bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental evolution supports signatures of sexual selection in genomic divergence
Authors: Wiberg R. Axel W. , Veltsos Paris , Snook Rhonda R. , Ritchie Michael G. 
Published: March 2021

AbstractComparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography, and neutral processes that occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here, we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of allele frequency divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in “islands,” many of which contain candidate genes implicated in mating behaviors and other sexually selected phenotypes. These are more often seen on the X chromosome, which also shows greater divergence in FST than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D within some of the divergent regions may imply that selective sweeps have occurred, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex-biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence between species and natural populations, and hence provide experimental support for the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.
Detection of fraud in lime juice using pattern recognition techniques and FT‐IR spectroscopy
Authors: Mohammadian Amirhossein , Barzegar Mohsen , Mani‐Varnosfaderani Ahmad 
Published: March 2021

AbstractThe lime juice is one of the products that has always fallen victim to fraud by manufacturers for reducing the cost of products. The aim of this research was to determine fraud in distributed lime juice products from different factories in Iran. In this study, 101 samples were collected from markets and also prepared manually and finally derived into 5 classes as follows: two natural classes (Citrus limetta, Citrus aurantifolia), including 17 samples, and three reconstructed classes, including 84 samples (made from Spanish concentrate, Chinese concentrate, and concentrate containing adulteration compounds). The lime juice samples were freeze‐dried and analyzed using FT‐IR spectroscopy. At first, principal component analysis (PCA) was applied for clustering, but the samples were not thoroughly clustered with respect to their original groups in score plots. To enhance the classification rates, different chemometric algorithms including variable importance in projection (VIP), partial least square‐discriminant analysis (PLS‐DA), and counter propagation artificial neural networks (CPANN) were used. The best discriminatory wavenumbers related to each class were selected using the VIP‐PLS‐DA algorithm. Then, the CPANN algorithm was used as a nonlinear mapping tool for classification of the samples based on their original groups. The lime juice samples were correctly designated to their original groups in CPANN maps and the overall accuracy of the model reached up to 0.96 and 0.87 for the training and validation procedures. This level of accuracy indicated the FT‐IR spectroscopy coupled with VIP‐PLS‐DA and CPANN methods can be used successfully for detection of authenticity of lime juice samples.
Derivation of site-specific selenium water quality criteria: A comparison of two methods and regulatory implications
Authors: Reash Robin J. , Thomas Jeffrey , Vondruska Joe T. 
Published: March 2021

Abstract
In 2016, the US Environmental Protection Agency (USEPA) issued revised aquatic life water quality criteria for selenium (Se). The criteria (“elements”) consisted of threshold concentrations applicable to fish tissue (three tissue types, though the egg and ovary tissue takes precedence over the whole-body and muscle tissue thresholds), and water column. The agency rationalized that measured concentrations of Se in fish tissue were more predictive of potential adverse reproductive effects than those measured in external media. The agency provided two mechanisms for derivation of site-specific Se water criteria: a bioaccumulation factor (BAF) approach, and a partitioning-based bioaccumulation model approach. The use of either approach assumes that fish tissue concentrations exceed one or more of the tissue criteria. We compared the two approaches using fish tissue samples from various species in the Ohio River to evaluate resulting similarities and differences in the calculated Se water quality criteria. Fish (five species) were collected near two coal-fired power plants at sites unaffected by Se from wastewater discharges. Using results for all species and all sites combined, the resulting site-specific Se criteria for the BAF and partitioning-based model approach (median values) were 2.0 and 1.5 µg/L, respectively. Considering all species, resulting criteria differed little between the two power plant locations. Resulting criteria for both methods were strongly influenced by a small (less than detection) background Se water concentration. At least for the upper Ohio River, the BAF approach (requiring less input data) seems adequate for derivation of site-specific Se water criteria. In the current study, however, none of the tissue samples exceeded USEPA's tissue criteria. Thus, the decision to derive site-specific Se water quality criteria should be evaluated on a case-by-case basis, because the process may result in either a more stringent or less stringent value, wholly dependent on local factors. Integr Environ Assess Manag 2021;17:1255–1262. © 2021 SETAC
KEY POINTS
USEPA offers methods to determine site-specific Se water quality criteria where the applicable tissue criteria may be exceeded. Two of these methods were evaluated side-by-side at two power plant sites on the Ohio River. Results indicated very similar site-specific Se water quality criteria for both methods, which was influenced highly by less than detection water concentrations.
MicroRNA‐216a targets WT1 expression and regulates KRT7 transcription to mediate the progression of pancreatic cancer—A transcriptome analysis
Authors: Wang Wei , Wang Jie , Yang Chuanxin , Wang Jian 
Published: March 2021

