bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid, precise quantification of large DNA excisions and inversions by ddPCR
Authors: Watry Hannah L. , Feliciano Carissa M. , Gjoni Ketrin , Takahashi Gou , Miyaoka Yuichiro , Conklin Bruce R. , Judge Luke M. 
Published: September 2020

AbstractThe excision of genomic sequences using paired CRISPR-Cas nucleases is a powerful tool to study gene function, create disease models and holds promise for therapeutic gene editing. However, our understanding of the factors that favor efficient excision is limited by the lack of a rapid, accurate measurement of DNA excision outcomes that is free of amplification bias. Here, we introduce ddXR (droplet digital PCR eXcision Reporter), a method that enables the accurate and sensitive detection of excisions and inversions independent of length. The method can be completed in a few hours without the need for next-generation sequencing. The ddXR method uncovered unexpectedly high rates of large (> 20 kb) excisions and inversions, while also revealing a surprisingly low dependence on linear distance, up to 170 kb. We further modified the method to measure precise repair of excision junctions and allele-specific excision, with important implications for disease modeling and therapeutic gene editing.
Case studies of clinical hemodialysis membranes: influences of membrane morphology and biocompatibility on uremic blood-membrane interactions and inflammatory biomarkers
Authors: Westphalen Heloisa , Saadati Shaghayegh , Eduok Ubong , Abdelrasoul Amira , Shoker Ahmed , Choi Phillip , Doan Huu , Ein-Mozaffari Farhad 
Published: September 2020

AbstractEnd stage renal disease (ESRD) patients depend on hemodialysis (HD) as a life-sustaining treatment, but HD membrane properties play a critical role in blood activation during HD and can lead to severe patient outcomes. This study reports on a series of investigations on the common clinical HD membranes available in Canadian hospitals to explore the key reasons behind their susceptibility to blood activation and unstable cytokine. Clinical HD membranes composed of cellulose triacetate (CTA) and polyvinylpyrrolidone: polyarylethersulfone (PAES: PVP) were thoroughly characterized in terms of morphology and chemical composition. Membrane-surface interactions with uremic blood samples after HD treatment were probed using Fourier Transform Infra-Red (FTIR) and Raman spectroscopic techniques in order to understand changes in chemistry on membrane fibers. In addition, as part of this innovative study, we utilized Molecular Modeling Docking to examine the interactions of human blood proteins and membrane models to gain an in-depth understanding of functional group types responsible for perceived interactions. In-vitro adsorption of fibrinogen on different clinical HD membranes was compared at similar clinical operating conditions. Samples were collected from dialysis patients to ascertain the extent of inflammatory biomarkers released, before, during (30 and 90 min) and after dialysis (4 h). Collected blood samples were analyzed using Luminex assays for the inflammatory biomarkers of Serpin/Antithrombin-III, Properdin, C5a, 1L-1α, 1L-1β, TNF-α, IL6, and vWF. We have likewise incubated uremic blood in vitro with the two membrane materials to determine the impact that membrane materials pose in favor of activation away from the hydrodynamics influences. The results of our morphological, chemical, spectroscopic, and in vitro incubation analyses indicate that CTA membranes have a smoother surface and higher biocompatibility than PAES: PVP membranes, however, it has smaller pore size distribution, which results in poor clearance of a broad spectrum of uremic toxins. However, the rougher surface and greater hydrophilicity of PAES: PVP membranes increases red blood cell rupture at the membrane surface, which promotes protein adsorption and biochemical cascade reactions. Molecular docking studies indicate sulfone functional groups play an important role in the adsorption of proteins and receptors. PAES: PVP membranes result in slower but greater adsorption of fibrinogen, but are more likely to experience reversible and irreversible fouling as well as backfiltration. Our major finding is that a single dialysis session, even with a more biocompatible membrane such as CTA, increases the levels of complement and inflammation factors, but to a milder extent than dialysis with a PAES membrane.
Asymmetry analysis of optical coherence tomography angiography macular perfusion density measurements in preperimetric and perimetric glaucoma
Authors: Chang Pei-Yao , Wang Jiun-Yi , Wang Jia-Kang , Yeh Shih-Cheng , Chang Shu-Wen 
Published: September 2020

