bluuebunny/crossref_metadata_2025 huggingface dataset:
Molybdenum Dioxide (MoS2)/Gadolinium (Gd) Containing Arginine-Glycine-Aspartic Acid (RGD) Sequences as New Nano-Contrast Agent for Cancer Magnetic Resonance Imaging (MRI)
Authors: Hao Xiaoguang , Li Weijing
Published: January 2021

Molybdenum dioxide-gadolinium-arginine/glycine/aspartic acid (MoS2-Gd-RGD) sequences targeting nano-contrast agents that specifically bind to human hepatocellular carcinoma (HCC) HepG2 cells were synthesized, and their targeting imaging effects on HCC cells and
models were evaluated. Zeta potential, particle size and Fourier Transform Infrared Spectrometer (FTIR) were used to characterize the nano-contrast agent, and its cytotoxicity was evaluated. The MoS2-Gd nanoparticles were used as control in vitro to determine the targeting
capability of the MoS2-Gd-RGD nanoparticles toward integrin αvβ3. During in vivo animal experiments, 12 nude mice with tumors were randomly divided into three groups to compare the imaging effects of the MoS2-Gd-RGD and MoS2-Gd
groups. The hydrodynamic diameter of MoS2-Gd-RGD nanoparticles was approximately 336.43±6.43 nm, and the polydispersity index (PDI) value reached 0.132. Transmission electron microscopy showed the uniform particle size and good dispersion of the nanoparticles. The relaxation
rate totaled 1.39 mM−1S−1. The signal value of the T1-weighted image of the HepG2 cells treated with MoS2-Gd-RGD was higher than that of the non-targeted materials (MoS2-Gd) (P < 0.01). The signal value
of the tumor increased significantly 15 min after the tail vein injection with MoS2-Gd-RGD, and it peaked at 60 min after injection. A significant difference in tumor signal values was observed between the two groups of nude mice injected with MoS2-Gd-RGD and MoS2-
Gd (P < 0.01). At the in vitro and in vivo experiments, the MoS2-Gd-RGD nanoparticles presented the characteristics of integrin αvβ3 targeting. Thus, MoS2-Gd-RGD nanoparticles feature potential as contrast agents for MRI.
Characteristics of Aluminum-Doped Zinc Oxide Films Grown Using Facing Target Sputtering for Transparent Electrode of Heterojunction Solar Cells
Authors: Kim Yujin , Kim Sangmo , Hong Jeongsoo , Kim Kyung Hwan
Published: January 2021

In general sputtering, material characteristics can be degraded by high-energy particles located inside the plasma owing to the thin film surface. However, facing target sputtering (FTS) can be used to produce high-quality thin films through maximum control over substrate damage and
the reduction of layer damage caused by high-energy particles impacting the substrate. Transparent conductive oxides (TCOs) are being applied to a variety of technologies, including displays and solar cells. The typical transparent electrode material is indium tin oxide (ITO), which contains
rare and expensive raw materials. Aluminum-doped zinc oxide (AZO) has attracted increasing attention as a substitute to ITO because it is composed of abundantly available resources and is generally inexpensive. In this study, an AZO thin film was prepared using an FTS system for heterojunction
solar cells. The effects of the deposition substrate temperature on the resulting electrical conductivity, structural properties, and optical properties of the AZO thin films were examined.
A Study on Carbon Capture and Storage and Its Feasibility in Energy-Environment Technologies
Authors: Kim Areum , Kwon Soon-Hyeong , Cui Yinhua , Gao Yuan , Jeong Soongon , Kim Kyung-Soo , Lee Sung Chul , Pyo Sung Gyu
Published: January 2021

Carbon capture and storage (CCS) has the potential to play an important role in managing global warming in the near future. Herein, we define the entire energy cycle from energy production to utilization considering energy-environment technologies and describe the technical classification
and brief technical principles of CCS technology. In addition, we evaluate data from actual scenarios and costs of various indicators established from diverse reports published by reliable institutes on various energy-environment technologies. Finally, the economic feasibility of CCS is determined
compared with that of fossil fuel power plants and renewable energy generation in terms of carbon credit for global trading. This techno-economic analysis and systematic review lays the groundwork for comprehensive research toward understanding energy-environment technologies by establishing
scenarios in terms of cost and data analysis that can provide an objective approach.
Comparison of Temperature Sensing Performance of 4H-SiC Schottky Barrier Diodes, Junction Barrier Schottky Diodes, and PiN Diodes
Authors: Min Seong-Ji , Schweitz Michael A. , Nguyen Ngoc Thi , Koo Sang-Mo
Published: January 2021

