bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caste development and sex ratio of the Ryukyu drywood termite Neotermes sugioi and its potential mechanisms
Authors: Miyaguni Y. , Agarie A. , Sugio K. , Tsuji K. , Kobayashi K. 
Published: July 2021

AbstractSex allocation is one of the most studied traits in evolutionary biology because its theoretical predictions match the empirical data. Here, using the Ryukyu dry-wood termiteNeotermes sugioi, we investigated several factors that could bias the sex allocation in three populations (Okinawa, Ishigaki/Iriomote, and Yonaguni). Our survey showed that there were more queen-only colonies than king-only colonies in these populations, suggesting a longer lifespan of the queens than that of the kings. In this condition, sex-asymmetric reproductive value (SRV) theory predicts female bias, because even after the short-lived kings die, the long-lived queens can continue reproduction with their sons. However, sex allocation in this species seemed to be biased toward males. Furthermore, we examined the possibility of intrasexual competition among siblings (ICS). If ICS is the cause of the bias, the allocation is expected to change depending on the total investment in sexual offspring. However, the biomass of both male and female alates increased linearly with the increase in the total biomass of the alates in these populations. Thus, neither the SRV nor the ICS theory could explain the male-biased sex ratio ofN. sugioi. On the basis of these results, we discuss the remaining possibilities in this species.
Inflammation-based assessment for the risk stratification of mortality in patients with heart failure
Authors: Itagaki Tadashi , Motoki Hirohiko , Otagiri Kyuhachi , Machida Keisuke , Takeuchi Takahiro , Kanai Masafumi , Kimura Kazuhiro , Higuchi Satoko , Minamisawa Masatoshi , Kitabayashi Hiroshi , Kuwahara Koichiro 
Published: July 2021

AbstractThe Glasgow Prognostic Score (GPS) has been established as a useful resource to evaluate inflammation and malnutrition and predict prognosis in several cancers. However, its prognostic significance in patients with heart failure (HF) is not well established. To investigate the association between the GPS and mortality in patients with HF, we assessed 870 patients who were 20 years old and more and had been admitted for acute decompensated HF. The GPS ranged from 0 to 2 points as previously reported. Over the 18-month follow-up (follow-up rate, 83.9%), 143 patients died. Increasing GPS was associated with higher HF severity assessed by New York Heart Association functional class and B-type natriuretic peptide (BNP) levels. Kaplan–Meier analysis showed significant associations for mortality and increased GPS. In multivariate analysis, compared to the GPS 0 group, the GPS 2 group was associated with high mortality (hazard ratio 2.92, 95% confidence interval 1.77–4.81, p < 0.001) after adjustment for age, sex, blood pressure, HF history, HF severity, hemoglobin, renal function, sodium, BNP, left ventricular ejection fraction, and anti-HF medications. In conclusion, high GPS was significantly associated with worse prognosis in patients with HF. Inflammation-based assessment by the GPS may enable simple evaluation of HF severity and prognosis.
The value of GATA6 immunohistochemistry and computer-assisted diagnosis to predict clinical outcome in advanced pancreatic cancer
Authors: Duan Kai , Jang Gun-Ho , Grant Robert C. , Wilson Julie M. , Notta Faiyaz , O’Kane Grainne M. , Knox Jennifer J. , Gallinger Steven , Fischer Sandra 
Published: July 2021

AbstractCombination chemotherapy, either modified FOLFIRINOX (mFFX) or gemcitabine–nabpaclitaxel, are used in the treatment of most patients with advanced pancreatic ductal adenocarcinoma (PDAC), yet robust biomarkers of outcome are currently lacking to guide regimen selection. Here, we tested GATA6 immunohistochemistry (IHC) as a putative biomarker in advanced PDAC. GATA6 is a transcription factor in normal pancreas development. Two pathologists, blinded to clinical and molecular data, independently assessed GATA6 IHC in biopsy specimens of 130 patients with advanced PDAC, in 2 distinct phases (without and with computer assistance using the open source software QuPath). Low GATA6 IHC expression was associated with shorter overall survival [median OS 6.2 months for patients with GATA6 low tumors vs. 11.5 months for patients with GATA6 high tumors, HR 1.66 (95% CI 1.15–2.40), P = 0.007]. Progression appears to be higher in GATA6-low tumors compared to GATA6-high tumors in patients treated with mFFX (P = 0.024) but not in patients treated with gemcitabine regimens. GATA6 IHC expression was significantly associated with molecular subtypes (P = 0.0003). Digital assistance markedly improved interrater concordance (Cohen’s kappa scores of 0.32 vs. 0.95). Our results provide strong evidence that GATA6 IHC can be used as a single biomarker in the clinic to predict clinical outcome in advanced PDAC, warranting further investigation in prospective clinical trials. These results provide the basis for an improved classification of PDAC and future biomarker design using digital pathology workflow.
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)
Authors: Zhang Tongqing , Yin Jiawen , Tang Shengkai , Li Daming , Gu Xiankun , Zhang Shengyu , Suo Weiguo , Liu Xiaowei , Liu Yanshan , Jiang Qicheng , Zhao Muzi , Yin Yue , Pan Jianlin 
Published: July 2021

