bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning and single cell RNA sequencing analysis identifies regeneration-related hepatocytes and highlights a Birc5-related model for identifying cell proliferative ability
Authors: Du Yuan , Jian Shuqin , Wang Xicheng , Shi Jun , li janfong 
Published: April 2023

Abstract
Background
Partial hepatectomy (PHx) has been shown to induce rapid regeneration of adult liver under emergency conditions. Therefore, an in-depth investigation of the underlying mechanisms that govern liver regeneration following PHx is crucial for a comprehensive understanding of this process.
Method
We analyzed scRNA-seq data from liver samples of normal and PHx-48-hour mice and identified a population of highly proliferative hepatocytes 48 hours after hepatectomy. Seven machine learning algorithms were utilized to screen and validate a gene signature that accurately identifies and predicts this population. We also used co-immunostaining of zonal markers with BIRC5 to investigate regional characteristics of hepatocytes post-PHx.
Results
Single cell sequencing results revealed a population of regeneration-related hepatocytes. Of note, transcription factor analysis emphasized the importance of Hmgb1 transcription factor in liver regeneration. HdWGCNA and machine learning algorithm screened and obtained the key signature characterizing this population, including a total of 17 genes, most of which have been confirmed to be related to liver regeneration, and the function enrichment analysis indicated their high correlation with cell cycle pathway. Furthermore, we found that the spatial characteristics of hepatocytes gradually weakened during regeneration and immunostaining further revealed that those hepatocytes with active proliferative ability primarily initiate in the midlobular zone and then repopulated peripheral region. It is note-worthy that we inferred that Hmgb1 might be vital in the regeneration-related hepatocytes of PHx_48h group. Parallelly, Birc5 might be closely related to the regulation of liver regeneration, and positively correlated with Hmgb1 while negatively correlated with portal vein and central vein characteristics.
Conclusions
Our study has identified a distinct population of hepatocytes that are closely associated with liver regeneration. Through machine learning algorithms, we have identified a set of 17 genes that are highly indicative of the regenerative capacity of hepatocytes. This gene signature has enabled us to assess the proliferation ability of in vitro cultured hepatocytes using sequencing data alone. Furthermore, our findings suggest that Birc5 may play a crucial role in regulating the proliferative potential of hepatocytes.
Systematic review of randomized clinical trials testing a pharmacological treatment in adults with autism spectrum disorder
Authors: Miguel Alicia Pérez , Moreno Mª Luisa Sánchez de Ocaña , Peiró Ana María Peiró , Gisbert Laura , Lugo-Marín Jorge , Martínez-Cayuelas Elena , Ballester Pura 
Published: April 2023

Abstract

Introduction: Autism Spectrum Disorder (ASD) affects 1 in 68 newborns. ASD is a neurodevelopmental condition characterized by deficits in social interaction, communication, and presence of restricted and repetitive interests. Despite this high prevalence and burden, there is no approved treatment for ASD’ core symptoms. Objective: This systematic review, using a rigorous methodological design, attempts to collect all clinical trials in adults with ASD have been published.
Methods: To ensure the retrieval of a maximum of articles, the systematic review used the databases Medline and Scopus. Retrieved manuscripts were evaluated reading the title, keywords, and abstract. CONSORT guidelines were used to evaluate the quality of included manuscripts (0-100% scale).
Results: A total of 17/86 (20%) clinical trials were selected with an average score of 70% in CONSORT. In general, sample sizes were low, ranged from 30 (single-center studies) to 115 participants (multiple inclusion sites), and an average age of 27 years-old. Pharmacological treatments studied were for improving a) social interaction and attachment (propranolol, oxytocin); b) cognitive abilities (cannabidiol); c) behavior (naltrexone, vasopressin V1a antagonists, dextromethorphan, quinidine, agomelatine, and citalopram); d) facial expression and emotion recognition (citalopram oxytocin, and V1a receptor antagonist).
Conclusion: regardless the methodological quality, there are few studies in this field with a low number of participants. Furthermore, different designs and measures to assess efficacy are used, and that avoids comparisons between them. Therefore, it is necessary to raise awareness in this field, and increase the number of clinical trials in the future with long-term side-effect monitoring.
Image based prognosis in head and neck cancer using convolutional neural networks: a case study in reproducibility and optimization
Authors: Mateus Pedro , Volmer Leroy , Wee Leonard , Aerts Hugo J.W.L. , Hoebers Frank , Dekker Andre , Bermejo Inigo 
Published: April 2023

