bluuebunny/crossref_metadata_2025_split huggingface dataset:
EMC rectifies the topology of multipass membrane proteins
Authors: Wu Haoxi , Smalinskaitė Luka , Hegde Ramanujan S. 
Published: November 2023

AbstractMost eukaryotic multipass membrane proteins are inserted into the membrane of the endoplasmic reticulum. Their transmembrane domains (TMDs) are thought to be inserted co-translationally as they emerge from a membrane-bound ribosome. Here we find that TMDs near the carboxyl terminus of mammalian multipass proteins are inserted post-translationally by the endoplasmic reticulum membrane protein complex (EMC). Site-specific crosslinking shows that the EMC’s cytosol-facing hydrophilic vestibule is adjacent to a pre-translocated C-terminal tail. EMC-mediated insertion is mostly agnostic to TMD hydrophobicity, favored for short uncharged C-tails and stimulated by a preceding unassembled TMD bundle. Thus, multipass membrane proteins can be released by the ribosome–translocon complex in an incompletely inserted state, requiring a separate EMC-mediated post-translational insertion step to rectify their topology, complete biogenesis and evade quality control. This sequential co-translational and post-translational mechanism may apply to ~250 diverse multipass proteins, including subunits of the pentameric ion channel family that are crucial for neurotransmission.
A labeled data set of underwater images of fish and crab species from five mesohabitats in Puget Sound WA USA
Authors: Farrell Dara M. , Ferriss Bridget , Sanderson Beth , Veggerby Karl , Robinson Lauren , Trivedi Anusua , Pathak Shreyaan , Muppalla Sreya , Wang Jane , Morris Dan , Dodhia Rahul 
Published: November 2023

AbstractThe sustainable management of fisheries and aquaculture requires an understanding of how these activities interact with natural fish populations. GoPro cameras were used to collect an underwater video data set on and around shellfish aquaculture farms in an estuary in the NE Pacific from June to August 2017 and June to August 2018 to better understand habitat use by the local fish and crab communities. Images extracted from these videos were labeled to produce a data set that is suitable for use in training computer vision models. The labeled data set contains 77,739 images sampled from the collected video; 67,990 objects (fishes and crustaceans) have been annotated in 30,384 images (the remainder have been annotated as “empty”). The metadata of the data set also indicates whether a physical magenta filter was used during video collection to counteract reduced visibility. These data have the potential to help researchers address system-level and in-depth regional shellfish aquaculture questions related to ecosystem services and shellfish aquaculture interactions.
Counting manatee aggregations using deep neural networks and Anisotropic Gaussian Kernel
Authors: Wang Zhiqiang , Pang Yiran , Ulus Cihan , Zhu Xingquan 
Published: November 2023

AbstractManatees are aquatic mammals with voracious appetites. They rely on sea grass as the main food source, and often spend up to eight hours a day grazing. They move slow and frequently stay in groups (i.e. aggregations) in shallow water to search for food, making them vulnerable to environment change and other risks. Accurate counting manatee aggregations within a region is not only biologically meaningful in observing their habit, but also crucial for designing safety rules for boaters, divers, etc., as well as scheduling nursing, intervention, and other plans. In this paper, we propose a deep learning based crowd counting approach to automatically count number of manatees within a region, by using low quality images as input. Because manatees have unique shape and they often stay in shallow water in groups, water surface reflection, occlusion, camouflage etc. making it difficult to accurately count manatee numbers. To address the challenges, we propose to use Anisotropic Gaussian Kernel (AGK), with tunable rotation and variances, to ensure that density functions can maximally capture shapes of individual manatees in different aggregations. After that, we apply AGK kernel to different types of deep neural networks primarily designed for crowd counting, including VGG, SANet, Congested Scene Recognition network (CSRNet), MARUNet etc. to learn manatee densities and calculate number of manatees in the scene. By using generic low quality images extracted from surveillance videos, our experiment results and comparison show that AGK kernel based manatee counting achieves minimum Mean Absolute Error (MAE) and Root Mean Square Error (RMSE). The proposed method works particularly well for counting manatee aggregations in environments with complex background.
Nitrogen isotopic composition as a gauge of tumor cell anabolism-to-catabolism ratio
Authors: Straub Marietta , Auderset Alexandra , de Leval Laurence , Piazzon Nathalie , Maison Damien , Vozenin Marie-Catherine , Ollivier Jonathan , Petit Benoît , Sigman Daniel M. , Martínez-García Alfredo 
Published: November 2023

