bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical and numerical investigation of thermal distribution for hybrid nanofluid through an oblique artery with mild stenosis
Authors: Jalili Payam , Sadeghi Ghahare Ahmad , Jalili Bahram , Domiri Ganji Davood 
Published: March 2023

AbstractIn this study, the accuracy of three methods to simulate the thermal diffusivity profile in oblique stenosis artery with hybrid nanofluid and the influence of volume fraction and heat sources in the hybrid nanofluid, including Al2O3 and Cu, is studied. Comparing the analytical methods for reliable answers is important in the new studies. Also, the influence of volume fraction and heat source parameter S in temperature evolution is studied. Akbari–Ganji Method (AGM), Finite Element Method (FEM), and Runge–Kutta method are studied to calculate the stenosis artery's heat profile. The results are compared by reference value, AGM is the more accurate method than FEM and Runge–Kutta methods by less than 7 percent error, and FEM is more accurate than Runge–Kutta by less than 9 percent error. The maximum difference between the three methods happened near the wall of the vessel. 0.02, 0.03, and 0.05 is the volume fraction chosen for studying. Changing the volume fraction of nanoparticles is studied by enhancing the volume fraction of Nanoparticles and presenting the Al2O3, and Cu decreases the max temperature profile and increases the heat source by increasing the maximum heat temperature. Al2O3 has more influence on maximum heat temperature and decreases the temperature profile more.
An Explainable Fully Dense Fusion Neural Network with Deep Support Vector Machine for Retinal Disease Determination
Authors: Kayadibi İsmail , Güraksın Gür Emre 
Published: March 2023

AbstractRetinal issues are crucial because they result in visual loss. Early diagnosis can aid physicians in initiating treatment and preventing visual loss. Optical coherence tomography (OCT), which portrays retinal morphology cross-sectionally and noninvasively, is used to identify retinal abnormalities. The process of analyzing OCT images, on the other hand, takes time. This study has proposed a hybrid approach based on a fully dense fusion neural network (FD-CNN) and dual preprocessing to identify retinal diseases, such as choroidal neovascularization, diabetic macular edema, drusen from OCT images. A dual preprocessing methodology, in other words, a hybrid speckle reduction filter was initially used to diminish speckle noise present in OCT images. Secondly, the FD-CNN architecture was trained, and the features obtained from this architecture were extracted. Then Deep Support Vector Machine (D-SVM) and Deep K-Nearest Neighbor (D-KNN) classifiers were proposed to reclassify those features and tested on University of California San Diego (UCSD) and Duke OCT datasets. D-SVM demonstrated the best performance in both datasets. D-SVM achieved 99.60% accuracy, 99.60% sensitivity, 99.87% specificity, 99.60% precision and 99.60% F1 score in the UCSD dataset. It achieved 97.50% accuracy, 97.64% sensitivity, 98.91% specificity, 96.61% precision, and 97.03% F1 score in Duke dataset. Additionally, the results were compared to state-of-the-art works on the both datasets. The D-SVM was demonstrated to be an efficient and productive strategy for improving the robustness of automatic retinal disease classification. Also, in this study, it is shown that the unboxing of how AI systems' black-box choices is made by generating heat maps using the local interpretable model-agnostic explanation method, which is an explainable artificial intelligence (XAI) technique. Heat maps, in particular, may contribute to the development of more stable deep learning-based systems, as well as enhancing the confidence in the diagnosis of retinal disease in the analysis of OCT image for ophthalmologists.
Planned missingness: An underused but practical approach to reducing survey and test length
Authors: Zhang Charlene , Sackett Paul R. 
Published: March 2023

AbstractI-O psychologists often face the need to reduce the length of a data collection effort due to logistical constraints or data quality concerns. Standard practice in the field has been either to drop some measures from the planned data collection or to use short forms of instruments rather than full measures. Dropping measures is unappealing given the loss of potential information, and short forms often do not exist and have to be developed, which can be a time-consuming and expensive process. We advocate for an alternative approach to reduce the length of a survey or a test, namely to implement a planned missingness (PM) design in which each participant completes a random subset of items. We begin with a short introduction of PM designs, then summarize recent empirical findings that directly compare PM and short form approaches and suggest that they perform equivalently across a large number of conditions. We surveyed a sample of researchers and practitioners to investigate why PM has not been commonly used in I-O work and found that the underusage stems primarily from a lack of knowledge and understanding. Therefore, we provide a simple walkthrough of the implementation of PM designs and analysis of data with PM, as well as point to various resources and statistical software that are equipped for its use. Last, we prescribe a set of four conditions that would characterize a good opportunity to implement a PM design.
DIVISIBILITY OF THE PARTITION FUNCTION BY POWERS OF AND
Authors: BARMAN RUPAM , SINGH GURINDER , SINGH AJIT 
Published: March 2023