Abstract
In the past decade, there has been a sharp increase in publications describing applications of convolutional neural networks (CNNs) in medical image analysis. However, recent reviews have warned of the lack of reproducibility of most such studies, which has impeded closer examination of the models and, in turn, their implementation in healthcare. On the other hand, the performance of these models is highly dependent on decisions on architecture and image pre-processing.
In this work, we assess the reproducibility of three studies that use CNNs for head and neck cancer (HNC) outcome prediction by attempting to reproduce the published results. In addition, we propose a new network structure and assess the impact of image pre-processing and model selection criteria on performance. We used two publicly available datasets: one with 298 patients for training and validation and another with 137 patients from a different institute for testing.
All three studies failed to report elements required to reproduce their results thoroughly, mainly the image pre-processing steps and the random seed. Our model either outperforms or achieves similar performance to the existing models with considerably fewer parameters. We also observed that the pre-processing efforts significantly impact the model's performance and that some model selection criteria may lead to suboptimal models. Although there have been improvements in the reproducibility of deep learning models, our work suggests that wider implementation of reporting standards is required to avoid a reproducibility crisis.
Sequential Antigen-loss and Branching Evolution in Lymphoma after Anti-CD19 and Anti-CD20 Targeted T Cell Redirecting Immunotherapy
Authors: Rasche Leo , Duell Johannes , Leipold Alexander , Appenzeller Silke , Fuhr Viktoria , Rauert-Wunderlich Hilka , Vià Matteo Claudio Da , Dietrich Oliver , Toussaint Christophe , Imdahl Fabian , Eisele Florian , Grundheber Lars , Einsele Hermann , Rosenwald Andreas , Topp Max S , Saliba Antoine-Emmanuel 
Published: April 2023

Abstract
CD19 CAR T cells and CD20 targeting T cell engaging bispecific antibodies have been approved in B-cell Non-Hodgkin lymphoma lately, heralding a new clinical setting where patients are treated with both approaches, sequentially. The aim of our study was to investigate the selective pressure of CD19 and CD20 directed therapy on the clonal architecture in lymphoma. Using a broad analytical pipeline, we identified truncating mutations in the gene encoding CD20 conferring antigen loss in 80% of patients relapsing from CD20 bispecs. Pronounced T cell exhaustion was identified in cases with progressive disease and retained CD20 expression. We also confirmed CD19 loss after CAR T cell therapy and report the case of sequential CD19 and CD20 loss. We observed branching evolution with re-emergence of CD20-positive subclones at later time points and spatial heterogeneity for CD20 expression in response to targeted therapy. Our results highlight immunotherapy as an evolutionary bottleneck selecting for antigen-loss variants but also complex evolutionary pathways underlying disease progression from these novel therapies.
Ascending motion of bottom-blown bubbles in vertical channels
Authors: Bowen Li , Jinyi Zhao , Zhenrong Liu , Chengjun Gao , Yuwei Hu , Rong Chen 
Published: April 2023

