bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient
in vivo
-inducible CRISPR interference system for group A
Streptococcus
genetic analysis and pathogenesis studies
Authors: Bjånes Elisabet , Stream Alexandra , Janssen Axel B. , Gibson Paddy S. , Bravo Afonso M. , Dahesh Samira , Baker Jonathon L. , Varble Andrew , Nizet Victor , Veening Jan-Willem 
Published: July 2024

ABSTRACT

While genome-wide transposon mutagenesis screens have identified numerous essential genes in the significant human pathogen
Streptococcus pyogenes
(group A
Streptococcus
or GAS), many of their functions remain elusive. This knowledge gap is attributed in part to the limited molecular toolbox for controlling GAS gene expression and the bacterium’s poor genetic transformability. CRISPR interference (CRISPRi), using catalytically inactive GAS Cas9 (dCas9), is a powerful approach to specifically repress gene expression in both bacteria and eukaryotes, but ironically, it has never been harnessed for controlled gene expression in GAS. In this study, we present a highly transformable and fully virulent serotype M1T1 GAS strain and introduce a doxycycline-inducible CRISPRi system for efficient repression of bacterial gene expression. We demonstrate highly efficient, oligo-based single guide RNA cloning directly to GAS, enabling the construction of a gene knockdown strain in just 2 days, in contrast to the several weeks typically required. The system is shown to be titratable and functional both
in vitro
and
in vivo
using a murine model of GAS infection. Furthermore, we provide direct
in vivo
evidence that the expression of the conserved cell division gene
ftsZ
is essential for GAS virulence, highlighting its promise as a target for emerging FtsZ inhibitors. Finally, we introduce SpyBrowse (
https://veeninglab.com/SpyBrowse
), a comprehensive and user-friendly online resource for visually inspecting and exploring GAS genetic features. The tools and methodologies described in this work are poised to facilitate fundamental research in GAS, contribute to vaccine development, and aid in the discovery of antibiotic targets.

IMPORTANCE

While group A
Streptococcus
(GAS) remains a predominant cause of bacterial infections worldwide, there are limited genetic tools available to study its basic cell biology. Here, we bridge this gap by creating a highly transformable, fully virulent M1T1 GAS strain. In addition, we established a tight and titratable doxycycline-inducible system and developed CRISPR interference (CRISPRi) for controlled gene expression in GAS. We show that CRISPRi is functional
in vivo
in a mouse infection model. Additionally, we present SpyBrowse, an intuitive and accessible genome browser (
https://veeninglab.com/SpyBrowse
). Overall, this work overcomes significant technical challenges of working with GAS and, together with SpyBrowse, represents a valuable resource for researchers in the GAS field.
Cytomegalovirus-induced peroxynitrite promotes virus entry and contributes to pathogenesis in a murine model of infection
Authors: Amratia Pragati S. , Kerr-Jones Lauren E. , Chapman Lucy , Marsden Morgan , Clement Mathew , Stanton Richard J. , Humphreys Ian R. 
Published: July 2024

ABSTRACT

There are no licensed vaccines for human cytomegalovirus (HCMV), and current antiviral drugs that target viral proteins are toxic and prone to resistance. Targeting host pathways essential for virus replication provides an alternate strategy that may reduce opportunities for drug resistance to occur. Oxidative stress is triggered by numerous viruses including HCMV. Peroxynitrite is a reactive nitrogen species that is formed during oxidative stress. Herein, we identified that HCMV rapidly induces the generation of intracellular peroxynitrite upon infection in a manner partially dependent upon xanthine oxidase generation. Peroxynitrite promoted HCMV infection in both cell-free and cell-associated infection systems in multiple cell types. Inhibiting peroxynitrite within the first 24 hours of infection prevented HCMV replication and peroxynitrite promoted cell entry and pp65 translocation into the host cell nuclei. Furthermore, using the murine cytomegalovirus model, we demonstrated that antagonizing peroxynitrite significantly reduces cytomegalovirus replication and pathogenesis
in vivo
. Overall, our study highlights a proviral role for peroxynitrite in CMV infection and implies that RNS and/or the mechanisms that induce their production could be targeted as a novel strategy to inhibit HCMV infection.