We present a comparison between the thermal sensing behaviors of 4H-SiC Schottky barrier diodes, junction barrier Schottky diodes, and PiN diodes in a temperature range from 293 K to 573 K. The thermal sensitivity of the devices was calculated from the slope of the forward voltage versus
temperature plot. At a forward current of 10 μA, the PiN diode presented the highest sensitivity peak (4.11 mV K−1), compared to the peaks of the junction barrier Schottky diode and the Schottky barrier diode (2.1 mV K−1 and 1.9 mV K−1,
respectively). The minimum temperature errors of the PiN and junction barrier Schottky diodes were 0.365 K and 0.565 K, respectively, for a forward current of 80 μA±10 μA. The corresponding value for the Schottky barrier diode was 0.985 K for a forward current of 150 μA±10
μA. In contrast to Schottky diodes, the PiN diode presents a lower increase in saturation current with temperature. Therefore, the nonlinear contribution of the saturation current with respect to the forward current is negligible; this contributes to the higher sensitivity of the PiN diode,
allowing for the design and fabrication of highly linear sensors that can operate in a wider temperature range than the other two diode types.
Effect of Cu Addition on the Precipitation Hardening and Mechanical Properties of Al–Mg Based Cast Alloys
Authors: Wahid Shah Abdul , Ha Seong-Ho , Kim Bong-Hwan , Yoon Young-Ok , Lim Hyun-Kyu , Kim Shae K.
Published: January 2021

This study examines the formation of different phases of Al-6 mass% Mg–xCu (x = 1 and 3 mass%) alloys in as-cast condition. Further, it investigates the dissolution of these phases upon solution heat treatment (SHT) and studies the precipitation behavior of these
ternary alloys. Scanning electron microscopy with energy-dispersive spectrometry and high resolution X-ray diffraction analyses show the presence of the second phases of Al3Mg2 (β), Al6CuMg4 (T), and Al2CuMg (S) in Alloy I (Al–6Mg–1Cu),
whereas Alloy II (Al–6Mg–3Cu) had only T and S second phases (with a much higher number of S phases). Upon SHT, a significant number of eutectic phases were dissolved in Alloy I, whereas in Alloy II, the number of undissolved S phases was relatively high. A differential scanning
calorimetry (DSC) analysis of experimental alloys in as-quenched states reveals two exothermic peaks related to the formation of nanoclusters and S″ or S′ metastable phases. Both alloys undergo a rapid hardening stage during the aging process, in which approximately 50%–60%
of total hardness was achieved. This is attributed to the formation of nanoclusters. The maximum yield strength achieved at the peak hardness condition was approximately 200 MPa for Alloy I, whereas it was approximately 160 MPa for alloy II. Alloy I took a long time to reach peak hardness,
which is correlated with the stability of nanoclusters for a longer time. Earlier peak hardness in Alloy II, despite having nanoclusters, is correlated with undissolved eutectic phases acting as heterogeneous nucleation sites for the formation of S″ or S′ metastable phases.
Combined Effect of Mg and Ca on Oxidation Behaviors of Zn–Mg Based Alloys Containing a Trace of Ca at High Temperature
Authors: Ha Seong-Ho , Kim Bong-Hwan , Yoon Young-Ok , Lim Hyun-Kyu , Kim Shae K.
Published: January 2021

In this study, the combined effect of Mg and Ca on the high temperature oxidation behaviors of Zn–Mg based alloys containing trace Ca was investigated. Phase diagrams for the oxygen partial pressure versus contents of constituent elements were conducted on the basis of thermodynamic
calculations to predict oxide scale behavior. Observation of Zn-1/3/5 mass%Mg alloys showed the distribution of a Zn–Zn11Mg2 eutectic phase after primary formation. As-cast microstructures of the Ca-containing alloys included the formation of a Ca-based intermetallic
phase. The change in oxidation resistance with variation of the Mg and Ca contents was experimentally examined via thermogravimetric analysis (TGA). The addition of trace Ca led to the formation of Zn13Ca and a CaO/MgO mixed oxide layer on the surface at 460 °C. After TGA at
460 °C under air atmosphere for 1 h, the Ca-free alloys showed rapid weight gain by oxidation, whereas the oxidation resistance of the Ca-added alloys was substantially increased.
Modelling and Evolution of Conducting Filament in TiOx Memristor Using Conducting Atomic Force Microscopy
Authors: Panda Debashis , Kumari Roshni , Pradhan Alaka
Published: January 2021

