bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active boundary layers in confined active nematics
Authors: Hardoüin Jerôme , Doré Claire , Laurent Justine , Lopez-Leon Teresa , Ignés-Mullol Jordi , Sagués Francesc 
Published: November 2022

AbstractThe role of boundary layers in conventional liquid crystals is commonly related to the mesogen anchoring on confining walls. In the classical view, anchoring enslaves the orientational field of the passive material under equilibrium conditions. In this work, we show that an active nematic can develop active boundary layers that topologically polarize the confining walls. We find that negatively-charged defects accumulate in the boundary layer, regardless of the wall curvature, and they influence the overall dynamics of the system to the point of fully controlling the behavior of the active nematic in situations of strong confinement. Further, we show that wall defects exhibit behaviors that are essentially different from those of their bulk counterparts, such as high motility or the ability to recombine with another defect of like-sign topological charge. These exotic behaviors result from a change of symmetry induced by the wall in the director field around the defect. Finally, we suggest that the collective dynamics of wall defects might be described in terms of a model equation for one-dimensional spatio-temporal chaos.
Membrane potential drives the exit from pluripotency and cell fate commitment via calcium and mTOR
Authors: Sempou Emily , Kostiuk Valentyna , Zhu Jie , Cecilia Guerra M. , Tyan Leonid , Hwang Woong , Camacho-Aguilar Elena , Caplan Michael J. , Zenisek David , Warmflash Aryeh , Owens Nick D. L. , Khokha Mustafa K. 
Published: November 2022

AbstractTransitioning from pluripotency to differentiated cell fates is fundamental to both embryonic development and adult tissue homeostasis. Improving our understanding of this transition would facilitate our ability to manipulate pluripotent cells into tissues for therapeutic use. Here, we show that membrane voltage (Vm) regulates the exit from pluripotency and the onset of germ layer differentiation in the embryo, a process that affects both gastrulation and left-right patterning. By examining candidate genes of congenital heart disease and heterotaxy, we identifyKCNH6, a member of the ether-a-go-go class of potassium channels that hyperpolarizes the Vmand thus limits the activation of voltage gated calcium channels, lowering intracellular calcium. In pluripotent embryonic cells, depletion ofkcnh6leads to membrane depolarization, elevation of intracellular calcium levels, and the maintenance of a pluripotent state at the expense of differentiation into ectodermal and myogenic lineages. Using high-resolution temporal transcriptome analysis, we identify the gene regulatory networks downstream of membrane depolarization and calcium signaling and discover that inhibition of the mTOR pathway transitions the pluripotent cell to a differentiated fate. By manipulating Vmusing a suite of tools, we establish a bioelectric pathway that regulates pluripotency in vertebrates, including human embryonic stem cells.
Ion rectification based on gel polymer electrolyte ionic diode
Authors: Jiang Fan , Poh Wei Church , Chen Juntong , Gao Dace , Jiang Feng , Guo Xiaoyu , Chen Jian , Lee Pooi See 
Published: November 2022

AbstractBiological ion channels rely on ions as charge carriers and unidirectional ion flow to produce and transmit signals. To realize artificial biological inspired circuitry and seamless human-machine communication, ion-transport-based rectification devices should be developed. In this research, poly(methyl methacrylate) (PMMA) and poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) gel polymer electrolytes (GPEs) are assembled to construct a novel ionic diode, enabling ion rectification through ion-diffusion/migration that emulates biological systems. This ion rectification results from the different diffusion/migration behaviors of mobile ions transporting in the GPE heterojunction. The electrical tests of the GPE heterojunction reveal outstanding rectifying ratio of 23.11. The GPE ionic diode operates in wide temperature window, from −20 °C (anti-freezing) to 125 °C (thermal tolerance). The absence of redox reactions is verified in the cyclic voltammogram. The GPE ionic diodes are used to construct ionic logic gates for signal communication. Furthermore, rectification of a triboelectric nanogenerator and potential for synaptic devices are demonstrated.
Systematic tissue annotations of genomics samples by modeling unstructured metadata
Authors: Hawkins Nathaniel T. , Maldaver Marc , Yannakopoulos Anna , Guare Lindsay A. , Krishnan Arjun 
Published: November 2022

