bluuebunny/crossref_metadata_2025_split huggingface dataset:
XDeathDB: a visualization platform for cell death molecular interactions
Authors: Gadepalli Venkat Sundar , Kim Hangil , Liu Yueze , Han Tao , Cheng Lijun 
Published: December 2021

AbstractLots of cell death initiator and effector molecules, signalling pathways and subcellular sites have been identified as key mediators in both cell death processes in cancer. The XDeathDB visualization platform provides a comprehensive cell death and their crosstalk resource for deciphering the signaling network organization of interactions among different cell death modes associated with 1461 cancer types and COVID-19, with an aim to understand the molecular mechanisms of physiological cell death in disease and facilitate systems-oriented novel drug discovery in inducing cell deaths properly. Apoptosis, autosis, efferocytosis, ferroptosis, immunogenic cell death, intrinsic apoptosis, lysosomal cell death, mitotic cell death, mitochondrial permeability transition, necroptosis, parthanatos, and pyroptosis related to 12 cell deaths and their crosstalk can be observed systematically by the platform. Big data for cell death gene-disease associations, gene-cell death pathway associations, pathway-cell death mode associations, and cell death-cell death associations is collected by literature review articles and public database from iRefIndex, STRING, BioGRID, Reactom, Pathway’s commons, DisGeNET, DrugBank, and Therapeutic Target Database (TTD). An interactive webtool, XDeathDB, is built by web applications with R-Shiny, JavaScript (JS) and Shiny Server Iso. With this platform, users can search specific interactions from vast interdependent networks that occur in the realm of cell death. A multilayer spectral graph clustering method that performs convex layer aggregation to identify crosstalk function among cell death modes for a specific cancer. 147 hallmark genes of cell death could be observed in detail in these networks. These potential druggable targets are displayed systematically and tailoring networks to visualize specified relations is available to fulfil user-specific needs. Users can access XDeathDB for free at https://pcm2019.shinyapps.io/XDeathDB/.
Genome-wide identification of microRNA targets reveals positive regulation of the Hippo pathway by miR-122 during liver development
Authors: Zhang Yin , Tan Ye-Ya , Chen Pei-Pei , Xu Hui , Xie Shu-Juan , Xu Shi-Jun , Li Bin , Li Jun-Hao , Liu Shun , Yang Jian-Hua , Zhou Hui , Qu Liang-Hu 
Published: December 2021

AbstractLiver development is a highly complex process that is regulated by the orchestrated interplay of epigenetic regulators, transcription factors, and microRNAs (miRNAs). Owing to the lack of global in vivo targets of all miRNAs during liver development, the mechanisms underlying the dynamic control of hepatocyte differentiation by miRNAs remain elusive. Here, using Argonaute (Ago) high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse liver at different developmental stages, we characterized massive Ago-binding RNAs and obtained a genome-wide map of liver miRNA-mRNA interactions. The dynamic changes of five clusters of miRNAs and their potential targets were identified to be differentially involved at specific stages, a dozen of high abundant miRNAs and their epigenetic regulation by super-enhancer were found during liver development. Remarkably, miR-122, a liver-specific and most abundant miRNA in newborn and adult livers, was found by its targetome and pathway reporter analyses to regulate the Hippo pathway, which is crucial for liver size control and homeostasis. Mechanistically, we further demonstrated that miR-122 negatively regulates the outcomes of the Hippo pathway transcription factor TEAD by directly targeting a number of hippo pathway regulators, including the coactivator TAZ and a key factor of the phosphatase complex PPP1CC, which contributes to the dephosphorylation of YAP, another coactivator downstream of the Hippo pathway. This study identifies for the first time the genome-wide miRNA targetomes during mouse liver development and demonstrates a novel mechanism of terminal differentiation of hepatocytes regulated by the miR-122/Hippo pathway in a coordinated manner. As the Hippo pathway plays important roles in cell proliferation and liver pathological processes like inflammation, fibrosis, and hepatocellular carcinoma (HCC), our study could also provide a new insight into the function of miR-122 in liver pathology.
Interleukin-7 receptor α mutational activation can initiate precursor B-cell acute lymphoblastic leukemia
Authors: Almeida Afonso R. M. , Neto João L. , Cachucho Ana , Euzébio Mayara , Meng Xiangyu , Kim Rathana , Fernandes Marta B. , Raposo Beatriz , Oliveira Mariana L. , Ribeiro Daniel , Fragoso Rita , Zenatti Priscila P. , Soares Tiago , de Matos Mafalda R. , Corrêa Juliana Ronchi , Duque Mafalda , Roberts Kathryn G. , Gu Zhaohui , Qu Chunxu , Pereira Clara , Pyne Susan , Pyne Nigel J. , Barreto Vasco M. , Bernard-Pierrot Isabelle , Clappier Emannuelle , Mullighan Charles G. , Grosso Ana R. , Yunes J. Andrés , Barata João T. 
Published: December 2021

