bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of inspiratory and expiratory lung and lobe volumes among supine, standing, and sitting positions using conventional and upright CT
Authors: Yamada Yoshitake , Yamada Minoru , Chubachi Shotaro , Yokoyama Yoichi , Matsuoka Shiho , Tanabe Akiko , Niijima Yuki , Murata Mitsuru , Fukunaga Koichi , Jinzaki Masahiro 
Published: October 2020

AbstractCurrently, no clinical studies have compared the inspiratory and expiratory volumes of unilateral lung or of each lobe among supine, standing, and sitting positions. In this prospective study, 100 asymptomatic volunteers underwent both low-radiation-dose conventional (supine position, with arms raised) and upright computed tomography (CT) (standing and sitting positions, with arms down) during inspiration and expiration breath-holds and pulmonary function test (PFT) on the same day. We compared the inspiratory/expiratory lung/lobe volumes on CT in the three positions. The inspiratory and expiratory bilateral upper and lower lobe and lung volumes were significantly higher in the standing/sitting positions than in the supine position (5.3–14.7% increases, all P < 0.001). However, the inspiratory right middle lobe volume remained similar in the three positions (all P > 0.15); the expiratory right middle lobe volume was significantly lower in the standing/sitting positions (16.3/14.1% decrease) than in the supine position (both P < 0.0001). The Pearson’s correlation coefficients (r) used to compare the total lung volumes on inspiratory CT in the supine/standing/sitting positions and the total lung capacity on PFT were 0.83/0.93/0.95, respectively. The r values comparing the total lung volumes on expiratory CT in the supine/standing/sitting positions and the functional residual capacity on PFT were 0.83/0.85/0.82, respectively. The r values comparing the total lung volume changes from expiration to inspiration on CT in the supine/standing/sitting positions and the inspiratory capacity on PFT were 0.53/0.62/0.65, respectively. The study results could impact preoperative CT volumetry of the lung in lung cancer patients (before lobectomy) for the prediction of postoperative residual pulmonary function, and could be used as the basis for elucidating undetermined pathological mechanisms. Furthermore, in addition to morphological evaluation of the chest, inspiratory and expiratory upright CT may be used as an alternative tool to predict lung volumes such as total lung capacity, functional residual capacity, and inspiratory capacity in situation in which PFT cannot be performed such as during an infectious disease pandemic, with relatively more accurate predictability compared with conventional supine CT.
Assessing harbour porpoise carcasses potentially subjected to grey seal predation
Authors: van Neer Abbo , Gross Stephanie , Kesselring Tina , Grilo Miguel L. , Ludes-Wehrmeister Eva , Roncon Giulia , Siebert Ursula 
Published: October 2020

AbstractAs a follow-up on the data presented for seals, we herein report and discuss outcomes resulting from a retrospective evaluation of harbour porpoise stranding and necropsy data from Schleswig–Holstein, Germany (n = 4463) to enable an objective evaluation of potential ecological effects of grey seal predation on porpoises. Results are compared to a recent case of definite grey seal predation as well as to reports from other countries. Porpoise carcasses potentially subject to grey seal predation show severe lacerations, with large parts of skin and underlying tissue being detached from the body. Loss of blubber tissue is common. Based on the occurrence frequencies of encountered lesions, a list of parameters as well as a complementary decision tree are suggested to be used for future assessments. The results shown add to an increasingly standardised assessment protocol of suspected grey seal predation cases making respective results comparable between different areas and countries. The usage of a standardised protocol may increase the awareness of grey seal predation and the reporting of such cases. By this, differences in the predation and feeding patterns as well as the potential ecological relevance of this behaviour may be elucidated.
Ab initio calculations of conduction band effective mass parameters of thermoelectric $${\hbox {Mg}}_{2} {\hbox {X}}_{1{-}x} {\hbox {Y}}_x$$ (X, Y = Si, Ge, Sn) alloys
Authors: Guerra Juan M. , Mahr Carsten , Giar Marcel , Czerner Michael , Heiliger Christian 
Published: October 2020

AbstractSince there are still research interests in the physical properties of quasi-binary thermoelectric $${\hbox {Mg}}_{2} {\hbox {X}}_{1-x}{\hbox {Y}}_{x}$$

