bluuebunny/crossref_metadata_2025_split huggingface dataset:
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins
Authors: Liu Yumeng , Wang Xiaolong , Liu Bin 
Published: February 2020

AbstractAs an important type of proteins, intrinsically disordered proteins/regions (IDPs/IDRs) are related to many crucial biological functions. Accurate prediction of IDPs/IDRs is beneficial to the prediction of protein structures and functions. Most of the existing methods ignore the fully ordered proteins without IDRs during training and test processes. As a result, the corresponding predictors prefer to predict the fully ordered proteins as disordered proteins. Unfortunately, these methods were only evaluated on datasets consisting of disordered proteins without or with only a few fully ordered proteins, and therefore, this problem escapes the attention of the researchers. However, most of the newly sequenced proteins are fully ordered proteins in nature. These predictors fail to accurately predict the ordered and disordered proteins in real-world applications. In this regard, we propose a new method called RFPR-IDP trained with both fully ordered proteins and disordered proteins, which is constructed based on the combination of convolution neural network (CNN) and bidirectional long short-term memory (BiLSTM). The experimental results show that although the existing predictors perform well for predicting the disordered proteins, they tend to predict the fully ordered proteins as disordered proteins. In contrast, the RFPR-IDP predictor can correctly predict the fully ordered proteins and outperform the other 10 state-of-the-art methods when evaluated on a test dataset with both fully ordered proteins and disordered proteins. The web server and datasets of RFPR-IDP are freely available at http://bliulab.net/RFPR-IDP/server.
DIMERBOW: exploring possible GPCR dimer interfaces
Authors: García-Recio Adrián , Navarro Gemma , Franco Rafael , Olivella Mireia , Guixà-González Ramon , Cordomí Arnau 
Published: February 2020

Abstract

Motivation
G protein-coupled receptors (GPCRs) can form homo-, heterodimers and larger order oligomers that exert different functions than monomers. The pharmacological potential of such complexes is hampered by the limited information available on the type of complex formed and its quaternary structure. Several GPCR structures in the Protein Data Bank display crystallographic interfaces potentially compatible with physiological interactions.

Results
Here, we present DIMERBOW, a database and web application aimed to visually browse the complete repertoire of potential GPCR dimers present in solved structures. The tool is suited to help finding the best possible structural template to model GPCR homomers.

Availability and implementation
DIMERBOW is available at http://lmc.uab.es/dimerbow/.

Supplementary information
Supplementary data are available at Bioinformatics online.
High levels of androgens cause chondrocyte accumulation and loss of smooth muscle in the mouse penile body†
Authors: Hiremath Deepak S , Geerling Elizabeth C , Hai Lan , Narayan Prema 
Published: February 2020

AbstractAndrogens are essential for penile development and for maintaining penile structural and functional integrity. Loss of androgen levels or function results in a decrease in smooth muscle content, accumulation of adipocytes in the corpora cavernosa, and inhibition of erectile function. Our previous studies with a mouse model (KiLHRD582G) of constitutive luteinizing hormone receptor activity also showed structural abnormalities in the penis caused by a decrease in smooth muscle content, accumulation of chondrocytes, and sexual dysfunction. As KiLHRD582G mice exhibit very high levels of testosterone at all postnatal ages, the goal of this study was to determine if the elevated androgen levels were responsible for the morphological changes in the penis. Implantation of testosterone capsules in wild-type mice at neonatal (2 weeks) and postpubertal (5 weeks) ages resulted in the accumulation of chondrocytes in the corpora cavernosa of the adult animals. Mice implanted with testosterone capsules at 2 weeks of age exhibited a 4-fold increase in serum testosterone with a 1.5-fold loss of smooth muscle at 24 weeks of age. Collagen content was unchanged. Only 57% of testosterone implanted mice were fertile at 24 weeks of age. Mice implanted with testosterone capsules at 5 weeks of age showed no decrease in smooth muscle content at 24 weeks, although serum testosterone levels were elevated 5-fold. Implantation with dihydrotestosterone also resulted in chondrocyte accumulation and a 2-fold loss in smooth muscle content. Together, these studies demonstrate that supraphysiological levels of androgens cause structural changes in the penile corpora cavernosa and impair fertility.
Qualification and Clinical Validation of an Immunodiagnostic Assay for Detecting 11 Additional Streptococcus pneumoniae Serotype–specific Polysaccharides in Human Urine
Authors: Kalina Warren V , Souza Victor , Wu Kangjian , Giardina Peter , McKeen Andrew , Jiang Qin , Tan Charles , French Roger , Ren Yanhua , Belanger Kelly , McElhiney Susan , Unnithan Manu , Cheng Huiming , Mininni Terri , Giordano-Schmidt Donna , Gessner Bradford D , Jansen Kathrin U , Pride Michael W 
Published: February 2020