Conducting filament evolution in TiOx based resistive switching memory fabricated by simple oxidation of Ti film is investigated. Formation of titanium oxide is confirmed from the X-ray diffraction study. Forming is required to initiate the switching process. A bipolar
analog switching is observed with a positive set and negative reset voltage. The switching properties in TiOx layer owing to the formation of conducting filament is confirmed from the conducting atomic force micrograph at different bias voltage. A significant change in surface
topography as a filament formation during set and reset is presented. Conduction mechanism inside the device at various voltage and effect of tunnel width on current is studied. The effective tunnel width of conduction filament and related parameters for device using device modelling (Threshold
Adaptive Memristor model) is studied. The device can be used for synaptic applications.
Magnesium Hydrogen Phosphate: An Efficient Catalyst for Acrylic Acid Production from Biorenewable Lactic Acid
Authors: Nekkala Nagaraju , Balla Putrakumar , Ginjupalli Srinivasarao , Mitta Harisekher , Hussain S. K. , Ponnala Bhanuchander , Chary K. V. R.
Published: January 2021

A series of Magnesium hydrogen phosphate (MgHP) catalysts with different magnesium to phosphorous (Mg/P) mole ratios at varying calcination temperatures has been synthesised, bearing in mind the effectiveness as well as the stability of MgHP to catalyse acrylic acid (AA) production
from biorenewable lactic acid (LA), a synthetic process applicable to biomass conversion. The physicochemical properties of the MgHP catalysts have been thoroughly characterised and the formation of Mg(NH4)PO4, MgHPO4 and Mg2P2O7
with different structural and acidic properties have been reported. The high catalytic performance of MgHP catalysts with high AA yields (100% conversion and 85% selectivity) at high space velocities (WHSVLA = 3.13 h−1) have been achieved at 360 °C. NH3-Temperature
programmed desorption (TPD) and pyridine FTIR have shown that the effectiveness of a catalyst is accounted for not primarily by the actual strength of acidic sites, but is due to the presence of Lewis acidic sites compared to Bronsted sites.
A Novel Room-Temperature Bonding Method Based on Electrohydrodynamic Printing
Authors: Wu Wenzheng , Yang Xue , Liu Rui , Yin Zhifu , Wang D. F. , Zou Helin , Hu Wei , Li Lu
Published: January 2021

Microfluidic chips made by traditional materials (glass and silicon) are still important for fluorescence tests, biocompatible experiments, and high temperature applications. However, the majority of the present bonding methods suffer from ultra-clean requirement, complicated fabrication
process, and low production efficiency. In the present work, an Electrohydrodynamic printing assist bonding method was proposed. By this method, the ultraviolet-cured-glue dots were printed onto the silicon substrate, and then the patterned glass and silicon substrate can be bonded together
at room temperature. The influence of printing condition (nozzle inner-diameter, applied voltage, printing height, and flow rate) on the diameter of printed dot was analyzed by experiments. By the optimized printing condition, the glass-silicon microfluidic chip can be well bonded. The bonding
strength and leakage test demonstrated the high bonding quality of the microfluidic chip (bonding strength of 28 MPa and leakage pressure of 3.5 MPa).
Fabrication of Mesoporous C60/Carbon Hybrids with 3D Porous Structure for Energy Storage Applications
Authors: Baskar Arun V. , Davidraj Jefrin M. , Ruban Ajanya M. , Joseph Stalin , Singh Gurwinder , Al-Muhtaseb Ala'a H. , Lee Jang Mee , Yi Jiabao , Vinu A.
Published: January 2021

