bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impacts of biomineralization and oil contamination on the compressive strength of waste plastic-filled mortar
Authors: Rux Kylee , Kane Seth , Espinal Michael , Ryan Cecily , Phillips Adrienne , Heveran Chelsea 
Published: December 2022

AbstractResearchers have made headway against challenges of increasing cement infrastructure and low plastic recycling rates by using waste plastic in cementitious materials. Past studies indicate that microbially induced calcium carbonate precipitation (MICP) to coat plastic in calcium carbonate may improve the strength. The objective of this study was to increase the amount of clean and contaminated waste plastic that can be added to mortar and to assess whether MICP treatment enhances the strength. The performance of plastic-filled mortar was investigated at 5%, 10%, and 20% volume replacement for cement. Untreated, clean plastics at a 20% cement replacement produced compressive strengths acceptable for several applications. However, a coating of MICP on clean waste plastic did not improve the strengths. At 10% replacement, both MICP treatment and washing of contaminated plastics recovered compressive strengths by approximately 28%, relative to mortar containing oil-coated plastics. By incorporating greater volumes of waste plastics into mortar, the sustainability of cementitious composites has the potential of being improved by the dual mechanisms of reduced cement production and repurposing plastic waste.
A descriptive study of routine laboratory testing in intensive care unit in nearly 140,000 patient stays
Authors: Allyn Jérôme , Devineau Marjolaine , Oliver Matthieu , Descombes Guillaume , Allou Nicolas , Ferdynus Cyril 
Published: December 2022

AbstractTo describe the relationship between the use of laboratory tests and changes in laboratory parameters in ICU patients is necessary to help optimize routine laboratory testing. A retrospective, descriptive study was conducted on the large eICU-Collaborative Research Database. The relationship between the use of routine laboratory tests (chemistry and blood counts) and changes in ten common laboratory parameters was studied. Factors associated with laboratory tests were identified in a multivariate regression analysis using generalized estimating equation Poisson models. The study included 138,734 patient stays, with an ICU mortality of 8.97%. For all parameters, the proportion of patients with at least one test decreased from day 0 to day 1 and then gradually increased until the end of the ICU stay. Paradoxically, the results of almost all tests moved toward normal values, and the daily variation in the results of almost all tests decreased over time. The presence of an arterial catheter or teaching hospitals were independently associated with an increase in the number of laboratory tests performed. The paradox of routine laboratory testing should be further explored by assessing the factors that drive the decision to perform routine laboratory testing in ICU and the impact of such testing on patient.
All-optical AZO-based modulator topped with Si metasurfaces
Authors: Vatani Sareh , Barahimi Behdad , Moravvej-Farshi Mohammad Kazem 
Published: December 2022

AbstractAll-optical communication systems are under continuous development to address different core elements of inconvenience. Here, we numerically investigate an all-optical modulator, realizing a highly efficient modulation depth of 22 dB and a low insertion loss of 0.32 dB. The tunable optical element of the proposed modulator is a layer of Al-doped Zinc Oxide (AZO), also known as an epsilon-near-zero transparent conductive oxide. Sandwiching the AZO layer between a carefully designed distributed Bragg reflector and a dielectric metasurface—i.e., composed of a two-dimensional periodic array of cubic Si—provides a guided-mode resonance at the OFF state of the modulator, preventing the incident signal reflection atλ = 1310 nm. We demonstrate the required pump fluence for switching between the ON/OFF states of the designed modulator is about a few milli-Joules per cm2. The unique properties of the AZO layer, along with the engineered dielectric metasurface above it, change the reflection from 1 to 93%, helping design better experimental configurations for the next-generation all-optical communication systems.
Transcriptomic differences between fibrotic and non-fibrotic testicular tissue reveal possible key players in Klinefelter syndrome-related testicular fibrosis
Authors: Willems Margo , Olsen Catharina , Caljon Ben , Vloeberghs Veerle , De Schepper Jean , Tournaye Herman , Van Saen Dorien , Goossens Ellen 
Published: December 2022

