bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative detection of KRAS mutated circulating tumor DNA is an independent risk factor for recurrence in colorectal cancer
Authors: Nakamura Yuki , Yokoyama Shozo , Matsuda Kenji , Tamura Koichi , Mitani Yasuyuki , Iwamoto Hiromitsu , Mizumoto Yuki , Murakami Daisuke , Kitahata Yuji , Yamaue Hiroki 
Published: January 2021

AbstractPreoperative ctDNA status in relation to recurrence in cases of CRC remains unclear. We examined preoperative ctDNA detection by targeting KRAS gene mutations as a predictive marker for recurrence after CRC surgery. We measured the preoperative KRAS mutated ctDNA status and analyzed the correlation with clinicopathologic features of 180 patients that underwent surgery for CRC. We studied the association between preoperative KRAS mutated ctDNA and postoperative recurrence in patients (n = 150) that underwent radical surgery. KRAS mutated ctDNA was detected in 59 patients (32.8%). Median mutant allele frequency of KRAS in ctDNA was 0.20%. KRAS status in ctDNA and lymph node metastasis and distant metastasis were not significantly different. Among patients that underwent radical resection, recurrence occurred in 21 (14.0%, median follow-up 24 months). In Kaplan–Meier analysis, preoperative detection of KRAS mutated ctDNA was associated with inferior recurrence-free interval (RFI) (p = 0.002) and recurrence-free survival (RFS) (p = 0.025). In a multivariate Cox proportional hazards model, preoperative detection of KRAS mutated ctDNA was an independent factor related to both RFI (HR = 3.08; p = 0.012) and RFS (HR = 2.18; p = 0.044). Preoperative measurement of KRAS mutated ctDNA could be useful to decide postoperative treatment.
Vision is protected against blue defocus
Authors: Benedi-Garcia Clara , Vinas Maria , Dorronsoro Carlos , Burns Stephen A. , Peli Eli , Marcos Susana 
Published: January 2021

AbstractDue to chromatic aberration, blue images are defocused when the eye is focused to the middle of the visible spectrum, yet we normally are not aware of chromatic blur. The eye suffers from monochromatic aberrations which degrade the optical quality of all images projected on the retina. The combination of monochromatic and chromatic aberrations is not additive and these aberrations may interact to improve image quality. Using Adaptive Optics, we investigated the optical and visual effects of correcting monochromatic aberrations when viewing polychromatic grayscale, green, and blue images. Correcting the eye’s monochromatic aberrations improved optical quality of the focused green images and degraded the optical quality of defocused blue images, particularly in eyes with higher amounts of monochromatic aberrations. Perceptual judgments of image quality tracked the optical findings, but the perceptual impact of the monochromatic aberrations correction was smaller than the optical predictions. The visual system appears to be adapted to the blur produced by the native monochromatic aberrations, and possibly to defocus in blue.
Role of PAI-1 in hepatic steatosis and dyslipidemia
Authors: Levine Joshua A. , Oleaga Carlota , Eren Mesut , Amaral Ansel P. , Shang Meng , Lux Elizabeth , Khan Sadiya S. , Shah Sanjiv J. , Omura Yasuhiro , Pamir Nathalie , Hay Joshua , Barish Grant , Miyata Toshio , Tavori Hagai , Fazio Sergio , Vaughan Douglas E. 
Published: January 2021