AbstractInterleukin-7 receptor α (encoded by IL7R) is essential for lymphoid development. Whether acute lymphoblastic leukemia (ALL)-related IL7R gain-of-function mutations can trigger leukemogenesis remains unclear. Here, we demonstrate that lymphoid-restricted mutant IL7R, expressed at physiological levels in conditional knock-in mice, establishes a pre-leukemic stage in which B-cell precursors display self-renewal ability, initiating leukemia resembling PAX5 P80R or Ph-like human B-ALL. Full transformation associates with transcriptional upregulation of oncogenes such as Myc or Bcl2, downregulation of tumor suppressors such as Ikzf1 or Arid2, and major IL-7R signaling upregulation (involving JAK/STAT5 and PI3K/mTOR), required for leukemia cell viability. Accordingly, maximal signaling drives full penetrance and early leukemia onset in homozygous IL7R mutant animals. Notably, we identify 2 transcriptional subgroups in mouse and human Ph-like ALL, and show that dactolisib and sphingosine-kinase inhibitors are potential treatment avenues for IL-7R-related cases. Our model, a resource to explore the pathophysiology and therapeutic vulnerabilities of B-ALL, demonstrates that IL7R can initiate this malignancy.
Integrated linkage-driven dexterous anthropomorphic robotic hand
Authors: Kim Uikyum , Jung Dawoon , Jeong Heeyoen , Park Jongwoo , Jung Hyun-Mok , Cheong Joono , Choi Hyouk Ryeol , Do Hyunmin , Park Chanhun 
Published: December 2021

AbstractRobotic hands perform several amazing functions similar to the human hands, thereby offering high flexibility in terms of the tasks performed. However, developing integrated hands without additional actuation parts while maintaining important functions such as human-level dexterity and grasping force is challenging. The actuation parts make it difficult to integrate these hands into existing robotic arms, thus limiting their applicability. Based on a linkage-driven mechanism, an integrated linkage-driven dexterous anthropomorphic robotic hand called ILDA hand, which integrates all the components required for actuation and sensing and possesses high dexterity, is developed. It has the following features: 15-degree-of-freedom (20 joints), a fingertip force of 34N, compact size (maximum length: 218 mm) without additional parts, low weight of 1.1 kg, and tactile sensing capabilities. Actual manipulation tasks involving tools used in everyday life are performed with the hand mounted on a commercial robot arm.
Tracking excited state decay mechanisms of pyrimidine nucleosides in real time
Authors: Borrego-Varillas Rocío , Nenov Artur , Kabaciński Piotr , Conti Irene , Ganzer Lucia , Oriana Aurelio , Jaiswal Vishal Kumar , Delfino Ines , Weingart Oliver , Manzoni Cristian , Rivalta Ivan , Garavelli Marco , Cerullo Giulio 
Published: December 2021

AbstractDNA owes its remarkable photostability to its building blocks—the nucleosides—that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.
Giant nonlinear Hall effect in twisted bilayer WTe2
Authors: He Zhihai , Weng Hongming 
Published: December 2021

