bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing Resources for Measuring Text Readability in Sesotho
Authors: Sibeko Johannes
Published: June 2023

This article presents a work-in-progress doctoral project that explores measuring text readability in Sesotho, a Bantu language spoken by more than 10 million speakers across Southern Africa. The main project adopts a classical readability formulas approach to text readability analysis. We aim to adapt nine existing readability metrics into Sesotho using English as a higher-resourced helper language. So far, five resources have been developed as part of the study. The rule-based and the TeX-based syllabification systems, the syllable annotated word list, and the grade 12 exam reading comprehension and summary writing corpus have been published on the South African Centre for Digital Language Resources' (SADiLaR) online repository. The machine-translated corpus is still under development. This article describes the progress of the PhD project by overviewing the basic digital language resources developed for the project. The metrics under consideration for adaptation into Sesotho are also briefly discussed.
WebLicht-Batch -- A Web-Based Interface for Batch Processing Large Input with the WebLicht Workflow Engine
Authors: Zinn Claus , Campbell Ben
Published: June 2023

WebLicht is a workflow engine that gives researchers access to a well-inhabited space of natural language processing tools that can be combined into tool chains to perform complex natural language analyses. In this paper, we present WebLicht-Batch, a web-based interface to WebLicht's chainer back-end. WebLicht-Batch helps users to automatically feed large input data, or input data of multiple files into WebLicht. It disassembles large input into smaller, more digestible sizes, feeds the resulting parts into WebLicht's pipelining and execution engine, and then assembles the results of such processing into files that preserve the usual input-output dichotomy.
Fully Convolutional Networks for Dense Water Flow Intensity Prediction in Swedish Catchment Areas
Authors: Pirinen Aleksis , Mogren Olof , Västerdal Mårten
Published: June 2023

Intensifying climate change will lead to more extreme weather events, including heavy rainfall and drought. Accurate streamflow prediction models which are adaptable and robust to new circumstances in a changing climate will be an important source of information for decisions on climate adaptation efforts, especially regarding mitigation of the risks of and damages associated with flooding. In this work we propose a machine learning-based approach for predicting water flow intensities in inland watercourses based on the physical characteristics of the catchment areas, obtained from geospatial data (including elevation and soil maps, as well as satellite imagery), in addition to temporal information about past rainfall quantities and temperature variations. We target the one-day-ahead regime, where a fully convolutional neural network model receives spatio-temporal inputs and predicts the water flow intensity in every coordinate of the spatial input for the subsequent day. To the best of our knowledge, we are the first to tackle the task of dense water flow intensity prediction; earlier works have considered the prediction of flow intensities at a sparse set of locations at a time. An extensive set of model evaluations and ablations are performed, which empirically justify our various design choices. Code and preprocessed data have been made publicly available at https://github.com/aleksispi/fcn-water-flow.
Aerial View Localization with Reinforcement Learning: Towards Emulating Search-and-Rescue
Authors: Pirinen Aleksis , Samuelsson Anton , Backsund John , Åström Kalle
Published: June 2023

Climate-induced disasters are and will continue to be on the rise, and thus search-and-rescue (SAR) operations, where the task is to localize and assist one or several people who are missing, become increasingly relevant. In many cases the rough location may be known and a UAV can be deployed to explore a given, confined area to precisely localize the missing people. Due to time and battery constraints it is often critical that localization is performed as efficiently as possible. In this work we approach this type of problem by abstracting it as an aerial view goal localization task in a framework that emulates a SAR-like setup without requiring access to actual UAVs. In this framework, an agent operates on top of an aerial image (proxy for a search area) and is tasked with localizing a goal that is described in terms of visual cues. To further mimic the situation on an actual UAV, the agent is not able to observe the search area in its entirety, not even at low resolution, and thus it has to operate solely based on partial glimpses when navigating towards the goal. To tackle this task, we propose AiRLoc, a reinforcement learning (RL)-based model that decouples exploration (searching for distant goals) and exploitation (localizing nearby goals). Extensive evaluations show that AiRLoc outperforms heuristic search methods as well as alternative learnable approaches, and that it generalizes across datasets, e.g. to disaster-hit areas without seeing a single disaster scenario during training. We also conduct a proof-of-concept study which indicates that the learnable methods outperform humans on average. Code and models have been made publicly available at https://github.com/aleksispi/airloc.
Understanding Large Language Models through the Lens of Artificial Agency
Authors: Van Lier Maud
Published: June 2023

This paper is motivated by Floridi’s recent claim that Large Language Models like ChatGPT can be seen as ‘intelligence-free’ agents. Where I do not agree with Floridi that such systems are intelligence-free, my paper does question whether they can be called agents, and if so, what kind. I argue for the adoption of a more restricted understanding of agent in AI-research, one that comes closer in its meaning to how the term is used in the philosophies of mind, action, and agency. I propose such a more narrowing understanding of agent, suggesting that an agent can be seen as entity or system that things can be ‘up to’, that can act autonomously in a way that is best understood on the basis of Husserl’s notion of indeterminate determinability.
Towards Better Product Quality: Identifying Legitimate Quality Issues through NLP & Machine Learning Techniques
Authors: Jabeen Rakhshanda , Ericsson Morgan , Nordqvist Jonas
Published: June 2023

