bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the Extracellular Matrix Transcriptome of Endometriosis
Authors: Cook Carson J. , Wiggin Noah , Fogg Kaitlin C. 
Published: October 2023

AbstractIn recent years, the matrisome, a set of proteins that make up the extracellular matrix (ECM) or are closely involved in ECM behavior, has been shown to have great importance for characterizing and understanding disease pathogenesis and progression. The matrisome is especially critical for examining diseases characterized by extensive tissue remodeling. Endometriosis is characterized by the extrauterine growth of endometrial tissue, making it an ideal condition to study through the lens of matrisome gene expression. While large gene expression datasets have become more available and gene dysregulation in endometriosis has been the target of several studies, the gene expression profile of the matrisome specifically in endometriosis has not been well characterized. In our study, we explored four Gene Expression Omnibus (GEO) DNA microarray datasets containing eutopic endometrium of people with and without endometriosis. After batch correction, menstrual cycle phase accounted for 53% of variance and disease accounted for 23%; thus, the data were separated by menstrual cycle phase before performing differential expression analysis, statistical and machine learning modeling, and enrichment analysis. We established that matrisome gene expression alone can effectively differentiate endometriosis samples from healthy ones, demonstrating the potential of matrisome gene expression for diagnostic applications. Furthermore, we identified specific matrisome genes and gene networks whose expression can distinguish endometriosis stages I/II from III/IV. Taken together, these findings may aid in developing future in vitro models of disease, offer insights into novel treatment strategies, and advance diagnostic tools for this underserved patient population.
Molecular mechanism of empagliflozin cardioprotection in 5-fluorouracil (5-FU)-induced cardiotoxicity via modulation of SGLT2 and TNFα/TLR/NF-κB signaling pathway in rats
Authors: Refaie Marwa Monier Mahmoud , Shehata Sayed , El-Hussieny Maram , Fawzy Michael Atef , Ahmed Nagwa Zenhom Mustafa , Marey Heba , Hishmat Asmaa Mohammed , Alkully Turki , Rahman Eman Shaaban Mahmoud Abd El 
Published: October 2023

AbstractOne of the commoly used chemotherapeutic agents is 5-Fluorouracil (5-FU). Unfortunately, the clinical administration of 5-FU is complicated with serious cardiotoxic effects and the safe use becomes an urgent task in cardio-oncology. Till now, there are no studies discussed the role of empagliflozin (EMP) against 5-FU cardiotoxicity. Thus, we investigated this effect and the involved mechanisms in 5-FU induced heart injury. Forty male rats of Wistar albino species were used and divided randomly into four groups. Group I is the control group, group II is EMP given group, group III is 5-FU cardiotoxic group and group IV is 5-FU plus EMP group. 5-FU (150 mg/kg) was administered as a single intraperitoneal (i.p.) dose on 1st day to induce cardiotoxicity with or without EMP (30 mg/kg/d) orally for 5 days. The dose of 5-FU is relevant to the human toxic dose. Our data showed that 5-FU given group caused cardiotoxicity with significant increase of serum cardiac enzymes, toll like receptors, enhancement of nuclear factor kappa B (NF-κB), interleukin1β (IL1β), IL6, myeloid-differentiation-factor 88 (MYD88), heart weight, malondialdehyde (MDA), tumor-necrosis-factor-alpha (TNFα), sodium glucose co-transporter 2 (SGLT2), P53 and caspase3 expression with clear histopathological features of cardiotoxicity. Moreover, there is a significant decrease in reduced glutathione (GSH) and total antioxidant capacity (TAC). Interestingly, co-administration of EMP could ameliorate 5-FU induced biochemical and histopathological changes. This effect may be due to modulation of SGLT2, decreasing inflammation, oxidative stress and apoptosis with downregulation of an essential inflammatory cascade that mediates 5-FU cardiotoxicity; TNFα/TLR/NF-κB.
NON-ISOMORPHIC SMOOTH COMPACTIFICATIONS OF THE MODULI SPACE OF CUBIC SURFACES
Authors: CASALAINA-MARTIN SEBASTIAN , GRUSHEVSKY SAMUEL , HULEK KLAUS , LAZA RADU 
Published: October 2023

