrio spp. were identified, and theVibrio spp. community at Port Dickson was more diverse (H′ = 1.94 ± 0.21). However species composition between Port Dickson and Port Klang were similar. Two frequently occurring Vibrio spp. were V. owensii and V. rotiferianus, which exhibited relatively higher growth rates (ANCOVA: F > 4.338, P < 0.05). Co-culture experiments between fast- and slow-growing Vibrio spp. revealed that fast-growing Vibrio spp. (r-strategists) were overwhelmed by slower-growing Vibrio spp. (K-strategists) when nutrient conditions were set towards oligotrophy. In response to resource availability, the intrinsic growth strategy of each Vibrio spp. determined its occurrence and the development of Vibrio spp. community composition.
Intraspecies cell–cell communication in yeast
Authors: Yashiroda Yoko , Yoshida Minoru
Published: November 2019

Although yeasts are unicellular microorganisms that can live independently, they can also communicate with other cells, in order to adapt to the environment. Two yeast species, the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe, engage in various kinds of intraspecies cell–cell communication using peptides and chemical molecules that they produce, constituting a sort of ‘language’. Cell–cell communication is a fundamental biological process, and its ultimate purpose is to promote survival by sexual reproduction and acquisition of nutrients from the environment. This review summarizes what is known about intraspecies cell–cell communication mediated by molecules including mating pheromones, volatile gases, aromatic alcohols and oxylipins in laboratory strains of S. cerevisiae and S. pombe.
Privatizations and efficiency. Evidences from the Italian iron and steel industry, 1979–2016
Authors: Brambilla Carlo , Lavista Fabio
Published: November 2019

Grounding on a new dataset gathering end-of-year financial statements of Italian steelmakers from 1979 to 2016, this article aims at assessing the effects of privatizations on the steelmaking industry, both in terms of changes in the industrial structure and of firms’ performance. It tries to verify whether privatizations fostered allocative efficiency and increased companies’ productive efficiency and innovative capabilities, and contributes to the debate on the alleged positive effects of privatizations on economic growth. In this respect, the article suggests some interesting insights both on the relationship between ownership and performance and on the outcomes of the Italian, as well as European, privatization processes of the fourth quarter of the 20th century.
Life expectancy of patients undergoing surgical aortic valve replacement compared with that of the general population
Authors: Hernandez-Vaquero Daniel , Diaz Rocio , Alperi Alberto , Almendarez Marcel G , Escalera Alain , Cubero-Gallego Hector , Avanzas Pablo , Moris Cesar , Pascual Isaac
Published: November 2019

OBJECTIVES

Surgical aortic valve replacement (SAVR) changes the natural history of severe aortic stenosis. However, whether the life expectancy of patients with severe aortic stenosis undergoing this surgical procedure is fully restored is unknown. The objective of this study was to assess if the life expectancy of patients aged >75 years is fully restored after undergoing surgery for severe aortic stenosis.

METHODS

We compared long-term survival of a group of patients aged >75 years, who underwent SAVR at our institution with the long-term survival of the general population. We matched each patient with 100 simulated individuals (control group) of the same age, sex and geographical region who died as indicated by the National Institute of Statistics. We compared survival curves and calculated hazard ratio (HR) or incidence rate ratio. Statistical significance existed if confidence intervals (CIs) did not overlap or did not include the value 1, as appropriate.

RESULTS

Average life expectancy of surgical patients who survived the postoperative period was 90.91 months (95% CI 82.99–97.22), compared to 92.94 months (95% CI 92.39–93.55) in the control group. One-, 5- and 8-year survival rates for SAVR patients who were discharged from the hospital were 94.9% (95% CI 92.74–96.43%), 71.66% (95% CI 67.37–75.5%) and 44.48% (95% CI 38.14–50.61%), respectively, compared to that of the general population: 95.8% (95% CI 95.64–95.95%), 70.64% (95% CI 70.28%–71%) and 47.91% (95% CI 47.52–48.31%), respectively (HR 1.07, 95% CI 0.94–1.22).

