bluuebunny/crossref_metadata_2025_split huggingface dataset:
EGFR signaling and pharmacology in oncology revealed with innovative BRET-based biosensors
Authors: Sabbagh Laurent , Gross Florence , Mancini Arturo , Breton Billy , Kobayashi Hiroyuki , Gouill Christian Le , Bouvier Michel , Schann Stephan , Leroy Xavier 
Published: June 2023

Abstract
Dysregulation of receptor tyrosine kinases (RTKs) is associated with the development of many cancers. Intrinsic and acquired mutations of RTKs modify receptor signaling contributing to drug resistance in clinical settings. We present enhanced bystander bioluminescence resonance energy transfer-based biosensors providing new insights into RTK biology and pharmacology critical for the development of more effective RTK-targeting drugs. The 12 distinct SH2-specific effector biosensors allow for real-time and spatiotemporal monitoring of signal transduction pathways engaged upon RTK activation. Using EGFR as a model system, we demonstrate the capacity of these biosensors to differentiate unique signaling signatures, at the plasma membrane or early endosome, with EGF and Epiregulin ligands displaying differences in efficacy, potency, and responses within different cellular compartments. We further demonstrate that EGFR single point mutations, found in Glioblastoma or non-small cell lung cancer, impact the constitutive activity of EGFR, its signaling profile and response to tyrosine kinase inhibitor. The BRET-based biosensors, are compatible with microscopy, allow extensive RTK signaling profiling in different cellular compartments and more importantly characterize the next generation of therapeutics directed against RTKs.
Investigations on a solar humidification dehumidification desalination system equipped with various packing materials and multi-stage bubble column dehumidifier
Authors: Shaikh Javed Sikandar , Ismail Saleel 
Published: June 2023

Abstract
This work presents the theoretical and experimental investigation of a solar-powered humidification dehumidification desalination (HDD) system with different humidifier packing materials and a two-stage bubble column dehumidifier (BCD). Naturally available coconut shells (CS) and coconut shells with drilled holes (CSH) on the surface to improve water permeability were used as packing materials in the humidifier, and their performance was compared with that of commercial-type pall ring (PR) and raschig ring (RR) packings. An in-house developed numerical model of the HDD system in conjunction with a flat plate solar water collector was used in this study. Steady-state experimental results showed that CSH packing exhibited the highest volumetric mass transfer coefficient (0.00852 kg/s), resulting in maximum humidifier efficiency (96%) and freshwater yield (2.16 kg/hr), followed by PR (0.00841 kg/s, 94%, and 2.137 kg/hr), CS (0.00831 kg/s, 90%, and 2.127 kg/hr), and RR (0.0081 kg/s, 81%, and 2.087 kg/hr) at feedwater mass flow rate of 1.5 kg/min and humidifier inlet temperature of 75\(℃\). Furthermore, transient outdoor test results showed that using a two-stage configuration in a BCD increased the daily average effectiveness to 0.93, as against 0.79 for a single-stage BCD. Employing CSH instead of PR and RR packings in the humidifier reduced freshwater costs by 6.2% and 7.6%, respectively.
Monolithic active-matrix full-color micro-LED micro-display using
InGaN/AlGaInP heterogeneous integration
Authors: QI Longheng , LI Peian , ZHANG Xu , WONG Ka Ming , Lau Kei 
Published: June 2023

Abstract
A prototype of active-matrix driven full-color micro-LED micro- display with a resolution of 200 × 80 is demonstrated using InGaN/AlGaInP heterogeneous integration. InGaN blue/green dual-color micro-LED arrays on a single MOCVD-grown GaN-on-Si epi-wafer and AlGaInP red micro-LED arrays were both monolithically fabricated, followed by the integration with a common CMOS backplane via flip-chip bonding technology to form a double-layer thin-film display structure. Full-color images with decent color gamut and brightness were successfully displayed by fine adjustment of the driving current densities of RGB subpixels. This integration method combines the benefits of the highly efficient InGaN blue/green emission with AlGaInP red light emission. The high pixel density demonstrated using the monolithic fabrication method shows the feasibility and promise for high brightness, good color performance and high-resolution micro-LED micro-displays towards future metaverse applications.
Induced alternative splicing: opportunity to study PCSK9 protein isoforms at physiologically relevant concentrations
Authors: Cale Jessica , Ham Kristin , Li Dunhui , McIntosh Craig , Watts Gerald F. , Wilton Steve , Aung-Htut May 
Published: June 2023