AbstractPlasminogen activator inhibitor 1 (PAI-1) is a functional biomarker of the metabolic syndrome. Previous studies have demonstrated that PAI-1 is a mechanistic contributor to several elements of the syndrome, including obesity, hypertension and insulin resistance. Here we show that PAI-1 is also a critical regulator of hepatic lipid metabolism. RNA sequencing revealed that PAI-1 directly regulates the transcriptional expression of numerous genes involved in mammalian lipid homeostasis, including PCSK9 and FGF21. Pharmacologic or genetic reductions in plasma PAI-1 activity ameliorates hyperlipidemia in vivo. These experimental findings are complemented with the observation that genetic deficiency of PAI-1 is associated with reduced plasma PCSK9 levels in humans. Taken together, our findings identify PAI-1 as a novel contributor to mammalian lipid metabolism and provides a fundamental mechanistic insight into the pathogenesis of one of the most pervasive medical problems worldwide.
Effect of CYP2C19 genotypes on tamoxifen metabolism and early-breast cancer relapse
Authors: Sanchez-Spitman A. B. , Swen J. J. , Dezentjé V. O. , Moes D. J. A. R. , Gelderblom H. , Guchelaar H. J. 
Published: January 2021

AbstractCYP2C19*2 and CYP2C19*17 might influence tamoxifen metabolism and clinical outcome. Our aim was to investigate the effect of CYP2C19 genotypes on tamoxifen concentrations and metabolic ratios (MRs) and breast cancer recurrence in a large cohort of Caucasian women. Genetic variants (CYP2D6 and CYP2C19 genotypes), tamoxifen and metabolites concentrations, baseline characteristics, and breast cancer recurrence from the CYPTAM study (NTR1509) were used. CYP2C19*2 and CYP2C19*17 genotypes were evaluated as alleles and as groups based on CYP2D6 genotypes (high, intermediate and low activity). Log-rank test and Kaplan–Meier analysis were used to evaluate differences in recurrence defined as relapse-free survival (RFS). Classification tree analyses (CTAs) were conducted to assess the levels of interactions per polymorphism (CYP2D6 and CYP2C19 genotypes) on endoxifen concentrations. No differences in mean concentrations and MRs were observed when comparing CYP2C19 genotypes (CYP2C19*1/*1; CYP2C19*1/*2; CYP2C19*2/*2; CYP2C19*1/*17; CYP2C19*17/*17; CYP2C19*2/*17). Only significant differences (p value < 0.05) in mean concentrations and MRs were observed when comparing tamoxifen activity groups (high, intermediate and low activity). A log-rank test did not find an association across CYP2C19 genotypes (p value 0.898). CTAs showed a significant relationship between CYP2D6 and endoxifen (p value < 0.0001), but no association with CYP2C19 genotypes was found. CYP2C19 polymorphisms do not have a significant impact on tamoxifen metabolism or breast cancer relapse.
Wetland hydroperiod predicts community structure, but not the magnitude of cross-community congruence
Authors: Daniel Jody , Rooney Rebecca C. 
Published: January 2021

AbstractA major focus in community ecology is understanding how biological interactions and environmental conditions shape horizontal communities. However, few studies have explored whether cross-community interactions are consistent or non-stationary across environmental gradients. Using the relative abundance of birds, aquatic macroinvertebrates and plants, we examined how cross-community congruence varied between short and long-hydroperiod prairie pothole wetlands in southern Alberta. These wetlands are structured by their hydroperiod: the length of time that ponded water is present in the wetland. We compared the strength of cross-community congruence and the strength of congruence between each horizontal community and wetland hydroperiod in wetlands that typically contain ponded water throughout the year to wetlands that dry up every summer. The strength of cross-community relationships was similar between more permanent and more ephemeral wetland classes, suggesting that biological interactions have a near equivalent role in shaping community composition, regardless of hydroperiod. However, because cross-community congruence, measured as the Procrustes pseudo-R value, was, on average, 77% ± SE 12% greater than that between each horizontal community and measures of wetland hydroperiod, we concluded that community structure is not shaped by hydroperiod alone. We attribute the observed cross-community congruence to (1) plants and aquatic macroinvertebrates influence birds through habitat and food provisioning, and (2) birds influence plants and aquatic macroinvertebrates by dispersing their propagules.
Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans
Authors: Hall Ashley N. , Turner Tychele N. , Queitsch Christine 
Published: January 2021