AbstractMacular retinal layer thickness asymmetry indices, particularly for the ganglion cell layer, are promising early indicators of glaucomatous damage. We evaluated macular perfusion density asymmetry (MPDA) among normal, preperimetric glaucoma (PPG), and perimetric glaucoma (PG) eyes, and we tested the performance of MPDA in differentiating between control and glaucoma eyes with or without visual field (VF) defects. In this study, 116 eyes (39 normal, 27 PPG, and 50 PG eyes) with optical coherence tomography angiography images of the macula were analysed. No significant difference was found in outer and inner MPDA between the control and PPG groups. However, outer MPDA was significantly higher in the PG group than in the PPG group (p = 0.009). Asymmetry of perfusion density and structural parameters was compared; no significant difference was found between controls and glaucoma patients. Outer MPDA had significantly higher discrimination ability between PPG and PG than did macular ganglion cell layer–inner plexiform layer thickness asymmetry (p = 0.039). In conclusion, the discriminant capability of MPDA for discriminating between glaucoma patients with and without VF defects is significantly higher than that of structural asymmetry. MPDA may be helpful in monitoring glaucoma progression in clinical practice.
Enhancing microtubule stabilization rescues cognitive deficits and ameliorates pathological phenotype in an amyloidogenic Alzheimer’s disease model
Authors: Fernandez-Valenzuela Juan Jose , Sanchez-Varo Raquel , Muñoz-Castro Clara , De Castro Vanessa , Sanchez-Mejias Elisabeth , Navarro Victoria , Jimenez Sebastian , Nuñez-Diaz Cristina , Gomez-Arboledas Angela , Moreno-Gonzalez Ines , Vizuete Marisa , Davila Jose Carlos , Vitorica Javier , Gutierrez Antonia 
Published: September 2020

AbstractIn Alzheimer’s disease (AD), and other tauopathies, microtubule destabilization compromises axonal and synaptic integrity contributing to neurodegeneration. These diseases are characterized by the intracellular accumulation of hyperphosphorylated tau leading to neurofibrillary pathology. AD brains also accumulate amyloid-beta (Aβ) deposits. However, the effect of microtubule stabilizing agents on Aβ pathology has not been assessed so far. Here we have evaluated the impact of the brain-penetrant microtubule-stabilizing agent Epothilone D (EpoD) in an amyloidogenic model of AD. Three-month-old APP/PS1 mice, before the pathology onset, were weekly injected with EpoD for 3 months. Treated mice showed significant decrease in the phospho-tau levels and, more interesting, in the intracellular and extracellular hippocampal Aβ accumulation, including the soluble oligomeric forms. Moreover, a significant cognitive improvement and amelioration of the synaptic and neuritic pathology was found. Remarkably, EpoD exerted a neuroprotective effect on SOM-interneurons, a highly AD-vulnerable GABAergic subpopulation. Therefore, our results suggested that EpoD improved microtubule dynamics and axonal transport in an AD-like context, reducing tau and Aβ levels and promoting neuronal and cognitive protection. These results underline the existence of a crosstalk between cytoskeleton pathology and the two major AD protein lesions. Therefore, microtubule stabilizers could be considered therapeutic agents to slow the progression of both tau and Aβ pathology.
A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)
Authors: Allain Thomas W. , Stentiford Grant D. , Bass David , Behringer Donald C. , Bojko Jamie 
Published: September 2020

AbstractThe Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).
Assessment of airborne particles and bioaerosols concentrations in a waste recycling environment in Brazil
Authors: Wikuats Caroline Fernanda Hei , Duarte Eduardo Henrique , Prates Kátia Valéria Marques Cardoso , Janiaski Laura Lahr Lourenço , de Oliveira Gabriel Bárbara , da Cunha Molina Alex , Martins Leila Droprinchinski 
Published: September 2020