CONCLUSION

For patients over the age of 75 years who underwent SAVR and survived the postoperative period, life expectancy and survival rates were similar to that of the general population.
Effects of copper hydroxychloride and distillers dried grains with solubles on intestinal microbial concentration and apparent ileal and total tract digestibility of energy and nutrients by growing pigs1
Authors: Espinosa Charmaine D , Fry R Scott , Kocher Matthew E , Stein Hans H
Published: November 2019

An experiment was conducted to test the hypothesis that Cu hydroxychloride improves nutrient digestibility and alters the concentration of microbial protein in the small intestine or large intestine by pigs fed a corn-soybean meal diet or a diet based on corn, soybean meal, and distillers dried grains with solubles (DDGS). Twenty-four barrows (33.3 ± 3.4 kg) that had a T-cannula installed in the distal ileum were allotted to a 2 × 2 factorial design with 2 levels of DDGS (0% or 45%) and 2 levels of supplemental Cu from Cu hydroxychloride (0 or 150 mg/kg). A 2-period switch back design with the 4 diets and 6 replicate pigs per diet in each period was used resulting in 12 replicate pigs per diet for the 2 periods. The initial 9 d of each period was considered an adaptation period to the experimental diets. For each period, feces were collected on days 10, 11, and 12, and ileal digesta were collected for 8 h on days 13 and 14. Results indicated that inclusion of 45% DDGS to diets reduced (P < 0.05) the apparent ileal digestibility (AID) of AA and the AID and the apparent total tract digestibility (ATTD) of dry matter, gross energy, and crude protein. In contrast, inclusion of DDGS to diets increased (P < 0.05) the AID and the ATTD of acid hydrolyzed ether extract and the concentration of microbial protein in the hindgut (P < 0.05). However, the total concentration of volatile fatty acids (VFA) in ileal digesta and in feces from pigs fed the DDGS diets were not different from concentrations in pigs fed diets without DDGS. The AID and ATTD of dry matter, gross energy, and crude protein were not affected by dietary Cu concentrations, but the AID and ATTD of acid hydrolyzed ether extract were greater (P < 0.05) in diets supplemented with Cu hydroxychloride compared with diets without Cu hydroxychloride. There was also a reduction (P < 0.05) in the concentration of microbial protein and a tendency for a reduction (P < 0.10) in the total concentration of VFA in feces when diets were supplemented with Cu hydroxychloride. In conclusion, supplementation of Cu hydroxychloride to diets improved AID and ATTD of acid hydrolyzed ether extract and reduced the concentration of microbial protein in the large intestine and this effect was observed in diets containing DDGS as well as in diets without DDGS.
Bone Mineral Density Mapping of Iliosacral Region: The Use of Hounsfield Units to Optimize Transsacral Screw Trajectory
Authors: Nakamura Tawney , Fredericks Donald R , Saxena Sameer , Helgeson Melvin D , Wagner Scott C
Published: November 2019

Introduction

Trauma, degenerative, pediatric, and neuromuscular deformities often require placement of implants into sacrum for construct stability. In these scenarios, fixation to the ilium is often added. To date, multiple studies have validated the correlation between Hounsfield units (HU) as measured on computed tomography and bone mineral density (BMD) on dual-energy X-ray absorptiometry to assess bone quality and fracture risk. We sought to map the BMD of the iliosacral region at the S1 and S2 levels using HU.

Materials and Methods

Pelvic CT scans of 100 patients were evaluated. HU measurements were taken from the anterior and posterior ilium, sacral ala, and sacral body using a best-fit circle encompassing a maximal amount of cancellous bone. Following the collection of all data points, an analysis of variance model was created to test the means and standard deviations of each anatomic region.