AbstractGene expression profiling has been broadly performed in the field of cancer research. This study aims to explore the key gene regulatory network and focuses on the functions of microRNA (miR)‐216a in pancreatic cancer (PC). PC datasets GSE15471, GSE16515, and GSE32676 were used to screen the differentially expressed genes (DEGs) in PC. A miRNA microarray analysis and gene oncology analysis suggested miR‐216a as an important differentially expressed miRNA in PC. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that miR‐216a and the DEGs are largely enriched on the phosphatidyl inositol 3‐kinase/protein kinase B (PI3K/AKT) signaling pathway. miR‐216a targeted Wilms Tumor 1 (WT1), while WT1 promoted transcription activity of keratin 7 (KRT7). Upregulation of miR‐216a reduced proliferation and invasiveness of PC cells, while further upregulation of WT1 blocked the functions of miR‐216a. Silencing of KRT7 diminished the oncogenic role of WT1. The in vitro results were reproduced in vivo. High expression of miR‐216a while poor expression of WT1 indicated better prognosis of PC patients. The miR‐216a/WT1/KRT7 axis influenced the activity of the PI3K/AKT pathway. To conclude, this study evidenced that miR‐216a suppressed WT1 expression and blocked KRT7 transcription, which inactivated the PI3K/AKT signaling and reduced PC progression.
Exosomal miR‐512‐3p derived from mesenchymal stem cells inhibits oxidized low‐density lipoprotein‐induced vascular endothelial cells dysfunction via regulating Keap1
Authors: Chen Sisi , Zhou Heng , Zhang Bofang , Hu Qi 
Published: March 2021

AbstractAtherosclerosis (AS) is a prevalent chronic inflammatory vascular disease. Upregulated oxidized low‐density lipoprotein (ox‐LDL) in the serum has been found to induce endothelial cells (ECs) apoptosis by increasing oxidative stress and promoting inflammatory response, which are essential mechanisms of AS development. Mesenchymal stem cells (MSCs), which secrete exosomes to transport microRNAs (miRNAs) and regulate cell functions, have become a research focus in recent years. The results of this study manifested that MSCs‐derived exosomes were phagocytosed by EC. In addition, miR‐512‐3p enriched by MSCs‐ derived exosomes markedly inhibited ox‐LDL‐mediated EC damage, namely, accelerated EC proliferation, inhibited Caspase‐3 activation and cell apoptosis, inhibited the levels of inflammatory cytokines (tumor necrosis factor‐α, interleukin (IL)‐1β, and IL‐6) and oxidative factor MDA, and increased the contents of SOD and GSH‐PX. Mechanistically, Keleh‐like ECH‐associated protein 1 (Keap1) was proved to be a functional target of miR‐512‐3p. Furthermore, silencing Keap1 limited ox‐LDL‐mediated EC cell dysfunction, while over‐expressing Keap1 mitigated the exosomal miR‐512‐3p‐mediated protective effect in Ox‐LDL‐induced EC. The above results confirmed that miR‐512‐3p shuttled by MSCs‐derived exosomes protected EC against ox‐LDL by targeting Keap1.
Higher infectivity of the SARS‐CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data
Authors: Khan Abbas , Zia Tauqir , Suleman Muhammad , Khan Taimoor , Ali Syed Shujait , Abbasi Aamir Ali , Mohammad Anwar , Wei Dong‐Qing 
Published: March 2021