AbstractStudies have suggested that cancerous tissue has a lower 15N/14N ratio than benign tissue. However, human data have been inconclusive, possibly due to constraints on experimental design. Here, we used high-sensitivity nitrogen isotope methods to assess the 15N/14N ratio of human breast, lung, and kidney cancer tissue at unprecedented spatial resolution. In lung, breast, and urothelial carcinoma, 15N/14N was negatively correlated with tumor cell density. The magnitude of 15N depletion for a given tumor cell density was consistent across different types of lung cancer, ductal in situ and invasive breast carcinoma, and urothelial carcinoma, suggesting similar elevations in the anabolism-to-catabolism ratio. However, tumor 15N depletion was higher in a more aggressive metaplastic breast carcinoma. These findings may indicate the ability of certain cancers to more effectively channel N towards growth. Our results support 15N/14N analysis as a potential tool for screening biopsies and assessing N metabolism in tumor cells.
Effect of statin use on head and neck cancer prognosis in a multicenter study using a Common Data Model
Authors: Seol Soobeen , Choi Jung Ran , Choi Byungjin , Kim Sungryeal , Jeon Ja Young , Park Ki Nam , Park Jae Hong , Park Min Woo , Eun Young-Gyu , Park Jung Je , Lee Byung-Joo , Shin Yoo Seob , Kim Chul-Ho , Park Rae Woong , Jang Jeon Yeob 
Published: November 2023

AbstractFew studies have found an association between statin use and head and neck cancer (HNC) outcomes. We examined the effect of statin use on HNC recurrence using the converted Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) in seven hospitals between 1986 and 2022. Among the 9,473,551 eligible patients, we identified 4669 patients with HNC, of whom 398 were included in the target cohort, and 4271 were included in the control cohort after propensity score matching. A Cox proportional regression model was used. Of the 4669 patients included, 398 (8.52%) previously received statin prescriptions. Statin use was associated with a reduced rate of 3- and 5-year HNC recurrence compared to propensity score-matched controls (risk ratio [RR], 0.79; 95% confidence interval [CI], 0.61–1.03; and RR 0.89; 95% CI 0.70–1.12, respectively). Nevertheless, the association between statin use and HNC recurrence was not statistically significant. A meta-analysis of recurrence based on subgroups, including age subgroups, showed similar trends. The results of this propensity-matched cohort study may not provide a statistically significant association between statin use and a lower risk of HNC recurrence. Further retrospective studies using nationwide claims data and prospective studies are warranted.
Proteomic discovery of prognostic protein biomarkers for persisting problems after mild traumatic brain injury
Authors: Lee Min-Yong , Son Minsoo , Lee Hyun Haeng , Kang Min-Gu , Yun Seo Jung , Seo Han Gil , Kim Youngsoo , Oh Byung-Mo 
Published: November 2023

AbstractSome individuals with mild traumatic brain injury (mTBI), also known as concussion, have neuropsychiatric and physical problems that last longer than a few months. Symptoms following mTBI are not only impacted by the kind and severity of the injury but also by the post-injury experience and the individual's responses to it, making the persistence of mTBI particularly difficult to predict. We aimed to identify prognostic blood-based protein biomarkers predicting 6-month outcomes, in light of the clinical course after the injury, in a longitudinal mTBI cohort (N = 42). Among 420 target proteins quantified by multiple-reaction monitoring-mass spectrometry assays of blood samples, 31, 43, and 15 proteins were significantly associated with the poor recovery of neuropsychological symptoms at < 72 h, 1 week, and 1 month after the injury, respectively. Sequential associations among clinical assessments (depressive symptoms and cognitive function) affecting the 6-month outcomes were evaluated. Then, candidate biomarker proteins indirectly affecting the outcome via neuropsychological symptoms were identified. Using the identified proteins, prognostic models that can predict the 6-month outcome of mTBI were developed. These protein biomarkers established in the context of the clinical course of mTBI may have potential for clinical application.
Inhibition of insulin-regulated aminopeptidase confers neuroprotection in a conscious model of ischemic stroke
Authors: Telianidis Jonathon , Hunter Andrew , Widdop Robert , Kemp-Harper Barbara , Pham Vi , McCarthy Claudia , Chai Siew Yeen 
Published: November 2023

