bluuebunny/crossref_metadata_2025 huggingface dataset:
Simultaneous Determination of Antazoline and Naphazoline by the Net Analyte Signal Standard Addition Method and Spectrophotometric Technique
Authors: Asadpour-Zeynali Karim , Ghavami Raoof , Esfandiari Roghayeh , Soheili-Azad Payam
Published: February 2020

A novel net analyte signal standard addition method (NASSAM) was used for simultaneous determination of the drugs anthazoline and naphazoline. The NASSAM can be applied for determination of analytes in the presence of known interferents. The proposed method is used to eliminate the calibration and prediction steps of multivariate calibration methods; the determination is carried out in a single step for each analyte. The accuracy of the predictions against the H-point standard addition method is independent of the shape of the analyte and interferent spectra. The net analyte signal concept was also used to calculate multivariate analytical figures of merit, such as LOD, selectivity, and sensitivity. The method was successfully applied to the simultaneous determination of anthazoline and naphazoline in a commercial eye drop sample.
Evaluation of Preservative Effectiveness of Liquid Crystalline Systems with Retynil Palmitate by the Challenge Test and D-value
Authors: Chorilli Marlus , Leonardi Gislaine Ricci , Nunes Salgado Hérida Regina , Scarpa Maria Virgínia
Published: February 2020

The objective of this work was to evaluate the preservative effectiveness of liquid crystalline systems containing retynil palmitate (RP) by the challenge test (CT) and D-value. A system was developed containing water, silicon glycol copolymer, and polyether functional siloxane with 1% RP added. The analyses were carried out by methods in the U.S. Pharmacopeia (USP 31, 2008) using the microorganisms Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans, and Aspergillus niger. The CT showed that after 7 days, all microorganisms were eliminated except A. niger, which maintained viability for at least 28 days after inoculation. Moreover, the microorganisms E. coli, P. aeruginosa, S. aureus, C. albicans and A. niger presented different growth behaviors, evidenced by differences among the D-values calculated. It was concluded that the CT and D-value were efficient methods for evaluation of the preservative property of these formulations.
Synchronous High-Performance Liquid Chromatography with a Photodiode Array Detector and Mass Spectrometry for the Determination of Citrinin, Monascin, Ankaflavin, and the Lactone and Acid Forms of Monacolin K in Red Mold Rice
Authors: Wu Cheng-Lun , Kuo Yao-Haur , Lee Chun-Lin , Hsu Ya-Wen , Pan Tzu-Ming
Published: February 2020

The Monascus fermentation product red mold rice (RMR) has been found to contain the cholesterol-lowering agent monacolin K (MK) in both its lactone (MKL) and acid (MKA) forms and the mycotoxin citrinin (CT). The yellow pigments in RMR, namely, monascin (MS) and ankaflavin (AK), have been reported to exhibit antimetastatic and antiangiogenic activities. Currently, MK and these yellow pigments are usually detected in RMR by different analytical methods that are inconvenient, expensive, and time-consuming. The goal of this study was to establish a rapid, synchronous analytical method for determination of the MKA, MKL, MS, AK, and CT levels in RMR. MKA, MKL, MS, AK, and CT were extracted by the same extraction method, then separated by RP-HPLC with a C18 column. The effluent from the column was passed through a photodiode array detector and then introduced directly into a fluorescence detector. The results showed that high recovery rates of MKA, MKL, MS, AK, and CT are possible if RMR powder is extracted with 75% ethanol (10 mL) at 80°C for 30 min. With regard to the optimal conditions of the HPLC, the peaks of MKA, MKL, MS, AK, and CT can be clearly separated from any noise peaks by isocratic elution with a mobile phase comprising 0.05% trifluoroacetic acid in acetonitrile–water (62.5 + 37.5, v/v).
A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance
Authors: Handy Sara M , Deeds Jonathan R , Ivanova Natalia V , Hebert Paul D N , Hanner Robert H , Ormos Andrea , Weigt Lee A , Moore Michelle M , Yancy Haile F
Published: February 2020

The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5′ end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.
Disposable Screen-Printed Electrode Coupled with Recombinant Drosophila melanogaster Acetylcholinesterase and Multiwalled Carbon Nanotubes for Rapid Detection of Pesticides
Authors: Tang Zhuzhao , Chen Haode , Song Shiping , Fan Chunhai , Zhang Dabing , Wu Aibo
Published: February 2020