AbstractLin introduced the partition function
$\text {PDO}_t(n)$
, which counts the total number of tagged parts over all the partitions of n with designated summands in which all parts are odd. Lin also proved some congruences modulo 3 and 9 for
$\text {PDO}_t(n)$
, and conjectured certain congruences modulo
$3^{k+2}$
for
$k\geq 0$
. He proved the conjecture for
$k=0$
and
$k=1$
[‘The number of tagged parts over the partitions with designated summands’, J. Number Theory184 (2018), 216–234]. We prove the conjecture for
$k=2$
. We also study the lacunarity of
$\text {PDO}_t(n)$
modulo arbitrary powers of 2 and 3. Using nilpotency of Hecke operators, we prove that there exists an infinite family of congruences modulo any power of 2 satisfied by
$\text {PDO}_t(n)$
.
Untangling the relationship between pre-service teachers’ development of intercultural effectiveness and their experiences in virtual exchange
Authors: Rets Irina , Rienties Bart , Lewis Tim 
Published: March 2023

AbstractSeveral studies have found that virtual exchange (VE) has a positive impact on intercultural effectiveness (IE) development. However, few VE studies have measured and unpacked perceived learning gains from VE in this area using data from multiple VEs and mixed-methods approaches. In this study, we explored the impact of VE on perceived IE development among pre-service teachers in two exchanges. Using k-means cluster analysis of reported gains in IE, we identified three groups of students who reported high-medium-low IE gains. Cluster analysis informed our qualitative analysis of students’ reflections on VE. Having analysed data from 486 diary entries at four successive time measurements, we identified three factors critical to students’ perceived IE development: students’ ability to overcome challenges during VE, level of engagement with their partners, and engagement with cultural difference. These findings shed light on what experiences in VE influence participants’ perceptions of their intercultural learning. The study provides recommendations for the design of online collaborative learning programmes, such as VE, that might help address students’ diverse needs.
Unusual peptide-binding proteins guide pyrroloindoline alkaloid formation in crocagin biosynthesis
Authors: Adam Sebastian , Zheng Dazhong , Klein Andreas , Volz Carsten , Mullen William , Shirran Sally L. , Smith Brian O. , Kalinina Olga V. , Müller Rolf , Koehnke Jesko 
Published: March 2023

AbstractRibosomally synthesized and post-translationally modified peptide natural products have provided many highly unusual scaffolds. This includes the intriguing alkaloids crocagins, which possess a tetracyclic core structure and whose biosynthesis has remained enigmatic. Here we use in vitro experiments to demonstrate that three proteins, CgnB, CgnC and CgnE, are sufficient for the production of the hallmark tetracyclic crocagin core from the precursor peptide CgnA. The crystal structures of the homologues CgnB and CgnE reveal them to be the founding members of a peptide-binding protein family and allow us to rationalize their distinct functions. We further show that the hydrolase CgnD liberates the crocagin core scaffold, which is subsequently N-methylated by CgnL. These insights allow us to propose a biosynthetic scheme for crocagins. Bioinformatic analyses based on these data led to the discovery of related biosynthetic pathways that may provide access to a structurally diverse family of peptide-derived pyrroloindoline alkaloids.
Sniper2L is a high-fidelity Cas9 variant with high activity
Authors: Kim Young-hoon , Kim Nahye , Okafor Ikenna , Choi Sungchul , Min Seonwoo , Lee Joonsun , Bae Seung-Min , Choi Keunwoo , Choi Janice , Harihar Vinayak , Kim Youngho , Kim Jin-Soo , Kleinstiver Benjamin P. , Lee Jungjoon K. , Ha Taekjip , Kim Hyongbum Henry 
Published: March 2023