Results

The highest mean BMD was found in the following locations (in descending order): S1 sacral body (279.72 HU, 95% confidence interval [CI], 261.75–297.69), S1 anterior ilium (254.45 HU, 95% CI, 236.64–272.27), S2 anterior ilium (229.88 HU, 95% CI, 211.39–248.36), and the S2 sacral body (191.58 HU, 95% CI, 173.31–209.85). Comparing the anterior ilium to the sacral ala, there was a higher BMD measurement at both the S1 level by 151.7 HU (p < 0.001) and the S2 level by 170.3 HU (p < 0.001). The anterior ilium also showed a significantly higher BMD when compared to measurements taken at the posterior ilium at the same level: at the S1 level by 100.5 HU (p < 0.001) and at the S2 level by 52.2 HU (p = 0.0006). The vertebral body had significantly higher mean BMD measurements when compared to the sacral ala at the S1 level by 176.9 HU (p < 0.001) and at the S2 level by 131.95 HU (p < 0.001).

Conclusions

The findings indicate that there is significantly higher BMD density of the anterior ilium and sacral body when compared to the sacral ala at both the S1 and S2 levels. In addition, the anterior ilium appears to provide more dense bone than the posterior ilium, as measured by mean HU.
Occult HBV Infection: A Case Series at a Military Treatment Facility
Authors: Pak Kevin , Ordway Sarah , Torres Dawn
Published: November 2019

Occult HBV infection (OBI) is defined as the presence of detectable hepatitis B virus (HBV) DNA in HBV surface antigen (HBsAg) negative individuals. Rarely, OBI is attributed to mutant HBV that cannot be detected by commercial assays, but most cases occur in the setting of chronic hepatitis B, particularly infection with wild-type viruses associated with strong HBV suppression. OBI is a high-risk diagnosis as it is associated with multiple complications: HBV reactivation in immunocompromised states, transmission of HBV, progression of liver disease, and hepatocellular carcinoma. The diagnosis is also easy to overlook, as the negative HBsAg in such cases can be falsely reassuring. This case series describes four male patients (mean age 51) who were diagnosed with OBI in the same military treatment facility between February 2018 and October 2018. Two of the four patients were active duty service members at the time of diagnosis. These patients had variable clinical presentations and outcomes. This case series illustrates the clinical significance of OBI and the importance of screening for OBI in HBsAg negative patients with signs of chronic or severe hepatic inflammation. It also prompts an intriguing question regarding the prevalence of both HBV and OBI in the United States military and whether or not routine screening for HBV should be implemented in this population. Further study is warranted to determine if adding HBV core antibody to a universally employed screening regimen would be beneficial.
SDSS-IV MaNGA: Bar pattern speed estimates with the Tremaine-Weinberg method and their error sources
Authors: Garma-Oehmichen L , Cano-Díaz M , Hernández-Toledo H , Aquino-Ort’iz E , Valenzuela O , Aguerri J A L , Sánchez S F , Merrifield M
Published: November 2019

Estimating the bar pattern speed (Ωbar) is one of the main challenges faced in understanding the role of stellar bars in galaxy dynamical evolution. This work aims to characterise different uncertainty sources affecting the Tremaine Weinberg (TW)-method to study the correlation between bar and galaxies physical parameters. We use a sample of 15 MaNGA SDSS-IV galaxies and 3 CALIFA galaxies from Aguerri et al. (2015). We studied the errors related with (i) galaxy centre determination, (ii) disc position angle (PA) emphasising the difficulties triggered by outer non-axisymmetric structures besides the bar, (iii) the slits length and (iv) the spatial resolution. In average, the PA uncertainties range $\sim 15 \%$, the slit length $\sim 9 \%$ and the centring error $\sim 5 \%$. Reducing the spatial resolution increases the sensitivity to the PA error. Through Monte Carlo simulations, we estimate the probability distribution of the $\mathcal {R}$ bar speed parameter. The present sample is composed of 7 slow, 4 fast and 7 ultrafast bars, with no trend with morphological types. Although uncertainties and low sample numbers may mask potential correlations between physical properties, we present a discussion of them: We observe an anti-correlation of Ωbar with the bar length and the stellar mass, suggesting that massive galaxies tend to host longer and slower bars. We also observe a correlation of the molecular gas fraction with $\mathcal {R}$, and a weak anti-correlation with Ωbar, suggesting that bars rotate slower in gaseous discs. Confirmation of such trends awaits future studies.
A Swift view of X-ray and UV radiation in the planet-forming T Tauri system PDS 70
Authors: Joyce Simon R G , Pye John P , Nichols Jonathan D , Page Kim L , Alexander Richard , Güdel Manuel , Metodieva Yanina
Published: November 2019

