bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing
Authors: Szyjka Courtney E. , Strobel Eric J. 
Published: November 2023

AbstractRNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription. Understanding how RNA folds into secondary and tertiary structures therefore requires methods for determining the structure of cotranscriptional folding intermediates. Cotranscriptional RNA chemical probing methods accomplish this by systematically probing the structure of nascent RNA that is displayed from an RNA polymerase. Here, we describe a concise, high-resolution cotranscriptional RNA chemical probing procedure called variable length Transcription Elongation Complex RNA structure probing (TECprobe-VL). We demonstrate the accuracy and resolution of TECprobe-VL by replicating and extending previous analyses of ZTP and fluoride riboswitch folding and mapping the folding pathway of a ppGpp-sensing riboswitch. In each system, we show that TECprobe-VL identifies coordinated cotranscriptional folding events that mediate transcription antitermination. Our findings establish TECprobe-VL as an accessible method for mapping cotranscriptional RNA folding pathways.
Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation
Authors: Ma Li , Wang Feng , Li Yangping , Wang Jing , Chang Qing , Du Yuanning , Sadan Jotham , Zhao Zhen , Fan Guoping , Yao Bing , Chen Jian-Fu 
Published: November 2023

AbstractHow early life experience is translated into storable epigenetic information leading to behavioral changes remains poorly understood. Here we found that Zika virus (ZIKV) induced-maternal immune activation (MIA) imparts offspring with anxiety- and depression-like behavior. By integrating bulk and single-nucleus RNA sequencing (snRNA-seq) with genome-wide 5hmC (5-hydroxymethylcytosine) profiling and 5mC (5-methylcytosine) profiling in prefrontal cortex (PFC) of ZIKV-affected male offspring mice, we revealed an overall loss of 5hmC and an increase of 5mC levels in intragenic regions, associated with transcriptional changes in neuropsychiatric disorder-related genes. In contrast to their rapid initiation and inactivation in normal conditions, immediate-early genes (IEGs) remain a sustained upregulation with enriched expression in excitatory neurons, which is coupled with increased 5hmC and decreased 5mC levels of IEGs in ZIKV-affected male offspring. Thus, MIA induces maladaptive methylome remodeling in brain and selectively regulates neuronal activity gene methylation linking to emotional behavioral abnormalities in offspring.
Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope
Authors: Wan Xiaomeng , Xiao Jiashun , Tam Sindy Sing Ting , Cai Mingxuan , Sugimura Ryohichi , Wang Yang , Wan Xiang , Lin Zhixiang , Wu Angela Ruohao , Yang Can 
Published: November 2023

AbstractThe rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our understanding of tissue spatial architecture and biology. Although current ST methods, whether based on next-generation sequencing (seq-based approaches) or fluorescence in situ hybridization (image-based approaches), offer valuable insights, they face limitations either in cellular resolution or transcriptome-wide profiling. To address these limitations, we present SpatialScope, a unified approach integrating scRNA-seq reference data and ST data using deep generative models. With innovation in model and algorithm designs, SpatialScope not only enhances seq-based ST data to achieve single-cell resolution, but also accurately infers transcriptome-wide expression levels for image-based ST data. We demonstrate SpatialScope’s utility through simulation studies and real data analysis from both seq-based and image-based ST approaches. SpatialScope provides spatial characterization of tissue structures at transcriptome-wide single-cell resolution, facilitating downstream analysis, including detecting cellular communication through ligand-receptor interactions, localizing cellular subtypes, and identifying spatially differentially expressed genes.
Non-canonical pathway for Rb inactivation and external signaling coordinate cell-cycle entry without CDK4/6 activity
Authors: Zhang Mimi , Kim Sungsoo , Yang Hee Won 
Published: November 2023