AbstractAlthough several high-fidelity SpCas9 variants have been reported, it has been observed that this increased specificity is associated with reduced on-target activity, limiting the applications of the high-fidelity variants when efficient genome editing is required. Here, we developed an improved version of Sniper–Cas9, Sniper2L, which represents an exception to this trade-off trend as it showed higher specificity with retained high activity. We evaluated Sniper2L activities at a large number of target sequences and developed DeepSniper, a deep learning model that can predict the activity of Sniper2L. We also confirmed that Sniper2L can induce highly efficient and specific editing at a large number of target sequences when it is delivered as a ribonucleoprotein complex. Mechanically, the high specificity of Sniper2L originates from its superior ability to avoid unwinding a target DNA containing even a single mismatch. We envision that Sniper2L will be useful when efficient and specific genome editing is required.
Phase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres
Authors: Spegg Vincent , Panagopoulos Andreas , Stout Merula , Krishnan Aswini , Reginato Giordano , Imhof Ralph , Roschitzki Bernd , Cejka Petr , Altmeyer Matthias 
Published: March 2023

AbstractRPA has been shown to protect single-stranded DNA (ssDNA) intermediates from instability and breakage. RPA binds ssDNA with sub-nanomolar affinity, yet dynamic turnover is required for downstream ssDNA transactions. How ultrahigh-affinity binding and dynamic turnover are achieved simultaneously is not well understood. Here we reveal that RPA has a strong propensity to assemble into dynamic condensates. In solution, purified RPA phase separates into liquid droplets with fusion and surface wetting behavior. Phase separation is stimulated by sub-stoichiometric amounts of ssDNA, but not RNA or double-stranded DNA, and ssDNA gets selectively enriched in RPA condensates. We find the RPA2 subunit required for condensation and multi-site phosphorylation of the RPA2 N-terminal intrinsically disordered region to regulate RPA self-interaction. Functionally, quantitative proximity proteomics links RPA condensation to telomere clustering and integrity in cancer cells. Collectively, our results suggest that RPA-coated ssDNA is contained in dynamic RPA condensates whose properties are important for genome organization and stability.
A low-cost smartphone fluorescence microscope for research, life science education, and STEM outreach
Authors: Schaefer Madison A. , Nelson Heather N. , Butrum John L. , Gronseth James R. , Hines Jacob H. 
Published: March 2023

AbstractMuch of our understanding of cell and tissue development, structure, and function stems from fluorescence microscopy. The acquisition of colorful and glowing images engages and excites users ranging from seasoned microscopists to STEM students. Fluorescence microscopes range in cost from several thousand to several hundred thousand US dollars. Therefore, the use of fluorescence microscopy is typically limited to well-funded institutions and biotechnology companies, research core facilities, and medical laboratories, but is financially impractical at many universities and colleges, primary and secondary schools (K-12), and in science outreach settings. In this study, we developed and characterized components that when used in combination with a smartphone or tablet, perform fluorescence microscopy at a cost of less than $50 US dollars per unit. We re-purposed recreational LED flashlights and theater stage lighting filters to enable viewing of green and red fluorophores including EGFP, DsRed, mRFP, and mCherry on a simple-to-build frame made of wood and plexiglass. These devices, which we refer to as glowscopes, were capable of 10 µm resolution, imaging fluorescence in live specimens, and were compatible with all smartphone and tablet models we tested. In comparison to scientific-grade fluorescence microscopes, glowscopes may have limitations to sensitivity needed to detect dim fluorescence and the inability to resolve subcellular structures. We demonstrate capability of viewing fluorescence within zebrafish embryos, including heart rate, rhythmicity, and regional anatomy of the central nervous system. Due to the low cost of individual glowscope units, we anticipate this device can help to equip K-12, undergraduate, and science outreach classrooms with fleets of fluorescence microscopes that can engage students with hands-on learning activities.
Initiation and modulation of Tau protein phase separation by the drug suramin
Authors: Prince Prabhu Rajaiah , Hochmair Janine , Brognaro Hévila , Gevorgyan Susanna , Franck Maximilian , Schubert Robin , Lorenzen Kristina , Yazici Selin , Mandelkow Eckhard , Wegmann Susanne , Betzel Christian 
Published: March 2023