Abstract
Splice modulating antisense oligomers (AOs) are increasingly used to modulate RNA processing. While most are investigated for their use as therapeutics, AOs can also be used for basic research. This study examined their use to investigate internally and terminally truncated proprotein convertase subtilisin/kexin type 9 (PCSK9) protein isoforms. Previous studies have used plasmid or viral-vector-mediated protein overexpression to study different PCSK9 protein isoforms, creating an artificial environment within the cell. Here we designed and tested AOs to remove specific exons that encode for PCSK9 protein domains and produced protein isoforms at more physiologically relevant levels. We evaluated the isoforms’ expression, secretion, and subsequent impact on the low-density lipoprotein (LDL) receptor and its activity in Huh-7 cells. We found that modifying the Cis-His-rich domain by targeting exons 10 or 11 negatively affected LDL receptor activity and hence did not enhance LDL uptake although the levels of LDL receptor were increased. On the other hand, removing the hinge region encoded by exon 8, or a portion of the prodomain encoded by exon 2, have the potential as therapeutics for hypercholesterolemia. Our findings expand the understanding of PCSK9 isoforms and their impact on the LDL receptor and its activity at physiologically relevant concentrations.
Coupled Nonlinear Schrodinger (CNLS) Equations for two interacting electrostatic wavepackets in a non-Maxwellian fluid plasma model
Authors: LAZARIDES NIKOLAOS , Kourakis Ioannis 
Published: June 2023

Abstract
The nonlinear dynamics of two co-propagating electrostatic wavepackets in a one-dimensional non-magnetized plasma fluid model is considered, from first principles. The coupled waves are characterized by different (carrier) wavenumbers and amplitudes. A plasma consisting of non-thermalized (κ−distributed) electrons evolving against a cold (stationary) ion background is considered. The original model is reduced, by means of a multiple-scale perturbation method, to a pair of coupled nonlinear Schr¨odinger (CNLS) equations for the dynamics of the wavepacket envelopes. For arbitrary wavenumbers, the resulting CNLS equations exhibit no known symmetry and thus intrinsically differ from the Manakov system, in general.
Exact analytical expressions have been derived for the dispersion, self-modulation (nonlinearity) and cross-modulation (coupling) coefficients involved in the CNLS equations, as functions of the wavenumbers (k1, k2) and of the spectral index κ characterizing the electron profile. An analytical investigation has thus been carried out of the modulational instability (MI) properties of this pair of wavepackets, focusing on the role of the intrinsic (variable) parameters. Modulational instability is shown to occur in most parts of the parameter space.
The instability window(s) and the corresponding growth rate are calculated numerically in a number of case studies. Two-wave interaction favors MI by extending its range of occurrence and by enhancing its growth rate. Growth rate patterns obtained for different κ index (values) suggest that deviation from thermal (Maxwellian) equilibrium, for low κ values, leads to enhances MI of the interacting wave pair.
Although we have focused on electrostatic wavepacket propagation in nonthermal (non-Maxwellian) plasma, the results of this study are generic and may be used as basis to model energy localization in nonlinear optics, in hydrodynamics or in dispersive media with Kerr-type nonlinearities where modulational instability is relevant.
Assessment of hybrid population immunity to SARS-CoV-2 following breakthrough infections of distinct SARS-CoV-2 variants
Authors: Hartog Gerco den , Andeweg Stijn P. , Hoeve Christina , Smits Gaby , Voordouw Bettie , Eggink Dirk , Knol Mirjam J. , Binnendijk Robert S. van 
Published: June 2023

