bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vascular calcification in different arterial beds in ex vivo ring culture and in vivo rat model
Authors: Muyor Karen , Laget Jonas , Cortijo Irene , Duranton Flore , Jover Bernard , Argilés Àngel , Gayrard Nathalie 
Published: July 2022

AbstractVascular calcification is a risk factor for cardiovascular and kidney diseases. Medial calcification may differently affect the arterial tree depending on vessel location and smooth muscle injury. The aim was to map the anatomical distribution of vascular calcifications on different arteries and artery locations, in cultured artery rings (ex vivo) and in a rat model of elastocalcinosis (in vivo). Vascular calcification was assessed histologically (von Kossa staining of the media) and by calcium content measurement. Arteries of different sizes were harvested from untreated rats for ring culture and from the vitamin D3-nicotine (VDN) rat model for direct observation. When cultured in pro-calcifying conditions, thoracic aorta exhibited similar calcification from the arch to the diaphragm. Calcification increased in abdominal aorta along with the reduction in cross sectional area. Carotid and renal arteries exhibited similar ex vivo calcification. In VDN rats, calcification was greater in carotid artery than in aorta, and was accompanied by fibrosis and apoptosis. Ex vivo, calcification was increased by the induction of lesions on arteries. Along the vascular tree, calcification of the arterial wall increases with the narrowing of vessels in ex vivo ring culture and in vivo. The observed differences represent local susceptibility of the vessels to the calcifying processes.
Investigation on the cellular mechanism of Prunetin evidenced through next generation sequencing and bioinformatic approaches against gastric cancer
Authors: Vetrivel Preethi , Nachimuthu Santhi , Abuyaseer Abusaliya , Bhosale Pritam Bhagwan , Ha Sang Eun , Kim Hun Hwan , Park Min Young , Kim Gon Sup 
Published: July 2022

AbstractGastric cancer is the common type of malignancy positioned at second in mortality rate causing burden worldwide with increasing treatment options. More accurate and reliable diagnostic methods/biomarkers are urgently needed. The application of transcriptomics technologies possesses the high efficiency of identifying key metabolic pathways and functional genes in cancer research. In this study, we performed a transcriptome analysis on Prunetin treated AGS cells. A total of 1,118 differentially expressed (DE) genes on Prunetin treated AGS cancer cells, among which 463 were up-regulated and 655 were down-regulated. Notably, around 40 genes were found to be related with necroptosis, among which 16 genes were found to be in close association with Receptor Interacting Protein Kinase (RIPK) family. Validation of the RIPK genes through GEPIA identified 8 genes (NRP1, MNX1, SSRP1, PRDX2, PLRG1, LGALS4, SNX5 and FXYD3) which are highly expressed in stomach cancer were significantly down-regulated in PRU treated samples. In conclusion, the sequencing data explores the expression of RIPK mediated genes through necroptosis signaling network in treating gastric cancer. The futuristic validations on the 8 genes as candidate biomarkers will offer a treatment approach against gastric cancer using PRU.
Physics of emergence beyond Berezinskii–Kosterlitz–Thouless transition for interacting topological quantum matter
Authors: Kumar Ranjith R. , Sarkar Sujit 
Published: July 2022

AbstractAn attempt is made to find different emergent quantum phases for interacting topological state of quantum matter. Our study is based on the quantum field theoretical renormalization group (RG) calculations. The behaviour of the RG flow lines give the emergence of different quantum phases for non-interacting and interacting topological state of quantum matter. We show explicitly electron-electron interaction can turn a topologically trivial phase into a topologically nontrivial one and also topologically nontrivial phase to topologically trivial phase. We show that physics of emergence goes beyond the quantum Berezinskii–Kosterlitz–Thouless transition. We also present the analysis of fixed point and show the behaviour of fixed point changes in presence and absence of interaction. This work provides a new perspective not only from the topological state of interacting quantum matter and but also for the correlated quantum many -body physics.
Exploring the association of organochlorine pesticides exposure and hearing impairment in United States adults
Authors: Long Lili , Tang Xinghua 
Published: July 2022

