bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derivation of unifying formulae for convective heat transfer in compressible flow fields
Authors: Zhao Bo 
Published: August 2021

AbstractAlthough many theoretical and experimental studies on convective heat transfer exist, the consistent analytical expression of advection heat flux vector in convection as well as its reference temperature in the thermal driving force remains unclear. Here we show theoretically and experimentally the unifying formulae for three-dimensional (3D) heat flux vector of forced and natural convections for compressible laminar flows based on the first law of thermodynamics. It is indicated for a single-phase compressible fluid that advection is no other than heat transfer owing to mass flow in the forms of enthalpy and mechanical energy by gross fluid movement, driven by the temperature difference between the fluid temperature and the potential temperature associated with the relevant adiabatic work done. A simple formula for the total convective heat flux vector of natural convection is also suggested and reformulated in terms of logarithmic density difference as the thermal driving force. The theoretical calculations agree well with the laminar flow experiment results. Our discovery of advection heat transfer for compressible flows caused by the temperature differential in which the potential temperature is regarded as the unifying reference temperature represents a previously unknown thermal driving mechanism. This work would bring fundamental insights into the physical mechanism of convective heat transfer, and opens up new avenue for the design, calculation and thermal management of the 3D convection heat flux problems using the novel thermal driving force for compressible laminar and turbulent flows.
A new tropical cyclone surge index incorporating the effects of coastal geometry, bathymetry and storm information
Authors: Islam Md. Rezuanul , Lee Chia-Ying , Mandli Kyle T. , Takagi Hiroshi 
Published: August 2021

AbstractThis study presents a new storm surge hazard potential index (SSHPI) for estimating tropical cyclone (TC) induced peak surge levels at a coast. The SSHPI incorporates parameters that are often readily available at real-time: intensity in 10-min maximum wind speed, radius of 50-kt wind, translation speed, coastal geometry, and bathymetry information. The inclusion of translation speed and coastal geometry information lead to improvements of the SSHPI to other existing surge indices. A retrospective analysis of SSHPI using data from 1978–2019 in Japan suggests that this index captures historical events reasonably well. In particular, it explains ~ 66% of the observed variance and ~ 74% for those induced by TCs whose landfall intensity was larger than 79-kt. The performance of SSHPI is not sensitive to the type of coastal geometry (open coasts or semi-enclosed bays). Such a prediction methodology can decrease numerical computation requirements, improve public awareness of surge hazards, and may also be useful for communicating surge risk.
DNA damage in circulating leukocytes measured with the comet assay may predict the risk of death
Authors: Bonassi Stefano , Ceppi Marcello , Møller Peter , Azqueta Amaya , Milić Mirta , Neri Monica , Brunborg Gunnar , Godschalk Roger , Koppen Gudrun , Langie Sabine A. S. , Teixeira João Paulo , Bruzzone Marco , Da Silva Juliana , Benedetti Danieli , Cavallo Delia , Ursini Cinzia Lucia , Giovannelli Lisa , Moretti Silvia , Riso Patrizia , Del Bo’ Cristian , Russo Patrizia , Dobrzyńska Malgorzata , Goroshinskaya Irina A. , Surikova Ekaterina I. , Staruchova Marta , Barančokova Magdalena , Volkovova Katarina , Kažimirova Alena , Smolkova Bozena , Laffon Blanca , Valdiglesias Vanessa , Pastor Susana , Marcos Ricard , Hernández Alba , Gajski Goran , Spremo-Potparević Biljana , Živković Lada , Boutet-Robinet Elisa , Perdry Hervé , Lebailly Pierre , Perez Carlos L. , Basaran Nursen , Nemeth Zsuzsanna , Safar Anna , Dusinska Maria , Collins Andrew ,   for the hCOMET project, Anderson Diana , Andrade Vanessa , Pereira Cristiana Costa , Costa Solange , Gutzkow Kristine B. , Ladeira Carina , Moretti Massimo , Costa Carla , Orlow Irene , Rojas Emilio , Pourrut Bertrand , Kruszewski Marcin , Knasmueller Siegfried , Shaposhnikov Sergey , Žegura Bojana , Stopper Helga 
Published: August 2021