Manufacturers of high-end professional products are committed to delivering outstanding customer-quality experiences. They maintain databases of customer complaints and repair service jobs data to monitor product quality. Analyzing the text data from service jobs can help identify common problems, recurring issues, and patterns that impact customer satisfaction, and aid manufacturers in taking corrective actions to improve product design, manufacturing processes, and customer support services. However, distinguishing legitimate quality issues from a brief, domain-specific text in service jobs remains a challenge. This study aims to automate the classification of technical service repair job data into legitimate quality issues or non-issues to assist individuals in the quality field department in a large company. To achieve this goal, we developed a comprehensive pipeline based on natural language processing and machine learning techniques including raw text preprocessing, dealing with imbalance class distribution, feature extraction, and classification. In this study, We evaluate several feature extraction and machine learning classification methods and perform the Friedman test followed by Nemenyi post-hoc analysis to find the best-performing model. Our results show that the passive-aggressive classifier achieved the highest average accuracy of 94% and 89% average macro F1-score when trained on TF-IDF vectors.
How Does the Language of ‘Threat’ Vary Across News Domains? A Semi-Supervised Pipeline for Understanding Narrative Components in News Contexts
Authors: Ryazanov Igor , Björklund Johanna
Published: June 2023

By identifying and characterising the narratives told in news media we can better understand political and societal processes. The problem is challenging from the perspective of natural language processing because it requires a combination of quantitative and qualitative methods. This paper reports on work in progress, which aims to build a human-in-the-loop pipeline for analysing how the variation of narrative themes across different domains, based on topic modelling and word embeddings. As an illustration, we study the language associated with the threat narrative in British news media.
Finite element evaluation of an American football helmet featuring liquid shock absorbers for protecting against concussive and subconcussive head impacts
Authors: Cecchi Nicholas J. , Vahid Alizadeh Hossein , Liu Yuzhe , Camarillo David B.
Published: June 2023

Introduction: Concern has grown over the potential long-term effects of repeated head impacts and concussions in American football. Recent advances in impact engineering have yielded the development of soft, collapsible, liquid shock absorbers, which have demonstrated the ability to dramatically attenuate impact forces relative to existing helmet shock absorbers.

Methods: To further explore how liquid shock absorbers can improve the efficacy of an American football helmet, we developed and optimized a finite element (FE) helmet model including 21 liquid shock absorbers spread out throughout the helmet. Using FE models of an anthropomorphic test headform and linear impactor, a previously published impact test protocol representative of concussive National Football League impacts (six impact locations, three velocities) was performed on the liquid FE helmet model and four existing FE helmet models. We also evaluated the helmets at three lower impact velocities representative of subconcussive football impacts. Head kinematics were recorded for each impact and used to compute the Head Acceleration Response Metric (HARM), a metric factoring in both linear and angular head kinematics and used to evaluate helmet performance. The head kinematics were also input to a FE model of the head and brain to calculate the resulting brain strain from each impact.

Results: The liquid helmet model yielded the lowest value of HARM at 33 of the 36 impact conditions, offering an average 33.0% (range: −37.5% to 56.0%) and 32.0% (range: −2.2% to 50.5%) reduction over the existing helmet models at each impact condition in the subconcussive and concussive tests, respectively. The liquid helmet had a Helmet Performance Score (calculated using a summation of HARM values weighted based on injury incidence data) of 0.71, compared to scores ranging from 1.07 – 1.21 from the other four FE helmet models. Resulting brain strains were also lower in the liquid helmet.

Discussion: The results of this study demonstrate the promising ability of liquid shock absorbers to improve helmet safety performance and encourage the development of physical prototypes of helmets featuring this technology. The implications of the observed reductions on brain injury risk are discussed.
Construction of an alpaca immune antibody library for the selection of nanobodies against Drosophila melanogaster proteins
Authors: Qiu Jianxiang , Li Jie , Zhang Zhen , Dong Shirui , Ling Xiaomei , Fang Zhixin , Ling Quanshou , Huang Zhixin
Published: June 2023

Introduction:Drosophila melanogaster is a model organism for studying developmental biology and human neural disorders. Nanobodies are the variable domains of the heavy chains of camelid heavy-chain antibodies (VHHs) with high affinity to their antigens and have applications in basic research, similar to traditional antibodies. In addition, nanobodies acting as functionalized antibodies or protein binders have become an additional valuable approach in Drosophila. This study aimed to develop a VHH library against Drosophila proteins and confirm its availability by retrieving some Drosophila protein-specific nanobodies from the library.

Methods: An alpaca was first immunized with Drosophila embryo lysate and then its lymphocytes were isolated. Total RNA was extracted and cDNA was synthesized. The vhh sequences were amplified by two round PCR, which were then ligated to a phage display vector pADL-10b. The ligation products were transduced into SS320 competent cells to generate a VHH library. From this library, nanobodies against CG7544, Myc, and CyclinE was enriched and screened by phage display technology and ELISA. DNA sequences of identified nanobodies were cloned into pADL-10b-Flag-His for expression and purification in Escherichia coli SS320. Binding ability of purified nanobodies with corresponding antigens were determined by ELISA and surface plasmon resonance in vitro.