AbstractHearing loss (HL) is a highly prevalent public health concern. Organochlorine pesticides (OCPs) are widely used environmental pollutants harmful to human health. Studies investigating the effects of OCPs exposure on the auditory system in the general population are rare. To explore the association between OCPs exposure and HL in adults, 366 adults aged 20–69 years who participated in the National Health and Nutrition Examination Survey (NHANES, 2003–2004) were investigated. HL was defined as a pure-tone average (PTA) ≥ 20 dB in the better ear. Multivariate linear and logistic regression analyses were conducted to evaluate the association of four selected serum OCPs with PTAs and the risk of HL. In participants aged < 60 years, hexachlorobenzene (HCB) and dichlorodiphenyldichloroethylene (p, p'-DDE) exposure was positively associated with low- and speech-frequency PTAs, and with low-frequency HL, respectively. Risk of HL increased in the highest tertile compared with the lowest tertile of serum HCB and p, p'-DDE (odds ratio [OR]: 4.38, 95% confidence interval [CI]: 0.97–19.80; OR: 16.66, 95% CI: 2.64–105.09, respectively). In this study of US adults aged < 60 years, HCB and p, p'-DDE exposure was positively associated with HL. HCB and p, p'-DDE may be potential risk factors for HL.
SARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis
Authors: Samy Asmaa , Maher Mohamed A. , Abdelsalam Nehal Adel , Badr Eman 
Published: July 2022

AbstractCOVID-19 is a global pandemic impacting the daily living of millions. As variants of the virus evolve, a complete comprehension of the disease and drug targets becomes a decisive duty. The Omicron variant, for example, has a notably high transmission rate verified in 155 countries. We performed integrative transcriptomic and network analyses to identify drug targets and diagnostic biomarkers and repurpose FDA-approved drugs for SARS-CoV-2. Upon the enrichment of 464 differentially expressed genes, pathways regulating the host cell cycle were significant. Regulatory and interaction networks featured hsa-mir-93-5p and hsa-mir-17-5p as blood biomarkers while hsa-mir-15b-5p as an antiviral agent. MYB, RRM2, ERG, CENPF, CIT, and TOP2A are potential drug targets for treatment. HMOX1 is suggested as a prognostic biomarker. Enhancing HMOX1 expression by neem plant extract might be a therapeutic alternative. We constructed a drug-gene network for FDA-approved drugs to be repurposed against the infection. The key drugs retrieved were members of anthracyclines, mitotic inhibitors, anti-tumor antibiotics, and CDK1 inhibitors. Additionally, hydroxyquinone and digitoxin are potent TOP2A inhibitors. Hydroxyurea, cytarabine, gemcitabine, sotalol, and amiodarone can also be redirected against COVID-19. The analysis enforced the repositioning of fluorouracil and doxorubicin, especially that they have multiple drug targets, hence less probability of resistance.
AI-based automatic segmentation of craniomaxillofacial anatomy from CBCT scans for automatic detection of pharyngeal airway evaluations in OSA patients
Authors: Orhan Kaan , Shamshiev Mamat , Ezhov Matvey , Plaksin Alexander , Kurbanova Aida , Ünsal Gürkan , Gusarev Maxim , Golitsyna Maria , Aksoy Seçil , Mısırlı Melis , Rasmussen Finn , Shumilov Eugene , Sanders Alex 
Published: July 2022