Recombinant Drosophila melanogaster acetylcholinesterase (R-DmAChE), multiwalled carbon nanotubes (MWCNTs), and Prussian blue have been combined for development of a three-electrode biosensor with more rapid responses and higher stability than in our previous study. A new disposable screen-printed electrode (SPE) was developed for rapid detection of organophosphate and carbamate pesticides. After optimization, 10 μg MWCNT and 5 μL enzyme immobilization solution consisting of 0.2% glutaraldehyde, 0.1% Nafion®, 0.2% bovine serum albumin, 0.1 g/L MWCNT, and 1.5 mU R-DmAChE were fixed on each of the R-DmAChE/MWCNT SPEs. The LOD of this biosensor was 0.5 μg/L for pesticide standards of dichlorvos (DDV) and carbofuran. The performance of this biosensor was tested for vegetable and water samples at various spiked levels, and good stability and sensitivity were found. The obtained recoveries were from 82.6 to 110.5% for DDV at levels of 0.5–5 μg/L and 73.4 to 118.4% for carbofuran at 1–10 μg/L in lake and sea water samples, demonstrating that the proposed approach is an alternative means for rapid detection of pesticide residues and contaminants in food safety and environmental monitoring.
Development of a Quantitative Multiclass/Multiresidue Method for 21 Veterinary Drugs in Shrimp
Authors: Li Hui , Kijak Philip J
Published: February 2020

A multiclass/multiresidue method has been developed and validated for the determination of 21 veterinary drug residues in shrimp, including sulfonamides (sulfadiazine, sulfamerazine, sulfamethazine, sulfachloropyridazine, sulfadimethoxine, and sulfaquinoxaline); tetracyclines (oxytetracycline, tetracycline, and chlortetracycline); (fluoro)quinolones (norfloxacin, ciprofloxacin, enrofloxacin, sarafloxacin, difloxacin, flumequine, oxolinic acid, and nalidixic acid); and cationic dyes (malachite green, gentian violet, leucomalachite green, and leucogentian violet), using HPLC/MS/MS. All drugs were quantifiable over a no less than 10-fold range with matrix-matched standards for linear external calibration, except for oxytetracycline, tetracycline, norfloxacin, and ciprofloxacin, for which norfloxacin-d5 was used as an internal standard. Two grams of preground shrimp sample was extracted twice with extractant at two different pH values. The combined supernatant was further diluted with an aqueous internal standard solution, and 50 L extract was injected into the HPLC instrument. An online SPE system was set up for automated sample cleanup. A triple quadrupole mass spectrometer equipped with an electrospray ionization source was operated in the multiple-reaction-monitoring mode to acquire data. The method has been validated at three levels within the designated linear ranges for each drug, with accuracies between 77 and 115, and most CV values below 15.
Development and Validation of a High-Performance Thin-Layer Chromatographic Method for Determination of Ofloxacin Residues on Pharmaceutical Equipment Surfaces
Authors: Vovk Irena , Simonovska Breda
Published: February 2020

An HPTLC method with densitometric quantification using fluorescence at 313 nm was developed and validated for the determination of ofloxacin residue in controlling pharmaceutical equipment cleanliness. Simulated samples at a residue level of 1 mg/m2 were prepared by spreading the calculated amount of ofloxacin solution on 1, 5, and 10 dm2 stainless steel surfaces. After evaporation of the solvent, the residue was removed by two ethanol wetted cotton swabs, which were thereafter extracted with the mixture of ethanol and Na2EDTA–water solution at pH 11 for 15 min with sonication. The extract and standards were applied on HPTLC silica gel 60 plates and then developed in a horizontal developing chamber from both sides using ethanol-conc. ammonia (4 + 1, v/v) as the mobile phase. The mean recovery (n = 6) at 1 mg/m2 from 1, 5, and 10 dm2 was 95.3, 88.6, and 89.7% with the CV values 3.78, 4.41, and 4.97%, respectively. The absolute detection limit was 0.6 ng and the quantitation limit was 2 ng, but it was shown that these can be improved by immersion of the developed plate into a solution of liquid paraffin–n-hexane (1 + 2, v/v) to approximately 0.25 and 0.9 ng, respectively. The LOD of the method using detection without paraffin–n-hexane was 3, 0.6, and 0.3 μg/m2 by swabbing 1, 5, and 10 dm2, respectively. The method can be applied to routine control of pharmaceutical equipment cleanliness by sampling from stainless steel surface areas of 1 to 10 dm2 with acceptable residue limit/surface of 1 mg/m2.
Advantages of Automation in Plasma Sample Preparation Prior to HPLC/MS/MS Quantification: Application to the Determination of Cilazapril and Cilazaprilat in a Bioequivalence Study
Authors: Kolocouri Filomila , Dotsikas Yannis , Apostolou Constantinos , Kousoulos Constantinos , Soumelas Georgios-Stefanos , Loukas Yannis L
Published: February 2020

