bluuebunny/crossref_metadata_2025 huggingface dataset:
FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots
Authors: Naznooshsadat Etminan , Elham Parvinnia , Ali Sharifi-Zarchi
Published: March 2020

Motivation

Multiple sequence alignment (MSA) is important and challenging problem of computational biology. Most of the existing methods can only provide a short length multiple alignments in an acceptable time. Nevertheless, when the researchers confront the genome size in the multiple alignments, the process has required a huge processing space/time. Accordingly, using the method that can align genome size rapidly and precisely has a great effect, especially on the analysis of the very long alignments. Herein, we have proposed an efficient method, called FAME, which vertically divides sequences from the places that they have common areas; then they are arranged in consecutive order. Then these common areas are shifted and placed under each other, and the subsequences between them are aligned using any existing MSA tool.

Results

The results demonstrate that the combination of FAME and the MSA methods and deploying minimizer are capable to be executed on personal computer and finely align long length sequences with much higher sum-of-pair (SP) score compared to the standalone MSA tools. As we select genomic datasets with longer length, the SP score of the combinatorial methods is gradually improved. The calculated computational complexity of methods supports the results in a way that combining FAME and the MSA tools leads to at least four times faster execution on the datasets.

Availability and implementation

The source code and all datasets and run-parameters are accessible free on http://github.com/naznoosh/msa.

Supplementary information

Supplementary data are available at Bioinformatics online.
Projected t-SNE for batch correction
Authors: Aliverti Emanuele , Tilson Jeffrey L , Filer Dayne L , Babcock Benjamin , Colaneri Alejandro , Ocasio Jennifer , Gershon Timothy R , Wilhelmsen Kirk C , Dunson David B
Published: March 2020

Motivation

Low-dimensional representations of high-dimensional data are routinely employed in biomedical research to visualize, interpret and communicate results from different pipelines. In this article, we propose a novel procedure to directly estimate t-SNE embeddings that are not driven by batch effects. Without correction, interesting structure in the data can be obscured by batch effects. The proposed algorithm can therefore significantly aid visualization of high-dimensional data.

Results

The proposed methods are based on linear algebra and constrained optimization, leading to efficient algorithms and fast computation in many high-dimensional settings. Results on artificial single-cell transcription profiling data show that the proposed procedure successfully removes multiple batch effects from t-SNE embeddings, while retaining fundamental information on cell types. When applied to single-cell gene expression data to investigate mouse medulloblastoma, the proposed method successfully removes batches related with mice identifiers and the date of the experiment, while preserving clusters of oligodendrocytes, astrocytes, and endothelial cells and microglia, which are expected to lie in the stroma within or adjacent to the tumours.

Availability and implementation

Source code implementing the proposed approach is available as an R package at https://github.com/emanuelealiverti/BC_tSNE, including a tutorial to reproduce the simulation studies.

Contact

aliverti@stat.unipd.it
Distinguishing the Roles of Antibiotic Stewardship and Reductions in Outpatient Visits in Generating a 5-Year Decline in Antibiotic Prescribing
Authors: Kissler Stephen M , Klevens R Monina , Barnett Michael L , Grad Yonatan H
Published: March 2020

Background

The mechanisms driving the recent decline in outpatient antibiotic prescribing are unknown. We estimated the extent to which reductions in the number of antibiotic prescriptions filled per outpatient visit (stewardship) and reductions in the monthly rate of outpatient visits (observed disease) for infectious disease conditions each contributed to the decline in outpatient antibiotic prescribing in Massachusetts between 2011 and 2015.

Methods

Outpatient medical and pharmacy claims from the Massachusetts All-Payer Claims Database were used to estimate rates of antibiotic prescribing and outpatient visits for 20 medical conditions and their contributions to the overall decline in antibiotic prescribing. Trends were compared with those in the National Ambulatory Medical Care Survey (NAMCS).

Results

Between 2011 and 2015, the January and July antibiotic-prescribing rates per 1000 individuals in Massachusetts declined by 18.9% and 13.6%, respectively. The monthly rate of outpatient visits per 1000 individuals in Massachusetts declined (P < .05) for respiratory infections and urinary tract infections. Nationally, outpatient visits for antibiotic-meriting medical conditions also declined between 2010 and 2015. Of the estimated 358 antibiotic prescriptions per 1000 individuals averted over the study period in Massachusetts, 59% (95% CI, 54–63%) were attributable to reduced observed disease and 41% (95% CI, 37–46%) to improved stewardship.

Conclusions

The decline in antibiotic prescribing in Massachusetts was driven both by a decline in observed disease and improved antibiotic stewardship, in agreement with national trends. A focus on infectious disease prevention should be considered alongside antibiotic stewardship as a means to reduce antibiotic prescribing.
Novel Coronavirus Disease 2019 (COVID-19) Pneumonia Progression Course in 17 Discharged Patients: Comparison of Clinical and Thin-Section Computed Tomography Features During Recovery
Authors: Han Xiaoyu , Cao Yukun , Jiang Nanchuan , Chen Yan , Alwalid Osamah , Zhang Xin , Gu Jin , Dai Meng , Liu Jie , Zhu Wanyue , Zheng Chuansheng , Shi Heshui
Published: March 2020

Background

Our objective was to retrospectively analyze the evolution of clinical features and thin-section computed tomography (CT) imaging of novel coronavirus disease 2019 (COVID-19) pneumonia in 17 discharged patients.

