bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography
Authors: Ihara Kentaro , Hato Masakatsu , Nakane Takanori , Yamashita Keitaro , Kimura-Someya Tomomi , Hosaka Toshiaki , Ishizuka-Katsura Yoshiko , Tanaka Rie , Tanaka Tomoyuki , Sugahara Michihiro , Hirata Kunio , Yamamoto Masaki , Nureki Osamu , Tono Kensuke , Nango Eriko , Iwata So , Shirouzu Mikako 
Published: November 2020

AbstractIn meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC17+4 mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A2A receptor (A2AR). The structures of EROCOC17+4-matrix grown A2AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A2AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC17+4/water system did not form the crystalline LC phase at least down to − 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline LC phase below about 17 °C. As the LC phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC17+4 will expand the utility of the in meso method.
Role of peripheral 5-HT5A receptors in 5-HT-induced cardiac sympatho-inhibition in type 1 diabetic rats
Authors: García-Pedraza José Ángel , Hernández-Abreu Oswaldo , Morán Asunción , Carretero José , García-Domingo Mónica , Villalón Carlos M. 
Published: November 2020

Abstract5-HT inhibits cardiac sympathetic neurotransmission in normoglycaemic rats, via 5-HT1B, 5-HT1Dand 5-HT5Areceptor activation. Since type 1 diabetes impairs the cardiac sympathetic innervation leading to cardiopathies, this study aimed to investigate whether the serotonergic influence on cardiac noradrenergic control is altered in type 1 diabetic rats. Diabetes was induced in male Wistar rats by streptozotocin (50 mg/kg, i.p.). Four weeks later, the rats were anaesthetized, pithed and prepared for producing tachycardic responses by electrical preganglionic stimulation (C7-T1) of the cardioaccelerator sympathetic outflow or i.v. noradrenaline bolus injections. Immunohistochemistry was performed to study 5-HT1B, 5-HT1Dand 5-HT5Areceptor expression in the stellate ganglion from normoglycaemic and diabetic rats. In the diabetic group, i) i.v. continuous infusions of 5-HT induced a cardiac sympatho-inhibition that was mimicked by the 5-HT1/5Aagonist 5-carboxamidotryptamine (without modifying noradrenaline-induced tachycardia), but not by the agonists indorenate (5-HT1A), CP 93,129 (5-HT1B), PNU 142633 (5-HT1D), or LY344864 (5-HT1F); ii) SB 699551 (5-HT5Aantagonist; i.v.) completely reversed 5-CT-induced cardiac sympatho-inhibition; and iii) 5-HT5Areceptors were more expressed in the stellate ganglion compared to normoglycaemic rats. These results show the prominent role of the peripheral 5-HT5Areceptors prejunctionally inhibiting the cardiac sympathetic drive in type 1 diabetic rats.
Giant refractometric sensitivity by combining extreme optical Vernier effect and modal interference
Authors: Gomes André D. , Kobelke Jens , Bierlich Jörg , Dellith Jan , Rothhardt Manfred , Bartelt Hartmut , Frazão Orlando 
Published: November 2020

AbstractThe optical Vernier effect consists of overlapping responses of a sensing and a reference interferometer with slightly shifted interferometric frequencies. The beating modulation thus generated presents high magnified sensitivity and resolution compared to the sensing interferometer, if the two interferometers are slightly out of tune with each other. However, the outcome of such a condition is a large beating modulation, immeasurable by conventional detection systems due to practical limitations of the usable spectral range. We propose a method to surpass this limitation by using a few-mode sensing interferometer instead of a single-mode one. The overlap response of the different modes produces a measurable envelope, whilst preserving an extremely high magnification factor, an order of magnification higher than current state-of-the-art performances. Furthermore, we demonstrate the application of that method in the development of a giant sensitivity fibre refractometer with a sensitivity of around 500 µm/RIU (refractive index unit) and with a magnification factor over 850.
Spatial patterns of pathogen prevalence in questing Ixodes ricinus nymphs in southern Scandinavia, 2016
Authors: Kjær Lene Jung , Klitgaard Kirstine , Soleng Arnulf , Edgar Kristin Skarsfjord , Lindstedt Heidi Elisabeth H. , Paulsen Katrine M. , Andreassen Åshild Kristine , Korslund Lars , Kjelland Vivian , Slettan Audun , Stuen Snorre , Kjellander Petter , Christensson Madeleine , Teräväinen Malin , Baum Andreas , Jensen Laura Mark , Bødker René 
Published: November 2020