Mg
2

X

1
-
x

Y
x

alloys, with X, Y = Si, Ge, Sn, we present an ab initio analysis that yields the relative formation energy and effective masses of the conduction bands, in the whole compositional range x. We base our calculations on the full-relativistic Korringa, Kohn and Rostocker (KKR) Green’s functions formalism within the coherent potential approximation (CPA). Formation energies, measured relative to the end $${\hbox {Mg}}_{2} \hbox {X}$$

Mg
2

X

compounds, show no excess energy for the $${\hbox {Mg}}_{2} \hbox {Si} {-} {\hbox {Mg}}_{2} \hbox {Ge}$$

Mg
2

Si
-

Mg
2

Ge

substitution thus indicating a complete solubility. In contrast, concave and asymmetric formation energies for intermediate compositions in the $${\hbox {Mg}}_{2} \hbox {X} {-} {\hbox {Mg}}_{2} \hbox {Sn}$$

Mg
2

X
-

Mg
2

Sn

alloys manifest a miscibility gap. With this basis, we compute and discuss the crossing of the conduction bands observed in n-type $${\hbox {Mg}}_{2} {\hbox {X}}_{1-x} {\hbox {Sn}}_x$$

Mg
2

X

1
-
x

Sn
x

materials. We present direction- and band-dependent effective masses using a generalized single parabolic band effective mass approximation to discuss anisotropic effects, to interpret available experimental and theoretical data, and to predict intermediate and not yet published transport parameters on these alloys.
Crystal structure of Epiphyas postvittana pheromone binding protein 3
Authors: Hamiaux Cyril , Carraher Colm , Löfstedt Christer , Corcoran Jacob A. 
Published: October 2020

AbstractThe insect olfactory system operates as a well-choreographed ensemble of molecules which functions to selectively translate volatile chemical messages present in the environment into neuronal impulses that guide insect behaviour. Of these molecules, binding proteins are believed to transport hydrophobic odorant molecules across the aqueous lymph present in antennal sensilla to receptors present in olfactory sensory neurons. Though the exact mechanism through which these proteins operate is still under investigation, these carriers clearly play a critical role in determining what an insect can smell. Binding proteins that transport important sex pheromones are colloquially named pheromone binding proteins (PBPs). Here, we have produced a functional recombinant PBP from the horticultural pest, Epiphyas postvittana (EposPBP3), and experimentally solved its apo-structure through X-ray crystallography to a resolution of 2.60 Å. Structural comparisons with related lepidopteran PBPs further allowed us to propose models for the binding of pheromone components to EposPBP3. The data presented here represent the first structure of an olfactory-related protein from the tortricid family of moths, whose members cause billions of dollars in losses to agricultural producers each year. Knowledge of the structure of these important proteins will allow for subsequent studies in which novel, olfactory molecule-specific insecticides can be developed.
Clinical utility of brain-derived neurotrophic factor as a biomarker with left ventricular echocardiographic indices for potential diagnosis of coronary artery disease
Authors: Monisha K. G. , Prabu Paramasivam , Chokkalingam M. , Murugesan Ram , Milenkovic Dragan , Ahmed Shiek S. S. J. 
Published: October 2020

AbstractBrain-derived neurotrophic factor (BDNF) plays a central pivotal role in the development of the cardiovascular system. Recent evidence suggests that BDNF has adverse subclinical cardiac remodeling in participants with cardiovascular disease risk factors. Relating serum BDNF levels with two-dimensional echocardiographic indices will provide insights into the BDNF mediated pathophysiology in coronary artery disease (CAD) that may shed light upon potential diagnostic biomarkers. For the study, 221 participants were recruited and classified based on coronary angiogram examination as control (n = 105) and CAD (n = 116). All participants underwent routine blood investigation, two-dimensional echocardiography, and serum BDNF estimation. As a result, total cholesterol, triglyceride, low-density lipid, high-density lipid, HbA1c (glycosylated hemoglobin), serum creatinine, eosinophils, lymphocyte, monocytes, neutrophils, and platelets were significantly elevated in CAD individuals compared to controls. Notably, the serum BDNF was significantly lower in individuals with CAD (30.69 ± 5.45 ng/ml) than controls (46.58 ± 7.95 ng/ml). Multivariate regression analysis showed neutrophils, total cholesterol, left ventricular mass index, mitral inflow E/A ratio, and pulmonary vein AR duration were associated with low BDNF in CAD. Four independent support vector machine (SVM) models performed to ensure the BDNF level in the classification of CAD from healthy controls. Particularly, the model with serum BDNF concentration and blood parameters of CAD achieved significant improvement from 90.95 to 98.19% in detecting CAD from healthy controls. Overall, our analysis provides a significant molecular linkage between the serum BDNF level and cardiovascular function. Our results contribute to the emerging evidence of BDNF as a potential diagnostic value in CAD that might lead to clinical application.
Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Authors: Takahashi Hiro , Miyaki Shido , Onouchi Hitoshi , Motomura Taichiro , Idesako Nobuo , Takahashi Anna , Murase Masataka , Fukuyoshi Shuichi , Endo Toshinori , Satou Kenji , Naito Satoshi , Itoh Motoyuki 
Published: October 2020

AbstractUpstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.
VEGF knockdown enhances radiosensitivity of nasopharyngeal carcinoma by inhibiting autophagy through the activation of mTOR pathway
Authors: Chen Li , Lin Guoxiang , Chen Kaihua , Wan Fangzhu , Liang Renba , Sun Yongchu , Chen Xishan , Zhu Xiaodong 
Published: October 2020

AbstractVascular endothelial growth factor (VEGF) is an important pro-angiogenic factor. VEGF was reported to promote the occurrence of autophagy, which enhanced the radioresistance of tumors. The purpose of this study was to investigate the influence of VEGF silencing on the radiosensitivity of nasopharyngeal carcinoma (NPC) cells and the underlying mechanisms. The radiosensitivity of NPC cells after VEGF silencing was detected by cell counting kit 8 (CCK-8) and clonogenic assay, while cell cycle and apoptosis were detected by flow cytometry. The processes of DNA damage, repair and autophagy were examined by immunofluorescence and western blotting. The interaction between VEGF and mTOR was confirmed by western blotting and co-immunoprecipitation studies. The effect of VEGF on radiosensitivity of NPC cells was investigated in vivo using a xenograft model. Furthermore, immunohistochemistry and TUNEL assays were used to verify the relationship between autophagy and radiosensitivity in NPC after VEGF depletion. Downregulation of VEGF significantly inhibited cell proliferation and induced apoptosis of NPC cells after radiotherapy in vitro and in vivo. In addition, VEGF knockdown not only decreased autophagy level, but also delayed the DNA damage repair in NPC cells after irradiation. Mechanistically, silencing VEGF suppressed autophagy through activation of the mTOR pathway. VEGF depletion increased radiosensitivity of NPC cells by suppressing autophagy via activation of the mTOR pathway.
Synthesis and structural characterization of Ca12Ga14O33
Authors: McCoy Sabrina E. A. , Salasin John R. , Everett S. Michelle , Rawn Claudia J. 
Published: October 2020

AbstractCa12Ga14O33 was successfully synthesized using a wet chemistry technique to promote the homogenous mixing of the Ca and Ga cations. Rietveld refinements on X-ray and neutron powder diffraction data confirm that the compound is isostructural to Ca12Al14O33, however, with a significantly larger lattice parameter allowing for the cages that result from the framework arrangement to expand. In naturally occurring Ca12Al14O33, the mineral mayenite, these cages are occupied by O2− anions, however, experimental studies exchanging the O2− anions with other anions has led to a host of applications, depending on the caged anion. The functional nature of the structure, where framework distortions coupled with cage occupants, are correlated to electronic band structure and modifications to the framework could lead to interesting physical properties. The phase evolution was tracked using thermogravimetric analysis and high temperature X-ray diffraction and showed a lower formation temperature for the Ca12Ga14O33 analogue compared to Ca12Al14O33 synthesized using the same wet chemistry technique. Analyzing both X-ray and neutron powder diffraction using the Rietveld method with two different starting models results in one structural model, with one Ca position and the caged O on a 24d special position, being preferred.
Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding
Authors: Wang Nan , Yuan Yibing , Wang Hui , Yu Diansi , Liu Yubo , Zhang Ao , Gowda Manje , Nair Sudha K. , Hao Zhuanfang , Lu Yanli , San Vicente Felix , Prasanna Boddupalli M. , Li Xinhai , Zhang Xuecai 
Published: October 2020