Abstract
Immunity induced by vaccination and infection, referred to as hybrid immunity, provides better protection against SARS-CoV-2 infections compared to immunity induced by vaccinations alone. To assess the development of hybrid immunity we investigated the induction of Nucleoprotein-specific antibodies in PCR-confirmed infections by Delta or Omicron in vaccinated individuals (n = 520). Eighty-two percent of the participants with a breakthrough infection reached N-seropositivity. N-seropositivity was accompanied by Spike S1 antibody boosting, and independent of vaccination status or virus variant. Following the infection relatively more antibodies to the infecting virus variant were detected. In conclusion, these data show that hybrid immunity through breakthrough infections is hallmarked by Nucleoprotein antibodies and repertoire broadening of Spike antibodies. Exposure to future SARS-CoV-2 variants may therefore continue to maintain and broaden vaccine-induced population immunity.
Revivify Modulates Healthy Gut Microbiomes and Short Chain Fatty Acids Evaluated by An In Vitro Model of Gut Microbiome Study.
Authors: Ashraf A H M Zuberi , Pantho Ahmed F , Kamal Samee , Caba Alyssa , Afroze Syeda H , Kuehl Thomas J , Hossain Liaquat , Uddin M. Nasir 
Published: June 2023

Abstract
Background. The diverse microbial community in our gastrointestinal (GI) helps in the fermentation of metabolites of Short Chain Fatty Acids (SCFAs), mainly acetate, propionate, butyrate, and small number of lactates. Acetate, propionate, and butyrate maintain colonic lining integrity and ideal colon activity. Butyrate is also known to be an energy source and assist in anti-inflammatory response. Maintaining an optimal ratio of these SCFAs reduce the risk of inflammation and promote a healthy colon. We evaluated the effect of Revivify Oral Liquid Gel (composition: US Patent 11 224 636) on gut microbiomes and SCFAs by an in vitro model of gut microbiome study. Gut microbes were cultured in 2 ml 96-well plates and treated with control, SOD, Prefibrotic fiber, Fruit juice, and Revivify gel for 48 hours followed by metaproteomic, chemical analysis (SCFA content), and microbiome profiling.
Results. We found that the amount of SCFAs increased by 2.5 folds, when treated with Revivify gel but the ratio of the SCFAs remain the same across all the treatment groups. Revivify gel promoted the growth of the Firmicutes spp., especially Lactobacillus, a probiotic organism.
Conclusions.Our study demonstrates that Revivify gel promotes a balanced increase of the SCFAs in a consistent manner, supporting a beneficial population of gut microbes for optimal gastrointestinal functionality.
Autophagy-related gene SQSTM1 predicts the prognosis of hepatocellular carcinoma
Authors: Zheng Zhiming , Xu Haijiong , Luo Lianxiang 
Published: June 2023

Abstract
Purpose: Studies have shown a clear correlation between autophagy-related genes and the development and progression of HCC. However, the mechanisms at work are not completely known. Our aim is to construct a prognostic model for HCC and to identify new molecular targets and develop effective therapies for HCC.
Methods: Using difference as well as prognostic analysis, a prognostic model was constructed based on lasso regression, and the hub gene SQSTM1 was selected based on PPI, and difference analysis, clinical analysis and drug sensitivity analysis were performed to determine whether SQSTM1 was the key gene for the induction of HCC.
Results: Finally, we built a prognostic model using 12 prognostic differential genes. We verified this model and discovered that the prediction was accurate and could be used as a standalone prognostic feature. We also discovered that SQSTM1, a crucial gene among these 12 genes, was inversely correlated with patient prognosis; this suggests that SQSTM1 may function as a separate prognostic factor. Additionally, we discovered that patients with HCC and high SQSTM1 expression are responsive to 17-AGG.
Conclusions：We developed a prognosis model based on 12 DEARGS that is predictive and may be applied to predict the prognostic mortality of HCC patients. By identifying the molecular and immunological components of our prognostic model, we were able to pinpoint potential therapeutic targets for HCC treatment. SQSTM1 is also a crucial gene for HCC therapy and for predicting the prognosis of patients. In order to treat hepatocellular cancer, 17-AGG can inhibit SQSTM1's function.
First year STEM curriculum co-created with Indigenous scientists improves intellectual growth, psychosocial factors associated with retention, and academic achievement of students from racially minoritized groups historically underrepresented in STEM.
Authors: Sprowles Amy E. , Margell Steven , Malloy Kerri J. , Hillman Lisa , Hillman L. Chook Chook , Rich Angela , Smith Jessica , Shaughnessy Frank J. , Hurst Matthew P. , Manor Sonja , Mazzag Borbala , Oliver Dale , Siering Patricia , Cashman Eileen , O'Dowd Alison P. , Goley P. Dawn , Black Gillian , Goldenberg Katlin O. , Johnson Matthew D. 
Published: June 2023