AbstractTick-borne pathogens cause diseases in animals and humans, and tick-borne disease incidence is increasing in many parts of the world. There is a need to assess the distribution of tick-borne pathogens and identify potential risk areas. We collected 29,440 tick nymphs from 50 sites in Scandinavia from August to September, 2016. We tested ticks in a real-time PCR chip, screening for 19 vector-associated pathogens. We analysed spatial patterns, mapped the prevalence of each pathogen and used machine learning algorithms and environmental variables to develop predictive prevalence models. All 50 sites had a pool prevalence of at least 33% for one or more pathogens, the most prevalent being Borrelia afzelii, B. garinii, Rickettsia helvetica, Anaplasma phagocytophilum, and Neoehrlichia mikurensis. There were large differences in pathogen prevalence between sites, but we identified only limited geographical clustering. The prevalence models performed poorly, with only models for R. helvetica and N. mikurensis having moderate predictive power (normalized RMSE from 0.74–0.75, R2 from 0.43–0.48). The poor performance of the majority of our prevalence models suggest that the used environmental and climatic variables alone do not explain pathogen prevalence patterns in Scandinavia, although previously the same variables successfully predicted spatial patterns of ticks in the same area.
Electrically stimulated hind limb muscle contractions increase adult hippocampal astrogliogenesis but not neurogenesis or behavioral performance in male C57BL/6J mice
Authors: Gardner Jennie C. , Dvoretskiy Svyatoslav V. , Yang Yanyu , Venkataraman Sanjana , Lange Dominica A. , Li Shiping , Boppart Alexandria L. , Kim Noah , Rendeiro Catarina , Boppart Marni D. , Rhodes Justin S. 
Published: November 2020

AbstractRegular exercise is crucial for maintaining cognitive health throughout life. Recent evidence suggests muscle contractions during exercise release factors into the blood which cross into the brain and stimulate adult hippocampal neurogenesis. However, no study has tested whether muscle contractions alone are sufficient to increase adult hippocampal neurogenesis and improve behavioral performance. Adult male, C57BL/6J mice were anesthetized and exposed to bilateral hind limb muscle contractions (both concentric and eccentric) via electrical stimulation (e-stim) of the sciatic nerve twice a week for 8 weeks. Each session lasted approximately 20 min and consisted of a total of 40 muscle contractions. The control group was treated similarly except without e-stim (sham). Acute neuronal activation of the dentate gyrus (DG) using cFos immunohistochemistry was measured as a negative control to confirm that the muscle contractions did not activate the hippocampus, and in agreement, no DG activation was observed. Relative to sham, e-stim training increased DG volume by approximately 10% and astrogliogenesis by 75%, but no difference in neurogenesis was detected and no improvement in behavioral performance was observed. E-stim also increased astrogliogenesis in CA1/CA2 hippocampal subfields but not in the cortex. Results demonstrate that muscle contractions alone, in absence of DG activation, are sufficient to increase adult hippocampal astrogliogenesis, but not neurogenesis or behavioral performance in mice.
Variations in the frequencies of polymorphisms in the CYP2C9 gene in six major ethnicities of Pakistan
Authors: Ahmed Sagheer , Altaf Nadeem , Ejaz Mahnoor , Altaf Aisha , Amin Aneela , Janjua Kholood , Khan Arif Ullah , Imran Imran , Khan Saeed 
Published: November 2020