AbstractThis study aims to generate and also validate an automatic detection algorithm for pharyngeal airway on CBCT data using an AI software (Diagnocat) which will procure a measurement method. The second aim is to validate the newly developed artificial intelligence system in comparison to commercially available software for 3D CBCT evaluation. A Convolutional Neural Network-based machine learning algorithm was used for the segmentation of the pharyngeal airways in OSA and non-OSA patients. Radiologists used semi-automatic software to manually determine the airway and their measurements were compared with the AI. OSA patients were classified as minimal, mild, moderate, and severe groups, and the mean airway volumes of the groups were compared. The narrowest points of the airway (mm), the field of the airway (mm2), and volume of the airway (cc) of both OSA and non-OSA patients were also compared. There was no statistically significant difference between the manual technique and Diagnocat measurements in all groups (p > 0.05). Inter-class correlation coefficients were 0.954 for manual and automatic segmentation, 0.956 for Diagnocat and automatic segmentation, 0.972 for Diagnocat and manual segmentation. Although there was no statistically significant difference in total airway volume measurements between the manual measurements, automatic measurements, and DC measurements in non-OSA and OSA patients, we evaluated the output images to understand why the mean value for the total airway was higher in DC measurement. It was seen that the DC algorithm also measures the epiglottis volume and the posterior nasal aperture volume due to the low soft-tissue contrast in CBCT images and that leads to higher values in airway volume measurement.
Proposal of time domain impedance spectroscopy to determine precise dimensionless figure of merit for thermoelectric modules within minutes
Authors: Hasegawa Yasuhiro , Takeuchi Mai 
Published: July 2022

AbstractSeveral techniques exist that use a thermoelectric element (TE) or module (TM) to measure precise dimensionless figure of merit (zT), both qualitatively and quantitatively. The techniques can be applied using both alternating (AC) and direct current (DC). Herein, the transient Harman (TH) and impedance spectroscopy (IS) methods were investigated as direct zT measurement techniques using identical TM, which showed that zT at 300 K was 0.767 and 0.811 within several minutes and several hours, respectively. The zT values differed despite the use of the same TM, which revealed that measuring ohmic resistance using DC and pulse DC is potentially misleading owing to the influence of Peltier heat on current flow. In this study, time domain impedance spectroscopy (TDIS) was proposed as a new technique to measure zT using proper DC and AC. zT obtained using TDIS was 0.811 within several minutes using the time and frequency domains, and was perfectly consistent with the result of the IS method. In conclusion, the TDIS is highly appropriate in estimating zT directly using only proper electrometric measurements, and without any heat measurements.
Comparison of gene expression profiles among caste differentiations in the termite Reticulitermes speratus
Authors: Saiki Ryota , Hayashi Yoshinobu , Toga Kouhei , Yaguchi Hajime , Masuoka Yudai , Suzuki Ryutaro , Fujiwara Kokuto , Shigenobu Shuji , Maekawa Kiyoto 
Published: July 2022

AbstractTermite castes express specialized phenotypes for their own tasks and are a good example of insect polyphenism. To understand the comprehensive gene expression profiles during caste differentiation, RNA-seq analysis based on the genome data was performed during the worker, presoldier, and nymphoid molts in Reticulitermes speratus. In this species, artificial induction methods for each molt have already been established, and the time scale has been clarified. Three different periods (before the gut purge (GP), during the GP, and after the molt) were discriminated in each molt, and two body parts (head and other body regions) were separately sampled. The results revealed that many differentially expressed genes (head: 2884, body: 2579) were identified in each molt. Based on the independent real-time quantitative PCR analysis, we confirmed the different expression patterns of seven out of eight genes in the presoldier molt. Based on the GO and KEGG enrichment analyses, the expressions of genes related to juvenile hormone titer changes (e.g., JH acid methyltransferase), nutrition status (e.g., Acyl-CoA Delta desaturase), and cell proliferation (e.g., insulin receptor), were shown to specifically fluctuate in each molt. These differences may have a crucial impact on caste differentiation. These data are important resources for future termite sociogenomics.
Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology
Authors: de Vries Ellen M. , Cogan Noel O. I , Gubala Aneta J. , Mee Peter T. , O’Riley Kim J. , Rodoni Brendan C. , Lynch Stacey E. 
Published: July 2022

AbstractOutbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
A novel nomogram model to predict the overall survival of patients with retroperitoneal leiomyosarcoma: a large cohort retrospective study
Authors: Huang Chao , Yu Qiu-Ping , Li Hao , Ding Zichuan , Zhou Zongke , Shi Xiaojun 
Published: July 2022

AbstractRetroperitoneal leiomyosarcomas (RLS) are the second most common type of retroperitoneal sarcoma and one of the most aggressive tumours. The lack of early warning signs and delay in regular checkups lead to a poor prognosis. This study aims to create a nomogram to predict RLS patients' overall survival (OS). Patients diagnosed with RLS in the Surveillance, Epidemiology, and End Results (SEER) database between 2000 and 2018 were enrolled in this study. First, univariable and multivariable Cox regression analyses were used to identify independent prognostic factors, followed by constructing a nomogram to predict patients' OS at 1, 3, and 5 years. Secondly, the nomogram's distinguishability and prediction accuracy were assessed using receiver operating characteristic (ROC) and calibration curves. Finally, the decision curve analysis (DCA) investigated the nomogram's clinical utility. The study included 305 RLS patients, and they were divided into two groups at random: a training set (216) and a validation set (89). The training set's multivariable Cox regression analysis revealed that surgery, tumour size, tumour grade, and tumour stage were independent prognostic factors. ROC curves demonstrated that the nomogram had a high degree of distinguishability. In the training set, area under the curve (AUC) values for 1, 3, and 5 years were 0.800, 0.806, and 0.788, respectively, while in the validation set, AUC values for 1, 3, and 5 years were 0.738, 0.780, and 0.832, respectively. As evidenced by the calibration curve, the nomogram had high prediction accuracy. Moreover, DCA revealed that the nomogram had high clinical utility. Furthermore, the risk stratification system based on the nomogram could effectively categorise patients into three mortality risk subgroups. Therefore, the developed nomogram and risk stratification system may aid in optimising the treatment decisions of RLS patients to improve treatment prognosis and maximise their healthcare outcomes.
Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model
Authors: Selvin Tove , Fasterius Erik , Jarvius Malin , Fryknäs Mårten , Larsson Rolf , Andersson Claes R. 
Published: July 2022

AbstractUnderstanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.
Purification of the full-length, membrane-associated form of the antiviral enzyme viperin utilizing nanodiscs
Authors: Patel Ayesha M. , Koebke Karl J. , Grunkemeyer Timothy J. , Riordan Colleen M. , Kim Youngsoo , Bailey Ryan C. , Marsh E. Neil G. 
Published: July 2022

AbstractViperin is a radical S-adenosylmethionine enzyme that catalyzes the formation of the antiviral ribonucleotide, 3’-deoxy-3’,4’-didehydroCTP. The enzyme is conserved across all kingdoms of life, and in higher animals viperin is localized to the ER-membrane and lipid droplets through an N-terminal extension that forms an amphipathic helix. Evidence suggests that the N-terminal extension plays an important role in viperin’s interactions with other membrane proteins. These interactions serve to modulate the activity of various other enzymes that are important for viral replication and constitute another facet of viperin’s antiviral properties, distinct from its catalytic activity. However, the full-length form of the enzyme, which has proved refractory to expression in E. coli, has not been previously purified. Here we report the purification of the full-length form of viperin from HEK293T cells transfected with viperin. The purification method utilizes nanodiscs to maintain the protein in its membrane-bound state. Unexpectedly, the enzyme exhibits significantly lower catalytic activity once purified, suggesting that interactions with other ER-membrane components may be important to maintain viperin’s activity.
The Campsis-Icterus association as a model system for avian nectar-robbery studies
Authors: Graves Gary R. 
Published: July 2022

