bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning multiple concepts in description logic through three perspectives
Authors: Melo Raphael , Revoredo Kate , Paes Aline 
Published: May 2021

AbstractAn ontology formalises a number of dependent and related concepts in a domain, encapsulated as a terminology. Manually defining such terminologies is a complex, time-consuming and error-prone task. Thus, there is great interest for strategies to learn terminologies automatically. However, most of the existing approaches induce a single concept definition at a time, disregarding dependencies that may exist among the concepts. As a consequence, terminologies that are difficult to interpret may be induced. Thus, systems capable of learning all concepts within a single task, respecting their dependency, are essential for reaching concise and readable ontologies. In this paper, we tackle this issue presenting three terminology learning strategies that aim at finding dependencies among concepts, before, during or after they have been defined. Experimental results show the advantages of regarding the dependencies among the concepts to achieve readable and concise terminologies, compared to a system that learns a single concept at a time. Moreover, the three strategies are compared and analysed towards discussing the strong and weak points of each one.
Children's comprehension of prosodically marked focus in Hungarian: How mandatory syntactic focus-marking affects the trajectory of acquisition
Authors: SURÁNYI Balázs , PINTÉR Lilla 
Published: May 2021

AbstractThis study investigates children's identification of prosodic focus in Hungarian, a language in which syntactic focus-marking is mandatory. Assuming that regular syntactic focus-marking diminishes the disambiguating role of prosodic marking in acquisition, we expected that in sentences in which focus is only disambiguated by prosody, adult-like comprehension of prosodic focus-marking should be delayed in comparison to the Germanic and Romance languages investigated previously using the same experimental method that we adopted. Our results, confirming this prediction, suggest that the developmental trajectory of the comprehension of prosodic focus-marking may be substantially affected by cross-linguistic grammatical variation in the marking of focus.
Turán-type results for intersection graphs of boxes
Authors: Tomon István , Zakharov Dmitriy 
Published: May 2021

AbstractIn this short note, we prove the following analog of the Kővári–Sós–Turán theorem for intersection graphs of boxes. If G is the intersection graph of n axis-parallel boxes in $${{\mathbb{R}}^d}$$ such that G contains no copy of Kt,t, then G has at most ctn( log n)2d+3 edges, where c = c(d)>0 only depends on d. Our proof is based on exploring connections between boxicity, separation dimension and poset dimension. Using this approach, we also show that a construction of Basit, Chernikov, Starchenko, Tao and Tran of K2,2-free incidence graphs of points and rectangles in the plane can be used to disprove a conjecture of Alon, Basavaraju, Chandran, Mathew and Rajendraprasad. We show that there exist graphs of separation dimension 4 having superlinear number of edges.
Prediction of Hypoxia in Eutrophic Polymictic Lakes
Authors: Cortés A. , Forrest A. L. , Sadro S. , Stang A. J. , Swann M. , Framsted N. T. , Thirkill R. , Sharp S. L. , Schladow S. G. 
Published: May 2021

AbstractQuantifying and predicting the drawdown of dissolved oxygen (DO) in lakes is important to ensuring healthy ecosystems and safe water sources. The characterization of DO depletion using available definitions and models requires extensive monitoring to obtain reliable results. These approaches have been mostly developed for seasonally stratified monomictic and dimictic lakes, limiting their applicability for polymictic systems which stratify and mix repeatedly. We compared the predicted duration of hypoxic events in the three basins of a large eutrophic polymictic lake (Clear Lake, CA, USA) by using three different one‐dimensional (1‐D) analytical approaches; two being original and requiring minimal input variables. Data on meteorology, lake temperature, and DO were all measured at multiple locations for one year and used to develop a novel method, named the Birge‐Winkler method. The daily net surface heat fluxes provided an energy term from which estimates of the onset and length of hypoxic periods could be made with minimal calibration. We used the Lake Number method to evaluate the level of accuracy of the Birge‐Winkler method. Finally, we estimated DO values next to the sediments using a Buoyancy Frequency method. Our results from the two original methods provided simple and effective tools for early warning of onset and duration of hypoxia, with a maximum of ±3–5 days uncertainty in the predictions. These indices can become powerful decision support tools for addressing aquatic ecological challenges triggered by hypoxia, including fish kills, internal nutrient loading, heavy metals release, and harmful algal blooms.
PAX8-AS1 knockdown facilitates cell growth and inactivates autophagy in osteoblasts via the miR-1252-5p/GNB1 axis in osteoporosis
Authors: Huang Caiqiang , Li Runguang , Yang Changsheng , Ding Rui , Li Qingchu , Xie Denghui , Zhang Rongkai , Qiu Yiyan 
Published: May 2021