AbstractThe well-studied moduli space of complex cubic surfaces has three different, but isomorphic, compact realizations: as a GIT quotient
${\mathcal {M}}^{\operatorname {GIT}}$
, as a Baily–Borel compactification of a ball quotient
${(\mathcal {B}_4/\Gamma )^*}$
, and as a compactified K-moduli space. From all three perspectives, there is a unique boundary point corresponding to non-stable surfaces. From the GIT point of view, to deal with this point, it is natural to consider the Kirwan blowup
${\mathcal {M}}^{\operatorname {K}}\rightarrow {\mathcal {M}}^{\operatorname {GIT}}$
, whereas from the ball quotient point of view, it is natural to consider the toroidal compactification
${\overline {\mathcal {B}_4/\Gamma }}\rightarrow {(\mathcal {B}_4/\Gamma )^*}$
. The spaces
${\mathcal {M}}^{\operatorname {K}}$
and
${\overline {\mathcal {B}_4/\Gamma }}$
have the same cohomology, and it is therefore natural to ask whether they are isomorphic. Here, we show that this is in fact not the case. Indeed, we show the more refined statement that
${\mathcal {M}}^{\operatorname {K}}$
and
${\overline {\mathcal {B}_4/\Gamma }}$
are equivalent in the Grothendieck ring, but not K-equivalent. Along the way, we establish a number of results and techniques for dealing with singularities and canonical classes of Kirwan blowups and toroidal compactifications of ball quotients.
Post-educator relaxation in the U-shaped curve: Evidence from a panel study of Tyneside (ing)
Authors: Grama James , Mechler Johanna , Bauernfeind Lea , Eiswirth Mirjam E. , Buchstaller Isabelle 
Published: October 2023

AbstractAge-grading—a cornerstone of sociolinguistic theorizing—is hypothesized to follow a U-shaped pattern. Vernacular forms peak in adolescence, abate in middle age, and increase again in retirement, forming a vernacular tail. A complete understanding of age-grading has been hampered by a lack of empirical evidence across the entire adult trajectory and a relatively narrow understanding of speakers’ motivations to change. This paper presents data from a dynamic panel dataset of Tyneside English speakers, covering successive cohorts over the entire adult lifespan. An analysis of (ing) reveals that the U-shaped curve is occupationally niched; only professional educators demonstrate clear retrenchment followed by a tail. Drawing on educational policy research, we argue this effect is largely driven by institutional (and heavily policed) expectations of UK educational policies. We are the first to demonstrate the occupationally niched nature of the U-shaped curve and provide quantitative evidence of the effect of educational policy on linguistic production.
Imaging the Spatiotemporal Evolution of Plate Coupling With Interferometric Radar (InSAR) in the Hikurangi Subduction Zone
Authors: Maubant L. , Frank W. B. , Wallace L. M. , Williams C. A. , Hamling I. 
Published: October 2023

AbstractThe coupling at the interface between tectonic plates is a key geophysical parameter to capture the frictional locking across plate boundaries and provides a means to estimate where tectonic strain is accumulating through time. Here, we use both interferometric radar (InSAR) and Global Navigation Satellite System (GNSS) data to investigate the plate coupling of the Hikurangi subduction zone beneath the North Island of New Zealand, where multiple slow slip cycles are superimposed on the long‐term loading. We estimate the plate coupling across the subduction zone over three multi‐year observational periods targeting different stages of the slow slip cycle. Our results highlight the importance of the observational time period when interpreting coupling maps, emphasizing the temporal variability of plate coupling. Leveraging multiple geodetic data sets, we demonstrate how InSAR provides powerful constraints on the spatial resolution of both plate coupling and slow fault slip, even in a region where a dense GNSS network exists.
Carbonyl Sulfide (OCS) in the Upper Troposphere/Lowermost Stratosphere (UT/LMS) Region: Estimates of Lifetimes and Fluxes
Authors: Karu Einar , Li Mengze , Ernle Lisa , Brenninkmeijer Carl A. M. , Lelieveld Jos , Williams Jonathan 
Published: October 2023