We report on the synthesis of 3D mesoporous fullerene/carbon hybrid materials with ordered porous structure and high surface area by mixing the solution of fullerene and sucrose molecules in the nanochannels of 3D mesoporous silica, KIT-6 via nanotemplating approach. The addition of
sucrose molecules in the synthesis offers a thin layer of carbon between the fullerene molecules which enhances not only the specific surface area and the specific pore volume but also the conductivity of the hybrid materials. The prepared hybrids exhibit 3D mesoporous structure and show a
much higher specific surface area than that of the pure mesoporous fullerene. The hybrids materials are used as the electrodes for supercapacitor and Li-ion battery applications. The optimised hybrid sample shows an excellent rate capability and a high specific capacitance of 254 F/g at the
current density of 0.5 A/g, which is much higher than that of the pure mesoporous fullerene, mesoporous carbon, activated carbon and multiwalled carbon nanotubes. When used as the electrode for Li-ion battery, the sample delivers the largest specific capacity of 1067 mAh/g upon 50 cycles at
the current density of 0.1 A/g with stability. These results reveal that the addition of carbon in the mesoporous fullerene with 3D structure makes a significant impact on the electrochemical properties of the hybrid samples, demonstrating their potential for applications in Li-ion battery
and supercapacitor devices.
Long Process Incus necrosis in Revision Stapedotomy: Retrospective Clinical Study
Authors: Massimilla Eva Aurora , Testa Domenico , Nunziata Michele , Donadio Anna , Romano Maria Loreto , Motta Gaetano
Published: January 2021

Objectives:

We describe our experience with long process incus (LPI) necrosis in revision stapedotomy and discuss the different management methods proposed in the literature to identify surgical techniques that can lead to satisfactory results over time.

Methods:

Twenty-two stapedotomy revisions, in 21 patients with the necrosis of the long process of the incus, are performed from 1997 to 2017. In cases of erosion or minimal necrosis of LPI, a new prosthesis of the same type or an angled prosthesis was applied higher on the residual incus stump. In cases of partial necrosis of LPI, a Donaldson type ventilation tube reshaped and placed on the residual incus stump to stabilize prosthesis, or glass ionomer bone cement was used. In cases of subtotal necrosis of LPI, a cup piston prosthesis in polycel was applied on incus residual stump. Pre- and postoperative (≥1 year) pure tone audiometry was performed for all cases. Air conduction threshold, bone conduction (BC) threshold, and air-bone gap (ABG) were documented according to the American Academy of Otolaryngology Head and Neck Surgery Committee of Hearing and Equilibrium guidelines.

Results:

At 1-year follow-up, postoperative ABG was reduced to ≤10 dB in 13 (59%) cases and ≤20 dB in 19 (86.4%) cases. The mean postoperative ABG significantly decreased in each group. There was no significant change in postoperative BC thresholds, and there were no cases with postoperative SNHL.

Conclusion:

Excellent functional results can also be achieved in cases of long incus process necrosis. The choice of technique should be considered according to the degree of necrosis. Piston replacement with the same type or angled type prosthesis, in cases of erosion or minimal LPI necrosis, and modified Donaldson type ventilation tube, in cases of partial LPI necrosis, provided excellent hearing results.
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
Authors: Solares Edwin A. , Tao Yuan , Long Anthony D. , Gaut Brandon S.
Published: January 2021

Background

Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

Results

Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb).

Conclusions

HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito’s largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.
Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm
Authors: Lu Jiaxing , Chen Ming , Qin Yufang
Published: January 2021

Background

Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing drug responses to the cancer, traditional experimental methods have been greatly hampered by the cost and sample size. At present, the public availability of large amounts of gene expression data makes it a challenging task to use machine learning methods to predict the drug sensitivity.

Results

In this study, we introduced the WRFEN-XGBoost cell viability prediction algorithm based on LINCS-L1000 cell signatures. We integrated the LINCS-L1000, CTRP and Achilles datasets and adopted a weighted fusion algorithm based on random forest and elastic net for key gene selection. Then the FEBPSO algorithm was introduced into XGBoost learning algorithm to predict the cell viability induced by the drugs. The proposed method was compared with some new methods, and it was found that our model achieved good results with 0.83 Pearson correlation. At the same time, we completed the drug sensitivity validation on the NCI60 and CCLE datasets, which further demonstrated the effectiveness of our method.

Conclusions

The results showed that our method was conducive to the elucidation of disease mechanisms and the exploration of new therapies, which greatly promoted the progress of clinical medicine.
nanotatoR: a tool for enhanced annotation of genomic structural variants
Authors: Bhattacharya Surajit , Barseghyan Hayk , Délot Emmanuèle C. , Vilain Eric
Published: January 2021

Background

Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity.

Results

We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.).

nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM.

Conclusions

The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.
Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data
Authors: Dzomba E. F. , Chimonyo M. , Pierneef R. , Muchadeyi F. C.
Published: January 2021

Background

Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands.

Results

A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns.