AbstractAvian nectar-robbing is common in some floras but its impact on plant-pollinator mutualisms, flowering phenology, and the evolution of floral traits remains largely unexplored. Surprisingly, there have been no quantitative studies of the topography and extent of floral damage inflicted on any flowering species by nectar-robbing birds. I studied nectar-robbing of orchard oriole (Icteridae: Icterus spurius) on the large reddish-orange flowers of trumpet creeper (Bignoniaceae: Campsis radicans), an ornithophilous liana of eastern North America. Floral traits that inhibit nectar-robbery by hummingbirds and bees, such as the thickened calyx and sympetalous corolla, are ineffective in deterring orioles. Orioles target the zygomorphic trumpet-shaped corollas at the 11:00 h or 01:00 h positions with a closed-bill puncture and then enlarge the incision with bill-gaping to reach the nectary. More than 92% of flowers were robbed when orioles were present. Fruit set was nil until orioles departed on fall migration in late July-early August. The timing suggests oriole nectary-robbery may be a potent selection agent for an extended flowering season or delay in the onset of flowering. The biological and geographic attributes of the Campsis-Icterus association make it a promising model system for studying the consequences of avian nectar-robbery on pollination biology and floral trait evolution.
Spatiotemporal expression of HMGB2 regulates cell proliferation and hepatocyte size during liver regeneration
Authors: Yano Koichi , Choijookhuu Narantsog , Ikenoue Makoto , Fidya  , Fukaya Tomohiro , Sato Katsuaki , Lee Deokcheol , Taniguchi Noboru , Chosa Etsuo , Nanashima Atsushi , Hishikawa Yoshitaka 
Published: July 2022

AbstractLiver regeneration is an extraordinarily complex process involving a variety of factors; however, the role of chromatin protein in hepatocyte proliferation is largely unknown. In this study, we investigated the functional role of high-mobility group box 2 (HMGB2), a chromatin protein in liver regeneration using wild-type and HMGB2-knockout (KO) mice. Liver tissues were sampled after 70% partial hepatectomy (PHx), and analyzed by immunohistochemistry, western blotting and flow cytometry using various markers of cell proliferation. In WT mice, hepatocyte proliferation was strongly correlated with the spatiotemporal expression of HMGB2; however, cell proliferation was significantly delayed in hepatocytes of HMGB2-KO mice. Quantitative PCR demonstrated that cyclin D1 and cyclin B1 mRNAs were significantly decreased in HMGB2-KO mice livers. Interestingly, hepatocyte size was significantly larger in HMGB2-KO mice at 36–72 h after PHx, and these results suggest that hepatocyte hypertrophy appeared in parallel with delayed cell proliferation. In vitro experiments demonstrated that cell proliferation was significantly decreased in HMGB2-KO cells. A significant delay in cell proliferation was also found in HMGB2-siRNA transfected cells. In summary, spatiotemporal expression of HMGB2 is important for regulation of hepatocyte proliferation and cell size during liver regeneration.
Dynamic manipulation of microwave polarization based on anisotropic graphene meta-device
Authors: Zhang Jin , Li Zhenfei , Zhang Chiben , Shao Linda , Zhu Weiren 
Published: July 2022

AbstractAs a unique two-dimensional atomic material, graphene offers excellent mechanical properties, dynamically tunable surface conductivity, ultra-high carrier mobility, and optical transparency, making it great potential for novel electromagnetic devices. However, dynamic manipulation of microwave polarization has not been experimentally realized in a graphene-assisted metasurface. In this paper, we present a general strategy for designing graphene-based active meta-device for achieving dynamic polarization control at microwave frequencies. When illuminated by a linear-polarized incident wave, the polarization angle of the reflected wave can be dynamically controlled by shifting the bias voltage applied to graphene. The simulated and measured results reveal that the proposed graphene-based meta-device offers a novel approach to the manipulation of microwave polarization and has potential applications in antenna, sensing, and communications.