bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stage-specific GATA3 induction promotes ILC2 development after lineage commitment
Authors: Furuya Hiroki , Toda Yosuke , Iwata Arifumi , Kanai Mizuki , Kato Kodai , Kumagai Takashi , Kageyama Takahiro , Tanaka Shigeru , Fujimura Lisa , Sakamoto Akemi , Hatano Masahiko , Suto Akira , Suzuki Kotaro , Nakajima Hiroshi 
Published: July 2024

AbstractGroup 2 innate lymphoid cells (ILC2s) are a subset of innate lymphocytes that produce type 2 cytokines, including IL-4, IL-5, and IL-13. GATA3 is a critical transcription factor for ILC2 development at multiple stages. However, when and how GATA3 is induced to the levels required for ILC2 development remains unclear. Herein, we identify ILC2-specific GATA3-related tandem super-enhancers (G3SE) that induce high GATA3 in ILC2-committed precursors. G3SE-deficient mice exhibit ILC2 deficiency in the bone marrow, lung, liver, and small intestine with minimal impact on other ILC lineages or Th2 cells. Single-cell RNA-sequencing and subsequent flow cytometry analysis show that GATA3 induction mechanism, which is required for entering the ILC2 stage, is lost in IL-17RB+PD-1− late ILC2-committed precursor stage in G3SE-deficient mice. Cnot6l, part of the CCR4-NOT deadenylase complex, is a possible GATA3 target during ILC2 development. Our findings implicate a stage-specific regulatory mechanism for GATA3 expression during ILC2 development.
Neuroimaging and fluid biomarkers in Parkinson’s disease in an era of targeted interventions
Authors: Zarkali Angeliki , Thomas George E. C. , Zetterberg Henrik , Weil Rimona S. 
Published: July 2024

AbstractA major challenge in Parkinson’s disease is the variability in symptoms and rates of progression, underpinned by heterogeneity of pathological processes. Biomarkers are urgently needed for accurate diagnosis, patient stratification, monitoring disease progression and precise treatment. These were previously lacking, but recently, novel imaging and fluid biomarkers have been developed. Here, we consider new imaging approaches showing sensitivity to brain tissue composition, and examine novel fluid biomarkers showing specificity for pathological processes, including seed amplification assays and extracellular vesicles. We reflect on these biomarkers in the context of new biological staging systems, and on emerging techniques currently in development.
In situ copper photocatalysts triggering halide atom transfer of unactivated alkyl halides for general C(sp3)-N couplings
Authors: Luo Hang , Yang Yupeng , Fu Yukang , Yu Fangnian , Gao Lei , Ma Yunpeng , Li Yang , Wu Kaifeng , Lin Luqing 
Published: July 2024

AbstractDirect reduction of unactivated alkyl halides for C(sp3)-N couplings under mild conditions presents a significant challenge in organic synthesis due to their low reduction potential. Herein, we introduce an in situ formed pyridyl-carbene-ligated copper (I) catalyst that is capable of abstracting halide atom and generating alkyl radicals for general C(sp3)-N couplings under visible light. Control experiments confirmed that the mono-pyridyl-carbene-ligated copper complex is the active species responsible for catalysis. Mechanistic investigations using transient absorption spectroscopy across multiple decades of timescales revealed ultrafast intersystem crossing (260 ps) of the photoexcited copper (I) complexes into their long-lived triplet excited states (>2 μs). The non-Stern-Volmer quenching dynamics of the triplets by unactivated alkyl halides suggests an association between copper (I) complexes and alkyl halides, thereby facilitating the abstraction of halide atoms via inner-sphere single electron transfer (SET), rather than outer-sphere SET, for the formation of alkyl radicals for subsequent cross couplings.
Genetically programmed synthetic cells for thermo-responsive protein synthesis and cargo release
Authors: Monck Carolina , Elani Yuval , Ceroni Francesca 
Published: July 2024

