bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellDeathPred: a deep learning framework for ferroptosis and apoptosis prediction based on cell painting
Authors: Schorpp Kenji , Bessadok Alaa , Biibosunov Aidin , Rothenaigner Ina , Strasser Stefanie , Peng Tingying , Hadian Kamyar 
Published: July 2023

AbstractCell death, such as apoptosis and ferroptosis, play essential roles in the process of development, homeostasis, and pathogenesis of acute and chronic diseases. The increasing number of studies investigating cell death types in various diseases, particularly cancer and degenerative diseases, has raised hopes for their modulation in disease therapies. However, identifying the presence of a particular cell death type is not an obvious task, as it requires computationally intensive work and costly experimental assays. To address this challenge, we present CellDeathPred, a novel deep-learning framework that uses high-content imaging based on cell painting to distinguish cells undergoing ferroptosis or apoptosis from healthy cells. In particular, we incorporate a deep neural network that effectively embeds microscopic images into a representative and discriminative latent space, classifies the learned embedding into cell death modalities, and optimizes the whole learning using the supervised contrastive loss function. We assessed the efficacy of the proposed framework using cell painting microscopy data sets from human HT-1080 cells, where multiple inducers of ferroptosis and apoptosis were used to trigger cell death. Our model confidently separates ferroptotic and apoptotic cells from healthy controls, with an average accuracy of 95% on non-confocal data sets, supporting the capacity of the CellDeathPred framework for cell death discovery.
Ability of a selfish B chromosome to evade genome elimination in the jewel wasp, Nasonia vitripennis
Authors: Lee Haena , Seo Pooreum , Teklay Salina , Yuguchi Emily , Benetta Elena Dalla , Werren John H. , Ferree Patrick M. 
Published: July 2023

AbstractB chromosomes are non-essential, extra chromosomes that can exhibit transmission-enhancing behaviors, including meiotic drive, mitotic drive, and induction of genome elimination, in plants and animals. A fundamental but poorly understood question is what characteristics allow B chromosomes to exhibit these extraordinary behaviors. The jewel wasp, Nasonia vitripennis, harbors a heterochromatic, paternally transmitted B chromosome known as paternal sex ratio (PSR), which causes complete elimination of the sperm-contributed half of the genome during the first mitotic division of fertilized embryos. This genome elimination event may result from specific, previously observed alterations of the paternal chromatin. Due to the haplo-diploid reproduction of the wasp, genome elimination by PSR causes female-destined embryos to develop as haploid males that transmit PSR. PSR does not undergo self-elimination despite its presence with the paternal chromatin until the elimination event. Here we performed fluorescence microscopic analyses aimed at understanding this unexplained property. Our results show that PSR, like the rest of the genome, participates in the histone-to-protamine transition, arguing that PSR does not avoid this transition to escape self-elimination. In addition, PSR partially escapes the chromatin-altering activity of the intracellular bacterium, Wolbachia, demonstrating that this ability to evade chromatin alteration is not limited to PSR’s own activity. Finally, we observed that the rDNA locus and other unidentified heterochromatic regions of the wasp’s genome also seem to evade chromatin disruption by PSR, suggesting that PSR’s genome-eliminating activity does not affect heterochromatin. Thus, PSR may target an aspect of euchromatin to cause genome elimination.
Fluorocarbonylation via palladium/phosphine synergistic catalysis
Authors: Zhao Mingxin , Chen Miao , Wang Tian , Yang Shuhan , Peng Qian , Tang Pingping 
Published: July 2023

AbstractDespite the growing importance of fluorinated organic compounds in pharmaceuticals, agrochemicals, and materials science, the introduction of fluorine into organic molecules is still a challenge, and no catalytic fluorocarbonylation of aryl/alkyl boron compounds has been reported to date. Herein, we present the development of palladium and phosphine synergistic redox catalysis of fluorocarbonylation of potassium aryl/alkyl trifluoroborate. Trifluoromethyl arylsulfonate (TFMS), which was used as a trifluoromethoxylation reagent, an easily handled and bench-scale reagent, has been employed as an efficient source of COF2. The reaction operates under mild conditions with good to excellent yields and tolerates diverse complex scaffolds, which allows efficient late-stage fluorocarbonylation of marked small-molecule drugs. Mechanistically, the key intermediates of labile Brettphos-Pd(II)-OCF3 complex and difluoro-Brettphos were synthesized and spectroscopically characterized, including X-ray crystallography. A detailed reaction mechanism involving the synergistic redox catalytic cycles Pd(II)/(0) and P(III)/(V) was proposed, and multifunction of phosphine ligand was identified based on 19F NMR, isotope tracing, synthetic, and computational studies.
The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes
Authors: Djakovic Lara , Hennig Thomas , Reinisch Katharina , Milić Andrea , Whisnant Adam W. , Wolf Katharina , Weiß Elena , Haas Tobias , Grothey Arnhild , Jürges Christopher S. , Kluge Michael , Wolf Elmar , Erhard Florian , Friedel Caroline C. , Dölken Lars 
Published: July 2023

