bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-evaluating the genotypes of patients with adenomatous polyposis of unknown etiology: a nationwide study
Authors: Karstensen John Gásdal , Hansen Thomas v. Overeem , Burisch Johan , Djursby Malene , Højen Helle , Madsen Majbritt Busk , Jespersen Niels , Jelsig Anne Marie 
Published: March 2024

AbstractIn the Danish Polyposis Register, patients with over 100 cumulative colorectal adenomas of unknown genetic etiology, named in this study colorectal polyposis (CP), is registered and treated as familial adenomatous polyposis (FAP). In this study, we performed genetic analyses, including whole genome sequencing (WGS), of all Danish patients registered with CP and estimated the detection rate of pathogenic variants (PV). We identified 231 families in the Polyposis Register, 31 of which had CP. A polyposis-associated gene panel was performed and, if negative, patients were offered WGS and screening for mosaicism in blood and/or adenomas. Next-generation sequencing (NGS) was carried out for 27 of the families (four declined). PVs were detected in 11 families, and WGS revealed three additional structural variants in APC. Mosaicism of a PV in APC was detected in two families. As the variant detection rate of eligible families was 60%, 93% of families in the register now have a known genetic etiology.
A shedding analysis after AAV8 CNS injection revealed fragmented viral DNA without evidence of functional AAV particles in mice
Authors: Krause Felix , Schmidtke Katja , de Vasconcelos Mailton Franca , Schmidt David , Cansiz Beyza , Theisen Franziska , Mark Melanie D. , Rybarski Max O. 
Published: March 2024

AbstractAdeno-associated viruses (AAV) are commonly used in the scientific field due to their diverse application range. However, AAV shedding, the release of virions from the host organism, can impact the safety of AAV-based approaches. An increasing number of authorities require the characterization of vector shedding in clinical trials. Recently, shedding of transduced laboratory animals has also gained attention regarding the necessary disposal measures of their waste products. However, no explicit international regulations for AAV-shedding waste exist. Generating insights into shedding dynamics becomes increasingly relevant to help authorities develop adequate regulations. To date, knowledge of AAV vector shedding in mice is very limited. Moreover, confirmation of functional shed AAV particles in mice is missing. Therefore, we examined feces, urine, and saliva of mice after CNS injection with AAV2/8. It revealed the presence of viral DNA fragments via qPCR for up to 4 days after injection. To examine AAV functionality we performed nested PCR and could not detect full-length viral genomes in any but two collected feces samples. Furthermore, a functional infection assay did not reveal evidence of intact AAV particles. Our findings are supposed to contribute murine shedding data as a foundation to help establish still lacking adequate biosafety regulations in the context of AAV shedding.
Numerosity estimation of virtual humans as a digital-robotic marker for hallucinations in Parkinson’s disease
Authors: Albert Louis , Potheegadoo Jevita , Herbelin Bruno , Bernasconi Fosco , Blanke Olaf 
Published: March 2024

AbstractHallucinations are frequent non-motor symptoms in Parkinson’s disease (PD) associated with dementia and higher mortality. Despite their high clinical relevance, current assessments of hallucinations are based on verbal self-reports and interviews that are limited by important biases. Here, we used virtual reality (VR), robotics, and digital online technology to quantify presence hallucination (vivid sensations that another person is nearby when no one is actually present and can neither be seen nor heard) in laboratory and home-based settings. We establish that elevated numerosity estimation of virtual human agents in VR is a digital marker for experimentally induced presence hallucinations in healthy participants, as confirmed across several control conditions and analyses. We translated the digital marker (numerosity estimation) to an online procedure that 170 PD patients carried out remotely at their homes, revealing that PD patients with disease-related presence hallucinations (but not control PD patients) showed higher numerosity estimation. Numerosity estimation enables quantitative monitoring of hallucinations, is an easy-to-use unobtrusive online method, reaching people far away from medical centers, translating neuroscientific findings using robotics and VR, to patients’ homes without specific equipment or trained staff.
The first demonstration of entirely roll-to-roll fabricated perovskite solar cell modules under ambient room conditions
Authors: Weerasinghe Hasitha C. , Macadam Nasiruddin , Kim Jueng-Eun , Sutherland Luke J. , Angmo Dechan , Ng Leonard W. T. , Scully Andrew D. , Glenn Fiona , Chantler Regine , Chang Nathan L. , Dehghanimadvar Mohammad , Shi Lei , Ho-Baillie Anita W. Y. , Egan Renate , Chesman Anthony S. R. , Gao Mei , Jasieniak Jacek J. , Hasan Tawfique , Vak Doojin 
Published: March 2024