Results: In this study, an immune VHH library against Drosophila embryo proteins was generated with a capacity of 3 × 107. From this library, eight nanobodies against three Drosophila proteins, Myc, CyclinE, and CG7544, were identified and the DNA sequences of these nanobodies were obtained. These nanobodies were successfully expressed and purified from Escherichia coli SS320, and were demonstrated to bind corresponding antigens with high affinity in vitro. Moreover, the equilibrium constant between the highest enriched nanobodies and corresponding antigens were calculated.

Conclusion: In summary, we report the availability of an immune VHH library and a highly efficient panning strategy for nanobodies against proteins in Drosophila.
Assessing agricultural gene editing regulation in Latin America: an analysis of how policy windows and policy entrepreneurs shape agricultural gene editing regulatory regimes
Authors: Zarate Sebastian , Cimadori Ilaria , Jones Michael S. , Roca Maria Mercedes , Barnhill-Dilling S. Kathleen
Published: June 2023

This article explores the new developments and challenges of agricultural Gene Editing (GED) regulation in primarily nine countries of Latin America and the Caribbean (LAC) Region: Argentina, Bolivia, Brazil, Colombia, Guatemala, Honduras, Mexico, Paraguay and Peru. As Gene Editing technology develops, Latin America and the Caribbean regulatory regimes struggle to keep pace. Developers and regulators face challenges such as consumer perceptions, intellectual property, R&D funding (private and public), training, environmental and social impact, and access to domestic and international markets. Some Latin America and the Caribbean countries (e.g., Argentina) interpret existing legislation to promulgate regulations for biotechnology and Genetically Modified Organisms (GMOs), while others (e.g., Brazil and Honduras) have specific legislation for Genetically Modified Organisms. In both those cases, often a case-by-case approach is chosen to determine whether a Gene Editing organism is subject to Genetically Modified Organisms regulations or not. Other countries such as Peru have opted to ban the technology due to its perceived resemblance to transgenic Genetically Modified Organisms. After presenting the regulatory landscape for agricultural Gene Editing in Latin America and the Caribbean, this article addresses some of the differences and similarities across the region. Some countries have had more foresight and have dedicated resources to increase capacity and develop regulations (e.g., Brazil, Argentina, Colombia, Guatemala, Honduras, Mexico before 2018) while others struggle with bureaucratic limitations and partisanship of policymaking (e.g., Paraguay, Bolivia, Peru, Mexico after 2018). We propose that the differences and similarities between these regulatory regimes have emerged in part as a result of policy entrepreneurs (influential individuals actively involved in policy making) taking advantage of policy windows (opportunities for shaping policy and regulation). The third and remaining sections of this study discuss our main findings. Based on 41 semi structured interviews with regulators, scientists, product developers, NGOs and activists, we arrived at three main findings. First, there seems to be a consensus among most regulators interviewed that having harmonized regimes is a positive step to facilitate product development and deployment, leading to commercialization. Second, reducing bureaucracy (e.g., paper work) and increasing flexibility in regulation go hand in hand to expedite the acquisition of key lab materials required by developers in countries with less robust regimes such as Peru and Bolivia. Finally, developing public and private partnerships, fostering transparency, and increasing the involvement of marginalized groups may increase the legitimacy of Gene Editing regulation.
Documenting the immune response in patients with COVID-19-induced acute respiratory distress syndrome
Authors: Lu Junyu , Zeng Xiaona , Lu Weisheng , Feng Jihua , Yang Yegui , Wei Yongxian , Chen Yin , Zhang Jianfeng , Pinhu Liao
Published: June 2023

Introduction: Coronavirus disease 2019 (COVID-19) can lead to acute respiratory distress syndrome (ARDS) and life-threatening multi-organ failure with increased levels of inflammatory mediators and viral load; however, little is known about its pathophysiology.

Methods: To better understand the cellular status of COVID-19-induced ARDS, we performed single-cell RNA sequencing on peripheral blood samples from patients with COVID-19-induced ARDS. Single-cell RNA sequencing combined with bioinformatics analysis was used to study dynamic changes in cell composition and transcriptional profiles.

Results: The single-cell RNA sequencing data revealed significant phenotypic differences between patients with COVID-19-induced ARDS and controls, mainly in monocytes, and CD8+ T and B cells. B-cell and monocyte abundances were significant in COVID-19-induced ARDS patients compared to controls, while CD8+ T cells were depleted. These data suggest that there is an imbalance between lymphocytes and monocytes in the blood of COVID-19-induced ARDS patients. In addition, cytokine interactions between T cells, monocytes and B cells are enhanced as evidenced by the intercellular communication analysis. In particular, T cell subsets target receptors on other cells via CCL5 and may play an important role in patients with COVID-19-induced ARDS.