AbstractHerpes simplex virus 1 (HSV-1) infection and stress responses disrupt transcription termination by RNA Polymerase II (Pol II). In HSV-1 infection, but not upon salt or heat stress, this is accompanied by a dramatic increase in chromatin accessibility downstream of genes. Here, we show that the HSV-1 immediate-early protein ICP22 is both necessary and sufficient to induce downstream open chromatin regions (dOCRs) when transcription termination is disrupted by the viral ICP27 protein. This is accompanied by a marked ICP22-dependent loss of histones downstream of affected genes consistent with impaired histone repositioning in the wake of Pol II. Efficient knock-down of the ICP22-interacting histone chaperone FACT is not sufficient to induce dOCRs in ΔICP22 infection but increases dOCR induction in wild-type HSV-1 infection. Interestingly, this is accompanied by a marked increase in chromatin accessibility within gene bodies. We propose a model in which allosteric changes in Pol II composition downstream of genes and ICP22-mediated interference with FACT activity explain the differential impairment of histone repositioning downstream of genes in the wake of Pol II in HSV-1 infection.
Wireless electromagnetic neural stimulation patch with anisotropic guidance
Authors: Jensen Bjarke Nørrehvedde , Wang Yuting , Le Friec Alice , Nabavi Sadegh , Dong Mingdong , Seliktar Dror , Chen Menglin 
Published: July 2023

AbstractThe human body is limited in healing neurological damage caused by diseases or traumatic injuries. Bioelectricity is a quintessential characteristic of neural tissue and has a crucial role in physiological and neurological therapeutics development. Here, a wireless electromagnetic neural stimulation patch was created, combining stimulation through electromagnetic induction with physical guidance cues through structural anisotropy. The melt electrowritten biocompatible, bioresorbable polycaprolactone anisotropic structure with glancing angle deposition of 80 nm gold directly endowed incorporation of a wireless energy harvesting component in the patch, as an electromagnetic stimulation delivery system directly interfacing with neural cells. The biocompatibility and the capacity of the patch to deliver electromagnetic stimulation and promote neurite outgrowth was confirmed in vitro. Electromagnetically (60 mV, 40 kHz, 2 h/day, 5 days) stimulated PC12 cells showed 73.2% increased neurite outgrowth compared to PC12 cells grown without electromagnetic stimulation. The neural stimulation patch shows great potential for wireless electromagnetic stimulation for non-invasive neurological therapeutics advancement.
A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion
Authors: Ildefonso Geena V. , Finley Stacey D. 
Published: July 2023

AbstractT cells play a key role in a variety of immune responses, including infection and cancer. Upon stimulation, naïve CD8+ T cells proliferate and differentiate into a variety of memory and effector cell types; however, failure to clear antigens causes prolonged stimulation of CD8+ T cells, ultimately leading to T cell exhaustion (TCE). The functional and phenotypic changes that occur during CD8+ T cell differentiation are well characterized, but the underlying gene expression state changes are not completely understood. Here, we utilize a previously published data-driven Boolean model of gene regulatory interactions shown to mediate TCE. Our network analysis and modeling reveal the final gene expression states that correspond to TCE, along with the sequence of gene expression patterns that give rise to those final states. With a model that predicts the changes in gene expression that lead to TCE, we could evaluate strategies to inhibit the exhausted state. Overall, we demonstrate that a common pathway model of CD8+ T cell gene regulatory interactions can provide insights into the transcriptional changes underlying the evolution of cell states in TCE.
Experimentally determined traits shape bacterial community composition one and five years following wildfire
Authors: Johnson Dana B. , Woolet Jamie , Yedinak Kara M. , Whitman Thea 
Published: July 2023

AbstractWildfires represent major ecological disturbances, burning 2–3% of Earth’s terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.
Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest
Authors: Honeker Linnea K. , Pugliese Giovanni , Ingrisch Johannes , Fudyma Jane , Gil-Loaiza Juliana , Carpenter Elizabeth , Singer Esther , Hildebrand Gina , Shi Lingling , Hoyt David W. , Chu Rosalie K. , Toyoda Jason , Krechmer Jordan E. , Claflin Megan S. , Ayala-Ortiz Christian , Freire-Zapata Viviana , Pfannerstill Eva Y. , Daber L. Erik , Meeran Kathiravan , Dippold Michaela A. , Kreuzwieser Jürgen , Williams Jonathan , Ladd S. Nemiah , Werner Christiane , Tfaily Malak M. , Meredith Laura K. 
Published: July 2023