Methods

Serial thin-section CT scans of 17 discharged patients with COVID-19 were obtained during recovery. Longitudinal changes of clinical parameters and a CT pattern were documented in all patients during the 4 weeks after admission. A CT score was used to evaluate the extent of the disease.

Results

There were marked improvements of fever, lymphocyte counts, C-reactive proteins, and erythrocyte sedimentation rates within the first 2 weeks after admission. However, the mean CT score rapidly increased from the first to the third week, with a top score of 8.2 obtained in the second week. During the first week, the main CT pattern was ground-glass opacities (GGO; 76.5%). The frequency of GGO (52.9%) decreased in the second week. Consolidation and mixed patterns (47.0%) were noted in the second week. Thereafter, consolidations generally dissipated into GGO, and the frequency of GGO increased in the third week (76.5%) and fourth week (71.4%). Opacities were mainly located in the peripheral (76.5%) and subpleural (47.1%) zones of the lungs; they presented as focal (35.3%) or multifocal (29.4%) in the first week and became more diffuse in the second (47.1%) and third weeks (58.8%), then showed a reduced extent in fourth week (50%).

Conclusions

The progression course of the CT pattern was later than the progression of the clinical parameters within the first 2 weeks after admission; however, there were synchronized improvements in both the clinical and radiologic features in the fourth week.
Divergent male and female mate preferences do not explain incipient speciation between lizard lineages
Authors: McLean Claire A , Bartle Richard A , Dong Caroline M , Rankin Katrina J , Stuart-Fox Devi
Published: March 2020

Diversification in sexual signals is often taken as evidence for the importance of sexual selection in speciation. However, in order for sexual selection to generate reproductive isolation between populations, both signals and mate preferences must diverge together. Furthermore, assortative mating may result from multiple behavioral mechanisms, including female mate preferences, male mate preferences, and male–male competition; yet their relative contributions are rarely evaluated. Here, we explored the role of mate preferences and male competitive ability as potential barriers to gene flow between 2 divergent lineages of the tawny dragon lizard, Ctenophorus decresii, which differ in male throat coloration. We found stronger behavioral barriers to pairings between southern lineage males and northern lineage females than between northern males and southern females, indicating incomplete and asymmetric behavioral isolating barriers. These results were driven by both male and female mate preferences rather than lineage differences in male competitive ability. Intrasexual selection is therefore unlikely to drive the outcome of secondary contact in C. decresii, despite its widely acknowledged importance in lizards. Our results are consistent with the emerging view that although both male and female mate preferences can diverge alongside sexual signals, speciation is rarely driven by divergent sexual selection alone.
Anomalous origin of coronary arteries from pulmonary artery in adults: a case series
Authors: Vergara-Uzcategui Carlos Eduardo , das Neves Barbara , Salinas Pablo , Fernández-Ortiz Antonio , Núñez-Gil Iván J
Published: March 2020

Background

Anomalous origin of a coronary artery from the pulmonary trunk is a small group of rare congenital anomalies present in up to 1% of the population. These patients, in absence of an adequate collateral supply, may present with congestive heart failure secondary to ischaemia, arrhythmia, or sudden cardiac death in up to 90% of cases within the first months of life.

Case summary

We present four cases diagnosed in adulthood over 10 years in two high-volume centres. The first patient presented with dyspnoea and orthopnoea. The second with chest pain and episodes of non-sustained ventricular tachycardia. The third patient presented during her third pregnancy with chest pain, palpitations, and arrhythmia (non-sustained ventricular tachycardia). The fourth patient presented with sudden cardiac death.

Discussion

In all cases with anomalous origin of coronary arteries, it is recommendable to consider surgical correction to avoid the progression of ischaemia, congestive heart failure, arrhythmia, and sudden death.
Atypical haemolytic uraemic syndrome: a case report of a rare cause of reversible cardiomyopathy
Authors: Campbell Courtney M , Cassol Clarissa , Cataland Spero R , Kahwash Rami
Published: March 2020

Background

Atypical haemolytic uraemic syndrome (aHUS) is a life-threatening, genetic disease of complement-mediated thrombotic microangiopathy that typically presents as anaemia, thrombocytopenia, and renal failure. Cardiomyopathy is seen in up to 10% of aHUS cases, but the aetiology is not well-understood.

Case summary

A 63-year-old man recently was diagnosed with a thrombotic microangiopathy most consistent with aHUS by renal biopsy after presentation with acute renal failure requiring haemodialysis. He was started on therapy with complement inhibitor, eculizumab. Six weeks after diagnosis, he presented with progressive dyspnoea on exertion and chest pain. An echocardiogram demonstrated an acute drop in left ventricular ejection fraction to 20–25% with global hypokinesis. Left heart catheterization showed moderate, non-obstructive coronary artery disease. Cardiac magnetic resonance imaging demonstrated diffuse myocardial oedema. Endomyocardial biopsy revealed an arteriole with obliterative changes and a few possible fragmented red blood cells suggestive of thrombotic microangiopathy. There was no biopsy evidence of immune complex deposition or myocarditis. He was treated for heart failure and was maintained on eculizumab. On repeat echocardiogram 3 months later, the patient had complete recovery of his ejection fraction (60–65%).