Conclusion: Our analysis suggested that a dysregulated adaptive immune response exists in patients with COVID-19-induced ARDS. Overall, we provided a cellular picture of the peripheral immune response in patients with COVID-19-induced ARDS.
Endothelial progenitor cells derived from embryonic stem cells prevent alveolar simplification in a murine model of bronchopulmonary dysplasia
Authors: Kolesnichenko Olena A. , Flood Hannah M. , Zhang Yufang , Ustiyan Vladimir , Cuervo Jimenez Hayde K. , Kalin Tanya V. , Kalinichenko Vladimir V.
Published: June 2023

Introduction: Vascular remodeling and compromised alveolar development are hallmarks of chronic pulmonary diseases such as bronchopulmonary dysplasia (BPD). Despite advances in neonatal healthcare the number of BPD cases worldwide continues to increase. One approach to overcoming the premature arrest in lung development seen in BPD is to stimulate neonatal angiogenesis via delivery and engraftment of endothelial progenitor cells (EPCs). One such population is resident to the pulmonary microvasculature and expresses both FOXF1 and c-KIT. Previous studies have shown that c-KIT+FOXF1+ EPCs are highly sensitive to elevated levels of oxygen (hyperoxia) and are decreased in premature infants with BPD and hyperoxia-induced BPD mouse models. We hypothesize that restoring EPCs through transplantation of c-KIT+FOXF1+ EPCs derived in vitro from pluripotent embryonic stem cells (ESCs), will stimulate neonatal angiogenesis and alveolarization in mice with hyperoxia-induced lung injury.

Methods: Utilizing a novel ESC line with a FOXF1:GFP reporter, we generated ESC-derived c-KIT+FOXF1+ EPCs in vitro. Using a second ESC line which contains FOXF1:GFP and tdTomato transgenes, we differentiated ESCs towards c-KIT+FOXF1+ EPCs and tracked them in vivo after injection into the neonatal circulation of hyperoxia-injured mice. After a recovery period in room air conditions, we analyzed c-KIT+FOXF1+ EPC engraftment and quantified the number of resident and circulating endothelial cells, the size of alveolar spaces, and the capillary density after EPC transplantations.

Results and conclusion: Herein, we demonstrate that addition of BMP9 to the directed endothelial differentiation protocol results in very efficient generation of c-KIT+FOXF1+ EPCs from pluripotent ESCs. ESC-derived c-KIT+FOXF1+ EPCs effectively engraft into the pulmonary microvasculature of hyperoxia-injured mice, promote vascular remodeling in alveoli, increase the number of resident and circulating endothelial cells, and improve alveolarization. Altogether, these results provide a proof-of-principle that cell therapy with ESC-derived c-KIT+FOXF1+ EPCs can prevent alveolar simplification in a hyperoxia-induced BPD mouse model.
Synthesis of acrylic resin and methacrylic resin microspheres by suspension polymerization
Authors: Yu Han , Liu Junjie , Zhao Lin , Liu Yonglin , Gu Lulu , Feng Lianxiang , Weng Yonggen , Duan Qingxu , Duan Baorong , Qu Jiale
Published: June 2023

The process of suspension polymerization was utilized to create acrylate resin microspheres with mesh numbers of 140–200 μm and particle sizes of 100 μm for implementation in mesh coating technology. The copolymer of methyl methacrylate (MMA) and methyl acrylate (MA) served as the primary polymer, with dibenzoyl peroxide (DBPO) functioning as the initiator, and a mixture of calcium carbonate and deionized water served as the dispersion medium. The surface morphology of the synthesized microspheres was analyzed through Fourier-transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) to confirm successful synthesis. The optimal reaction conditions for the synthesis of these microspheres were determined to be a dispersant dosage of 30 g of calcium carbonate with a monomer ratio of 4:1, a reaction time of 1 h, an initiator dosage of 1.2 g of BPO, and a reaction temperature of approximately 75–80 C, resulting in microspheres with a regular spherical shape and smooth surface.
Seismic prediction of porosity in tight reservoirs based on transformer
Authors: Su Zhaodong , Cao Junxing , Xiang Tao , Fu Jingcheng , Shi Shaochen
Published: June 2023

Porosity is a crucial index in reservoir evaluation. In tight reservoirs, the porosity is low, resulting in weak seismic responses to changes in porosity. Moreover, the relationship between porosity and seismic response is complex, making accurate porosity inversion prediction challenging. This paper proposes a Transformer-based seismic multi-attribute inversion prediction method for tight reservoir porosity to address this issue. The proposed method takes multiple seismic attributes as input data and porosity as output data. The Transformer mapping transformation network consists of an encoder, a multi-head attention layer, and a decoder and is optimized for training with a gating mechanism and a variable selection module. Applying this method to actual data from a tight sandstone gas exploration area in the Sichuan Basin yielded a porosity prediction coincidence rate of 95% with the well data.
Life cycle assessment of energy consumption and GHG emission for sewage sludge treatment and disposal: a review
Authors: Yu Shilin , Deng Shuanghui , Zhou Ao , Wang Xuebin , Tan Houzhang
Published: June 2023