AbstractThere are currently >1.3 million human –omics samples that are publicly available. This valuable resource remains acutely underused because discovering particular samples from this ever-growing data collection remains a significant challenge. The major impediment is that sample attributes are routinely described using varied terminologies written in unstructured natural language. We propose a natural-language-processing-based machine learning approach (NLP-ML) to infer tissue and cell-type annotations for genomics samples based only on their free-text metadata. NLP-ML works by creating numerical representations of sample descriptions and using these representations as features in a supervised learning classifier that predicts tissue/cell-type terms. Our approach significantly outperforms an advanced graph-based reasoning annotation method (MetaSRA) and a baseline exact string matching method (TAGGER). Model similarities between related tissues demonstrate that NLP-ML models capture biologically-meaningful signals in text. Additionally, these models correctly classify tissue-associated biological processes and diseases based on their text descriptions alone. NLP-ML models are nearly as accurate as models based on gene-expression profiles in predicting sample tissue annotations but have the distinct capability to classify samples irrespective of the genomics experiment type based on their text metadata. Python NLP-ML prediction code and trained tissue models are available athttps://github.com/krishnanlab/txt2onto.
Hippocampal convergence during anticipatory midbrain activation promotes subsequent memory formation
Authors: Poh Jia-Hou , Vu Mai-Anh T. , Stanek Jessica K. , Hsiung Abigail , Egner Tobias , Adcock R. Alison 
Published: November 2022

AbstractThe hippocampus has been a focus of memory research since H.M’s surgery abolished his ability to form new memories, yet its mechanistic role in memory remains debated. Here, we identify a candidate memory mechanism: an anticipatory hippocampal “convergence state”, observed while awaiting valuable information, and which predicts subsequent learning. During fMRI, participants viewed trivia questions eliciting high or low curiosity, followed seconds later by its answer. We reasoned that encoding success requires a confluence of conditions, so that hippocampal states more conducive to memory formation should converge in state space. To operationalize convergence of neural states, we quantified the typicality of multivoxel patterns in the medial temporal lobes during anticipation and encoding of trivia answers. We found that the typicality of anticipatory hippocampal patterns increased during high curiosity. Crucially, anticipatory hippocampal pattern typicality increased with dopaminergic midbrain activation and uniquely accounted for the association between midbrain activation and subsequent recall. We propose that hippocampal convergence states may complete a cascade from motivation and midbrain activation to memory enhancement, and may be a general predictor of memory formation.
GZMKhigh CD8+ T effector memory cells are associated with CD15high neutrophil abundance in non-metastatic colorectal tumors and predict poor clinical outcome
Authors: Tiberti Silvia , Catozzi Carlotta , Croci Ottavio , Ballerini Mattia , Cagnina Danilo , Soriani Chiara , Scirgolea Caterina , Gong Zheng , He Jiatai , Macandog Angeli D. , Nabinejad Amir , Nava Lauson Carina B. , Quinte’ Arianna , Bertalot Giovanni , Petz Wanda L. , Ravenda Simona P. , Licursi Valerio , Paci Paola , Rasponi Marco , Rotta Luca , Fazio Nicola , Ren Guangwen , Fumagalli-Romario Uberto , Schaefer Martin H. , Campaner Stefano , Lugli Enrico , Nezi Luigi , Manzo Teresa 
Published: November 2022

AbstractCD8+T cells are a major prognostic determinant in solid tumors, including colorectal cancer (CRC). However, understanding how the interplay between different immune cells impacts on clinical outcome is still in its infancy. Here, we describe that the interaction of tumor infiltrating neutrophils expressing high levels of CD15 with CD8+T effector memory cells (TEM) correlates with tumor progression. Mechanistically, stromal cell-derived factor-1 (CXCL12/SDF-1) promotes the retention of neutrophils within tumors, increasing the crosstalk with CD8+T cells. As a consequence of the contact-mediated interaction with neutrophils, CD8+T cells are skewed to produce high levels of GZMK, which in turn decreases E-cadherin on the intestinal epithelium and favors tumor progression. Overall, our results highlight the emergence of GZMKhighCD8+TEMin non-metastatic CRC tumors as a hallmark driven by the interaction with neutrophils, which could implement current patient stratification and be targeted by novel therapeutics.
Economic interests cloud hazard reductions in the European regulation of substances of very high concern
Authors: Coria Jessica , Kristiansson Erik , Gustavsson Mikael 
Published: November 2022