AbstractGenetic variation in cytochrome P450 (CYP) 2C9 is known to cause significant inter-individual differences in drug response and adverse effects. The frequencies of CYP2C9*2 and CYP2C9*3, both of which are responsible for the low activity of the enzyme, are not known in the Pakistani population. Therefore, we screened various ethnic groups residing in Pakistan for these polymorphisms. A total of 467 healthy human volunteers were recruited from six major ethnicities of Pakistan after written informed consent. Our results indicate that about 20% of the Pakistani population has a genotype containing at least one low activity allele. Ethnic Punjabi and Pathan populations had the highest frequencies of wild type genotypes while Urdu, Seraiki, and Sindhi populations showed higher rates of both low activity genotypes. The Baloch population showed the highest rates of low activity genotypes with less than 50% of the samples showing wild type genotypes, suggesting that more than half of the Baloch population possesses low activity genotypes. The frequencies found in various ethnic groups in Pakistan were comparable with ethnicities in the South Asian region except for the Baloch population. These results suggest that pharmacogenetics screening for low activity genotypes may be a helpful tool for clinicians while prescribing medications metabolized by CYP2C9.
Cryopreservation of testicular tissue from Murray River Rainbowfish, Melanotaenia fluviatilis
Authors: Rivers Nicola , Daly Jonathan , Jones Robert , Temple-Smith Peter 
Published: November 2020

AbstractGlobally, fish populations are in decline from overfishing, habitat destruction and poor water quality. Recent mass fish deaths in Australia’s Murray–Darling Basin highlight the need for improved conservation methods for endangered fish species. Cryopreservation of testicular tissue allows storage of early sperm precursor cells for use in generating new individuals via surrogacy. We describe successful isolation and cryopreservation of spermatogonia in an Australian rainbowfish. Testis histology showed rainbowfish spermatogonia are large (> 10 μm) and stain positive for Vasa, an early germ line-specific protein. Using size-based flow cytometry, testis cell suspensions were sorted through “A” (> 9 μm) and “B” gates (2–5 μm); the A gate produced significantly more Vasa-positive cells (45.0% ± 15.2%) than the “B” gate (0.0% ± 0.0%) and an unsorted control (22.9% ± 9.5%, p < 0.0001). The most successful cryoprotectant for “large cell” (> 9 μm) viability (72.6% ± 10.5%) comprised 1.3 M DMSO, 0.1 M trehalose and 1.5% BSA; cell viability was similar to fresh controls (78.8% ± 10.5%) and significantly better than other cryoprotectants (p < 0.0006). We have developed a protocol to cryopreserve rainbowfish testicular tissue and recover an enriched population of viable spermatogonia. This is the first step in developing a biobank of reproductive tissues for this family, and other Australian fish species, in the Australian Frozen Zoo.
Gold cauldrons as efficient candidates for plasmonic tweezers
Authors: Khosravi Mohammad Ali , Aqhili Abolfazl , Vasini Shoaib , Khosravi Mohammad Hossein , Darbari Sara , Hajizadeh Faegheh 
Published: November 2020

AbstractIn this report, gold cauldrons are proposed and proved as efficient candidates for plasmonic tweezers. Gold cauldrons benefit from high field localization in the vicinity of their apertures, leading to particle trapping by a reasonably low power source. The plasmonic trapping capability of a single gold cauldron and a cauldrons cluster are studied by investigating the plasmon-induced variations of the optical trap stiffness in a conventional optical tweezers configuration. This study shows that the localized plasmonic fields and the consequent plasmonic forces lead to enhanced trap stiffness in the vicinity of the cauldrons. This observation is pronounced for the cauldrons cluster, due to the additive plasmonic fields of the neighboring cauldrons. Strong direct plasmonic tweezing by the gold cauldrons cluster is also investigated and confirmed by our simulations and experimental results. In addition to the presented plasmonic trapping behavior, gold cauldrons benefit from a low cost and simple fabrication process with acceptable controllability over the structural average dimensions and plasmonic behavior, making them attractive for emerging lab-on-a-chip optophoresis applications.
Environmental dust repelling from hydrophilic/hydrophobic surfaces under sonic excitations
Authors: Abubakar Abba Abdulhamid , Yilbas Bekir Sami , Al-Qahtani Hussain , Alzaydi Ammar 
Published: November 2020