AbstractIn a system with broken inversion symmetry, a second-order nonlinear Hall effect can survive even in the presence of time-reversal symmetry. In this work, we show that a giant nonlinear Hall effect can exist in twisted bilayer WTe2 system. The Berry curvature dipole of twisted bilayer WTe2 (θ = 29.4°) can reach up to ~1400 Å, which is much larger than that in previously reported nonlinear Hall systems. In twisted bilayer WTe2 system, there exist abundant band anticrossings and band inversions around the Fermi level, which brings a complicated distribution of Berry curvature, and leads to the nonlinear Hall signals that exhibit dramatically oscillating behavior in this system. Its large amplitude and high tunability indicate that the twisted bilayer WTe2 can be an excellent platform for studying the nonlinear Hall effect.
Potato leafroll virus reduces Buchnera aphidocola titer and alters vector transcriptome responses
Authors: Patton MacKenzie F. , Hansen Allison K. , Casteel Clare L. 
Published: December 2021

AbstractViruses in the Luteoviridae family, such as Potato leafroll virus (PLRV), are transmitted by aphids in a circulative and nonpropagative mode. This means the virions enter the aphid body through the gut when they feed from infected plants and then the virions circulate through the hemolymph to enter the salivary glands before being released into the saliva. Although these viruses do not replicate in their insect vectors, previous studies have demonstrated viruliferous aphid behavior is altered and the obligate symbiont of aphids, Buchnera aphidocola, may be involved in transmission. Here we provide the transcriptome of green peach aphids (Myzus persicae) carrying PLRV and virus-free control aphids using Illumina sequencing. Over 150 million paired-end reads were obtained through Illumina sequencing, with an average of 19 million reads per library. The comparative analysis identified 134 differentially expressed genes (DEGs) between the M. persicae transcriptomes, including 64 and 70 genes that were up- and down-regulated in aphids carrying PLRV, respectively. Using functional classification in the GO databases, 80 of the DEGs were assigned to 391 functional subcategories at category level 2. The most highly up-regulated genes in aphids carrying PLRV were cytochrome p450s, genes related to cuticle production, and genes related to development, while genes related to heat shock proteins, histones, and histone modification were the most down-regulated. PLRV aphids had reduced Buchnera titer and lower abundance of several Buchnera transcripts related to stress responses and metabolism. These results suggest carrying PLRV may reduce both aphid and Buchnera genes in response to stress. This work provides valuable basis for further investigation into the complicated mechanisms of circulative and nonpropagative transmission.
Alginate-amphotericin B nanocomplexes covered by nanocrystals from bacterial cellulose: physico-chemical characterization and in vitro toxicity
Authors: Soeiro Victória Soares , Silva-Carvalho Ricardo , Martins Daniela , Parpot Pier , Grotto Denise , Chaud Marco Vinicius , da Gama Francisco Miguel Portela , Jozala Angela Faustino 
Published: December 2021

AbstractNanocomplexes systems made up natural poylymers have pharmacotechnical advantages such as increase of water solubility and a decrease of drugs toxicity. Amphotericin B (AmB) is a drug apply as anti-leishmanial and anti-fungal, however it has low water solubility and high toxicity, limiting its therapeutic application. With this in mind, the present study aimed to produce nanocomplexes composed by alginate (Alg), a natural polymer, with AmB covered by nanocrystals from bacterial cellulose (CNC). For this reason, the nanocomplexes were produced utilizing sodium alginate, amphotericin B in a borate buffer (pH 11.0). The CNC was obtained by enzymatic hydrolysis of the bacterial cellulose. To CNC cover the nanocomplexes 1 ml of the nanocomplexes was added into 1 ml of 0.01% CNC suspension. The results showed an ionic adsorption of the CNC into the Alg-AmB nanocomplexes surface. This phenomena was confirmed by an increase in the particle size and PDI decrease. Besides, nanocomplexes samples covered by CNC showed uniformity. The amorphous inclusion of AmB complex into the polysaccharide chain network in both formulations. AmB in the nanocomplexes was in supper-aggregated form and showed good biocompatibility, being significantly less cytotoxic in vitro against kidney cells and significantly less hemolytic compared to the free-drug. The in vitro toxicity results indicated the Alg-AmB nanocomplexes can be considered a non-toxic alternative to improve the AmB therapeutic effect. All process to obtain nanocomplexes and it coat was conduce without organic solvents, can be considered a green process, and allowed to obtain water soluble particles. Furthermore, CNC covering the nanocomplexes brought additional protection to the system can contribut advancement in the pharmaceutical.
Postoperative proliferative vitreoretinopathy development is linked to vitreal CXCL5 concentrations
Authors: Zandi Souska , Pfister Isabel B. , Garweg Justus G. 
Published: December 2021