Discussion

In this report, we describe complete recovery of aHUS-associated heart failure with eculizumab therapy and demonstrate for the first time that the aetiology of aHUS-associated heart failure is likely an acute thrombotic microangiopathy involving small intramyocardial arterioles, as demonstrated by cardiac biopsy.
Gaps in patient-reported outcome measures in randomized clinical trials of cardiac catheter ablation: a systematic review
Authors: Chen Yang , Nagendran Myura , Gomes Manuel , Wharton Peter V , Raine Rosalind , Lambiase Pier D
Published: March 2020

The aim of this systematic review was to evaluate randomized clinical trials (RCTs) of cardiac catheter ablation (CCA) and to assess the prevalence, characteristics and reporting standards of clinically relevant patient-reported outcome measures (PROMs). Electronic database searches of Medline, Embase, CENTRAL, and the WHO Trial Registry were conducted in March 2019. The study protocol was registered on PROSPERO (CRD42019133086). Of 7125 records identified, 237 RCTs were included for analysis, representing 35 427 patients with a mean age of 59 years. Only 43 RCTs (18%) reported PROMs of which 27 included a generic PROM that measured health-related quality of life (HRQL) necessary to conduct comparative effectiveness research. There was notable under-representation of certain patient groups—only 31% were women and only 8% were of non-Caucasian ethnicity, in trials which reported such data. The reporting standard of PROMs was highly variable with 8–62% adherence against CONSORT PRO-specific items. In summary, PROMs play a crucial role in determining the clinical and cost-effectiveness of treatments which primarily offer symptomatic improvement, such as CCA. Their underuse significantly limits evaluation of the comparative effectiveness of treatments. Using CCA as an exemplar, there are additional issues of infrequent assessment, poor reporting and under-representation of many population groups. Greater use of PROMs, and specifically validated HRQL questionnaires, is paramount in giving patients a voice in studies, generating more meaningful comparisons between treatments and driving better patient-centred clinical and policy-level decision-making.
The mixology of precursory strain partitioning approaching brittle failure in rocks
Authors: McBeck J , Ben-Zion Y , Renard F
Published: March 2020

We examine the strain accumulation and localization process throughout 12 triaxial compression experiments on six rock types deformed in an X-ray transparent apparatus. In each experiment, we acquire 50–100 tomograms of rock samples at differential stress steps during loading, revealing the evolving 3-D distribution of X-ray absorption contrasts, indicative of density. Using digital volume correlation (DVC) of pairs of tomograms, we build time-series of 3-D incremental strain tensor fields as the rocks are deformed towards failure. The Pearson correlation coefficients between components of the local incremental strain tensor at each stress step indicate that the correlation strength between pairs of local strain components, including dilation, contraction and shear strain, are moderate-strong in 11 of 12 experiments. In addition, changes in the local strain components from one DVC calculation to the next show differences in the correlations between pairs of strain components. In particular, the correlation of the local changes in dilation and shear strain tends to be stronger than the correlation of changes in dilation-contraction and contraction-shear strain. In 11 of 12 experiments, the most volumetrically frequent mode of strain accommodation includes a synchronized increase in multiple strain components. Early in loading, under lower differential stress, the most frequent strain accumulation mode involves the paired increase in dilation and contraction at neighbouring locations. Under higher differential stress, the most frequent mode is the paired increase in dilation and shear strain. This mode is also the first or second most frequent throughout each complete experiment. Tracking the mean values of the strain components in the sample and the volume of rock that each component occupies reveals fundamental differences in the nature of strain accumulation and localization between the volumetric and shear strain modes. As the dilative strain increases in magnitude throughout loading, it tends to occupy larger volumes within the rock sample and thus delocalizes. In contrast, the increasing shear strain components (left- or right-lateral) do not necessarily occupy larger volumes and so involve localization. Consistent with these evolutions, the correlation length of the dilatational strains tends to increase by the largest amounts of the strain components from lower to higher differential stress. In contrast, the correlation length of the shear strains does not consistently increase or decrease with increasing differential stress.
Reviewing the Potential of Psychedelics for the Treatment of PTSD
Authors: Krediet Erwin , Bostoen Tijmen , Breeksema Joost , van Schagen Annette , Passie Torsten , Vermetten Eric
Published: March 2020

There are few medications with demonstrated efficacy for the treatment of posttraumatic stress disorder (PTSD). Treatment guidelines have unequivocally designated psychotherapy as a first line treatment for PTSD. Yet, even after psychotherapy, PTSD often remains a chronic illness, with high rates of psychiatric and medical comorbidity. Meanwhile, the search for and development of drugs with new mechanisms of action has stalled. Therefore, there is an urgent need to explore not just novel compounds but novel approaches for the treatment of PTSD. A promising new approach involves the use of psychedelic drugs. Within the past few years, 2 psychedelics have received breakthrough designations for psychiatric indications from the US Food and Drug Administration, and several psychedelics are currently being investigated for the treatment of PTSD. This review discusses 4 types of compounds: 3,4-methylenedioxymethamphetamine, ketamine, classical psychedelics (e.g., psilocybin and lysergic acid diethylamide), and cannabinoids. We describe the therapeutic rationale, the setting in which they are being administered, and their current state of evidence in the treatment of PTSD. Each compound provides unique qualities for the treatment of PTSD, from their use to rapidly target symptoms to their use as adjuncts to facilitate psychotherapeutic treatments. Several questions are formulated that outline an agenda for future research.
Strong convergence of a half-explicit Euler scheme for constrained stochastic mechanical systems
Authors: Lindner Felix , Stroot Holger
Published: March 2020

