bluuebunny/crossref_metadata_2025_split huggingface dataset:
A time-resolved, multi-symbol molecular recorder via sequential genome editing
Authors: Choi Junhong , Chen Wei , Minkina Anna , Chardon Florence M. , Suiter Chase C. , Regalado Samuel G. , Domcke Silvia , Hamazaki Nobuhiko , Lee Choli , Martin Beth , Daza Riza M. , Shendure Jay 
Published: July 2022

AbstractDNA is naturally well suited to serve as a digital medium for in vivo molecular recording. However, contemporary DNA-based memory devices are constrained in terms of the number of distinct ‘symbols’ that can be concurrently recorded and/or by a failure to capture the order in which events occur1. Here we describe DNA Typewriter, a general system for in vivo molecular recording that overcomes these and other limitations. For DNA Typewriter, the blank recording medium (‘DNA Tape’) consists of a tandem array of partial CRISPR–Cas9 target sites, with all but the first site truncated at their 5′ ends and therefore inactive. Short insertional edits serve as symbols that record the identity of the prime editing guide RNA2 mediating the edit while also shifting the position of the ‘type guide’ by one unit along the DNA Tape, that is, sequential genome editing. In this proof of concept of DNA Typewriter, we demonstrate recording and decoding of thousands of symbols, complex event histories and short text messages; evaluate the performance of dozens of orthogonal tapes; and construct ‘long tape’ potentially capable of recording as many as 20 serial events. Finally, we leverage DNA Typewriter in conjunction with single-cell RNA-seq to reconstruct a monophyletic lineage of 3,257 cells and find that the Poisson-like accumulation of sequential edits to multicopy DNA tape can be maintained across at least 20 generations and 25 days of in vitro clonal expansion.
Biosynthesis of strychnine
Authors: Hong Benke , Grzech Dagny , Caputi Lorenzo , Sonawane Prashant , López Carlos E. Rodríguez , Kamileen Mohamed Omar , Hernández Lozada Néstor J. , Grabe Veit , O’Connor Sarah E. 
Published: July 2022

AbstractStrychnine is a natural product that, through isolation, structural elucidation and synthetic efforts, shaped the field of organic chemistry. Currently, strychnine is used as a pesticide to control rodents1because of its potent neurotoxicity2,3. The polycyclic architecture of strychnine has inspired chemists to develop new synthetic transformations and strategies to access this molecular scaffold4, yet it is still unknown how plants create this complex structure. Here we report the biosynthetic pathway of strychnine, along with the related molecules brucine and diaboline. Moreover, we successfully recapitulate strychnine, brucine and diaboline biosynthesis inNicotiana benthamianafrom an upstream intermediate, thus demonstrating that this complex, pharmacologically active class of compounds can now be harnessed through metabolic engineering approaches.
Fatigue dataset of high-entropy alloys
Authors: Chen Shiyi , Fan Xuesong , Steingrimsson Baldur , Xiong Qingang , Li Weidong , Liaw Peter K. 
Published: July 2022

AbstractFatigue failure of metallic structures is of great concern to industrial applications. A material will not be practically useful if it is prone to fatigue failures. To take the advantage of lately emerged high-entropy alloys (HEAs) for designing novel fatigue-resistant alloys, we compiled a fatigue database of HEAs from the literature reported until the beginning of 2022. The database is subdivided into three categories, i.e., low-cycle fatigue (LCF), high-cycle fatigue (HCF), and fatigue crack growth rate (FCGR), which contain 15, 23, and 28 distinct data records, respectively. Each data record in any of three categories is characteristic of a summary, which is comprised of alloy compositions, key fatigue properties, and additional information influential to, or interrelated with, fatigue (e.g., material processing history, phase constitution, grain size, uniaxial tensile properties, and fatigue testing conditions), and an individual dataset, which makes up the original fatigue testing curve. Some representative individual datasets in each category are graphically visualized. The dataset is hosted in an open data repository, Materials Cloud.
LepTraits 1.0 A globally comprehensive dataset of butterfly traits
Authors: Shirey Vaughn , Larsen Elise , Doherty Andra , Kim Clifford A. , Al-Sulaiman Faisal T. , Hinolan Jomar D. , Itliong Micael Gabriel A. , Naive Mark Arcebal K. , Ku Minji , Belitz Michael , Jeschke Grace , Barve Vijay , Lamas Gerardo , Kawahara Akito Y. , Guralnick Robert , Pierce Naomi E. , Lohman David J. , Ries Leslie 
Published: July 2022