An HPLC/MS/MS method characterized by complete automation and high throughput was developed for the determination of cilazapril and its active metabolite cilazaprilat in human plasma. All sample preparation and analysis steps were performed by using 2.2 mL 96 deep-well plates, while robotic liquid handling workstations were utilized for all liquid transfer steps, including liquid–liquid extraction. The whole procedure was very fast compared to a manual procedure with vials and no automation. The method also had a very short chromatographic run time of 1.5 min. Sample analysis was performed by RP-HPLC/MS/MS with positive electrospray ionization using multiple reaction monitoring. The calibration curve was linear in the range of 0.500–300 and 0.250–150 ng/mL for cilazapril and cilazaprilat, respectively. The proposed method was fully validated and proved to be selective, accurate, precise, reproducible, and suitable for the determination of cilazapril and cilazaprilat in human plasma. Therefore, it was applied to a bioequivalence study after per os administration of 2.5 mg tablet formulations of cilazapril.
Determination of Fat-Soluble Vitamins and Carotenoids in Standard Reference Material 3280 Multivitamin/Multielement Tablets by Liquid Chromatography with Absorbance Detection
Authors: Thomas Jeanice B , Sharpless Katherine E , Yen James H , Rimmer Atherine
Published: February 2020

The concentrations of selected fat-soluble vitamins and carotenoids in Standard Reference Material (SRM) 3280 Multivitamin/Multielement Tablets have been determined by two independent LC methods, with measurements performed by the National Institute of Standards and Technology (NIST). This SRM has been prepared as part of a collaborative effort between NIST and the National Institutes of Health Office of Dietary Supplements. The SRM is also intended to support the Dietary Supplement Ingredient Database that is being established by the U.S. Department of Agriculture. The methods used at NIST to determine the concentration levels of vitamins A and E, and β-carotene in the SRM used RPLC with absorbance detection. The relative precision of these methods ranged from 2 to 8% for the analytes measured. SRM 3280 is primarily intended for use in validating analytical methods for the determination of selected vitamins, carotenoids, and elements in multivitamin/multielement tablets and similar matrixes.
Determination of Disulfiram by Micellar Liquid Chromatography in Illicit Preparations
Authors: mourya Sandeep-Kumar , Dubey Swati , Durgabanshi Abhilasha , Kumar Shukla Sudheer , Esteve-Romero Josep , Bose Devasish
Published: February 2020

Presently, disulfram is used in aversion therapy for recovering alcoholics. It acts by inhibiting aldehyde dehydrogenase, leading to high blood levels of acetaldehyde. A simple direct injection micellar liquid chromatographic procedure was developed to determine disulfram in illicit preparations (ayurvedic, herbal, divine ash, and traditional medicine), as well as inpharmaceuticals and biological samples (urine). After application of a predictive optimization strategy, the proposed method was developed using a 0.1 M sodium dodecyl sulfate-butanol 4% (v/v) buffered to pH 7 as the mobile phase at a ﬂow rate of 1 mL/min, an octyl silyl (C8) 150 mm column, and diode array detection at 248 nm. Under the above conditions, the analysis time was below 8 min. Validation studies were based on U.S. Food and Drug Administration guidelines. The LOD (3 × SD criterion) was 15 ng/mL and LOQ (10 × SD criterion) was 70 ng/mL for disulfram. The intraday and interday precisions were below 3.5%, recoveries were in the range of 97–102%, and robustness was below 3%. The optimized and validated micellar liquid chromatographic method was successfully applied to the determination of disulfram in ayurvedic, herbal, divine ash, and other samples. The procedure developed could also be used in the felds of QC, routine analysis, and pharmacokinetic studies.
Development of Standard Method Performance Requirements for Biological Threat Agent Detection Methods
Authors: Coates Scott G , Brunelle Sharon L , Davenport Matthew G
Published: February 2020

Standards and third-party testing are necessary to demonstrate the performance and limitations of biological threat agent (biothreat) detection technologies to allow appropriate response actions by end-users and responders. In order to address this need, the Department of Homeland Security, Science and Technology Directorate has funded AOAC INTERNATIONAL to develop standards and perform conformity assessment. AOAC formed the Stakeholder Panel on Agent Detection Assays to develop consensus performance criteria (standard method performance requirements; SMPRs) for methods that detect biothreats. This paper documents the development of the frst fve biothreat SMPRs, including the voluntary consensus process, the components of an SMPR, the use of SMPRs in developing validation protocols, and a description of the development efforts and considerations for each of the current SMPRs.
Evaluation of Applied Biosystems MicroSEQ® Real-Time PCR System for Detection of Listeria monocytogenes in Food
Authors: Tebbs Robert S , Balachandran Priya , Wong Lily Y , Zoder Patrick , Furtado Manohar R , Petrauskene Olga V , Cao Yanxiang
Published: February 2020