AbstractKlinefelter syndrome (KS; 47,XXY) affects 1–2 in 1000 males. Most men with KS suffer from an early germ cell loss and testicular fibrosis from puberty onwards. Mechanisms responsible for these processes remain unknown. Previous genomics studies on testis tissue from men with KS focused on germ cell loss, while a transcriptomic analysis focused on testicular fibrosis has not yet been performed. This study aimed to identify factors involved in the fibrotic remodelling of KS testes by analysing the transcriptome of fibrotic and non-fibrotic testicular tissue. RNA sequencing was performed to compare the genes expressed in testicular samples with (KS and testis atrophy) and without (Sertoli cell-only syndrome and fertile controls) fibrosis (n = 5, each). Additionally, differentially expressed genes (DEGs) between KS and testis atrophy samples were studied to reveal KS-specific fibrotic genes. DEGs were considered significant when p < 0.01 and log2FC > 2. Next, downstream analyses (GO and KEGG) were performed. Lastly, RNA in situ hybridization was performed to validate the results. The first analysis (fibrotic vs non-fibrotic) resulted in 734 significant DEGs (167 up- and 567 down-regulated). Genes involved in the extracellular structure organization (e.g. VCAM1) were found up-regulated. KEGG analysis showed an up-regulation of genes involved in the TGF-β pathway. The KS vs testis atrophy analysis resulted in 539 significant DEGs (59 up- and 480 down-regulated). Chronic inflammatory response genes were found up-regulated. The overlap of X-linked DEGs from the two analyses revealed three genes: matrix-remodelling associated 5 (MXRA5), doublecortin (DCX) and variable charge X-Linked 3B (VCX3B). RNA in situ hybridization showed an overexpression of VCAM1, MXRA5 and DCX within the fibrotic group compared with the non-fibrotic group. To summarize, this study revealed DEGs between fibrotic and non-fibrotic testis tissue, including VCAM1. In addition, X-linked fibrotic genes were revealed, e.g. MXRA5, DCX and VCX3B. Their potential role in KS-related testicular fibrosis needs further study.
The predictors of health-enhancing physical activity among working women in Singapore two years into COVID-19: a cross-sectional study
Authors: Lim Ellene , Ramachandran Hadassah Joann , Er Joyce Biaw Theng , Ng Pearlyn , Tam Wilson Wai San , Jiang Ying 
Published: December 2022

AbstractPhysical activity (PA) levels may have changed since the COVID-19 pandemic. However, these changes are not well understood. The study aimed to describe the PA level and examine the predictive factors of a health-enhancing PA level among working women in Singapore two years into the COVID-19 pandemic. We undertook a cross-sectional descriptive correlational study. Three hundred participants were recruited and completed the online questionnaire between October and November 2021. In the PA analysis of 217 participants, only 32.7% of the participants achieved a health-enhancing PA level, while 44.7% of the total sample sat for 7 h or more daily. In the univariate analysis, occupation, nationality, monthly income, and average daily sitting hours were significantly associated with a high PA level. The current mode of work, living arrangement, and health-promoting lifestyle profile II_physical activity score remained significant in both univariate and multivariate analyses. Participants who worked from home and stayed with their families were less likely to achieve a health-enhancing PA level than those who had a regular workplace and did not stay with their families. Working women with a health-promoting physically active lifestyle were likelier to achieve a health-enhancing PA level. The long daily sitting time and suboptimal health-enhancing PA participation underscore the need for health promotion initiatives for working women.
Effects of pre-existing anti-adenovirus antibodies on transgene expression levels and therapeutic efficacies of arming oncolytic adenovirus
Authors: Ono Ryosuke , Nishimae Fumitaka , Wakida Takuro , Sakurai Fuminori , Mizuguchi Hiroyuki 
Published: December 2022