AbstractHere, we present the largest, global dataset of Lepidopteran traits, focusing initially on butterflies (ca. 12,500 species records). These traits are derived from field guides, taxonomic treatments, and other literature resources. We present traits on wing size, phenology,voltinism, diapause/overwintering stage, hostplant associations, and habitat affinities (canopy, edge, moisture, and disturbance). This dataset will facilitate comparative research on butterfly ecology and evolution and our goal is to inspire future research collaboration and the continued development of this dataset.
The interplay of chemical structure, physical properties, and structural design as a tool to modulate the properties of melanins within mesopores
Authors: Pira Alessandro , Amatucci Alberto , Melis Claudio , Pezzella Alessandro , Manini Paola , d’Ischia Marco , Mula Guido 
Published: July 2022

AbstractThe design of modern devices that can fulfil the requirements for sustainability and renewable energy applications calls for both new materials and a better understanding of the mixing of existing materials. Among those, surely organic–inorganic hybrids are gaining increasing attention due to the wide possibility to tailor their properties by accurate structural design and materials choice. In this work, we’ll describe the tight interplay between porous Si and two melanic polymers permeating the pores. Melanins are a class of biopolymers, known to cause pigmentation in many living species, that shows very interesting potential applications in a wide variety of fields. Given the complexity of the polymerization process beyond the formation and structure, the full understanding of the melanins' properties remains a challenging task. In this study, the use of a melanin/porous Si hybrid as a tool to characterize the polymer’s properties within mesopores gives new insights into the conduction mechanisms of melanins. We demonstrate the dramatic effect induced on these mechanisms in a confined environment by the presence of a thick interface. In previous studies, we already showed that the interactions at the interface between porous Si and eumelanin play a key role in determining the final properties of composite materials. Here, thanks to a careful monitoring of the photoconductivity properties of porous Si filled with melanins obtained by ammonia-induced solid-state polymerization (AISSP) of 5,6-dihydroxyindole (DHI) or 1,8-dihydroxynaphthalene (DHN), we investigate the effect of wet, dry, and vacuum cycles of storage from the freshly prepared samples to months-old samples. A computational study on the mobility of water molecules within a melanin polymer is also presented to complete the understanding of the experimental data. Our results demonstrate that: (a) the hydration-dependent behavior of melanins is recovered in large pores (≈ 60 nm diameter) while is almost absent in thinner pores (≈ 20 nm diameter); (b) DHN-melanin materials can generate higher photocurrents and proved to be stable for several weeks and more sensitive to the wet/dry variations.
Whole-body transcriptome analysis provides insights into the cascade of sequential expression events involved in growth, immunity, and metabolism during the molting cycle in Scylla paramamosain
Authors: Liu Lei , Liu Xiao , Fu Yuanyuan , Fang Wei , Wang Chunlin 
Published: July 2022

AbstractThe molecular mechanisms underlying the dynamic process of crab molting are still poorly understood at the individual level. We investigated global expression changes in the mud crab, Scylla paramamosain, at the transcriptome level and revealed a cascade of sequential expression events for genes involved in various aspects of the molting process using whole-body sequencing of juvenile crabs. RNA-sequencing (RNA-seq) produced 139.49 Gb of clean reads and 20,436 differentially expressed genes (DEGs) among different molting stages. The expression patterns for genes involved in several molecular events critical for molting, such as cuticle reconstruction, cytoskeletal structure remodeling, hormone regulation, immune responses, and metabolism, were characterized and considered as mechanisms underlying molting in S. paramamosain. Among these genes, we identified 10,695 DEGs in adjacent molting stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that significantly enriched pathways included structural constituents of cuticle, binding and chitin metabolic processes, steroid hormone biosynthesis, insulin resistance, and amino sugar metabolic processes. The expression profiles of 12 functional genes detected via RNA-seq were corroborated via real-time RT-PCR assays. The results revealed gene expression profiles across the molting cycle and identified possible activation pathways for future investigation of the underlying molecular mechanisms.
Assessing the impact of free-roaming dog population management through systems modelling
Authors: Smith Lauren M. , Quinnell Rupert J. , Goold Conor , Munteanu Alexandru M. , Hartmann Sabine , Collins Lisa M. 
Published: July 2022

