bluuebunny/crossref_metadata_2025_split huggingface dataset:
An overview of mouse models of hepatocellular carcinoma
Authors: Zheng Hua-chuan , Xue Hang , Yun Wen-Jing 
Published: September 2023

AbstractHepatocellular carcinoma (HCC) has become a severe burden on global health due to its high morbidity and mortality rates. However, effective treatments for HCC are limited. The lack of suitable preclinical models may contribute to a major failure of drug development for HCC. Here, we overview several well-established mouse models of HCC, including genetically engineered mice, chemically-induced models, implantation models, and humanized mice. Immunotherapy studies of HCC have been a hot topic. Therefore, we will introduce the application of mouse models of HCC in immunotherapy. This is followed by a discussion of some other models of HCC-related liver diseases, including non-alcoholic fatty liver disease (NAFLD), hepatitis B and C virus infection, and liver fibrosis and cirrhosis. Together these provide researchers with a current overview of the mouse models of HCC and assist in the application of appropriate models for their research.
Total network controllability analysis discovers explainable drugs for Covid-19 treatment
Authors: Wei Xinru , Pan Chunyu , Zhang Xizhe , Zhang Weixiong 
Published: September 2023

Abstract
Background
The active pursuit of network medicine for drug repurposing, particularly for combating Covid-19, has stimulated interest in the concept of structural controllability in cellular networks. We sought to extend this theory, focusing on the defense rather than control of the cell against viral infections. Accordingly, we extended structural controllability to total structural controllability and introduced the concept of control hubs. Perturbing any control hub may render the cell uncontrollable by exogenous stimuli like viral infections, so control hubs are ideal drug targets.

Results
We developed an efficient algorithm to identify all control hubs, applying it to a largest homogeneous network of human protein interactions, including interactions between human and SARS-CoV-2 proteins. Our method recognized 65 druggable control hubs with enriched antiviral functions. Utilizing these hubs, we categorized potential drugs into four groups: antiviral and anti-inflammatory agents, drugs acting on the central nervous system, dietary supplements, and compounds enhancing immunity. An exemplification of our approach’s effectiveness, Fostamatinib, a drug initially developed for chronic immune thrombocytopenia, is now in clinical trials for treating Covid-19. Preclinical trial data demonstrated that Fostamatinib could reduce mortality rates, ICU stay length, and disease severity in Covid-19 patients.

Conclusions
Our findings confirm the efficacy of our novel strategy that leverages control hubs as drug targets. This approach provides insights into the molecular mechanisms of potential therapeutics for Covid-19, making it a valuable tool for interpretable drug discovery. Our new approach is general and applicable to repurposing drugs for other diseases.
Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia
Authors: Gofton Alexander William , Popa-Baez Angel , Takano Ai , Soennichsen Kari , Michie Michelle , Short Makenna , Supriyono Supriyono , Pascoe Jack , Cusbert Sue , Mulley Robert 
Published: September 2023

Abstract
Background
Borrelia are important disease-causing tick- and louse-borne spirochaetes than can infect a wide variety of vertebrates, including humans and reptiles. Reptile-associated (REP) Borrelia, once considered a peculiarity, are now recognised as a distinct and important evolutionary lineage, and are increasingly being discovered worldwide in association with novel hosts. Numerous novel Borrelia spp. associated with monitor lizards (Varanus spp.) have been recently identified throughout the Indo-Pacific region; however, there is a lack of genomic data on these Borrelia.

Methods
We used metagenomic techniques to sequence almost complete genomes of novel Borrelia spp. from Varanus varius and Varanus giganteus from Australia, and used long- and short-read technologies to sequence the complete genomes of two strains of a novel Borrelia sp. previously isolated from ticks infesting Varanus salvator from Indonesia. We investigated intra- and interspecies genomic diversity, including plasmid diversity and relatedness, among Varanus-associated Borrelia and other available REP Borrelia and, based on 712 whole genome orthologues, produced the most complete phylogenetic analysis, to the best of our knowledge, of REP Borrelia to date.