AbstractCyclin-dependent kinases 4 and 6 (CDK4/6) are critical for initiating cell proliferation by inactivating the retinoblastoma (Rb) protein. However, mammalian cells can bypass CDK4/6 for Rb inactivation. Here we show a non-canonical pathway for Rb inactivation and its interplay with external signals. We find that the non-phosphorylated Rb protein in quiescent cells is intrinsically unstable, offering an alternative mechanism for initiating E2F activity. Nevertheless, this pathway incompletely induces Rb-protein loss, resulting in minimal E2F activity. To trigger cell proliferation, upregulation of mitogenic signaling is required for stabilizing c-Myc, thereby augmenting E2F activity. Concurrently, stress signaling promotes Cip/Kip levels, competitively regulating cell proliferation with mitogenic signaling. In cancer, driver mutations elevate c-Myc levels, facilitating adaptation to CDK4/6 inhibitors. Differentiated cells, despite Rb-protein loss, maintain quiescence through the modulation of c-Myc and Cip/Kip levels. Our findings provide mechanistic insights into an alternative model of cell-cycle entry and the maintenance of quiescence.
Placental Streptococcus agalactiae DNA is associated with neonatal unit admission and foetal pro-inflammatory cytokines in term infants
Authors: Gaccioli Francesca , Stephens Katie , Sovio Ulla , Jessop Flora , Wong Hilary S. , Lager Susanne , Cook Emma , de Goffau Marcus C. , Le Doare Kirsty , Peacock Sharon J. , Parkhill Julian , Charnock-Jones D. Stephen , Smith Gordon C. S. 
Published: November 2023

AbstractStreptococcus agalactiae (Group B Streptococcus; GBS) is a common cause of sepsis in neonates. Previous work detected GBS DNA in the placenta in ~5% of women before the onset of labour, but the clinical significance of this finding is unknown. Here we re-analysed this dataset as a case control study of neonatal unit (NNU) admission. Of 436 infants born at term (≥37 weeks of gestation), 7/30 with placental GBS and 34/406 without placental GBS were admitted to the NNU (odds ratio (OR) 3.3, 95% confidence interval (CI) 1.3–7.8). We then performed a validation study using non-overlapping subjects from the same cohort. This included a further 239 cases of term NNU admission and 686 term controls: 16/36 with placental GBS and 223/889 without GBS were admitted to the NNU (OR 2.4, 95% CI 1.2–4.6). Of the 36 infants with placental GBS, 10 were admitted to the NNU with evidence of probable but culture-negative sepsis (OR 4.8, 95% CI 2.2–10.3), 2 were admitted with proven GBS sepsis (OR 66.6, 95% CI 7.3–963.7), 6 were admitted and had chorioamnionitis (inflammation of the foetal membranes) (OR 5.3, 95% CI 2.0–13.4), and 5 were admitted and had funisitis (inflammation of the umbilical cord) (OR 6.7, 95% CI 12.5–17.7). Foetal cytokine storm (two or more pro-inflammatory cytokines >10 times median control levels in umbilical cord blood) was present in 36% of infants with placental GBS DNA and 4% of cases where the placenta was negative (OR 14.2, 95% CI 3.6–60.8). Overall, ~1 in 200 term births had GBS detected in the placenta, which was associated with infant NNU admission and morbidity.
A dynamic and collaborative database for morphogeometric information of trilobites
Authors: Serra Fernanda , Balseiro Diego , Monnet Claude , Randolfe Enrique , Bignon Arnaud , Rustán Juan J. , Bault Valentin , Muñoz Diego F. , Vaccari N. Emilio , Martinetto Malena , Crônier Catherine , Waisfeld Beatriz G. 
Published: November 2023

AbstractModern morphometric-based approaches provide valuable metrics to quantify and understand macroevolutionary and macroecological patterns and processes. Here we describe TriloMorph, an openly accessible database for morpho-geometric information of trilobites, together with a landmark acquisition protocol. In addition to morphological traits, the database contains contextual data on chronostratigraphic age, geographic location, taxonomic information and lithology of landmarked specimens. In this first version, the dataset has broad taxonomic and temporal coverage and comprises more than 55% of all trilobite genera and 85% of families recorded in the Paleobiology Database through the Devonian. We provide a release of geometric morphometric data of 277 specimens linked to published references. Additionally, we established a Github repository for constant input of morphometric data by multiple contributors and present R functions that help with data retrieval and analysis. This is the first attempt of an online, dynamic and collaborative morphometric repository. By bringing this information into a single open database we enhance the possibility of performing global palaeobiological research, providing a major complement to current occurrence-based databases.
Positron emission tomography dataset of [11C]carbon dioxide storage in coal for geo-sequestration application
Authors: Jing Yu , Kumaran Aaron Uthaia , Stimson Damion Howard Read , Mardon Karine , Najdovski Ljubco , Armstrong Ryan T. , Mostaghimi Peyman 
Published: November 2023