AbstractHere we investigate how the conflicts between hazard reduction and economic interests have shaped the regulation of substances of very high concern (SVHCs) under the Authorization program of the European chemical regulation Registration, Evaluation, Authorization, and Restriction of Chemicals (REACH). Since regulation starts with listing SVHCs on the Candidate List, we analyze the relative importance of toxicological properties, economic motivations, and available scientific knowledge on the probability of inclusion on the Candidate List. We find that the most important factor in whether a substance is listed is whether it is being produced in, or imported into, the European Economic Area (EEA), with the regulators less likely to place a substance on the list if it is currently being produced or imported in the EEA. This evidence suggests that regulators have listed chemicals of secondary importance leading to lesser than anticipated hazard reductions, either because production and imports had already ceased before the listing, or because the compound has never been produced or imported in the EEA at all.
Peptide-enhanced tough, resilient and adhesive eutectogels for highly reliable strain/pressure sensing under extreme conditions
Authors: Zhang Yan , Wang Yafei , Guan Ying , Zhang Yongjun 
Published: November 2022

AbstractNatural gels and biomimetic hydrogel materials have been able to achieve outstanding integrated mechanical properties due to the gain of natural biological structures. However, nearly every natural biological structure relies on water as solvents or carriers, which limits the possibility in extreme conditions, such as sub-zero temperatures and long-term application. Here, peptide-enhanced eutectic gels were synthesized by introducing α-helical “molecular spring” structure into deep eutectic solvent. The gel takes full advantage of the α-helical structure, achieving high tensile/compression, good resilience, superior fracture toughness, excellent fatigue resistance and strong adhesion, while it also inherits the benefits of the deep eutectic solvent and solves the problems of solvent volatilization and freezing. This enables unprecedentedly long and stable sensing of human motion or mechanical movement. The electrical signal shows almost no drift even after 10,000 deformations for 29 hours or in the −20 °C to 80 °C temperature range.
Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers
Authors: Shah Jennifer B. , Pueschl Dana , Wubbenhorst Bradley , Fan Mengyao , Pluta John , D’Andrea Kurt , Hubert Anna P. , Shilan Jake S. , Zhou Wenting , Kraya Adam A. , Llop Guevara Alba , Ruan Catherine , Serra Violeta , Balmaña Judith , Feldman Michael , Morin Pat J. , Nayak Anupma , Maxwell Kara N. , Domchek Susan M. , Nathanson Katherine L. 
Published: November 2022

AbstractRecurrence is a major cause of death amongBRCA1/2mutation carriers with breast (BrCa) and ovarian cancers (OvCa). Herein we perform multi-omic sequencing on 67 paired primary and recurrent BrCa and OvCa from 27BRCA1/2mutation carriers to identify potential recurrence-specific drivers.PARP1amplifications are identified in recurrences (False Discovery Rate q = 0.05), andPARP1is significantly overexpressed across primary BrCa and recurrent BrCa and OvCa, independent of amplification status. RNA sequencing analysis finds twoBRCA2isoforms,BRCA2-201/LongandBRCA2-001/Short, respectively predicted to be sensitive and insensitive to nonsense-mediated decay.BRCA2-001/Shortis expressed more frequently in recurrences and associated with reduced overall survival in breast cancer (87 vs. 121 months; Hazard Ratio = 2.5 [1.18–5.5]). Loss of heterozygosity (LOH) status is discordant in 25% of patient’s primary and recurrent tumors, with switching between both LOH and lack of LOH found. Our study reveals multiple potential drivers of recurrent disease inBRCA1/2mutation-associated cancer, improving our understanding of tumor evolution and suggesting potential biomarkers.
Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice
Authors: Gul Seref , Akyel Yasemin Kubra , Gul Zeynep Melis , Isin Safak , Ozcan Onur , Korkmaz Tuba , Selvi Saba , Danis Ibrahim , Ipek Ozgecan Savlug , Aygenli Fatih , Taskin Ali Cihan , Akarlar Büşra Aytül , Ozlu Nurhan , Ozturk Nuri , Ozturk Narin , Ünal Durişehvar Özer , Guzel Mustafa , Turkay Metin , Okyar Alper , Kavakli Ibrahim Halil 
Published: November 2022

AbstractCryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing the level of endogenous CRY1 in mammals will affect circadian rhythm and the relation of such a decrease with apoptosis. Here, we discovered a molecule (M47) that destabilizes Cryptochrome 1 (CRY1) both in vitro and in vivo. The M47 selectively enhanced the degradation rate of CRY1 by increasing its ubiquitination and resulted in increasing the circadian period length of U2OSBmal1-dLuccells. In addition, subcellular fractionation studies from mice liver indicated that M47 increased degradation of the CRY1 in the nucleus. Furthermore, M47-mediated CRY1 reduction enhanced oxaliplatin-induced apoptosis in Ras-transformedp53null fibroblast cells. Systemic repetitive administration of M47 increased the median lifespan ofp53−/−mice by ~25%. Collectively our data suggest that M47 is a promising molecule to treat forms of cancer depending on thep53mutation.
Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1
Authors: Chung Scisung , Kang Mi-Sun , Alimbetov Dauren S. , Mun Gil-Im , Yunn Na-Oh , Kim Yunjin , Kim Byung-Gyu , Wie Minwoo , Lee Eun A. , Ra Jae Sun , Oh Jung-Min , Lee Donghyun , Lee Keondo , Kim Jihan , Han Seung Hyun , Kim Kyong-Tai , Chung Wan Kyun , Nam Ki Hyun , Park Jaehyun , Lee ByungHoon , Kim Sunghoon , Zhao Weixing , Ryu Sung Ho , Lee Yun-Sil , Myung Kyungjae , Cho Yunje 
Published: November 2022

AbstractAminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I. Here, we present the crystal structure of the chicken IARS1 UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1). UNE-I consists of tandem ubiquitin regulatory X (UBX) domains that interact with a distinct hairpin loop on EARS1 and protect its neighboring proteins in the multi-synthetase complex from degradation. Phosphomimetic mutation of the two serine residues in the hairpin loop releases IARS1 from the complex. IARS1 interacts with BRCA1 in the nucleus, regulates its stability by inhibiting ubiquitylation via the UBX domains, and controls DNA repair function.
Carbon nanotube-based flexible high-speed circuits with sub-nanosecond stage delays
Authors: Long Guanhua , Jin Wanlin , Xia Fan , Wang Yuru , Bai Tianshun , Chen Xingxing , Liang Xuelei , Peng Lian-Mao , Hu Youfan 
Published: November 2022

AbstractHigh-speed flexible circuits are required in flexible systems to realize real-time information analysis or to construct wireless communication modules for emerging applications. Here, we present scaled carbon nanotube-based thin film transistors (CNT-TFTs) with channel lengths down to 450 nm on 2-μm-thick parylene substrates, achieving state-of-the-art performances of high on-state current (187.6 μA μm−1) and large transconductance (123.3 μS μm−1). Scaling behavior analyses reveal that the enhanced performance introduced by scaling is attributed to channel resistance reduction while the contact resistance (180 ± 50 kΩ per tube) remains unchanged, which is comparable to that achieved in devices on rigid substrates, indicating great potential in ultimate scaled flexible CNT-TFTs with high performance comparable to their counterparts on rigid substrates where contact resistance dominates the performance. Five-stage flexible ring oscillators are built to benchmark the speed of scaled devices, demonstrating a 281 ps stage delay at a low supply voltage of 2.6 V.
Designing mechanically tough graphene oxide materials using deep reinforcement learning
Authors: Zheng Bowen , Zheng Zeyu , Gu Grace X. 
Published: November 2022

AbstractGraphene oxide (GO) is playing an increasing role in many technologies. However, it remains unanswered how to strategically distribute the functional groups to further enhance performance. We utilize deep reinforcement learning (RL) to design mechanically tough GOs. The design task is formulated as a sequential decision process, and policy-gradient RL models are employed to maximize the toughness of GO. Results show that our approach can stably generate functional group distributions with a toughness value over two standard deviations above the mean of random GOs. In addition, our RL approach reaches optimized functional group distributions within only 5000 rollouts, while the simplest design task has 2 × 1011 possibilities. Finally, we show that our approach is scalable in terms of the functional group density and the GO size. The present research showcases the impact of functional group distribution on GO properties, and illustrates the effectiveness and data efficiency of the deep RL approach.
Investigate the role of fungal communities associated with a historical manuscript from the 17th century in biodegradation
Authors: Fouda Amr , Abdel-Nasser Mahmoud , Khalil Ahmed Mohamed Aly , Hassan Saad El-Din , Abdel-Maksoud Gomaa 
Published: November 2022