AbstractTau is an intrinsically disordered neuronal protein in the central nervous system. Aggregated Tau is the main component of neurofibrillary tangles observed in Alzheimer’s disease. In vitro, Tau aggregation can be triggered by polyanionic co-factors, like RNA or heparin. At different concentration ratios, the same polyanions can induce Tau condensates via liquid–liquid phase separation (LLPS), which over time develop pathological aggregation seeding potential. Data obtained by time resolved Dynamic Light Scattering experiments (trDLS), light and electron microscopy show that intermolecular electrostatic interactions between Tau and the negatively charged drug suramin induce Tau condensation and compete with the interactions driving and stabilizing the formation of Tau:heparin and Tau:RNA coacervates, thus, reducing their potential to induce cellular Tau aggregation. Tau:suramin condensates do not seed Tau aggregation in a HEK cell model for Tau aggregation, even after extended incubation. These observations indicate that electrostatically driven Tau condensation can occur without pathological aggregation when initiated by small anionic molecules. Our results provide a novel avenue for therapeutic intervention of aberrant Tau phase separation, utilizing small anionic compounds.
Combined adipose-derived mesenchymal stem cell and antibiotic therapy can effectively treat periprosthetic joint infection in rats
Authors: Yamamuro Yuki , Kabata Tamon , Nojima Takayuki , Hayashi Katsuhiro , Tokoro Masaharu , Kajino Yoshitomo , Inoue Daisuke , Ohmori Takaaki , Yoshitani Junya , Ueno Takuro , Ueoka Ken , Taninaka Atsushi , Kataoka Tomoyuki , Saiki Yoshitomo , Yanagi Yu , Tsuchiya Hiroyuki 
Published: March 2023

AbstractPeriprosthetic joint infection (PJI) is characterized by biofilm infection, which is difficult to alleviate while preserving implant integrity. Furthermore, long-term antibiotic therapy may increase the prevalence of drug-resistant bacterial strains, necessitating a non-antibacterial approach. Adipose-derived stem cells (ADSCs) exert antibacterial effects; however, their efficacy in PJI remains unclear. This study investigates the efficacy of combined intravenous ADSCs and antibiotic therapy in comparison to antibiotic monotherapy in a methicillin-sensitive Staphylococcus aureus (MSSA)-infected PJI rat model. The rats were randomly assigned and equally divided into 3 groups: no-treatment group, antibiotic group, ADSCs with antibiotic group. The ADSCs with antibiotic group exhibited the fastest recovery from weight loss, with lower bacterial counts (p = 0.013 vs. no-treatment group; p = 0.024 vs. antibiotic group) and less bone density loss around the implants (p = 0.015 vs. no-treatment group; p = 0.025 vs. antibiotic group). The modified Rissing score was used to evaluate localized infection on postoperative day 14 and was the lowest in the ADSCs with antibiotic group; however, no significant difference was observed between the antibiotic group and ADSCs with antibiotic group (p < 0.001 vs. no-treatment group; p = 0.359 vs. antibiotic group). Histological analysis revealed a clear, thin, and continuous bony envelope, a homogeneous bone marrow, and a defined, normal interface in the ADSCs with antibiotic group. Moreover, the expression of cathelicidin expression was significantly higher (p = 0.002 vs. no-treatment group; p = 0.049 vs. antibiotic group), whereas that of tumor necrosis factor (TNF)-α and interleukin(IL)-6 was lower in the ADSCs with antibiotic group than in the no-treatment group (TNF-α, p = 0.010 vs. no-treatment group; IL-6, p = 0.010 vs. no-treatment group). Thus, the combined intravenous ADSCs and antibiotic therapy induced a stronger antibacterial effect than antibiotic monotherapy in a MSSA-infected PJI rat model. This strong antibacterial effect may be related to the increased cathelicidin expression and decreased inflammatory cytokine expression at the site of infection.
Pseudomonas alcaliphila NEWG-2 as biosorbent agent for methylene blue dye: optimization, equilibrium isotherms, and kinetic processes
Authors: Ghoniem Abeer A. , Moussa Zeiad , Alenzi Asma Massad , Alotaibi Amenah S. , Fakhry Hala , El-Khateeb Ayman Y. , Saber WesamEldin I. A. , Elsayed Ashraf 
Published: March 2023

