bluuebunny/crossref_metadata_2025 huggingface dataset:
Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance
Authors: Zatreanu Diana , Robinson Helen M. R. , Alkhatib Omar , Boursier Marie , Finch Harry , Geo Lerin , Grande Diego , Grinkevich Vera , Heald Robert A. , Langdon Sophie , Majithiya Jayesh , McWhirter Claire , Martin Niall M. B. , Moore Shaun , Neves Joana , Rajendra Eeson , Ranzani Marco , Schaedler Theresia , Stockley Martin , Wiggins Kimberley , Brough Rachel , Sridhar Sandhya , Gulati Aditi , Shao Nan , Badder Luned M. , Novo Daniela , Knight Eleanor G. , Marlow Rebecca , Haider Syed , Callen Elsa , Hewitt Graeme , Schimmel Joost , Prevo Remko , Alli Christina , Ferdinand Amanda , Bell Cameron , Blencowe Peter , Bot Chris , Calder Mathew , Charles Mark , Curry Jayne , Ekwuru Tennyson , Ewings Katherine , Krajewski Wojciech , MacDonald Ellen , McCarron Hollie , Pang Leon , Pedder Chris , Rigoreau Laurent , Swarbrick Martin , Wheatley Ed , Willis Simon , Wong Ai Ching , Nussenzweig Andre , Tijsterman Marcel , Tutt Andrew , Boulton Simon J. , Higgins Geoff S. , Pettitt Stephen J. , Smith Graeme C. M. , Lord Christopher J.
Published: June 2021

To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance.
CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation
Authors: Zabrady Katerina , Zabrady Matej , Kolesar Peter , Li Arthur W. H. , Doherty Aidan J.
Published: June 2021

CRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation.
BNT162b2 vaccine uptake and effectiveness in UK healthcare workers – a single centre cohort study
Authors: Azamgarhi Tariq , Hodgkinson Michelle , Shah Ashik , Skinner John A. , Hauptmannova Iva , Briggs Tim W. R. , Warren Simon
Published: June 2021

In this single centre cohort study we assessed BNT162B2 vaccine uptake and effectiveness among UK healthcare workers (HCWs) during a time of high community COVID-19 prevalence. Early uptake among HCWs was 62.3% (1409/2260), however there were significant differences in uptake between age groups, ethnic origins, and job roles. Uptake increased to 72.9% after a vaccine hesitancy working group implemented specific measures. In the 42 days after vaccination, 49 new cases of COVID-19 were identified, of which 7 (14.3%) occurred in HCWs who were beyond 10 days of vaccination. Kaplan–Meier curves for partially vaccinated and unvaccinated groups were congruent until day 14 and continued to diverge up to 42 days. Cox regression analysis showed a 70.0% (95%CI 6.0–91.0; p=0.04) risk reduction for COVID-19 infection in partially vaccinated HCWs. Here we report early vaccination rates among HCWs are generally high although uptake is lower in certain groups. It is possible to improve vaccine uptake and efforts should focus on this, however, significant resource is required. The BNT162B2 vaccine is effective from 14 days post-vaccination in a frontline clinical setting and protection continues beyond 21 days post 1st dose without a 2nd dose, being given.
C(sp3)−C(sp3) bond formation via nickel-catalyzed deoxygenative homo-coupling of aldehydes/ketones mediated by hydrazine
Authors: Cao Dawei , Li Chen-Chen , Zeng Huiying , Peng Yong , Li Chao-Jun
Published: June 2021

Aldehydes and ketones are widely found in biomass resources and play important roles in organic synthesis. However, the direct deoxygenative coupling of aldehydes or ketones to construct C(sp3)−C(sp3) bond remains a scientific challenge. Here we report a nickel−catalyzed reductive homo-coupling of moisture- and air-stable hydrazones generated in-situ from naturally abundant aldehydes and ketones to construct challenging C(sp3)−C(sp3) bond. This transformation has great functional group compatibility and can suit a broad substrate scope with innocuous H2O, N2 and H2 as the by-products. Furthermore, the application in several biological molecules and the transformation of PEEK model demonstrate the generality, practicability, and applicability of this novel methodology.
MolDiscovery: learning mass spectrometry fragmentation of small molecules
Authors: Cao Liu , Guler Mustafa , Tagirdzhanov Azat , Lee Yi-Yuan , Gurevich Alexey , Mohimani Hosein
Published: June 2021

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.
Efficient precise in vivo base editing in adult dystrophic mice
Authors: Xu Li , Zhang Chen , Li Haiwen , Wang Peipei , Gao Yandi , Mokadam Nahush A. , Ma Jianjie , Arnold W. David , Han Renzhi
Published: June 2021