IMPORTANCE
Human cytomegalovirus (HCMV) causes significant disease in individuals with impaired or immature immune systems, such as transplant patients and after congenital infection. Antiviral drugs that target the virus directly are toxic and are susceptible to antiviral drug resistance due to virus mutations. An alternate strategy is to target processes within host cells that are required by the virus for replication. Herein, we show that HCMV infection triggers a highly reactive molecule, peroxynitrite, during the initial stages of infection. Peroxynitrite was required for the initial entry of the virus into the cell and promotes virus replication in multiple cell types, suggesting a broad pro-viral function. Importantly, targeting peroxynitrite dramatically inhibited cytomegalovirus replication in cells in the laboratory and in mice, suggesting that therapeutic targeting of this molecule and/or the cellular functions it regulates could represent a novel strategy to inhibit HCMV infection.
Second-generation checkpoint inhibitors and Treg depletion synergize with a mouse cancer vaccine in accordance with tumor microenvironment characterization
Authors: Becker William , Olkhanud Purevdorj B , Seishima Noriko , Moreno Paloma A , Goldfarbmuren Katherine C , Maeng Hoyoung M , Berzofsky Jay A 
Published: July 2024

BackgroundDespite advances in checkpoint inhibitor (CPI) therapy for cancer treatment, many cancers remain resistant. Tumors deemed “cold” based on lack of T cell infiltration show reduced potential for CPI therapy. Cancer vaccines may overcome the inadequacy of existing T cells by inducing the needed antitumor T cell response to synergize with CPIs and overcome resistance.MethodsCT26 and TC1 tumor cells were injected subcutaneously into mice. Mice were treated with combinations of CPIs alone or a cancer vaccine specific to the tumor antigen E7 present in TC1 cells. CPIs for the TC1 model were selected because of immunophenotyping TC1 tumors. Antitumor and protumor immunity, tumor size and survival, sequence and timing of vaccine and CPI administration, and efficacy of treatment in young and aged mice were probed.ResultsWhile “hot” CT26 tumors are treatable with combinations of second-generation CPIs alone or with anti-TGFβ, “cold” TC1 tumor reduction requires the synergy of a tumor-antigen-specific vaccine in combination with two CPIs, anti-TIGIT and anti-PD-L1, predicted by tumor microenvironment (TME) characterization. The synergistic triple combination delays tumor growth better than any pairwise combination and improves survival in a CD8+T cell-dependent manner. Depletion of CD4+T cells improved the treatment response, and depleting regulatory T cells (Treg) revealed Tregs to be inhibiting the response as also predicted from TME analysis. We found the sequence of CPI and vaccine administration dictates the success of the treatment, and the triple combination administered concurrently induces the highest E7-specific T cell response. Contrary to young mice, in aged mice, the cancer vaccine alone is ineffective, requiring the CPIs to delay tumor growth.ConclusionsThese findings show how pre-existing or vaccine-mediated de novo T cell responses can both be amplified by and facilitate synergistic CPIs and Treg depletion that together lead to greater survival, and how analysis of the TME can help rationally design combination therapies and precision medicine to enhance clinical response to CPI and cancer vaccine therapy.
Citizen science for social physics: digital tools and participation
Authors: Perelló Josep , Larroya Ferran , Bonhoure Isabelle , Peter Franziska 
Published: July 2024

AbstractSocial physics is an active and diverse field in which many scientists with formal training in physics study a broad class of complex social phenomena. Social physics investigates societal problems but most often does not count on the active and conscious participation of the citizens. We here want to support the idea that citizen science, and more particularly citizen social science, can contribute to the broad field of social physics. The current manuscript is not a review paper of citizen science projects from the context of social physics as there are still too few experiences in this context. We, in contrast, present a selection of our own experiences during the last decade to extract key learnings and further reflect on citizen science practices for social physics. We first describe several human mobility experiments in urban contexts with the participation of concerned young students, old women, or other different groups of neighbors. We second share how we have studied community mental healthcare provision in collaboration with a civil society organization and with the intense involvement of persons with lived experience in mental health. In both cases, we narrow down the discussion to digital tools being used and the involved participatory dynamics. In this way, we share key learnings to enhance a synergistic relationship between social physics and citizen science and with the aim of increasing the societal impact of the research on complex social phenomena.
Numerical intercomparison of PHITS and Geant4 Monte Carlo codes for fast neutron inelastic scattering applications
Authors: Meleshenkovskii I. , Van den Brandt K. , Ogawa T. , Datema C. , Mauerhofer E. 
Published: July 2024