AbstractThis study aims to assess the concentrations of size-fractioned particle mass (PM1.0, PM2.5, PM4.0, PM10) and number (PNC0.3, PNC0.5, PNC1.0, PNC2.5), bacteria, and fungi in a Materials Recycling Facility (MRF) in Brazil. The measurements were performed inside the waste processing shed (P1) and in the outdoor environment (P2) during working days in winter and spring of 2017, and summer of 2019. A total of 2,400 min of PM, 1,440 min of PNC, and 216 samples of bioaerosols were collected in the morning and afternoon. P1 has the strongest air contamination with mean values of 475.5 ± 563.7 µg m−3 for PM10, 58.6 ± 36.0 cm−3 for PNC0.3, 1,088.8 ± 825.2 colony-forming units per cubic meter (CFU m−3) for bacteria, and 2,738.3 ± 1,381.3 CFU m−3 for fungi. The indoor/outdoor ratios indicated the large influence of indoor sources due to the activities performed inside P1 that promote the generation and resuspension of pollutants. Gram-positive bacteria dominated with 58.6% of indoor samples. Overall, our results show a critical indoor air quality situation in a Brazilian MRF, which may cause several health risks for waste pickers. Finally, we call attention to the lack of occupational exposure limits for bioaerosols in industrial workplaces and mainly in MRFs.
Corneal topography in keratoconus evaluated more than 30 years after penetrating keratoplasty: a Fourier harmonic analysis
Authors: Ono Takashi , Kawasaki Yuki , Chen Lily Wei , Toyono Tetsuya , Shirakawa Rika , Yoshida Junko , Aihara Makoto , Miyai Takashi 
Published: September 2020

AbstractThe aim of this observational study was to examine the characteristics of anterior and posterior corneal topography in keratoconic eyes more than 30 years after penetrating keratoplasty (PK). Patients who maintained clear grafts for more than 30 years after PK were included and divided into the keratoconus (KC) group or other diseases (Others) group, based on the primary indication. Twenty-six eyes of 26 patients were included. The KC group and the Others group included 14 eyes and 12 eyes, respectively. The KC group participants were younger at the time of surgery (P = 0.03). No differences were found in best-spectacle-corrected visual acuity, keratometric power, and central-corneal-thickness. Based on corneal topography using Fourier harmonic analyses, regular astigmatism in the anterior cornea was significantly larger (P = 0.047) and the spherical component in the posterior cornea was significantly lower (P = 0.01) in the KC group. The area under the receiver operating characteristic curve of the spherical component, regular astigmatism, asymmetry component, and higher-order irregularity were 66.07%, 63.10%, 57.14%, and 59.23%, respectively, in the anterior cornea and 80.65%, 52.98%, 63.10%, and 63.99%, respectively, in the posterior cornea. Our results suggested that Fourier harmonic analysis of corneal topography could be useful for patients with KC long after PK.
Polyphenols profile of pomegranate leaves and their role in green synthesis of silver nanoparticles
Authors: Swilam Noha , Nematallah Khaled A. 
Published: September 2020

AbstractThe current study reports on polyphenols profile of pomegranate leaves (PL) Punica granatum grown in Egypt and exhibiting their role in development of an eco-friendly method of green synthesis of silver nanoparticles (AgNPs). PL aqueous alcohol extract was fractionated, the major phenolic compound was isolated from the polyphenols rich fraction (ethyl acetate fraction) and identified by conventional and spectroscopic methods of analysis as ellagic acid. Furthermore, the fraction was standardized and analysed using UPLC-PDA-UV and LC–MS-MS techniques revealing tentative identification of 23 polyphenolic compounds, quantifying ellagic acid as 43.14 ± 0.57 μg/mg of the fraction. AgNPs were successfully synthesized with the aid of polyphenols rich fraction. This is the first report revealing the systematic optimization of the green synthesis process using various independent variables. AgNPs were characterized by adopting UV–Vis spectroscopy, FTIR, XRD, and SEM, which revealed strong SPR band within average of λ max 425 nm and polygonal shaped nanoparticles of 26.22 nm size, respectively. The antimicrobial efficacies of AgNPs and polyphenols rich fraction were tested against Gram-positive bacteria (Bacillus subtilis, Staphylococcus aureus, and Sarcina lutea), Gram-negative bacteria (Salmonella paratyphi, Escherichia coli, and Pseudomonas aeruginosa) and fungi (Candida albicans). AgNPs showed a concentration-dependent activity against all the tested microorganisms.
The synergistic interaction of thermal stress coupled with overstocking strongly modulates the transcriptomic activity and immune capacity of rainbow trout (Oncorhynchus mykiss)
Authors: Rebl Alexander , Korytář Tomáš , Borchel Andreas , Bochert Ralf , Strzelczyk Joanna Ewa , Goldammer Tom , Verleih Marieke 
Published: September 2020