AbstractThe rapid development of organic-inorganic hybrid perovskite solar cells has resulted in laboratory-scale devices having power conversion efficiencies that are competitive with commercialised technologies. However, hybrid perovskite solar cells are yet to make an impact beyond the research community, with translation to large-area devices fabricated by industry-relevant manufacturing methods remaining a critical challenge. Here we report the first demonstration of hybrid perovskite solar cell modules, comprising serially-interconnected cells, produced entirely using industrial roll-to-roll printing tools under ambient room conditions. As part of this development, costly vacuum-deposited metal electrodes are replaced with printed carbon electrodes. A high-throughput experiment involving the analysis of batches of 1600 cells produced using 20 parameter combinations enabled rapid optimisation over a large parameter space. The optimised roll-to-roll fabricated hybrid perovskite solar cells show power conversion efficiencies of up to 15.5% for individual small-area cells and 11.0% for serially-interconnected cells in large-area modules. Based on the devices produced in this work, a cost of ~0.7 USD W−1 is predicted for a production rate of 1,000,000 m² per year in Australia, with potential for further significant cost reductions.
Inhibition of 7-dehydrocholesterol reductase prevents hepatic ferroptosis under an active state of sterol synthesis
Authors: Yamada Naoya , Karasawa Tadayoshi , Ito Junya , Yamamuro Daisuke , Morimoto Kazushi , Nakamura Toshitaka , Komada Takanori , Baatarjav Chintogtokh , Saimoto Yuma , Jinnouchi Yuka , Watanabe Kazuhisa , Miura Kouichi , Yahagi Naoya , Nakagawa Kiyotaka , Matsumura Takayoshi , Yamada Ken-ichi , Ishibashi Shun , Sata Naohiro , Conrad Marcus , Takahashi Masafumi 
Published: March 2024

AbstractRecent evidence indicates ferroptosis is implicated in the pathophysiology of various liver diseases; however, the organ-specific regulation mechanism is poorly understood. Here, we demonstrate 7-dehydrocholesterol reductase (DHCR7), the terminal enzyme of cholesterol biosynthesis, as a regulator of ferroptosis in hepatocytes. Genetic and pharmacological inhibition (with AY9944) of DHCR7 suppress ferroptosis in human hepatocellular carcinoma Huh-7 cells. DHCR7 inhibition increases its substrate, 7-dehydrocholesterol (7-DHC). Furthermore, exogenous 7-DHC supplementation using hydroxypropyl β-cyclodextrin suppresses ferroptosis. A 7-DHC-derived oxysterol metabolite, 3β,5α-dihydroxycholest-7-en-6-one (DHCEO), is increased by the ferroptosis-inducer RSL-3 in DHCR7-deficient cells, suggesting that the ferroptosis-suppressive effect of DHCR7 inhibition is associated with the oxidation of 7-DHC. Electron spin resonance analysis reveals that 7-DHC functions as a radical trapping agent, thus protecting cells from ferroptosis. We further show that AY9944 inhibits hepatic ischemia-reperfusion injury, and genetic ablation of Dhcr7 prevents acetaminophen-induced acute liver failure in mice. These findings provide new insights into the regulatory mechanism of liver ferroptosis and suggest a potential therapeutic option for ferroptosis-related liver diseases.
PHEIGES: all-cell-free phage synthesis and selection from engineered genomes
Authors: Levrier Antoine , Karpathakis Ioannis , Nash Bruce , Bowden Steven D. , Lindner Ariel B. , Noireaux Vincent 
Published: March 2024

AbstractBacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.
Circulating tumor DNA validity and potential uses in metastatic breast cancer
Authors: Amato Ottavia , Giannopoulou Nefeli , Ignatiadis Michail 
Published: March 2024

AbstractFollowing the first characterization of circulating tumor DNA (ctDNA) in the 1990s, recent advances led to its introduction in the clinics. At present, the European Society Of Medical Oncology (ESMO) recommendations endorse ctDNA testing in routine clinical practice for tumor genotyping to direct molecularly targeted therapies in patients with metastatic cancer. In studies on metastatic breast cancer, ctDNA has been utilized for treatment tailoring, tracking mechanisms of drug resistance, and for predicting disease response before imaging. We review the available evidence regarding ctDNA applications in metastatic breast cancer.
Single-cell integrative analysis reveals consensus cancer cell states and clinical relevance in breast cancer
Authors: Pang Lin , Xiang Fengyu , Yang Huan , Shen Xinyue , Fang Ming , Li Ran , Long Yongjin , Li Jiali , Yu Yonghuan , Pang Bo 
Published: March 2024

AbstractHigh heterogeneity and complex interactions of malignant cells in breast cancer has been recognized as a driver of cancer progression and therapeutic failure. However, complete understanding of common cancer cell states and their underlying driver factors remain scarce and challenging. Here, we revealed seven consensus cancer cell states recurring cross patients by integrative analysis of single-cell RNA sequencing data of breast cancer. The distinct biological functions, the subtype-specific distribution, the potential cells of origin and the interrelation of consensus cancer cell states were systematically elucidated and validated in multiple independent datasets. We further uncovered the internal regulons and external cell components in tumor microenvironments, which contribute to the consensus cancer cell states. Using the state-specific signature, we also inferred the abundance of cells with each consensus cancer cell state by deconvolution of large breast cancer RNA-seq cohorts, revealing the association of immune-related state with better survival. Our study provides new insights for the cancer cell state composition and potential therapeutic strategies of breast cancer.
Towards standardising retinal OCT angiography image analysis with open-source toolbox OCTAVA
Authors: Untracht Gavrielle R. , Durkee Madeleine S. , Zhao Mei , Kwok-Cheung Lam Andrew , Sikorski Bartosz L. , Sarunic Marinko V. , Andersen Peter E. , Sampson David D. , Chen Fred K. , Sampson Danuta M. 
Published: March 2024

AbstractQuantitative assessment of retinal microvasculature in optical coherence tomography angiography (OCTA) images is important for studying, diagnosing, monitoring, and guiding the treatment of ocular and systemic diseases. However, the OCTA user community lacks universal and transparent image analysis tools that can be applied to images from a range of OCTA instruments and provide reliable and consistent microvascular metrics from diverse datasets. We present a retinal extension to the OCTA Vascular Analyser (OCTAVA) that addresses the challenges of providing robust, easy-to-use, and transparent analysis of retinal OCTA images. OCTAVA is a user-friendly, open-source toolbox that can analyse retinal OCTA images from various instruments. The toolbox delivers seven microvascular metrics for the whole image or subregions and six metrics characterising the foveal avascular zone. We validate OCTAVA using images collected by four commercial OCTA instruments demonstrating robust performance across datasets from different instruments acquired at different sites from different study cohorts. We show that OCTAVA delivers values for retinal microvascular metrics comparable to the literature and reduces their variation between studies compared to their commercial equivalents. By making OCTAVA publicly available, we aim to expand standardised research and thereby improve the reproducibility of quantitative analysis of retinal microvascular imaging. Such improvements will help to better identify more reliable and sensitive biomarkers of ocular and systemic diseases.
Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators
Authors: Diaz Soria Carmen L. , Attenborough Teresa , Lu Zhigang , Fontenla Santiago , Graham Jennie , Hall Christopher , Thompson Sam , Andrews Toby G. R. , Rawlinson Kate A. , Berriman Matthew , Rinaldi Gabriel 
Published: March 2024