Abstract
Only 40–50% of first-year collegiate science, technology, engineering or math (STEM) students complete a Bachelor of Science degree. Persistence and graduation rates of students from racially minoritized groups that historically have been underrepresented in STEM (URG) is significantly lower. Culturally responsive programming that incorporates the values, perspectives, cultures, and the empathy and equity matters of non-majority populations can empower students from diverse backgrounds to achieve their educational goals. This paper describes the outcomes of first-year place-based learning community students who participated in a water quality laboratory that integrates the science, culture, values, and social justice concerns of the Indigenous people of the Klamath River Basin. The curriculum was designed by university faculty and Indigenous scientists from The Karuk Tribe of California. A combination of survey data and thematic analysis was used to evaluate the impact of our program on intellectual growth, gains in psychosocial factors associated with first year student success, and academic achievement. All student participants demonstrated intellectual growth and gains in psychosocial factors associated with STEM retention, but the effects were most pronounced for students who identified parallels between issues faced by Native American communities and their home community. The most significant gains in STEM retention and academic achievement occurred for URG students who learned about Native American culture through the water quality laboratory. The majority of all students expressed the importance of understanding the cultural, environmental, and/or social justice issues of Native American people to their future careers. We believe ours is one of the first studies that specifically examines the power of collaborating with contemporary Indigenous communities to create opportunities for first-year collegiate STEM students to participate in interdisciplinary, place-based curricular and co-curricular activities.
Deep Learning model-based malicious node detection system in wireless multimedia sensor Network
Authors: JOHN AROCKIA JAYADHAS SOOSAI , Roslin Emalda , Wilfred Florin 
Published: June 2023

Abstract
Wireless sensor networks (WMSNs) are becoming increasingly popular in many fields, from academia to transportation, environmental monitoring, wildlife preservation, and military espionage. Therefore, examining potential threats, power consumption, vulnerability recognition, and systemic vulnerability characteristics is essential to develop a reliable information security approach for WSNs. As a result, it is becoming increasingly crucial for the technical community to conduct intrusion recognition method evaluations. Since this is the case, using deep learning techniques in creating intrusion identification and mitigation systems for wireless multimedia sensor networks is essential. This article examines how well different machine learning and deep learning algorithms perform in attack identification systems. Testing the efficacy of different methods on the WMSN-DS database through experimentation is essential. In this work, we combine the power of a Convolutional Neural Network classifier with a Random forest. In order to accomplish this, a Convolutional Neural Network with a Random Forest Classifier is used. The intrusion detection system (IDS) is a crucial technique proposed in this study for WMSN. To address this issue, the current study proposal uses deep Learning with a Random Forest classifier to detect and prevent attacks and to promote efficient forwarding in WMSNs. Multiple WMSN assaults have been investigated, and the results of these investigations have been critically evaluated.
Activation of transsulfuration pathway to maintain cysteine is a thermogenic checkpoint for the conservation of energy
Authors: Dixit Vishwa , Lee Aileen , Sugiura Yuki , Youm Yun-Hee , Dlugos Tamara , Maeda Rae , Coman Daniel , Spadaro Olga , Sidorov Sviatoslav , Shcukina Irina , Andhey Prabhakar Sairam , Smith Steven , Ravussin Eric , Hyder Fahmeed , Artyomov Maxim 
Published: June 2023

Abstract
The authors have requested that this preprint be removed from Research Square.
Urinary protein changes during the short-term growth and development of rats
Authors: Liu Yuqing , Yang Minhui , Wang Haitong , Chen Yuzhen , Gao Youhe 
Published: June 2023