AbstractOsteoporosis (OP) is the most common systematic bone disorder among elderly individuals worldwide. Long noncoding RNAs (lncRNAs) are involved in biological processes in various human diseases. It has been previously revealed that PAX8 antisense RNA 1 (PAX8-AS1) is upregulated in OP. However, its molecular mechanism in OP remains unclear. Therefore, we specifically designed this study to determine the specific role of PAX8-AS1 in OP. We first established a rat model of OP and then detected PAX8-AS1 expression in the rats with RT-qPCR. Next, to explore the biological function of PAX8-AS1 in osteoblasts, in vitro experiments, such as Cell Counting Kit-8 (CCK-8) assays, flow cytometry, western blotting and immunofluorescence (IF) staining, were conducted. Subsequently, we performed bioinformatic analysis and luciferase reporter assays to predict and identify the relationships between microRNA 1252-5p (miR-1252-5p) and both PAX8-AS1 and G protein subunit beta 1 (GNB1). Additionally, rescue assays in osteoblasts clarified the regulatory network of the PAX8-AS1/miR-1252-5p/GNB1 axis. Finally, in vivo loss-of-function studies verified the role of PAX8-AS1 in OP progression. The results illustrated that PAX8-AS1 was upregulated in the proximal tibia of OP rats. PAX8-AS1 silencing promoted the viability and inhibited the apoptosis and autophagy of osteoblasts. PAX8-AS1 interacted with miR-1252-5p. GNB1 was negatively regulated by miR-1252-5p. In addition, the impacts of PAX8-AS1 knockdown on osteoblasts were counteracted by GNB1 overexpression. PAX8-AS1 depletion suppressed OP progression by inhibiting apoptosis and autophagy in osteoblasts. In summary, PAX8-AS1 suppressed the viability and activated the autophagy of osteoblasts via the miR-1252-5p/GNB1 axis in OP.
Internal OH− induced cascade quenching of upconversion luminescence in NaYF4:Yb/Er nanocrystals
Authors: Feng Yansong , Li Zhi , Li Qiqing , Yuan Jun , Tu Langping , Ning Lixin , Zhang Hong 
Published: May 2021

AbstractInternal hydroxyl impurity is known as one of the main detrimental factors affecting the upconversion (UC) efficiency of upconversion luminescence (UCL) nanomaterials. Different from surface/ligand-related emission quenching which can be effectively diminished by, e.g., core/shell structure, internal hydroxyl is easy to be introduced in synthesis but difficult to be quantified and controlled. Therefore, it becomes an obstacle to fully understand the relevant UC mechanism and improve UC efficiency of nanomaterials. Here we report a progress in quantifying and large-range adjustment of the internal hydroxyl impurity in NaYF4 nanocrystals. By combining the spectroscopy study and model simulation, we have quantitatively unraveled the microscopic interactions underlying UCL quenching between internal hydroxyl and the sensitizers and activators, respectively. Furthermore, the internal hydroxyl-involved UC dynamical process is interpreted with a vivid concept of “Survivor effect,” i.e., the shorter the migration path of an excited state, the larger the possibility of its surviving from hydroxyl-induced quenching. Apart from the consistent experimental results, this concept can be further evidenced by Monte Carlo simulation, which monitors the variation of energy migration step distribution before and after the hydroxyl introduction. The new quantitative insights shall promote the construction of highly efficient UC materials.
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development
Authors: Turnham Kira E , Wham Drew C , Sampayo Eugenia , LaJeunesse Todd C 
Published: May 2021