AbstractThe objective of the present study is to identify and evaluate informative indicators for the welfare of rainbow trout exposed to (A) a water temperature of 27 °C and (B) a stocking density of 100 kg/m3combined with a temperature of 27 °C. The spleen-somatic and condition index, haematocrit and the concentrations of haemoglobin, plasma cortisol and glucose revealed non-significant differences between the two stress groups and the reference group 8 days after the onset of the experiments. The transcript abundance of almost 1,500 genes was modulated at least twofold in in the spleen of rainbow trout exposed to a critical temperature alone or a critical temperature combined with crowding as compared to the reference fish. The number of differentially expressed genes was four times higher in trout that were simultaneously challenged with high temperature and crowding, compared to trout challenged with high temperature alone. Based on these sets of differentially expressed genes, we identified unique and common tissue- and stress type-specific pathways. Furthermore, our subsequent immunologic analyses revealed reduced bactericidal and inflammatory activity and a significantly altered blood-cell composition in challenged versus non-challenged rainbow trout. Altogether, our data demonstrate that heat and overstocking exert synergistic effects on the rainbow trout’s physiology, especially on the immune system.
Identifying metastasis-initiating miRNA-target regulations of colorectal cancer from expressional changes in primary tumors
Authors: Lee Jongmin , Hong Hye Kyung , Peng Sheng-Bin , Kim Tae Won , Lee Woo Yong , Yun Seong Hyun , Kim Hee Cheol , Liu Jiangang , Ebert Philip J. , Aggarwal Amit , Jung Sungwon , Cho Yong Beom 
Published: September 2020

AbstractColorectal cancer (CRC) is prevalent with high mortality, with liver metastasis contributing as a major factor that worsens the survival of patients. The roles of miRNAs in CRC have been elucidated, subsequent to recent studies that suggest the involvement of miRNAs in cancer biology. In this study, we compare the miRNA and gene expression profiles of primary tumors between two groups of patients (with and without liver metastasis) to identify the metastasis-initiating microRNA-target gene regulations. Analysis from 33 patients with metastasis and 14 patients without metastasis revealed that 17 miRNAs and their 198 predicted target genes are differentially expressed, where the target genes showed association with cancer progression and metastasis with statistical significance. In order to evaluate the clinical implications of the findings, we classified CRC patients of independent data into two groups based on the identified miRNA-target regulations, where one group was closer to primary tumors with metastasis than the other group. The comparison of survival showed statistically significant difference, thereby implying the roles of the identified miRNA-target regulations in cancer progression and metastasis. The identification of metastasis-initiating miRNA-target regulations in this study will lead to better understanding of the roles of miRNAs in CRC progression.
Effects of introducing eels on the yields and availability of fertilizer nitrogen in an integrated rice–crayfish system
Authors: Lv Weiwei , Yuan Quan , Lv Weiguang , Zhou Wenzong 
Published: September 2020

AbstractRecently, many new rice–fish co-culture models have been developed to increase economic and ecological benefits. In this study, we added eels (Monopterus albus) to a rice–crayfish system and conducted a 3-year field investigation to compare the yields and availability of fertilizer N among groups with a low density of eels, high density of eels and no eels. We performed a mesocosm experiment and used an isotope tracer technique to detect the fate of fertilizer N. The results showed that the rice yields significantly improved after the introduction of the eels. However, the introduction of a high density of eels significantly limited the crayfish yield, increased water N and N2O emissions and decreased soil N content. The mesocosm experiment suggested that the use efficiency of fertilizer N was significantly increased after the introduction of the eels. The fertilizer N used by rice was significantly higher in rice–crayfish–eel system than in rice–crayfish system. This study indicated that the introduction of eels may be a good practice for improving yields and availability of fertilizer N in a rice–crayfish system.
Oxidation and electrical properties of chromium–iron alloys in a corrosive molten electrolyte environment
Authors: Esmaily M. , Mortazavi A. N. , Birbilis N. , Allanore A. 
Published: September 2020