Results
The genomic architecture of Varanus-associated Borrelia spp. is similar to that of Borrelia spp. that cause relapsing fever (RF), and includes a highly conserved megaplasmid and numerous smaller linear and circular plasmids that lack structural consistency between species. Analysis of PF32 and PF57/62 plasmid partitioning genes indicated that REP Borrelia plasmids fall into at least six distinct plasmid families, some of which are related to previously defined Borrelia plasmid families, whereas the others appear to be unique. REP Borrelia contain immunogenic variable major proteins that are homologous to those found in Borrelia spp. that cause RF, although they are limited in copy number and variability and have low sequence identities to RF variable major proteins. Phylogenetic analyses based on single marker genes and 712 single copy orthologs also definitively demonstrated the monophyly of REP Borrelia as a unique lineage.

Conclusions
In this work we present four new genomes from three novel Borrelia, and thus double the number of REP Borrelia genomes publicly available. The genomic characterisation of these Borrelia clearly demonstrates their distinctiveness as species, and we propose the names Borrelia salvatorii, ‘Candidatus Borrelia undatumii’, and ‘Candidatus Borrelia rubricentralis’ for them.

Graphical Abstract
Integrated transcriptomic and proteomic analyses of plerocercoid and adult Spirometra mansoni reveal potential important pathways in the development of the medical tapeworm
Authors: Wang Rui Jie , Li Wen , Liu Shi Nan , Wang Si Yao , Jiang Peng , Wang Zhong Quan , Zhang Xi 
Published: September 2023

Abstract
Background
Spirometra mansoni can parasitize animals and humans through food and water, causing parasitic zoonosis. Knowledge of the developmental process of S. mansoni is crucial for effective treatment; thus, it is important to characterize differential and specific proteins and pathways associated with parasite development.

Methods
In this study, we performed a comparative proteomic analysis of the plerocercoid and adult stages using a tandem mass tag-based quantitative proteomic approach. Additionally, integrated transcriptomic and proteomic analyses were conducted to obtain the full protein expression profiles of different life cycle stages of the tapeworm.

Results
Approximately 1166 differentially expressed proteins (DEPs) were identified in adults versus plerocercoids, of which 641 DEPs were upregulated and 525 were downregulated. Gene Ontology (GO), Clusters of Orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most DEPs related to genetic information processing and metabolism of energy in adults seem to be more activated. In the plerocercoid stage, compared to metabolism, genetic information processing appears more dynamic. Protein-protein interaction (PPI) revealed six key proteins (phosphomannomutase, glutathione transferase, malate dehydrogenase, cytoplasmic, 40S ribosomal protein S15, ribosomal protein L15 and 60S acidic ribosomal protein P2) that may play active roles in the growth and development of S. mansoni. Finally, the combination of transcriptomic and proteomic data suggested that three pathways (ubiquitin-mediated proteolysis, phagosome and spliceosome) and five proteins closely related to these pathways might have a significant influence in S. mansoni.

Conclusions
These findings contribute to increasing the knowledge on the protein expression profiles of S. mansoni and provide new insights into functional studies on the molecular mechanisms of the neglected medical tapeworm.

Graphical Abstract
Differential sensitivity of the 2020 revised comprehensive diagnostic criteria and the 2019 ACR/EULAR classification criteria across IgG4-related disease phenotypes: results from a Norwegian cohort
Authors: Vikse Jens , Midtvedt Øyvind , Fevang Bjørg-Tilde Svanes , Garen Torhild , Palm Øyvind , Wallenius Marianne , Bakland Gunnstein , Norheim Katrine Brække , Molberg Øyvind , Hoffmann-Vold Anna-Maria 
Published: September 2023

Abstract
Background
We investigated sensitivity of the 2020 Revised Comprehensive Diagnostic Criteria (RCD) and the 2019 ACR/EULAR classification criteria across the four identified IgG4-related disease (IgG4-RD) phenotypes: “Pancreato-Hepato-Biliary”, “Retroperitoneum and Aorta”, “Head and Neck-limited” and “Mikulicz’ and Systemic” in a well-characterized patient cohort.