With increasing population and urbanization, the amount of municipal sewage sludge generated is huge and growing rapidly. In order to minimize resource inputs and pollutant emissions in the sludge disposal process, it is crucial to carry out an environmental impact analysis and sustainability assessment of different strategies based on life cycle assessment (LCA). LCA provides a flexible framework for quantifying the consumption and emissions of different processes to determine the energy consumption and environmental impact of sewage sludge treatment and disposal. The aim of this review is to compare the energy consumption and GHG emissions of existing sludge management options for energy and nutrient recovery. At the same time, the characteristics of sewage sludge and the potential to convert sludge from waste to valuable products were assessed. While the excessive moisture content and ash content make sludge unsuitable for use as fuel, and the potential risk of contamination with heavy metals makes it less suitable for use as organic fertilizer, energy and material recovery during disposal can reduce disposal costs and environmental impacts. In the context of the current limitations reviewed, the level of potential GHG emissions of existing sludge treatment and disposal routes is: composting > anaerobic digestion > pyrolysis > incineration. With suitable sludge treatment routes, negative GHG emissions could potentially be achieved by substituting fossil fuels for heat and electricity generation, or as a fertilizer substitute. The development and application of future sludge management strategies should aim at reduction and harmless disposal, thereby reducing the operating costs and environmental burdens through resources.
Extreme heat alters the performance of hosts and pathogen
Authors: Porras Mitzy F. , Navas Carlos A. , Agudelo-Cantero Gustavo A. , Santiago-Martínez Michel Geovanni , Loeschcke Volker , Sørensen Jesper Givskov , Crandall Sharifa G. , Biddinger David , Rajotte Edwin G.
Published: June 2023

The frequency and intensity of extreme heat in the environment have increased in the last decade. Extreme heating events (EHE) have wide-ranging impacts on biological systems from the molecular to the community level. However, the impacts of EHE have been poorly studied in pathogen–host systems. Here, we explore how EHE affects the interaction among the insect hosts,Osmia cornifronsandOsmia lignaria, and a protozoan pathogen,Crithidia mellificae. We compared changes in the upper limit for locomotion of hosts (Ctmax), thermal boldness (voluntary exposure to Extreme Temperature Zones – ETZ) between healthy and infected host exposed to EHE, and the effect of host Ctmaxon pathogen growth rate. Our results showed that 1-day EHE significantly reduced the upper limit for locomotion of hosts by an average of 4 °C in healthy and 7 °C in infected hosts. Further, EHE significantly reduced the protozoan pathogen growth rate. EHE also reduced the hosts’ voluntary exposure to (or transit across) extreme (hot or cold) temperature zones (ETZ). Our results show that EHE reduces both hosts’ heat tolerance and pathogen fitness, and shed light on the implications of EHE on host–pathogen dynamics under warmer world.
Multidimensional hydrological modeling of a forested catchment in a German low mountain range using a modular runoff and water balance model
Authors: Schäfer Christian , Fäth Julian , Kneisel Christof , Baumhauer Roland , Ullmann Tobias
Published: June 2023

Sufficient plant-available water is one of the most important requirements for vital, stable, and well-growing forest stands. In the face of climate change, there are various approaches to derive recommendations considering tree species selection based on plant-available water provided by measurements or simulations. Owing to the small-parcel management of Central European forests as well as small-spatial variation of soil and stand properties, in situ data collection for individual forest stands of large areas is not feasible, considering time and cost effort. This problem can be addressed using physically based modeling, aiming to numerically simulate the water balance. In this study, we parameterized, calibrated, and verified the hydrological multidimensional WaSiM-ETH model to assess the water balance at a spatial resolution of 30 m in a German forested catchment area (136.4 km2) for the period 2000–2021 using selected in situ data, remote sensing products, and total runoff. Based on the model output, drought-sensitive parameters, such as the difference between potential and effective stand transpiration (Tdiff) and the water balance, were deduced from the model, analyzed, and evaluated. Results show that the modeled evapotranspiration (ET) correlated significantly (R2 = 0.80) with the estimated ET using MODIS data (MOD16A2GFv006). Compared with observed daily, monthly, and annual runoff data, the model shows a good performance (R2: 0.70|0.77|0.73; Kling–Gupta efficiency: 0.59|0.62|0.83; volumetric efficiency: 0.52|0.60|0.83). The comparison with in situ data from a forest monitoring plot, established at the end of 2020, indicated good agreement between observed and simulated interception and soil water content. According to our results, WaSiM-ETH is a potential supplement for forest management, owing to its multidimensionality and the ability to model soil water balance for large areas at comparable high spatial resolution. The outputs offer, compared to non-distributed models (like LWF-Brook90), spatial differentiability, which is important for small-scale parceled forests, regarding stand structure and soil properties. Due to the spatial component offered, additional verification possibilities are feasible allowing a reliable and profound verification of the model and its parameterization.
Clustering single-cell multimodal omics data with jrSiCKLSNMF
Authors: Ellis Dorothy , Roy Arkaprava , Datta Susmita
Published: June 2023

Introduction: The development of multimodal single-cell omics methods has enabled the collection of data across different omics modalities from the same set of single cells. Each omics modality provides unique information about cell type and function, so the ability to integrate data from different modalities can provide deeper insights into cellular functions. Often, single-cell omics data can prove challenging to model because of high dimensionality, sparsity, and technical noise.

Methods: We propose a novel multimodal data analysis method called joint graph-regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization (jrSiCKLSNMF, pronounced “junior sickles NMF”) that extracts latent factors shared across omics modalities within the same set of single cells.

Results: We compare our clustering algorithm to several existing methods on four sets of data simulated from third party software. We also apply our algorithm to a real set of cell line data.