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.
Enhanced brightness of bacterial luciferase by bioluminescence resonance energy transfer
Authors: Kaku Tomomi , Sugiura Kazunori , Entani Tetsuyuki , Osabe Kenji , Nagai Takeharu 
Published: July 2021

AbstractUsing the lux operon (luxCDABE) of bacterial bioluminescence system as an autonomous luminous reporter has been demonstrated in bacteria, plant and mammalian cells. However, applications of bacterial bioluminescence-based imaging have been limited because of its low brightness. Here, we engineered the bacterial luciferase (heterodimer of luxA and luxB) by fusion with Venus, a bright variant of yellow fluorescent protein, to induce bioluminescence resonance energy transfer (BRET). By using decanal as an externally added substrate, color change and ten-times enhancement of brightness was achieved in Escherichia coli when circularly permuted Venus was fused to the C-terminus of luxB. Expression of the Venus-fused luciferase in human embryonic kidney cell lines (HEK293T) or in Nicotiana benthamiana leaves together with the substrate biosynthesis-related genes (luxC, luxD and luxE) enhanced the autonomous bioluminescence. We believe the improved luciferase will forge the way towards the potential development of autobioluminescent reporter system allowing spatiotemporal imaging in live cells.
Quantification of tumor microenvironment acidity in glioblastoma using principal component analysis of dynamic susceptibility contrast enhanced MR imaging
Authors: Akbari Hamed , Kazerooni Anahita Fathi , Ware Jeffrey B. , Mamourian Elizabeth , Anderson Hannah , Guiry Samantha , Sako Chiharu , Raymond Catalina , Yao Jingwen , Brem Steven , O’Rourke Donald M. , Desai Arati S. , Bagley Stephen J. , Ellingson Benjamin M. , Davatzikos Christos , Nabavizadeh Ali 
Published: July 2021

AbstractGlioblastoma (GBM) has high metabolic demands, which can lead to acidification of the tumor microenvironment. We hypothesize that a machine learning model built on temporal principal component analysis (PCA) of dynamic susceptibility contrast-enhanced (DSC) perfusion MRI can be used to estimate tumor acidity in GBM, as estimated by pH-sensitive amine chemical exchange saturation transfer echo-planar imaging (CEST-EPI). We analyzed 78 MRI scans in 32 treatment naïve and post-treatment GBM patients. All patients were imaged with DSC-MRI, and pH-weighting that was quantified from CEST-EPI estimation of the magnetization transfer ratio asymmetry (MTRasym) at 3 ppm. Enhancing tumor (ET), non-enhancing core (NC), and peritumoral T2 hyperintensity (namely, edema, ED) were used to extract principal components (PCs) and to build support vector machines regression (SVR) models to predict MTRasym values using PCs. Our predicted map correlated with MTRasym values with Spearman’s r equal to 0.66, 0.47, 0.67, 0.71, in NC, ET, ED, and overall, respectively (p < 0.006). The results of this study demonstrates that PCA analysis of DSC imaging data can provide information about tumor pH in GBM patients, with the strongest association within the peritumoral regions.
Bimanual coupling effect during a proprioceptive stimulation
Authors: Biggio M. , Bisio A. , Garbarini F. , Bove Marco 
Published: July 2021

AbstractCircle-line drawing paradigm is used to study bimanual coupling. In the standard paradigm, subjects are asked to draw circles with one hand and lines with the other hand; the influence of the concomitant tasks results in two “elliptical” figures. Here we tested whether proprioceptive information evoked by muscle vibration inducing a proprioceptive illusion (PI) of movement at central level, was able to affect the contralateral hand drawing circles or lines. A multisite 80 Hz-muscle vibration paradigm was used to induce the illusion of circle- and line-drawing on the right hand of 15 healthy participants. During muscle vibration, subjects had to draw a congruent or an incongruent figure with the left hand. The ovalization induced by PI was compared with Real and Motor Imagery conditions, which already have proved to induce bimanual coupling. We showed that the ovalization of a perceived circle over a line drawing during PI was comparable to that observed in Real and Motor Imagery condition. This finding indicates that PI can induce bimanual coupling, and proprioceptive information can influence the motor programs of the contralateral hand.
pH-controlled synthesis of sustainable lauric acid/SiO2 phase change material for scalable thermal energy storage
Authors: Ishak Shafiq , Mandal Soumen , Lee Han-Seung , Singh Jitendra Kumar 
Published: July 2021