Abstract
Can the urine proteome reflect short-term changes in the growth and development of animals? Do short-term developmental effects on urinary protein need to be considered when performing urine marker studies using model animals with faster growing periods? In this study, urine samples were collected from 10 Wistar rats aged 6–8 weeks 3 and 6 days apart. The results showed that the urine proteome could sensitively reflect short-term growth and development in rats. For example, comparing the urine proteome of Day 0 and Day 6, 195 differential proteins were identified after screening (FC ≥ 1.5 or ≤ 0.67, P < 0.05), and verified by randomization, the average number of randomly generated differential proteins was 17.99. At least 90.77% of the differential proteins were not randomly generated. This finding demonstrates that the differential proteins identified in the samples collected at different time points were not randomly generated. A large number of biological processes and pathways related to growth and development were enriched, which shows that the urine proteome reflects the short-term growth and development of rats, and provides a means for in-depth and meticulous study of growth and development. Moreover, an interfering factor in animal experiments using 6- to 8-week-old rats to construct models was identified. The results of this study demonstrated that there were differences in the urinary proteome in rats aged 6–8 weeks only 3–6 days apart, which suggests that the sensitivity of urinary proteomics is high and shows the sensitive and precise response of the urinary proteome to body changes.
Electric properties of the magnetopause boundary layer
Authors: Gao Lai , Shen Chao , Ji Yong , Zhou Yufei 
Published: June 2023

Abstract
The magnetopause plays a pivotal role in the coupling between solar wind and the magnetosphere. By analysing magnetopause crossing events by Magnetospheric Multiscale mission, we reveal a local non-neutrality of electric charges and the associated electric field in the magnetopause boundary layer. There are two types of electric structures. In one group that typically occurs on the dusk-side, the electric field is directed towards the Earth. In the other structure that occurs on the whole dayside, the field is directed away from the Earth. The spatial extent of this electric non-neutrality spans approximately 600 km, which is at the scale of ion gyrational motion. These findings provide valuable insights into the fine structures of the magnetopause and the coupling between solar wind and the magnetosphere.
Machine learning identifies right index finger tenderness as key signal of DAS28- CRP based psoriatic arthritis activity
Authors: Rischke Samuel , Poor Sorwe Mojtahed , Gurke Robert , Hahnefeld Lisa , Köhm Michaela , Ultsch Alfred , Geisslinger Gerd , Behrens Frank , Lötsch Jörn 
Published: June 2023

Abstract
Background
Psoriatic arthritis (PsA) is a chronic inflammatory systemic disease that is often categorized based on the Disease Activity Score 28 (DAS-28 CRP). However, since DAS28-CRP was originally designed for rheumatoid arthritis, it may not perfectly reflect PsA, and periodic re-evaluation has been recommended.
Methods
A cohort of 80 PsA patients (44 women and 36 men, aged 56.3 ± 12 years) with a range of disease activity from remission to moderate was analyzed using unsupervised and supervised methods applied to the DAS28-CRP components.
Results
Machine learning-based permutation importance identified tenderness in the metacarpophalangeal joint of the right index finger as the most informative item for PsA activity staging. This symptom alone allowed a random forest classifier to identify PsA remission with 67% balanced accuracy in new cases. Projection of the DAS28-CRP data onto an emergent self-organizing map of artificial neurons identified outliers, who following enhancement of group sizes by generative artificial intelligence (AI) could be defined as subgroups particularly characterized by either joint tenderness or swelling.
Conclusions
AI-assisted re-evaluation of the DAS28-CRP for PsA has narrowed the score items to a most relevant symptom, and generative AI has been useful for identifying and characterizing small subgroups of patients whose symptom patterns differ from the majority. These findings represent an important step toward precision medicine that can address outliers.
The retinoblastoma-related gene RBL901 can trigger drought response actions in potato
Authors: Sołtys-Kalina Dorota , Macko-Podgórni Alicja , Plich Jarosław , Boguszewska-Mańkowska Dominika , Szajko Katarzyna , Smyda-Dajmund Paulina , Grzebelus Dariusz , Marczewski Waldemar 
Published: June 2023

Abstract
The cultivated potato (Solanum tuberosum L.) is one of the most important crops in the world. It is estimated that, globally, over the next few decades, drought will decrease potential potato yields and quality, which are the main determinants of potato tolerance to drought stress. Potato plants are sensitive to drought stress, although cultivar-dependent variability in the response to water deficiency has been observed (Nasir and Toth 2022). Photosynthesis in leaves provides the supplies needed for biomass accumulation, whereas potato tubers are strong sink organs. Understanding the biological basis of decreases in potato tuber yields and quality in response to water shortage, considering the responses of leaves, is a serious agronomic challenge (Boguszewska-Mańkowska et al. 2020).