Abstract

Background
Identifying Streptococcus pneumoniae serotypes by urinary antigen detection (UAD) assay is the most sensitive way to evaluate the epidemiology of nonbacteremic community-acquired pneumonia (CAP). We first described a UAD assay to detect the S. pneumoniae serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F, covered by the licensed 13-valent S. pneumoniae conjugate vaccine. To assess the substantial remaining pneumococcal disease burden after introduction of several pneumococcal vaccines, a UAD-2 assay was developed to detect 11 additional serotypes (2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F) in individuals with radiographically confirmed CAP.

Methods
The specificity of the UAD-2 assay was achieved by capturing pneumococcal polysaccharides with serotype-specific monoclonal antibodies, using Luminex technology. Assay qualification was used to assess accuracy, precision, and sample linearity. Serotype positivity was based on cutoffs determined by nonparametric statistical evaluation of urine samples from individuals without pneumococcal disease. The sensitivity and specificity of the positivity cutoffs were assessed in a clinical validation, using urine samples obtained from a large study that measured the proportion of radiographically confirmed CAP caused by S. pneumoniae serotypes in hospitalized US adults.

Results
The UAD-2 assay was shown to be specific and reproducible. Clinical validation demonstrated assay sensitivity and specificity of 92.2% and 95.9% against a reference standard of bacteremic pneumonia. In addition, the UAD-2 assay identified a S. pneumoniae serotype in 3.72% of nonbacteremic CAP cases obtained from hospitalized US adults. When combined with bacteremic CAP cases, the proportion of pneumonias with a UAD-2 serotype was 4.33%.

Conclusions
The qualified/clinically validated UAD-2 method has applicability in understanding the epidemiology of nonbacteremic S. pneumoniae CAP and for assessing the efficacy of future pneumococcal conjugate vaccines that are under development.
Vascular endothelial S1pr1 ameliorates adverse cardiac remodelling via stimulating reparative macrophage proliferation after myocardial infarction
Authors: Kuang Yashu , Li Xiaolin , Liu Xiuxiang , Wei Lu , Chen Xiaoli , Liu Jie , Zhuang Tao , Pi Jingjiang , Wang Yanfang , Zhu Chenying , Gong Xin , Hu Hao , Yu Zuoren , Li Jiming , Yu Ping , Fan Huimin , Zhang Yuzhen , Liu Zhongmin , Zhang Lin 
Published: February 2020

Abstract

Aims
Endothelial cell (EC) homoeostasis plays an important role in normal physiological cardiac functions, and its dysfunction significantly influences pathological cardiac remodelling after myocardial infarction (MI). It has been shown that the sphingosine 1-phosphate receptor 1 (S1pr1) was highly expressed in ECs and played an important role in maintaining endothelial functions. We thus hypothesized that the endothelial S1pr1 might be involved in post-MI cardiac remodelling.

Methods and results
Our study showed that the specific loss of endothelial S1pr1 exacerbated post-MI cardiac remodelling and worsened cardiac dysfunction. We found that the loss of endothelial S1pr1 significantly reduced Ly6clow macrophage accumulation, which is critical for the resolution of inflammation and cardiac healing following MI. The reduced reparative macrophages in post-MI myocardium contributed to the detrimental effects of endothelial S1pr1 deficiency on post-MI cardiac remodelling. Further investigations showed that the loss of endothelial S1pr1-reduced Ly6clow macrophage proliferation, while the pharmacological activation of S1pr1-enhanced Ly6clow macrophage proliferation, thereby ameliorated cardiac remodelling after MI. A mechanism study showed that S1P/S1pr1 activated the ERK signalling pathway and enhanced colony-stimulating factor 1 (CSF1) expression, which promoted Ly6clow macrophage proliferation in a cell-contact manner. The blockade of CSF1 signalling reversed the enhancing effect of S1pr1 activation on Ly6clow macrophage proliferation and worsened post-MI cardiac remodelling.