Discussion: We show overwhelmingly better clustering performance than several existing methods on the simulated data. On a real multimodal omics dataset, we also find our method to produce scientifically accurate clustering results.
Lipids as a key element of insect defense systems
Authors: Wrońska Anna Katarzyna , Kaczmarek Agata , Boguś Mieczysława Irena , Kuna Anna
Published: June 2023

The relationship between insect pathogenic fungi and their insect hosts is a classic example of a co-evolutionary arms race between pathogen and target host: parasites evolve towards mechanisms that increase their advantage over the host, and the host increasingly strengthens its defenses. The present review summarizes the literature data describing the direct and indirect role of lipids as an important defense mechanism during fungal infection. Insect defense mechanisms comprise anatomical and physiological barriers, and cellular and humoral response mechanisms. The entomopathogenic fungi have the unique ability to digest the insect cuticle by producing hydrolytic enzymes with chitin-, lipo- and proteolytic activity; besides the oral tract, cuticle pays the way for fungal entry within the host. The key factor in insect resistance to fungal infection is the presence of certain types of lipids (free fatty acids, waxes or hydrocarbons) which can promote or inhibit fungal attachment to cuticle, and might also have antifungal activity. Lipids are considered as an important source of energy, and as triglycerides are stored in the fat body, a structure analogous to the liver and adipose tissue in vertebrates. In addition, the fat body plays a key role in innate humoral immunity by producing a range of bactericidal proteins and polypeptides, one of which is lysozyme. Energy derived from lipid metabolism is used by hemocytes to migrate to the site of fungal infection, and for phagocytosis, nodulation and encapsulation. One polyunsaturated fatty acid, arachidonic acid, is used in the synthesis of eicosanoids, which play several crucial roles in insect physiology and immunology. Apolipoprotein III is important compound with antifungal activity, which can modulate insect cellular response and is considered as important signal molecule.
Liposomes loaded with vitamin D3 induce regulatory circuits in human dendritic cells
Authors: Nagy Noémi Anna , Lozano Vigario Fernando , Sparrius Rinske , van Capel Toni M. M. , van Ree Ronald , Tas Sander W. , de Vries I. Jolanda M. , Geijtenbeek Teunis B. H. , Slütter Bram , de Jong Esther C. ,   for the DC4Balance consortium
Published: June 2023

Introduction

Nanomedicine provides a promising platform for manipulating dendritic cells (DCs) and the ensuing adaptive immune response. For the induction of regulatory responses, DCs can be targeted in vivo with nanoparticles incorporating tolerogenic adjuvants and auto-antigens or allergens.

Methods

Here, we investigated the tolerogenic effect of different liposome formulations loaded with vitamin D3 (VD3). We extensively phenotyped monocyte-derived DCs (moDCs) and skin DCs and assessed DC-induced regulatory CD4+ T cells in coculture.

Results

Liposomal VD3 primed-moDCs induced the development of regulatory CD4+ T cells (Tregs) that inhibited bystander memory T cell proliferation. Induced Tregs were of the FoxP3+ CD127low phenotype, also expressing TIGIT. Additionally, liposome-VD3 primed moDCs inhibited the development of T helper 1 (Th1) and T helper 17 (Th17) cells. Skin injection of VD3 liposomes selectively stimulated the migration of CD14+ skin DCs.

Discussion

These results suggest that nanoparticulate VD3 is a tolerogenic tool for DC-mediated induction of regulatory T cell responses.
Pancreatic adverse events of immune checkpoint inhibitors therapy for solid cancer patients: a systematic review and meta-analysis
Authors: Zhao Zhe , Zhang Weike , Pang Longbin , Zeng Liangjie , Liu Surui , Liu Jie
Published: June 2023

Objective

This review aims to determine the incidence and risk of pancreatic adverse events (AEs) associated with immune checkpoint inhibitors (ICIs) therapy for solid tumors.

Methods

We conducted a comprehensive systematic literature search in PubMed, Embase, and Cochrane Library up to March 15, 2023, to identify all randomized controlled trials comparing ICIs with standard treatment in solid tumors. We included studies that reported immune-related pancreatitis or elevation of serum amylase or lipase levels. Following protocol registration in PROSPERO, we conducted a systematic review and meta-analysis.

Results

59 unique randomized controlled trials with at least one ICI-containing arm (41 757 patients) were retrieved. The incidences for all-grade pancreatitis, amylase elevation and lipase elevation were 0.93% (95% CI 0.77-1.13), 2.57% (95% CI 1.83-3.60) and 2.78% (95% CI 1.83-4.19), respectively. The incidences for grade ≥3 pancreatitis, amylase elevation and lipase elevation were 0.68% (95% CI 0.54-0.85), 1.17% (95% CI 0.83-1.64) and 1.71% (95% CI 1.18-2.49), respectively. The use of ICIs was associated with an increased risk of all-grade pancreatic immune-related AEs (irAEs) including pancreatitis (OR=2.04, 95% CI 1.42-2.94, P =0.0001), amylase elevation (OR=1.91, 95% CI 1.47-2.49, P < 0.0001) and lipase elevation (OR=1.77, 95% CI 1.37-2.29, P < 0.0001). In addition to these, the post-hoc analysis found that PD-1 inhibitors had a significant higher risk of pancreatic AEs compared with PD-L1 inhibitors and the patients undergoing dual ICI therapy were at a significantly higher risk of pancreatic AEs than the patients receiving single ICI therapy.

