bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unbiased assessment of genome integrity and purging of adverse outcomes at the target locus upon editing of CD4+ T‐cells for the treatment of Hyper IgM1
Authors: Canarutto Daniele , Asperti Claudia , Vavassori Valentina , Porcellini Simona , Rovelli Elisabetta , Paulis Marianna , Ferrari Samuele , Varesi Angelica , Fiumara Martina , Jacob Aurelien , Sergi Sergi Lucia , Visigalli Ilaria , Ferrua Francesca , González‐Granado Luis Ignacio , Lougaris Vassilios , Finocchi Andrea , Villa Anna , Radrizzani Marina , Naldini Luigi 
Published: November 2023

AbstractHyper IgM1 is an X‐linked combined immunodeficiency caused by CD40LG mutations, potentially treatable with CD4+ T‐cell gene editing with Cas9 and a “one‐size‐fits‐most” corrective template. Contrary to established gene therapies, there is limited data on the genomic alterations following long‐range gene editing, and no consensus on the relevant assays. We developed drop‐off digital PCR assays for unbiased detection of large on‐target deletions and found them at high frequency upon editing. Large deletions were also common upon editing different loci and cell types and using alternative Cas9 and template delivery methods. In CD40LG edited T cells, on‐target deletions were counter‐selected in culture and further purged by enrichment for edited cells using a selector coupled to gene correction. We then validated the sensitivity of optical genome mapping for unbiased detection of genome wide rearrangements and uncovered on‐target trapping of one or more vector copies, which do not compromise functionality, upon editing using an integrase defective lentiviral donor template. No other recurring events were detected. Edited patient cells showed faithful reconstitution of CD40LG regulated expression and function with a satisfactory safety profile. Large deletions and donor template integrations should be anticipated and accounted for when designing and testing similar gene editing strategies.
Investigation of carbapenem-resistant Enterobacterales isolates at a tertiary laboratory in Pretoria, South Africa
Authors: Ramashia Mbudzeni , Phofa Thabiso D. , Nkawane Granny M. , Nogbou Noel-David , Bolukaoto John Y. , Nchabeleng Maphoshane , Musyoki Andrew M. 
Published: November 2023

AbstractThis study aimed to investigate phenotypic and genotypic characteristics of carbapenem-resistant Enterobacterales isolates (CRE) at a tertiary laboratory in South Africa. A total of 99 CRE isolates were collected between 2019 and 2021. Carbapenemase production was tested using modified carbapenem inhibitory method. Colistin susceptibility testing was performed using the ComASP™ Colistin broth microdilution method. Conventional PCR assays were conducted for detection of mcr-1 gene and common carbapenemase genes (blaVIM, blaNDM, blaIMP, blaKPC, blaOXA-23, blaOXA-51 and blaOXA-48). Rep-PCR assay was conducted to determine the genetic relatedness of the study isolates. Majority of the isolates were Klebsiella pneumoniae (83%). Carbapenem resistant K. pneumoniae cluster was observed from ICU and surgical ward samples. Colistin resistance was observed in 13% (12/93) of the isolates namely, in 11 K. pneumoniae and one Enterobacter cloacae. The blaOXA-48 (65%) was the most prevalent gene detected followed by blaNDM (25%) and blaVIM (22%). Several K. pneumoniae isolates concomitantly carried multiple carbapenemase genes with one isolate carry up to 5 five genes blaVIM, blaNDM, blaOXA-48, blaOXA-23 and blaOXA-51. The mcr-1 gene was not detected in the isolates. Rep-PCR assay showed that most isolates matched cluster A (50%). The high prevalence of blaOXA-48, blaNDM and emerging colistin resistant isolates is of concern for patient management at this institution and needs close monitoring. Rep-PCR is a valuable tool in establishing infection clusters in resource-limited settings.
Multi-DBN Weighted Voting Algorithm for Multi-Targets Classification in WSN
Authors: Zhang Heng , Zhou Yang 
Published: November 2023