PDS 70 is a ∼5-Myr-old star with a gas and dust disc in which several protoplanets have been discovered. We present the first ultraviolet (UV) detection of the system along with X-ray observations taken with the Neil Gehrels Swift Observatory satellite. PDS 70 has an X-ray flux of 3.4 × 10−13 erg cm−2 s−1 in the 0.3–10.0 keV range, and UV flux (U band) of 3.5 × 10−13 erg cm−2 s−1 . At the distance of 113.4 pc determined from Gaia Data Release 2, this gives luminosities of 5.2 × 1029 and 5.4 × 1029 erg s−1, respectively. The X-ray luminosity is consistent with coronal emission from a rapidly rotating star close to the log $\frac{L_{\mathrm{X}}}{L_{\mathrm{bol}}} \sim -3$ saturation limit. We find the UV luminosity is much lower than would be expected if the star were still accreting disc material and suggest that the observed UV emission is coronal in origin.
Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage
Authors: Yubuki Naoji , Galindo Luis Javier , Reboul Guillaume , López-García Purificación , Brown Matthew W , Pollet Nicolas , Moreira David
Published: November 2019

Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.
Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation
Authors: Moran Rachel L , Catchen Julian M , Fuller Rebecca C
Published: November 2019

Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have examined prezygotic isolation in darters (Percidae), investigations into postzygotic barriers have remained rare due to long generation times and a lack of genomic resources. Orangethroat and rainbow darters naturally hybridize and provide a remarkable example of male-driven speciation via character displacement. Backcross hybrids suffer from high mortality, which appears to promote behavioral isolation in sympatry. To investigate the genomic architecture of postzygotic isolation, we used Illumina and PacBio sequencing to generate a chromosome-level, annotated assembly of the orangethroat darter genome and high-density linkage maps for orangethroat and rainbow darters. We also analyzed genome-wide RADseq data from wild-caught adults of both species and laboratory-generated backcrosses to identify genomic regions associated with hybrid incompatibles. Several putative chromosomal translocations and inversions were observed between orangethroat and rainbow darters, suggesting structural rearrangements may underlie postzygotic isolation. We also found evidence of selection against recombinant haplotypes and transmission ratio distortion in backcross hybrid genomes, providing further insight into the genomic architecture of genetic incompatibilities. Notably, regions with high levels of genetic divergence between species were enriched for genes associated with developmental and meiotic processes, providing strong candidates for postzygotic isolating barriers. These findings mark significant contributions to our understanding of the genetic basis of reproductive isolation between species undergoing character displacement. Furthermore, the genomic resources presented here will be instrumental for studying speciation in darters, the most diverse vertebrate group in North America.
Game theory, learning, and control systems
Authors: Shamma Jeff S
Published: November 2019

Game theory is the study of interacting decision makers, whereas control systems involve the design of intelligent decision-making devices. When many control systems are interconnected, the result can be viewed through the lens of game theory. This article discusses both long standing connections between these fields as well as new connections stemming from emerging applications.
The CHROME Study, a Real-world Experience of Single- and Multiple-Dose Oritavancin for Treatment of Gram-Positive Infections
Authors: Redell Mark , Sierra-Hoffman Miguel , Assi Maha , Bochan Markian , Chansolme David , Gandhi Anurag , Sheridan Kathleen , Soosaipillai Ivan , Walsh Thomas , Massey Jill
Published: November 2019

Background

Oritavancin (ORI) is a long-acting lipoglycopeptide indicated for the treatment of adult patients with acute bacterial skin and skin structure infections (ABSSSIs) caused or suspected to be caused by susceptible Gram-positive (GP) pathogens.