Abstract
The application of molecular genetics has reinvigorated and improved how species are defined and investigated scientifically, especially for morphologically cryptic micro-organisms. Here we show how species recognition improves understanding of the ecology and evolution of mutualisms between reef-building corals and their mutualistic dinoflagellates (i.e. Symbiodiniaceae). A combination of genetic, ecological, and morphological evidence defines two sibling species of Cladocopium (formerly Symbiodinium Clade C), specific only to host corals in the common genus Pocillopora, which transmit their obligate symbionts during oogenesis. Cladocopium latusorum sp. nov. is symbiotic with P. grandis/meandrina while the smaller-celled C. pacificum sp. nov. associates with P. verrucosa. Both symbiont species form mutualisms with Pocillopora that brood their young. Populations of each species, like their hosts, are genetically well connected across the tropical and subtropical Pacific Ocean, indicating a capacity for long-range dispersal. A molecular clock approximates their speciation during the late Pliocene or early Pleistocene as Earth underwent cycles of precipitous cooling and warming; and corresponds to when their hosts were also diversifying. The long temporal and spatial maintenance of high host fidelity, as well as genetic connectivity across thousands of kilometers, indicates that distinct ecological attributes and close evolutionary histories will restrain the adaptive responses of corals and their specialized symbionts to rapid climate warming.
The metabolite α-KG induces GSDMC-dependent pyroptosis through death receptor 6-activated caspase-8
Authors: Zhang Jia-yuan , Zhou Bo , Sun Ru-yue , Ai Yuan-li , Cheng Kang , Li Fu-nan , Wang Bao-rui , Liu Fan-jian , Jiang Zhi-hong , Wang Wei-jia , Zhou Dawang , Chen Hang-zi , Wu Qiao 
Published: May 2021

AbstractPyroptosis is a form of regulated cell death mediated by gasdermin family members, among which the function of GSDMC has not been clearly described. Herein, we demonstrate that the metabolite α-ketoglutarate (α-KG) induces pyroptosis through caspase-8-mediated cleavage of GSDMC. Treatment with DM-αKG, a cell-permeable derivative of α-KG, elevates ROS levels, which leads to oxidation of the plasma membrane-localized death receptor DR6. Oxidation of DR6 triggers its endocytosis, and then recruits both pro-caspase-8 and GSDMC to a DR6 receptosome through protein-protein interactions. The DR6 receptosome herein provides a platform for the cleavage of GSDMC by active caspase-8, thereby leading to pyroptosis. Moreover, this α-KG-induced pyroptosis could inhibit tumor growth and metastasis in mouse models. Interestingly, the efficiency of α-KG in inducing pyroptosis relies on an acidic environment in which α-KG is reduced by MDH1 and converted to L-2HG that further boosts ROS levels. Treatment with lactic acid, the end product of glycolysis, builds an improved acidic environment to facilitate more production of L-2HG, which makes the originally pyroptosis-resistant cancer cells more susceptible to α-KG-induced pyroptosis. This study not only illustrates a pyroptotic pathway linked with metabolites but also identifies an unreported principal axis extending from ROS-initiated DR6 endocytosis to caspase-8-mediated cleavage of GSDMC for potential clinical application in tumor therapy.
Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness
Authors: Baron Lia , Atar Shimshi , Zur Hadas , Roopin Modi , Goz Eli , Tuller Tamir 
Published: May 2021

AbstractViral genomes not only code the protein content, but also include silent, overlapping codes which are important to the regulation of the viral life cycle and affect its evolution. Due to the high density of these codes, their non-modular nature and the complex intracellular processes they encode, the ability of current approaches to decipher them is very limited. We describe the first computational-experimental pipeline for studying the effects of viral silent and non-silent information on its fitness. The pipeline was implemented to study the Porcine Circovirus type 2 (PCV2), the shortest known eukaryotic virus, and includes the following steps: (1) Based on the analyses of 2100 variants of PCV, suspected silent codes were inferred. (2) Five hundred variants of the PCV2 were designed to include various ‘smart’ silent mutations. (3) Using state of the art synthetic biology approaches, the genomes of these five hundred variants were generated. (4) Competition experiments between the variants were performed in Porcine kidney-15 (PK15) cell-lines. (5) The variant titers were analyzed based on novel next-generation sequencing (NGS) experiments. (6) The features related to the titer of the variants were inferred and their analyses enabled detection of various novel silent functional sequence and structural motifs. Furthermore, we demonstrate that 50 of the silent variants exhibit higher fitness than the wildtype in the analyzed conditions.
Visual analysis of density and velocity profiles in dense 3D granular gases
Authors: Puzyrev Dmitry , Fischer David , Harth Kirsten , Trittel Torsten , Hidalgo Raúl Cruz , Falcon Eric , Noirhomme Martial , Opsomer Eric , Vandewalle Nicolas , Garrabos Yves , Lecoutre Carole , Palencia Fabien , Stannarius Ralf 
Published: May 2021

