bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma
Authors: Yu Zhixiang , He Haiyan , Chen Yanan , Ji Qiuhe , Sun Min 
Published: June 2021

AbstractOvarian cancer (OV) is a common type of carcinoma in females. Many studies have reported that ferroptosis is associated with the prognosis of OV patients. However, the mechanism by which this occurs is not well understood. We utilized Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) to identify ferroptosis-related genes in OV. In the present study, we applied Cox regression analysis to select hub genes and used the least absolute shrinkage and selection operator to construct a prognosis prediction model with mRNA expression profiles and clinical data from TCGA. A series of analyses for this signature was performed in TCGA. We then verified the identified signature using International Cancer Genome Consortium (ICGC) data. After a series of analyses, we identified six hub genes (DNAJB6, RB1, VIMP/ SELENOS, STEAP3, BACH1, and ALOX12) that were then used to construct a model using a training data set. The model was then tested using a validation data set and was found to have high sensitivity and specificity. The identified ferroptosis-related hub genes might play a critical role in the mechanism of OV development. The gene signature we identified may be useful for future clinical applications.
High-throughput phenotyping methods for quantifying hair fiber morphology
Authors: Lasisi Tina , Zaidi Arslan A. , Webster Timothy H. , Stephens Nicholas B. , Routch Kendall , Jablonski Nina G. , Shriver Mark D. 
Published: June 2021

AbstractQuantifying the continuous variation in human scalp hair morphology is of interest to anthropologists, geneticists, dermatologists and forensic scientists, but existing methods for studying hair form are time-consuming and not widely used. Here, we present a high-throughput sample preparation protocol for the imaging of both longitudinal (curvature) and cross-sectional scalp hair morphology. Additionally, we describe and validate a new Python package designed to process longitudinal and cross-sectional hair images, segment them, and provide measurements of interest. Lastly, we apply our methods to an admixed African-European sample (n = 140), demonstrating the benefit of quantifying hair morphology over classification, and providing evidence that the relationship between cross-sectional morphology and curvature may be an artefact of population stratification rather than a causal link.
Comparative analysis of the gut microbiota of mice fed a diet supplemented with raw and cooked beef loin powder
Authors: Kim Hye-Jin , Kim Dongwook , Kim Kwan-Woo , Lee Sang-Hoon , Jang Aera 
Published: June 2021

AbstractWe used 16S ribosomal RNA sequencing to evaluate changes in the gut microbiota of mice fed a diet supplemented with either raw or cooked beef loin powder for 9 weeks. Male BALB/c mice (n = 60) were randomly allocated to five groups: mice fed AIN-93G chow (CON), chow containing 5% (5RB) and 10% (10RB) raw beef loin powder, and chow containing 5% (5CB) and 10% (10CB) cooked beef loin powder. Dietary supplementation with both RB and CB increased the relative abundance of Clostridiales compared to the CON diet (p < 0.05). Mice fed 10RB showed a significantly higher relative abundance of Firmicutes (p = 0.018) and Lactobacillus (p = 0.001) than CON mice, and the ratio of Firmicutes/Bacteroidetes showed an increasing trend in the 10RB mice (p > 0.05). Mice fed 10CB showed a higher abundance of Peptostreptococcaceae and a lower abundance of Desulfovibrionaceae compared with the CON mice (p < 0.05). Genes for glycan biosynthesis, which result in short-chain fatty acid synthesis, were enriched in the CB mice compared to the RB mice, which was correlated to a high abundance of Bacteroides. Overall, dietary RB and CB changed the gut microbiota of mice (p < 0.05).
Differentiation between non-small cell lung cancer and radiation pneumonitis after carbon-ion radiotherapy by 18F-FDG PET/CT texture analysis
Authors: Suga Makito , Nishii Ryuichi , Miwa Kenta , Kamitaka Yuto , Yamazaki Kana , Tamura Kentaro , Yamamoto Naoyoshi , Kohno Ryosuke , Kobayashi Masato , Tanimoto Katsuyuki , Tsuji Hiroshi , Higashi Tatsuya 
Published: June 2021