AbstractThe ribosomal RNA genes (rDNA) are tandemly arrayed in most eukaryotes and exhibit vast copy number variation. There is growing interest in integrating this variation into genotype–phenotype associations. Here, we explored a possible association of rDNA copy number variation with autism spectrum disorder and found no difference between probands and unaffected siblings. Because short-read sequencing estimates of rDNA copy number are error prone, we sought to validate our 45S estimates. Previous studies reported tightly correlated, concerted copy number variation between the 45S and 5S arrays, which should enable the validation of 45S copy number estimates with pulsed-field gel-verified 5S copy numbers. Here, we show that the previously reported strong concerted copy number variation may be an artifact of variable data quality in the earlier published 1000 Genomes Project sequences. We failed to detect a meaningful correlation between 45S and 5S copy numbers in thousands of samples from the high-coverage Simons Simplex Collection dataset as well as in the recent high-coverage 1000 Genomes Project sequences. Our findings illustrate the challenge of genotyping repetitive DNA regions accurately and call into question the accuracy of recently published studies of rDNA copy number variation in cancer that relied on diverse publicly available resources for sequence data.
Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation
Authors: Hashemkhani Shahnazari Ghazaleh , Darvish Ganji Masoud 
Published: January 2021

AbstractThe characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase–Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.
The Aβ(1–38) peptide is a negative regulator of the Aβ(1–42) peptide implicated in Alzheimer disease progression
Authors: Quartey Maa O. , Nyarko Jennifer N. K. , Maley Jason M. , Barnes Jocelyn R. , Bolanos Maria A. C. , Heistad Ryan M. , Knudsen Kaeli J. , Pennington Paul R. , Buttigieg Josef , De Carvalho Carlos E. , Leary Scot C. , Parsons Matthew P. , Mousseau Darrell D. 
Published: January 2021

AbstractThe pool of β-Amyloid (Aβ) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for Aβ peptides. We examined how a naturally occurring variant, e.g. Aβ(1–38), interacts with the AD-related variant, Aβ(1–42), and the predominant physiological variant, Aβ(1–40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that Aβ(1–38) interacts differently with Aβ(1–40) and Aβ(1–42) and, in general, Aβ(1–38) interferes with the conversion of Aβ(1–42) to a β-sheet-rich aggregate. Functionally, Aβ(1–38) reverses the negative impact of Aβ(1–42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an Aβ(1–42) phenotype in Caenorhabditis elegans. Aβ(1–38) also reverses any loss of MTT conversion induced by Aβ(1–40) and Aβ(1–42) in HT-22 hippocampal neurons and APOE ε4-positive human fibroblasts, although the combination of Aβ(1–38) and Aβ(1–42) inhibits MTT conversion in APOE ε4-negative fibroblasts. A greater ratio of soluble Aβ(1–42)/Aβ(1–38) [and Aβ(1–42)/Aβ(1–40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that Aβ(1–38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant Aβ(1–42).
Degree day-based model predicts pink bollworm phenology across geographical locations of subtropics and semi-arid tropics of India
Authors: Fand Babasaheb B. , Nagrare V. S. , Bal S. K. , Naik V. Chinna Babu , Naikwadi B. V. , Mahule D. J. , Gokte-Narkhedkar Nandini , Waghmare V. N. 
Published: January 2021

AbstractThere is a global concern about the effects of climate change driven shifts in species phenology on crop pests. Using geographically and temporally extensive data set of moth trap catches and temperatures across the cotton growing states of India, we predicted the phenology of cotton pink bollworm Pectinophora gossypiella (Saunders). Our approach was centered on growing degree days (GDD), a measure of thermal accumulation that provides a mechanistic link between climate change and species’ phenology. The phenology change was predicted by calculating absolute error associated with DD and ordinal date, an alternative predictor of phenology, for peak moth abundance. Our results show that GDD outperformed the ordinal dates in predicting peak moth abundance in 6 out of 10 selected locations. Using established thresholds of 13.0/34.0 °C, mean DD accumulated between the consecutive moth peaks across different years were estimated at 504.05 ± 4.84. Seven generations were determined for pink bollworm in a cropping season, the length of which varied between 35 and 73 days in response to temperature. Pink bollworm population reached its peak during third generation which can be the target for management actions. The study provides essential information for developing pink bollworm management strategies under climate change.
Metabarcoding profiling of microbial diversity associated with trout fish farming
Authors: Mahmoud Mohamed A. A. , Magdy Mahmoud 
Published: January 2021