AbstractPositron Emission Tomography (PET) imaging has demonstrated its capability in providing time-lapse fluid flow visualisation for improving the understanding of flow properties of geologic media. To investigate the process of CO2 geo-sequestration using PET imaging technology, [11C]CO2 is the most optimal and direct radiotracer. However, it has not been extensively used due to the short half-life of Carbon-11 (20.4 minutes). In this work, a novel laboratory protocol is developed to use [11C]CO2 as radiolabelled tracer to visualise and quantify in-situ CO2 adsorption, spreading, diffusion, and advection flow in coal. This protocol consists of generation and delivering of [11C]CO2, lab-based PET scanning, subsequent micro-CT scanning, and data processing. The lab-based PET scanning setup integrates in-situ core flooding tests with PET scanning. The real-time PET images are acquired under different storage conditions, including early gas production stage, depleted stage, and late storage stage. These datasets can be used to study across-scale theoretical and experimental study of CO2 flow behaviour in coal with the application to CO2 geo-sequestration.
Characteristic dynamic functional connectivity during sevoflurane-induced general anesthesia
Authors: Miao Jingya , Tantawi Mohamed , Alizadeh Mahdi , Thalheimer Sara , Vedaei Faezeh , Romo Victor , Mohamed Feroze B. , Wu Chengyuan 
Published: November 2023

AbstractGeneral anesthesia (GA) during surgery is commonly maintained by inhalational sevoflurane. Previous resting state functional MRI (rs-fMRI) studies have demonstrated suppressed functional connectivity (FC) of the entire brain networks, especially the default mode networks, transitioning from the awake to GA condition. However, accuracy and reliability were limited by previous administration methods (e.g. face mask) and short rs-fMRI scans. Therefore, in this study, a clinical scenario of epilepsy patients undergoing laser interstitial thermal therapy was leveraged to acquire 15 min of rs-fMRI while under general endotracheal anesthesia to maximize the accuracy of sevoflurane level. Nine recruited patients had fMRI acquired during awake and under GA, of which seven were included in both static and dynamic FC analyses. Group independent component analysis and a sliding-window method followed by k-means clustering were applied to identify four dynamic brain states, which characterized subtypes of FC patterns. Our results showed that a low-FC brain state was characteristic of the GA condition as a single featuring state during the entire rs-fMRI session; In contrast, the awake condition exhibited frequent fluctuations between three distinct brain states, one of which was a highly synchronized brain state not seen in GA. In conclusion, our study revealed remarkable dynamic connectivity changes from awake to GA condition and demonstrated the advantages of dynamic FC analysis for future studies in the assessments of the effects of GA on brain functional activities.
Morphological characteristics of coronoid process and revisiting definition of coronoid hyperplasia
Authors: Shujaat Sohaib , Politis Constantinus , Van Den Bogaert Tom , Vueghs Pieter , Smeets Maximiliaan , Verhelst Pieter-Jan , Grymonprez Edouard , Jacobs Reinhilde 
Published: November 2023

AbstractThe aim of this study was to assess the morphological characteristics of the coronoid process (CP) and define coronoid hyperplasia (CH) using cadaveric mandibles of a Caucasian population. A sample of 151 adult dry cadaveric mandibles (302 CPs) was acquired. Three distances were measured, which included the width, height, and length of CP. The surface area measurements involved area A: above the width distance line; area B: between incisura mandibulae—Alveolar ridge line and width distance line; area C: between distance lines of width and height. Finally, angulations of the CP and gonial angles were identified. Both length and surface area A + B acted as hyperplastic indicators. Based on the selection criteria, a sample of 197 CPs was included. The hooked shape (59%) was most commonly observed. No significant difference existed between left and right sides (p > 0.05). The mean values of length and surface area A + B were 2.2 ± 0.3 cm and 3.3 ± 0.8 cm2, and any values above 2.7 cm (n = 5 CPs- 2.5%) and 5.0 cm2 (n = 9 CPs- 4.6%) were described as hyperplastic, respectively. The presented data could act as quantitative reference for differentiating between normal and hyperplastic conditions.
Gender inequality in cum laude distinctions for PhD students
Authors: Bol Thijs 
Published: November 2023