AbstractOncolytic adenoviruses (OAds), most of which are based on species C human adenovirus serotype 5 (Ad5) (OAd5), have recently received much attention as potential anticancer agents. High seroprevalence of anti-Ad5 neutralizing antibodies is a major hurdle for Ad5-based gene therapy. However, the impacts of anti-Ad5 neutralizing antibodies on OAd5-mediated transgene expression in the tumor and antitumor effects remain to be fully elucidated. In this study, we examined the impact of anti-Ad5 neutralizing antibodies on the OAd5-mediated antitumor effects and OAd5-mediated transgene expression. The luciferase expression of OAd-tAIB-Luc, which contains the cytomegalovirus promoter-driven luciferase gene, was inhibited in human cultured cells in the presence of human serum. Although the inhibitory effects of human serum possessing the low anti-Ad5 neutralizing antibody titers were overcome by long-term infection, the in vitro tumor cell lysis activities of OAd-tAIB-Luc were entirely attenuated by human serum containing the high titers of anti-Ad5 neutralizing antibodies. OAd-tAIB-Luc-mediated luciferase expression in the subcutaneous tumors 3 days after administration and tumor growth suppression levels following intratumoral administration were significantly lower in mice possessing the high titers of anti-Ad5 neutralizing antibodies, compared to those in control mice. These results suggested that pre-existing anti-Ad5 antibodies attenuated both transgene expression and potential antitumor effects of OAd5 following intratumoral administration.
Heat and mass transfer for MHD peristaltic flow in a micropolar nanofluid: mathematical model with thermophysical features
Authors: Abd-Alla A. M. , Abo-Dahab S. M. , Thabet Esraa N. , Abdelhafez M. A. 
Published: December 2022

AbstractAccording to a survey of the literature, nanofluids are superior to traditional fluids at transferring heat. A detailed analysis of the models mentioned above is crucial since there are large gaps in the illumination of current solutions for improving heat transfer in nanomaterials. The ongoing investigation's purpose is to ascertain the tiny size gold particles drift in free with the heat and mass transfer, buoyancy forces, thermophoresis, and Brownian motion of a micropolar nanofluid being transported through a porous medium in an asymmetric channel with a uniform magnetic field using a long-wavelength and low Reynolds number approximation. The resulting dimensionless nonlinear governing equations have been numerically solved using a MATLAB software and the Runge–Kutta–Fehlberg integration scheme. Two comparisons with previously investigated problems are also made to confirm our findings, and an excellent concurrence is discovered. As a result, trustworthy results are being given. Numerical solutions are used to describe the effects of different thermal-fluidic parameters on velocity profiles, temperature, concentration, micropolar rotation, pressure gradient, shear stress, heat flux, and nanoparticle volume flux, etc. Tables, graphs, and bar charts are used to present and discuss numerical results that have been produced. A comparison of the resulting numerical solution to earlier literature also reveals a satisfactory level of agreement. Insight into real-world applications such nanofluidic, energy conservation, friction reduction, and power generation are provided by this work. Furthermore, the Brownian and thermophoresis parameters behave significantly differently in a concentration field. On the other hand, the study puts forward an important note that for peristaltic flow of a micropolar fluid with nanoparticles can be controlled by suitably adjusting the micropolar parameter, thermophoresis parameter, nanoparticle Grashof number, and Brownian motion parameter.
Quantification of prostate tumour diameter and volume from MR images using 3D ellipsoid model and its impact on PI-RADS v2.1 assessment
Authors: Singh Dharmesh , Das Chandan J. , Kumar Virendra , Singh Anup , Mehndiratta Amit 
Published: December 2022

AbstractMaximum diameter and volume of the tumour provide important clinical information and are decision-making parameters for patients suspected with prostate cancer (PCa). The objectives of this study were to develop an automated method for 3D tumour measurement and compare it with the radiologist’s manual assessment, as well as to investigate the impact of 3D tumour measurement on Prostate Imaging-Reporting and Data System version-2.1 (PI-RADS v2.1) scoring of prostate cancer. Tumour maximum diameter and volume were calculated using automated ellipsoid-fit method. For all PI-RADS scores, mean ± standard deviation range of tumour maximum diameter and volume measured using ellipsoid-fit method were 1.36 ± 0.28 to 1.97 ± 0.67 cm and 0.49 ± 0.31 to 1.05 ± 0.78 cc and manual assessment were in range of 0.73 ± 0.12 to 1.14 ± 0.25 cm and 0.36 ± 0.21 to 0.93 ± 0.39 cc, respectively. Ellipsoid-fit method showed significantly (p < 0.05) higher values for maximum diameter and volume than manual assessment. 3D measurement of tumour using ellipsoid-fit method was found to have higher maximum diameter and volume values (in 40–61% patients) compared to conventional assessment by radiologist, which may have an impact on PI-RADS v2.1 scoring system.
Simulation study of gas sensor using periodic phononic crystal tubes to detect hazardous greenhouse gases
Authors: Zaky Zaky A. , Alamri Sagr , Zohny Ensjam I. , Aly Arafa H. 
Published: December 2022