AbstractThe comet assay or single cell gel electrophoresis, is the most common method used to measure strand breaks and a variety of other DNA lesions in human populations. To estimate the risk of overall mortality, mortality by cause, and cancer incidence associated to DNA damage, a cohort of 2,403 healthy individuals (25,978 person-years) screened in 16 laboratories using the comet assay between 1996 and 2016 was followed-up. Kaplan–Meier analysis indicated a worse overall survival in the medium and high tertile of DNA damage (p < 0.001). The effect of DNA damage on survival was modelled according to Cox proportional hazard regression model. The adjusted hazard ratio (HR) was 1.42 (1.06–1.90) for overall mortality, and 1.94 (1.04–3.59) for diseases of the circulatory system in subjects with the highest tertile of DNA damage. The findings of this study provide epidemiological evidence encouraging the implementation of the comet assay in preventive strategies for non-communicable diseases.
Notch1 haploinsufficiency in mice accelerates adipogenesis
Authors: Yamaguchi Kazutoshi , Hayashi Motoharu , Uchida Yasuhiro , Cheng Xian Wu , Nakayama Takayuki , Matsushita Tadashi , Murohara Toyoaki , Takeshita Kyosuke 
Published: August 2021

AbstractNotch signaling has been recognized recently as a key regulator of metabolism. Here, we determined the role of Notch1 in adipogenesis in wild-type (WT) and Notch1 hetero-mutant (N1+/−) mice provided with 12-week normal or high-fat diet. Haploinsufficiency of Notch1 was associated with adipose tissue accumulation despite similar food intake. White adipose tissue (WAT) of N1+/− showed accumulation of adipogenic cells (CD34+CD68+ cells), crown-like structures, and upregulation of cell proliferation markers (cyclin D1 and Ki67). Notch1 expression in WAT reached peak levels in 8-week-old WT mice in parallel with fat accumulation, especially under HF/HS-feeding, whereas such increment was blunted in N1+/− mice. Downstream of Notch1 haploinsufficiency, over-expression of adipogenic factors PPARγ and C/EBPα was noted following down-regulation of downstream transcriptional factors of Notch signaling (Hes-1, Pref-1, and Sox9). Both pharmacological Notch signal inhibition and Notch1 knockdown enhanced adipogenesis of 3T3-L1 preadipocytes. N1+/− mice showed impaired glucose and insulin tolerance with downregulation of IRS-1 and GLUT4 in WAT after high-fat diet. Taken together, our results suggest that haploinsufficiency of Notch1 promotes fat accumulation and adipogenesis and provides a mechanistic link between Notch signaling and development of metabolic syndrome.
The Penn State Protein Ladder system for inexpensive protein molecular weight markers
Authors: Santilli Ryan T. , Williamson John E. , Shibata Yoshitaka , Sowers Rosalie P. , Fleischman Andrew N. , Tan Song 
Published: August 2021

AbstractWe have created the Penn State Protein Ladder system to produce protein molecular weight markers easily and inexpensively (less than a penny a lane). The system includes plasmids which express 10, 15, 20, 30, 40, 50, 60, 80 and 100 kD proteins inE. coli. Each protein migrates appropriately on SDS-PAGE gels, is expressed at very high levels (10–50 mg per liter of culture), is easy to purify via histidine tags and can be detected directly on Western blots via engineered immunoglobulin binding domains. We have also constructed plasmids to express 150 and 250 kD proteins. For more efficient production, we have created two polycistronic expression vectors which coexpress the 10, 30, 50, 100 kD proteins or the 20, 40, 60, 80 kD proteins. 50 ml of culture is sufficient to produce 20,000 lanes of individual ladder protein or 3750 lanes of each set of coexpressed ladder proteins. These Penn State Protein Ladder expression plasmids also constitute useful reagents for teaching laboratories to demonstrate recombinant expression inE. coliand affinity protein purification, and to research laboratories desiring positive controls for recombinant protein expression and purification.
Metabolic, structural, and proteomic changes in Candida albicans cells induced by the protein-carbohydrate fraction of Dendrobaena veneta coelomic fluid
Authors: Fiołka Marta J. , Czaplewska Paulina , Wójcik-Mieszawska Sylwia , Lewandowska Aleksandra , Lewtak Kinga , Sofińska-Chmiel Weronika , Buchwald Tomasz 
Published: August 2021