AbstractGenotyping-by-Sequencing (GBS) is a low-cost, high-throughput genotyping method that relies on restriction enzymes to reduce genome complexity. GBS is being widely used for various genetic and breeding applications. In the present study, 2240 individuals from eight maize populations, including two association populations (AM), backcross first generation (BC1), BC1F2, F2, double haploid (DH), intermated B73 × Mo17 (IBM), and a recombinant inbred line (RIL) population, were genotyped using GBS. A total of 955,120 of raw data for SNPs was obtained for each individual, with an average genotyping error of 0.70%. The rate of missing genotypic data for these SNPs was related to the level of multiplex sequencing: ~ 25% missing data for 96-plex and ~ 55% for 384-plex. Imputation can greatly reduce the rate of missing genotypes to 12.65% and 3.72% for AM populations and bi-parental populations, respectively, although it increases total genotyping error. For analysis of genetic diversity and linkage mapping, unimputed data with a low rate of genotyping error is beneficial, whereas, for association mapping, imputed data would result in higher marker density and would improve map resolution. Because imputation does not influence the prediction accuracy, both unimputed and imputed data can be used for genomic prediction. In summary, GBS is a versatile and efficient SNP discovery approach for homozygous materials and can be effectively applied for various purposes in maize genetics and breeding.
The duality between particle methods and artificial neural networks
Authors: Alexiadis A. , Simmons M. J. H. , Stamatopoulos K. , Batchelor H. K. , Moulitsas I. 
Published: October 2020

AbstractThe algorithm behind particle methods is extremely versatile and used in a variety of applications that range from molecular dynamics to astrophysics. For continuum mechanics applications, the concept of ‘particle’ can be generalized to include discrete portions of solid and liquid matter. This study shows that it is possible to further extend the concept of ‘particle’ to include artificial neurons used in Artificial Intelligence. This produces a new class of computational methods based on ‘particle-neuron duals’ that combines the ability of computational particles to model physical systems and the ability of artificial neurons to learn from data. The method is validated with a multiphysics model of the intestine that autonomously learns how to coordinate its contractions to propel the luminal content forward (peristalsis). Training is achieved with Deep Reinforcement Learning. The particle-neuron duality has the advantage of extending particle methods to systems where the underlying physics is only partially known, but we have observations that allow us to empirically describe the missing features in terms of reward function. During the simulation, the model evolves autonomously adapting its response to the available observations, while remaining consistent with the known physics of the system.
Mid-infrared spectroscopic screening of metabolic alterations in stress-exposed gilthead seabream (Sparus aurata)
Authors: de Magalhães Cláudia Raposo , Carrilho Raquel , Schrama Denise , Cerqueira Marco , Rosa da Costa Ana M. , Rodrigues Pedro M. 
Published: October 2020

AbstractStress triggers a battery of physiological responses in fish, including the activation of metabolic pathways involved in energy production, which helps the animal to cope with the adverse situation. Prolonged exposure to stressful farming conditions may induce adverse effects at the whole-animal level, impairing welfare. Fourier transform infrared (FTIR) spectroscopy is a rapid biochemical fingerprinting technique, that, combined with chemometrics, was applied to disclose the metabolic alterations in the fish liver as a result of exposure to standard stressful practices in aquaculture. Gilthead seabream (Sparus aurata) adults exposed to different stressors were used as model species. Spectra were preprocessed before multivariate statistical analysis. Principal components analysis (PCA) was used for pattern recognition and identification of the most discriminatory wavenumbers. Key spectral features were selected and used for classification using the k-nearest neighbour (KNN) algorithm to evaluate whether the spectral changes allowed for the reliable discrimination between experimental groups. PCA loadings suggested that major variations in the hepatic infrared spectra responsible for the discrimination between the experimental groups were due to differences in the intensity of absorption bands associated with proteins, lipids and carbohydrates. This broad-range technique can thus be useful in an exploratory approach before any targeted analysis.
Designing a multi-epitope peptide based vaccine against SARS-CoV-2
Authors: Singh Abhishek , Thakur Mukesh , Sharma Lalit Kumar , Chandra Kailash 
Published: October 2020