AbstractFree-roaming dogs can present significant challenges to public health, wildlife conservation, and livestock production. Free-roaming dogs may also experience poor health and welfare. Dog population management is widely conducted to mitigate these issues. To ensure efficient use of resources, it is critical that effective, cost-efficient, and high-welfare strategies are identified. The dog population comprises distinct subpopulations characterised by their restriction status and level of ownership, but the assessment of dog population management often fails to consider the impact of the interaction between subpopulations on management success. We present a system dynamics model that incorporates an interactive and dynamic system of dog subpopulations. Methods incorporating both fertility control and responsible ownership interventions (leading to a reduction in abandonment and roaming of owned dogs, and an increase in shelter adoptions) have the greatest potential to reduce free-roaming dog population sizes over longer periods of time, whilst being cost-effective and improving overall welfare. We suggest that future management should be applied at high levels of coverage and should target all sources of population increase, such as abandonment, births, and owners of free-roaming dogs, to ensure effective and cost-efficient reduction in free-roaming dog numbers.
Hsa-miR-143-3p inhibits Wnt-β-catenin and MAPK signaling in human corneal epithelial stem cells
Authors: Kalaimani Lavanya , Devarajan Bharanidharan , Namperumalsamy Venkatesh Prajna , Veerappan Muthukkaruppan , Daniels Julie T. , Chidambaranathan Gowri Priya 
Published: July 2022

AbstractOur previous study demonstrated hsa-miR-143-3p as one of the highly expressed miRNAs in enriched corneal epithelial stem cells (CESCs). Hence this study aims to elucidate the regulatory role of hsa-miR-143-3p in the maintenance of stemness in CESCs. The target genes of hsa-miR-143-3p were predicted and subjected to pathway analysis to select the targets for functional studies. Primary cultured limbal epithelial cells were transfected with hsa-miR-143-3p mimic, inhibitor or scrambled sequence using Lipofectamine 3000. The transfected cells were analysed for (i) colony forming potential, (ii) expression of stem cell (SC) markers/ transcription factors (ABCG2, NANOG, OCT4, KLF4, ΔNp63), (iii) differentiation marker (Cx43), (iv) predicted five targets of hsa-miR-143-3p (DVL3, MAPK1, MAPK14, KRAS and KAT6A), (v) MAPK signaling regulators and (vi) Wnt-β-catenin signaling regulators by qPCR, immunofluorescence staining and/or Western blotting. High expression of hsa-miR-143-3p increased the colony forming potential (10.04 ± 1.35%, p < 0.001) with the ability to form holoclone-like colonies in comparison to control (3.33 ± 0.71%). The mimic treated cells had increased expression of SC markers but reduced expression of Cx43 and hsa-miR-143-3p targets involved in Wnt-β-catenin and MAPK signaling pathways. The expression of β-catenin, active β-catenin and ERK2 in hsa-miR-143-3p inhibitor transfected cells were higher than the control cells and the localized nuclear expression indicated the activation of Wnt and MAPK signaling. Thus, the probable association of hsa-miR-143-3p in the maintenance of CESCs through inhibition of Wnt and MAPK signaling pathways was thus indicated.
Expression pattern of Stomatin-domain proteins in the peripheral olfactory system
Authors: Gonzalez-Velandia Kevin Y. , Hernandez-Clavijo Andres , Menini Anna , Dibattista Michele , Pifferi Simone 
Published: July 2022