AbstractSynthetic cells containing genetic programs and protein expression machinery are increasingly recognized as powerful counterparts to engineered living cells in the context of biotechnology, therapeutics and cellular modelling. So far, genetic regulation of synthetic cell activity has been largely confined to chemical stimuli; to unlock their potential in applied settings, engineering stimuli-responsive synthetic cells under genetic regulation is imperative. Here we report the development of temperature-sensitive synthetic cells that control protein production by exploiting heat-responsive mRNA elements. This is achieved by combining RNA thermometer technology, cell-free protein expression and vesicle-based synthetic cell design to create cell-sized capsules able to initiate synthesis of both soluble proteins and membrane proteins at defined temperatures. We show that the latter allows for temperature-controlled cargo release phenomena with potential implications for biomedicine. Platforms like the one presented here can pave the way for customizable, genetically programmed synthetic cells under thermal control to be used in biotechnology.
Climate data for building simulations with urban heat island effects and nature-based solutions
Authors: Lu Henry , Gaur Abhishek , Lacasse Michael 
Published: July 2024

AbstractAs cities face a changing climate, buildings will be subjected to increasing energy demand, heat stress, thermal comfort issues, and decreased service life. Therefore, evaluating building performance under climate change is essential for maintaining sustainable and resilient communities. To better prepare building simulation climate data with urban effects, a computationally efficient approach is used to generate “urbanized” data, where the city’s unique signature is obtained through the dynamic Weather Research and Forecasting model for the Ottawa, Canada region. We demonstrate this process using existing climate data and extend it to prepare projections for scenarios where nature-based solutions, such as increased greenery and albedo, were implemented. The data consists of several 31-year time series of climate variables such as temperature, humidity, wind speed and direction, pressure, cloud cover, and precipitation over different global warming thresholds. Such a dataset allows building practitioners to evaluate building performance under both historical and future climate conditions, as well as to evaluate the impacts of nature-based solutions to mitigate future climate change risks.
Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets
Authors: O’Leary Nuala A. , Cox Eric , Holmes J. Bradley , Anderson W. Ray , Falk Robert , Hem Vichet , Tsuchiya Mirian T. N. , Schuler Gregory D. , Zhang Xuan , Torcivia John , Ketter Anne , Breen Laurie , Cothran Jonathan , Bajwa Hena , Tinne Jovany , Meric Peter A. , Hlavina Wratko , Schneider Valerie A. 
Published: July 2024

AbstractTo explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data.
Correlation analysis of whole genome sequencing of a pathogenic Escherichia coli strain of Inner Mongolian origin
Authors: Jia Yan , Zhang Kai , Cao Jinshan , Mao Wei 
Published: July 2024

AbstractAnal swabs of 1-month-old Holstein calves with diarrhea were collected from an intensive cattle farm, and a highly pathogenic Escherichia coli strain was obtained by isolation and purification. To study the virulence and resistance genes of pathogenic E.coli that cause diarrhea in calves, a strain of E. coli E12 isolated from calf diarrhea samples was used as experimental material in this experiment, and the virulence of the E12 strain were identified by the mouse infection test, and the whole genome map of the E12 strain were obtained by whole-genome sequencing and analyzed for genome characterization. The results showed that the lethality of strain E12 was 100%, the total length of E12-encoded genes was 4,294,530 bp, Cluster of Orthologous Groups of proteins (COG) annotated to 4,194 functional genes, and the virulence genes of sequenced strain E12 were compared with the virulence genes of sequenced strain E12 from the Virulence Factors of Pathogenic Bacteria (VFDB), which contained a total of 366 virulence genes in sequenced strain E12. The analysis of virulence genes of E12 revealed a total of 52 virulence genes in the iron transferrin system, 56 virulence genes in the secretory system, 41 virulence genes in bacterial toxins, and a total of 217 virulence genes in the Adhesin and Invasins group. The antibiotic resistance genes of sequenced strain E12 were identified through the Antibiotic Resistance Genes Database (ARDB) and Comprehensive Antibiotic Research Database, and it was found that its chromosome and plasmid included a total of 127 antibiotic resistance genes in four classes, and that E12 carried 71 genes related to the antibiotic efflux pumps, 36 genes related to antibiotic inactivation, and 14 antibiotic target alteration and reduced penetration into antibiotics, and 6 antibiotic resistance genes, and the resistance phenotypes were consistent with the genotypes. The pathogenic E. coli that causes diarrhea in calves on this ranch contains a large number of virulence and resistance genes. The results provide a theoretical basis for the prevention and treatment of diarrhea and other diseases caused by E. coli disease.
Adsorption characteristics and applications of andesite in removing some pollutants from wastewater
Authors: Khedr Abdalla M. , Elwakiel Nadia , Halawia Sameh E. , Mansour Ramadan Abdelghany 
Published: July 2024