Methods
We included adult patients diagnosed with IgG4-RD after comprehensive clinical assessment at Oslo University Hospital in Norway. We assigned patients to IgG4-RD phenotypes based on pattern of organ involvement and assessed fulfillment of RCD and 2019 ACR/EULAR classification criteria. Differences between phenotype groups were analyzed using one-way ANOVA for continuous variables, and contingency tables for categorical variables.

Results
The study cohort included 79 IgG4-RD patients assigned to the “Pancreato-Hepato-Biliary” (22.8%), Retroperitoneum and Aorta” (22.8%) “Head and Neck-limited” (29.1%), and “Mikulicz’ and Systemic” (25.3%) phenotype groups, respectively. While 7﻿2/79 (91.1%) patients in total fulfilled the RCD, proportion differed across phenotype groups and was lowest in the “Retroperitoneum and Aorta” group (﻿66.7%, p < 0.001). Among the 57 (72.2%) patients meeting the 2019 ACR/EULAR classification criteria, proportion was again lowest in the “Retroperitoneum and Aorta” group (27.8%, p < 0.001).

Conclusion
The results from this study indicate that IgG4-RD patients having the “Retroperitoneum and Aorta” phenotype less often fulfill diagnostic criteria and classification criteria than patients with other IgG4-RD phenotypes. Accordingly, this phenotype is at risk of being systematically selected against in observational studies and randomized clinical trials, with potential implications for patients, caregivers and future definitions of IgG4-RD.
Learning domain-heterogeneous speaker recognition systems with personalized continual federated learning
Authors: Chen Zhiyong , Xu Shugong 
Published: September 2023

AbstractSpeaker recognition, the process of automatically identifying a speaker based on individual characteristics in speech signals, presents significant challenges when addressing heterogeneous-domain conditions. Federated learning, a recent development in machine learning methods, has gained traction in privacy-sensitive tasks, such as personal voice assistants in home environments. However, its application in heterogeneous multi-domain scenarios for enhancing system customization remains underexplored. In this paper, we propose the utilization of federated learning in heterogeneous situations to enable adaptation across multiple domains. We also introduce a personalized federated learning algorithm designed to effectively leverage limited domain data, resulting in improved learning outcomes. Furthermore, we present a strategy for implementing the federated learning algorithm in practical, real-world continual learning scenarios, demonstrating promising results. The proposed federated learning method exhibits superior performance across a range of synthesized complex conditions and continual learning settings, compared to conventional training methods.
RETRACTED ARTICLE: Application of deep learning in Mandarin Chinese lip-reading recognition
Authors: Xing Guangxin , Han Lingkun , Zheng Yelong , Zhao Meirong 
Published: September 2023

AbstractLip-reading is an emerging technology in recent years, and it can be applied to the field of language recovery, criminal investigation, identity authentication, etc. We aim to recognize what the speaker is saying without audio but only video. Because of the different mouth shapes and the influence of homophones, the current Mandarin Chinese lip-reading network is proposed, an end-to-end model based on long short-term memory (LSTM) encoder-decoder architecture. The model incorporates the LSTM encoder-decode architecture, the spatiotemporal convolutional neural network (STCNN), Word2Vec, and the Attention model. The STCNN captures continuously encoded motion information, Word2Vec converts words into word vectors for feature encoding, and the Attention model assigns weights to the target words. Based on the video dataset we built, we completed training and testing. Experiments have proved that the accuracy of the Mandarin Chinese lip-reading model is about 72%. Therefore, MCLRN can be used to identify the words spoken by the speaker.
Energy efficient resource allocation for re-configurable intelligent surface-assisted wireless networks
Authors: Bidabadi Samaneh , Ahmed Ouameur Messaoud , Bagaa Miloud , Massicotte Daniel 
Published: September 2023