Abstract
The gas-liquid two-phase flow is widely applied in engineering. Studying the bubble movement in the liquid phase is valuable for achieving efficient operation of relevant reactors. In this study, the ascending morphology of single-pore bubbles and double-pore bubbles in liquids was photographed by building a visualization experimental setup. Together with MATLAB, the effects of different variables on the ascending of bottom-blown bubbles were analyzed. Experimental results showed the bubble departure diameter was enlarged with the increase of pore inner diameter. At larger pore inner diameter, the bubble orbits were more disorderly, and the ultimate bubble velocity was smaller. At larger gas flow rate, the orbit of single bubbles was closer to a straight line, and the disturbance of double bubbles was intensified, leading to coalescence. The ultimate bubble velocity in water was accelerated with the increase of gas flow rate, and when the number of pores changed, the flow rate was more influential than the pore inner diameter on the ultimate bubble velocity. The centroid orbits of single bubbles were not significantly different between the two liquid-phase conditions, but the swinging amplitude of double bubbles in water was smaller than that in the 0.75% NaCl solution. The horizontal velocities were not significantly different, but the first velocity and ultimate velocity of bubbles at the vertical level in the 0.75% NaCl solution were both larger than those in water. These findings offer basic data for research on bubble strengthening and blending effects in vertical channels.
Correlation Between Renal Artery Doppler Indices and Renal Function Test in Young Adult Hypertension
Authors: Ali Marzoug Ahmed , Abdelrahim Ahmed , Hussein Abdulaziz 
Published: April 2023

Abstract
Background: Hypertension is a chronic elevation in blood pressure (BP) 140/90. It is subjected to various disorders which produce alteration in the morphology and function of kidneys with renal artery blood flow. Doppler ultrasound (US) of the renal artery is sensitive for evaluating the kidneys and provides the accurate diagnosis of early kidneys function, morphology, and blood flow effect. This study aimed to determine whether there was a correlation between renal artery Doppler indices and renal function tests in young adult hypertension.
Methods: A total of 100 patients with hypertension were examined using the Doppler ultrasonography for renal artery and renal function tests. Measurements of the renal artery Doppler indices and renal function tests were performed on adult hypertension patients.
Results: There was a significant negative correlation between end-diastolic velocity (EDV) in the right kidney with urea -.33, P-value= 0.001 and creatinine -.26, P-value=0.008 also a significant negative correlation between end-diastolic velocity (EDV) in the left kidney with urea -.49, P-value= 0.000 and creatinine -.43, P-value=0.000. Significant positive correlation between resistive index (RI) in right kidney with urea +.37, P-value=000, and creatinine=.38, P-value=000 also Significant positive correlations between pulsatile index (PI) in right kidney with urea +.32, P-value=000 and creatinine=.42, P-value=000. Significant positive correlation between resistive index (RI) in left kidney with urea +.64, P-value=00,0, and creatinine+.60, P-value=000 also Significant positive correlations between pulsatile index (PI) in left kidney with urea +.45, P-value=000 and creatinine+.57, P-value=000.
Conclusion: Individuals with hypertension have reduced blood flow at an end-diastolic velocity (EDV) correlated with increase urea and creatinine also increase blood flow resistance at resistive index (RI) and pulsatile index (PI) correlated with increase urea and creatinine.
Synthesis of Polyethylenes with In-Chain Isolated Carbonyls from CO2 and Ethylene
Authors: Zhou Fulin , Dai HaoJie , Tang Shan , Zhou Yongfeng 
Published: April 2023

Abstract
Aiming at accessing polyethylenes bearing in-chain degradable functionality, copolymerization of carbon dioxide (CO2) with ethylene has long been recognized as a significant but highly challenging transformation. Nevertheless, most trials resulted in ethylene homopolymerization because of the endothermic property and high energy barriers of CO2 insertion during polymer chain propagation. Here we report an unprecedented protocol synthesis of polyethylenes with low content carbonyls from CO2 and ethylene by the combination of photocatalytic CO2 reduction and palladium catalyzed coordination/insertion polymerization. The introduction of photocatalytic systems provides an easy way to tune the carbonyl content and insertion selectivity of the polyethylene copolymers. Significantly, excellent selectivity (up to >99%) for incorporating isolated carbonyls in the main polymer chain has been achieved, which allows the copolymers to retain the properties of polyethylene but makes them photodegradable.
Detailed profiling with MaChIAto reveals various genomic and epigenomic features affecting the efficacy of knock-out, short homology-based knock-in and Prime Editing.
Authors: Nakamae Kazuki , Takenaga Mitsumasa , Nakade Shota , Awazu Akinori , Sakamoto Naoaki , Yamamoto Takashi , Sakuma Tetsushi 
Published: April 2023

