bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mechanistic insight intoNigella sativamediated anticancer effect on breast cancer through regulation of various miRNAs: Anin vitro&in vivostudy
Authors: Das Shaswati , Ghosh Avijit , Upadhyay Priyanka , Sarker Sushmita , Bhattacharjee Mousumi , Gupta Payal , Ghosh Swatilekha , Chattopadhyay Sreya , Dhar Pubali , Adhikary Arghya 
Published: October 2022

ABSTRACTBackgroundCancer continues to threat the mortal alongside scientific community with its burgeoning grasp. Although efforts have been directed to tame cancer by radiotherapy, photodynamic therapy, chemotherapy it came at a cost of fatal side effects.PurposePlant derived bioactive compounds carries an inevitable advantage of being safer, bioavailable & less toxic compared to contemporary chemotherapeutics. This study analyzed anti-cancerous potential of volatile oil, extracted fromNigella sativa, in-vitro against MDA-MB-231, MCF-7 & in-vivo on tumor growth in mice after successful oral administration.Study DesignOur strategic approach employed solvent extraction of black seed oil (BSO) to highlight orchestrated use of its potent integrants - TQ, Carvacrol & TA which in modest amounts show anti-cancerous properties compared to their individual treatment.We attempted to show this cost effective, safe & bioavailable form of dealing with the atrocities of breast cancer by means of MTT, Apoptotic, Western Blot Assays besides Transwell & Wound healing Assay. Reduction in the solid tumour in-vivo & near normalcy restoration of tissue section architecture from the BSO treated tumour sets are indicative of the better anti-tumorigenic potential of BSO.MethodsBSO’s Solvent extraction was performed followed by its characterization. MTT aided cytotoxicity study of BSO alongside major components in PBMC & cancer cells while its efficacy was presented by flow cytometric ROS analysis, cell cycle arrest & apoptosis assessment. Anti-migratory potential evaluated by Wound Healing, Transwell Migration & Western Blot while the expression study of a wide range of proteins, miRNAs & the in-vivo studies undertaken climaxed the confirmation of the anti-cancerous potential of BSO.ResultsComparatively reduced concentrations of TQ, TA & Carvacrol in BSO played a synergistic role to enhance apoptotic potential via Caspase 7 & 9, through enhanced ROS & expression of apoptotic family of proteins, miRNAs besides uplifting the anti-migratory perspective by effectively enhancing E-cad & downregulating lamellipodia, filopodia assembly & MMPs in MCF-7 & MDA-MB-231. Similar observations in-vivo outlined the therapeutic potential of BSO.ConclusionThis study culminates isolation & processing of BSO in a simplified procedure, thereby aiming at a more lucrative paradigm to be accepted in contemporary phytomedicine research.
Transcriptome characterization of the common cockle (Cerastoderma edule) after exposure to aMarteilia cochilliaoutbreak
Authors: Pardo B. G. , Fernández C. , Pampín M. , Blanco A. , Iglesias D. , Cao A. , Carballal M.J. , Villalba A. , Martínez P. 
Published: October 2022

AbstractThe edible cockle (Cerastoderma edule) is a widely cultivated bivalve with relevant ecological value roles and high value for shellfisheries in different European regions. The emergence of new threats, such as the parasiteMarteilia cochillia, has impaired the production and ecosystem of shellfish beds where the parasite was detected. Knowledge of the molecular mechanisms involved in cockle immune response to this parasite is essential to devise strategies for its control. With this aim, a transcriptomic study of the digestive gland (target organ of the parasite) and the whole cockle meat in response toM. cochilliainfection was carried out in heavily impacted area in the Northwest of Spain (Lombos do Ulla, Ria de Arousa). A total of 2079 million raw RNA-seq reads were obtained after filtering and used for annotation of 9049 genes following a conservative bioinformatic pipeline using the chromosome-level cockle genome as reference. Gene expression analysis identified a total of 973 consistent differentially expressed genes (DEGs) between comparisons across a temporal series involving cockles with different degrees of infection. DEGs increased with the level of infection within each temporal sample, but the higher DEGs number were detected when comparing temporal samples. Enrichment analysis of DEGs showed an increased expression of molecular functions related to hydrolase, peptidase activity, carbohydrate binding and active transmembrane transporter activity; cellular components such as extracellular matrix and extracellular regions; and a few biological functions associated with immunity and defence response. This information will be valuable for further studies focused on DEGs and associated SNP markers to develop reliant cockle strains to marteiliosis.
Body temperature rebounds on sea ice and is elevated by mercury contamination in a keystone predator
Authors: Grunst Melissa L. , Grunst Andrea S. , Grémillet David , Sato Akiko , Gentès Sophie , Fort Jérôme 
Published: October 2022