AbstractThis paper focuses on energy-efficient resource allocation in reconfigurable intelligent surface (RIS)-assisted multiple-input-single-output (MISO) communication systems. Specifically, it revisits the solution to the energy efficiency (EE) problem using the alternating optimization (AO) approach. In each AO iteration, the RIS phase optimization is achieved using the gradient descent method, which unfortunately does not guarantee convergence. To overcome this limitation, we propose two alternatives: the Wolfe-based gradient-descent (GAW) EE maximization Algorithm and the trust region (TR)-based EE maximization algorithm. Additionally, we use Dinkelbach’s algorithm to obtain the optimal transmit power allocation. Our results demonstrate that the proposed methods outperform the existing approach that uses sequential fractional programming (SFP) for phase optimization and the traditional relay-based method.
Guilty or not guilty by reason of insanity? a comparative study of murderers referred for psychiatric examination by court order
Authors: Antar Anat Yaron 
Published: September 2023

AbstractBackgroundSome murders are committed under the influence of a psychotic state resulting from a mental disorder, mainly schizophrenia. According to the law in many countries, people with mental disorders do not have criminal responsibility. They are defined as not guilty due to insanity (insanity defense) and therefore cannot be punished. In Israel, in recent years, more lawyers are requesting psychiatric opinions for the murder defendants they represent. This study aims to explore the differences between two groups of murderers: individuals who committed murder and were found not guilty by reason of insanity (NGRI) and individuals who committed murder and were found responsible and guilty. The comparison is made from a broad perspective by examining sociodemographic factors and psychiatric factors as well as criminological and forensic factors.MethodsThis study, conducted in Israel, analyzes the sociodemographic and forensic differences between 72 individuals who committed murder and were found not guilty by reason of insanity (NGRI) and 56 individuals who committed murder and were found responsible for their actions and fit to stand trial (guilty).ResultsThe findings show that NGRI participants were more likely to be from central areas, to be Jewish (rather than Arab), to be diagnosed with schizophrenia and have a background of hospitalizations before committing the murder, to have remained at the murder scene and/or called for help, and to be less likely to have committed the murder with a partner.ConclusionsThe study’s findings are explained and the limitations discussed. The findings add to the existing knowledge base about murder by reason of insanity and the differences between NGRI and criminal murderers. The characteristics of the NGRI group found here can help to identify risk groups and to develop and implement prevention programs for people with mental disorders who are at risk of violent behavior.
A novel approach to determining augmented bone volume in intraoral bone block augmentation using an intraoral scanner: an in vitro study
Authors: Frederic Weichel , Lukas Kalchthaler , Reinald Kühle , Christopher Büsch , Oliver Ristow , Michael Engel , Christian Freudlsperger , Jürgen Hoffmann , Christian Mertens 
Published: September 2023

Abstract
Introduction
Bone augmentation procedures are established tools for reshaping the alveolar ridge and increasing bone volume. Different approaches are being used to measure postoperative bone volume gain. This study aimed to develop an objective and automated volume measurement tool equally as precise as manual slice-by-slice annotation.

Materials and methods
To evaluate the proposed workflow, we performed an in vitro study with 20 pig mandibles that were grafted using three different grafting techniques—autogenous full block, split block bone and shell augmentation. The pig jaws were scanned pre- and postoperatively using an intraoral scanner. The resulting surface files (baseline, full block, split block, shell) were processed using the new volume-measuring workflow as well as using manual slice-by-slice annotation at baseline (t0) and at 6 months (t1) using the same population. Two TOSTs (Test of One-Sided Significance) and NHSTs (Null Hypothesis Significance Test) were used to compare the two workflows. The intra-rater reliability between t0 and t1 was determined using intraclass correlation coefficients.

Results
The mean difference for the full block augmentation technique was − 0.015 cm3 (p < 0.001); for the split block technique, it was − 0.034 cm3p = 0.01, and for the shell technique, it was − 0.042 cm3. All results were statistically not different from zero and statistically equivalent to zero. The results also showed an excellent absolute intra-rater agreement.

Conclusions
The semiautomatic volume measurement established in this article achieves comparable results to manual slice-by-slice measuring in determining volumes on STL files generated by intraoral scanners and shows an excellent intra-rater reliability.