AbstractThe isolated protein-polysaccharide fraction (AAF) from the coelomic fluid of Dendrobaena veneta earthworm shows effective activity against Candida albicans yeast. Fungal cells of the clinical strain after incubation with the active fraction were characterized by disturbed cell division and different morphological forms due to the inability to separate the cells from each other. Staining of the cells with acridine orange revealed a change in the pH of the AAF-treated cells. It was observed that, after the AAF treatment, the mitochondrial DNA migrated towards the nuclear DNA, whereupon both merged into a single nuclear structure, which preceded the apoptotic process. Cells with a large nucleus were imaged with the scanning electron cryomicroscopy (Cryo-SEM) technique, while enlarged mitochondria and the degeneration of cell structures were shown by transmission electron microscopy (TEM). The loss of the correct cell shape and cell wall integrity was visualized by both the TEM and SEM techniques. Mass spectrometry and relative quantitative SWATH MS analysis were used to determine the reaction of the C. albicans proteome to the components of the AAF fraction. AAF was observed to influence the expression of mitochondrial and oxidative stress proteins. The oxidative stress in C. albicans cells caused by the action of AAF was demonstrated by fluorescence microscopy, proteomic methods, and XPS spectroscopy. The secondary structure of AAF proteins was characterized by Raman spectroscopy. Analysis of the elemental composition of AAF confirmed the homogeneity of the preparation. The observed action of AAF, which targets not only the cell wall but also the mitochondria, makes the preparation a potential antifungal drug killing the cells of the C. albicans pathogen through apoptosis.
RT-QuIC detection of CWD prion seeding activity in white-tailed deer muscle tissues
Authors: Li Manci , Schwabenlander Marc D. , Rowden Gage R. , Schefers Jeremy M. , Jennelle Christopher S. , Carstensen Michelle , Seelig Davis , Larsen Peter A. 
Published: August 2021

AbstractChronic wasting disease (CWD) is a prion disease circulating in wild and farmed cervid populations throughout North America (United States and Canada), Europe (Finland, Norway, Sweden), and South Korea. CWD is a long-term threat to all cervid populations and to cervid hunting heritage, with the potential to cause substantial economic losses across multiple sectors. In North America, hunting and farming industries focused on the processing and consumption of white-tailed deer (WTD) venison are particularly vulnerable to CWD prion contamination, as millions of WTD are consumed annually. Real-time quaking-induced conversion (RT-QuIC) is a highly sensitive assay amplifying misfolded CWD prions in vitro and has facilitated CWD prion detection in a variety of tissues and excreta. To date, no study has comprehensively examined CWD prion content across bulk skeletal muscle tissues harvested from individual CWD infected WTD. Here, we use RT-QuIC to characterize prion-seeding activity in a variety of skeletal muscles from both wild and farmed CWD-positive WTD. We successfully detected CWD prions in muscles commonly used for consumption (e.g., backstrap, tenderloin, etc.) as well as within tongue and neck samples of WTD. Our results suggest that CWD prions are distributed across the skeletal muscles of infected WTD. We posit that RT-QuIC will be a useful tool for monitoring CWD prions in venison and that the method (with additional protocol optimization and high-throughput functionality) could be used to reduce and/or prevent CWD prions from entering animal and human food chains.
Anatomy of Cowper’s gland in humans suggesting a secretion and emission mechanism facilitated by cooperation of striated and smooth muscles
Authors: Muro Satoru , Suriyut Janyaruk , Akita Keiichi 
Published: August 2021

AbstractThis study presents the detailed anatomy of the Cowper’s gland in humans. Elucidating the mechanism of secretion and emission of the Cowper’s gland requires analysis of the muscles around the Cowper’s gland. We hypothesized that the Cowper’s gland involves not only smooth muscle but also the striated muscles of the pelvic floor. Here, we provide comprehensive and three-dimensional anatomy of the Cowper’s gland and its surrounding structures, which overcomes the current local and planar understanding. In this study, seven male corpses of body donors were used to conduct macroscopic anatomy, histology, and three-dimensional reconstruction. The Cowper’s gland was surrounded laterally and posterosuperiorly by striated and smooth muscles, respectively. The striated muscle bundle was connected from the superficial transverse perineal muscle, levator ani, and external anal sphincter to the external urethral sphincter (rhabdosphincter). The smooth muscle was part of the deep transverse perineal muscle and entered between the bilateral Cowper’s glands and lobules. Our findings indicate that the secretion and emission of the Cowper’s gland in humans are carried out through the cooperation of striated and smooth muscles.
Long noncoding RNA landscapes specific to benign and malignant thyroid neoplasms of distinct histological subtypes
Authors: Yakushina Valentina D. , Strelnikov Vladimir V. , Tanas Alexander S. , Lavrov Alexander V. 
Published: August 2021