AbstractStroke is a leading cause of mortality and morbidity with a paucity of effective pharmacological treatments. We have previously identified insulin-regulated aminopeptidase (IRAP) as a potential target for the development of a new class of drugs for the treatment of stroke, as global deletion of this gene in mice significantly protected against ischemic damage. In the current study, we demonstrate that small molecular weight IRAP inhibitors reduce infarct volume and improve neurological outcome in a hypertensive animal model of ischemic stroke. The effects of two structurally distinct IRAP inhibitors (HFI419 or SJM164) were investigated in a model of stroke where the middle cerebral artery was transiently occluded with endothelin-1 in the conscious spontaneously hypertensive rat. IRAP inhibitor was administered into the lateral ventricle at 2 or 6 h after stroke, with subsequent doses delivered at 24, 48 and 70 h post-stroke. Functional outcomes were assessed prior to drug treatment, and on day 1 and 3 post-stroke. Histological analyses and neuroinflammatory cytokine profiling were conducted at 72 and 24 h post-stroke respectively. IRAP inhibitor treatment following stroke significantly reduced infarct volume and improved neurological and motor deficits. These protective effects were maintained even when the therapeutic window was extended to 6 h. Examination of the cellular architecture at 72 h post-stroke demonstrated that IRAP expression was upregulated in CD11b positive cells and activated astrocytes. Furthermore, IRAP inhibitor treatment significantly increased gene expression for interleukin 6 and C–C motif chemokine ligand 2 in the ischemic core. This study provides proof-of-principle that selective inhibition of IRAP activity with two structurally distinct IRAP inhibitors reduces infarct volume and improves functional outcome even when the first dose is administered 6 h post-stroke. This is the first direct evidence that IRAP inhibitors are a class of drug with potential use in the treatment of ischemic stroke.
A sensitive method to determine 210Po and 210Pb in environmental samples by alpha spectrometry using CuS micro-precipitation
Authors: Walsh Stephanie , Bond Matthew J. , Guérin Nicolas , Blais Jules M. , Rowan David J. 
Published: November 2023

AbstractA new sensitive method to determine polonium-210 (210Po) and lead-210 (210Pb) in a diversity of environmental samples was developed. For fresh and marine waters, Po was pre-concentrated using a titanium (III) hydroxide (Ti(OH)3) co-precipitation. Solid environmental samples were digested with nitric acid (HNO3) and hydrogen peroxide (H2O2). The alpha thin layer source was prepared using CuS micro-precipitation and 210Po was measured by alpha spectrometry. Lead-210 was left to decay for up to a year and indirectly measured via its progeny, 210Po. The chemical recoveries for 210Po and 210Pb were high, 90% and 97%, respectively, for a large variety of samples and a very low minimum detectable activity (MDA) was obtained. The method was validated using standardized solutions and certified reference materials.
Study on optimization of layout parameters of high-level boreholes in Pingdingshan coal mine
Authors: Wang Yapeng , Zhang Yongli 
Published: November 2023

AbstractTo reduce the gas disaster of high gas coal seam and improve the efficiency of gas extraction by high drilling, the layout parameters of drilling holes in Pingdingshan coal mine are optimized. Based on the analysis and calculation of the "three zones" of the movement towards the overly strata of No.10 coal in Pingdingshan coal mine, the height of caving zone and fissure zone in 24,130 working face are 10.06–14.46 m and 38.75–49.95 m respectively. The elevation angle, azimuth angle and the length of high-level boreholes are studied and analyzed by COMSOL numerical simulation software. The simulation results show that the optimum layout parameters of high-level boreholes are as follows: The elevation angle of borehole should be controlled at 9°–12°, the azimuth angle should be 30°–45°, and the length of borehole should be 150 m. Then the optimum layout parameters of high-level boreholes are determined for engineering application of 24,130 working face. Borehole data onto actual mine show that the optimum layout parameters of high-level boreholes were elevation angle between 8°and 11°, azimuth angle between 30° and 42°, and length of boreholes between 145 and 155 m. The simulation results are basically consistent with the measured data. The maximum gas concentration in working face, upper corner and return air roadway is stably controlled below 1%. The safe mining of 24,130 working face is ensured, which provided a certain reference value of gas control in the goaf of Pingdingshan mine and adjacent mines.
Multifocal optical projection microscopy enables label-free 3D measurement of cardiomyocyte cluster contractility
Authors: Belay Birhanu , Figueiras Edite , Hyttinen Jari , Ahola Antti 
Published: November 2023