Conclusions

Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.
Comparative transcriptomic analysis reveals female-biased olfactory genes potentially involved in plant volatile-mediated oviposition behavior of Bactrocera dorsalis
Authors: Xu Li , Tang Kai-Yue , Chen Xiao-Feng , Tao Yong , Jiang Hong-Bo , Wang Jin-Jun
Published: January 2021

Background

Olfactory systems take on important tasks to distinguish salient information from a complex olfactory environment, such as locating hosts, mating, aggression, selecting oviposition sites, and avoiding predators. The olfactory system of an adult insect consists of two pairs of main olfactory appendages on the head, the antennae, and the palps, which are covered with sensilla. Benzothiazole and 1-octen-3-ol could elicit oviposition behavior in gravid B. dorsalis are regarded as oviposition stimulants. However, the mechanism for how B. dorsalis percepts benzothiazole and 1-octen-3-ol still remains unknown.

Results

We conducted a comparative analysis of the antennal transcriptomes in different genders of B. dorsalis using Illumina RNA sequencing (RNA-seq). We identified a total of 1571 differentially expressed genes (DEGs) among the two sexes, including 450 female-biased genes and 1121 male-biased genes. Among these DEGs, we screened out 24 olfaction-related genes and validated them by qRT-PCR. The expression patterns of these genes in different body parts were further determined. In addition, we detected the expression profiles of the screened female-biased chemosensory genes in virgin and mated female flies. Furthermore, the oviposition stimulants-induced expression profilings were used to identify chemosensory genes potentially responsible for benzothiazole and 1-octen-3-ol perception in this fly.

Conclusions

The results from this study provided fundamental data of chemosensory DEGs in the B. dorsalis antenna. The odorant exposure assays we employed lay a solid foundation for the further research regarding the molecular mechanism of benzothiazole and 1-octen-3-ol mediated oviposition behavior in B. dorsalis.
Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene
Authors: Jeong Jiseong , Park Sunhee , Im Jeong Hui , Yi Hankuil
Published: January 2021

Background

TheGretchen Hagen 3(GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors.GH3genes, especially Group III subgroup 6GH3genes, and their expression patterns in economically importantB. oleraceavar.oleraceahave not been systematically identified.

Results

As a first step to understand regulation and molecular functions of Group III subgroup 6GH3genes, 34GH3genes including four subgroup 6 genes were identified inB. oleraceavar.oleracea. Synteny found around subgroup 6GH3genes inB. oleraceavar.oleraceaandArabidopsis thalianaindicated that these genes are evolutionarily related. Although expression of four subgroup 6GH3genes inB. oleraceavar.oleraceais not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6GH3genes inB. oleraceavar.oleracea, onlyBoGH3.13–1is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenicA. thalianasubgroup 6GH3genes. Detailed analyses of promoter activities further showed thatBoGH3.13–1is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones.

Conclusions

Sixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) inBoGH3.13–1promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenicBrassicaplants.
Galectins from Onchocerca ochengi and O. volvulus and their immune recognition by Wistar rats, Gudali zebu cattle and human hosts
Authors: Ngwasiri Ngwafu Nancy , Brattig Norbert W. , Ndjonka Dieudonné , Liebau Eva , Paguem Archile , Leusder Dustin , Kingsley Manchang Tanyi , Eisenbarth Albert , Renz Alfons , Daniel Achukwi Mbunkah
Published: January 2021

Background

During the last two decades research on animal filarial parasites, especiallyOnchocerca ochengi,infecting cattle in savanna areas of Africa revealed thatO. ochengias an animal model has biological features that are similar to those ofO. volvulus,the aetiological agent of human onchocerciasis. There is, however, a paucity of biochemical, immunological and pathological data forO. ochengi. Galectins can be generated by parasites and their hosts. They are multifunctional molecules affecting the interaction between filarial parasites and their mammalian hosts including immune responses. This study characterizedO. ochengigalectin, verified its immunologenicity and established its immune reactivity and that ofOnchocerca volvulusgalectin.

Results

The phylogenetic analysis showed the high degree of identity between the identifiedO. ochengiand theO. volvulusgalectin-1 (ß-galactoside-binding protein-1) consisting only in one exchange of alanine for serine.O. ochengigalectin induced IgG antibodies during 28 days after immunization of Wistar rats. IgG fromO. ochengi-infected cattle andO. volvulus-infected humans cross-reacted with the corresponding galectins. Under the applied experimental conditions in a cell proliferation test,O. ochengigalectin failed to significantly stimulate peripheral blood mononuclear cells (PBMCs) fromO. ochengi-infected cattle, regardless of their parasite load.