AbstractFast neutron inelastic scattering is a promising non-destructive assay technique for various analytical applications. As an active neutron interrogation technique, its performance is a function of various different factors and parameters that require optimization. Monte Carlo simulation codes are indispensable for such tasks. However, the internal simulation routines implemented in such codes can rely on different physical models that can yield discrepancies in the simulation results. In this work we conduct an intercomparison of PHITS and Geant4 codes performance in application to fast neutron inelastic scattering simulations. The goal of this paper is twofold. First, we explain the differences in code configuration with respect to gamma and neutron transport, as well as internal simulation routines. Second, we conduct a performance assessment of the two codes using two different measurement configurations. One configuration consisted of a source of gamma rays in a broad energy range (100–9000 keV) and a CeBr3 detector. The other configuration consisted of a monoenergetic 2.5 MeV fast neutron source, Fe, Nd, Dy, B targets and a CeBr3 detector. Selected simulation configurations were chosen with a goal to compare the performance differences in neutron energy distribution, produced prompt gamma rays and energy deposition in CeBr3 detector between the two codes. Results of our study reveal a good coherence of both codes performance in the application of fast neutron inelastic scattering simulations. The simulation geometries and observed differences are described in detail.
NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation
Authors: Zhu Xiangfei , Li Yishan , Shao Zhiying , Lu Xiaoyuan , Chen Youguo 
Published: July 2024

Abstract
Endometrial cancer is one of the predominant tumors of the female reproductive system. In this current study, we investigated the functions and related mechanisms of nucleosome assembly protein 1 like 1 (NAP1L1)/ DEAD-box helicase 5 (DDX5) in endometrial cancer. This retrospective study analyzed the medical records of patients with endometrial cancer, collected tissue samples for NAP1L1 and DDX5 staining, and conducted survival analysis using the Kaplan–Meier method. To evaluate the impact of NAP1L1 and/or DDX5 on cellular processes in endometrial cancer cells, several techniques were employed. These included Cell Counting Kit-8 assay, wound healing assay, Transwell assay, as well as overexpression or knockdown of target gene expression. Additionally, chromatin immunoprecipitation, dual luciferase reporter gene, and coimmunoprecipitation (Co-IP) assay were utilized to confirm the interaction between NAP1L1, E1A-binding protein p300 (EP300), and DDX5. Furthermore, qRT-PCR, Western blot, and Co-IP assay were performed to analyze the modulation of NAP1L1/DDX5 in Wnt/β-catenin. NAP1L1 and DDX5 expression were upregulated in endometrial cancer tissues, and correlated with poor prognosis. NAP1L1/DDX5 promoted endometrial cancer cell proliferation, migration, and invasion. NAP1L1 promotes acetylation and transcription by recruiting EP300 to the DDX5 promoter. DDX5 could activate Wnt/β-catenin signal by binding to β-catenin. In animal models, knockdown of NAP1L1 inhibits endometrial cancer tumor growth and lung metastasis. To sum up, our study demonstrated that NAP1L1 promoted the malignant phenotypes of endometrial cancer cells via recruiting EP300 to promote DDX5 acetylation, thus activating the Wnt/β-catenin signaling pathway.
Implications: Our research findings indicate that targeting the NAP1L1/EP300/DX5 axis might be a new potential treatment option for endometrial cancer.
Enhancing Colorectal Cancer Screening with Droplet Digital PCR Analysis of Fusobacterium nucleatum in Fecal Immunochemical Test Samples
Authors: Datorre José G. , dos Reis Mariana B. , de Carvalho Ana C. , Porto Jun , Rodrigues Gabriela H. , Lima Adhara B. , Reis Monise T. , Hirai Welinton , Hashimoto Claudio L. , Guimarães Denise P. , Reis Rui M. 
Published: July 2024