Increasingly, more food companies are relying on molecular methods, such as PCR, for pathogen detection due to their improved simplicity, sensitivity, and rapid time to results. this report describes the validation of a new Real-time PCR method to detect Listeria monocytogenes in nine different food matrixes. the complete system consists of the MicroSEQ®L. monocytogenes Detection Kit, sample preparation, the Applied Biosystems 7500 Fast Real-time PCR instrument, and RapidFinder™ Express software. two sample preparation methods were validated: the PrepSEQ® Nucleic Acid extraction kit and the PrepSEQ Rapid Spin sample preparation kit. the test method was compared to the ISO 11290-1 reference method using an unpaired-study design to detect L. monocytogenes in roast beef, cured bacon, lox (smoked salmon), lettuce, whole cow's milk, dry infant formula, ice cream, salad dressing, and mayonnaise. the MicroSEQ L. monocytogenes Detection Kit and the ISO 11290-1 reference method showed equivalent detection based on Chi-square analysis for all food matrixes when the samples were prepared using either of the two sample preparation methods. An independent validation confirmed these findings on smoked salmon and whole cow's milk. the MicroSEQ kit detected all 50 L. monocytogenes strains tested, and none of the 30 nontargeted bacteria strains.
Modification of the BAX®Salmonella Test Kit to Include a Hot Start Functionality (Modification of AOAC Official MethodSM 2003.09)
Authors: Wallace F Morgan , DiCosimo Deana , Farnum Andrew , Tice George , Andaloro Bridget , Davis Eugene , Burns Frank R
Published: February 2020

In 2010, the BAX® System PCR assay for Salmonella was modified to include a hot start functionality designed to keep the reaction enzyme inactive until PCR begins. To validate the assay's Official Methods of Analysis status to include this procedure modification, an evaluation was conducted on four food types that were simultaneously analyzed with the BAX System and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual or the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook reference method for detecting Salmonella. Identical performance between the BAX System method and the reference methods was observed. Additionally, lysates were analyzed using both the BAX System Classic and BAX System Q7 instruments with identical results using both platforms for all samples tested. Of the 100 samples analyzed, 34 samples were positive for both the BAX System and reference methods, and 66 samples were negative by both the BAX System and reference methods, demonstrating 100% correlation. No instrument platform variation was observed. Additional inclusivity and exclusivity testing using the modified test kit demonstrated the test kit to be 100% accurate in evaluation of test panels of 352 Salmonella strains and 46 non-Salmonella strains.
Differential roles of two DDX17 isoforms in the formation of membraneless organelles
Authors: Hirai Yuya , Domae Eisuke , Yoshikawa Yoshihiro , Tomonaga Keizo
Published: February 2020

The RNA helicase, DDX17 is a member of the DEAD-box protein family. DDX17 has two isoforms: p72 and p82. The p82 isoform has additional amino acid sequences called intrinsically disordered regions (IDRs), which are related to the formation of membraneless organelles (MLOs). Here, we reveal that p72 is mostly localized to the nucleoplasm, while p82 is localized to the nucleoplasm and nucleoli. Additionally, p82 exhibited slower intranuclear mobility than p72. Furthermore, the enzymatic mutants of both p72 and p82 accumulate into the stress granules. The enzymatic mutant of p82 abolishes nucleolar localization of p82. Our findings suggest the importance of IDRs and enzymatic activity of DEAD-box proteins in the intracellular distribution and formation of MLOs.
Production decline analysis of shale gas based on a probability density distribution function
Authors: Yuan Yingzhong , Qi Zhilin , Chen Zhangxing , Yan Wende , Zhao Zhiheng
Published: February 2020

Production decline analysis is a simple and efficient method to forecast production dynamics of shale gas. The traditional Arps decline model is also widely used in the production decline analysis of shale gas, but an obvious error is often generated. Based on the Weibull and χ2 probability density distribution function, the monotonic decreasing production prediction equations of shale gas are established. It is deduced that recently, the widely used Duong model is essentially a Weibull probability density distribution model. Decline analysis results of production data from actual shale gas well and numerical simulations indicate that the fitting results of the Weibull (Duong) model and χ2 distribution model are better than the Arps model whose deviation of early data is large. For a shale gas reservoir with very low permeability, pressure conformance area is small and it is obviously influenced by fractures. Early shale gas production rate mainly contributed to by fractures declines quickly and the later production rate mainly contributed to by the matrix declines slowly over time. The production decline curve has obvious long-tail distribution characteristics and it is a better fit to the data with a χ2 distribution model. As for the increase of permeability, the fitting accuracy of the Weibull (Duong) model gradually becomes better than the χ2 distribution model. Research results provide theoretical guidance for choosing a reasonable production decline model of a shale gas reservoir with a different permeability.
Infrared variability due to magnetic pressure-driven jets, dust ejection and quasi-puffed-up inner rims
Authors: Liffman Kurt , Bryan Geoffrey , Hutchison Mark , Maddison Sarah T
Published: February 2020