Methods

Data collected from a retrospective observational program (2014–2017), Clinical and Historic Registry and Orbactiv Medical Evaluation (CHROME), describe the utilization, outcomes, and adverse events (AEs) associated with ORI in 440 patients treated at 26 US sites for ABSSSI and other GP infections.

Results

Clinical success in evaluable patients receiving at least 1 dose of oritavancin was 88.1% (386/438). In a subgroup of patients who received ORI for skin and soft tissue infections (n = 401) and bacteremia (n = 7), clinical success was achieved in 89.0% and 100%, respectively. A cohort of 32 patients received 2–10 ORI doses separated by no more than 14 days for complicated GP infections. Clinical success was observed in 30 of 32 patients (93.8%), including 10 of 11 (90.9%) patients with bone and joint infections and 7 of 8 (87.5%) patients with osteomyelitis. In the safety evaluable population, the overall rate of AEs was 6.6%.

Conclusions

We describe results from a real-world program that includes the largest multicenter, retrospective, observational study in patients who received at least 1 dose of ORI for the treatment of GP infections. This study confirms that ORI is an effective, well-tolerated antibiotic used in single and multiple doses for the treatment of ABSSSIs and complicated GP infections.
Extracellular SPARC cooperates with TGF-β signalling to induce pro-fibrotic activation of systemic sclerosis patient dermal fibroblasts
Authors: Carvalheiro Tiago , Malvar Fernández Beatriz , Ottria Andrea , Giovannone Barbara , Marut Wioleta , Reedquist Kris A , Garcia Samuel , Radstake Timothy R
Published: November 2019

Objectives

SSc is an autoimmune disease characterized by inflammation, vascular injury and excessive fibrosis in multiple organs. Secreted protein acidic and rich in cysteine (SPARC) is a matricellular glycoprotein that regulates processes involved in SSc pathology, such as inflammation and fibrosis. In vivo and in vitro studies have implicated SPARC in SSc, but it is unclear if the pro-fibrotic effects of SPARC on fibroblasts are a result of intracellular signalling or fibroblast interactions with extracellular SPARC hampering further development of SPARC as a potential therapeutic target. This study aimed to analyse the potential role of exogenous SPARC as a regulator of fibrosis in SSc.

Methods

Dermal fibroblasts from both healthy controls and SSc patients were stimulated with SPARC alone or in combination with TGF-β1, in the absence or presence of a TGF receptor 1 inhibitor. mRNA and protein expression of extracellular matrix components and other fibrosis-related mediators were measured by quantitative PCR and western blot.

Results

Exogenous SPARC induced mRNA and protein expression of collagen I, collagen IV, fibronectin 1, TGF-β and SPARC by dermal fibroblasts from SSc patients, but not from healthy controls. Importantly, exogenous SPARC induced the activation of the tyrosine kinase SMAD2 and pro-fibrotic gene expression induced by SPARC in SSc fibroblasts was abrogated by inhibition of TGF-β signalling.