AbstractDust repelling from transparent polyvinyl chloride film surface via sonic excitation is examined and dynamics of repelled (inflight) dust particles are analyzed. An experimental rig is designed and built to assess the vibrational characteristics of the polyvinyl chloride film at different frequencies of sonic excitation. A high speed recording system and tracking program are utilized monitoring and evaluating the dynamics of the inflight particles. The dynamics of inflight particles are also simulated numerically and the predictions are compared with those of the experimental data. In order to examine the influence of dust particle adhesion on the dynamics of the inflight particles, the polyvinyl chloride film surface is hydrophobized through dip coating by functionalized nano-silica particles. Improvement of the optical transmittance of the dust mitigated film is determined via outdoor tests. The findings demonstrate that sonic excitation repels the particles from the film surface and it is more pronounced at 64 Hz excitation frequency while demonstrating that sonic excitation can be used for dust removal from transparent surfaces. The mitigation via sonic excitation improves the optical transmittance of the dusty surface by 77%, which becomes more apparent for hydrophobic surfaces.
Roles for the RNA polymerase III regulator MAFR-1 in regulating sperm quality in Caenorhabditis elegans
Authors: Hammerquist Amy M. , Curran Sean P. 
Published: November 2020

AbstractThe negative regulator of RNA polymerase (pol) III mafr-1 has been shown to affect RNA pol III transcript abundance, lipid biosynthesis and storage, progeny output, and lifespan. We deleted mafr-1 from the Caenorhabditis elegans genome and found that animals lacking mafr-1 replicated many phenotypes from previous RNAi-based studies and discovered a new sperm-specific role. Utilizing a yeast two-hybrid assay, we discovered several novel interactors of MAFR-1 that are expressed in a sperm- and germline-enriched manner. In support of a role for MAFR-1 in the male germline, we found mafr-1 null males have smaller spermatids that are less capable in competition for fertilization; a phenotype that was dependent on RNA pol III activity. Restoration of MAFR-1 expression specifically in the germline rescued the spermatid-related phenotypes, suggesting a cell autonomous role for MAFR-1 in nematode male fertility. Based on the high degree of conservation of Maf1 activity across species, our study may inform similar roles for Maf1 and RNA pol III in mammalian male fertility.
Prediction of age and brachial-ankle pulse-wave velocity using ultra-wide-field pseudo-color images by deep learning
Authors: Nagasato Daisuke , Tabuchi Hitoshi , Masumoto Hiroki , Kusuyama Takanori , Kawai Yu , Ishitobi Naofumi , Furukawa Hiroki , Adachi Shouto , Murao Fumiko , Mitamura Yoshinori 
Published: November 2020

AbstractThis study examined whether age and brachial-ankle pulse-wave velocity (baPWV) can be predicted with ultra-wide-field pseudo-color (UWPC) images using deep learning (DL). We examined 170 UWPC images of both eyes of 85 participants (40 men and 45 women, mean age: 57.5 ± 20.9 years). Three types of images were included (total, central, and peripheral) and analyzed by k-fold cross-validation (k = 5) using Visual Geometry Group-16. After bias was eliminated using the generalized linear mixed model, the standard regression coefficients (SRCs) between actual age and baPWV and predicted age and baPWV from the UWPC images by the neural network were calculated, and the prediction accuracies of the DL model for age and baPWV were examined. The SRC between actual age and predicted age by the neural network was 0.833 for all images, 0.818 for central images, and 0.649 for peripheral images (all P < 0.001) and between the actual baPWV and the predicted baPWV was 0.390 for total images, 0.419 for central images, and 0.312 for peripheral images (all P < 0.001). These results show the potential prediction capability of DL for age and vascular aging and could be useful for disease prevention and early treatment.
In situ formation of photoactive B-ring reduced chlorophyll isomer in photosynthetic protein LH2
Authors: Saga Yoshitaka , Otsuka Yuji , Funakoshi Daichi , Masaoka Yuto , Kihara Yu , Hidaka Tsubasa , Hatano Hiroka , Asakawa Hitoshi , Nagasawa Yutaka , Tamiaki Hitoshi 
Published: November 2020