One of the most important applications in the wireless sensor networks (WSN) is to classify mobile targets in the monitoring area. In this paper, a multi-DBN weighted voting classification algorithm is proposed on the basis of the Deep Belief Network (DBN) classifier and combined with the idea of voting method, which is implemented on the nodes of the WSN monitoring system by means of &quot;upper training, lower transplantation&quot; appraoch. The performance of the algorithm is verified by using real-world experimental data, and the results show that the proposed method has a higher accuracy in classifying the target signal features, achieving an average classification accuracy of 84.63% across four different types of moving targets. The experiment reveals that the multi-DBN weighted voting algorithm enhances the target classification accuracy by approximately 5% in comparison to the single DBN classifier, but the memory and computation time required for the algorithm to run are also increased at the same time. Compared to the FFNN classifier, which exhibited the highest classification accuracy among the four selected methods, the algorithm achieves an improvement of approximately 8.8% in classification accuracy. However, it incurs greater time overhead to run.
Persepsi Guru terhadap Bahan Ajar Sejarah Sekolah Menengah Atas
Authors: Djono Djono 
Published: November 2023

<p>Persepsi guru tentang bahan ajar sejarah sangat beragam. Penelitian ini memiliki tujuan untuk memahami perspektif guru terhadap bahan ajar sejarah dari aspek kognitif, afektif, dan psikomotor<em>. </em>Penelitian ini merupakan penelitian<em> </em>deskriptif. Subjek penelitian ini yaitu 28 responden guru sejarah sekolah menengah atas di beberapa wilayah Indonesia. Penelitian dilaksanakan selama bulan November tahun 2022. Instrumen penelitian menggunakan angket. Teknik analisis data menggunakan <em>anaysis Interactive</em> meliputi reduksi data, penyajian data, dan penarikan kesimpulan. Hasil penelitian ini menunjukkan bahwa persepsi guru terhadap bahan ajar sejarah telah mencakup aspek kognitif dengan nilai rerata 3.45 (86.44%), afektif dengan nilai rerata 3.48 (87.27%), dan psikomotor dengan nilai rerata 3.55 (88.93%). Secara spesifik, pada ranah kognitif, bahan ajar sejarah telah memenuhi indikator yaitu s<em>elf-instruction</em> (89.03%), <em>self-contained</em> (88.81%), <em>stand-alone</em> (79.93%), adaptif (85.36%), dan <em>user friendly</em> (89.07%). Pada ranah afektif, bahan ajar telah memenuhi indikator <em>self-instruction </em>(88.65%),<em> self-contained</em> (89.69%), <em>stand-alone </em>(83.22%), adaptif (85.96%), dan <em>user friendly</em> <em>(</em>88.81%). Pada ranah psikomotorik, bahan ajar sejarah telah memenuhi indikator <em>self-instruction </em>(87.66%), <em>self-contained</em> (89.80%), <em>stand-alone</em> (89.47%), adaptif (87.82%), dan <em>user friendly</em> (89.91%). Maka, dapat disimpulkan bahwa persepsi guru terhadap bahan ajar sejarah telah memenuhi aspek kognitif, afektif, dan psikomotorik.</p>
Identification of CERS5 as a novel biomarker for prognosis and immunity in hepatocellular carcinoma: a bioinformatics analysis and functional validation study
Authors: Qiu Peng , Feng Yunxiang , Zhao Kai , Shi Yuanxin , Li Xiangyu , Yao Wei , Deng Zhengdong , Wang Jianming 
Published: November 2023

Abstract
Objective
Hepatocellular carcinoma (HCC) is an extremely deadly cancer with few effective therapeutic options available. Ceramide synthases (CERS), a family of enzymes that regulate sphingolipid metabolism, have been suggested to play a role in cancer initiation and progression. Whereas the specific functions of CERS in HCC pathogenesis have not yet been fully elucidated.
Methods
The TCGA and ICGC databases were employed to analyze the expression levels and clinical relevance of CERS genes in HCC. Functional enrichment analyses were performed to identify pathways and functions associated with CERS5. The correlation between CERS5 and the tumor immune microenvironment was investigated. The mutation landscape and immunotherapy efficacy were evaluated. Functional experiments in vitro were conducted to assess CERS5’s impact on HCC cell proliferation and invasion.
Results
Aberrant expression of the CERS family was detected not only in HCC but also in other cancers, and has been linked to both overall survival and disease-free survival. Among the CERS family members, CERS5 was identified as the only prognosis-related gene, with up-regulated in HCC validated in the ICGC database and clinical tissue samples. Higher expression levels of CERS5 were associated with a poorer prognosis as well as an advanced pathologic stage and grade, as confirmed by the TCGA and ICGC databases. Besides, a prognostic nomogram combining pathologic stage, tumor status, and the expression of CERS5 was established and further validated, which suggested a favorable value for prognosis prediction. Functional enrichment analyses showed that the overexpression of CERS5 resulted in enriched pathways associated with carcinogenesis, drug metabolism, the PI3K/AKT/mTOR signaling pathway, and cancer immune-related pathways. In addition, the overexpression of CERS5 correlated positively with the expression of genes associated with immunogenic cell death modulators and immune checkpoints, levels of immune cell infiltration, and immunotherapy response, which was featured in an immunologically “hot” environment in the tumor microenvironment. Finally, the functional experiments showed that CERS5 knockdown has been shown to inhibit the growth and invasion of hepatocellular carcinoma, potentially through targeting the PI3K/AKT/mTOR signaling pathway.
Conclusions
Based on our findings, CERS5 appears to have great potential as both a precise prognostic biomarker and a novel therapeutic target in HCC.
Wave Mechanics of Microwave Absorption Films: Part 3 - Multilayered Films
Authors: Liu Yue , Liu Ying , Drew Michael G. B. 
Published: November 2023