AbstractHuman induced pluripotent stem cell (hiPSC)-derived cardiomyocyte (CM) models have become an attractive tool for in vitro cardiac disease modeling and drug studies. These models are moving towards more complex three-dimensional microphysiological organ-on-chip systems. Label-free imaging-based techniques capable of quantifying contractility in 3D are needed, as traditional two-dimensional methods are ill-suited for 3D applications. Here, we developed multifocal (MF) optical projection microscopy (OPM) by integrating an electrically tunable lens to our in-house built optical projection tomography setup for extended depth of field brightfield imaging in CM clusters. We quantified cluster biomechanics by implementing our previously developed optical flow-based CM video analysis for MF-OPM. To demonstrate, we acquired and analyzed multiangle and multifocal projection videos of beating hiPSC-CM clusters in 3D hydrogel. We further quantified cluster contractility response to temperature and adrenaline and observed changes to beating rate and relaxation. Challenges emerge from light penetration and overlaying textures in larger clusters. However, our findings indicate that MF-OPM is suitable for contractility studies of 3D clusters. Thus, for the first time, MF-OPM is used in CM studies and hiPSC-CM 3D cluster contraction is quantified in multiple orientations and imaging planes.
Combustion of raw Camelina sativa oil in CI engine equipped with common rail system
Authors: Pawlak Grzegorz , Skrzek Tomasz 
Published: November 2023

AbstractDuring the world energy transformation, using some vegetable oils as fuel enables the production of clean and inexpensive energy with the application of the well-known technology of the CI engine. The common rail (CR) fuel system gives many opportunities related to creating an air–fuel mixture and its efficient combustion. Can the system dedicated to diesel oil be used to inject vegetable oil and control its combustion effectively? This paper presents some results of the application of the injection strategy for raw Camelina sativa (CS) oil fueling. The test was conducted on the AVL single-cylinder CI engine equipped with a CR system for engine speed n = 1500 rpm and different excess air coefficients (1.1 < λ < 2.1). The engine parameters and performance obtained for raw CS oil were compared with the results obtained for diesel oil fueling for the same and slightly modified injection strategy. The experiment demonstrated how much the combustion process and its effects differ for these two fuels. In addition, several aspects related to the cultivation and use of Camelina sativa oil as a renewable energy source are presented.
Integration of high-resolution imaging through scattering medium into a disposable micro-endoscope via projection of 2D spots-array
Authors: Elkabetz Shimon , Herman Oran , Meiri Amihai , Shahmoon Asaf , Zalevsky Zeev 
Published: November 2023

AbstractThe objective of this research includes integration of high-resolution imaging through scattering medium, such as blood, into a disposable micro-endoscope. A fiber laser integrated into the micro-endoscope as part of its illumination channel, allows to project a tunable array of spots of light onto an object, that is located behind the scattering medium. We have a laser fiber as part of the illumination channel of a disposable micro-endoscope. By using proper optics, we convert the temporal modulation of the laser into spatial distribution. Thus, the result is generation of spatial spots when using a pulsed laser. The detection channel is a holographic recording of the collected back scattered light, that allows extraction of the electrical field. By time integrating the field we obtain the realization of the spatial array of illumination spots formed on top of the inspected object and behind the scattering medium. By changing the temporal modulation of the illumination laser (changing its temporal photonic signals), we can tune the positions of the spots in the illumination array. If the distance between the projected spots is larger than the imaging resolution, then by applying localization microscopy algorithms together with scanning of the position of the spots in the array, will yield a high-resolution reconstruction of the inspected object. We theoretically and experimentally demonstrate the discussed operation principle and show the potential of the proposed concept as a modality in medical endoscopic procedures.
Morphological description of the glochidia of Buldowskia suifunica (Bivalvia: Unionidae)
Authors: Sayenko Elena M. , Nikischenko Viktoria E. , Dyachuk Vyacheclav A. 
Published: November 2023