AbstractAndesite was employed to effectively extract mercury(II) in an aqueous solution. After evaluating its characteristics, andesite was characterized by applying modern techniques such as BET and TGA methods. The study employed SEM and TEM measurements to analyze the variation in the surface shape and crystallinity of the metal due to adsorption. Using the EDX process, the chemical composition, weight, and atomic percentage of each element of andesite were determined. FTIR techniques were also used to confirm the TEM–EDX findings. Zeta potential was estimated. Cycles of regeneration and desorption have been examined. 99.03% was the highest uptake percentage. Adsorbent quantity (0.0025–0.05) g/L, contact time (5–60) min, pH (2–10), temperature (25–60) °C, and dose (0.0027, 0.0044, 0.0125, 0.0155, and 0.0399) mg/L all affect the amount of removal that increases with the increase in contact time, pH, dose, and temperature but drops as the metal ion concentration rises. The ideal values for contact time, pH, metal ion concentration, dose, and temperature were found to be, respectively, 30 min, 0.0155 mg/l, 0.02 g/l, and 40 °C. The calculation of thermodynamic parameters, including ΔH, ΔG, and ΔS, was imperative in establishing that the mechanism of heavy metal adsorption on andesite was endothermic, exhibiting a physical nature that escalated with temperature rise. The Freundlich adsorption equation's linear form is matched by the adsorption of mercury(II) on andesite; constant n was 1.85, 1.06, 1.1, and 1.1, whereas the Langmuir constant qmwas found to be 1.85, 2.41, 3.54, and 2.28 mg/g at 25–60 °C. Furthermore, adsorption follows a pseudo-second-order rate constant of (3.08, 3.24, 3.24, and 13) g/mg/min under identical temperature conditions, as opposed to a first-order rate constant of 4, 3, 2.6, and 2. Hg2+, NH4+, Cl−, Br−, NO3−, SO42−, Na+, K+, H2S, and CH3SH were all extracted from wastewater by this application.
A retrospective study on the impact of radiotherapy on the survival outcomes of small cell lung cancer patients based on the SEER database
Authors: Chen Yao , Yao Ling , Chen Qingquan , Hu Yiming , Zhu Xi , Dai Rongrong , Chen Xiaoyang , Zeng Yifu , Zhu Yong , Song Duanhong , Zhang Yixiang 
Published: July 2024