Conclusion

AnO. ochengigalectin gene was identified and the recombinantly expressed protein was immunogenic. IgG fromOnchocerca-infected humans and cattle showed similar cross-reaction with both respective galectins. The present findings reflect the phylogenetic relationship between the two parasites and endorse the appropriateness of the cattleO. ochengimodel forO. volvulusinfection research.
Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis
Authors: Ma Dongmei , Liu Bei , Ge Lingqiao , Weng Yinyin , Cao Xiaohui , Liu Fang , Mao Peisheng , Ma Xiqing
Published: January 2021

Background

Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the production of alfalfa hay and seeds. However, the underlying molecular mechanisms of flowering time regulation in alfalfa are not well understood.

Results

In this study, an early-flowering alfalfa genotype 80 and a late-flowering alfalfa genotype 195 were characterized for the flowering phenotype. Our analysis revealed that the lower jasmonate (JA) content in new leaves and the downregulation of JA biosynthetic genes (i.e. lipoxygenase, the 12-oxophytodienoate reductase-like protein, and salicylic acid carboxyl methyltransferase) may play essential roles in the early-flowering phenotype of genotype 80. Further research indicated that genes encode pathogenesis-related proteins [e.g. leucine rich repeat (LRR) family proteins, receptor-like proteins, and toll-interleukin-like receptor (TIR)-nucleotide-binding site (NBS)-LRR class proteins] and members of the signaling receptor kinase family [LRR proteins, kinases domain of unknown function 26 (DUF26) and wheat leucine-rich repeat receptor-like kinase10 (LRK10)-like kinases] are related to early flowering in alfalfa. Additionally, those involved in secondary metabolism (2-oxoglutarate/Fe (II)-dependent dioxygenases and UDP-glycosyltransferase) and the proteasome degradation pathway [really interesting new gene (RING)/U-box superfamily proteins and F-box family proteins] are also related to early flowering in alfalfa.

Conclusions

Integrated phenotypical, physiological, and transcriptomic analyses demonstrate that hormone biosynthesis and signaling pathways, pathogenesis-related genes, signaling receptor kinase family genes, secondary metabolism genes, and proteasome degradation pathway genes are responsible for the early flowering phenotype in alfalfa. This will provide new insights into future studies of flowering time in alfalfa and inform genetic improvement strategies for optimizing this important trait.
Targeted amplicon sequencing + next-generation sequencing–based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)
Authors: Takeshima Ryoma , Ogiso-Tanaka Eri , Yasui Yasuo , Matsui Katsuhiro
Published: January 2021

Background

Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines. However, genetic loci and selection markers associated with PHS in buckwheat have not been reported.

Results

By next-generation sequencing (NGS) of whole-genome of parental lines, we developed a genome-wide set of 300 markers. By NGS- based bulked segregant analysis (NGS-BSA), we developed 100 markers linked to PHS tolerance. To confirm the effectiveness of marker development from NGS-BSA data, we developed 100 markers linked to the self-compatibility (SC) trait from previous NGS-BSA data. Using these markers, we developed genetic maps with AmpliSeq technology, which can quickly detect polymorphisms by amplicon-based multiplex targeted NGS, and performed quantitative trait locus (QTL) analysis for PHS tolerance in combination with NGS-BSA. QTL analysis detected two major and two minor QTLs for PHS tolerance in a segregating population developed from a cross between the PHS-tolerant ‘Kyukei 29’ and the self-compatible susceptible ‘Kyukei SC7’. We found different major and minor QTLs in other segregating populations developed from the PHS-tolerant lines ‘Kyukei 28’ and ‘NARO-FE-1’. Candidate markers linked to PHS developed by NGS-BSA were located near these QTL regions. We also investigated the effectiveness of markers linked to these QTLs for selection of PHS-tolerant lines among other segregating populations.

Conclusions

We efficiently developed genetic maps using a method combined with AmpliSeq technology and NGS-BSA, and detected QTLs associated with preharvest sprouting tolerance in common buckwheat. This is the first report to identify QTLs for PHS tolerance in buckwheat. Our marker development system will accelerate genetic research and breeding in common buckwheat.
Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation
Authors: Yu Zhenming , Zhang Guihua , Teixeira da Silva Jaime A. , Li Mingzhi , Zhao Conghui , He Chunmei , Si Can , Zhang Mingze , Duan Jun
Published: January 2021

Background

DNA methylation is a conserved and important epigenetic modification involved in the regulation of numerous biological processes, including plant development, secondary metabolism, and response to stresses. However, no information is available regarding the identification of cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes in the orchid Dendrobium officinale.