AbstractSchistosomiasis is a major Neglected Tropical Disease, caused by the infection with blood flukes in the genus Schistosoma. To complete the life cycle, the parasite undergoes asexual and sexual reproduction within an intermediate snail host and a definitive mammalian host, respectively. The intra-molluscan phase provides a critical amplification step that ensures a successful transmission. However, the cellular and molecular mechanisms underlying the development of the intra-molluscan stages remain poorly understood. Here, single cell suspensions from S. mansoni mother sporocysts were produced and sequenced using the droplet-based 10X Genomics Chromium platform. Six cell clusters comprising two tegument, muscle, neuron, parenchyma and stem/germinal cell clusters were identified and validated by in situ hybridisation. Gene Ontology term analysis predicted key biological processes for each of the clusters, including three stem/germinal sub-clusters. Furthermore, putative transcription factors predicted for stem/germinal and tegument clusters may play key roles during parasite development and interaction with the intermediate host.
Imaging predictors of hemorrhagic progression of a contusion after traumatic brain injury: a systematic review and meta-analysis
Authors: Peng Jie , Luo Tao , Li Xiaoyu , Li Bin , Cheng Yuan , Huang Qin , Su Jun 
Published: March 2024

AbstractThe hemorrhagic progression of a contusion (HPC) after Traumatic brain injury (TBI) is one of the important causes of death in trauma patients. The purpose of this meta-analysis was to evaluate the predictive effect of imaging features of Computed tomography (CT) on HPC after TBI. A comprehensive systematic search was performed using PubMed, EMBASE, and WEB OF SCIENCE databases to identify all relevant literature. A total of 8 studies involving 2543 patients were included in this meta-analysis. Meta-analysis showed that subarachnoid hemorrhage (OR 3.28; 95% CI 2.57–4.20), subdural hemorrhage (OR 4.35; 95% CI 3.29–5.75), epidural hemorrhage (OR 1.47;95% CI 1.15–1.89), contrast extravasation (OR 11.81; 95% CI 4.86–28.71) had a predictive effect on the occurrence of HPC. Skull fracture (OR 1.64; 95% CI 0.84–3.19) showed no statistical significance, and midline displacement > 5 mm (OR 4.66; 95% CI 1.87–11.62) showed high heterogeneity. The results of this meta-analysis showed that some imaging features were effective predictors of HPC after TBI. Well-designed prospective studies are needed to more accurately assess the effective predictors of HPC after TBI.
Application of machine learning algorithms for accurate determination of bilirubin level on in vitro engineered tissue phantom images
Authors: Yuan Yijia , Huang Jiayao , Yu Jiachen , Tan Justin Kok Soon , Chng Kevin Ziyang , Lee Jiun , Kim Sangho 
Published: March 2024

AbstractNeonatal Jaundice is a common occurrence in neonates. High excess bilirubin would lead to hyperbilirubinemia, leading to irreversible adverse damage such as kernicterus. Therefore, it is necessary and important to monitor neonates’ bilirubin levels in real-time for immediate intervention. However, current screening protocols have their inherent limitations, necessitating more convenient measurements. In this proof-of-concept study, we evaluated the feasibility of using machine learning for the screening of hyperbilirubinemia in neonates from smartphone-acquired photographs. Different machine learning models were compared and evaluated to gain a better understanding of feature selection and model performance in bilirubin determination. An in vitro study was conducted with a bilirubin-containing tissue phantom to identify potential biological and environmental confounding factors. The findings of this study present a systematic characterization of the confounding effect of various factors through separate parametric tests. These tests uncover potential techniques in image pre-processing, highlighting important biological features (light scattering property and skin thickness) and external features (ISO, lighting conditions and white balance), which together contribute to robust model approaches for accurately determining bilirubin concentrations. By obtaining an accuracy of 0.848 in classification and 0.812 in regression, these findings indicate strong potential in aiding in the design of clinical studies using patient-derived images.
Data-driven autonomous operation of VOCs removal system
Authors: Kang Myeonginn , Han Jongmin , Kim Yangjoon , Kim Seongcheon , Kang Seokho 
Published: March 2024