AbstractSmall cell lung cancer (SCLC) patients exhibit significant heterogeneity in tumor burden, physical condition, and responses to initial treatment. This diversity in treatment responses can result in varying treatment outcomes. The primary objective of this study was to explore the patient demographics associated with improved survival outcomes through radiotherapy. Based on the SEER database, we identified 42,824 SCLC patients enrolled between 2004 and 2015. These patients were stratified into radiotherapy (n = 20,360) and non-radiotherapy groups (n = 22,464). We controlled for confounding factors using propensity score matching (PSM) analysis. Subsequently, Kaplan–Meier (KM) analysis was employed to evaluate the impact of radiotherapy on patients’ overall survival (OS) and cancer-specific survival (CSS). Cancer-specific mortality was further analyzed using competitive risk models. Cox analysis was also conducted to examine additional variables potentially affecting the survival of SCLC patients. We identified a total of 42,824 eligible patients, and following PSM, 13,329 patients were successfully matched in both the radiotherapy and non-radiotherapy groups. The KM analysis showed that the median OS was 9 months in the radiotherapy group and 6 months in the non-radiotherapy group. The median CSS was 10 months in the radiotherapy group and 7 months in the non-radiotherapy group. The 5-year OS and 10-year OS rates were 6.2% versus 1.6% in the radiotherapy group and 2.6% versus 0.8% in the non-radiotherapy group (P < 0.001). Competitive risk analysis showed that cancer-specific mortality was significantly higher in the non-radiotherapy group than in the radiotherapy group (P < 0.001). Multivariate Cox analysis showed that the radiotherapy group (relative non-radiotherapy group) showed a significant positive effect on survival outcomes (OS: HR 0.658 95% CI [0.642, 0.675] P < 0.001; CSS: HR 0.662 95% CI [0.645, 0.679], P < 0.001). In addition, age, gender, race, primary tumor site, T stage, N stage, M stage, chemotherapy, and surgery were also considered as important predictors of SCLC outcome. The results of the subgroup analysis showed that the radiotherapy group showed a significant survival advantage regardless of age, sex, race, primary tumor site, M stage, chemotherapy, and surgery (P < 0.001). Radiotherapy may improve both OS and CSS in SCLC patients. Patients with SCLC may benefit from radiotherapy regardless of age, sex, race, primary tumor site, M stage, chemotherapy, and surgery.
Exploring the ecological security evaluation of water resources in the Yangtze River Basin under the background of ecological sustainable development
Authors: Zhou Jie-Rong , Li Xiao-Qing , Yu Xin , Zhao Tian-Cheng , Ruan Wen-Xi 
Published: July 2024

AbstractThe Yangtze River (hereafter referred to as the YZR), the largest river in China, is of paramount importance for ensuring water resource security. The Yangtze River Basin (hereafter referred to as the YRB) is one of the most densely populated areas in China, and complex human activities have a significant impact on the ecological security of water resources. Therefore, this paper employs theories related to ecological population evolution and the Driving Force-Pressure-State-Impact-Response (DPSIR) model to construct an indicator system for the ecological security of water resources in the YRB. The report evaluates the ecological security status of water resources in each province of the YRB from 2010 to 2019, clarifies the development trend of its water resource ecological security, and proposes corresponding strategies for regional ecological security and coordinated economic development. According to the results of the ecological population evolution competition model, the overall indicator of the ecological security of water resources in the YRB continues to improve, with the safety level increasing annually. Maintaining sound management of water resources in the YRB is crucial for sustainable socioeconomic development. To further promote the ecological security of water resources in the YRB and the coordinated development of the regional economy, this paper proposes policy suggestions such as promoting the continuous advancement of sustainable development projects, actively adjusting industrial structure, continuously enhancing public environmental awareness, and actively participating in international ecological construction and seeking cooperation among multiple departments.
AI driven analysis of MRI to measure health and disease progression in FSHD
Authors: Riem Lara , DuCharme Olivia , Cousins Matthew , Feng Xue , Kenney Allison , Morris Jacob , Tapscott Stephen J. , Tawil Rabi , Statland Jeff , Shaw Dennis , Wang Leo , Walker Michaela , Lewis Leann , Jacobs Michael A. , Leung Doris G. , Friedman Seth D. , Blemker Silvia S. 
Published: July 2024

AbstractFacioscapulohumeral muscular dystrophy (FSHD) affects roughly 1 in 7500 individuals. While at the population level there is a general pattern of affected muscles, there is substantial heterogeneity in muscle expression across- and within-patients. There can also be substantial variation in the pattern of fat and water signal intensity within a single muscle. While quantifying individual muscles across their full length using magnetic resonance imaging (MRI) represents the optimal approach to follow disease progression and evaluate therapeutic response, the ability to automate this process has been limited. The goal of this work was to develop and optimize an artificial intelligence-based image segmentation approach to comprehensively measure muscle volume, fat fraction, fat fraction distribution, and elevated short-tau inversion recovery signal in the musculature of patients with FSHD. Intra-rater, inter-rater, and scan-rescan analyses demonstrated that the developed methods are robust and precise. Representative cases and derived metrics of volume, cross-sectional area, and 3D pixel-maps demonstrate unique intramuscular patterns of disease. Future work focuses on leveraging these AI methods to include upper body output and aggregating individual muscle data across studies to determine best-fit models for characterizing progression and monitoring therapeutic modulation of MRI biomarkers.
Vaccination homophily in ego contact networks during the COVID-19 pandemic
Authors: Stefkovics Ádám , Albert Fruzsina , Ligeti Anna Sára , Dávid Beáta , Rudas Szilvia , Koltai Júlia 
Published: July 2024