Conclusion

Our study provides an overview of the incidence and risk of ICI-associated pancreatitis and pancreatic enzyme elevations in the treatment of solid tumors. Our findings may help raise awareness among clinicians of the potential for ICI-associated pancreatic AEs in clinical practice.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO, identifier 345350.
Identification of PTPN20 as an innate immunity-related gene in gastric cancer with Helicobacter pylori infection
Authors: Ma Lianjun , Liu Yang , Wang Yizhao , Yang Jiaxing , Lu Jordan , Feng Huijin , Ye Shujun , Liu Yanqing
Published: June 2023

Background

Gastric cancer (GC) is among the deadliest diseases with countless incidences and deaths each year. Helicobacter pylori (Hp) is the primary type of microbe that colonizes the stomach. In recent years, increasing evidence has demonstrated that Hp infection is one of the main risk factors for GC. Elucidating the molecular mechanism of how Hp leads to GC will not only benefit the treatment of GC, but also boost the development of therapeutics for other gastric disorders caused by Hp infection. In this study, we aimed to identify innate immunity-related genes in GC and investigate their potentials as prognostic markers and therapeutic targets for Hp-related GC.

Methods

Firstly, we analyzed the differentially expressed innate immunity-related genes in GC samples from the TCGA database. Then prognostic correlation analysis was carried out to explore the prognostic value of these candidate genes. By combing transcriptome data, somatic mutation data, and clinical data, co-expression analysis, functional enrichment analysis, tumor mutational burden analysis, and immune infiltration analysis were performed to reveal the pathological relevance of the candidate gene. Finally, ceRNA network was constructed to identify the genes and pathways for the regulation of the candidate gene.

Results

We revealed that protein tyrosine phosphatase non-receptor type 20 (PTPN20) is a significant prognostic marker in Hp-related GC. Thus, PTPN20 levels have the potential to efficiently predict the survival of Hp-related GC patients. In addition, PTPN20 is associated with immune cell infiltration and tumor mutation burden in these GC patients. Moreover, we have also identified PTPN20-related genes, PTPN20 protein-protein interactions, and the PTPN20 ceRNA network.

Conclusion

Our data suggest that PTPN20 may have critical functions in Hp-related GC. Targeting PTPN20 may be a promising way to treat Hp-related GC.
Aspergillus niger confers health benefits and modulates the gut microbiota of juvenile Pacific white shrimp (Penaeus vannamei) under farming conditions
Authors: Zhang Ming , Liang Huifen , Lei Yifan , Zhang Yiwen , Tan Zhigang , Chen Wenzhen , Li Shengkang , Peng Xianfeng , Tran Ngoc Tuan
Published: June 2023

Introduction

The fungus Aspergillus niger is found to be predominant in the body of Pacific white shrimp (Penaeus vannamei); however, its role in shrimp’s health has not been explored. This study aimed to evaluate the influences of A. niger on growth, antioxidative activity, immune response, and gut microbiota of juvenile Pacific white shrimps under farming conditions.

Methods

Shrimps (2.30±1.05 g) were fed diets supplemented with 0 (control), 1.5 (A1.5), or 3.0 g/kg diet of A. niger (A3.0) for one month. At the end of the study, the growth, antioxidant enzyme activity and immune parameters, and gut microbiota in shrimps fed with different experimental diets were analyzed.

Results

The results showed a significant increase in weight gain, specific growth rate, and length gain of shrimps in A1.5, compared with other groups (P<0.05). With the exception of lysozyme in both A1.5 and A3.0, which were lower than in the control, the activity of superoxide dismutase (SOD), catalase, acid phosphatase, alkaline phosphatase, and phenol oxidase was higher than those in the control. Gene expressions of SOD, anti-lipopolysaccharide factor-ALF1, and ALF2 (in A1.5 and A3.0) and nitric oxide synthase, penaeidin-PEN2 (in A1.5) and PEN3 and PEN4 (in A3.0) were significantly up-regulated compared to the control (P<0.05). The addition of A. niger increased diversity and separated the microbial community in the gut of shrimps. At the phylum level, Firmicutes and Bacteroidota were dominant, and Proteobacteria was less abundant in the A1.5 and A3.0, as compared to the control. At the genus level, the relative abundance of Vibrio, Marivita, and Roseobacter was increased but Ruegeria was decreased in A1.5 and A3.0 when compared to the control. The genera Edwardsiella, Clostridium sensu stricto 1, and Shimia in the A1.5 were higher than in the control.

Discussion

These findings demonstrated the beneficial effects of A. niger on growth, health, and changes in the gut microbiota in shrimps under farming conditions. The recommended concentration of A. niger in the diet for shrimps is 1.5 g/kg diet.
Fracture and dislodgment of a guidewire retrieved by a Solitaire AB neurovascular remodeling device
Authors: Liu Zhengli , Zhao Boxiang , He Xu , Gu Jianping , Gong Maofeng , Kong Jie
Published: June 2023

Background: Guidewire fracture and dislodgment are very rare but can cause serious complications.

Method: A case was reported where part of the guidewire was blocked to the posterior tibial. We attempted to remove it using a Solitaire AB Neurovascular Remodeling Device.