The interaction between a YSO stellar magnetic field and its protostellar disc can result in stellar accretional flows and outflows from the inner disc rim. Gas flows with a velocity component perpendicular to disc mid-plane subject particles to centrifugal acceleration away from the protostar, resulting in particles being catapulted across the face of the disc. The ejected material can produce a ‘dust fan’, which may be dense enough to mimic the appearance of a ‘puffed-up’ inner disc rim. We derive analytical equations for the time-dependent disc toroidal field, the disc magnetic twist, the size of the stable toroidal disc region, the jet speed, and the disc region of maximal jet flow speed. We show how the observed infrared variability of the pre-transition disc system LRLL 31 can be modelled by a dust ejecta fan from the inner-most regions of the disc whose height is partially dependent on the jet flow speed. The greater the jet flow speed, the higher is the potential dust fan scale height. An increase in mass accretion on to the star tends to increase the height and optical depth of the dust ejection fan, increasing the amount of 1–8 µm radiation. The subsequent shadow reduces the amount of light falling on the outer disc and decreases the 8–40 µm radiation. A decrease in the accretion rate reverses this scenario, thereby producing the observed ‘see-saw’ infrared variability.
Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response
Authors: Aichmüller Christian F , Iskar Murat , Jones David T W , Korshunov Andrey , Radlwimmer Bernhard , Kool Marcel , Ernst Aurelie , Pfister Stefan M , Lichter Peter , Zapatka Marc
Published: February 2020

Background

Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well studied, data of the complete methylome, tumor cell composition, and immune infiltration are scarce.

Methods

We generated whole genome bisulfite sequence (WGBS) data of 9 PAs and 16 control samples and integrated available 154 PA and 57 control methylation array data. RNA sequence data of 49 PAs and 11 control samples as well as gene expression arrays of 248 PAs and 28 controls were used to assess transcriptional activity.

Results

DNA-methylation patterns of partially methylated domains suggested high stability of the methylomes during tumorigenesis. Comparing tumor and control tissues of infra- and supratentorial location using methylation arrays revealed a site specific pattern. Analysis of WGBS data revealed 9381 significantly differentially methylated regions (DMRs) in PA versus control tissue. Enhancers and transcription factor (TF) motifs of five distinct TF families were found to be enriched in DMRs. Methylation together with gene expression data–based in silico tissue deconvolution analysis indicated a striking variation in the immune cell infiltration in PA. A TF network analysis showed a regulatory relation between basic leucine zipper (bZIP) transcription factors and genes involved in immune-related processes.

Conclusion

We provide evidence for a link of focal methylation differences and differential gene expression to immune infiltration.
Downregulation of a Mitochondrial NAD+ Transporter (NDT2) Alters Seed Production and Germination in Arabidopsis
Authors: Feitosa-Araujo Elias , de Souza Chaves Izabel , Florian Alexandra , da Fonseca-Pereira Paula , Condori Apfata Jorge Alberto , Heyneke Elmien , Medeiros David Barbosa , Pires Marcel Viana , Mettler-Altmann Tabea , Neuhaus H Ekkehard , Palmieri Ferdinando , Ara�jo Wagner L , Obata Toshihiro , Weber Andreas P M , Linka Nicole , Fernie Alisdair R , Nunes-Nesi Adriano
Published: February 2020

Despite the fundamental importance of nicotinamide adenine dinucleotide (NAD+) for metabolism, the physiological roles of NAD+ carriers in plants remain unclear. We previously characterized the Arabidopsis thaliana gene (At1g25380), named AtNDT2, encoding a protein located in the mitochondrial inner membrane, which imports NAD+ from the cytosol using ADP and AMP as counter-exchange substrates for NAD+. Here, we further investigated the physiological roles of NDT2, by isolating a T-DNA insertion line, generating an antisense line and characterizing these genotypes in detail. Reduced NDT2 expression affected reproductive phase by reducing total seed yield. In addition, reduced seed germination and retardation in seedling establishment were observed in the mutant lines. Moreover, remarkable changes in primary metabolism were observed in dry and germinated seeds and an increase in fatty acid levels was verified during seedling establishment. Furthermore, flowers and seedlings of NDT2 mutants displayed upregulation of de novo and salvage pathway genes encoding NAD+ biosynthesis enzymes, demonstrating the transcriptional control mediated by NDT2 activity over these genes. Taken together, our results suggest that NDT2 expression is fundamental for maintaining NAD+ balance amongst organelles that modulate metabolism, physiology and developmental processes of heterotrophic tissues.
Disciplining Difference(s): Reproducing Inequalities through Disciplinary Interactions in Preschool
Authors: Gansen Heidi M
Published: February 2020