Conclusion
This study reveals that cardiac microvascular endothelium promotes reparative macrophage proliferation in injured hearts via the S1P/S1PR1/ERK/CSF1 pathway and thus ameliorates post-MI adverse cardiac remodelling.
Nitrogen concentration affects amphotericin B and fluconazole tolerance of pathogenic cryptococci
Authors: Bosch Caylin , Toplis Barbra , Vreulink Jo-Marie , Volschenk Heinrich , Botha Alfred 
Published: February 2020

ABSTRACT
Environmental stress often causes phenotypic changes among pathogenic cryptococci, such as altered antifungal susceptibility, changes in capsule and melanin formation, as well as altered levels of the membrane sterol and antifungal target, ergosterol. We therefore hypothesised that nitrogen limitation, a prevalent environmental stress in the natural habitat of these yeasts, might affect virulence and antifungal susceptibility. We tested the effect of different nitrogen concentrations on capsule, melanin and ergosterol biosynthesis, as well as amphotericin B (AmB) and fluconazole (FLU) susceptibility. This was achieved by culturing cryptococcal strains representing Cryptococcus neoformans and Cryptococcus gattii in media with high (0.53 g/l), control (0.42 g/l) and low (0.21 g/l) NH4Cl concentrations. India ink staining was used to determine capsule thickness microscopically, while melanin and ergosterol content were determined spectrophotometrically. We found that lower nitrogen concentrations enhanced both ergosterol and capsule biosynthesis, while a variable effect was observed on melanisation. Evaluation of drug tolerance using time-kill methodology, as well as tests for FLU heteroresistance, revealed that the low nitrogen cultures had the highest survival percentages in the presence of both AmB and FLU, and showed the highest frequency of FLU heteroresistance, suggesting that nitrogen concentration may indeed influence drug tolerance.
On the generation and segregation of helicity in geodynamo simulations
Authors: Ranjan A , Davidson P A , Christensen U R , Wicht J 
Published: February 2020

SUMMARY
Helicity, the inner product of velocity and vorticity, is considered an important ingredient for the maintenance of a dipolar magnetic field in the geodynamo. Outside the tangent cylinder—an imaginary cylinder which circumscribes the inner core—a spatial segregation of helicity has been observed in several simulations, being negative in the north and positive in the south. Such a segregation pattern is important for a dynamo that relies on the α-effect. However, the origin of this pattern in these simulations is poorly understood. In this paper, we use three strongly forced numerical dynamo solutions to study the various sources of helicity, including those due to buoyancy $({H_T})$, Coriolis, Lorentz and viscous forces. We find a strong spatial correlation between the segregation pattern of helicity and ${H_T}$ both in the instantaneous and the time-averaged results. Our results show that, outside the tangent cylinder, ${H_T}$ is dominated by the product $- {u_z}\partial T/\partial \varphi $, where ${u_z}$ is the vertical velocity component and T is the temperature perturbation. It is known that when inertial waves are launched from a localized buoyant anomaly, ${H_T}$ takes the same sign as the local helicity. We conjecture that this is the reason for the spatial correlation between ${H_T}$ and helicity in our simulation results. The flow in our simulations being strongly turbulent, this effect seems to be a statistical one and manifests itself most clearly in the averaged quantities.
Effects of salinity and pH on the spectral induced polarization signals of graphite particles
Authors: Wu Yuxin , Peruzzo Luca 
Published: February 2020

SUMMARY
The electrical property of micrometre-sized graphite particles was investigated under different particle concentration, particle size, fluid conductivity and pH conditions. Due to its large internal electronic conductivity and ability to polarize under external potential field, significant enhancement of its spectral induced polarization (SIP) responses is observed when graphite is included in sand mixtures. While a small amount of graphite inclusion significantly increases the SIP response of its mixtures with sand, further concentration increase does not necessarily lead to a proportional increase of the SIP response. This is shown to be related to the formation of graphite aggregates at higher concentrations. Changes of fluid salinity have a significant effect on graphite's SIP behaviour. This includes a positive impact on normalized chargeability and imaginary conductivity, but a negative impact on chargeability and relaxation time constant. The effect of pH on the SIP response of graphite is small but shows consistent trend, where pH increase leads to a decrease of both the chargeability and relaxation time constant. The underlying cause of this effect is not clear.
On the influence of different misfit functions for attenuation estimation in viscoelastic full-waveform inversion: synthetic study
Authors: Pan Wenyong , Wang Yanfei 
Published: February 2020