AbstractThe main types of thyroid neoplasms, follicular adenoma (FA), follicular thyroid carcinoma (FTC), classical and follicular variants of papillary carcinoma (clPTC and fvPTC), and anaplastic thyroid carcinoma (ATC), differ in prognosis, progression rate and metastatic behaviour. Specific patterns of lncRNAs involved in the development of clinical and morphological features can be presumed. LncRNA landscapes within distinct benign and malignant histological variants of thyroid neoplasms were not investigated. The aim of the study was to discover long noncoding RNA landscapes common and specific to major benign and malignant histological subtypes of thyroid neoplasms. LncRNA expression in FA, FTC, fvPTC, clPTC and ATC was analysed with comprehensive microarray and RNA-Seq datasets. Putative biological functions were evaluated via enrichment analysis of coexpressed coding genes. In the results, lncRNAs common and specific to FTC, clPTC, fvPTC, and ATC were identified. The discovered lncRNAs are putatively involved in L1CAM interactions, namely, pre-mRNA processing (lncRNAs specific to FTC); PCP/CE and WNT pathways (lncRNAs specific to fvPTC); extracellular matrix organization (lncRNAs specific to clPTC); and the cell cycle (lncRNAs specific to ATC). Known oncogenic and suppressor lncRNAs (RMST, CRNDE, SLC26A4-AS1, NR2F1-AS1, and LINC00511) were aberrantly expressed in thyroid carcinomas. These findings enhance the understanding of lncRNAs in the development of subtype-specific features in thyroid cancer.
Longitudinal analysis of antibody decay in convalescent COVID-19 patients
Authors: Xia Weiming , Li Mingfei , Wang Ying , Kazis Lewis E. , Berlo Kim , Melikechi Noureddine , Chiklis Gregory R. 
Published: August 2021

AbstractDetermining the sustainability of antibodies targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for predicting immune response against the Coronavirus disease 2019 (COVID-19). To quantify the antibody decay rates among the varying levels of anti-nucleocapsid (anti-N) Immunoglobulin G (IgG) in convalescent COVID-19 patients and estimate the length of time they maintained SARS-CoV-2 specific antibodies, we have collected longitudinal blood samples from 943 patients over the course of seven months after their initial detection of SARS-CoV-2 virus by RT-PCR. Anti-N IgG levels were then quantified in these blood samples. The primary study outcome was the comparison of antibody decay rates from convalescent patients with high or low initial levels of antibodies using a mixed linear model. Additional measures include the length of time that patients maintain sustainable levels of anti-N IgG. Antibody quantification of blood samples donated by the same subject multiple times shows a gradual decrease of IgG levels to the cutoff index level of 1.4 signal/cut-off (S/C) on the Abbott Architect SARS-CoV-2 IgG test. In addition, this study shows that antibody reduction rate is dependent on initial IgG levels, and patients with initial IgG levels above 3 S/C show a significant 1.68-fold faster reduction rate compared to those with initial IgG levels below 3 S/C. For a majority of the donors naturally occurring anti-N antibodies were detected above the threshold for only four months after infection with SARS-CoV-2. This study is clinically important for the prediction of immune response capacity in COVID-19 patients.
Numerical investigation of effects of incisor angle on production of sibilant /s/
Authors: Lu HsuehJui , Yoshinaga Tsukasa , Li ChungGang , Nozaki Kazunori , Iida Akiyoshi , Tsubokura Makoto 
Published: August 2021

AbstractThe effects of the inclination angle of the incisor on the speech production of the fricative consonant /s/ was investigated using an implicit compressible flow solver. The hierarchical structure grid was applied to reduce the grid generation time for the vocal tract geometry. The airflow and sound during the pronunciation of /s/ were simulated using the adaptively switched time stepping scheme, and the angle of the incisor in the vocal tract was changed from normal position up to 30°. The results showed that increasing the incisor angle affected the flow configuration and moved the location of the high turbulence intensity region thereby decreased the amplitudes of the sound in the frequency range from 8 to 12 kHz. Performing the Fourier transform on the velocity fluctuation, we found that the position of large magnitudes of the velocity at 10 kHz shifted toward the lip outlet when the incisor angle was increased. In addition, separate acoustic simulations showed that the shift in the potential sound source position decreased the far-field sound amplitudes above 8 kHz. These results provide the underlying insights necessary to design dental prostheses for the production of sibilant fricatives.
Secretome screening reveals immunomodulating functions of IFNα-7, PAP and GDF-7 on regulatory T-cells
Authors: Ding Mei , Malhotra Rajneesh , Ottosson Tomas , Lundqvist Magnus , Mebrahtu Aman , Brengdahl Johan , Gehrmann Ulf , Bäck Elisabeth , Ross-Thriepland Douglas , Isaksson Ida , Magnusson Björn , Sachsenmeier Kris F. , Tegel Hanna , Hober Sophia , Uhlén Mathias , Mayr Lorenz M. , Davies Rick , Rockberg Johan , Schiavone Lovisa Holmberg 
Published: August 2021