AbstractHere, we investigate a gas sensor model based on phononic crystals of alternating tubes using the transfer matrix method to detect hazardous greenhouse gases. The effect of the thicknesses and cross-sections of all tubes on the performance of the proposed sensor is studied. The results show that longitudinal acoustic speed is a pivotal parameter rather than the mass density variations of the gas samples on the position of the resonant peaks due to its significant impact on the propagation of the acoustic wave. The suggested sensor can be considered very simple and low-cost because it does not need a complicated process to deposit multilayers of different mechanical properties’ materials.
Resampling and harmonization for mitigation of heterogeneity in image parameters of baseline scans
Authors: Singh Apurva , Horng Hannah , Chitalia Rhea , Roshkovan Leonid , Katz Sharyn I. , Noël Peter , Shinohara Russell T. , Kontos Despina 
Published: December 2022

AbstractOur study investigates the effects of heterogeneity in image parameters on the reproducibility of prognostic performance of models built using radiomic biomarkers. We compare the prognostic performance of models derived from the heterogeneity-mitigated features with that of models obtained from raw features, to assess whether reproducibility of prognostic scores improves upon application of our methods. We used two datasets: The Breast I-SPY1 dataset—Baseline DCE-MRI scans of 156 women with locally advanced breast cancer, treated with neoadjuvant chemotherapy, publicly available via The Cancer Imaging Archive (TCIA); The NSCLC IO dataset—Baseline CT scans of 107 patients with stage 4 non-small cell lung cancer (NSCLC), treated with pembrolizumab immunotherapy at our institution. Radiomic features (n = 102) are extracted from the tumor ROIs. We use a variety of resampling and harmonization scenarios to mitigate the heterogeneity in image parameters. The patients were divided into groups based on batch variables. For each group, the radiomic phenotypes are combined with the clinical covariates into a prognostic model. The performance of the groups is assessed using the c-statistic, derived from a Cox proportional hazards model fitted on all patients within a group. The heterogeneity-mitigation scenario (radiomic features, derived from images that have been resampled to minimum voxel spacing, are harmonized using the image acquisition parameters as batch variables) gave models with highest prognostic scores (for e.g., IO dataset; batch variable: high kernel resolution—c-score: 0.66). The prognostic performance of patient groups is not comparable in case of models built using non-heterogeneity mitigated features (for e.g., I-SPY1 dataset; batch variable: small pixel spacing—c-score: 0.54, large pixel spacing—c-score: 0.65). The prognostic performance of patient groups is closer in case of heterogeneity-mitigated scenarios (for e.g., scenario—harmonize by voxel spacing parameters: IO dataset; thin slice—c-score: 0.62, thick slice—c-score: 0.60). Our results indicate that accounting for heterogeneity in image parameters is important to obtain more reproducible prognostic scores, irrespective of image site or modality. For non-heterogeneity mitigated models, the prognostic scores are not comparable across patient groups divided based on batch variables. This study can be a step in the direction of constructing reproducible radiomic biomarkers, thus increasing their application in clinical decision making.
Differential critical residues on the overlapped region of the non-structural protein-1 recognized by flavivirus and dengue virus cross-reactive monoclonal antibodies
Authors: Luangaram Prasit , Tamdet Chamaiporn , Saengwong Chananya , Prommool Tanapan , Kraivong Romchat , Nilchan Napon , Punyadee Nuntaya , Avirutnan Panisadee , Srisawat Chatchawan , Malasit Prida , Kasinrerk Watchara , Puttikhunt Chunya 
Published: December 2022

AbstractThe non-structural protein-1 (NS1) of dengue virus (DENV) contributes to several functions related to dengue disease pathogenesis as well as diagnostic applications. Antibodies against DENV NS1 can cross-react with other co-circulating flaviviruses, which may lead to incorrect diagnosis. Herein, five anti-DENV NS1 monoclonal antibodies (mAbs) were investigated. Four of them (1F11, 2E3, 1B2, and 4D2) cross-react with NS1 of all four DENV serotypes (pan-DENV mAbs), whereas the other (2E11) also reacts with NS1 of other flaviviruses (flavi-cross-reactive mAb). The binding epitopes recognized by these mAbs were found to overlap a region located on the disordered loop of the NS1 wing domain (amino acid residues 104 to 123). Fine epitope mapping employing phage display technology and alanine-substituted DENV2 NS1 mutants indicates the critical binding residues W115, K116, and K120 for the 2E11 mAb, which are conserved among flaviviruses. In contrast, the critical binding residues of four pan-DENV mAbs include both flavi-conserved residues (W115 to G119) and DENV-conserved flanking residues (K112, Y113, S114 and A121, K122). Our results highlight DENV-conserved residues in cross-reactive epitopes that distinguish pan-DENV antibodies from the flavi-cross-reactive antibody. These antibodies can be potentially applied to differential diagnosis of DENV from other flavivirus infections.
Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer
Authors: Deb Dhruba , Wu Yangfan , Coker Courtney , Harimoto Tetsuhiro , Huang Ruoqi , Danino Tal 
Published: December 2022