AbstractThe evolution of the SARS‐CoV‐2 new variants reported to be 70% more contagious than the earlier one is now spreading fast worldwide. There is an instant need to discover how the new variants interact with the host receptor (ACE2). Among the reported mutations in the Spike glycoprotein of the new variants, three are specific to the receptor‐binding domain (RBD) and required insightful scrutiny for new therapeutic options. These structural evolutions in the RBD domain may impart a critical role to the unique pathogenicity of the SARS‐CoV‐2 new variants. Herein, using structural and biophysical approaches, we explored that the specific mutations in the UK (N501Y), South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y), and hypothetical (N501Y‐E484K) variants alter the binding affinity, create new inter‐protein contacts and changes the internal structural dynamics thereby increases the binding and eventually the infectivity. Our investigation highlighted that the South African (K417N‐E484K‐N501Y), Brazilian (K417T‐E484K‐N501Y) variants are more lethal than the UK variant (N501Y). The behavior of the wild type and N501Y is comparable. Free energy calculations further confirmed that increased binding of the spike RBD to the ACE2 is mainly due to the electrostatic contribution. Further, we find that the unusual virulence of this virus is potentially the consequence of Darwinian selection‐driven epistasis in protein evolution. The triple mutants (South African and Brazilian) may pose a serious threat to the efficacy of the already developed vaccine. Our analysis would help to understand the binding and structural dynamics of the new mutations in the RBD domain of the Spike protein and demand further investigation in in vitro and in vivo models to design potential therapeutics against the new variants.
The double corpus luteum: A novel sonographic sign of heterotopic pregnancy
Authors: Kluckman Matthew L. , Schwope Ryan B. , Provagna Alyssa J. , Yauger Belinda J. , Ramirez Christina I. 
Published: March 2021

AbstractHeterotopic pregnancy is a rare and highly morbid condition with simultaneous intrauterine and extra‐uterine pregnancies. The early diagnosis of heterotopic pregnancy is difficult, owing to rarity of the condition and nonspecific clinical and laboratory findings. This case report introduces the “double corpus luteum” sign, a new sonographic and magnetic resonance imaging sign which is easily detectable and should raise the index of suspicion for heterotopic pregnancy. We present a surgically confirmed spontaneous heterotopic and angular pregnancy in a young woman without risk factors or assisted reproductive therapy to illustrate the utility of this novel sign.
Use of a sensitive multisugar test for measuring segmental intestinal permeability in critically ill, mechanically ventilated adults: A pilot study
Authors: Tatucu‐Babet Oana A. , Forsyth Adrienne , Udy Andrew , Radcliffe Jessica , Benheim Devin , Calkin Caroline , Ridley Emma J. , Gantner Dashiell , Jois Markandeya , Itsiopoulos Catherine , Tierney Audrey C. 
Published: March 2021

AbstractBackgroundIncreased intestinal permeability (IP) is associated with sepsis in the intensive care unit (ICU). This study aimed to pilot a sensitive multisugar test to measure IP in the nonfasted state.MethodsCritically ill, mechanically ventilated adults were recruited from 2 ICUs in Australia. Measurements were completed within 3 days of admission using a multisugar test measuring gastroduodenal (sucrose recovery), small‐bowel (lactulose‐rhamnose [L‐R] and lactulose‐mannitol [L‐M] ratios), and whole‐gut permeability (sucralose‐erythritol ratio) in 24‐hour urine samples. Urinary sugar concentrations were compared at baseline and after sugar ingestion, and IP sugar recoveries and ratios were explored in relation to known confounders, including renal function.ResultsTwenty‐one critically ill patients (12 males; median, 57 years) participated. Group median concentrations of all sugars were higher following sugar administration; however, sucrose and mannitol increases were not statistically significant. Within individual patients, sucrose and mannitol concentrations were higher in baseline than after sugar ingestion in 9 (43%) and 4 (19%) patients, respectively. Patients with impaired (n = 9) vs normal (n = 12) renal function had a higher L‐R ratio (median, 0.130 vs 0.047; P = .003), lower rhamnose recovery (median, 15% vs 24%; P = .007), and no difference in lactulose recovery.ConclusionSmall‐bowel and whole‐gut permeability measurements are possible to complete in the nonfasted state, whereas gastroduodenal permeability could not be measured reliably. For small‐bowel IP measurements, the L‐R ratio is preferred over the L‐M ratio. Alterations in renal function may reduce the reliability of the multisugar IP test, warranting further exploration.
Quantifying the impact of chemicals on stable carbon and oxygen isotope values of raw pollen
Authors: Müller Carolina , Hennig Julian , Riedel Frank , Helle Gerhard 
Published: March 2021