This article offers an expansive conceptualization and examination of young children’s experiences of school discipline inequalities, which includes the variety of behavior management approaches (i.e., punitive discipline and positive discipline) that preschool teachers differentially use in response to students’ behavior (e.g., noncompliance). I draw on data from ethnographic observations in three preschools (nine classrooms total) with different racial and socioeconomic classroom compositions. I find that teachers’ varying approaches to behavior management for students from particular racial, gender, and socioeconomic backgrounds (i.e., low-SES girls and middle-class black boys) contributes to children’s hierarchical identity groups within preschool classrooms: “good kids” vs. “troublemaking kids.” Specifically, the messages children at Imagination Center received from teachers’ differential disciplinary responses to low-SES girls’ behaviors, and the messages children at Kids Company received from teachers’ differential disciplinary responses to middle-class black boys’ behaviors, shaped their understandings of whom they should or should not associate with. The findings reveal how school-level disciplinary practices/cultures (e.g., positive discipline rather than punitive discipline) can help to alleviate disciplinary inequalities apparent in some preschool classrooms. Additionally, these data illuminate how preschool teachers’ differential approaches to behavior management affect some marginalized students’ experiences of discipline inequalities as early as preschool.
Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification
Authors: Yeo Darren , Srivathsan Amrita , Meier Rudolf
Published: February 2020

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($>$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94–407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($>$200 bp). Only very short mini-barcodes (<200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $>$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.]
Predicting successes and failures of clinical trials with an ensemble LS-SVR
Authors: Hong Zhen-Yu , Shim Jooyong , Son Woo Chan , Hwang Changha
Published: February 2020

Abstract

For a variety of reasons, most drug candidates cannot eventually pass the drug approval process. Thus, developing reliable methods for predicting clinical trial outcomes of drug candidates is crucial in improving the success rate of drug discovery and development. In this study, we propose an ensemble classifier based on weighted least squares support vector regression (LS-SVR) for predicting successes and failures of clinical trials. The efficacy of the proposed ensemble classifier is demonstrated through an experimental study on PrOCTOR dataset, which consists of informative chemical features of the drugs and target-based features. Comparing random forest and other models, the proposed ensemble classifier obtains the highest value for the area under the receiver operator curve (AUC). The results of this study demonstrate that the proposed ensemble classifier can be used to effectively predict drug approvals.
Nomogram for the prediction of in-hospital incidence of acute respiratory distress syndrome in patients with acute pancreatitis
Authors: Ding Ning , Guo Cuirong , Huang Yuchai , Li Changluo , Zhou Yang , Yang Guifang , Chai Xiangping
Published: February 2020

Objective

The aim of this study was to formulate and validate an individualized predictive nomogram for in-hospital incidence of acute respiratory distress syndrome (ARDS) in patients with acute pancreatitis(AP).

Design

It was a retrospective cohort study.

Setting

Departments of Emergency Medicine of two university-affiliated tertiary hospitals, Changsha, China.

Participants

From January 2017 to December 2018, 779 individuals with AP were included in this study.

Primary outcome measures

The in-hospital incidence of ARDS was assessed.

Results

AP patients were randomly distributed into primary cohort(n=560)and validation cohort(n=219). Based on the primary cohort, risk factors were identified by logistic regression model and a nomogram was performed. Five independent factors including white blood counts(WBC),prothrombin time(PT),albumin(ALB),serum creatinine(SCR) and triglyceride (TG) were associated with in-hospital incidence of ARDS in AP patients. A nomogram was constructed based on the five independent factors with primary cohort of AUC 0.821 and validation cohort of AUC 0.822. Calibration curve analysis indicated that the predicted probability was in accordance with the observed probability in both primary and validation cohorts.

Conclusions

The study developed an intuitive nomogram with easily available laboratory parameters for the prediction of in-hospital incidence of ARDS in patients with AP. The incidence of ARDS for an individual patient can be fast and conveniently evaluated by our nomogram.

Strengths and limitations of this study

This is the first study to develop a nomogram for predicting the in-hospital incidence of ARDS in AP patients.

For each AP patient, our nomogram enables physicians to directly and conveniently calculate a numeric probability of ARDS.