AbstractChromium–iron (CrFe) binary alloys have recently been proposed to serve as the “inert” anode for molten oxide electrolysis (MOE). Herein, the effects of anodic polarization on physical and functional properties of CrFe anodes in the corrosive environment of MOE are studied via empirical observations and theoretical calculations. The findings indicate that the alloys form an inner chromia–alumina solid-solution covered by an MgCr2O4 spinel layer. A survey into the electrical properties of the detected oxides suggests that the layered oxide scale function as an efficient conductor of electricity at elevated temperature. The formation mechanism of the oxides is also investigated.
Mating and blood-feeding induce transcriptome changes in the spermathecae of the yellow fever mosquito Aedes aegypti
Authors: Camargo Carolina , Ahmed-Braimah Yasir H. , Amaro I. Alexandra , Harrington Laura C. , Wolfner Mariana F. , Avila Frank W. 
Published: September 2020

AbstractAedes aegyptimosquitoes are the primary vectors of numerous viruses that impact human health. As manipulation of reproduction has been proposed to suppress mosquito populations, elucidation of biological processes that enable males and females to successfully reproduce is necessary. One essential process is female sperm storage in specialized structures called spermathecae.Aedes aegyptifemales typically mate once, requiring them to maintain sperm viably to fertilize eggs they lay over their lifetime. Spermathecal gene products are required forDrosophilasperm storage and sperm viability, and a spermathecal-derived heme peroxidase is required for long-termAnopheles gambiaefertility. Products of theAe. aegyptispermathecae, and their response to mating, are largely unknown. Further, although female blood-feeding is essential for anautogenous mosquito reproduction, the transcriptional response to blood-ingestion remains undefined in any reproductive tissue. We conducted an RNAseq analysis of spermathecae from unfed virgins,mated only, and mated and blood-fed females at 6, 24, and 72 h post-mating and identified significant differentially expressed genes in each group at each timepoint. A blood-meal following mating induced a greater transcriptional response in the spermathecae than mating alone. This study provides the first view of elicited mRNA changes in the spermathecae by a blood-meal in mated females.
Usefulness of heart rhythm complexity in heart failure detection and diagnosis
Authors: Tsai Cheng-Hsuan , Ma Hsi-Pin , Lin Yen-Tin , Hung Chi-Sheng , Huang Shan-Hsuan , Chuang Bei-Lin , Lin Chen , Lo Men-Tzung , Peng Chung-Kang , Lin Yen-Hung 
Published: September 2020

AbstractHeart failure (HF) is a major cardiovascular disease worldwide, and the early detection and diagnosis remain challenges. Recently, heart rhythm complexity analysis, derived from non-linear heart rate variability (HRV) analysis, has been proposed as a non-invasive method to detect diseases and predict outcomes. In this study, we aimed to investigate the diagnostic value of heart rhythm complexity in HF patients. We prospectively analyzed 55 patients with symptomatic HF with impaired left ventricular ejection fraction and 97 participants without HF symptoms and normal LVEF as controls. Traditional linear HRV parameters and heart rhythm complexity including detrended fluctuation analysis (DFA) and multiscale entropy (MSE) were analyzed. The traditional linear HRV, MSE parameters and DFAα1 were significantly lower in HF patients compared with controls. In regression analysis, DFAα1 and MSE scale 5 remained significant predictors after adjusting for multiple clinical variables. Among all HRV parameters, MSE scale 5 had the greatest power to differentiate the HF patients from the controls in receiver operating characteristic curve analysis (area under the curve: 0.844). In conclusion, heart rhythm complexity appears to be a promising tool for the detection and diagnosis of HF.