This paper is concerned with the numerical approximation of stochastic mechanical systems with nonlinear holonomic constraints. The considered systems are described by second-order stochastic differential-algebraic equations involving an implicitly given Lagrange multiplier process. The explicit representation of the Lagrange multiplier leads to an underlying stochastic ordinary differential equation, the drift coefficient of which is typically not globally one-sided Lipschitz continuous. We investigate a half-explicit, drift-truncated Euler scheme that fulfills the constraint exactly. Pathwise uniform $L_p$-convergence is established. The proof is based on a suitable decomposition of the discrete Lagrange multipliers and on norm estimates for the single components, enabling the verification of consistency, semistability and moment growth properties of the scheme.
Rapid Kinetic Spectrophotometric Determination of Phosalone (Zolone) in a Commercial Formulation
Authors: Espinosa-Mansilla Anunciación , Cabanillas Agustina Guiberteau , Salinas Francisco , Mora Nielena , Zamoro Angel
Published: March 2020

A kinetic study of the degradation of phosalone in an alkaline medium was undertaken by using a pneumatic stopped-flow system. A rapid semiautomatic method is proposed for determining phosalone. Linear calibration graphs up to 8.0 × 10−5M (detection limit = 1.40 × 10−6M) were obtained, with a measurement period of only 3.5 s per sample and a relative standard deviation of 1.4%. Several pesticides were assayed as interference species, and several did not interfere even at a 6:1, M:M foreign species/phosalone ratio. A strong interference (ratio < 1) was generated by azinphos-methyl and carbaryl. The proposed method was applied to the analysis of a commercial formulation, and the results were validated by comparison with those for a chromatographic method.
Determination of Egg Proteins in Food Products by Enzyme Immunoassay
Authors: Yeung Jupiter M , Newsome W Harvey , Abbott Michael A
Published: March 2020

An enzyme-linked immunosorbent assay (ELISA) was developed to determine the presence of egg proteins in foods. The polyclonal antibodies developed were specific to whole egg proteins and did not cross-react with any of the 38 nuts, legumes, or other common food ingredients tested. The concentrations of egg proteins that will inhibit 50% of antibody–antigen binding, IC50, were 3–7 ng/mL, and the linear range was 0.5–62.5 ng/mL. The detection limit was 0.2 ppm for various foods. Recoveries ranged from 67 to 96%. The intra- and inter-assay coefficients of variation in this procedure were 10–13% for ice cream spiked at 0.8 and 1.6 ppm. The ELISA has been applied to ice creams, noodles, pasta, and breads. Egg proteins were identified in all declared egg products, and no false positives were found.
Determination of Malathion, Coumaphos, and Fluvalinate Residues in Honey by Gas Chromatography with Nitrogen–Phosphorus or Electron Capture Detectors
Authors: Menkissoglu-Spiroudi Urania , Diamantidis Grigorios C , Georgiou Vassiliki E , Thrasyvoulou Andreas T
Published: March 2020

A rapid, reliable, and inexpensive extraction method was developed to determine acaricide residues in honey by gas chromatography (GC) with nitrogen–phosphorus (NP) or electron capture (EC) detectors. Because of the high selectivity of the NP detector, no interfering peaks were present and no cleanup was necessary. A simple cleanup step is proposed for the GC–ECD analysis. Recoveries from spiked honey samples ranged from 79 to 94.4%, with coefficients of variation of 0.3–18.5%. The quantitation limit obtained was 0.015 mg/kg for malathion, 0.020 mg/kg for coumaphos, and 0.005 mg/kg for fluvalinate. The method was used to determine the disappearance of malathion and coumaphos residues from honey samples collected from beehives treated with these acaricides. The disappearance of both acaricides was rapid and followed a first-order model for the duration of the experiment.
Determination of Six Metals in Galician Red Wines (in Northwestern Spain) by Capillary Electrophoresis
Authors: Núñez Mar , Peña Rosa M , Herrero Carlos , García Sagrario
Published: March 2020

A simple technique is described for the routine simultaneous capillary electrophoretic determination of 6 cations in wine. Separation was achieved on a fused silica capillary column with a UV-Cat-1, α-hydroxysobutyric acid and 18-crown-6-ether buffer at pH 4.5 and indirect UV detection at 214 nm. The content of magnesium, sodium, potassium, calcium, manganese, and lithium was determined. The method is quantitative, with recoveries in the 92–102% range, and linear over more than one order of magnitude. The precision is better than 2.5–3.4%. The method is sensible, with detection limits between 0.01 and 0.06 mg/L. Twenty-five red wines with a Certified Brand of Origin from Galicia (northwestern Spain) were analyzed by the proposed method. Various wines showed very similar electrophoretic profiles, but significant quantitative differences were observed.
Determination of 4-Hexylresorcinol in Shrimp by Liquid Chromatography with Fluorescence Detection
Authors: Jonker Klaas M , Dekker Colinda P
Published: March 2020