AbstractVaccine hesitancy is an inevitable risk for societies as it contributes to outbreaks of diseases. Prior research suggests that vaccination decisions of individuals tend to spread within social networks, resulting in a tendency to vaccination homophily. The clustering of individuals resistant to vaccination can substantially make the threshold necessary to achieve herd immunity harder to reach. In this study, we examined the extent of vaccination homophily among social contacts and its association with vaccine uptake during the COVID-19 pandemic in Hungary using a contact diary approach in two cross-sectional surveys. The results indicate strong clustering among both vaccinated and unvaccinated groups. The most powerful predictor of vaccine uptake was the perceived vaccination rate within the egos’ social contact network. Vaccination homophily and the role of the interpersonal contact network in vaccine uptake were particularly pronounced in the networks of close relationships, including family, kinship, and strong social ties of the ego. Our findings have important implications for understanding COVID-19 spread dynamics by showing that the strong clustering of unvaccinated individuals posed a great risk in preventing the spread of the disease.
3D engineered scaffold for large-scale Vigil immunotherapy production
Authors: Kerneis Fabienne , Bognar Ernest , Stanbery Laura , Moon Seongjun , Kim Do Hoon , Deng Yuxuan , Hughes Elliot , Chun Tae-Hwa , Tharp Darron , Zupanc Heidi , Jay Chris , Walter Adam , Nemunaitis John , Lahann Joerg 
Published: July 2024

AbstractPreviously, we reported successful cellular expansion of a murine colorectal carcinoma cell line (CT-26) using a three-dimensional (3D) engineered extracellular matrix (EECM) fibrillar scaffold structure. CCL-247 were grown over a limited time period of 8 days on 3D EECM or tissue culture polystyrene (TCPS). Cells were then assayed for growth, electroporation efficiency and Vigil manufacturing release criteria. Using EECM scaffolds, we report an expansion of CCL-247 (HCT116), a colorectal carcinoma cell line, from a starting concentration of 2.45 × 105 cells to 1.9 × 106 cells per scaffold. Following expansion, 3D EECM-derived cells were assessed based on clinical release criteria of the Vigil manufacturing process utilized for Phase IIb trial operation with the FDA. 3D EECM-derived cells passed all Vigil manufacturing release criteria including cytokine expression. Here, we demonstrate successful Vigil product manufacture achieving the specifications necessary for the clinical trial product release of Vigil treatment. Our results confirm that 3D EECM can be utilized for the expansion of human cancer cell CCL-247, justifying further clinical development involving human tissue sample manufacturing including core needle biopsy and minimal ascites samples.
Probabilistic prediction and context tree identification in the Goalkeeper game
Authors: Hernández Noslen , Galves Antonio , García Jesús E. , Gubitoso Marcos D. , Vargas Claudia D. 
Published: July 2024

AbstractIn this article we address two related issues on the learning of probabilistic sequences of events. First, which features make the sequence of events generated by a stochastic chain more difficult to predict. Second, how to model the procedures employed by different learners to identify the structure of sequences of events. Playing the role of a goalkeeper in a video game, participants were told to predict step by step the successive directions—left, center or right—to which the penalty kicker would send the ball. The sequence of kicks was driven by a stochastic chain with memory of variable length. Results showed that at least three features play a role in the first issue: (1) the shape of the context tree summarizing the dependencies between present and past directions; (2) the entropy of the stochastic chain used to generate the sequences of events; (3) the existence or not of a deterministic periodic sequence underlying the sequences of events. Moreover, evidence suggests that best learners rely less on their own past choices to identify the structure of the sequences of events.