AbstractThe specific changes linked to de novo development of postoperative PVR have remained elusive and were the object of the underlying study. Vitreous fluid (VF) was obtained at the beginning of vitrectomy from 65 eyes that underwent vitrectomy for primary rhegmatogenous retinal detachment (RRD) without preoperative PVR. Eyes developing postoperative PVR within 6 months after re-attachment surgery were compared to those which did not regarding the preoperative concentrations of 43 cytokines and chemokines in the VF, using multiplex beads analysis. For all comparisons Holm’s correction was applied in order to control for multiple comparisons. Twelve out of 65 eyes (18.5%) developed PVR postoperatively. While 12 of the chemokines and cytokines presented concentration differences on a statistical level of p < 0.05 (CXCL5, CCL11, CCL24, CCL26, GM-CSF, IFN-γ, CCL8, CCL7, MIF, MIG/CXCL9, CCL19, and CCL25), CXCL5 was the only cytokine with sufficiently robust difference in its VF concentrations to achieve significance in eyes developing postoperative PVR compared to eyes without PVR. CXCL5 may represent a potent biomarker for the de novo development of postoperative PVR. In line with its pathophysiological role in the development of PVR, it might serve as a basis for the development of urgently needed preventive options.
Learning of a mimic odor combined with nectar nonsugar compounds enhances honeybee pollination of a commercial crop
Authors: Estravis-Barcala M. Cecilia , Palottini Florencia , Farina Walter M. 
Published: December 2021

AbstractThe increasing demand on pollination services leads food industry to consider new strategies for management of pollinators to improve their efficiency in agroecosystems. Recently, it was demonstrated that feeding beehives food scented with an odorant mixture mimicking the floral scent of a crop (sunflower mimic, SM) enhanced foraging activity and improved recruitment to the target inflorescences, which led to higher density of bees on the crop and significantly increased yields. Besides, the oral administration of nonsugar compounds (NSC) naturally found in nectars (caffeine and arginine) improved short and long-term olfactory memory retention in conditioned bees under laboratory conditions. To test the effect of offering of SM-scented food supplemented with NSC on honeybees pollinating sunflower for hybrid seed production, in a commercial plantation we fed colonies SM-scented food (control), and SM-scented food supplemented with either caffeine, arginine, or a mixture of both, in field realistic concentrations. Their foraging activity was assessed at the hive and on the crop up to 90 h after treatment, and sunflower yield was estimated prior to harvest. Our field results show that SM + Mix-treated colonies exhibited the highest incoming rates and densities on the crop. Additionally, overall seed mass was significantly higher by 20% on inflorescences close to these colonies than control colonies. Such results suggest that combined NSC potentiate olfactory learning of a mimic floral odor inside the hive, promoting faster colony-level foraging responses and increasing crop production.
Genome analysis provides insight into hyper-virulence of Streptococcus suis LSM178, a human strain with a novel sequence type 1005
Authors: Hu Yong , Fu Shiming , Zou Geng , Kerdsin Anusak , Chen Xiabing , Dong Xingxing , Teng Lin , Li Jinquan 
Published: December 2021