AbstractRemoval of volatile organic compounds (VOCs) from the air has been an important issue in many industrial fields. Traditionally, the operation of VOCs removal systems has relied on fixed operating conditions determined by domain experts based on their expertise and intuition. In practice, this manual operation cannot respond immediately to changes in the system environment. To facilitate the autonomous operation of the system, the operating conditions should be optimized properly in real time to adapt to the changes in the system environment. Recently, optimization frameworks have been widely applied to real-world industrial systems across various domains using different approaches. The primary motivation for this study is the effective implementation of an optimization framework targeting a VOCs removal system. In this paper, we present a data-driven autonomous operation method for optimizing the operating conditions of a VOCs removal system to enhance the overall performance. An optimization problem is formulated with the decision variables denoting the parameters associated with the operating condition, the environmental variables representing the measurements for the system environment, the constraints specifying the control ranges of the parameters, and the objective function representing the system performance as determined by the operating conditions and environment. Using the previous operation data from the system, a neural network is trained to model the system performance as a function of the decision and environmental variables to approximate the objective function. For the current state of the system environment, the optimal operating condition is derived by solving the optimization problem. A case study of a targeted VOCs removal system demonstrates that the proposed method effectively optimizes the operating conditions for improved system performance without intervention from domain experts.
From instable directional switching to controlled unidirectional operation in a nonlinear fiber ring laser
Authors: Hartung Alexander , Arshad Muhammad Assad , Jäger Matthias 
Published: March 2024

AbstractWe investigate a new phenomenon, where a reciprocal fiber ring laser switches from bidirectional to unidirectional operation above a certain pump power threshold. Significant simplifications regarding earlier experiments are presented, which for the first time allow the identification of individual nonlinear effects. We highlight the unique role of stimulated Raman scattering in triggering unidirectional operation, and that additional conditions apply. The threshold is reduced from 30 to 3.8 W, which eases potential applications.
Association study of morpho-phenological traits in quinoa (Chenopodium quinoa Willd.) using SSR markers
Authors: Souri Laki Ebrahim , Rabiei Babak , Marashi Hassan , Jokarfard Vahid , Börner Andreas 
Published: March 2024

AbstractIn this study, the genetic and molecular diversity of 60 quinoa accessions was assessed using agronomically important traits related to grain yield as well as microsatellite (SSR) markers, and informative markers linked to the studied traits were identified using association study. The results showed that most of the studied traits had a relatively high diversity, but grain saponin and protein content showed the highest diversity. High diversity was also observed in all SSR markers, but KAAT023, KAAT027, KAAT036, and KCAA014 showed the highest values for most of the diversity indices and can be introduced as the informative markers to assess genetic diversity in quinoa. Population structure analysis showed that the studied population probably includes two subclusters, so that out of 60 quinoa accessions, 29 (48%) and 23 (38%) accessions were assigned to the first and second subclusters, respectively, and eight (13%) accessions were considered as the mixed genotypes. The study of the population structure using Structure software showed two possible subgroups (K = 2) in the studied population and the results of the bar plot confirmed it. Association study using the general linear model (GLM) and mixed linear model (MLM) identified the number of 35 and 32 significant marker-trait associations (MTAs) for the first year (2019) and 37 and 35 significant MTAs for the second year (2020), respectively. Among the significant MTAs identified for different traits, the highest number of significant MTAs were obtained for grain yield and 1000-grain weight with six and five MTAs, respectively.