Abstract
Highly efficient gene knock-out and knock-in have been achieved by harnessing CRISPR-Cas9 and its advanced technologies such asPrime Editor. In addition, various bioinformatics resources have become available to quantify and qualify the efficiency and accuracy of CRISPR edits, which significantly increased the user-friendliness of the general next-generation sequencing (NGS) analysis in the context of genome editing. However, there is no specialized and integrated software for investigating the preference in the genomic context involved in the efficiency and accuracy of genome editing using CRISPR-Cas9 and beyond. Here, we address this issue by establishing a novel analysis platform of NGS data for profiling the outcome of template-free knock-out and short homology-based editing, named MaChIAto (Microhomology-associated Chromosomal Integration/editing Analysis tools)
Identification and validation of a prognostic Risk-Scoring Model based on LATS2 expression in acute myeloid leukemia
Authors: Liu Bin , Zhang Jian , Wang Jing , Wang Qian , Liu Xiaoman , Sun Hui 
Published: April 2023

Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by the accumulation of immature myeloid precursors with resultant peripheral blood cytopenias. We obtained gene expression profiles and corresponding clinical information of AML cases from the TCGA (TCGA-LAML), GEO (GSE108266), and GEO (GSE71014) databases. We analyzed the LATS2 expression using our collected 13 bone marrow specimens and a GEO cohort, confirmed the higher LATS2 expression. AML patients could be grouped into LATS2 high- and low-expression groups, and low-expression patients showed better survival than high-expression patients. Based on the LATS2 expression, a prognostic risk-scoring model containing seven signature genes, including POU3F1, RPGR, PTP4A3, SOCS1, FAM83G, GREB1 and COL2A1, were developed. According to the risk score, patients were divided into High- and Low-risk groups. In the training set, area under the curve values of 1, 3, and 5 years were 0.876, 0.877 and 0.937, respectively, which indicates a good predictive efficacy. In the test group, area under the curve values of 1, 3, and 5 years were 0.974, 0.878 and 0.976. In an external GEO (GSE71014) dataset, we validate that the low-risk group was also significantly better prognostic outcomes, area under the curve values of 1, 3, and 5 years were 0.847, 0.857 and 0.822 respectively.
Audience Perception and Cognition towards Moving Images: Review of Short Film Delirium
Authors: RV Shynu , R.D Sambath , Pandey Lalita 
Published: April 2023

Abstract
This short paper discusses the creator's video project Delirium recorded in India. The video aims to explore the viewer's perception and cognition towards this moving image. Also, the genre was designed in the realm of psychology to explore both complex parts of storytelling and viewers' point of narration. This short film examines the efficiency of storytelling to attain the audience's attention engagement level. The film experimented with questioning the law of physics related to time throughout the film. The film developed with several visual aspects and audios for the same. The results of the study show that the film concept was very effective in maintaining their curiosity. Viewer's perceptions and cognition are essential to explore and understand how moving images engage them as entertainment media. This study suggests the scope of extending the investigation towards the motion picture parameters such as visual and audio in a larger format. We identified that more than 48% of our participants attended physical objects screened in the movie while 28% of participants perceived and recalled more subjective quality of the film (the facial expression of the character, the rhythm of the scene, and syncing of music with visuals, connotative meaning of the plot including the lighting). We recommend further investigation in larger film format on perception and cognition for the research domain like age and gender categories. We anticipate that our research methodology would aid in understanding how cinema affects the viewer and in designing a film to have a more excellent visual experience.
Salt corrections for RNA secondary structures in the ViennaRNA package
Authors: Yao Hua-Ting , Lorenz Ronny , Hofacker Ivo L. , Stadler Peter F. 
Published: April 2023