AbstractThe differentiation of non-small cell lung cancer (NSCLC) and radiation pneumonitis (RP) is critically essential for selecting optimal clinical therapeutic strategies to manage post carbon-ion radiotherapy (CIRT) in patients with NSCLC. The aim of this study was to assess the ability of 18F-FDG PET/CT metabolic parameters and its textural image features to differentiate NSCLC from RP after CIRT to develop a differential diagnosis of malignancy and benign lesion. We retrospectively analyzed 18F-FDG PET/CT image data from 32 patients with histopathologically proven NSCLC who were scheduled to undergo CIRT and 31 patients diagnosed with RP after CIRT. The SUV parameters, metabolic tumor volume (MTV), total lesion glycolysis (TLG) as well as fifty-six texture parameters derived from seven matrices were determined using PETSTAT image-analysis software. Data were statistically compared between NSCLC and RP using Wilcoxon rank-sum tests. Diagnostic accuracy was assessed using receiver operating characteristics (ROC) curves. Several texture parameters significantly differed between NSCLC and RP (p < 0.05). The parameters that were high in areas under the ROC curves (AUC) were as follows: SUVmax, 0.64; GLRLM run percentage, 0.83 and NGTDM coarseness, 0.82. Diagnostic accuracy was improved using GLRLM run percentage or NGTDM coarseness compared with SUVmax (p < 0.01). The texture parameters of 18F-FDG uptake yielded excellent outcomes for differentiating NSCLC from radiation pneumonitis after CIRT, which outperformed SUV-based evaluation. In particular, GLRLM run percentage and NGTDM coarseness of 18F-FDG PET/CT images would be appropriate parameters that can offer high diagnostic accuracy.
Benthic estuarine communities' contribution to bioturbation under the experimental effect of marine heatwaves
Authors: Dolbeth M. , Babe O. , Costa D. A. , Mucha A. P. , Cardoso P. G. , Arenas F. 
Published: June 2021

AbstractMarine heatwaves are increasing worldwide, with several negative impacts on biological communities and ecosystems. This 24-day study tested heatwaves' effect with distinct duration and recovery periods on benthic estuarine communities' diversity and contribution to ecosystem functioning experimentally. The communities were obtained from a temperate estuary, usually subjected to high daily thermal amplitudes. Our goal was to understand the communities' response to the thermal change, including the community descriptors and behavioural changes expected during heat extremes. We measured community composition and structural changes and the bioturbation process and nutrient release as ecosystem functioning measurements. Overall, our findings highlight the potential tolerance of studied estuarine species to the temperature ranges tested in the study, as community composition and structure were similar, independently of the warming effect. We detected a slight trend for bioturbation and nutrient release increase in the communities under warming, yet these responses were not consistent with the heatwaves exposure duration. Overall, we conclude on the complexity of estuarine communities’ contribution to functioning under warming, and the importance of scalable experiments with benthic organisms' responses to climate variability, accommodating longer time scales and replication. Such an approach would set more efficient expectations towards climate change mitigation or adaptation in temperate estuarine ecosystems.
Combined bio-chemical fertilizers ameliorate agro-biochemical attributes of black cumin (Nigella sativa L.)
Authors: Moradzadeh Samira , Siavash Moghaddam Sina , Rahimi Amir , Pourakbar Latifeh , Sayyed R. Z. 
Published: May 2021