AbstractEarthy and musty off-flavors are routinely observed in farmed trout worldwide. The microbial association to the production of those off-flavors was previously reported. The current manuscript aimed to catalog the microbial enrichment (eukaryotes and prokaryotes) in semi-intensive aquaculture freshwater sources that might influence the trout aquaculture quality production. The 16S rRNA and ITS metabarcoding analyses were applied on the inflow- and pond-water samples from trout farms previously recorded a malodor fish products and located alongside Moosach and Sempt Rivers in Bavaria province, Germany. The results showed that more than 99% of the detected prokaryotic OTUs (Operational Taxonomic Unit identification) were bacteria as of ~ 75.57% were Proteobacteria, and ~ 14.4% were Bacteroidetes. Meanwhile, 118 out of 233 of the eukaryotic OTUs were known species. Of these, ~ 45% were plant pathogens, and ~ 28% were mushroom/yeasts. Based on the comparative analysis between inflow- and pond-water samples, several pro- and eukaryotic microorganisms that affect the trout aquaculture water quality and industry have been detected, including the malodor-producing microorganisms, e.g., Cyanobacteria and Actinobacteria, along with fish infectious microorganisms, e.g., Chilodonella cyprinid, Metschnikowia bicuspidate. Additionally, the effect of the human- and industrial-related activities around the sampling area on the microbiota of the investigated farms were highlighted.
Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model
Authors: Devall Matthew , Plummer Sarah J. , Bryant Jennifer , Jennelle Lucas T. , Eaton Stephen , Dampier Christopher H. , Huyghe Jeroen R. , Peters Ulrike , Powell Steven M. , Casey Graham 
Published: January 2021

AbstractAlcohol is a consistently identified risk factor for colon cancer. However, the molecular mechanism underlying its effect on normal colon crypt cells remains poorly understood. We employed RNA-sequencing to asses transcriptomic response to ethanol exposure (0.2% vol:vol) in 3D organoid lines derived from healthy colon (n = 34). Paired regression analysis identified 2,162 differentially expressed genes in response to ethanol. When stratified by colon location, a far greater number of differentially expressed genes were identified in organoids derived from the left versus right colon, many of which corresponded to cell-type specific markers. To test the hypothesis that the effects of ethanol treatment on colon organoid populations were in part due to differential cell composition, we incorporated external single cell RNA-sequencing data from normal colon biopsies to estimate cellular proportions following single cell deconvolution. We inferred cell-type-specific changes, and observed an increase in transit amplifying cells following ethanol exposure that was greater in organoids from the left than right colon, with a concomitant decrease in more differentiated cells. If this occurs in the colon following alcohol consumption, this would lead to an increased zone of cells in the lower crypt where conditions are optimal for cell division and the potential to develop mutations.
A novel deep learning-based quantification of serial chest computed tomography in Coronavirus Disease 2019 (COVID-19)
Authors: Pan Feng , Li Lin , Liu Bo , Ye Tianhe , Li Lingli , Liu Dehan , Ding Zezhen , Chen Guangfeng , Liang Bo , Yang Lian , Zheng Chuansheng 
Published: January 2021