ABSTRACTPurification protocols to extract pollen from lake sediments contain chemicals that alter the carbon and oxygen pollen‐isotope values according to pollen characteristics and family affiliation. Modern (raw) pollen of broad‐leaved (Alnus glutinosa, Betula pendula, Carpinus betulus, Corylus avellana, Fagus sylvatica and Quercus robur) and coniferous tree species (Picea abies and Pinus sylvestris) were treated with potassium hydroxide (KOH), hydrofluoric acid (HF), sodium hypochlorite (NaClO) and sulphuric acid (H2SO4) to test the impact on δ13Cpollen and δ18Opollen and assess the applicability in purification protocols. Pollen of broad‐leaved and coniferous trees reacted differently to chemical exposure, but response patterns are generally alike. Alterations of δ13Cpollen values vary between + 1.0‰ (B. pendula, NaClO‐treatment) and −5.0‰ (P. sylvestris, H2SO4‐treatment). The δ13Cpollen values of raw and chemically treated samples seem to be related after treatments with KOH, NaClO and HF, whereas the application of H2SO4 led to inconsistent changes among species. The impact of chemicals on δ18Opollen are more diverse and offsets range between +1.1‰ (C. avellana, NaClO‐treatment) and −17.9‰ (P. sylvestris, H2SO4‐treatment). In general, the use of isotope‐altering chemicals in purification protocols should be brought to a minimum, but the application of KOH and NaClO seems mostly unproblematic before δ13Cpollen and δ18Opollen analysis.
Compact, fast‐response, continuous, and wide‐angle laser beam steerers
Authors: He Ziqian , Wu Shin‐Tson 
Published: March 2021

AbstractA liquid crystal‐cladding waveguide with resistive electrode configuration is proposed for laser beam steering applications. It can achieve wide‐angle, continuous coverage, two‐dimensional beam control with fast response time. With numerical validation, we find that in comparison with previous prismatic electrode approach, our device demonstrates higher compatibility with high birefringence liquid crystal materials, and thus, a more compact form factor can be realized. Such a beam steerer is attractive for a wide range of applications including automotive LiDAR, eye‐tracking for near‐eye displays, and high‐precision 3D printing.
Hybrid Aptamer‐Molecularly Imprinted Polymer (aptaMIP) Nanoparticles from Protein Recognition—A Trypsin Model
Authors: Sullivan Mark V. , Clay Oliver , Moazami Michael P. , Watts Jonathan K. , Turner Nicholas W. 
Published: March 2021

AbstractAptamers offer excellent potential for replacing antibodies for molecular recognition purposes however their performance can compromise with biological/environmental degradation being a particular problem. Molecularly imprinted Polymers (MIPs) offer an alternative to biological materials and while these offer the robustness and ability to work in extreme environmental conditions, they often lack the same recognition performance. By slightly adapting the chemical structure of a DNA aptamer it is incorporated for use as the recognition part of a MIP, thus creating an aptamer‐MIP hybrid or aptaMIP. Here these are developed for the detection of the target protein trypsin. The aptaMIP nanoparticles offer superior binding affinity over conventional MIP nanoparticles (nanoMIPs), with KD values of 6.8 × 10−9 (±0.2 × 10−9) m and 12.3 × 10−9 (±0.4 × 10−9) m for the aptaMIP and nanoMIP, respectively. The aptaMIP also outperforms the aptamer only (10.3 × 10−9 m). Good selectivity against other protein targets is observed. Using surface plasmon resonance, the limit of detection for aptaMIP nanoparticles is twofold lower (2 nm) compared to the nanoMIP (4 nm). Introduction of the aptamer as a “macro‐monomer” into the MIP scaffold has beneficial effects and offers potential to improve this class of polymers significantly.
Polyrotaxane Crosslinked Self‐Healing Hydrogels for Switchable Bioadhesion
Authors: Wang Yushi , Dong Jiyu , Jin Jiahong , Jia Yong‐Guang 
Published: March 2021