AbstractDespite overall stability, plasticity in endothermic body temperature (Tb) occurs, which may facilitate maintenance of crucial activities in the face of climate change-related environmental variations. However, this plasticity may be limited by physiological or energetic constraints, which are potentially exacerbated by other environmental stressors. For instance, chemical contamination may elevate energetic costs and have endocrine disrupting effects that undermine thermoregulation. We leveraged advanced biologging techniques to elucidate how Tbvaries with different behavioral states and environmental conditions in a keystone Arctic seabird, the little auk (Alle alle). We additionally evaluated whether mercury (Hg) contamination independently affected Tb, or limited or increased state-dependent changes in Tb. Tbwas highest and relatively invariable when birds were at the colony, and rebounded when birds were resting on sea ice, following declines while foraging (diving) in polar waters. These results suggest that the colony and sea ice function as thermal refuges for little auks. In addition, Tbincreased with ambient temperature and relative humidity across behavioral states, and increased with wind speed when birds were flying. Little auks with higher Hg levels had higher, less variable, Tbacross behaviors and environmental contexts, perhaps reflecting increased metabolic rates linked to detoxification costs. Results provide evidence for environment- and contaminant-related effects on Tb, but not interactive effects between the two, and suggest that loss of sea ice and increased environmental contamination under global change may have serious implications for Tbregulation and energy balance.
L-lactic and 2-ketoglutaric acids, odors from human skin, govern attraction and landing in host-seeking femaleAedes aegyptimosquitoes
Authors: Sumner Benjamin D. , Amos Brogan A. , Bello Jan E. , Cardé Ring T. 
Published: October 2022

AbstractAedes aegypti, presented with a source of L-lactic and 2-ketoglutaric acid in a wind-tunnel bioassay, takeoff, fly upwind, and land on the blend at rates comparable those exhibited by mosquitoes presented with a skin odor stimulus. Addition of carbon dioxide decreased takeoff latency but was not required to elicit upwind flight nor landings. Ketoglutaric acid, a recently identified component of human skin odor, combined with lactic acid elicits the full repertoire of mosquito host-seeking behaviors.
Broad-scale factors shaping the ecological niche and geographic distribution ofSpirodela polyrhiza
Authors: Cobos Marlon E. , Peterson A. Townsend 
Published: October 2022

AbstractThe choice of appropriate independent variables to create models characterizing ecological niches of species is of critical importance in distributional ecology. This set of dimensions in which a niche is defined can inform about what factors limit the distributional potential of a species. We used a multistep approach to select relevant variables for modeling the ecological niche of the aquaticSpirodela polyrriza,taking into account variability arising from using distinct algorithms, calibration areas, and spatial resolutions of variables. We found that, even after an initial selection of meaningful variables, the final set of variables selected based on statistical inference varied considerably depending on the combination of algorithm, calibration area, and spatial resolution used. However, variables representing extreme temperatures and dry periods were more consistently selected than others, highlighting their importance in shaping the distribution of this species. Other variables related to seasonality of solar radiation, summer solar radiation, and some soil proxies of nutrients in water, were selected commonly but not as frequently as the ones mentioned above. We suggest that the these later variables are also important to understanding the distributional potential of the species, but that their effects may be less pronounced at the scale at which they are represented for the needs of this type of modeling.
Suppression of vitamin D metabolizing enzyme CYP24A1 provides increased sensitivity to chemotherapeutic drugs in breast cancer
Authors: Kamiya Sakura , Yuna Nakamori , Takasawa Akira , Takasawa Kumi , Kyuno Daisuke , Ono Yusuke , Magara Kazufumi , Osanai Makoto 
Published: October 2022