AbstractNigella sativaL. is a medicinal plant with extensive, nutritional, pharmaceutical, and health applications. Nowadays, reducing the application of chemical fertilizers (synthetic fertilizers) is one of the main goals of sustainable agriculture to allow the production of safe crops. Therefore, the combined effect of urea and biofertilizers was studied on the quantitative and qualitative traits ofN. sativaL. in a randomized complete block design with 10 treatments and three replications. The treatments included control (no fertilization), U (100% chemical fertilizer as urea at 53.3 kg ha−1, Nb (Biofertilizer, Azotobacter vinelandii), Pb (Biofertilizer, Pantoea agglomerans and Pseudomonas putida), Kb (Biofertilizer, Bacillus spp.), NPKb (NPK, biofertilizer), Nb + 50% U, Pb + 50% U, Kb + 50%U and NPKb + 50% U. The NPK(b) + U50% was related to the highest quantity of plant height, branch diameter, capsule (follicle) number per plant, auxiliary branches, seed yield per plant, thousand-seed weight, essential oil content, total phenolic compounds, flavonoid content, DPPH free radical scavenging, nitric oxide (NO) radical scavenging, superoxide radical scavenging, chain-breaking activity, phosphorus content, and potassium content, along with U for the highest biological yield and (Pb) + U50% for the highest essential oil percentage which is close to (NPKb) + U50%. The lowest value was observed in all traits related to the control treatment except for branch diameter that was related to (NPKb). Hence, the application of (NPKb) + U50% as bio-chemical fertilizers improvedN. sativaL. Traits, so it can be recommended.
The heavy chain of 4F2 antigen promote prostate cancer progression via SKP-2
Authors: Maimaiti Maihulan , Sakamoto Shinichi , Sugiura Masahiro , Kanesaka Manato , Fujimoto Ayumi , Matsusaka Keisuke , Xu Minhui , Ando Keisuke , Saito Shinpei , Wakai Ken , Imamura Yusuke , Nakayama Keiichi , Kanai Yoshikatsu , Kaneda Atsushi , Ikehara Yuzuru , Ikeda Jun-Ichiro , Anzai Naohiko , Ichikawa Tomohiko 
Published: June 2021

Abstract
The 4F2 cell-surface antigen heavy chain (4F2hc) forms a heterodimeric complex with L-type amino acid transporter 1 (LAT1) and transports large neutral essential amino acids. However, in contrast to the traditional role of LAT1 in various cancers, the role of 4F2hc has largely remained unknown. The role of 4F2hc in prostate cancer was studied. Treatment of C4-2 cells with si4F2hc was found to suppress cellular growth, migratory and invasive abilities, with this effect occurring through the cell cycle, with a significant decrease in S phase and a significant increase in G0/G1 phase, suggesting cell cycle arrest. In addition, it was proven by RNA seq that the key to 4F2hc’s impact on cancer is SKP2. si4F2hc upregulates the protein expression of cyclin-dependent kinase inhibitors (P21cip1, P27kip1) through the downstream target SKP2. Furthermore, the expression of 4F2hc and LAT1 in prostate cancer cells suggests the importance of 4F2hc. Multivariate analysis showed that high 4F2hc expression was an independent prognostic factor for progression-free survival (HR 11.54, p = 0.0357). High 4F2hc was related to the clinical tumour stage (p = 0.0255) and Gleason score (p = 0.0035). Collectively, 4F2hc contributed significantly to prostate cancer (PC) progression. 4F2hc may be a novel marker and therapeutic target in PC.
Output of a valveless Liebau pump with biologically relevant vessel properties and compression frequencies
Authors: Davtyan Rubina , Sarvazyan Narine A. 
Published: June 2021

AbstractLiebau pump is a tubular, non-peristaltic, pulsatile pump capable of creating unidirectional flow in the absence of valves. It requires asymmetrical positioning of the pincher relative to the attachment sites of its elastic segment to the rest of the circuit. Biological feasibility of such valveless pumps remains a hotly debated topic. To test the feasibility of the Liebau-based pumping in vessels with biologically relevant properties we quantified the output of Liebau pumps with their compliant segments made of a silicone rubber that mimicked the Young modulus of soft tissues. The lengths, the inner diameters, thicknesses of the tested compliant segments ranged from 1 to 5 cm, 3 to 8 mm and 0.3 to 1 mm, respectively. The compliant segment of the setup was compressed at 0.5–2.5 Hz frequencies using a 3.5-mm-wide rectangular piston. A nearest-neighbor tracking algorithm was used to track movements of 0.5-mm carbon particles within the system. The viscosity of the aqueous solution was varied by increased percentage of glycerin. Measurements yielded quantitative relationships between viscosity, frequency of compression and the net flowrate. The use of the Liebau principle of valveless pumping in conjunction with physiologically sized vessel and contraction frequencies yields flowrates comparable to peristaltic pumps of the same dimensions. We conclude that the data confirm physiological feasibility of Liebau-based pumping and warrant further testing of its mechanism using excised biological conduits or tissue engineered components. Such biomimetic pumps can serve as energy-efficient flow generators in microdevices or to study the function of embryonic heart during its normal development or in diseased states.
A time-dependent parameter estimation framework for crop modeling
Authors: Akhavizadegan Faezeh , Ansarifar Javad , Wang Lizhi , Huber Isaiah , Archontoulis Sotirios V. 
Published: June 2021