AbstractAs an effective alternative to suture in wound closure, tissue adhesives often need to have excellent biocompatibility and suitable bioadhesion. To achieve long‐term adhesion on moist tissue, polyrotaxane (PR) crosslinked self‐healing hydrogels have been prepared by the introduction of dynamic borate bonds between PR bearing phenylboronic acid moieties (PR‐PBA) and dopamine grafted poly(vinyl alcohol) (PVA‐DOP). Synthesis of these precursor polymers PR‐PBA and PVA‐DOP is quite simple and the hydrogels combine dynamic borate bonds with the sliding motion of the phenylboronic acid moieties on PR. The sliding nature of the crosslinking points along the axle in the PR is thought to enhance the mechanical properties and adhesion ability of the resultant hydrogels. Meanwhile, catechol groups on dopamine units have been protected by borate bonds under alkaline conditions to avoid oxidation, and they then are released to react with various functional groups on tissue surface to ensure the switchable tissue adhesion. The self‐healing test and adhesion of hydrogels on pigskin demonstrate the ability to restore the original performance after repeated strain cycles and maintain strong tissue adhesion. The components of these hydrogels have satisfying biocompatibility. These results indicate that these self‐healing hydrogels have great potentials in tissue adhesion.
MRzero ‐ Automated discovery of MRI sequences using supervised learning
Authors: Loktyushin A. , Herz K. , Dang N. , Glang F. , Deshmane A. , Weinmüller S. , Doerfler A. , Schölkopf B. , Scheffler K. , Zaiss M. 
Published: March 2021

PurposeA supervised learning framework is proposed to automatically generate MR sequences and corresponding reconstruction based on the target contrast of interest. Combined with a flexible, task‐driven cost function this allows for an efficient exploration of novel MR sequence strategies.MethodsThe scanning and reconstruction process is simulated end‐to‐end in terms of RF events, gradient moment events in x and y, and delay times, acting on the input model spin system given in terms of proton density, and , and . As a proof of concept, we use both conventional MR images and maps as targets and optimize from scratch using the loss defined by data fidelity, SAR penalty, and scan time.ResultsIn a first attempt, MRzero learns gradient and RF events from zero, and is able to generate a target image produced by a conventional gradient echo sequence. Using a neural network within the reconstruction module allows arbitrary targets to be learned successfully. Experiments could be translated to image acquisition at the real system (3T Siemens, PRISMA) and could be verified in the measurements of phantoms and a human brain in vivo.ConclusionsAutomated MR sequence generation is possible based on differentiable Bloch equation simulations and a supervised learning approach.
A Nonlethal Genetic Assay for Discriminating Sex in Brook Trout
Authors: Webster N. , Price S. , Gowan C. , Coster S. S. 
Published: March 2021

Abstract
Identifying sex in salmonids using nonlethal methods is valuable for controlled breeding in aquaculture and understanding behavior and dispersal for conservation. Although salmonids are male heterogametic, genetic sex identification has been problematic because a specific sex determination locus has been elusive. We implemented a blind analysis to identify sex in Brook Trout Salvelinus fontinalis using genetic primers (sdY) developed for Brown Trout Salmo trutta along with cytochrome c oxidase subunit I (COI_BT1) as an internal control. Fin clips were taken from 35 Brook Trout and analyzed via PCR and gel electrophoresis, and fish were simultaneously sacrificed and dissected to identify sex via gonads. The genetic and phenotypic analysis matched in 97% of the Brook Trout that were sampled, suggesting that this primer combination is successful in genetic sex determination. The ability to sex Brook Trout genetically will allow scientists to observe the difference in male and female Brook Trout behavior in the lab and natural stream ecosystems without using lethal methods.