AbstractSynthetic biology enables the engineering of bacteria to safely deliver potent payloads to tumors for effective anti-cancer therapies. However, a central challenge for translation is determining ideal bacterial therapy candidates for specific cancers and integrating them with other drug treatment strategies to maximize efficacy. To address this, we designed a screening and evaluation pipeline for characterization of bacterial therapies in lung cancer models. We screened 10 engineered bacterial toxins across 6 non-small cell lung cancer patient-derived cell lines and identified theta toxin as a promising therapeutic candidate. Using a bacteria-spheroid co-culture system (BSCC), analysis of differentially expressed transcripts and gene set enrichment revealed significant changes in at least 10 signaling pathways with bacteria-producing theta toxin. We assessed combinatorial treatment of small molecule pharmaceutical inhibitors targeting 5 signaling molecules and of 2 chemotherapy drugs along with bacterially-produced theta toxin and showed improved dose-dependent response. This combination strategy was further tested and confirmed, with AKT signaling as an example, in a mouse model of lung cancer. In summary, we developed a pipeline to rapidly characterize bacterial therapies and integrate them with current targeted therapies for lung cancer.
Efficient simultaneous double DNA knock-in in murine embryonic stem cells by CRISPR/Cas9 ribonucleoprotein-mediated circular plasmid targeting for generating gene-manipulated mice
Authors: Ozawa Manabu , Taguchi Jumpei , Katsuma Kento , Ishikawa-Yamauchi Yu , Kikuchi Mio , Sakamoto Reiko , Yamada Yasuhiro , Ikawa Masahito 
Published: December 2022

AbstractGene targeting of embryonic stem (ES) cells followed by chimera production has been conventionally used for developing gene-manipulated mice. Although direct knock-in (KI) using murine zygote via CRISPR/Cas9-mediated genome editing has been reported, ES cell targeting still has merits, e.g., high throughput work can be performed in vitro. In this study, we first compared the KI efficiency of mouse ES cells with CRISPR/Cas9 expression vector and ribonucleoprotein (RNP), and confirmed that KI efficiency was significantly increased by using RNP. Using CRISPR/Cas9 RNP and circular plasmid with homologous arms as a targeting vector, knock-in within ES cell clones could be obtained efficiently without drug selection, thus potentially shortening the vector construction or cell culture period. Moreover, by incorporating a drug-resistant cassette into the targeting vectors, double DNA KI can be simultaneously achieved at high efficiency by a single electroporation. This technique will help to facilitate the production of genetically modified mouse models that are fundamental for exploring topics related to human and mammalian biology.
Interpretable prognostic modeling of endometrial cancer
Authors: Zagidullin Bulat , Pasanen Annukka , Loukovaara Mikko , Bützow Ralf , Tang Jing 
Published: December 2022

AbstractEndometrial carcinoma (EC) is one of the most common gynecological cancers in the world. In this work we apply Cox proportional hazards (CPH) and optimal survival tree (OST) algorithms to the retrospective prognostic modeling of disease-specific survival in 842 EC patients. We demonstrate that linear CPH models are preferred for the EC risk assessment based on clinical features alone, while interpretable, non-linear OST models are favored when patient profiles can be supplemented with additional biomarker data. We show how visually interpretable tree models can help generate and explore novel research hypotheses by studying the OST decision path structure, in which L1 cell adhesion molecule expression and estrogen receptor status are correctly indicated as important risk factors in the p53 abnormal EC subgroup. To aid further clinical adoption of advanced machine learning techniques, we stress the importance of quantifying model discrimination and calibration performance in the development of explainable clinical prediction models.