There might be patient selection biases owing to retrospective nature of our study.
Comparison of High-Throughput Single-Cell RNA Sequencing Data Processing Pipelines
Authors: Gao Mingxuan , Ling Mingyi , Tang Xinwei , Wang Shun , Xiao Xu , Qiao Ying , Yang Wenxian , Yu Rongshan
Published: February 2020

With the development of single-cell RNA sequencing (scRNA-seq) technology, it has become possible to perform large-scale transcript profiling for tens of thousands of cells in a single experiment. Many analysis pipelines have been developed for data generated from different high-throughput scRNA-seq platforms, bringing a new challenge to users to choose a proper workflow that is efficient, robust and reliable for a specific sequencing platform. Moreover, as the amount of public scRNA-seq data has increased rapidly, integrated analysis of scRNA-seq data from different sources has become increasingly popular. How-ever, it remains unclear whether such integrated analysis would be biased if the data were processed by different upstream pipelines. In this study, we encapsulated seven existing high-throughput scRNA-seq data processing pipelines with Nextflow, a general integrative workflow management framework, and evaluated their performances in terms of running time, computational resource consumption, and data processing consistency using nine public datasets generated from five different high-throughput scRNA-seq platforms. Our work provides a useful guideline for the selection of scRNA-seq data processing pipelines based on their performances on different real datasets. In addition, these guidelines can serve as a performance evaluation framework for future developments in high-throughput scRNA-seq data processing.
Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures
Authors: Ruffolo Jeffrey A. , Guerra Carlos , Mahajan Sai Pooja , Sulam Jeremias , Gray Jeffrey J.
Published: February 2020

Antibody structure is largely conserved, except for a complementarity-determining region featuring six variable loops. Five of these loops adopt canonical folds which can typically be predicted with existing methods, while the remaining loop (CDR H3) remains a challenge due to its highly diverse set of observed conformations. In recent years, deep neural networks have proven to be effective at capturing the complex patterns of protein structure. This work proposes DeepH3, a deep residual neural network that learns to predict inter-residue distances and orientations from antibody heavy and light chain sequence. The output of DeepH3 is a set of probability distributions over distances and orientation angles between pairs of residues. These distributions are converted to geometric potentials and used to discriminate between decoy structures produced by RosettaAntibody. When evaluated on the Rosetta Antibody Benchmark dataset of 49 targets, DeepH3-predicted potentials identified better, same, and worse structures (measured by root-mean-squared distance [RMSD] from the experimental CDR H3 loop structure) than the standard Rosetta energy function for 30, 13, and 6 targets, respectively, and improved the average RMSD of predictions by 21.3% (0.48 Å). Analysis of individual geometric potentials revealed that inter-residue orientations were more effective than inter-residue distances for discriminating near-native CDR H3 loop structures.
Low-Bias Amplification for Robust DNA Data Readout
Authors: Gao Yanmin , Chen Xin , Hao Jianye , Zhang Chengwei , Qiao Hongyan , Ke Yonggang , Qi Hao
Published: February 2020

In DNA data storage, the massive sequence complexity creates challenges in repeatable and efficient information readout. Here, our study clearly demonstrated that canonical polymerase chain reaction (PCR) created significant DNA amplification biases, which greatly hinder fast and stable data retrieving from hundred-thousand synthetic DNA sequences encoding over 2.85 megabyte (MB) digital data. To mitigate the amplification bias, we adapted an isothermal DNA amplification for low-bias amplification of DNA pool with massive sequence complexity, and named the new method isothermal DNA reading (iDR). By using iDR, we were able to robustly and repeatedly retrieve the data stored in DNA strands attached on magnetic beads (MB) with significantly decreased sequencing reads, compared with the PCR method. Therefore, we believe that the low-bias iDR method provides an ideal platform for robust DNA data storage, and fast and reliable data readout.
Urn models for regulated gene expression yield physically intuitive solutions for probability distributions of single-cell counts
Authors: Choudhary Krishna , Narang Atul
Published: February 2020

Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the count distributions of mRNA and protein molecules in single cells can yield valuable insights into mechanisms of gene regulation. Solutions of chemical master equations are available for various kinetic schemes but, even for the models of regulation with a basic ON-OFF switch, they take complex forms with generating functions given as hypergeometric functions. Gene expression studies that have used these to fit the data have interpreted the parameters as burst size and frequency. However, this is consistent with the hypergeometric functions only if a gene stays active for short time intervals separated by relatively long intervals of inactivity. Physical insights into the probability mass functions are essential to ensure proper interpretations but are lacking for models of gene regulation. We fill this gap by developing urn models for regulated gene expression, which are of immense value to interpret probability distributions. Our model consists of a master urn, which represents the cytosol. We sample RNA polymerases and ribosomes from it and assign them to recipient urns of two or more colors, which represent time intervals with a homogeneous propensity for gene expression. Colors of the recipient urns represent sub-systems of the promoter states, and the assignments to urns of a specific color represent gene expression. We use elementary principles of discrete probability theory to derive the solutions for a range of kinetic models, including the Peccoud-Ycart model, the Shahrezaei-Swain model, and models with an arbitrary number of promoter states. For activated genes, we show that transcriptional lapses, which are events of gene inactivation for short time intervals separated by long active intervals, quantify the transcriptional dynamics better than bursts. Our approach reveals the physics underlying the solutions, which has important implications for single-cell data analysis.
Wheat pathogenZymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism
Authors: Fedoryshchak Roman O. , Ocasio Cory A. , Strutton Ben , Mattocks Jo , Corran Andrew J. , Tate Edward W.
Published: February 2020

Zymoseptoria triticiis the causative agent ofSeptoria triticiblotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogenZ. triticivia inhibition ofN-myristoyltransferase (NMT). We characterizeZ. triticiNMT biochemically for the first time, profile thein vivo Z. triticimyristoylated proteome and identify and validate the firstZ. triticiNMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity inZ. triticithrough the application of comparative bioinformatics to deconvolute function from the previously largely unannotatedZ. triticiproteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studyingZ. tritici.
Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their distinct aggregation propensities
Authors: Chakraborty Debayan , Straub John E. , Thirumalai D.
Published: February 2020

The early events in the aggregation of the intrinsically disordered peptide, Aβ, involve transitions from the disordered lowest free energy ground state to assembly-competent states. Are the finger-prints of order found in the amyloid fibrils encoded in the conformations that the monomers access at equilibrium? If so, could the enhanced aggregation rate of Aβ42 compared to Aβ40 be rationalized from the sparsely populated high free energy states of the monomers? Here, we answer these questions in the affirmative using coarse-grained simulations of the SOP-IDP model of Aβ40 and Aβ42. Although both the peptides have practically identical ensemble-averaged properties, characteristic of random coils (RCs), the conformational ensembles of the two monomers exhibit sequence-specific heterogeneity. Hierarchical clustering of conformations reveals that both the peptides populate high free energy aggregation-prone (N*) states, which resemble the monomers in the fibril structure. The free energy gap between the ground (RC) and theN* states of Aβ42 peptide is smaller than for Aβ40. By relating the populations of excited states of the two peptides to the fibril formation time scales using an empirical formula, we explain nearly quantitatively the faster aggregation rate of Aβ42 relative to Aβ40. TheN* concept accounts for fibril polymorphs, leading to the prediction that the less stableN* state of Aβ42, encoding for the U-bend fibril, should form earlier than the structure with the S-bend topology, which is in accord with the Ostwald’s rule rationalizing crystal polymorph formation.

Significance Statement

Alzheimer’s disease (AD), a rampant neurodegenerative disorder, is caused by the accumulation of pathological aggregates, primarily composed of the two isoforms Aβ40 and Aβ42. Experiments have shown that Aβ42 is more aggregation-prone compared to Aβ40. However, the molecular origin of this apparent anomaly remains elusive. Here, we provide a microscopic basis for the different aggregation rates in terms of the distinct populations of high free energy excited fibril-like states (N*) that are encoded in the monomer spectra. The N* theory explains the emergence of fibril polymorphs, and predicts the relative kinetic stabilities of Aβ42 fibrils using Ostwald’s rule of stages. Our work shows that sequence-specific conformational heterogeneity of the monomer ensembles provides important cues for understanding protein aggregation.
Distance and Colour-based Scores for Blood Test Risk Stratification
Authors: Zenil Hector , Hernández-Quiroz Francisco , Hérnandez-Orozco Santiago , Saeb-Parsy Kourosh , Hernández De la Cerda Héctor , Riedel Jürgen
Published: February 2020

We introduce a numerical and a colour-based risk stratification score to quantify abnormal blood analyte values. The score indicates how removed values of an individual are from considered healthy ranges from the literature or derived from empirical data such as medical surveys. The scores’ behaviour can be adjusted to incorporate medical knowledge by assigning multipliers or ‘weights’ to individual components and is rooted on a numerical and a colour-based scheme. We test the score against real and synthetic data from medically relevant cases, extremes cases, and empirical blood cell count data from the CDC NHANES survey spanning 13 years, from 2003 to 2016. We find that both the numerical and colour-based scores are informative in distinguishing healthy individuals from those with diseases manifested with abnormal blood results.