AbstractDrought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking 13C from position-specific 13C-pyruvate into CO2 and VOCs in parallel with multi-omics. During drought, efflux of 13C-enriched acetate, acetone and C4H6O2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,13C-CO2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.
Isothermal self-assembly of multicomponent and evolutive DNA nanostructures
Authors: Rossi-Gendron Caroline , El Fakih Farah , Bourdon Laura , Nakazawa Koyomi , Finkel Julie , Triomphe Nicolas , Chocron Léa , Endo Masayuki , Sugiyama Hiroshi , Bellot Gaëtan , Morel Mathieu , Rudiuk Sergii , Baigl Damien 
Published: July 2023

AbstractThermal annealing is usually needed to direct the assembly of multiple complementary DNA strands into desired entities. We show that, with a magnesium-free buffer containing NaCl, complex cocktails of DNA strands and proteins can self-assemble isothermally, at room or physiological temperature, into user-defined nanostructures, such as DNA origamis, single-stranded tile assemblies and nanogrids. In situ, time-resolved observation reveals that this self-assembly is thermodynamically controlled, proceeds through multiple folding pathways and leads to highly reconfigurable nanostructures. It allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. Strikingly, upon the appearance of a new energy minimum, DNA origamis isothermally shift from one initially stable shape to a radically different one, by massive exchange of their constitutive staple strands. This method expands the repertoire of shapes and functions attainable by isothermal self-assembly and creates a basis for adaptive nanomachines and nanostructure discovery by evolution.
Critical slowing down near a magnetic quantum phase transition with fermionic breakdown
Authors: Yang Chia-Jung , Kliemt Kristin , Krellner Cornelius , Kroha Johann , Fiebig Manfred , Pal Shovon 
Published: July 2023

AbstractWhen a system close to a continuous phase transition is subjected to perturbations, it takes an exceptionally long time to return to equilibrium. This critical slowing down is observed universally in the dynamics of bosonic excitations, such as order-parameter collective modes, but it is not generally expected to occur for fermionic excitations. Here using terahertz time-domain spectroscopy, we find evidence for fermionic critical slowing down in YbRh2Si2 close to a quantum phase transition between an antiferromagnetic phase and a heavy Fermi liquid. In the latter phase, the relevant quasiparticles are a quantum superposition of itinerant and localized electronic states with a strongly enhanced effective mass. As the temperature is lowered on the heavy-Fermi-liquid side of the transition, the heavy-fermion spectral weight builds up until the Kondo temperature TK ≈ 25 K, then decays towards the quantum phase transition and is, thereafter, followed by a logarithmic rise of the quasiparticle excitation rate below 10 K. A two-band heavy-Fermi-liquid theory shows that this is indicative of the fermionic critical slowing down associated with heavy-fermion breakdown near the quantum phase transition. The critical exponent of this breakdown could be used to classify this system among a wider family of fermionic quantum phase transitions that is yet to be fully explored.
Zolbetuximab plus CAPOX in CLDN18.2-positive gastric or gastroesophageal junction adenocarcinoma: the randomized, phase 3 GLOW trial
Authors: Shah Manish A. , Shitara Kohei , Ajani Jaffer A. , Bang Yung-Jue , Enzinger Peter , Ilson David , Lordick Florian , Van Cutsem Eric , Gallego Plazas Javier , Huang Jing , Shen Lin , Oh Sang Cheul , Sunpaweravong Patrapim , Soo Hoo Hwoei Fen , Turk Haci Mehmet , Oh Mok , Park Jung Wook , Moran Diarmuid , Bhattacharya Pranob , Arozullah Ahsan , Xu Rui-Hua 
Published: July 2023

AbstractThere is an urgent need for first-line treatment options for patients with human epidermal growth factor receptor 2 (HER2)-negative, locally advanced unresectable or metastatic gastric or gastroesophageal junction (mG/GEJ) adenocarcinoma. Claudin-18 isoform 2 (CLDN18.2) is expressed in normal gastric cells and maintained in malignant G/GEJ adenocarcinoma cells. GLOW (closed enrollment), a global, double-blind, phase 3 study, examined zolbetuximab, a monoclonal antibody that targets CLDN18.2, plus capecitabine and oxaliplatin (CAPOX) as first-line treatment for CLDN18.2-positive, HER2-negative, locally advanced unresectable or mG/GEJ adenocarcinoma. Patients (n = 507) were randomized 1:1 (block sizes of two) to zolbetuximab plus CAPOX or placebo plus CAPOX. GLOW met the primary endpoint of progression-free survival (median, 8.21 months versus 6.80 months with zolbetuximab versus placebo; hazard ratio (HR) = 0.687; 95% confidence interval (CI), 0.544–0.866; P = 0.0007) and key secondary endpoint of overall survival (median, 14.39 months versus 12.16 months; HR = 0.771; 95% CI, 0.615–0.965; P = 0.0118). Grade ≥3 treatment-emergent adverse events were similar with zolbetuximab (72.8%) and placebo (69.9%). Zolbetuximab plus CAPOX represents a potential new first-line therapy for patients with CLDN18.2-positive, HER2-negative, locally advanced unresectable or mG/GEJ adenocarcinoma. ClinicalTrials.gov identifier: NCT03653507.
A type-augmented knowledge graph embedding framework for knowledge graph completion
Authors: He Peng , Zhou Gang , Yao Yao , Wang Zhe , Yang Hao 
Published: July 2023