AbstractResource allocation in academia is highly skewed, and peer evaluation is the main method used to distribute scarce resources. A large literature documents gender inequality in evaluation, and the explanation for this inequality is homophily: male evaluators give more favorable ratings to male candidates. We investigate this by focusing on cum laude distinctions for PhD students in the Netherlands, a distinction that is only awarded to 5 percent of all dissertations and has as its sole goal to distinguish the top from the rest. Using data from over 5000 PhD recipients of a large Dutch university for the period 2011–2021, we find that female PhD students were almost two times less likely to get a cum laude distinction than their male counterparts, even when they had the same doctoral advisor. This gender gap is largest when dissertations are evaluated by all-male committees and decreases as evaluation committees include more female members.
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
Authors: Castellano Kate R. , Batta-Lona Paola , Bucklin Ann , O’Neill Rachel J. 
Published: November 2023

AbstractOcean warming favors pelagic tunicates, such as salps, that exhibit increasingly frequent and rapid population blooms, impacting trophic dynamics and composition and human marine-dependent activities. Salp blooms are a result of their successful reproductive life history, alternating seasonally between asexual and sexual protogynous (i.e. sequential) hermaphroditic stages. While predicting future salp bloom frequency and intensity relies on an understanding of the transitions during the sexual stage from female through parturition and subsequent sex change to male, these transitions have not been explored at the molecular level. Here we report the development of the first complete genome of S. thompsoni and the North Atlantic sister species S. aspera. Genome and comparative analyses reveal an abundance of repeats and G-quadruplex (G4) motifs, a highly stable secondary structure, distributed throughout both salp genomes, a feature shared with other tunicates that perform alternating sexual-asexual reproductive strategies. Transcriptional analyses across sexual reproductive stages for S. thompsoni revealed genes associated with male sex differentiation and spermatogenesis are expressed as early as birth and before parturition, inconsistent with previous descriptions of sequential sexual differentiation in salps. Our findings suggest salp are poised for reproductive success at birth, increasing the potential for bloom formation as ocean temperatures rise.
A study of text-theoretical approach to S-box construction with image encryption applications
Authors: Mahboob Abid , Nadeem Muhammad , Rasheed Muhammad Waheed 
Published: November 2023

AbstractData protection is regarded as one of the biggest issues facing companies that have been using public data for a long time. Numerous encryption techniques have been used to address these issues and safeguard data from any malicious attempts and assaults. A substitution box (S-box) is the basic component for modern block ciphers, which helps to ensure robust security of plain data while encryption and permits its lawful decipherment. The goal of this paper is to recommend an effective, original, and straightforward technique for the creation of robust S-boxes. A sample S-box is generated in the proposed work using the word “UNITY” but other words can also be used to generate many powerful S-boxes. The ASCII code is used to translate the word “UNITY” into binary form, after which a distinct matrix is constructed for each character of the word. In the next phase, a linear fractional transformation is constructed using these matrices, which is then utilized to generate the S-box. The constructed S-box was then evaluated against typical security standards to support its high cryptographic authority. The generated S-box's statistical and algebraic resilience is demonstrated by its very low linear probability and differential probability scores of 0.125 and 0.039, respectively, and a high non-linearity score of 111.5. To evaluate the effectiveness of the image encryption scheme, digital images are encoded using the created S-box. The performance and comparative research demonstrate that the suggested S-box is a real candidate for applications in the field of image encryption and has a stronger performance base.
Effect of laser fluence on the optoelectronic properties of nanostructured GaN/porous silicon prepared by pulsed laser deposition
Authors: Fakhri Makram A. , Jabbar Haneen D. , AbdulRazzaq Mohammed Jalal , Salim Evan T. , Azzahrani Ahmad S. , Ibrahim Raed Khalid , Ismail Raid A. 
Published: November 2023