A method was developed to determine 4-hexylresorcinol in shrimp meat. The procedure is based on extraction of test portions with methanol followed by liquid chromatographic analysis of the extracts, using a reversed-phase column and fluorimetric detection (excitation: 280 nm, and emission: 310 nm). The confidence interval of the recovery in working range of 1.5–2.5 mg/kg was 81.6 ± 0.8%. The relative standard deviation in the working range was 2.1%. Limits of quantitation and detection were 6.59 and 1.98 ng/mL extract, respectively, corresponding to 0.26 and 0.08 mg/kg in shrimp.
New Monitoring System for Ninety Pesticides and Related Compounds in River Water by Solid-Phase Extraction with Determination by Gas Chromatography/Mass Spectrometry
Authors: Tanabe Akiko , Mitobe Hideko , Kawata Kuniaki , Sakai Masaaki , Yasuhara Akio
Published: March 2020

A new monitoring system was established for the determination of 90 pesticides and 10 pesticide degradation products in river water. The pesticides consisted of 18 fungicides, 30 insecticides, and 42 herbicides. The pesticides were extracted with a solid-phase, styrene-divinylbenzene copolymer, eluted with acetone, hexane, and ethyl acetate, and determined by gas chromatography/mass spectrometry. Overall recoveries ranged from 72 to 118%. The limits of detection were 0.01–0.1 μg/L. This system determines most of the pesticides used in Japan and was successfully applied to practical monitoring of water polluted with pesticides and related compounds.
Detection of Pork in Heat-Processed Meat Products by Monoclonal Antibody-Based ELISA
Authors: Chen Fur-Chi , Hsieh Y-H Peggy
Published: March 2020

An enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody to a porcine thermal-stable muscle protein was developed for detection of pork in cooked meat products. The assay specifically detects porcine skeletal muscle, but not cardiac muscle, smooth muscle, blood, and nonmuscle organs. No cross-reactivity was observed with common food proteins. Validity of the assay was evaluated with laboratory formulated and commercial meat samples. The detection limit was determined as 0.5% (w/w) pork in heterologous meat mixtures. Overall, intra- and inter-assay coefficients of variation were 5.8 and 7.9%, respectively. The accuracy in analyzing market samples was 100% as verified by product labeling and confirmed by a commercial polycolonal antibody test kit.
On the Statistical Testing Methods for Single Laboratory Validation of Qualitative Microbiological Assays with an Unpaired Design
Authors: Wang Shizhen S
Published: March 2020

Background

There exists several statistical methods for detecting a difference of detection rates between alternative and reference qualitative microbiological assays in a single laboratory validation study with an unpaired design.

Objective

We compared performance of eight methods including Fisher’s exact test, unequal variance two-sample t-test, Wilcoxon rank-sum test, z-test, and methods based on Wilson confidence intervals, complementary log-log regression, Firth’s logistic regression, and ordinary logistic regression.

Method

We first compared the minimum detectable difference in the proportion of detections between the alternative and reference methods among these statistical methods for a varied number of test portions. We then compared power and size of test of these methods using simulated data.

Results

Firth’s logistic regression and the unequal variance two-sample t-test had the lowest minimum detectable difference and highest power. None of these statistical methods had an estimated size of test always within a 95% confidence interval of the nominal value 0.05 with small numbers of test portions (n = 12, 20, 30). Fisher’s exact test, the Wilcoxon rank-sum test, and the z-test were conservative even with a moderately large number of test portions (n = 40), while Firth’s logistic regression and the unequal variance two-sample t-test had a size of test closer to 0.05 than other methods.

Conclusions

Firth's logistic regression and the unequal variance two-sample t-test are better choices than other competing methods.

Highlights

We recommend the unequal variance two-sample t-test over Firth’s logistic regression because the unequal variance two-sample t-test is better known and easier to use. We provide an example using real data.
Rapid Method for the Determination of Thiamine and Pantothenic Acid in Infant Formula and Milk-Based Nutritional Products by Liquid Chromatography‒Tandem Mass Spectrometry
Authors: Gill Brendon D , Saldo Sheila C , McGrail Iain J , Wood Jackie E , Indyk Harvey E
Published: March 2020

Background

Thiamine and pantothenic acid play a critical role in numerous metabolic reactions and are typically supplemented in infant and adult nutritional formulas as thiamine chloride hydrochloride and calcium pantothenate salts.

Objective

A rapid compliance method for the analysis of thiamine and pantothenic acid applicable to infant formula and milk-based nutritional products is described.

Method

Proteins are removed by centrifugal ultrafiltration, followed by analysis by reversed-phase liquid chromatography‒tandem mass spectrometry (LC-MS/MS), with quantitation accomplished by internal standard technique.

Results

The method was shown to be accurate, with acceptable recovery (thiamine, 99.3–101.1%; pantothenic acid, 99.2–108.6%). A certified reference material (NIST 1849a), showed no statistical bias (α = 0.05) for thiamine (P = 0.64); although a statistically significant bias (P < 0.01) for pantothenic acid was found, the nominal bias was only 4.7% (mean = 7.1 mg/hg; certified value = 6.8 mg/hg). A comparison of results by LC-MS/MS and current methods showed negligible bias (mean bias: thiamine, 0.01 mg/hg; pantothenic acid, 0.17 mg/hg) and no statistical significance (α = 0.05; thiamine, P = 0.399; pantothenic acid, P = 0.058). Acceptable precision was demonstrated with a repeatability of 7.2% repeatability relative standard deviation (RSDr) (HorRat: 0.6) and an intermediate precision of 7.0% RSD for thiamine, and a repeatability of 5.7% RSDr (HorRat: 0.5) and an intermediate precision of 6.1% RSD for pantothenic acid.