AbstractCOVID-19 pandemic has resulted in 16,114,449 cases with 646,641 deaths from the 217 countries, or territories as on July 27th 2020. Due to multifaceted issues and challenges in the implementation of the safety and preventive measures, inconsistent coordination between societies-governments and most importantly lack of specific vaccine to SARS-CoV-2, the spread of the virus that initially emerged at Wuhan is still uprising after taking a heavy toll on human life. In the present study, we mapped immunogenic epitopes present on the four structural proteins of SARS-CoV-2 and we designed a multi-epitope peptide based vaccine that, demonstrated a high immunogenic response with a vast application on world’s human population. On codon optimization and in-silico cloning, we found that candidate vaccine showed high expression in E. coli and immune simulation resulted in inducing a high level of both B-cell and T-cell mediated immunity. The results predicted that exposure of vaccine by administrating three injections significantly subsidized the antigen growth in the system. The proposed candidate vaccine found promising by yielding desired results and hence, should be validated by practical experimentations for its functioning and efficacy to neutralize SARS-CoV-2.
Prevalence and risk factors of intrahepatic cholestasis of pregnancy in a Chinese population
Authors: Gao Xing-Xing , Ye Meng-Ying , Liu Yan , Li Jin-Yan , Li Li , Chen Wei , Lu Xue , Nie Guiying , Chen Yuan-Hua 
Published: October 2020

AbstractStudies on the risk factors for intrahepatic cholestasis of pregnancy (ICP) in a population-based cohort are lacking. We assess the prevalence and risk factors of ICP in a Chinese population. In this study, a cohort study was conducted that included 12,200 eligible pregnant women. The overall incidence of ICP in this cohort was 6.06%. With increasing maternal age, the incidence of ICP decreased in women younger than 30 years of age but increased in those older than 30. With increasing pre-pregnancy BMI, the incidence of ICP decreased if the pre-pregnancy BMI was less than 23 kg/m2 but increased if it was 23 kg/m2 or higher. Further analysis showed that the risk of ICP increased when maternal age was < 25 years (Adjusted RR  2.01; 95% CI 1.64–2.47) or ≥ 35 years (Adjusted RR  1.34; 95% CI 1.02–1.76). Furthermore, an increased risk of ICP was associated with pre-pregnancy underweight (adjusted RR  1.27; 95% CI 1.04–1.56), inadequate gestational weight gain (GWG) (adjusted RR  1.58; 95% CI 1.28–1.96), lower maternal education (adjusted RR  2.96; 95% CI 2.35–3.74), multiparity (adjusted RR  1.54; 95% CI 1.23–1.93), and twin/multiple pregnancies (adjusted RR  2.12; 95% CI 1.25–3.58). Maternal age (< 25 or ≥ 35 years), underweight, inadequate GWG, lower maternal education, multiparity, and twin/multiple pregnancies were identified as risk factors of ICP.
Bidirectional-nonlinear threshold switching behaviors and thermally robust stability of ZnTe selectors by nitrogen annealing
Authors: Jang Gabriel , Park Mihyun , Hyeon Da Seul , Kim WooJong , Yang JungYup , Hong JinPyo 
Published: October 2020

AbstractThree-dimensional stackable memory frames involving the integration of two-terminal scalable crossbar arrays are expected to meet the demand for high-density memory storage, fast switching speed, and ultra-low power operation. However, two-terminal crossbar arrays introduce an unintended sneak path, which inevitably requires bidirectional nonlinear selectors. In this study, the advanced threshold switching (TS) features of ZnTe chalcogenide material-based selectors provide bidirectional threshold switching behavior, nonlinearity of 104, switching speed of less than 100 ns, and switching endurance of more than 107. In addition, thermally robust ZnTe selectors (up to 400 ℃) can be obtained through the use of nitrogen-annealing treatment. This process can prevent possible phase separation phenomena observed in generic chalcogenide materials during thermal annealing which occurs even at a low temperature of 250 ℃. The possible characteristics of the electrically and thermally advanced TS nature are described by diverse structural and electrical analyses through the Poole–Frankel conduction model.