AbstractRecent data show that Stomatin-like protein 3 (STOML3), a member of the stomatin-domain family, is expressed in the olfactory sensory neurons (OSNs) where it modulates both spontaneous and evoked action potential firing. The protein family is constituted by other 4 members (besides STOML3): STOM, STOML1, STOML2 and podocin. Interestingly, STOML3 with STOM and STOML1 are expressed in other peripheral sensory neurons: dorsal root ganglia. In here, they functionally interact and modulate the activity of the mechanosensitive Piezo channels and members of the ASIC family. Therefore, we investigated whether STOM and STOML1 are expressed together with STOML3 in the OSNs and whether they could interact. We found that all three are indeed expressed in ONSs, although STOML1 at very low level. STOM and STOML3 share a similar expression pattern and STOML3 is necessary for STOM to properly localize to OSN cilia. In addition, we extended our investigation to podocin and STOML2, and while the former is not expressed in the olfactory system, the latter showed a peculiar expression pattern in multiple cell types. In summary, we provided a first complete description of stomatin-domain protein family in the olfactory system, highlighting the precise compartmentalization, possible interactions and, finally, their functional implications.
Enrichment of 150Nd for neutrinoless double-beta decay detection
Authors: Suryanarayana M. V. 
Published: July 2022

AbstractA 562 nm–627 nm–597 nm three-step resonant photoionization scheme has been studied using the density matrix formalism for the enrichment of 150Nd in weighable quantities for the neutrinoless double-beta decay detection. The effect of bandwidth of the excitation laser and charge exchange collisions, on the production rates and degree of enrichment has also been studied. Optimum conditions for the efficient enrichment of 150Nd isotope have been derived. It has been shown that it might be possible to produce 50 kg of 66% enriched 150Nd isotope in about five months (16 h/day) using the conditions derived through this investigation. This enables to reach the 0νββ decay half-life limit of ≈ 1.8 × 1025 year for the 150Nd isotope.
Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene
Authors: Toffoli Marco , Chen Xiao , Sedlazeck Fritz J. , Lee Chiao-Yin , Mullin Stephen , Higgins Abigail , Koletsi Sofia , Garcia-Segura Monica Emili , Sammler Esther , Scholz Sonja W. , Schapira Anthony H. V. , Eberle Michael A. , Proukakis Christos 
Published: July 2022

AbstractGBA variants carriers are at increased risk of Parkinson’s disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to structural variants, complicating genetic analysis. We present two methods to resolve recombinant alleles and other variants in GBA: Gauchian, a tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore sequencing after PCR enrichment. Both methods were concordant for 42 samples carrying a range of recombinants and GBAP1-related mutations, and Gauchian outperformed the GATK Best Practices pipeline. Applying Gauchian to sequencing of over 10,000 individuals shows that copy number variants (CNVs) spanning GBAP1 are relatively common in Africans. CNV frequencies in PD and LBD are similar to controls. Gains may coexist with other mutations in patients, and a modifying effect cannot be excluded. Gauchian detects more GBA variants in LBD than PD, especially severe ones. These findings highlight the importance of accurate GBA analysis in these patients.
Combining visible-light induction and copper catalysis for chemo-selective nitrene transfer for late-stage amination of natural products
Authors: Xing Qi , Jiang Ding , Zhang Jiayin , Guan Liangyu , Li Ting , Zhao Yi , Di Man , Chen Huangcan , Che Chao , Zhu Zhendong 
Published: July 2022

AbstractNitrene transfer chemistry is an effective strategy for introducing C–N bonds, which are ubiquitous in pharmaceuticals, agrochemicals and diverse bioactive natural products. The development of chemical methodology that can functionalize unique sites within natural products through nitrene transfer remains a challenge in the field. Herein, we developed copper catalyzed chemoselective allylic C–H amination and catalyst-free visible-light induced aziridination of alkenes through nitrene transfer. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Furthermore, combination of these two methods enable the intermolecular chemo-selective late-stage amination of biologically active natural products, leading to C–H amination or C=C aziridination products in a tunable way. A series of control experiments indicate two-step radical processes were involved in both reaction systems.
Correlated disorder as a way towards robust superconductivity
Authors: Neverov Vyacheslav D. , Lukyanov Alexander E. , Krasavin Andrey V. , Vagov Alexei , Croitoru Mihail D. 
Published: July 2022