Abstract

In the field of microwave absorption, the quarter-wavelength theory (QWM) is commonly employed for films with multiple layers. However, this study demonstrates the inadequacy of QWM as it is fundamentally flawed. The conventional results pertaining to films with or without a metal backing are typically applied to the central layers of multilayer films. Nevertheless, this approach is flawed, as it overlooks the presence of incident microwaves on both sides of the central layer, focusing solely on those in front of the film. To address this gap, our work introduces a novel theoretical framework for multilayer films, filling the void in existing literature. This research introduces a new, robust physical approach to understanding Multilayered films.
In Vitro Explant Sterilization and Bud Proliferation Studies on Some Imported Peach Rootstocks
Authors: Eliwa Galal I. , El-Dengawy El-Refaey F. , Gawish Mohamed S. , Yamany Mona M. 
Published: November 2023

Abstract
The present investigation was conducted in the Laboratory of Tissue Culture, Horticulture Department, Faculty of Agriculture, Damietta University, Egypt. The objective of this study was to establish a micropropagation protocol suitable for three imported peach rootstocks {Okinawa (P. persica), Nemared (P. persica × P. davidiana) × P. persica) and Garnem (P. dulcis × P. persica)} In vitro. According to the results, soaking the explants in sodium hypochlorite (NaOCl) at 20% for 15 min achieved the highest value of responsive (82.81%) and survived (96.61%) with a minimum value of dead (3.14%) and contaminated (0.24%). Garnem genotype explants had achieved the best response (89.12%) and Survived (90.62%) with minimum dead (0.00%) and maximum contamination (9.37%). The shoot tips showed the highest responsive, Survived, and dead% (100, 87.40 and12.59% respectively) and minimum significant contaminated (0.00%) in comparison with axillary buds. Also, the explants differed significantly in their percentages of responsive, survived, dead, and contaminated at the different collected dates. The 6-benzylaminopurine (BAP) concentrations used (3 to 5.0 mg/L-1) demonstrated similar behavior in terms of in vitro proliferation, with rates of 3.77 to 6.11, 4.33 to 8.88 and 3.33 to 7.44 shoots per explant for Okinawa, Nemared, and Garnem peach rootstocks respectively, indicating that the number of shoots proliferation is genotype dependent. Moreover, using 5.0 mg/L-1 BAP in combination with 0.2 mg/L-1 IBA produced higher significant values of average shoot proliferation % (96.29%) as well as number of shoots per explant (7.48) and average Leaves number/explant (16.33) than the other treatments. From these results, we could conclude that indole-butyric acid (IBA) synergists with 6-benzylaminopurine (BAP) improved adventitious bud development in vitro multiplication of Okinawa, Nemared, and Garnem peach rootstocks.
Pathways to a Carbon-Neutral Uzbekistan: Evaluating CO2 Emission Estimation and Decarbonization Measures for Sustainability
Authors: Turakulov Zafar , Kamolov Azizbek , Norkobilov Adham , Variny Miroslav , Fallanza Marcos 
Published: November 2023