Conclusion

These results indicate that exogenous SPARC is an important pro-fibrotic mediator contributing to the pathology driving SSc but in a TGF-β dependent manner. Therefore, SPARC could be a promising therapeutic target for reducing fibrosis in SSc patients, even in late states of the disease.
NUMERICAL ANALYSIS OF SAFETY ZONE OF A LARGE FLAT-PLATE BOUNDED-WAVE EMP SIMULATOR
Authors: Huang Liuhong , Meng Cui , Li Yuebo , Yang Jie , Xiong Jiuliang , Wu Ping , Jiang Yunsheng
Published: November 2019

The safety zone of a large flat-plate bounded-wave electromagnetic pulse simulator was analyzed using the 3D electromagnetic simulation software Computer Simulation Technology. First, the double-limit requirement cited from the GB 8702 for an instantaneous pulse was clarified compared with the International Commission on Non-Ionizing Radiation Protection guidelines. This means that both the amplitude of the time-domain waveforms and all frequency components should be satisfied with the respective exposure limits. Then, the leakage field of a large flat-plate bounded-wave simulator was simulated. After analyzing the peak amplitude of an instantaneous electric field in a certain area, the observation points along six directions were specified, and the corresponding amplitudes were given. Furthermore, it was verified that the time-domain electric field of the critical points was satisfied with the frequency-domain exposure limits. Finally, the safety distances lower than the reference levels were given, and the safety zones corresponding to the three common exposure limits were obtained.
Ideological Legitimacy, Color-blindness, and Racially Conservative Organizations
Authors: Ebert Kim
Published: November 2019

Although scholars of racial inequality have investigated the transformation of racial ideologies in the post-Civil Rights Era, comparatively little research has been done on a corresponding transformation in racial advocacy organizing. Using an original dataset, I introduce racially conservative organizations, provide a history of their growth from 1960 to 2000, and estimate their formation in metropolitan areas over three decades to better specify the factors that led to their emergence. Measures of organizational strength, stability, and growth reveal that racially conservative organizations thrived relative to white extremist organizations in the second half of the 20th century, alongside the de-legitimation of explicit racism and rise of color-blind racism. The multivariate analysis indicates that metropolitan areas with increased political opportunities witnessed a greater likelihood of organizational formation among racial conservatives. In the 1970s, threats to dominant group interests emboldened racial conservatives and incited mobilization. However, in later decades, these conditions weakened dominant group interests in a way that deterred collective action. Racially conservative organizations are more likely to form in contexts that provide them with legitimacy to mobilize around racially sensitive issues. The findings challenge past research that conflates racial conservatism and white extremism and assumes that they share the same determinants.
Inquiry-oriented differential equations: a guided journey of learning
Authors: Habre Samer
Published: November 2019

This study conducted at the Lebanese American University in spring 2018 reports on an inquiry-oriented differential equations class where the course curriculum falls within the realm of Realistic Mathematics Education. The focus of the study is on some curriculum tasks and how they assist students reinvent successfully key mathematical notions covered in most introductory differential equations courses. While the results show remarkable cognitive gains in understanding and thinking, reinventing knowledge was demanding and in some cases required the intervention of the instructor to control and lead the discussion. Results also show that the lack of appropriate mathematical knowledge was sometimes an obstacle for the reinvention process, and the traditional view of mathematical learning a hindrance for accepting that an inquiry-oriented approach can fulfil the course outcomes.
Maternal and fetal blood pharmacokinetics and organ distribution of atrazine, propazine, simazine and their metabolites in pregnant rats after chronic oral administration
Authors: Brandhonneur Nolwenn , Hutin Vincent , Chevrier Cécile , Cordier Sylvaine , Le Corre Pascal
Published: November 2019

Environmental contamination by chlorotriazines has been evidenced in mother-child cohort suggesting more detailed risk assessment of these compounds in drinking water. Exposure of rodents to atrazine has been associated to alterations of endocrine and reproductive functions by disrupting neuroendocrine control at hypothalamus level. Perinatal exposure to low doses of atrazine has been associated to reproductive dysfunction, and to behavioral abnormalities in adult exposed during embryogenesis. The objectives of the current investigation were to (1) evaluate the influence of physico-chemical properties of chlorotriazines on tissue distribution in pregnant rats and in fetuses, (2) gain a better understanding of fetal distribution of chlorotriazines in specific tissues, particularly in brain.