AbstractCarbonyl sulfide (OCS or COS) is a ubiquitous trace gas and plays a role in forming stratospheric sulfate aerosol particles, thereby influencing climate. In this study, whole‐air samples containing OCS were collected onboard a passenger aircraft (IAGOS‐CARIBIC) from the upper troposphere/lowermost stratosphere (UT/LMS, 10–12 km) region and analyzed with CryoTrap–GC–AED system in the laboratory. Global OCS mixing ratios are presented and by using the OCS measurements in conjunction with other trace gases, an atmospheric OCS lifetime of 2.1 ± 1.3 years, and lowermost stratospheric OCS lifetime of 47 ± 16 years were determined. A total flux of 137 GgS a−1 of OCS from the troposphere into the stratosphere was estimated, and the stratospheric sink estimate yielded 55 ± 23 GgS a−1 of OCS. The 60% smaller sink can be interpreted as 82 GgS a−1 OCS which is transported back from the stratosphere into the troposphere.
Non‐Uniqueness in ITCZ Latitude Due To Radiation‐Circulation Coupling in an Idealized GCM
Authors: Zurita‐Gotor Pablo , Held Isaac M. , Merlis Timothy M. , Chang Chiung‐Yin , Hill Spencer A. , MacDonald Cameron G. 
Published: October 2023

AbstractAn idealized aquaplanet moist global atmospheric model with realistic radiative transfer but no clouds and no convective parameterization is found to possess multiple climate equilibria. When forced symmetrically about the equator, in some cases the Inter Tropical Convergence Zone (ITCZ) migrates to an off‐equatorial equilibrium position. Mechanism denial experiments prescribing relative humidity imply that radiation‐circulation coupling is essential to this instability. The cross‐equatorial asymmetry occurs only when the underlying slab ocean is sufficiently deep and the atmosphere's spectral dynamical core is sufficiently coarse (∼T170 or less with our control parameters). At higher resolutions, initializing with an asymmetric state indicates metastability with very slow (thousands of days) return to hemispheric symmetry. There is some sensitivity to the model timestep, which affects the time required to transition to the asymmetric state, with little effect on the equilibrium climate. The instability is enhanced when the planetary boundary layer scheme favors deeper layers or by a prescribed meridional heat transport away from the equator within the slab. The instability is not present when the model is run with a convective parameterization scheme commonly utilized in idealized moist models. We argue that the instability occurs when the asymmetric heating associated with a spontaneous ITCZ shift drives a circulation that rises poleward of the perturbed ITCZ. These results serve as a warning of the potential for instability and non‐uniqueness of climate that may complicate studies with idealized models of the tropical response to perturbations in forcing.
Modulating biofilm can potentiate activity of novel plastic-degrading enzymes
Authors: Howard Sophie A. , McCarthy Ronan R. 
Published: October 2023

AbstractPlastic pollution is an increasing global issue desperately requiring a solution. Only 9% of all plastic waste has been recycled, and whilst recycling gives a second life to plastic, it is costly and there are limited downstream uses of recycled plastic, therefore an alternative is urgently needed. Biodegradation of plastic by microorganisms is a developing field of interest with the potential for bioreactors to be used alongside recycling to degrade plastic that may otherwise be sent to landfill. Here, we have identified two novel polyethylene terephthalate (PET) degrading enzymes through genomic mining and characterised their activity, including their ability to degrade PET. One of the main roadblocks facing the development of microbial enzymes as a plastic biodegradation solution, is that their efficiency is too low to facilitate development as bioremediation tools. In an innovative approach to tackle this roadblock, we hypothesised that enhancing a bacteria’s ability to attach to and form a biofilm on plastic could maximise the local concentration of the enzyme around the target substrate, therefore increasing the overall rate of plastic degradation. We found that increasing biofilm levels, by manipulating the levels of the second messenger, Cyclic-di-GMP, led to increased levels of polyester degradation in cells expressing novel and well characterised polyester-degrading enzymes. This indicates that modulating biofilm formation is a viable mechanism to fast track the development of bacterial plastic bioremediation solutions.
Endomapper dataset of complete calibrated endoscopy procedures
Authors: Azagra Pablo , Sostres Carlos , Ferrández Ángel , Riazuelo Luis , Tomasini Clara , Barbed O. León , Morlana Javier , Recasens David , Batlle Víctor M. , Gómez-Rodríguez Juan J. , Elvira Richard , López Julia , Oriol Cristina , Civera Javier , Tardós Juan D. , Murillo Ana C. , Lanas Angel , Montiel José M. M. 
Published: October 2023