AbstractGranular multiparticle ensembles are of interest from fundamental statistical viewpoints as well as for the understanding of collective processes in industry and in nature. Extraction of physical data from optical observations of three-dimensional (3D) granular ensembles poses considerable problems. Particle-based tracking is possible only at low volume fractions, not in clusters. We apply shadow-based and feature-tracking methods to analyze the dynamics of granular gases in a container with vibrating side walls under microgravity. In order to validate the reliability of these optical analysis methods, we perform numerical simulations of ensembles similar to the experiment. The simulation output is graphically rendered to mimic the experimentally obtained images. We validate the output of the optical analysis methods on the basis of this ground truth information. This approach provides insight in two interconnected problems: the confirmation of the accuracy of the simulations and the test of the applicability of the visual analysis. The proposed approach can be used for further investigations of dynamical properties of such media, including the granular Leidenfrost effect, granular cooling, and gas-clustering transitions.
Roaming pathways and survival probability in real-time collisional dynamics of cold and controlled bialkali molecules
Authors: Kłos Jacek , Guan Qingze , Li Hui , Li Ming , Tiesinga Eite , Kotochigova Svetlana 
Published: May 2021

AbstractPerfectly controlled molecules are at the forefront of the quest to explore chemical reactivity at ultra low temperatures. Here, we investigate for the first time the formation of the long-lived intermediates in the time-dependent scattering of cold bialkali $$^{23}\hbox {Na}^{87}$$

23

Na
87

Rb molecules with and without the presence of infrared trapping light. During the nearly 50 nanoseconds mean collision time of the intermediate complex, we observe unconventional roaming when for a few tens of picoseconds either NaRb or $$\hbox {Na}_2$$

Na
2

and $$\hbox {Rb}_2$$

Rb
2

molecules with large relative separation are formed before returning to the four-atom complex. We also determine the likelihood of molecular loss when the trapping laser is present during the collision. We find that at a wavelength of 1064 nm the $$\hbox {Na}_2\hbox {Rb}_2$$

Na
2

Rb
2

complex is quickly destroyed and thus that the $$^{23}\hbox {Na}^{87}$$

23

Na
87

Rb molecules are rapidly lost.
Experiential ownership and body ownership are different phenomena
Authors: Liang Caleb , Lin Wen-Hsiang , Chang Tai-Yuan , Chen Chi-Hong , Wu Chen-Wei , Chen Wen-Yeo , Huang Hsu-Chia , Lee Yen-Tung 
Published: May 2021

AbstractBody ownership concerns what it is like to feel a body part or a full body as mine, and has become a prominent area of study. We propose that there is a closely related type of bodily self-consciousness largely neglected by researchers—experiential ownership. It refers to the sense that I am the one who is having a conscious experience. Are body ownership and experiential ownership actually the same phenomenon or are they genuinely different? In our experiments, the participant watched a rubber hand or someone else’s body from the first-person perspective and was touched either synchronously or asynchronously. The main findings: (1) The sense of body ownership was hindered in the asynchronous conditions of both the body-part and the full-body experiments. However, a strong sense of experiential ownership was observed in those conditions. (2) We found the opposite when the participants’ responses were measured after tactile stimulations had ceased for 5 s. In the synchronous conditions of another set of body-part and full-body experiments, only experiential ownership was blocked but not body ownership. These results demonstrate for the first time the double dissociation between body ownership and experiential ownership. Experiential ownership is indeed a distinct type of bodily self-consciousness.
Grain Fe and Zn content, heterosis, combining ability and its association with grain yield in irrigated and aerobic rice
Authors: Anusha G. , Rao D. Sanjeeva , Jaldhani V. , Beulah P. , Neeraja C. N. , Gireesh C. , Anantha M. S. , Suneetha K. , Santhosha R. , Prasad A. S. Hari , Sundaram R. M. , Madhav M. Sheshu , Fiyaz A. , Brajendra P. , Tuti M. D. , Bhave M. H. V. , Krishna K. V. Radha , Ali J. , Subrahmanyam D. , Senguttuvel P. 
Published: May 2021