Result: A Solitaire AB Neurovascular Remodeling Device was successfully used to remove the fracture and dislodgment of a guidewire. There were no complications during the removal of the guidewire.

Conclusion: A Solitaire AB can be used to remove a fractured guidewire, which is a simple and effective method to reduce complications. The Solitaire stent gradually crimped and tightened to form a dense inverted conical meshwork, similar to the “trans embolic protection device.” We can use minimally invasive methods to remove a broken and displaced guidewire within the vascular lumen.
Classification of clinical skin lesions with double-branch networks
Authors: Wang Hui , Qi Qianqian , Sun Weijia , Li Xue , Yao Chunli
Published: June 2023

Introduction

Malignant skin lesions pose a great threat to the health of patients. Due to the limitations of existing diagnostic techniques, such as poor accuracy and invasive operations, malignant skin lesions are highly similar to other skin lesions, with low diagnostic efficiency and high misdiagnosis rates. Automatic medical image classification using computer algorithms can effectively improve clinical diagnostic efficiency. However, existing clinical datasets are sparse and clinical images have complex backgrounds, problems with noise interference such as light changes and shadows, hair occlusions, etc. In addition, existing classification models lack the ability to focus on lesion regions in complex backgrounds.

Methods

In this paper, we propose a DBN (double branch network) based on a two-branch network model that uses a backbone with the same structure as the original network branches and the fused network branches. The feature maps of each layer of the original network branch are extracted by our proposed CFEBlock (Common Feature Extraction Block), the common features of the feature maps between adjacent layers are extracted, and then these features are combined with the feature maps of the corresponding layers of the fusion network branch by FusionBlock, and finally the total prediction results are obtained by weighting the prediction results of both branches. In addition, we constructed a new dataset CSLI (Clinical Skin Lesion Images) by combining the publicly available dataset PAD-UFES-20 with our collected dataset, the CSLI dataset contains 3361 clinical dermatology images for six disease categories: actinic keratosis (730), cutaneous basal cell carcinoma (1136), malignant melanoma (170) cutaneous melanocytic nevus (391), squamous cell carcinoma (298) and seborrheic keratosis (636).

Results

We divided the CSLI dataset into a training set, a validation set and a test set, and performed accuracy, precision, sensitivity, specificity, f1score, balanced accuracy, AUC summary, visualisation of different model training, ROC curves and confusion matrix for various diseases, ultimately showing that the network performed well overall on the test data.

Discussion

The DBN contains two identical feature extraction network branches, a structure that allows shallow feature maps for image classification to be used with deeper feature maps for information transfer between them in both directions, providing greater flexibility and accuracy and enhancing the network's ability to focus on lesion regions. In addition, the dual branch structure of DBN provides more possibilities for model structure modification and feature transfer, and has great potential for development.
The effects of probiotics, prebiotics, and synbiotics on polycystic ovarian syndrome: an overview of systematic reviews
Authors: Angoorani Pooneh , Ejtahed Hanieh-Sadat , Ettehad Marvasti Fateme , Taghavi MinaSadat , Mohammadpour Ahranjani Behzad , Hasani-Ranjbar Shirin , Larijani Bagher
Published: June 2023

Introduction

Accumulating evidence has highlighted the critical role of the gut microbiota and its potential action as a regulator of metabolic disorders including insulin resistance, obesity, and systemic inflammation in polycystic ovarian syndrome (PCOS). Microbiota-modulating interventions, such as probiotics, prebiotics, and synbiotics, could be effective in PCOS management.

Methods

We conducted an overview of systematic reviews (SRs) and meta-analyses to summarize reviews regarding the effectiveness of probiotics/prebiotics/synbiotics on the management of PCOS through a systematic literature search in PubMed, Web of Science, and Scopus databases until September 2021.

Results

Eight SRs and meta-analyses were included in this study. Our overview confirmed that probiotic supplementation had a potentially beneficial effect on some PCOS-related parameters including body mass index (BMI), fasting plasma glucose (FPG), and lipid profiles. Evidence shows that synbiotics in comparison with probiotics were less effective on these parameters. The methodological quality of SRs was assessed using the AMSTAR-2 assessment tool and was determined as high for four SRs, low for two SRs, and critically low for one SR. Due to limited evidence and high heterogeneity of the studies, it remains difficult to identify optimal probiotics strains, prebiotics types, length of duration, and doses.

Discussion

Future clinical trials with higher quality are recommended to clarify the efficacy of probiotics/prebiotics/synbiotics on the management of PCOS and provide more accurate evidence.
Subepithelial white deposition in the cornea associated with silicone oil and surgical management: a case report
Authors: Shao Yuting , Liu Xin , Shu Yiyang , Lv Xiao , Bi Yanlong
Published: June 2023

A 36-year-old patient presented with a complaint of an extensive “white scar” in his right eye without pain after silicone oil presence in the vitreous cavity for 12 years. Slit-lamp microscopy revealed extensive corneal leukoplakia and mild limbus neovascularization. Anterior segment optical coherence tomography revealed marked eccentric thickening of the subepithelium and normal thickness of the stroma. We proceeded with silicone oil removal and intraocular and anterior chamber lavage at first, followed by epithelial lesion excision combined with amniotic membrane transplantation 3 months later. The patient was satisfied with the clear cornea appearance.