AbstractIn comparison to physicochemical and chemical methods, microbial dye biosorption is regarded as an eco-effective and economically viable alternative and is a widely applied method due to its high efficiency and compatibility with the environment. Therefore, the idea of this study is to clarify to what extent the viable cells and the dry biomass of Pseudomonas alcaliphila NEWG-2 can improve the biosorption of methylene blue (MB) from a synthetic wastewater sample. The array of Taguchi paradigm has been conducted to ascertain five variables affecting the biosorption of MB by broth forms of P. alcaliphila NEWG. The data of MB biosorption were familiar to the predicted ones, indicating the precision of the Taguchi model’s prediction. The maximum biosorption of MB (87.14%) was achieved at pH 8, after 60 h, in a medium containing 15 mg/ml MB, 2.5% glucose, and 2% peptone, with sorting the highest signal-to-noise ratio (38.80). FTIR spectra detected various functional groups (primary alcohol, α, β-unsaturated ester, symmetric NH2 bending, and strong C–O stretching) on the bacterial cell wall that participated in the biosorption of MB. Furthermore, the spectacular MB biosorption ability was validated by equilibrium isotherms and kinetic studies (the dry biomass form), which were derived from the Langmuir model (qmax = 68.827 mg/g). The equilibrium time was achieved in about 60 min, with 70.5% of MB removal. The biosorption kinetic profile might be adequately represented by pseudo-second order and Elovich models. The changes in the bacterial cells before and after the biosorption of MB were characterized using a scanning electron microscope. As realized from the aforementioned data, the bacterium is a talented, effective, eco-friendly, and low-cost bio-sorbent for the decolorization and remedy of an industrial effluent containing MB from an aqueous environment. The current outcomes in the biosorption of MB molecules promote the use of the bacterial strain as viable cells and/or dry biomass in ecosystem restoration, environmental cleanup, and bioremediation studies.
Evaluation of the clinical performance of an AI-based application for the automated analysis of chest X-rays
Authors: Niehoff Julius Henning , Kalaitzidis Jana , Kroeger Jan Robert , Schoenbeck Denise , Borggrefe Jan , Michael Arwed Elias 
Published: March 2023

AbstractThe AI-Rad Companion Chest X-ray (AI-Rad, Siemens Healthineers) is an artificial-intelligence based application for the analysis of chest X-rays. The purpose of the present study is to evaluate the performance of the AI-Rad. In total, 499 radiographs were retrospectively included. Radiographs were independently evaluated by radiologists and the AI-Rad. Findings indicated by the AI-Rad and findings described in the written report (WR) were compared to the findings of a ground truth reading (consensus decision of two radiologists after assessing additional radiographs and CT scans). The AI-Rad can offer superior sensitivity for the detection of lung lesions (0.83 versus 0.52), consolidations (0.88 versus 0.78) and atelectasis (0.54 versus 0.43) compared to the WR. However, the superior sensitivity is accompanied by higher false-detection-rates. The sensitivity of the AI-Rad for the detection of pleural effusions is lower compared to the WR (0.74 versus 0.88). The negative-predictive-values (NPV) of the AI-Rad for the detection of all pre-defined findings are on a high level and comparable to the WR. The seemingly advantageous high sensitivity of the AI-Rad is partially offset by the disadvantage of a high false-detection-rate. At the current stage of development, therefore, the high NPVs may be the greatest benefit of the AI-Rad giving radiologists the possibility to re-insure their own negative search for pathologies and thus boosting their confidence in their reports.
Effect of BIM expression on the prognostic value of PD-L1 in advanced non-small cell lung cancer patients treated with EGFR-TKIs
Authors: Chu Chang-Yao , Lin Chien-Yu , Lin Chien-Chung , Li Chien-Feng , Wu Shang-Yin , Tsai Jeng-Shiuan , Yang Szu-Chun , Chen Chian-Wei , Lin Chia-Yin , Chang Chao-Chun , Yen Yi-Ting , Tseng Yau-Lin , Su Po-Lan , Su Wu-Chou 
Published: March 2023

AbstractThe role of Programmed Cell Death Ligand 1 (PD-L1) expression in predicting epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKIs) efficacy remains controversial. Recent studies have highlighted that tumor-intrinsic PD-L1 signaling can be modulated by STAT3, AKT, MET oncogenic pathway, epithelial–mesenchymal transition, or BIM expression. This study aimed to investigate whether these underlying mechanisms affect the prognostic role of PD-L1. We retrospectively enrolled patients with EGFR mutant advanced stage NSCLC who received first-line EGFR-TKI between January 2017 and June 2019, the treatment efficacy of EGFR-TKI was assessed. Kaplan–Meier analysis of progression-free survival (PFS) revealed that patients with high BIM expression had shorter PFS, regardless of PD-L1 expression. This result was also supported by the COX proportional hazard regression analysis. In vitro, we further proved that the knockdown of BIM, instead of PDL1, induced more cell apoptosis following gefitinib treatment. Our data suggest that among the pathways affecting tumor-intrinsic PD-L1 signaling, BIM is potentially the underlying mechanism that affects the role of PD-L1 expression in predicting response to EGFR TKI and mediates cell apoptosis under treatment with gefitinib in EGFR-mutant NSCLC. Further prospective studies are required to validate these results.