SUMMARY
Estimating subsurface attenuation distribution is essential to compensate the amplitude and phase distortions in seismic imaging and characterize attenuative reservoirs. Full-waveform inversion (FWI) methods represent promising techniques to invert for both velocity and attenuation models with arbitrary spatial distributions. However, simultaneously determining velocity and attenuation properties introduces the problem of interparameter trade-off in viscoelastic FWI. Ignoring attenuation effects can result in inaccurate velocity estimations. Velocity errors may produce significant parameter crosstalk artefacts in the inverted attenuation models. An appropriate misfit function measuring specific seismic attribute is essential to capture the influence of attenuation on the seismic data and thus is expected to reduce the influences of velocity errors for attenuation estimation. In this study, we evaluate the performances of different misfit functions for attenuation estimation in viscoelastic FWI accompanied with a two-stage sequential inversion strategy. Synthetic examples with different acquisition surveys are given to show that in the presence of strong velocity errors, the amplitude-based misfit functions, including envelope-difference, root-mean-square amplitude-ratio and spectral amplitude-ratio, can invert for the attenuation models more reliably, compared to the waveform-difference and instantaneous phase misfit functions. With the two-stage inversion approach, more reliable velocity and attenuation models can be obtained using viscoelastic FWI.
Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies
Authors: Wong Chao-Jen , Wang Leo H , Friedman Seth D , Shaw Dennis , Campbell Amy E , Budech Chris B , Lewis Leann M , Lemmers Richard J F L , Statland Jeffrey M , van der Maarel Silvère M , Tawil Rabi N , Tapscott Stephen J 
Published: February 2020

Abstract
Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to the discovery of candidate therapeutics, and it is important to identify markers of disease activity to inform clinical trial design. For drugs that inhibit DUX4 expression, measuring DUX4 or DUX4-target gene expression might be an interim measure of drug activity; however, only a subset of FHSD muscle biopsies shows evidence of DUX4 expression. Our prior study showed that MRI T2-STIR-positive muscles had a higher probability of showing DUX4 expression than muscles with normal MRI characteristics. In the current study, we performed a 1-year follow-up assessment of the same muscle with repeat MRI and muscle biopsy. There was little change in MRI characteristics over the 1-year period and, similar to the initial evaluation, MRI T2-STIR-postive muscles had a higher expression of DUX4-regulated genes, as well as genes associated with inflammation, extracellular matrix and cell cycle. Compared to the initial evaluation, overall the level of expression in these gene categories remained stable over the 1-year period; however, there was some variability for each individual muscle biopsied. The pooled data from both the initial and 1-year follow-up evaluations identified several FSHD subgroups based on gene expression, as well as a set of genes—composed of DUX4-target genes, inflammatory and immune genes and cell cycle control genes—that distinguished all of the FSHD samples from the controls. These candidate markers of disease activity need to be replicated in independent datasets and, if validated, may provide useful measures of disease progression and response to therapy.
Simultaneous Determination of Vitamins B1 and B6 by Nuclear Magnetic Resonance Spectrometry
Authors: Hassan Saad S M 
Published: February 2020

Abstract
A new, simple, and rapid quantitative nuclear magnetic resonance method has been developed for simultaneous determination of vitamins B1 and B6 in mixtures in the presence of vitamin B2 without prior separation. The peak areas of 2 resonance lines at δ2.55 and 2.65 ppm are used. Maleic acid (δ = 6.6 ppm) is used as a reference standard, and the integral peak areas are referred to it. The method was tested with synthetically prepared mixtures containing from 0.05 to 1.5mM of each vitamin and was applied to the analysis of some pharmaceutical preparations. The results show an average recovery of 98% of both vitamins. Vitamin B2 does not interfere, if present.
Analysis of Fat-Soluble Vitamins. XVII. Comparison of Chemical and Biological Assays of Vitamin D
Authors: Mulder Frits J , Strik Roel 
Published: February 2020