Results

In this study, we performed a genome-wide analysis of DoC5-MTase and DodMTase gene families in D. officinale. Integrated analysis of conserved motifs, gene structures and phylogenetic analysis showed that eight DoC5-MTases were divided into four subfamilies (DoCMT, DoDNMT, DoDRM, DoMET) while three DodMTases were divided into two subfamilies (DoDML3, DoROS1). Multiple cis-acting elements, especially stress-responsive and hormone-responsive ones, were found in the promoter region of DoC5-MTase and DodMTase genes. Furthermore, we investigated the expression profiles of DoC5-MTase and DodMTase in 10 different tissues, as well as their transcript abundance under abiotic stresses (cold and drought) and at the seedling stage, in protocorm-like bodies, shoots, and plantlets. Interestingly, most DoC5-MTases were downregulated whereas DodMTases were upregulated by cold stress. At the seedling stage, DoC5-MTase expression decreased as growth proceeded, but DodMTase expression increased.

Conclusions

These results provide a basis for elucidating the role of DoC5-MTase and DodMTase in secondary metabolite production and responses to abiotic stresses in D. officinale.
Coronary artery vasculitis: a review of current literature
Authors: Khanna Shaun , Garikapati Kartheek , Goh Daniel S. L. , Cho Kenneth , Lo Phillip , Bhojaraja Mohan V. , Tarafdar Surjit
Published: January 2021

Cardiac vasculitis is recognized as a heterogeneous disease process with a wide spectrum of manifestations including pericarditis, myocarditis, valvular heart disease and less frequently, coronary artery vasculitis (CAV). CAV encompasses an emerging field of diseases which differ from conventional atherosclerotic disease and have a proclivity for the younger population groups. CAV portends multiple complications including the development of coronary artery aneurysms, coronary stenotic lesions, and thrombosis, all which may result in acute coronary syndromes. There are several aetiologies for CAV; with Kawasaki’s disease, Takayasu's arteritis, Polyarteritis Nodosa, and Giant-Cell Arteritis more frequently described clinically, and in literature. There is a growing role for multi-modality imaging in assisting the diagnostic process; including transthoracic echocardiography, cardiac magnetic resonance imaging, computed tomography coronary angiography, fluorodeoxyglucose-positron emission tomography and conventional coronary angiogram with intravascular ultrasound. Whilst the treatment paradigms fundamentally vary between different aetiologies, there are overlaps with pharmacological regimes in immunosuppressive agents and anti-platelet therapies. Interventional and surgical management are is a consideration in select populations groups, within a multi-disciplinary context. Further large-scale studies are required to better appropriately outline management protocols in this niche population.
The evaluation of annuloplasty in bicuspid aortic valve repair using cardiac magnetic resonance
Authors: Jasinski Marek J. , Miszalski-Jamka Karol , Kosiorowska Kinga , Gocol Radoslaw , Wenzel-Jasinska Izabella , Bielicki Grzegorz , Berezowski Mikolaj , Lukaszewski Marceli , Kansy Andrzej , Deja Marek A.
Published: January 2021

Background

The incompetent bicuspid aortic valve (BAV) can be replaced or repaired using various surgical techniques. This study sought to assess the efficacy of external annuloplasty and postoperative reverse remodelling using cardiac magnetic resonance (CMR) and compare the results of external and subcommissural annuloplasty.

Methods

Out of a total of 200 BAV repair performed between 2004 and 2018, 21 consecutive patients (median age 54 years) with regurgitation requiring valve repair with annuloplasty without concomitant aortic root surgery were prospectively referred for CMR and transthoracic echocardiography (TTE) one year after the operation. Two aortic annulus stabilization techniques were used: external, circumferential annuloplasty (EA), and subcommissural annuloplasty (SCA).