Conclusions

This rapid method is intended for use in high-throughput laboratories as part of routine product compliance release testing of thiamine and pantothenic acid in manufactured infant and milk-based nutritional products.
Development and Validation of a Reversed Phase High Performance Liquid Chromatography-Photodiode Array Detection Method for Simultaneous Identification and Quantification of Coumarin, Precocene-I, β-Caryophyllene Oxide, α-Humulene, and β-Caryophyllene in Ageratum Conyzoides Extracts and Essential Oils from Plants
Authors: Shah Sonal , Dhanani Tushar , Sharma Sonu , Singh Raghuraj , Kumar Satyanshu , Kumar Bhanu , Srivastava Sharad , Ghosh Srikant , Kumar Rajesh , Juliet Sanis
Published: March 2020

Background

Ageratum conyzoides is an aromatic plant. It is considered as an invasive and cosmopolite weed, widely spread in tropical and subtropical regions. Phytochemicals such as benzopyrenes, flavonoids, and terpenoids are reported from A. conyzoides.

Objective

Development and validation of a reversed-phase HPLC-photodiode array (PDA) detection method for simultaneous identification and quantification of coumarin, precocene-I, β-caryophyllene oxide, α-humulene, and β-caryophyllene in extracts of A. conyzoides and essential oils was carried out.

Methods

Separation of analytes was achieved on a RP-18 (250 mm × 4.6 mm, 5 µm) column using a solvent system comprising of a mixture of acetonitrile and water with 0.05% trifluoroacetic acid in gradient elution mode at ambient temperature with flow rate of 1 mL/min.

Results

The retention time of coumarin, precocene-I, β-caryophyllene oxide, α-humulene, and β-caryophyllene was 4.38, 12.86, 20.10, 33.34, and 35.11 min, respectively. Limits of detection for coumarin, precocene-I, β-caryophyllene oxide, α-humulene, and β-caryophyllene were 2.5, 2.5, 2.5, 0.025, and 2.5 µg/mL, respectively. Similarly, LOQ were 10, 10, 10, 0.10, and 10 µg/mL for coumarin, precocene-I, β-caryophyllene oxide, α-humulene, and β- caryophyllene, respectively. Repeatabilities (RSD, %) values for intraday and interday precision for coumarin, precocene-I, β-caryophyllene oxide, α-humulene, and β-caryophyllene was 0.765–2.086 and 0.886–2.128; 0.879–1.672 and 0.979–1.825; 0.696–2.418 and 0.768–2.592; 1.728–2.362 and 1.965–2.378; 1.615–2.897 and 1.658–2.906, respectively.

Conclusions

The separation of five analytes was achieved within 50 min. The developed and validated HPLC-PDA method was successfully applied for identification and quantification of above five analytes in A. conyzoides extracts and essential oils. The method could be used for meeting the characterization criteria of phytoformulations.
Characterization of Insect Stains Deposited by Calliphora vicina (Diptera: Calliphoridae) on Shirt Fabrics
Authors: Rivers David B , Dunphy Brendan , Hammerschmidt Claire , Carrigan Alexandra
Published: March 2020

Despite the fact that necrophagous flies are known to alter bloodstains and create unique artifacts, no research has occurred to date that has examined the characteristics of insect stains on textiles or fabrics. This study represents the first effort to characterize artifacts produced by adult Calliphora vicina Robineau-Desvoidy deposited on a range of shirt fabrics that varied in type, color, orientation, and yarn tension. In general, artifact morphology on any type of fabric was distorted in comparison to those observed on smooth and/or nonporous surfaces in previous studies. Consequently, distinction of artifact type could only be made broadly as digestive artifacts and transfer patterns, in which the latter was predominantly detected as tarsal tracks. None of the artifacts displayed satellite stains typical of human bloodstains found on textiles. Wicking was evident on all fabrics but was most pronounced with dri wick and jersey knit polyester in comparison to cotton knit. Digestive artifacts on any colored fabric, but especially with green and yellow shirt samples, resembled the reported color, size, and morphology of bloodstains generated in laboratory studies on a range of fabrics. Unique digestive artifacts were also detected as small, black, and nearly spherical. These defecatory stains did not appear to wet or wick into any of the fabrics. Digestive artifacts and tarsal tracks differentially interacted with front face stitch loops of clothing fabrics to yield distinct stain patterns. The implications of these observations in reference to bloodstain pattern analysis at crime scenes are discussed.
The white dwarf planet WD J0914+1914 b: barricading potential rocky pollutants?
Authors: Veras Dimitri
Published: March 2020