AbstractComputer-assisted systems are becoming broadly used in medicine. In endoscopy, most research focuses on the automatic detection of polyps or other pathologies, but localization and navigation of the endoscope are completely performed manually by physicians. To broaden this research and bring spatial Artificial Intelligence to endoscopies, data from complete procedures is needed. This paper introduces the Endomapper dataset, the first collection of complete endoscopy sequences acquired during regular medical practice, making secondary use of medical data. Its main purpose is to facilitate the development and evaluation of Visual Simultaneous Localization and Mapping (VSLAM) methods in real endoscopy data. The dataset contains more than 24 hours of video. It is the first endoscopic dataset that includes endoscope calibration as well as the original calibration videos. Meta-data and annotations associated with the dataset vary from the anatomical landmarks, procedure labeling, segmentations, reconstructions, simulated sequences with ground truth and same patient procedures. The software used in this paper is publicly available.
Multi-year belowground data of minirhizotron facilities in Selhausen
Authors: Lärm Lena , Bauer Felix Maximilian , Hermes Normen , van der Kruk Jan , Vereecken Harry , Vanderborght Jan , Nguyen Thuy Huu , Lopez Gina , Seidel Sabine Julia , Ewert Frank , Schnepf Andrea , Klotzsche Anja 
Published: October 2023

AbstractThe production of crops secure the human food supply, but climate change is bringing new challenges. Dynamic plant growth and corresponding environmental data are required to uncover phenotypic crop responses to the changing environment. There are many datasets on above-ground organs of crops, but roots and the surrounding soil are rarely the subject of longer term studies. Here, we present what we believe to be the first comprehensive collection of root and soil data, obtained at two minirhizotron facilities located close together that have the same local climate but differ in soil type. Both facilities have 7m-long horizontal tubes at several depths that were used for crosshole ground-penetrating radar and minirhizotron camera systems. Soil sensors provide observations at a high temporal and spatial resolution. The ongoing measurements cover five years of maize and wheat trials, including drought stress treatments and crop mixtures. We make the processed data available for use in investigating the processes within the soil–plant continuum and the root images to develop and compare image analysis methods.
Improving diagnosis accuracy with an intelligent image retrieval system for lung pathologies detection: a features extractor approach
Authors: Souid Abdelbaki , Alsubaie Najah , Soufiene Ben Othman , Alqahtani Mohammed S. , Abbas Mohamed , Jambi Layal K. , Sakli Hedi 
Published: October 2023

AbstractDetecting lung pathologies is critical for precise medical diagnosis. In the realm of diagnostic methods, various approaches, including imaging tests, physical examinations, and laboratory tests, contribute to this process. Of particular note, imaging techniques like X-rays, CT scans, and MRI scans play a pivotal role in identifying lung pathologies with their non-invasive insights. Deep learning, a subset of artificial intelligence, holds significant promise in revolutionizing the detection and diagnosis of lung pathologies. By leveraging expansive datasets, deep learning algorithms autonomously discern intricate patterns and features within medical images, such as chest X-rays and CT scans. These algorithms exhibit an exceptional capacity to recognize subtle markers indicative of lung diseases. Yet, while their potential is evident, inherent limitations persist. The demand for abundant labeled data during training and the susceptibility to data biases challenge their accuracy. To address these formidable challenges, this research introduces a tailored computer-assisted system designed for the automatic retrieval of annotated medical images that share similar content. At its core lies an intelligent deep learning-based features extractor, adept at simplifying the retrieval of analogous images from an extensive chest radiograph database. The crux of our innovation rests upon the fusion of YOLOv5 and EfficientNet within the features extractor module. This strategic fusion synergizes YOLOv5's rapid and efficient object detection capabilities with EfficientNet's proficiency in combating noisy predictions. The result is a distinctive amalgamation that redefines the efficiency and accuracy of features extraction. Through rigorous experimentation conducted on an extensive and diverse dataset, our proposed solution decisively surpasses conventional methodologies. The model's achievement of a mean average precision of 0.488 with a threshold of 0.9 stands as a testament to its effectiveness, overshadowing the results of YOLOv5 + ResNet and EfficientDet, which achieved 0.234 and 0.257 respectively. Furthermore, our model demonstrates a marked precision improvement, attaining a value of 0.864 across all pathologies—a noteworthy leap of approximately 0.352 compared to YOLOv5 + ResNet and EfficientDet. This research presents a significant stride toward enhancing radiologists' workflow efficiency, offering a refined and proficient tool for retrieving analogous annotated medical images.
Addressable superconductor integrated circuit memory from delay lines
Authors: Volk Jennifer , Wynn Alex , Golden Evan , Sherwood Timothy , Tzimpragos Georgios 
Published: October 2023