AbstractGenetic improvement of rice for grain micronutrients, viz., iron (Fe) and zinc (Zn) content is one of the important breeding objectives, in addition to yield improvement under the irrigated and aerobic ecosystems. In view of developing genetic resources for aerobic conditions, line (L) × tester (T) analysis was conducted with four restorers, four CMS lines and 16 hybrids. Both hybrids and parental lines were evaluated in irrigated and aerobic field conditions for grain yield, grain Fe and Zn content. General Combining Ability (GCA) effects of parents and Specific Combining Ability (SCA) effects of hybrids were observed to be contrasting for the micronutrient content in both the growing environments. The grain Fe and Zn content for parental lines were negatively correlated with grain yield in both the contrasting growing conditions. However, hybrids exhibited positive correlation for grain Fe and Zn with grain yield under limited water conditions. The magnitude of SCA mean squares was much higher than GCA mean squares implying preponderance of dominance gene action and also role of complementary non-allelic gene(s) interaction of parents and suitability of hybrids to the aerobic system. The testers HHZ12-SAL8-Y1-SAL1 (T1) and HHZ17-Y16-Y3-Y2 (T2) were identified as good combiners for grain Zn content under irrigated and aerobic conditions respectively.
Targeted neuromodulation of pelvic floor nerves in aging and multiparous rabbits improves continence
Authors: Hernandez-Reynoso Ana G. , Corona-Quintanilla Dora L. , López-García Kenia , Horbovetz Ana A. , Castelán Francisco , Zimmern Philippe , Martínez-Gómez Margarita , Romero-Ortega Mario I. 
Published: May 2021

AbstractPelvic floor muscle stretch injury during pregnancy and birth is associated with the incidence of stress urinary incontinence (SUI), a condition that affects 30–60% of the female population and is characterized by involuntary urine leakage during physical activity, further exacerbated by aging. Aging and multiparous rabbits suffer pelvic nerve and muscle damage, resulting in alterations in pelvic floor muscular contraction and low urethral pressure, resembling SUI. However, the extent of nerve injury is not fully understood. Here, we used electron microscopy analysis of pelvic and perineal nerves in multiparous rabbits to describe the extent of stretch nerve injury based on axon count, axon size, myelin-to-axon ratio, and elliptical ratio. Compared to young nulliparous controls, mid-age multiparous animals showed an increase in the density of unmyelinated axons and in myelin thickness in both nerves, albeit more significant in the bulbospongiosus nerve. This revealed a partial but sustained damage to these nerves, and the presence of some regenerated axons. Additionally, we tested whether electrical stimulation of the bulbospongiosus nerve would induce muscle contraction and urethral closure. Using a miniature wireless stimulator implanted on this perineal nerve in young nulliparous and middle age multiparous female rabbits, we confirmed that these partially damaged nerves can be acutely depolarized, either at low (2–5 Hz) or medium (10–20 Hz) frequencies, to induce a proportional increase in urethral pressure. Evaluation of micturition volume in the mid-age multiparous animals after perineal nerve stimulation, effectively reversed a baseline deficit, increasing it 2-fold (p = 0.02). These results support the notion that selective neuromodulation of pelvic floor muscles might serve as a potential treatment for SUI.
Intranasal delivery of mitochondria for treatment of Parkinson’s Disease model rats lesioned with 6-hydroxydopamine
Authors: Chang Jui-Chih , Chao Yi-Chun , Chang Huei-Shin , Wu Yu-Ling , Chang Hui-Ju , Lin Yong-Shiou , Cheng Wen-Ling , Lin Ta-Tsung , Liu Chin-San 
Published: May 2021

AbstractThe feasibility of delivering mitochondria intranasally so as to bypass the blood–brain barrier in treating Parkinson's disease (PD), was evaluated in unilaterally 6-OHDA-lesioned rats. Intranasal infusion of allogeneic mitochondria conjugated with Pep-1 (P-Mito) or unconjugated (Mito) was performed once a week on the ipsilateral sides of lesioned brains for three months. A significant improvement of rotational and locomotor behaviors in PD rats was observed in both mitochondrial groups, compared to sham or Pep-1-only groups. Dopaminergic (DA) neuron survival and recovery > 60% occurred in lesions of the substantia nigra (SN) and striatum in Mito and P-Mito rats. The treatment effect was stronger in the P-Mito group than the Mito group, but the difference was insignificant. This recovery was associated with restoration of mitochondrial function and attenuation of oxidative damage in lesioned SN. Notably, P-Mito suppressed plasma levels of inflammatory cytokines. Mitochondria penetrated the accessory olfactory bulb and doublecortin-positive neurons of the rostral migratory stream (RMS) on the ipsilateral sides of lesions and were expressed in striatal, but not SN DA neurons, of both cerebral hemispheres, evidently via commissural fibers. This study shows promise for intranasal delivery of mitochondria, confirming mitochondrial internalization and migration via RMS neurons in the olfactory bulb for PD therapy.