AbstractThe performance of crop models in simulating various aspects of the cropping system is sensitive to parameter calibration. Parameter estimation is challenging, especially for time-dependent parameters such as cultivar parameters with 2–3 years of lifespan. Manual calibration of the parameters is time-consuming, requires expertise, and is prone to error. This research develops a new automated framework to estimate time-dependent parameters for crop models using a parallel Bayesian optimization algorithm. This approach integrates the power of optimization and machine learning with prior agronomic knowledge. To test the proposed time-dependent parameter estimation method, we simulated historical yield increase (from 1985 to 2018) in 25 environments in the US Corn Belt with APSIM. Then we compared yield simulation results and nine parameter estimates from our proposed parallel Bayesian framework, with Bayesian optimization and manual calibration. Results indicated that parameters calibrated using the proposed framework achieved an 11.6% reduction in the prediction error over Bayesian optimization and a 52.1% reduction over manual calibration. We also trained nine machine learning models for yield prediction and found that none of them was able to outperform the proposed method in terms of root mean square error and R2. The most significant contribution of the new automated framework for time-dependent parameter estimation is its capability to find close-to-optimal parameters for the crop model. The proposed approach also produced explainable insight into cultivar traits’ trends over 34 years (1985–2018).
Dual interleukin-17A/F deficiency protects against acute and chronic response to cigarette smoke exposure in mice
Authors: Wada Hiroo , Nakamura Masuo , Inoue Shin-Ichi , Kudo Akihiko , Hanawa Tomoko , Iwakura Yoichiro , Kobayashi Fumie , Kamma Hiroshi , Kamiya Shigeru , Ito Kazuhiro , Barnes Peter J. , Takizawa Hajime 
Published: June 2021

AbstractIL-17A and IL-17F are both involved in the pathogenesis of neutrophilic inflammation observed in COPD and severe asthma. To explore this, mice deficient in bothIl17aandIl17fand wild type (WT) mice were exposed to cigarette smoke or environmental air for 5 to 28 days and changes in inflammatory cells in bronchoalveolar lavage (BAL) fluid were determined. We also measured the mRNA expression of keratinocyte derived chemokine (Kc), macrophage inflammatory protein-2 (Mip2), granulocyte–macrophage colony stimulating factor (Gmcsf)and matrix metalloproteinase-9 (Mmp9) in lung tissue after 8 days, and lung morphometric changes after 24 weeks of exposure to cigarette smoke compared to air-exposed control animals. Macrophage counts in BAL fluid initially peaked at day 8 and again on day 28, while neutrophil counts peaked between day 8 and 12 in WT mice. Mice dual deficient withIl17a and 1l17fshowed similar kinetics with macrophages and neutrophils, but cell numbers at day 8 and mRNA expression ofKc,GmcsfandMmp9were significantly reduced. Furthermore, airspaces in WT mice became larger after cigarette smoke exposure for 24 weeks, whereas this was not seen dualIl17a and 1l17fdeficient mice. CombinedIl17aandIl17fdeficiency resulted in significant attenuation of neutrophilic inflammatory response and protection against structural lung changes after long term cigarette smoke exposure compared with WT mice. Dual IL-17A/F signalling plays an important role in pro-inflammatory responses associated with histological changes induced by cigarette smoke exposure.
Electrically controllable active plasmonic directional coupler of terahertz signal based on a periodical dual grating gate graphene structure
Authors: Morozov Mikhail Yu. , Popov Vyacheslav V. , Fateev Denis V. 
Published: June 2021