Abstract
As the climate change becomes the greatest issue of this century, countries are looking for sustainable solutions to effectively control their greenhouse gas (GHG) emissions. In this way, the transition to a carbon neutral economy is likely to be the top priority in the sustainable management strategies and policies of each country. Uzbekistan, being one of the most vulnerable countries to climate change effects, is taking notable actions to transition towards a low-carbon economy. This study estimates the carbon dioxide (CO2) — the main GHG — emissions trends in Uzbekistan and their sector-by-sector contribution. Additionally, various carbon emissions reduction pathways are discussed emphasizing on the potential for the transition to renewable energy sources (RES) and carbon capture, storage, and utilization (CCSU) technology integration. Apart from that, the possible opportunities and barriers of RES power generation, CCSU integration, and trading infrastructure among Central Asian countries are comprehensively investigated. CO2 concentration of flue gases from different sources is also estimated in order to preliminary calculation of CO2 capture cost. In the end, CO2 utilization pathways and potentials for Uzbekistan is briefly discussed. This paper gives valuable recourses for researchers and decision-makers aiming to reduce the GHG emissions via RES promotion, fossil fuel based industry optimization, and CCSU integration in Uzbekistan.
WITHDRAWN: Soil remediation modulates Cd content and CH4 emission in a karst rice paddy
Authors: Zeng Guangneng , Lu Wangbiao , Song Jiangju , Ni Maofei , Guo Shuangqin , Zhang Qi , Huang Chengling , Yang Cheng , Du Haijun , Luo Weijun 
Published: November 2023

Abstract
Rice (Oryza sativa L.) paddies are increasingly threatened by cadmium (Cd) pollution, and potentially serve as methane (CH4) emitters to the atmosphere. Remediation agents widely mitigate Cd pollution in paddy soil, however, we know little about their regulations on CH4 emission. Here, via adding biochar (B), sulfhydryl-modified palygorskite (SMP), and selenium foliar fertilizer (SFF), we conducted a pot experiment to investigate soil and rice Cd changes together with in-situ CH4 fluxes. We suggest that SMP, SFF, and mixed B-SMP significantly facilitate Cd remediation. CH4 outgassing increased gradually along the growing season, with the cumulative CH4 fluxes ranging between 338.82 and 619.13 kg∙hm− 2. Agents 7% B, 7% B-0.01% SMP and SFF reduced CH4 emissions by 8.46%, 5.30%, and 4.11%, respectively. Our results highlight that mixed 7% B-0.01% SMP and SFF showed collaborative effects on Cd remediation and CH4 emission. This study reveals the feasibility of reducing Cd pollution and CH4 evasion in a karst rice paddy, which hopes to supplement knowledge of collaborative controls on soil remediation and carbon emission.
Spatiotemporal evolution characteristics and driving forces of vegetation cover variations in the Chengdu-Chongqing region of China under the background of rapid urbanization
Authors: Zhang Luoqi , Zhang Yan , Wang Junyi , Liang Xinyu , Wei Yali 
Published: November 2023

Abstract

The research on the spatiotemporal changes and driving factors of ecosystems in rapidly urbanizing regions has always been a topic of widespread concern. As the fourth pole of China's economic development, the research on the Chengdu-Chongqing region has reference significance for the urbanization process of developing countries such as India, Brazil, and South Africa.The normalized difference vegetation index (NDVI) has been widely applied in studies of plant and ecosystem changes. Based on MODIS NDVI data from 2001 to 2020 and meteorological data of the same period, this study reveal the evolution of NDVI in the Chengdu-Chongqing region from three aspects: the spatiotemporal variation characteristics of NDVI, the prediction of future trends in vegetation coverage, and the response of vegetation to climate change and human activities. During the period of plant growth, the mean NDVI achieved a value of 0.78, and the vegetation coverage rate is increasing year by year. According to the Hurst index, the future NDVI in Chengdu-Chongqing region will tend to decrease, and its trend is opposite to that of the past period of time. The Chengdu-Chongqing region vegetation positively affected by human activities are greater than those negatively affected, and in terms of vegetation degradation, the impact of human activities is greater than climate change.
Study on water entry of a 3D torpedo based on the improved smooth particle hydrodynamics method
Authors: Zhang Jun , Ding Yanchao , Wu Wei , Li Wenjie , Zhang Zhaoming , JIAO YANMEI 
Published: November 2023