AbstractHerein, the deteriorating aspects of a historical manuscript (papers and leather bookbinding) dated back to the 17th century were evaluated with reference to the role of the associated fungal communities. The deterioration signs were investigated using visual assessment, SEM, ATR-FTIR, XRD, color changes, and pH values compared with control. Data showed that the most deterioration aspects were represented by the dust, dirt, erosion, stains, bores, weakness, missed parts, decreasing in paper crystallinity, shifting of wavenumbers of cellulosic band, and changing of color and pH. The dependent-culturable technique showed that thirteen fungal strains were associated with historical manuscript and identified using traditional and molecular methods as Aspergillus niger (three isolates), A. fumigatus (two isolates), A. quadrilineatus (three isolates), Penicillium citrinum (two isolates), and P. chrysogenium (three isolates). These fungal strains showed high efficacy to secretion various hydrolytic enzymes including cellulase, amylase, gelatinase, and pectinase which play a critical role in biodeterioration.
Biosoluble ceramic fiber reinforced poly(L-lactic acid) bone scaffold: degradation and bioactivity
Authors: Shuai Cijun , Wang Zhicheng , Zhang Haiyang , Jia Jiye , Huang Liping , Wang Dong , Chen Shijie , Feng Pei 
Published: November 2022

Abstract
Poly (l-lactic acid) (PLLA) exhibits great potential as a kind of scaffold material for bone defect repair because of its good biocompatibility and processability, while the too slow degradation rate hinders its further application. In this study, the biosoluble ceramic fiber (BCF) was introduced into PLLA matrix, and the PLLA/BCF composite scaffold was manufactured by selective laser sintering (SLS). It was observed that water contact angle of the composite scaffold decreased from 87.4° to 61.1° with the increasing content of BCF, while the pH value raised from 6.6 to 7.8, and the molecular weight of PLLA decreased after immersion for 4 weeks. The mechanism of degradation acceleration was that the dissolution of BCF not only released OH− into solution environment and produced alkaline microenvironment, but also formed capillary channels on the interface between BCF and PLLA matrix, beneficial for the infiltration of water into the hydrophobic PLLA matrix, which contributed to the degradation both on the surface and in the interior of the matrix. Besides, the dissolution of BCF released Ca2+, Si2+ and Mg2+ simultaneously and absorbed PO43− from the environment, contributing to the formation of bone bonding between the scaffold and host bone. In addition, the introduced BCF improved the mechanical capacities of the scaffold via fiber breakage, fiber debond and fiber separation, and so on.
A population-based study on social inequality and barriers to healthcare-seeking with lung cancer symptoms
Authors: Sætre Lisa Maria Sele , Rasmussen Sanne , Balasubramaniam Kirubakaran , Søndergaard Jens , Jarbøl Dorte Ejg 
Published: November 2022

AbstractHealthcare-seeking with lung cancer symptoms is a prerequisite for improving timely diagnosis of lung cancer. In this study we aimed to explore barriers towards contacting the general practitioner (GP) with lung cancer symptoms, and to analyse the impact of social inequality. The study is based on a nationwide survey with 69,060 individuals aged ≥40 years, randomly selected from the Danish population. The survey included information on lung cancer symptoms, GP contacts, barriers to healthcare-seeking and smoking status. Information about socioeconomics was obtained by linkage to Danish Registers. Descriptive statistics and multivariate logistic regression model were used to analyse the data. “Being too busy” and “Being worried about wasting the doctor’s time” were the most frequent barriers to healthcare-seeking with lung cancer symptoms. Individuals out of workforce and individuals who smoked more often reported “Being worried about what the doctor might find” and “Being too embarrassed” about the symptoms. The social inequality in barriers to healthcare-seeking with lung cancer symptoms is noticeable, which emphasises the necessity of focus on vulnerable groups at risk of postponing relevant healthcare-seeking.