AbstractVitamin D is an essential nutrient for the human body that plays an important role in homeostasis and contributes to cell fate decision including proliferation, differentiation and cell viability. Accumulated epidemiological data suggest a relationship between vitamin D deficiency and carcinogenesis in various organs. However, the underlying mechanism remains to be further clarified. In this study, we showed that vitamin D metabolizing enzyme CYP24A1 promotes the oncogenic property of breast carcinoma cells. In addition, expression of CYP24A1 is elevated in invasive breast carcinoma and decreases the overall survival. Importantly, CYP24A1 suppression significantly enhances cell death sensitivity to two pharmacologically different acting anticancer drugs, cisplatin and gefitinib. The results of our study suggest the possibility of CYP24A1-inhibiting therapy for breast malignancy.
Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation
Authors: van Creveld Shiri Graff , Coesel Sacha N. , Blaskowski Stephen , Groussman Ryan D. , Schatz Megan J. , Armbrust E. Virginia 
Published: October 2022

AbstractPhytoplankton rely on diverse mechanisms to adapt to the decreased iron bioavailability and oxidative stress-inducing conditions of today’s oxygenated oceans, including replacement of the iron-requiring ferredoxin electron shuttle protein with a less-efficient iron-free flavodoxin under iron limiting conditions. And yet, diatoms transcribe flavodoxins in high-iron regions in contrast to other phytoplankton. Here, we show that the two clades of flavodoxins present within diatoms exhibit a functional divergence, with only clade II flavodoxins displaying the canonical role in adaptation to iron limitation. We created CRISPR/Cas9 knock-outs of the clade I flavodoxin from the model diatomThalassiosira pseudonanaand found these cell lines are hypersensitive to oxidative stress, while maintaining a wild-type response to iron limitation. Within natural diatom communities, clade I flavodoxin transcript abundance is regulated over the diel cycle rather than in response to iron availability, whereas clade II transcript abundances increase either in iron-limiting regions or under artificially induced iron-limitation. The observed functional specialization of two flavodoxin variants within diatoms reiterates two major stressors associated with contemporary oceans and illustrates diatom strategies to flourish in diverse aquatic ecosystems.
A developmental program that regulates mammalian organ size offsets evolutionary distance
Authors: Shimamura Yuko , Tanaka Junichi , Kakiuchi Miwako , Sarmah Hemanta , Miura Akihiro , Hwang Youngmin , Sawada Anri , Ninish Zurab , Yamada Kazuhiko , Cai James J. , Mori Munemasa 
Published: October 2022

AbstractPigs are evolutionarily more distant from humans than mice, but their physiological organs are closest to humans. The molecular program leading to a more than 1,000-fold increase in organ size in pigs and humans over that of mice across evolution has not been elucidated. We generated large-scale transcriptional landscapes throughout swine lung development. Our cross-species single-cell molecular atlas let us discover swine progenitor identities, stage-specific markers, and a core organ-size regulation program (COSRP), well-conserved in swine and humans but less so in mice. Across eight mammalian species, human COSRP promoters showed higher homologies to evolutionary-distant large animals, including pigs, than evolutionary-close small animals. Our study provides a molecular foundation during swine lung development that unveils animal size regulation conserved in the COSRP promoter, independent of genome-wide evolution. COSRP is a critical paradigm for studying thousands-fold changes in biological sizes in evolution, development, cancer, zoology, respirology, organoids, and biotechnology, particularly human-compatible organ generation.One Sentence SummaryA cross-species developmental molecular atlas identified the indicator of lung and animal size beyond evolution
Hymenoptera (Insecta) telomerase RNAs switched to plant/ciliate-like biogenesis
Authors: Fajkus Petr , Adamik Matej , Nelson Andrew D.L. , Kilar Agata M. , Franek Michal , Bubenik Michal , Capkova Radmila Frydrychova , Votavova Alena , Sykorova Eva , Fajkus Jiri , Peska Vratislav 
Published: October 2022