Abstract
Fecal immunochemical test (FIT) followed by colonoscopy in positive cases is commonly used for population-based colorectal cancer screening. However, specificity of FIT for colorectal cancer is not ideal and has poor performance for advanced adenoma detection. Fecal Fusobacterium nucleatum (Fn) detection has been proposed as a potential noninvasive biomarker for colorectal cancer and advanced adenoma detection. We aimed to evaluate the diagnostic performance of Fn detection using droplet digital PCR (ddPCR) in FIT samples from individuals enrolled in a colorectal cancer screening program with colorectal adenoma or cancer. We evaluated Fn presence in DNA isolated from FIT leftover material of 300 participants in a colorectal cancer screening program using ddPCR. The Fn DNA amount was classified as Fn-low/negative and Fn-high, and the association with patients’ clinicopathological features and accuracy measurements was calculated. Fn-high levels were more prevalent in FIT-positive (47.2%, n = 34 of 72) than FIT-negative samples (28.9%, n = 66 of 228; P &lt; 0.04). Among FIT-positive samples, high Fn levels were significantly more frequent in patients with cancer (CA, n = 8) when compared to normal (NT, n = 16; P = 0.02), non-advanced adenomas (NAA, n = 36; P = 0.01), and advanced adenomas (AA, n = 12; P = 0.01). Performance analysis of Fn in FIT-positive samples for colorectal cancer detection yielded an AUC of 0.8203 [confidence interval (CI), 0.6464–0.9942], with high sensitivity (100%) and specificity of 50%. Concluding, we showed the feasibility of detecting Fn in FIT leftovers using the ultrasensitive ddPCR technique. Furthermore, we highlighted the potential use of Fn levels in fecal samples to ameliorate colorectal cancer detection.
Prevention Relevance: Fusobacterium nucleatum detection by droplet digital PCR could prioritize the selection of fecal immunochemical test–positive individuals who might benefit the most from the colonoscopy procedure.
Modulation of U.S. Tornado Activity by Year-Round North American Weather Regimes
Authors: Tippett Michael K. , Malloy Kelsey , Lee Simon H. 
Published: July 2024

Abstract
Here, we examine the relation between U.S. tornado activity and a new year-round classification of North American weather regimes. The regime classification is based on 500-hPa geopotential height anomalies and classifies each day as Pacific Trough, Pacific Ridge, Alaskan Ridge, Greenland High, or No regime. During the period 1979–2022, we find statistically significant relations between average tornado report numbers and weather regimes in all months except June–August. Tornado activity is enhanced on Pacific Ridge days during late winter and spring, reduced on Pacific Trough days in spring, and reduced on Alaskan Ridge and Greenland High days during fall and early winter. During active regimes, the probability of many tornadoes occurring also increases, and there is greater variability in the number of tornadoes reported each day. A reanalysis-based tornado index reproduces the regional features of the modulation of tornado activity by the weather regimes and attributes them to changes in storm relative helicity, convective available potential energy, and convective precipitation. The phase of El Niño–Southern Oscillation (ENSO) also plays a role. In winter and spring, Pacific Ridge days occur more often and average more reports per day during cool ENSO conditions. During warm ENSO conditions, Pacific Trough days occur more often and are associated with widespread reduced tornado activity.

Significance Statement
Daily weather patterns over North America can be classified into five categories. The purpose of this study was to examine whether the number of U.S. tornado reports on a given day depends on the weather category of that day. We found robust relations between the average number of tornado reports and the weather pattern category in all months except June–August, with some weather patterns associated with increased tornado numbers and others with decreased tornado numbers. The El Niño–Southern Oscillation (ENSO) phenomenon plays a role, with weather patterns that are favorable for tornadoes being more frequent and having more tornadoes per day during cool ENSO conditions.
LncRNA TRPM2-AS promotes endometrial carcinoma progression and angiogenesis via targeting miR-497-5p/SPP1 axis
Authors: Ma Hanbo , Weng Fengyun , Tong Xiaowen , Li Huaifang , Yao Yinan , Yuan Jiangjing 
Published: July 2024

Abstract
Background
Anti-angiogenic therapy has become one of the effective treatment methods for tumors. Long noncoding RNAs (lncRNAs) are emerging as important regulators of tumorigenesis and angiogenesis in EC. However, the underlying mechanisms of lncRNA TRPM2-AS in EC are still not clear.

Methods
We screened the differently expressed lncRNAs that were highly associated with poor prognosis and angiogenesis of EC by bioinformatics analysis, and constructed a ceRNA network based on the prognostic lncRNAs. The subcellular localization of TRPM2-AS was determined by fluorescence in situ hybridization (FISH) and nuclear cytoplasmic fractionation assay. CCK-8, EdU, transwell, western blot, qRT-PCR and endothelial tube formation assay were used to evaluate the effects of TRPM2-AS on the proliferation, invasion, migration of EC cells and angiogenesis. The targeted microRNA (miRNA) of TRPM2-AS was predicted by bioinformatic methods. The interaction between TRPM2-AS and miR497-5p, miR497-5p and SPP1 were analyzed by RNA immunoprecipitation and dual-luciferase reporter assay. A subcutaneous tumor model was used to explore TRPM2-AS’s function in vivo. CIBERSORT was used to analyze the correlation between TRPM2-AS and immune cell immersion in EC.