Abstract
Background RNA features a highly negatively charged phosphate backbone that attracts a of cloud counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled by currently available secondary stucture prediction algorithms. Combining Debye-Hückel potentials for line charges and Manning's counter-ion condensation theory, Einert et al. [Biophys. J. 100: 2745-2753 (2011)] modeled the energetic effects contributions monovalent cations on loops and helices.
Results The model of Einert et al. is adapted to match the structure of the dynamic programming recursion of RNA secondary structure prediction algorithms. An empirical term describing the dependence salt dependence of the duplex initiation energy is added to improve co-folding predictions for two or more RNA strands. The slightly modified model is implemented in the ViennaRNA package in such way that only the energy parameters but not the algorithmic structure is affected. A comparison with data from the literature show that predicted free energies and melting temperatures are in reasonable agreement with experiments.
Conclusion The new feature in the ViennaRNA package makes it possible to study effects of salt concentrations on RNA folding in a systematic manner. Strictly speaking, the model pertains only to mono-valent cations, and thus covers the most important parameter, i.e., the NaCl concentration. It remains a question for future research to what extent unspecific effects of bi- and tri-valent cations can be approximated in a similar manner.
Availability: Corrections for the concentration of monovalent cations are available in the ViennaRNA package starting from version 2.6.0.
The inhibition performance of a novel iron (III), copper (II), and nickel (II) complexes with Schiff base ligand derived from salicylaldehyde and p–phenylene diamine on Polyvinyl chloride photodegradation
Authors: Mohamed E. A. , Negm N. A. , Youssef A. O. , Sayed G. H. 
Published: April 2023

Abstract
The stabilization of polyvinyl chloride polymer has a great concern for researchers due to its high instability in the environmental conditions of heat and ultraviolet arrays. Herein, three metal complexes of Schiff base ligand were prepared and their chemical structures were confirmed using elemental analysis, FTIR, 1H-NMR, and UV/Vis spectra. The prepared metal complexes were incorporated in PVC as photo-stabilizers. Only 0.5% by weight of these prepared Schiff bases metal complexes was blended with the PVC polymer to form films with a width of (50 µm). The prepared samples were exposed to ultraviolet irradiation time was varied ranging from 0 to 300 h and the impact of irradiation scheduled upon the PVC stabilization was examined each 50 h. The degree of degradation of PVC in the presence and absence of the different stabilizers was determined using various techniques, including the degree of oxygenated compounds formed, degree of unsaturation, viscosity, and degree of deterioration. The results showed that in the native PVC, the degradation progressively increased over time at the conditions of the experiments. The addition of the stabilizers decreased the degradation considerably. The formation of carbonyl, hydroxyl, and unsaturated intermediates was decreased in the presence of Cu-L, and Ni-L. While Fe-L stabilizer showed weak efficiency. The reasons for the stabilization and the mechanism of the degradation/stabilization processes were discussed based on the electronegativity of the metal ions and the antioxidant activities of the different metal complexes.
Interstate Trade Exacerbates Agricultural Pollution in Food Bowls of India
Authors: Goyal Shekhar Sharan , Dave Raviraj , Kumar Rohini , Bhatia Udit 
Published: April 2023

Abstract
Maintaining food surplus for growing populace while reducing agriculture’s environmental impact poses significant challenge. Intensive agricultural practices fueled green revolutions in nations, which helped them achieve self-sufficiency. However, the fertilizer-intensive agricultural practices and exploitative trade systems eventually created a legacy of unsustainable agrarian systems. To understand the environmental consequences of the national cereal trade, we map Nitrogen, Phosphorous, and Potassium transferred through interstate wheat and rice trade in India over the decade. We quantify the fate of leftover nutrient surplus across the traded network. Nation’s food bowls, while contributing significantly towards national food demand, are becoming pollution-rich by sustaining 1.19 TgNyr-1, and 0.35 TgPyr-1 surplus that accounts for 61% of total surplus arising from trade transfer, indicating a growing disparity in agricultural nutrient budget. Given India’s role in global food security, identifying the nation’s environmental vulnerability can help to design appropriate policy interventions for sustainable development.