AbstractThis study aims to explore and compare a novel deep learning-based quantification with the conventional semi-quantitative computed tomography (CT) scoring for the serial chest CT scans of COVID-19. 95 patients with confirmed COVID-19 and a total of 465 serial chest CT scans were involved, including 61 moderate patients (moderate group, 319 chest CT scans) and 34 severe patients (severe group, 146 chest CT scans). Conventional CT scoring and deep learning-based quantification were performed for all chest CT scans for two study goals: (1) Correlation between these two estimations; (2) Exploring the dynamic patterns using these two estimations between moderate and severe groups. The Spearman’s correlation coefficient between these two estimation methods was 0.920 (p < 0.001). predicted pulmonary involvement (CT score and percent of pulmonary lesions calculated using deep learning-based quantification) increased more rapidly and reached a higher peak on 23rd days from symptom onset in severe group, which reached a peak on 18th days in moderate group with faster absorption of the lesions. The deep learning-based quantification for COVID-19 showed a good correlation with the conventional CT scoring and demonstrated a potential benefit in the estimation of disease severities of COVID-19.
Structure and spectroscopy of methionyl-methionine for aquaculture
Authors: Parker Stewart F. , Funnell Nicholas P. , Shankland Kenneth , Kabova Elena A. , Häußner Thomas , Hasselbach Hans-Joachim , Braune Sascha , Kobler Christoph , Albers Peter W. 
Published: January 2021

AbstractThe amino acid l-methionine is an essential amino acid and is commonly used as a feed supplement in terrestrial animals. It is less suitable for marine organisms because it is readily excreted. It is also highly water soluble and this results in loss of the feed and eutrophication of the water. To address these problems, the dipeptide dl-methionyl-dl-methionine (trade name: AQUAVI Met-Met) has been developed as a dedicated methionine source for aquaculture. The commercial product is a mixture of a racemic crystal form of d-methionyl-d-methionine/l-methionyl-l-methionine and a racemic crystal form of d-methionyl-l-methionine/l-methionyl-d-methionine. In this work, we have computationally, structurally, spectroscopically and by electron microscopy characterised these materials. The microscopy and spectroscopy demonstrate that there is no interaction between the dd–ll and dl–ld racemates on any length scale from the macroscopic to the nanoscale.
Comprehensive impedance investigation of low-cost anion exchange membrane electrolysis for large-scale hydrogen production
Authors: Vincent Immanuel , Lee Eun-Chong , Kim Hyung-Man 
Published: January 2021

AbstractAnion exchange membrane (AEM) electrolysis is a promising solution for large-scale hydrogen production from renewable energy resources. However, the performance of AEM electrolysis is still lower than what can be achieved with conventional technologies. The performance of AEM electrolysis is limited by integral components of the membrane electrode assembly and the reaction kinetics, which can be measured by ohmic and charge transfer resistances. We here investigate and then quantify the contributions of the ohmic and charge transfer resistances, and the rate-determining steps, involved in AEM electrolysis by using electrochemical impedance spectroscopy analysis. The factors that have an effect on the performance, such as voltage, flow rate, temperature and concentration, were studied at 1.5 and 1.9 V. Increased voltage, flow rate, temperature and concentration of the electrolyte strongly enhanced the anodic activity. We observed that here the anodic reaction offered a greater contribution to the overpotential than the cathode did.
A novel hybrid termination structure for vertical gallium nitride Schottky barrier diode by using technology computer aided design simulation
Authors: Li Jian , Lin Feng , Chen Yong , He Wei , Liu Xinke 
Published: January 2021

AbstractGallium nitride based high‐power electronic devices are now in full swing. However, the phenomenon that the gallium nitride Schottky diodes break down prematurely without reaching the gallium nitride material limit is unsolved. This paper proposes a novel hybrid termination structure for vertical gallium nitride Schottky diodes to improve breakdown voltage. This work is carried out to simulate the breakdown voltage and reverse characteristics of the vertical gallium nitride Schottky diode by using technology computer aided design (TCAD) simulation. Under the same testing conditions, we demonstrate that compared with the control vertical Schottky diode, the breakdown voltage of the proposed Schottky diode can be significantly advanced, which has increased by 350 V and reached 850 V.