Abstract
Two methods, the chemical assay using maleic anhydride addition and the British Standard Institution chick bioassay, were used to analyze samples from vitamin D3 resin batches manufactured over a period of about 4 years. Statistical analysis of data obtained for vitamin D shows that (1) the reproducibility of the chemical assay has a coefficient of variation of 0.7% ; (2) the chemical assay is suitable for controlling the dilution procedure of resins in oil, the product variability being represented by a coefficient of variation of 1.7% ; (3) the agreement between the average values obtained by the bioassay and the chemical method is satisfactory (geometric mean ratio = 99.7%, n = 39); (4) the chick bioassay has 95% limits of variation of about ±30% for single results.
Multiple Internal Standard Technique for the Gas-Liquid Chromatographic Determination of Indole in Shrimp
Authors: Staruszkiewicz Walter F , Bond John F 
Published: February 2020

Abstract
A multiple internal standard technique has been developed for the official first action gas-liquid chromatographic (GLC) method for determining indole in shrimp. The modification was developed because interfering GLC peaks are occasionally observed when 2-methylindole is used as the internal standard. An internal standard solution containing 1-methylindole, 2- methylindole, and diphenylamine was added to extracts of shrimp before silica gel cleanup and separation by GLC. All of the compounds were quantitatively recovered and were separated on the GLC column under identical experimental conditions. Extracts of acceptable shrimp to which indole was added at levels of 3–10 μg/ 100 g and extracts of decomposed shrimp were stored at room temperature for 2 weeks. Average and maximum changes (μg indole/100 g) during storage were, respectively, for each internal standard: average 0.6, 0.4, and 1.1; maximum 1.7, 0.9, and 2.9.
Collaborative Study of Three Methods for the Determination of Fluoride in Vegetation
Authors: Jacobson Jay S , Heller Laurence I 
Published: February 2020

Abstract
A procedure is described for determining Kepone (decachlorooctahydro-l,3,4-metheno-2ffcyclobuta[ cd]pentalene-2-one) residues in avian egg, liver, and tissue. Samples were extracted with benzene-isopropanol, and the extract was cleaned up with fuming H2S04-concentrated H2SO4. Kepone was separated from organochlorine pesticides and polychlorinated biphenyls on a Florisil column and analyzed by electron capture gas-liquid chromatography (GLC). The average recovery from spiked tissues was 86%. The analyses performed on 14 bald eagle carcasses and livers, 3 bald eagle eggs, and 14 osprey eggs show measurable levels which indicate that Kepone accumulates in the tissues of fish-eating birds. Residues were confirmed by GLC-mass spectrometry
Foam-Charcoal Chromatography for Analysis of Polychlorinated Dibenzodioxins in Herbicide Orange
Authors: Huckins James N , Stalling David L , Smith William A 
Published: February 2020

Abstract
Herbicide Orange (HO) is a mixture of n-butyl esters of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). The 2,4,5-T is known to contain 2,3, 7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) and other chlorinated aromatic contaminants. Adsorption of TCDD from HO on small amounts of powdered charcoal results in sample cleanup adequate for electron capture gas-liquid chromatographic (GLC) analysis. Column flow restrictions with powdered charcoal are overcome by using polyurethane foams as a dispersive support, HO is dissolved in chloroform and percolated through a column containing a mixture of PX-21 activated carbon suspended on clean polyurethane foam (14.9% charcoal/ 85.1% foam, w/w). Subsequently, the column is washed with benzene, and TCDD is recovered with toluene-benzene (1+1). Samples containing less than 1 μg TCDD/ml required additional sample cleanup on activated alumina prior to GLC analysis. The average recovery of TCDD determined from 4 replicate radiometric measurements was 91.4% (standard error = 4.0). TCDD residues greater than 0.02 μg/ml in HO samples were quantitated by electron capture GLC after cleanup. The presence of TCDD and pentachlorodibenzo-p-dioxin was confirmed by GLC-mass spectroscopy. In addition, tetrachloro- and pentachlorodibenzofurans were inferred by GLC-mass spectrometry.
Automated Determination of Phosphorus in Fertilizers Collaborative Study
Authors: Johnson Frank J 
Published: February 2020

Abstract
An automated method for determining total and direct available P2O5 in fertilizers was compared to the official final action gravimetric quinolinium molybdophosphate and spectrophotometric molybdovanadate methods in a collaborative study. Ten samples were sent to 10 collaborators for analysis. Eight complete sets of data were returned, and the ninth collaborator returned data for direct available phosphorus by the automated method only. The data were statistically analyzed by the technique of closely matched pairs. No significant overall difference was found between methods or among collaborators. The automated method has been adopted as official first action for phosphorus.