Serial blood samples were obtained from pregnant rats after administration of atrazine (ATZ), propazine (PRO) and simazine (SIM) via oral route at a dose of 10 mg/kg from day 15 to day 19. Maternal and fetal tissues were harvested at day 20, 24 hrs after the last dosing.

The metabolic extraction ratio was estimated to 87% suggesting a significant first-pass effect explaining the low oral bioavailability. Blood exposure to parent compounds (ATZ, PRO and SIM) was negligible (lower than 5%) compared to metabolite exposure. The main metabolite exposure involved diamino-s-chlorotriazine (DACT), ranging from 60 to 90% depending on the molecules administered. A correlation between tissue-to-blood ratio and physico-chemical descriptors were observed for fat and mammary gland tissues but not for brain in adult rats. A more pronounced distribution in fetal brain was observed for ATZ and PRO, the two most lipophilic compounds.
Role of pharmacogenetics in rifampicin pharmacokinetics and the potential effect on TB–rifampicin sensitivity among Ugandan patients
Authors: Mukonzo Jackson K , Kengo Allan , Kutesa Bisaso , Nanzigu Sarah , Pohanka Anton , McHugh Timothy D , Zumla Alimuddin , Aklillu Eleni
Published: November 2019

Background

Suboptimal anti-TB drugs exposure may cause multidrug-resistant TB. The role of African predominant SLCO1B1 variant alleles on rifampicin pharmacokinetics and the subsequent effect on the occurrence of Mycobacterium tuberculosis–rifampicin sensitivity needs to be defined. We describe the rifampicin population pharmacokinetics profile and investigate the relevance of SLCO1B1 genotypes to rifampicin pharmacokinetics and rifampicin-TB sensitivity status.

Methods

Fifty patients with TB (n=25 with rifampicin-resistant TB and n=25 with rifampicin-susceptible TB) were genotyped for SLOC1B1 rs4149032 (g.38664C>T), SLOC1B1*1B (c.388A>G) and SLOC1B1*5 (c.521 T>C). Steady state plasma rifampicin levels were determined among patients infected with rifampicin-sensitive TB. Data were analysed using NONMEM to estimate population rifampicin pharmacokinetics as well as the effect of SLOC1B1 genotypes on rifampicin pharmacokinetics and on rifampicin-TB sensitivity status.

Results

Overall allele frequencies of SLOC1B1 rs4149032, *1B and *5 were 0.66, 0.90 and 0.01, respectively. Median (IQR) Cmax and Tmax were 10.2 (8.1–12.5) mg/L and 1.7 (1.125–2.218) h, respectively. Twenty-four percent of patients exhibited Cmax below the recommended 8–24 mg/L range. SLOC1B1 genotypes, gender and age did not influence rifampicin pharmacokinetics or TB-rifampicin sensitivity.

Conclusions

Although SLOC1B1 genotype, age and gender do not influence either rifampicin pharmacokinetics or rifampicin-TB sensitivity status, one in every four Ugandan TB patients achieve subtherapeutic plasma rifampicin concentrations.
Molecular phylogeny of Ceriantharia (Cnidaria: Anthozoa) reveals non-monophyly of traditionally accepted families
Authors: Forero Mejia Anny C , Molodtsova Tina , Östman Carina , Bavestrello Giorgio , Rouse Greg W
Published: November 2019