An ice giant planet was recently reported orbiting white dwarf WD J0914+1914 at an approximate distance of 0.07 au. The striking non-detection of rocky pollutants in this white dwarf’s photosphere contrasts with the observations of nearly every other known white dwarf planetary system. Here, I analyse the prospects for exterior extant rocky asteroids, boulders, cobbles, and pebbles to radiatively drift inward past the planet due to the relatively high luminosity ($0.1 \, \mathrm{L}_{\odot }$) of this particularly young (13 Myr) white dwarf. Pebbles and cobbles drift too slowly from Poynting–Robertson drag to bypass the planet, but boulders and asteroids are subject to the much stronger Yarkovsky effect. In this paper, I (i) place lower limits on the time-scales for these objects to reach the planet’s orbit, (ii) establish 3 m as the approximate limiting radius above which a boulder drifts too slowly to avoid colliding with the planet, and (iii) compute bounds on the fraction of boulders that succeed in traversing mean motion resonances and the planet’s Hill sphere to eventually pollute the star. Overall, I find that the planet acts as a barrier against rather than a facilitator for radiatively driven rocky pollution, suggesting that future rocky pollutants would most likely originate from distant scattering events.
RAiSE X: searching for radio galaxies in X-ray surveys
Authors: Turner Ross J , Shabala Stanislav S
Published: March 2020

We model the X-ray surface brightness distribution of emission associated with Fanaroff & Riley type-II radio galaxies. Our approach builds on the RAiSE dynamical model which describes broad-band radio frequency synchrotron evolution of jet-inflated lobes in a wide range of environments. The X-ray version of the model presented here includes: (1) inverse-Compton upscattering of cosmic microwave background radiation; (2) the dynamics of the shocked gas shell and associated bremsstrahlung radiation; and (3) emission from the surrounding ambient medium. We construct X-ray surface brightness maps for a mock catalogue of extended FR-IIs based on the technical characteristics of the eRosita telescope. The integrated X-ray luminosity function at low redshifts (z ≤ 1) is found to strongly correlate with the density of the ambient medium in all but the most energetic sources, whilst at high-redshift (z > 1) the majority of objects are dominated by inverse-Compton lobe emission due to the stronger cosmic microwave background radiation. By inspecting our mock spatial brightness distributions, we conclude that any extended X-ray detection can be attributed to AGN activity at redshifts z ≥ 1. We compare the expected detection rates of active and remnant high-redshift radio AGNs for eRosita and LOFAR, and future more sensitive surveys. We find that a factor of ten more remnants can be detected using X-ray wavelengths over radio frequencies at z > 2.2, increasing to a factor of 100 for redshifts z > 3.1.
Searching for multiple populations in the integrated light of the young and extremely massive clusters in the merger remnant NGC 7252
Authors: Bastian Nate , Lardo Carmela , Usher Christopher , Kamann Sebastian , Larsen Søren S , Cabrera-Ziri Ivan , Chantereau William , Martocchia Silvia , Salaris Maurizio , Asa’d Randa , Hilker Michael
Published: March 2020

Recent work has shown that the properties of multiple populations (MPs) within massive stellar clusters (i.e. in the extent of their abundance variations as well as the fraction of stars that show the anomalous chemistry) depend on the mass as well as the age of the host cluster. Such correlations are largely unexpected in current models for the formation of MPs and hence provide essential insight into their origin. Here, we extend our previous study into the presence or absence of MPs using integrated light spectroscopy of the ∼600 Myr, massive (∼107–108 M⊙) clusters, W3 and W30, in the galactic merger remnant, NGC 7252. Due to the extreme mass of both clusters, the expectation is that they should host rather extreme abundance spreads, manifested through high mean [Na/Fe] abundances. However, we do not find evidence for a strong [Na/Fe] enhancement, with the observations being consistent with the solar value. This suggests that age is playing a key role, or alternatively that MPs only manifest below a certain stellar mass, as the integrated light at all ages above ∼100 Myr is dominated by stars near or above the main-sequence turn-off.
Positive Selection and Inactivation in the Vision and Hearing Genes of Cetaceans
Authors: McGowen Michael R , Tsagkogeorga Georgia , Williamson Joseph , Morin Phillip A , Rossiter and Stephen J
Published: March 2020

The transition to an aquatic lifestyle in cetaceans (whales and dolphins) resulted in a radical transformation in their sensory systems. Toothed whales acquired specialized high-frequency hearing tied to the evolution of echolocation, whereas baleen whales evolved low-frequency hearing. More generally, all cetaceans show adaptations for hearing and seeing underwater. To determine the extent to which these phenotypic changes have been driven by molecular adaptation, we performed large-scale targeted sequence capture of 179 sensory genes across the Cetacea, incorporating up to 54 cetacean species from all major clades as well as their closest relatives, the hippopotamuses. We screened for positive selection in 167 loci related to vision and hearing and found that the diversification of cetaceans has been accompanied by pervasive molecular adaptations in both sets of genes, including several loci implicated in nonsyndromic hearing loss. Despite these findings, however, we found no direct evidence of positive selection at the base of odontocetes coinciding with the origin of echolocation, as found in studies examining fewer taxa. By using contingency tables incorporating taxon- and gene-based controls, we show that, although numbers of positively selected hearing and nonsyndromic hearing loss genes are disproportionately high in cetaceans, counts of vision genes do not differ significantly from expected values. Alongside these adaptive changes, we find increased evidence of pseudogenization of genes involved in cone-mediated vision in mysticetes and deep-diving odontocetes.
Eosinophil and lymphocyte counts predict bevacizumab response and survival in recurrent glioblastoma
Authors: Vaios Eugene J , Winter Sebastian F , Muzikansky Alona , Nahed Brian V , Dietrich Jorg
Published: March 2020

Background

There is a lack of biomarkers to identify glioblastoma (GBM) patients who may benefit from specific salvage therapies, such as the anti-angiogenic agent bevacizumab. We hypothesized that circulating blood counts may serve as biomarkers for treatment response and clinical outcomes.