AbstractRegulatory T cells (Tregs) are the key cells regulating peripheral autoreactive T lymphocytes. Tregs exert their function by suppressing effector T cells. Tregs have been shown to play essential roles in the control of a variety of physiological and pathological immune responses. However, Tregs are unstable and can lose the expression of FOXP3 and suppressive functions as a consequence of outer stimuli. Available literature suggests that secreted proteins regulate Treg functional states, such as differentiation, proliferation and suppressive function. Identification of secreted proteins that affect Treg cell function are highly interesting for both therapeutic and diagnostic purposes in either hyperactive or immunosuppressed populations. Here, we report a phenotypic screening of a human secretome library in human Treg cells utilising a high throughput flow cytometry technology. Screening a library of 575 secreted proteins allowed us to identify proteins stabilising or destabilising the Treg phenotype as suggested by changes in expression of Treg marker proteins FOXP3 and/or CTLA4. Four proteins including GDF-7, IL-10, PAP and IFNα-7 were identified as positive regulators that increased FOXP3 and/or CTLA4 expression. PAP is a phosphatase. A catalytic-dead version of the protein did not induce an increase in FOXP3 expression. Ten interferon proteins were identified as negative regulators that reduced the expression of both CTLA4 and FOXP3, without affecting cell viability. A transcriptomics analysis supported the differential effect on Tregs of IFNα-7 versus other IFNα proteins, indicating differences in JAK/STAT signaling. A conformational model experiment confirmed a tenfold reduction in IFNAR-mediated ISG transcription for IFNα-7 compared to IFNα-10. This further strengthened the theory of a shift in downstream messaging upon external stimulation. As a summary, we have identified four positive regulators of FOXP3 and/or CTLA4 expression. Further exploration of these Treg modulators and their method of action has the potential to aid the discovery of novel therapies for both autoimmune and infectious diseases as well as for cancer.
The effects of feeding and starvation on antioxidant defence, fatty acid composition and lipid peroxidation in reared Oncorhynchus mykiss fry
Authors: Zengin Hatayi 
Published: August 2021

AbstractThe effects of feeding and starvation have been studied with respect to oxidative stress and enzymatic antioxidant activities in the whole body of 4 cm rainbow trout fry Oncorhynchus mykiss (Walbaum 1792). The experiment was conducted for 28 days. The selected biomarkers for the study were determined, including non-enzymic scavengers glutathione (GSH), oxidized glutathione (GSSG) and malondialdehyde (MDA) contents and a number of enzymes are known to have major antioxidant activity, such as activities of süperoksit dismutaz (SOD), catalase (CAT), glutatyon peroksidaz (GSHpx), glutatyon Redüktaz (GR) and Glutatyon-S-Transferaz (GST). There is an endogenous cellular glutathione pool which consists of two forms of glutathione, i.e. the GSH and the GSSG. Oxidative damage was measured by the formation of MDA as an indication of lipid peroxidation. The activities of SOD in 14th and 28th day and the activity of CAT in 14th day were increased significantly during the 28 days of starvation. GSHpx and GR activities in starved fry decreased significantly in 28th day. GST activity in all starved fry showed the most significant increases the period of 28 days starving. The highest ΣSFA (Total Saturated Fatty Acid) content was obtained from 28 day starved fry. In starved fry, there was an apparent preference in utilization of C18:1n-9 than in the fed fry. In both starved and fed fry, C16:1n-7 was preferentially kept during the same period. Fry kept 28 days under starvation conditions exhausted C15:0, C17:0, C18:3n-6, C22:0, C24:0. They utilized less C20:5n-3 acid and conserved strongly C22:6n-3 acid. Concentrations of C20:5n-3, C22:5n-3, C22:6n-3 and total n-3 fatty acids significantly increased and C18:3n-3 significantly decreased in the whole body of starved fry during starvation period. A significant increase in the concentrations of C22:5n-3 and C22:6n-3 was determined in the fed fries in the last 2 weeks. Fat-soluble vitamins, cholesterol, stigmasterol and β-sitosterol levels were also determined in the same period of O. mykiss fry.