ABSTRACTIn contrast to the catalytic subunit of telomerase, its RNA subunit (TR) is highly divergent in size, sequence and biogenesis pathways across eukaryotes. Current views on TR evolution assume a common origin of TRs transcribed with RNA polymerase II in Opisthokonta (the supergroup including Animalia and Fungi) and Trypanosomida on one hand, and TRs transcribed with RNA polymerase III under the control of type 3 promoter, found in TSAR and Archaeplastida supergroups (including e.g., ciliates and Viridiplantae taxa, respectively). Here we focus on unknown TRs in one of the largest Animalia order - Hymenoptera (Arthropoda) with more than 300 available representative genomes. Using a combination of bioinformatic and experimental approaches, we identify their TRs. In contrast to the presumed type of TRs (H/ACA box snoRNAs transcribed with RNA Polymerase II) corresponding to their phylogenetic position, we find here short TRs of the snRNA type, likely transcribed with RNA polymerase III under the control of the type 3 promoter. The newly described insect TRs thus question the hitherto assumed monophyletic origin of TRs across Animalia and point to an evolutionary switch in TR type and biogenesis that was associated with the divergence of Arthropods.Graphical abstract
Using a Bayesian network model to predict effects of pesticides on aquatic community endpoints in a rice field – A southern European case study
Authors: Mentzel Sophie , Martínez-Megías Claudia , Grung Merete , Rico Andreu , Tollefsen Knut Erik , Van den Brink Paul J. , Moe S. Jannicke 
Published: October 2022

AbstractIn recent years, Bayesian network (BN) models have become more popular as a tool to support probabilistic environmental risk assessments (ERA). They can better account for and communicate uncertainty compared to the deterministic approaches currently used in traditional ERA. In this study, we used the BN as a meta-model to predict the potential effect of various pesticides on different biological levels in the aquatic ecosystem. The meta-model links the inputs and outputs of a process-based exposure model (RICEWQ), that is run with various scenarios combination built on meteorological, hydrological, and agricultural scenarios, and a probabilistic case-based effect model (PERPEST), which bases its prediction on a database of microcosm and mesocosm experiments. The research focused on the pesticide exposure in rice fields surrounding a Spanish Natural Park, considering three selected pesticides for this case study: acetamiprid (insecticide), MCPA (herbicide), and azoxystrobin (fungicide). For each of the pesticide types, the developed BN model enabled the prediction of their effects on biological endpoints, endpoint groups, and community in an aquatic ecosystem. Also, it enables comparison between the different pesticide types, their effects on endpoint groups and community. While directly linking future scenarios of climate and agricultural practice to the exposure concentration and indirectly linking them to the effect on biological endpoints as well as community. In summary, azoxystrobin and MCPA seem to have a higher predicted risk for the community with at least one of the biological endpoint being effected compared to acetamiprid. Generally, the developed approach facilitates the communication of uncertainties associated with the predicted effect on different biological levels of the aquatic ecosystem. This transparency in all model components can aid risk management and decision making.
Identification of pre-synaptic density networks using SV2A PET imaging and ICA in healthy and diseased mice
Authors: Akkermans Jordy , Zajicek Franziska , Miranda Alan , Adhikari Mohit , Bertoglio Daniele 
Published: October 2022

AbstractBackgroundSynaptic vesicle glycoprotein 2A (SV2A) is a vesicle glycoprotein involved in neurotransmitter release. SV2A is located on the pre-synaptic terminals of neurons and visualized using the radioligand [11C]UCB-J and positron emission tomography (PET) imaging. Thus, SV2A PET imaging can provide a proxy for pre-synaptic density in health and disease. This study aims to apply independent component analysis (ICA) to SV2A PET data acquired in mice to identify pre-synaptic density networks (pSDNs), explore how ageing affects these pSDNs, and determine the impact of a neurological disorder on these networks.MethodsWe used [11C]UCB-J PET imaging data (n=135) available at different ages (3, 7, 10, and 16 months) in wild-type (WT) C57BL/6J mice and in diseased mice (mouse model of Huntington’s disease, HD). First, ICA was performed on a healthy dataset after it was split into two equal-sized samples (n=36 each) and the analysis was repeated 50 times in different partitions. We tested different model orders (8, 12, and 16) and identified the pSDNs. Next, we investigated the effect of age on the loading weights of the identified pSDNs. Additionally, the identified pSDNs were compared to those of diseased mice to assess the impact of disease on each pSDNs.ResultsModel order 12 resulted in the preferred choice to provide six reliable and reproducible independent components (ICs) as supported by the cluster-quality index (IQ) and regression coefficients (β) values. Temporal analysis showed age-related statistically significant changes on the loading weights in four ICs. ICA in an HD model revealed a statistically significant disease-related effect on the loading weights in several pSDNs in line with the progression of the disease.ConclusionThis study validated the use of ICA on SV2A PET data acquired with [11C]UCB-J for the identification of cerebral pre-synaptic density networks in mice in a rigorous and reproducible manner. Furthermore, we showed that different pSDNs change with age and are affected in a disease condition. These findings highlight the potential value of ICA in understanding pre-synaptic density networks in the mouse brain.
Training stochastic stabilized supralinear networks by dynamics-neutral growth
Authors: Soo Wayne W.M. , Lengyel Máté 
Published: October 2022