AbstractLauric acid (LA) has been recommended as economic, eco-friendly, and commercially viable materials to be used as phase change materials (PCMs). Nevertheless, there is lack of optimized parameters to produce microencapsulated PCMs with good performance. In this study, different amounts of LA have been chosen as core materials while tetraethyl orthosilicate (TEOS) as the precursor solution to form silicon dioxide (SiO2) shell. The pH of precursor solution was kept at 2.5 for all composition of microencapsulated LA. The synthesized microencapsulated LA/SiO2 has been characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-Ray photoelectron spectroscopy (XPS), Scanning electron microscopy (SEM), and Transmission electron microscopy (TEM). The SEM and TEM confirm the microencapsulation of LA with SiO2. Thermogravimetric analysis (TGA) revealed better thermal stability of microencapsulated LA/SiO2 compared to pure LA. PCM with 50% LA i.e. LAPC-6 exhibited the highest encapsulation efficiency (96.50%) and encapsulation ratio (96.15%) through Differential scanning calorimetry (DSC) as well as good thermal reliability even after 30th cycle of heating and cooling process.
Comparison of ocular surface assessment and adherence between preserved and preservative-free latanoprost in glaucoma: a parallel-grouped randomized trial
Authors: Kim Dai Woo , Shin Jonghoon , Lee Chang Kyu , Kim Myungjin , Lee Sohyeon , Rho Seungsoo 
Published: July 2021

AbstractGiven that nonadherence is related to subject characteristics and drug tolerance and preserved eye drops tend to be more intolerable than preservative-free ones, we conducted a phase 4, parallel-grouped, investigator-blind, active-control, randomized, multicenter study. A total of 51 patients with intraocular pressure (IOP) ≥ 15 mmHg diagnosed with open-angle glaucoma or ocular hypertension were randomly assigned to the preserved latanoprost group (n = 26) and the preservative-free latanoprost group (n = 25). The efficacy variables were corneal/conjunctival staining grade, Ocular Surface Disease Index (OSDI), adherence at 12 weeks after the first administration; corneal/conjunctival staining grade at 4 weeks; and IOP, tear break-up time (TBUT), and hyperemia score at 4 and 12 weeks. The safety variables included visual acuity and drug tolerance questionnaire results. There was no statistically significant difference in corneal/conjunctival staining grade, OSDI, or TBUT between the groups at 4 and 12 weeks. However, the adherence rate was higher and the hyperemia score was lower in the preservative-free group than in the preserved group. The severity and duration of stinging/burning sensation were lower in the preservative-free group than in the preserved group. Overall, preservative-free latanoprost showed better ocular tolerance assessed by hyperemia scores and stinging/burning symptoms following higher adherence than preserved latanoprost.
Strong near band-edge excited second-harmonic generation from multilayer 2H Tin diselenide
Authors: Biswas Rabindra , Dandu Medha , Prosad Asish , Das Sarthak , Menon Sruti , Deka Jayanta , Majumdar Kausik , Raghunathan Varun 
Published: July 2021

AbstractWe report strong second-harmonic generation (SHG) from 2H polytype of multilayer Tin diselenide (SnSe2) for fundamental excitation close to the indirect band-edge in the absence of excitonic resonances. Comparison of SHG and Raman spectra from exfoliated SnSe2 flakes of different polytypes shows strong (negligible) SHG and Raman Eg mode at 109 cm−1 (119 cm−1), consistent with 2H (1T) polytypes. The difference between the A1g–Eg Raman peak positions is found to exhibit significant thickness dependent for the 1T form, which is found to be absent for the 2H form. The observed thickness dependence of SHG with rapid oscillations in signal strength for small changes in flake thickness are in good agreement with a nonlinear wave propagation model considering nonlinear polarization with alternating sign from each monolayer. The nonlinear optical susceptibility extracted from SHG signal comparison with standard quartz samples for 1040 nm excitation is found to be more than 4-times higher than that at 1550 nm. This enhanced nonlinear response at 1040 nm is attributed to the enhanced nonlinear optical response for fundamental excitation close to the indirect band-edge. We also study SHG from heterostructures of monolayer MoS2/multilayer SnSe2 which allows us to unambiguously compare the nonlinear optical response of SnSe2 with MoS2. We find the SHG signal and any interference effect in the overlap region to be dominated by the SnSe2 layer for the excitation wavelengths considered. The comparison of SHG from SnSe2 and MoS2 underscores that the choice of the 2D material for a particular nonlinear optical application is contextual on the wavelength range of interest and its optical properties at those wavelengths. The present works further highlights the usefulness of near band-edge enhancement of nonlinear processes in emerging 2D materials towards realizing useful nanophotonic devices.
Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae
Authors: Chang Zih-Ting , Huang Yu-Feng , Chen Yue-Wen , Yen Ming-Ren , Hsu Po-Ya , Chen Tzu-Han , Li Yi-Hsuan , Chiu Kuo-Ping , Nai Yu-Shin 
Published: July 2021