Results
We found that the expression of TRPM2-AS and SPP1 was aberrantly upregulated, while miR-497-5p expression was significantly downregulated in EC tissues and cells. TRPM2-AS was closely correlated with the angiogenesis and poor prognosis in EC patients. Mechanistically, TRPM2-AS could sponge miR-497-5p to release SPP1, thus promoting the proliferation, invasion and migration of EC cells and angiogenesis of HUVECs. Knockdown of TRPM2-AS in xenograft mouse model inhibited tumor proliferation and angiogenesis in vivo. In addition, TRPM2-AS plays a vital role in regulating the tumor immune microenvironment of EC, overexpression of TRPM2-AS in EC cells stimulated the polarization of M2 macrophages and angiogenesis through secreting SPP1 enriched exosomes.

Conclusion
The depletion of TRPM2-AS inhibits the oncogenicity of EC by targeting the miR-497-5p/SPP1 axis. This study offers a better understanding of TRPM2-AS’s role in regulating angiogenesis and provides a novel target for EC treatment.
Extracellular vesicle miRNAs for predicting the efficacy of late-line treatment with anlotinib in patients with lung adenocarcinoma
Authors: Huang Aimi , Zhang Fuchuang , Zhang Jiyang , Xu Xiaoya , Li Zhikuan , Chen Sheng , Nian Baoning , Zhang Dadong , Han Baohui , Gu Aiqin , Wang Weimin 
Published: July 2024

Abstract
Background
Anlotinib is a targeted therapy indicated for some malignancies, including advanced non-small cell lung cancer (NSCLC). However, noninvasive biomarkers for identifying patients who will benefit from this disease remain lacking.

Methods
Here, we investigated the potential of small extracellular vesicle (sEV) microRNAs (miRNAs) as predictive biomarkers for anlotinib efficacy. A total of 20 advanced NSCLC patients were enrolled. Patients were classified as having stable disease (SD) or progressive disease (PD) after the initial efficacy assessment.

Results
Seven differentially expressed miRNAs (DEMs) were identified. Among them, miR-941 was significantly upregulated in the PD group, while the others were downregulated. Furthermore, these six downregulated miRNAs (miR-30a-3p, miR-150-5p, miR-122-5p, miR-10b-5p, miR-92a-3p, and miR-150-3p) were more pronounced in nonsmoking patients.

Conclusions
It was found that sEV miRNAs have the potential to predict the benefit of anlotinib.
Application of remote sensing to understand the role of Galician feral horses in the biomass reduction of a shrub-grassland-dominated landscape
Authors: Janeiro-Otero Andrea , Álvarez Xana , Dormann Carsten F. 
Published: July 2024

AbstractGalician forests in northwestern Spain are subject to frequent wildfires with high environmental and economic costs. In addition, due to the consequences of climate change, these fires are becoming more virulent, occurring throughout the year, and taking place in populated areas, in some cases involving the loss of human life. Therefore, forest fire prevention is even more relevant than mitigating its consequences. Given the costs involved in forestry work, alternative measures to reduce fuel load and create vegetation gaps are needed. One involves grazing by an endemic species of feral horses (Equus ferus atlanticus) that feed on thicket-forming gorse (Ulex europaeus). In a 100-ha forest fenced study area stocked with 11 horses, four 50 m2 enclosed plots prevented the access of these wild animals to the vegetation, with the aim of manipulating their impact on the reduction of forest biomass. The measurement of biomass volumes is an important method that can describe the assessment of wildfire risks, unfortunately, high-resolution data collection at the regional scale is very time-consuming. The best result can be using drones (unmanned aerial vehicles - UAVs) as a method of collecting remotely sensed data at low cost. From September 2018 to November 2020, we collected information about aboveground biomass from these four enclosed plots and their surrounding areas available for horses to forage, via UAV. These data, together with environmental variables from the study site, were used as input for a fire model to assess the differences in the surface rate of spread (SROS) among grazed and ungrazed areas. Our results indicated a consistent but small reduction in the SROS between 0.55 and 3.10 m/min in the ungrazed enclosured plots in comparison to their grazed surrounding areas (which have an SROS between 15 and 25 m/min). The research showed that radar remote sensing (UAV) can be used to map forest aboveground biomass, and emphasized the importance and role of feral horses in Galicia as a prevention tool against wildfires in gorse-dominated landscapes.