Abstract
The water entry of a torpedo is a complex nonlinear problem, involving transient impact, free surface deformation, droplet splashing, and fluid-solid coupling, which poses severe challenges to traditional mesh methods. The meshless smooth particle hydrodynamics (SPH) method shows unique advantages in capturing the complex features of the water entry of the torpedo. However, it still suffers from some inherent shortcomings, such as low surface discretization accuracy, poor discretization flexibility, and low calculation efficiency. In this study, an improved adaptive SPH algorithm is proposed to accurately and efficiently investigate the water entry of the torpedo. This method integrates meshless point generation and adaptive techniques simultaneously. Numerical results demonstrate that when the torpedo vertically enters the water at different velocities, the induced impact loads acting on the head of the torpedo fluctuate significantly with two peak values at the initial stage and thereafter stabilize at a later stage. The impact load acting on the torpedo, the entry depth of the torpedo, the splash height of the droplets, and the size of the cavity generated around the torpedo increase with the increment of the entry velocity. When the torpedo enters the water at different enter angles under the same initial enter velocity, both the vertical and the horizontal movements of the torpedo are observed, which results in more complex variations of parameters along the x- and y-axes. The findings and the corresponding numerical method in this study can provide a certain basis for the future designs of the entry trajectory and the structural bearing capacity of torpedoes.
Photoinduced and electrochemical induced degradation of the 4th EU watchlist compound venlafaxine
Authors: Voigt Melanie , Dluziak Jean-Michel , Wellen Nils , Langerbein Victoria , Jaeger Martin 
Published: November 2023

Abstract
The European Union require environmental monitoring of the antidepressant drug venlafaxine. Advanced oxidation processes provide a remedy against spread of micropollutants. In this study, the photoinduced and electrochemical decompositions of venlafaxine were investigated in terms of mechanism and efficacy using high-performance liquid chromatography coupled to high-resolution multifragmentation mass spectrometry. Kinetic analysis, structure elucidation, matrix variation and radical scavenging indicated the dominance of a hydroxyl mediated indirect mechanism during photo-degradation, hydroxyl and direct electrochemical oxidation for electrochemical degradation. Oxidants, sulfate and chloride ions acted as accelerants. Humic acid decelerated degradation during UV irradiation, but accelerated during electrochemical oxidation. In silico QSAR analysis predicted decreased environmental hazard after AOP treatment. In general, photo-irradiation proved more efficient due to faster decomposition and slightly less toxic transformation products. Yet, matrix effects would have to be carefully evaluated when potential applications as a fourth purification stage were to be considered.
XX sex chromosome complement modulates immune responses to heat-killed Streptococcus pneumoniae immunization in a microbiome-dependent manner
Authors: Amato-Menker Carly , Hopen Quinn , Pettit Andrea , Gandhi Jasleen , Hu Gangqing , Schafer Rosana , Franko Jennifer 
Published: November 2023

Abstract
Background
Differences in male vs. female immune responses are well-documented and have significant clinical implications. While the immunomodulatory effects of sex hormones are well established, the contributions of sex chromosome complement (XX vs. XY) and gut microbiome diversity on immune sexual dimorphisms have only recently become appreciated. Here we investigate the individual and collaborative influences of sex chromosome complements and gut microbiome bacteria on humoral immune activation.
Methods
Sham-operated and gonadectomized male and female Four Core Genotype (FCG) mice were immunized with heat-killed Streptococcus pneumoniae (HKSP). Humoral immune responses were assessed, and X-linked immune-related gene expression was evaluated to explain the identified XX-dependent phenotypes. Ex vivo studies investigated the functional role of Kdm6a, an X-linked epigenetic regulatory gene of interest, in mitogenic B cell activation. Additionally, we examined whether gut microbiome communities, or their metabolites, differentially influence immune cell activation in a sex chromosome-dependent manner. Endogenous gut microbiomes were antibiotically depleted and reconstituted with select short-chain fatty acid (SCFA)-producing bacteria prior to HKSP immunization and immune responses assessed.
Results
XX mice exhibited higher HKSP-specific IgM-secreting B cells and plasma cell frequencies than XY mice, regardless of gonadal sex. Although Kdm6a was identified as an X-linked gene overexpressed in XX B cells, inhibition of its enzymatic activity did not affect mitogen-induced plasma cell differentiation or antibody production in a sex chromosome-dependent manner ex vivo. Enhanced humoral responses in XX vs. XY immunized FCG mice were eliminated after microbiome depletion, indicating that the microbiome contributes to the identified XX-dependent immune enhancement. Reconstituting microbiota-depleted mice with select SCFA-producing bacteria increased humoral responses in XX, but not XY, FCG mice. This XX-dependent enhancement appears to be independent of SCFA production in males, while female XX-dependent responses relied on SCFAs.
Conclusions
FCG mice have been used to assess the influence of sex hormones and sex chromosome complements on various sexually dimorphic traits. The current study indicates that the gut microbiome impacts humoral responses in an XX-dependent manner, suggesting that the collaborative influence of gut bacteria and other sex-specific factors should be considered when interpreting data aimed at delineating the mechanisms that promote sexual dimorphism.