AbstractKnowledge graphs (KGs) are of great importance to many artificial intelligence applications, but they usually suffer from the incomplete problem. Knowledge graph embedding (KGE), which aims to represent entities and relations in low-dimensional continuous vector spaces, has been proved to be a promising approach for KG completion. Traditional KGE methods only concentrate on structured triples, while paying less attention to the type information of entities. In fact, incorporating entity types into embedding learning could further improve the performance of KG completion. To this end, we propose a universal Type-augmented Knowledge graph Embedding framework (TaKE) which could utilize type features to enhance any traditional KGE models. TaKE automatically captures type features under no explicit type information supervision. And by learning different type representations of each entity, TaKE could distinguish the diversity of types specific to distinct relations. We also design a new type-constrained negative sampling strategy to construct more effective negative samples for the training process. Extensive experiments on four datasets from three real-world KGs (Freebase, WordNet and YAGO) demonstrate the merits of our proposed framework. In particular, combining TaKE with the recent tensor factorization KGE model SimplE can achieve state-of-the-art performance on the KG completion task.
Droplet duos on water display pairing, autonomous motion, and periodic eruption
Authors: Sumino Yutaka , Yamashita Ryo , Miyaji Kazuki , Ishikawa Hiroaki , Otani Maho , Yamamoto Daigo , Okita Erika , Okamoto Yasunao , Krafft Marie Pierre , Yoshikawa Kenichi , Shioi Akihisa 
Published: July 2023

AbstractUnder non-equilibrium conditions, liquid droplets dynamically couple with their milieu through the continuous flux of matter and energy, forming active systems capable of self-organizing functions reminiscent of those of living organisms. Among the various dynamic behaviors demonstrated by cells, the pairing of heterogeneous cell units is necessary to enable collective activity and cell fusion (to reprogram somatic cells). Furthermore, the cyclic occurrence of eruptive events such as necroptosis or explosive cell lysis is necessary to maintain cell functions. However, unlike the self-propulsion behavior of cells, cyclic cellular behavior involving pairing and eruption has not been successfully modeled using artificial systems. Here, we show that a simple droplet system based on quasi-immiscible hydrophobic oils (perfluorodecalin and decane) deposited on water, mimics such complex cellular dynamics. Perfluorodecalin and decane droplet duos form autonomously moving Janus or coaxial structures, depending on their volumes. Notably, the system with a coaxial structure demonstrates cyclic behavior, alternating between autonomous motion and eruption. Despite their complexity, the dynamic behaviors of the system are consistently explained in terms of the spreading properties of perfluorodecalin/decane duplex interfacial films.
Novel treatment of chalazion using light-guided-tip intense pulsed light
Authors: Zhu Yirui , Zhao Hanhe , Huang Xiaodan , Lin Lin , Huo Yanan , Qin Zhenwei , Lu Jiale , Jin Xiuming 
Published: July 2023

AbstractWe assessed the effectiveness of light-guided-tip intense pulsed light (IPL) with meibomian gland expression (MGX) in chalazion treatment. Ninety-five eyes with chalazion received a light-guided-tip IPL-MGX treatment (IPL-MGX group), and another 95 eyes with chalazion received incision with curettage treatment (Control group). Prior to IPL or incision, as well as 1 month after the final treatment, data were gathered pertaining to the lesion location and size, hyperemia, lesions regression or recurrence, and a comprehensive ophthalmic examination. The total size of the chalazia in the IPL-MGX group was significantly reduced after the final treatment, with an average resolution rate of 70.5%, which is comparable to excision surgery. A significant decrease in chalazion recurrence rate was apparent after treatment in the IPL-MGX group compared with control. Moreover, the IPL-MGX demonstrated significant advancements throughout noninvasive tear film breakup time (NIBUT) as well as meibum grade in comparison to baseline and those in the the Control group. The use of IPL-MGX was found to be an efficient therapy for reducing the size and recurring frequency of chalazia, as well as for improving the meibomian gland function. It may be considered as a first-line treatment for cases of primary or recurrent chalazia with inflammation.