Results

11 patients received EA and 10 patients were treated using SCA. There was no in-hospital mortality and all patients survived the follow-up period (median: 12.6 months (first quartile: 6.6; third quartile: 14.1). CMR showed strong correlation between postoperative aortic recurrent regurgitant fraction and left ventricular end-diastolic volume (r = 0.62; p = 0.003) as well as left ventricular ejection fraction (r = -0.53; p = 0.01). Patients treated with EA as compared with SCA had larger anatomic aortic valve area measured by CMR (3.5 (2.5; 4.0) vs. 2.5 cm2(2.0; 3.4); p = 0.04). In both EA and SCA group, aortic valve area below 3.5 cm2correlated with no regurgitation recurrency. EA (vs. SCA) was associated with lower peak transvalvular aortic gradients (10 (6; 17) vs. 21 mmHg (15; 27); p = 0.04).

Conclusions

The repair of the bicuspid aortic valve provides significant postoperative reverse remodelling, provided no recurrent regurgitation and durable reduction annuloplasty can be achieved. EA is associated with lower transvalvular gradients and higher aortic valve area assessed by CMR, compared to SCA.
Multiple imputation validation study: addressing unmeasured survey data in a longitudinal design
Authors:   for the Millennium Cohort Study Team, Kolaja Claire A. , Porter Ben , Powell Teresa M. , Rull Rudolph P.
Published: January 2021

Background

Questionnaires used in longitudinal studies may have questions added or removed over time for numerous reasons. Data missing completely at a follow-up survey is a unique issue for longitudinal studies. While such excluded questions lack information at one follow-up survey, they are collected at other follow-up surveys, and covariances observed at other follow-up surveys may allow for the recovery of the missing data. This study utilized data from a large longitudinal cohort study to assess the efficiency and feasibility of using multiple imputation (MI) to recover this type of information.

Methods

Millennium Cohort Study participants completed the 9-item Patient Health Questionnaire (PHQ) depression module at 2 time points (2004, 2007). The suicidal ideation item in the module was set to missing for the 2007 assessment. Several single-level MI models using different sets of predictors and forms of suicidal ideation were used to compare self-reported values and imputed values for this item in 2007. Additionally, associations with sleep duration and smoking status, which are related constructs, were compared between self-reported and imputed values of suicidal ideation.

Results

Among 63,028 participants eligible for imputation analysis, 4.05% reported suicidal ideation on the 2007 survey. The imputation models successfully identified suicidal ideation, with a sensitivity ranging between 34 and 66% and a positive predictive value between 36 and 42%. Specificity remained above 96% and negative predictive value above 97% for all imputed models. Similar associations were found for all imputation models on related constructs, though the dichotomous suicidal ideation imputed from the model using only PHQ depression items yielded estimates that were closest with the self-reported associations for all adjusted analyses.

Conclusions

Although sensitivity and positive predictive value were relatively low, applying MI techniques allowed for inclusion of an otherwise missing variable. Additionally, correlations with related constructs were estimated near self-reported values. Therefore, the other 8 depression items can be used to estimate suicidal ideation that was completely missing from a survey using MI. However, these imputed values should not be used to estimate population prevalence.
Quantifying the under-reporting of uncorrelated longitudal data: the genital warts example
Authors: Moriña David , Fernández-Fontelo Amanda , Cabaña Alejandra , Puig Pedro , Monfil Laura , Brotons Maria , Diaz Mireia
Published: January 2021

Background

Genital warts are a common and highly contagious sexually transmitted disease. They have a large economic burden and affect several aspects of quality of life. Incidence data underestimate the real occurrence of genital warts because this infection is often under-reported, mostly due to their specific characteristics such as the asymptomatic course.

Methods

Genital warts cases for the analysis were obtained from the Catalan public health system database (SIDIAP) for the period 2009-2016. People under 15 and over 94 years old were excluded from the analysis as the incidence of genital warts in this population is negligible. This work introduces a time series model based on a mixture of two distributions, capable of detecting the presence of under-reporting in the data. In order to identify potential differences in the magnitude of the under-reporting issue depending on sex and age, these covariates were included in the model.

Results

This work shows that only about 80% in average of genital warts incidence in Catalunya in the period 2009-2016 was registered, although the frequency of under-reporting has been decreasing over the study period. It can also be seen that this issue has a deeper impact on women over 30 years old.

Conclusions

Although this study shows that the quality of the registered data has improved over the considered period of time, the Catalan public health system is underestimating genital warts real burden in almost 10,000 cases, around 23% of the registered cases. The total annual cost is underestimated in about 10 million Euros respect the 54 million Euros annually devoted to genital warts in Catalunya, representing 0.4% of the total budget.