AbstractDeformed wing virus (DWV) prevalence is high in honey bee (Apis mellifera) populations. The virus infects honey bees through vertical and horizontal transmission, leading to behavioural changes, wing deformity, and early mortality. To better understand the impacts of viral infection in the larval stage of honey bees, artificially reared honey bee larvae were infected with DWV (1.55 × 1010 copies/per larva). No significant mortality occurred in infected honey bee larvae, while the survival rates decreased significantly at the pupal stage. Examination of DWV replication revealed that viral replication began at 2 days post inoculation (d.p.i.), increased dramatically to 4 d.p.i., and then continuously increased in the pupal stage. To better understand the impact of DWV on the larval stage, DWV-infected and control groups were subjected to transcriptomic analysis at 4 d.p.i. Two hundred fifty-five differentially expressed genes (DEGs) (fold change ≥ 2 or ≤ -2) were identified. Of these DEGs, 168 genes were downregulated, and 87 genes were upregulated. Gene Ontology (GO) analysis showed that 141 DEGs (55.3%) were categorized into molecular functions, cellular components and biological processes. One hundred eleven genes (38 upregulated and 73 downregulated) were annotated by KO (KEGG Orthology) pathway mapping and involved metabolic pathways, biosynthesis of secondary metabolites and glycine, serine and threonine metabolism pathways. Validation of DEGs was performed, and the related gene expression levels showed a similar tendency to the DEG predictions at 4 d.p.i.; cell wall integrity and stress response component 1 (wsc1), cuticular protein and myo-inositol 2-dehydrogenase (iolG) were significantly upregulated, and small conductance calcium-activated potassium channel protein (SK) was significantly downregulated at 4 d.p.i. Related gene expression levels at different d.p.i. revealed that these DEGs were significantly regulated from the larval stage to the pupal stage, indicating the potential impacts of gene expression levels from the larval to the pupal stages. Taken together, DWV infection in the honey bee larval stage potentially influences the gene expression levels from larvae to pupae and reduces the survival rate of the pupal stage. This information emphasizes the consequences of DWV prevalence in honey bee larvae for apiculture.
RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis
Authors: Figueroa Álvaro , Brante Antonio , Cárdenas Leyla 
Published: July 2021

AbstractThe polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.
Rapid detection of phenotypes Bombay sedel and nonsecretor rs200157007 SNP (302C > T) by real-time PCR-based methods
Authors: Soejima Mikiko , Koda Yoshiro 
Published: July 2021

AbstractThesedelallele is one of the nonsecretor alleles (se) ofFUT2generated by an Alu-mediated recombination event and was first found in Indian Bombay phenotype individuals who have anti-H, anti-A, and anti-B antibodies in their serum. As well as anti-A, and anti-B antibodies, anti-H is clinically significant because it causes sever hemolytic transfusion reactions. Likesedel,se302having a missense single nucleotide polymorphism (SNP), 302C > T, is characteristic of South Asians with a frequency of 10–30%. We developed a real-time PCR melting curve analysis for detection ofsedelusing a 127-bp amplicon encompassing the breakpoint junction. In addition, by performing duplex PCR by amplifying a 65-bp amplicon of theFUT2coding region at the same time, we could determine the zygosity ofsedelin a single tube. We also developed an Eprobe-mediated PCR assay (Eprobe-PCR) for detection of 302C > T ofFUT2.These methods were validated by analyzing 58 Tamils and 54 Sinhalese in Sri Lanka. Both the duplex PCR melting curve analysis for determination ofsedelzygosity and the Eprobe-PCR assay for detection of 302C > T exactly determined three genotypes. In addition, the results of the present methods were in complete agreement with those obtained by previously established methods. The two present methods were reliable and seem to be advantageous for large-scale association studies ofFUT2polymorphisms in South Asian populations.
Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions
Authors: Weiel Marie , Götz Markus , Klein André , Coquelin Daniel , Floca Ralf , Schug Alexander 
Published: July 2021

AbstractMolecular simulations are a powerful tool to complement and interpret ambiguous experimental data on biomolecules to obtain structural models. Such data-assisted simulations often rely on parameters, the choice of which is highly non-trivial and crucial to performance. The key challenge is weighting experimental information with respect to the underlying physical model. We introduce FLAPS, a self-adapting variant of dynamic particle swarm optimization, to overcome this parameter selection problem. FLAPS is suited for the optimization of composite objective functions that depend on both the optimization parameters and additional, a priori unknown weighting parameters, which substantially influence the search-space topology. These weighting parameters are learned at runtime, yielding a dynamically evolving and iteratively refined search-space topology. As a practical example, we show how FLAPS can be used to find functional parameters for small-angle X-ray scattering-guided protein simulations.