AbstractRecent advances in logic schemes and fabrication processes have renewed interest in using superconductor electronics for energy-efficient computing and quantum control processors. However, scalable superconducting memory still poses a challenge. To address this issue, we present an alternative to approaches that solely emphasize storage cell miniaturization by exploiting the minimal attenuation and dispersion properties of superconducting passive transmission lines to develop a delay-line memory system. This fully superconducting design operates at speeds between 20 and 100 GHz, with ± 24% and ± 13% bias margins, respectively, and demonstrates data densities in the 10s of Mbit/cm2 with the MIT Lincoln Laboratory SC2 fabrication process. Additionally, the circulating nature of this design allows for minimal control circuitry, eliminates the need for data splitting and merging, and enables inexpensive implementations of sequential access and content-addressable memories. Further advances in fabrication processes suggest data densities of 100s of Mbit/cm2 and beyond.
Human papillomavirus and prostate cancer: systematic review and meta-analysis
Authors: Tsydenova Irina A. , Ibragimova Marina K. , Tsyganov Matvey M. , Litviakov Nikolai V. 
Published: October 2023

AbstractThe involvement of human papillomavirus (HPV) in the prostate carcinogenesis is a controversial issue. The presented meta-analysis was carried out to systematize the currently available research results regarding this question. The meta-analysis includes case–control studies from 1991 to 2022, which were collected from publicly available bibliometric databases. The meta-analysis was performed using Meta-Essentials_1.5 software. We used Begg’s and Egger’s methods to assess publication bias. Cochran’s Q test was used to assess heterogeneity and the I2 index was employed for calculating the variation in the pooled estimations. The analysis was based on data from 27 case–control studies, which in total yielded 1607 tumour tissue samples of prostate and 1515 control samples (317 samples of normal tissue, 1198 samples of benign prostatic hyperplasia (BPH)). According to the data obtained, there was high risk of prostate cancer by HPV infection in both cases. HPV was found in prostate cancer in 25.8% of cases, while in normal tissue samples the virus was detected in 9.2% of cases and in 17.4% with BPH as a control. In particular, more studies on the association of HPV and prostate cancer are needed to prove the role of HPV in the development of prostate cancer. In addition to the controversial question of whether HPV infection is associated with prostate cancer risk, it is worth considering whether the samples used as a control have an impact on the results. The impact of HPV in prostate tumour tissue samples on outcome should also be investigated.
Effect of phospholipid head group on ultrasound-triggered drug release and cellular uptake of immunoliposomes
Authors: Awad Nahid S. , Paul Vinod , AlSawaftah Nour M. , Husseini Ghaleb A. 
Published: October 2023

AbstractLiposomes are the most successful nanoparticles used to date to load and deliver chemotherapeutic agents to cancer cells. They are nano-sized vesicles made up of phospholipids, and targeting moieties can be added to their surfaces for the active targeting of specific tumors. Furthermore, Ultrasound can be used to trigger the release of the loaded drugs by disturbing their phospholipid bilayer structure. In this study, we have prepared pegylated liposomes using four types of phospholipids with similar saturated hydrocarbon tails including a phospholipid with no head group attached to the phosphate head (DPPA) and three other phospholipids with different head groups attached to their phosphate heads (DPPC, DPPE and DPPG). The prepared liposomes were conjugated to the monoclonal antibody trastuzumab (TRA) to target the human epidermal growth factor receptor 2 (HER2) overexpressed on HER2-positive cancer cells (HER2+). We have compared the response of the different formulations of liposomes when triggered with low-frequency ultrasound (LFUS) and their cellular uptake by the cancer cells. The results showed that the different formulations had similar size, polydispersity, and stability. TRA-conjugated DPPC liposomes showed the highest sensitivity to LFUS. On the other hand, incubating the cancer cells with TRA-conjugated DPPA liposomes triggered with LFUS showed the highest uptake of the loaded calcein by the HER2+ cells.