AbstractNatural chlorophylls have a D-ring reduced chlorin π-system; however, no naturally occurring photosynthetically active B-ring reduced chlorins have been reported. Here we report a B-ring reduced chlorin, 17,18-didehydro-bacteriochlorophyll (BChl) a, produced by in situ oxidation of B800 bacteriochlorophyll (BChl) a in a light-harvesting protein LH2 from a purple photosynthetic bacterium Phaeospirillum molischianum. The regioselective oxidation of the B-ring of B800 BChl a is rationalized by its molecular orientation in the protein matrix. The formation of 17,18-didehydro-BChl a produced no change in the local structures and circular arrangement of the LH2 protein. The B-ring reduced 17,18-didehydro-BChl a functions as an energy donor in the LH2 protein. The photoactive B-ring reduced Chl isomer in LH2 will be helpful for understanding the photofunction and evolution of photosynthetic cyclic tetrapyrrole pigments.
Structural and proteomic analyses of vitelline membrane proteins of blackbird (Turdus merula) and song thrush (Turdus philomelos)
Authors: Damaziak Krzysztof , Kieliszek Marek , Gozdowski Dariusz 
Published: November 2020

AbstractIn this study, we aimed to perform structural and proteomic analysis of the vitelline membrane (VM) of two species birds belonging to the family Turdidae: blackbird (Turdus merula) and song thrush (Turdus philomelos). We performed structural analyses using scanning electron microscopy. The VM proteins were identified and compared to the best-known chicken VM proteins. According to our results, VM of both species has a typical three-layered structure: the outer layer, inner layer, and the continuous membrane between them. An unusual observation was the finding of “convexity” formed by the inner layer in blackbird. The role of these convex structures is not known, but they can be typical for the species and can be used in their identification. In addition, we identified two proteins in the VM of both species of birds, of which U3KEZ1 FICAL was not previously identified in any other bird species, and the U3JXV8 FICAL protein was confirmed only once in cockatiel parrot VM. The function of these proteins is not exactly known, but their structure shows similarities to the SERPIN proteins that are involved in microbiological defense, i.e., they are immune proteins. This study contributes to the current knowledge about the structure and composition of proteins of VM, especially because similar analyses have never been performed for Turdidae family. Knowledge of the structure and specific proteins of blackbird and song thrush VM can be beneficial in research on ecology and bird biology and also helpful in developing noninvasive and nongenetic identification methods.
Generating high-fidelity synthetic patient data for assessing machine learning healthcare software
Authors: Tucker Allan , Wang Zhenchen , Rotalinti Ylenia , Myles Puja 
Published: November 2020

AbstractThere is a growing demand for the uptake of modern artificial intelligence technologies within healthcare systems. Many of these technologies exploit historical patient health data to build powerful predictive models that can be used to improve diagnosis and understanding of disease. However, there are many issues concerning patient privacy that need to be accounted for in order to enable this data to be better harnessed by all sectors. One approach that could offer a method of circumventing privacy issues is the creation of realistic synthetic data sets that capture as many of the complexities of the original data set (distributions, non-linear relationships, and noise) but that does not actually include any real patient data. While previous research has explored models for generating synthetic data sets, here we explore the integration of resampling, probabilistic graphical modelling, latent variable identification, and outlier analysis for producing realistic synthetic data based on UK primary care patient data. In particular, we focus on handling missingness, complex interactions between variables, and the resulting sensitivity analysis statistics from machine learning classifiers, while quantifying the risks of patient re-identification from synthetic datapoints. We show that, through our approach of integrating outlier analysis with graphical modelling and resampling, we can achieve synthetic data sets that are not significantly different from original ground truth data in terms of feature distributions, feature dependencies, and sensitivity analysis statistics when inferring machine learning classifiers. What is more, the risk of generating synthetic data that is identical or very similar to real patients is shown to be low.