Methods

Complete blood counts, clinical data, and radiographic information were collected retrospectively from 84 recurrent GBM patients receiving bevacizumab (10 mg/kg every 2 weeks). Significant biomarkers were categorized into quartiles and the association with clinical outcomes was assessed using the Kaplan–Meier method.

Results

The median treatment duration and survival on bevacizumab (OS-A) was 88 and 192 days, respectively. On multivariate analysis, MGMT promoter methylation (hazard ratio [HR] 0.504, P = .031), increases in red blood cells (HR 0.496, P = .035), and increases in eosinophils (HR 0.048, P = .054) during treatment predicted improved OS-A. Patients in the first and fourth quartiles of eosinophil changes had a 12-month survival probability of 5.6% and 41.2% (P < .0001), respectively. Treatment response was associated with increases in eosinophil counts (P = .009) and improved progression-free survival (P = .013). On multivariate analysis, increases in lymphocyte counts among responders predicted improved OS-A (HR 0.389, P = .044). Responders in the first and fourth quartiles of lymphocyte changes had a 12-month survival probability of 0% and 44.4% (P = .019), respectively. Changes in platelet counts differed before and after radiographic response (P = .014).

Conclusions

Changes in circulating eosinophil, lymphocyte, and platelet counts may predict treatment response and clinical outcomes in patients with recurrent GBM receiving bevacizumab.
Anisotropic fluoride nanocrystals modulated by facet-specific passivation and their disordered surfaces
Authors: Yang Ziyu , Zhang Huihui , Xu Junjie , Ma Renzhi , Sasaki Takayoshi , Zeng Yu-Jia , Ruan Shuangchen , Hou Yanglong
Published: March 2020

Rutile-type fluorides have been proven to be active components in the context of emerging antiferr-omagnetic devices. However, controlled synthesis of low-dimensional, in particular two-dimensional (2D), fluorides in a predictable and deterministic manner remains unrealized because of a lack of efficient anisotropic control, which impedes their further development in reduced dimensions. We report here that altered passivation of {110} growing facets can direct the synthesis of rutile-type fluoride nanocrystals into well-defined zero-dimensional (0D) particulates, one-dimensional (1D) rods and 2D sheets in a colloidal approach. The obtained nanocrystals show positive exchange bias and enhanced magnetic transition temperature from the coexistence of long-range antiferromagnetic order and disordered surface spins, making them strong alternatives for flexible magnetic devices and sensors.
De Minimis Normativism: a New Theory of Full Aptness
Authors: Carter J Adam
Published: March 2020

Full aptness is the most important concept in performance-based virtue epistemology. The structure of full aptness, in epistemology and elsewhere, is bilevelled. At the first level, we evaluate beliefs, like performances, on the basis of whether they are successful, competent, and apt—viz successful because competent. But the fact that aptness itself can be fragile—as it is when an apt performance could easily have been inapt—points to a higher zone of quality beyond mere aptness. To break in to this zone, one must not merely perform aptly but also in doing so safeguard in skilled ways against certain risks to inaptness. But how must this be done, exactly? This paper has two central aims. First, I challenge the credentials of mainstream thinking about full aptness by raising some new and serious problems for the view. I then propose a novel account of full aptness—what I call de minimis normativism—which keeps all the advantages of the canonical view, avoids its problems entirely, and offers some additional payoffs.
Linking Pelvic Floor Muscle Function Terminology to the International Classification of Functioning, Disability and Health
Authors: Saltiel Fernanda , Miranda-Gazzola Ana Paula Gonçalves , Vitória Rayane Oliveira , Sampaio Rosana Ferreira , Figueiredo Elyonara Mello
Published: March 2020

Objective

A previous systematic review on pelvic floor muscle function (PFMF) identified a miscellaneity of terms. The lack of consensual terminology might have come from the complexity of neuromusculoskeletal function itself. This study sought to link the previously identified PFMF terms to the International Classification of Functioning, Disability and Health (ICF) terminology.

Methods

In this secondary analysis study, 10 linkage rules were applied to link 196 previously identified PFMF terms to the ICF. Two researchers performed the linking process independently. Disagreements were solved by open dialogue with a third researcher. Percentage agreement was computed for main outcome.

Results

A total of 184 (93.9%) PFMF terms were subsumed into the following 6 ICF terms: tone, involuntary movement reaction, control, coordination, strength, and endurance. The most frequently investigated PFMF was strength (25.5%), followed by involuntary movement reaction (22.9%), endurance (17.2%), control (14.1%), coordination (9.9%), and tone (4.2%). Only 6.2% PFMF could not be linked to ICF terminology. A wide variation of instruments/methods was used to measure PFMF. Vaginal palpation was the only method employed to measure all 6 PFMF. Percentage agreement between raters was 100%.

Conclusions

Linking PFMF terminology to the ICF was feasible and valid. It allowed the identification of the most investigated PFMF and their measuring methods. ICF terminology to describe PFMF should be used since it may improve communication, data gathering, and the advance in scientific knowledge.

Impact

Standardized terminology anchored in a theoretical framework is crucial to data gathering, communication, and dissemination of evidence-based practice. PFMF terminology based on ICF can be used to improve data pooling and communication.