AbstractWe propose a concept of an electrically controllable plasmonic directional coupler of terahertz signal based on a periodical structure with an active (with inversion of the population of free charge carriers) graphene with a dual grating gate and numerically calculate its characteristics. Proposed concept of plasmon excitation by using the grating gate offers highly effective coupling of incident electromagnetic wave to plasmons as compared with the excitation of plasmons by a single diffraction element. The coefficient which characterizes the efficiency of transformation of the electromagnetic wave into the propagating plasmon has been calculated. This transformation coefficient substantially exceeds the unity (exceeding 6 in value) due to amplification of plasmons in the studied structure by using pumped active graphene. We have shown that applying different dc voltages to different subgratings of the dual grating gate allows for exciting the surface plasmon in graphene, which can propagate along or opposite the direction of the structure periodicity, or can be a standing plasma wave for the same frequency of the incident terahertz wave. The coefficient of unidirectionality, which is the ratio of the plasmon power flux propagating along (opposite) the direction of the structure periodicity to the sum of the absolute values of plasmon power fluxes propagating in both directions, could reach up to 80 percent. Two different methods of the plasmon propagation direction switching are studied and possible application of the found effects are suggested.
Cascaded processing enables continuous upstream processing with E. coli BL21(DE3)
Authors: Kittler Stefan , Slouka Christoph , Pell Andreas , Lamplot Roman , Besleaga Mihail , Ablasser Sarah , Herwig Christoph , Spadiut Oliver , Kopp Julian 
Published: June 2021

AbstractIn many industrial sectors continuous processing is already the golden standard to maximize productivity. However, when working with living cells, subpopulation formation causes instabilities in long-term cultivations. In cascaded continuous cultivation, biomass formation and recombinant protein expression can be spatially separated. This cultivation mode was found to facilitate stable protein expression using microbial hosts, however mechanistic knowledge of this cultivation strategy is scarce. In this contribution we present a method workflow to reduce workload and accelerate the establishment of stable continuous processes with E. coli BL21(DE3) exclusively based on bioengineering methods.
Fewer bat passes are detected during small, commercial drone flights
Authors: Ednie Gabrielle , Bird David M. , Elliott Kyle H. 
Published: June 2021

AbstractAdvances in technological capabilities, operational simplicity and cost efficiency have promoted the rapid integration of unmanned aerial vehicles (UAVs) into ecological research, providing access to study taxa that are otherwise difficult to survey, such as bats. Many bat species are currently at risk, but accurately surveying populations is challenging for species that do not roost in large aggregations. Acoustic recorders attached to UAVs provide an opportunity to survey bats in challenging habitats. However, UAVs may alter bat behaviour, leading to avoidance of the UAV, reduced detection rates and inaccurate surveys. We evaluated the number of bat passes detected with and without the presence of a small, commercial UAV in open habitats. Only 22% of bat passes were recorded in the presence of the UAV (0.23 ± 0.09 passes/min) compared to control periods without the UAV (1.03 ± 0.17 passes/min), but the effect was smaller on the big brown bat/silver-haired bat (Eptesicus fuscus/Lasionycteris noctivagans) acoustic complex. Noise interference from the UAV also reduced on-board bat detection rates. We conclude that acoustic records attached to UAVs may inaccurately survey bat populations due to low and variable detection rates by such recorders.
Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet
Authors: Aguirre-Rojas Lina M. , Scully Erin D. , Trick Harold N. , Zhu Kun Yan , Smith C. Michael 
Published: June 2021

AbstractDectes texanus is an important coleopteran pest of soybeans and cultivated sunflowers in the Midwestern United States that causes yield losses by girdling stems of their host plants. Although sunflower and giant ragweed are primary hosts of D. texanus, they began colonizing soybeans approximately 50 years ago and no reliable management method has been established to prevent or reduce losses by this pest. To identify genes putatively involved when feeding soybean, we compared gene expression of D. texanus third-instar larvae fed soybean to those fed sunflower, giant ragweed, or artificial diet. Dectes texanus larvae differentially expressed 514 unigenes when fed on soybean compared to those fed the other diet treatments. Enrichment analyses of gene ontology terms from up-regulated unigenes in soybean-fed larvae compared to those fed both primary hosts highlighted unigenes involved in oxidoreductase and polygalacturonase activities. Cytochrome P450s, carboxylesterases, major facilitator superfamily transporters, lipocalins, apolipoproteins, glycoside hydrolases 1 and 28, and lytic monooxygenases were among the most commonly up-regulated unigenes in soybean-fed larvae compared to those fed their primary hosts. These results suggest that D. texanus larvae differentially expressed unigenes involved in biotransformation of allelochemicals, digestion of plant cell walls and transport of small solutes and lipids when feeding in soybean.