AbstractStreptococcus suis has been well-recognized as a zoonotic pathogen worldwide, and the diversity and unpredictable adaptive potential of sporadic human strains represent a great risk to the public health. In this study, S. suis LSM178, isolated from a patient in contact with pigs and raw pork, was assessed as a hyper-virulent strain and interpreted for the virulence based on its genetic information. The strain was more invasive for Caco-2 cells than two other S. suis strains, SC19 and P1/7. Sequence analysis designated LSM178 with serotype 2 and a novel sequence type 1005. Phylogenetic analysis showed that LSM178 clustered with highly virulent strains including all human strains and epidemic strains. Compared with other strains, these S. suis have the most and the same virulent factors and a type I-89 K pathogenicity island. Further, groups of genes were identified to distinguish these highly virulent strains from other generally virulent strains, emphasizing the key roles of genes modeling transcription, cell barrier, replication, recombination and repair on virulence regulation. Additionally, LSM178 contains a novel prophage conducive potentially to pathogenicity.
From positron emission tomography to cell analysis of the 18-kDa Translocator Protein in mild traumatic brain injury
Authors: Delage Clément , Vignal Nicolas , Guerin Coralie , Taib Toufik , Barboteau Clément , Mamma Célia , Khacef Kahina , Margaill Isabelle , Sarda-Mantel Laure , Rizzo-Padoin Nathalie , Hontonnou Fortune , Marchand-Leroux Catherine , Lerouet Dominique , Hosten Benoit , Besson Valérie 
Published: December 2021

AbstractTraumatic brain injury (TBI) leads to a deleterious neuroinflammation, originating from microglial activation. Monitoring microglial activation is an indispensable step to develop therapeutic strategies for TBI. In this study, we evaluated the use of the 18-kDa translocator protein (TSPO) in positron emission tomography (PET) and cellular analysis to monitor microglial activation in a mild TBI mouse model. TBI was induced on male Swiss mice. PET imaging analysis with [18F]FEPPA, a TSPO radiotracer, was performed at 1, 3 and 7 days post-TBI and flow cytometry analysis on brain at 1 and 3 days post-TBI. PET analysis showed no difference in TSPO expression between non-operated, sham-operated and TBI mice. Flow cytometry analysis demonstrated an increase in TSPO expression in ipsilateral brain 3 days post-TBI, especially in microglia, macrophages, lymphocytes and neutrophils. Moreover, microglia represent only 58.3% of TSPO+ cells in the brain. Our results raise the question of the use of TSPO radiotracer to monitor microglial activation after TBI. More broadly, flow cytometry results point the lack of specificity of TSPO for microglia and imply that microglia contribute to the overall increase in TSPO in the brain after TBI, but is not its only contributor.
Multi-step atomic mechanism of platinum nanocrystals nucleation and growth revealed by in-situ liquid cell STEM
Authors: Dachraoui Walid , Henninen Trond R. , Keller Debora , Erni Rolf 
Published: December 2021

AbstractThe understanding of crystal growth mechanisms has broadened substantially. One significant advancement is based in the conception that the interaction between particles plays an important role in the growth of nanomaterials. This is in contrast to the classical model, which neglects this process. Direct imaging of such processes at atomic-level in liquid-phase is essential for establishing new theoretical models that encompass the full complexity of realistic scenarios and eventually allow for tailoring nanoparticle growth. Here, we investigate at atomic-scale the exact growth mechanisms of platinum nanocrystals from single atom to final crystals by in-situ liquid phase scanning transmission electron microscopy. We show that, after nucleation, the nanocrystals grow via two main stages: atomic attachment in the first stage, where the particles initially grow by attachment of the atoms until depletion of the surrounding zone. Thereafter, follows the second stage of growth, which is based on particle attachment by different atomic pathways to finally form mature nanoparticles. The atomic mechanisms underlying these growth pathways are distinctly different and have different driving forces and kinetics as evidenced by our experimental observations.