AbstractOrdinary superconductors are widely assumed insensitive to small concentrations of random nonmagnetic impurities, whereas strong disorder suppresses superconductivity and even makes superconductor-insulator transition occur. In between these limiting cases, a most fascinating regime can take place where disorder enhances superconductivity. Hitherto, almost all theoretical studies have been conducted under the assumption that disorder is completely independent and random. In real materials, however, positions of impurities and defects tend to correlate with each other. This work shows that these correlations have a strong impact on superconductivity making it more robust and less sensitive to the disorder potential. Superconducting properties can therefore be controlled not only by the overall density of impurities and defects, but by their spatial correlations as well.
Forces that control self-organization of chemically-propelled Janus tori
Authors: Wang Jiyuan , Huang Mu-Jie , Baker-Sediako Remmi D. , Kapral Raymond , Aranson Igor S. 
Published: July 2022

AbstractControl of the individual and collective behavior of self-propelled synthetic micro-objects has immediate application for nanotechnology, robotics, and precision medicine. Despite significant progress in the synthesis and characterization of self-propelled Janus (two-faced) particles, predictive understanding of their behavior remains challenging, especially if the particles have anisotropic forms. Here, by using molecular simulation, we describe the interactions of chemically-propelled microtori near a wall. The results show that a torus hovers at a certain distance from the wall due to a combination of gravity and hydrodynamic flows generated by the chemical activity. Moreover, electrostatic dipolar interactions between the torus and the wall result in a spontaneous tilt and horizontal translation, in a qualitative agreement with experiment. Simulations of the dynamics of two and four tori near a wall provide evidence for the formation of stable self-propelled bound states. Our results illustrate that self-organization at the microscale occurs due to a combination of multiple factors, including hydrodynamic, chemical, electrostatic and steric interactions.
Predicting the formation of fractionally doped perovskite oxides by a function-confined machine learning method
Authors: Zhai Ximei , Ding Fei , Zhao Zeyu , Santomauro Aaron , Luo Feng , Tong Jianhua 
Published: July 2022

AbstractFractionally doped perovskites oxides (FDPOs) have demonstrated ubiquitous applications such as energy conversion, storage and harvesting, catalysis, sensor, superconductor, ferroelectric, piezoelectric, magnetic, and luminescence. Hence, an accurate, cost-effective, and easy-to-use methodology to discover new compositions is much needed. Here, we developed a function-confined machine learning methodology to discover new FDPOs with high prediction accuracy from limited experimental data. By focusing on a specific application, namely solar thermochemical hydrogen production, we collected 632 training data and defined 21 desirable features. Our gradient boosting classifier model achieved a high prediction accuracy of 95.4% and a high F1 score of 0.921. Furthermore, when verified on additional 36 experimental data from existing literature, the model showed a prediction accuracy of 94.4%. With the help of this machine learning approach, we identified and synthesized 11 new FDPO compositions, 7 of which are relevant for solar thermochemical hydrogen production. We believe this confined machine learning methodology can be used to discover, from limited data, FDPOs with other specific application purposes.
Distributed secure transmission for covert communication under multi‐user network
Authors: Huang Ying , Lei Jing 
Published: July 2022

AbstractIn order to counter the double attack with wardens and eavesdroppers in the practical scenario, a distributed transmission scheme with security and covertness is proposed, which combines coding techniques and transmission protocol. The covert message is encoded by rateless codes and transmitted embedded in normal frames. The security is based on the random essence of rateless coding, and the covertness is achieved by ignoring the error frames and maintaining the signal waveform. The inter‐collusion between multiple wardens and eavesdroppers greatly increases the potential security hazards, which is first discussed in this paper. The authors can counter the inter‐collusion attack by adjusting the ratio of covert frame transmission in the distributed transmission scheme with security and covertness. Compared with the related work, this paper has many advantages, such as good robustness, lower extra complexity, and the insurance of the performance for both normal message and covert message. The analysis and simulation results show that our distributed transmission scheme with security and covertness can achieve both covertness and security based on the effective design under the existing communication system.