AbstractFreshwater mussels of the genus Buldowskia (Bivalvia, Unionidae) are distributed from the Amur River basin in Russia and China southward to the Korean Peninsula and some Japanese islands. This work is an integrative morphological study of Buldowskia suifunica glochidia from locations in the Primorsky Territory, the Russian Far East. Glochidia of B. suifunica, taken from the same gill have asynchronous development. The external and internal morphology of its shell has been characterized. The morphology of its sensory system, within three stages of larval development (immature, intermediate and mature glochidia), consists of hair cells as well as nonhair cells. Their muscle system is composed of massive adductor and minor muscle bundles. The FMRFamid-ergic nervous system turned out to be a complex system includes basal cells (neurons), their neurites and anterior neurons. FMRFamide and tubulin was found in all neurons. Glochidia of B. suifunica have only four 5-HT-lir neurons. We concluded that B. suifunica glochidial nervous system differs from those of the larval systems of planktotrophic marine mollusks.
Constrained DFT-based magnetic machine-learning potentials for magnetic alloys: a case study of Fe–Al
Authors: Kotykhov Alexey S. , Gubaev Konstantin , Hodapp Max , Tantardini Christian , Shapeev Alexander V. , Novikov Ivan S. 
Published: November 2023

AbstractWe propose a machine-learning interatomic potential for multi-component magnetic materials. In this potential we consider magnetic moments as degrees of freedom (features) along with atomic positions, atomic types, and lattice vectors. We create a training set with constrained DFT (cDFT) that allows us to calculate energies of configurations with non-equilibrium (excited) magnetic moments and, thus, it is possible to construct the training set in a wide configuration space with great variety of non-equilibrium atomic positions, magnetic moments, and lattice vectors. Such a training set makes possible to fit reliable potentials that will allow us to predict properties of configurations in the excited states (including the ones with non-equilibrium magnetic moments). We verify the trained potentials on the system of bcc Fe–Al with different concentrations of Al and Fe and different ways Al and Fe atoms occupy the supercell sites. Here, we show that the formation energies, the equilibrium lattice parameters, and the total magnetic moments of the unit cell for different Fe–Al structures calculated with machine-learning potentials are in good correspondence with the ones obtained with DFT. We also demonstrate that the theoretical calculations conducted in this study qualitatively reproduce the experimentally-observed anomalous volume-composition dependence in the Fe–Al system.
The potential immunomodulatory role of the gut microbiota in the pathogenesis of asthma: an in vitro study
Authors: Kleniewska Paulina , Kopa-Stojak Paulina Natalia , Hoffmann Arkadiusz , Pawliczak Rafał 
Published: November 2023

AbstractThe aim of this study was to investigate the influence of Bacteroides vulgatus (BV), Clostridium perfringens (CP), Parabacteroides distasonis (PD) and Ruminococcus albus (RA) lysates on secretion of selected cytokines by PBMC, MDM and HT-29 cells, as well as to determine the potential mechanisms of their action in the development of asthma. Enzyme-linked immunosorbent assays were used to analyze the effect of BV, CP, PD and RA lysates on the secretion of IL-1β, IL-6, IL-10 and TNF-α by human PBMC, MDM and HT-29 cells. BV and CP lysates significantly lowered IL-1β secretion by MDM vs. control (p < 0.05 and p < 0.001 respectively) but only at a dose of 400 µg lysate. The secretions of IL-6 by PBMC and MDM were elevated significantly above control values (p < 0.05) after administration of CP and PD lysates. BV, CP and PD lysates (100 µg) significantly increased IL-10 secretion by PBMC vs. control (p < 0.05). CP, PD and RA lysates (400 µg) significantly increased IL-10 secretion by MDM vs. control (p < 0.001). BV lysate (400 µg) also significantly increased IL-10 secretion by MDM as compared to control (p < 0.05). In PBMC and MDM, the production levels of the anti-inflammatory cytokine were increased by all the bacterial lysates used in a dose-dependent manner.