AbstractIn this study, the fabrication of nanostructured GaN/porous Si by pulsed laser deposition (PLD) was demonstrated. The porous silicon was prepared using laser-assisted electrochemical etching (LAECE). The structural, optical, and electrical properties of GaN films were investigated as a function of laser fluence. XRD studies revealed that the GaN films deposited on porous silicon were nanocrystalline, exhibiting a hexagonal wurtzite structure along the (100) plane. Spectroscopic property results revealed that the photoluminescence PL emission peaks of the gallium nitride over porous silicon (GaN/PSi) sample prepared at 795 mJ/mm2 were centered at 260 nm and 624 nm. According to topographical and morphological analyses, the deposited film consisted of spherical grains with an average diameter of 178.8 nm and a surface roughness of 50.61 nm. The surface of the prepared films exhibited a cauliflower-like morphology. The main figures of merit of the nanostructured GaN/P-Si photodetectors were studied in the spectral range of 350–850 nm. The responsivity, detectivity, and external quantum efficiency of the photodetector at 575 nm under − 3 V were 19.86 A/W, 8.9 × 1012 Jones, and 50.89%, respectively. Furthermore, the photodetector prepared at a laser fluence of 795 mJ/mm2 demonstrates a switching characteristic, where the rise time and fall time are measured to be 363 and 711 μs, respectively.
Norepinephrine prevents hypotension in older patients under spinal anesthesia with intravenous propofol sedation: a randomized controlled trial
Authors: Kim Hyungtae , Lee Sooho , Koh Won Uk , Cho Jooyeon , Park Sung Wook , Kim Keon Sik , Ro Young-Jin , Kim Ha-Jung 
Published: November 2023

AbstractReducing hypotension is crucial as hypotension is the most common side effect of spinal anesthesia, and in older patients with various comorbidities, it can lead to fatality. We hypothesized that continuous infusion of norepinephrine could effectively prevent hypotension in older patients undergoing hip surgery under spinal anesthesia with propofol sedation. The study randomly assigned patients aged ≥ 70 years to either a control (Group C, n = 35) or a norepinephrine group (Group N, n = 35). After spinal anesthesia, continuous infusion of propofol and normal saline or norepinephrine was initiated. The number of hypotensive episodes, the primary outcome, as well as other intraoperative hemodynamic events and postoperative complications were compared. In total, 67 patients were included in the final analysis. The number of hypotensive episodes was significantly higher in Group C than in Group N (p < 0.001). Furthermore, Group C required a greater amount of fluid to maintain normovolemia (p = 0.008) and showed less urine output (p = 0.019). However, there was no difference in postoperative complications between the two groups. Continuous intravenous infusion of prophylactic norepinephrine prevented hypotensive episodes, reduced the requirement of fluid, and increased the urine output in older patients undergoing unilateral hip surgery under spinal anesthesia with propofol sedation.Clinical trial registration number: KCT0005046 (https://cris.nih.go.kr). IRB number: 2020-0533 (Institutional Review Board of Asan Medical Center, approval date: 13/APR/2020).
Nanocomposite fibers based on cellulose acetate loaded with fullerene for cancer therapy: preparation, characterization and in-vitro evaluation
Authors: El Fawal Gomaa , Abu-Serie Marwa M. , Ali Safaa M. , Elessawy Noha A. 
Published: November 2023

AbstractThe current prevalence of cancerous diseases necessitates the exploration of materials that can effectively treat these conditions while minimizing the occurrence of adverse side effects. This study aims to identify materials with the potential to inhibit the metastasis of cancerous diseases within the human body while concurrently serving as therapeutic agents for their treatment. A novel approach was employed to enhance the anti-cancer properties of electrospun cellulose fibers by incorporating fullerene nanoparticles (NPs) into cellulose acetate (CA) fibers, resulting in a composite material called Fullerene@CA. This development aimed at utilizing the anti-cancer properties of fullerenes for potential therapeutic applications. This process has been demonstrated in vitro against various types of cancer, and it was found that Fullerene@CA nanocomposite fibers displayed robust anticancer activity. Cancer cells (Caco-2, MDA-MB 231, and HepG-2 cells) were inhibited by 0.3 and 0.5 mg.g−1 fullerene doses by 58.62–62.87%, 47.86–56.43%, and 48.60–57.73%, respectively. The tested cancer cells shrink and lose their spindle shape due to morphological changes. The investigation of the prepared nanocomposite reveals its impact on various genes, such as BCL2, NF-KB, p53, Bax, and p21, highlighting the therapeutic compounds' effectiveness. The experimental results demonstrated that the incorporation of NPs into CA fibers resulted in a significant improvement in their anti-cancer efficacy. Therefore, it is suggested that these modified fibers could be utilized as a novel therapeutic approach for the treatment and prevention of cancer metastasis.