Graphical Abstract
Heat exposure and hospitalizations for chronic kidney disease in China: a nationwide time series study in 261 major Chinese cities
Authors: Wang Fu-Lin , Wang Wan-Zhou , Zhang Fei-Fei , Peng Su-Yuan , Wang Huai-Yu , Chen Rui , Wang Jin-Wei , Li Peng-Fei , Wang Yang , Zhao Ming-Hui , Yang Chao , Zhang Lu-Xia 
Published: September 2023

Abstract
Background
Climate change profoundly shapes the population health at the global scale. However, there was still insufficient and inconsistent evidence for the association between heat exposure and chronic kidney disease (CKD).

Methods
In the present study, we studied the association of heat exposure with hospitalizations for cause-specific CKD using a national inpatient database in China during the study period of hot season from 2015 to 2018. Standard time-series regression models and random-effects meta-analysis were developed to estimate the city-specific and national averaged associations at a 7 lag-day span, respectively.

Results
A total of 768,129 hospitalizations for CKD was recorded during the study period. The results showed that higher temperature was associated with elevated risk of hospitalizations for CKD, especially in sub-tropical cities. With a 1 °C increase in daily mean temperature, the cumulative relative risks (RR) over lag 0–7 d were 1.008 [95% confidence interval (CI) 1.003–1.012] for nationwide. The attributable fraction of CKD hospitalizations due to high temperatures was 5.50%. Stronger associations were observed among younger patients and those with obstructive nephropathy. Our study also found that exposure to heatwaves was associated with added risk of hospitalizations for CKD compared to non-heatwave days (RR = 1.116, 95% CI 1.069–1.166) above the effect of daily mean temperature.

Conclusions
Short-term heat exposure may increase the risk of hospitalization for CKD. Our findings provide insights into the health effects of climate change and suggest the necessity of guided protection strategies against the adverse effects of high temperatures.
Large-scale energy storage system: safety and risk assessment
Authors: Moa Ernest Hiong Yew , Go Yun Ii 
Published: September 2023

AbstractThe International Renewable Energy Agency predicts that with current national policies, targets and energy plans, global renewable energy shares are expected to reach 36% and 3400 GWh of stationary energy storage by 2050. However, IRENA Energy Transformation Scenario forecasts that these targets should be at 61% and 9000 GWh to achieve net zero carbon emissions by 2050 and limit the global temperature rise within the twenty-first century to under 2 °C. Despite widely known hazards and safety design of grid-scale battery energy storage systems, there is a lack of established risk management schemes and models as compared to the chemical, aviation, nuclear and the petroleum industry. Incidents of battery storage facility fires and explosions are reported every year since 2018, resulting in human injuries, and millions of US dollars in loss of asset and operation. Traditional risk assessment practices such as ETA, FTA, FMEA, HAZOP and STPA are becoming inadequate for accident prevention and mitigation of complex energy power systems. This work describes an improved risk assessment approach for analyzing safety designs in the battery energy storage system incorporated in large-scale solar to improve accident prevention and mitigation, via incorporating probabilistic event tree and systems theoretic analysis. The causal factors and mitigation measures are presented. The risk assessment framework presented is expected to benefit the Energy Commission and Sustainable Energy Development Authority, and Department of Standards in determining safety engineering guidelines and protocols for future large-scale renewable energy projects. Stakeholders and Utility companies will benefit from improved safety and reliability by avoiding high-cost asset damages and downtimes due to accident events.
How to manage a scientific project in biological nitrogen fixation (BNF) and the topics that needed to be searched?
Authors: Shamseldin Abdelaal 
Published: September 2023

AbstractPlanning to have a good scientific project generally or specifically in BNF is a main target for young scientists and PhD students worldwide. Therefore, it is hardly urgent to well manage the project, which defined the use of knowledge, skills and methods to achieve objectives of the project in the determined time without delay. Consequently, in this letter I will explain the main points that needed to be covered to manage a research project in BNF and which subjects of research are requested to be covered in the future.