AbstractThere continues to be a trade-off between the biological realism and performance of neural networks. Contemporary deep learning techniques allow neural networks to be trained to perform challenging computations at (near) human-level, but these networks typically violate key biological constraints. More detailed models of biological neural networks can incorporate many of these constraints but typically suffer from subpar performance and trainability. Here, we narrow this gap by developing an effective method for training a canonical model of cortical neural circuits, the stabilized supralinear network (SSN), that in previous work had to be constructed manually or trained with undue constraints. SSNs are particularly challenging to train for the same reasons that make them biologically realistic: they are characterized by strongly-connected excitatory cells and expansive firing rate non-linearities that together make them prone to dynamical instabilities unless stabilized by appropriately tuned recurrent inhibition. Our method avoids such instabilities by initializing a small network and gradually increasing network size via the dynamics-neutral addition of neurons during training. We first show how SSNs can be trained to perform typical machine learning tasks by training an SSN on MNIST classification. We then demonstrate the effectiveness of our method by training an SSN on the challenging task of performing amortized Markov chain Monte Carlo-based inference under a Gaussian scale mixture generative model of natural image patches with a rich and diverse set of basis functions – something that was not possible with previous methods. These results open the way to training realistic cortical-like neural networks on challenging tasks at scale.
Remodeling and compaction of the inactive X is regulated byXistduring female B cell activation
Authors: Sierra Isabel , Nguyen Son C. , Barnett R. Jordan , Cook Ashley L. , Ryu Han-Seul , Beethem Zachary T. , Philips-Cremins Jennifer E. , Joyce Eric F. , Anguera Montserrat C. 
Published: October 2022

ABSTRACTX Chromosome Inactivation (XCI) equalizes X-linked gene expression between sexes. B cells exhibit unusually dynamic XCI, as Xist RNA/heterochromatic marks on the inactive X (Xi) are absent in naïve B cells, but return following mitogenic stimulation. Xi gene expression analysis supports dosage compensation, but reveals high levels of XCI escape genes in both naive and activated B cells. Allele-specific OligoPaints indicate similar Xi and Xa territories in B cells that is less compact than in fibroblasts. Allele-specific Hi-C maps reveal a lack of TAD-like structures on the Xi of naïve B cells, and alterations in TADs and stronger TAD boundaries at Xi escape genes after mitogenic stimulation. Notably,Xistdeletion in B cells reduces Xi compaction and changes TAD boundaries, independent of its localization to the Xi. Our findings provide the first evidence that Xi compaction/small scale organization in lymphocytes impact XCI maintenance and female biased X-linked gene expression.
MTM: a multi-task learning framework to predict individualized tissue gene expression profiles
Authors: He Guangyi , Chen Maiyue , Bian Yingnan , Yang Ence 
Published: October 2022

AbstractPredicting tissue expression profiles from peripheral ‘surrogate’ samples, especially blood transcriptome, has become an effective alternative when invasive procedures are not ideal. However, existing approaches ignore tissue-shared intrinsic relevance, inevitably limiting predictive performance. Here, we propose a unified deep learning-based multi-task learning framework, Multi-tissue Transcriptome Mapping (MTM), enabling the prediction of individualized expression profiles from any available tissue of an individual. By jointly leveraging individualized cross-tissue information through multi-task learning, MTM achieves superior sample-level and gene-level performance. With the high prediction accuracy and the ability to preserve individualized biological variations, MTM could facilitate both fundamental and clinical biomedical research.