We present an integrative study with molecular phylogenetic reconstructions and morphological assessment across the three Ceriantharia families: Arachnactidae, Botrucnidiferidae and Cerianthidae. The Arachnactidae specimens (Isarachnanthus spp.) form a well-supported clade, whereas Cerianthidae and Botrucnidiferidae are not recovered as monophyletic. Consequently, the validity of the suborder Spirularia is questioned. Cerianthus was recovered as polyphyletic and Ceriantheomorphe may prove to be a junior synonym of Cerianthus. The taxonomic position of Cerianthus cf. mortenseni is also discussed. All specimens identified on morphology as belonging to Pachycerianthus are recovered as a clade. Further revision of taxa within Ceriantharia is necessary. Molecular phylogenetic analyses based on six mitochondrial or nuclear loci place Ceriantharia as sister to Hexacorallia s.s., but with no significant support relative to an alternative hypothesis that it is the sister taxon to Octocorallia. Further molecular sequence data and taxon sampling will be needed to resolve the position of Ceriantharia.
Efficacy and Profitability of Insecticide Treatments for Tomato Spotted Wilt Management on Peanut in South Carolina
Authors: Anco Daniel J. , Thomas James S. , Monfort Walter S.
Published: November 2019

Tomato spotted wilt (TSW) is a common and serious disease of peanut (Arachis hypogaea L.) caused by Tomato spotted wilt virus (TSWV; family Tospoviridae, genus Orthotospovirus). Management frequently uses an integrated approach, with cultivar resistance and application of in-furrow insecticide as two critical components. In-furrow insecticides help suppress thrips, which can injure and stunt young growing plants and transmit TSWV, with postemergent application of acephate capable of providing additional thrips control. To examine effects of systemic insecticides (imidacloprid, imidacloprid plus fluopyram, phorate, and acephate) on TSW management, yield, and economic return across cultivar susceptibilities (susceptible, moderately susceptible, and resistant) in South Carolina, a meta-analysis was used to synthesize results from 32 studies conducted between 2009 and 2018. Although efficacy and magnitude of individual treatments varied with susceptibility, imidacloprid increased, whereas phorate generally decreased TSW incidence relative to nontreated controls. In-furrow treatments followed by acephate further reduced TSW incidence and increased profitability. All examined treatments improved yield compared with untreated peanuts except for susceptible cultivars treated with imidacloprid. Imidacloprid plus fluopyram increased yield more than imidacloprid alone for the susceptible group, although there was little difference between these treatments in association with moderately susceptible cultivars. When comparing individual applications, phorate was overall the most profitable option across susceptibilities, although imidacloprid plus fluopyram exhibited analogous profitability for susceptible cultivars. Results from this study can be used to assist producer selection of management options for TSW in peanut.
Resistance of Wheat Genotypes to Root-Lesion Nematode (Pratylenchus thornei) Can be Used to Predict Final Nematode Population Densities, Crop Greenness, and Grain Yield in the Field
Authors: Thompson J. P. , Sheedy J. G. , Robinson N. A.
Published: November 2019

The root-lesion nematode Pratylenchus thornei is a major pathogen of wheat (Triticum aestivum) in many regions globally. Resistance of wheat genotypes to P. thornei can be determined from final nematode population densities in glasshouse experiments but combining results across multiple experiments presents challenges. Here, we use a factor analytic method for multiexperiment analysis of final population densities of P. thornei for 1,096 unique wheat genotypes in 22 glasshouse experiments. The resistance to P. thornei of the genotypes was effectively represented by a two-factor model with rotation of the axes to a principal components solution. Principal axes 1 and 2 (PA1 and PA2) accounted for 79 and 11% of the genetic variance, respectively, over all experiments. Final population densities of P. thornei as empirical best linear unbiased predictors (PA[1+2]-eBLUPs) from the combined glasshouse experiments were highly predictive (P < 0.001) of final nematode population densities in the soil profile, crop canopy greenness (normalized difference vegetation index), and grain yield of wheat genotypes in P. thornei-infested fields in the Australian subtropical grain region. Nine categories of resistance ratings for wheat genotypes from resistant to very susceptible were based on subdivision of the range of PA(1+2)-eBLUPs for use in growers’ sowing guides. Nine genotypes were nominated as references for future resistance experiments. Most (62%) Australian wheat genotypes were in the most susceptible three categories (susceptible, susceptible to very susceptible, and very susceptible). However, resistant germplasm characterized in this study could be used in plant breeding to considerably improve the overall resistance of Australian wheat crops.