Recent advances in base editing have created an exciting opportunity to precisely correct disease-causing mutations. However, the large size of base editors and their inherited off-target activities pose challenges for in vivo base editing. Moreover, the requirement of a protospacer adjacent motif (PAM) nearby the mutation site further limits the targeting feasibility. Here we modify the NG-targeting adenine base editor (iABE-NGA) to overcome these challenges and demonstrate the high efficiency to precisely edit a Duchenne muscular dystrophy (DMD) mutation in adult mice. Systemic delivery of AAV9-iABE-NGA results in dystrophin restoration and functional improvement. At 10 months after AAV9-iABE-NGA treatment, a near complete rescue of dystrophin is measured in mdx4cv mouse hearts with up to 15% rescue in skeletal muscle fibers. The off-target activities remains low and no obvious toxicity is detected. This study highlights the promise of permanent base editing using iABE-NGA for the treatment of monogenic diseases.
Model-based prediction of spatial gene expression via generative linear mapping
Authors: Okochi Yasushi , Sakaguchi Shunta , Nakae Ken , Kondo Takefumi , Naoki Honda
Published: June 2021

Decoding spatial transcriptomes from single-cell RNA sequencing (scRNA-seq) data has become a fundamental technique for understanding multicellular systems; however, existing computational methods lack both accuracy and biological interpretability due to their model-free frameworks. Here, we introduce Perler, a model-based method to integrate scRNA-seq data with reference in situ hybridization (ISH) data. To calibrate differences between these datasets, we develop a biologically interpretable model that uses generative linear mapping based on a Gaussian mixture model using the Expectation–Maximization algorithm. Perler accurately predicts the spatial gene expression of Drosophila embryos, zebrafish embryos, mammalian liver, and mouse visual cortex from scRNA-seq data. Furthermore, the reconstructed transcriptomes do not over-fit the ISH data and preserved the timing information of the scRNA-seq data. These results demonstrate the generalizability of Perler for dataset integration, thereby providing a biologically interpretable framework for accurate reconstruction of spatial transcriptomes in any multicellular system.
Triboelectrification induced self-powered microbial disinfection using nanowire-enhanced localized electric field
Authors: Huo Zheng-Yang , Kim Young-Jun , Suh In-Yong , Lee Dong-Min , Lee Jeong Hwan , Du Ye , Wang Si , Yoon Hong-Joon , Kim Sang-Woo
Published: June 2021

Air-transmitted pathogens may cause severe epidemics showing huge threats to public health. Microbial inactivation in the air is essential, whereas the feasibility of existing air disinfection technologies meets challenges including only achieving physical separation but no inactivation, obvious pressure drops, and energy intensiveness. Here we report a rapid disinfection method toward air-transmitted bacteria and viruses using the nanowire-enhanced localized electric field to damage the outer structures of microbes. This air disinfection system is driven by a triboelectric nanogenerator that converts mechanical vibration to electricity effectively and achieves self-powered. Assisted by a rational design for the accelerated charging and trapping of microbes, this air disinfection system promotes microbial transport and achieves high performance: >99.99% microbial inactivation within 0.025 s in a fast airflow (2 m/s) while only causing low pressure drops (<24 Pa). This rapid, self-powered air disinfection method may fill the urgent need for air-transmitted microbial inactivation to protect public health.
Efficient ethylene purification by a robust ethane-trapping porous organic cage
Authors: Su Kongzhao , Wang Wenjing , Du Shunfu , Ji Chunqing , Yuan Daqiang
Published: June 2021

The removal of ethane (C2H6) from its analogous ethylene (C2H4) is of paramount importance in the petrochemical industry, but highly challenging due to their similar physicochemical properties. The use of emerging porous organic cage (POC) materials for C2H6/C2H4 separation is still in its infancy. Here, we report the benchmark example of a truncated octahedral calix[4]resorcinarene-based POC adsorbent (CPOC-301), preferring to adsorb C2H6 than C2H4, and thus can be used as a robust absorbent to directly separate high-purity C2H4 from the C2H6/C2H4 mixture. Molecular modelling studies suggest the exceptional C2H6 selectivity is due to the suitable resorcin[4]arene cavities in CPOC-301, which form more multiple C–H···π hydrogen bonds with C2H6 than with C2H4 guests. This work provides a fresh avenue to utilize POC materials for highly selective separation of industrially important hydrocarbons.
Mechanistic analysis of multiple processes controlling solar-driven H2O2 synthesis using engineered polymeric carbon nitride
Authors: Zhao Yubao , Zhang Peng , Yang Zhenchun , Li Lina , Gao Jingyu , Chen Sheng , Xie Tengfeng , Diao Caozheng , Xi Shibo , Xiao Beibei , Hu Chun , Choi Wonyong
Published: June 2021

Solar-driven hydrogen peroxide (H2O2) production presents unique merits of sustainability and environmental friendliness. Herein, efficient solar-driven H2O2production through dioxygen reduction is achieved by employing polymeric carbon nitride framework with sodium cyanaminate moiety, affording a H2O2production rate of 18.7 μmol h−1mg−1and an apparent quantum yield of 27.6% at 380 nm. The overall photocatalytic transformation process is systematically analyzed, and some previously unknown structural features and interactions are substantiated via experimental and theoretical methods. The structural features of cyanamino group and pyridinic nitrogen-coordinated soidum in the framework promote photon absorption, alter the energy landscape of the framework and improve charge separation efficiency, enhance surface adsorption of dioxygen, and create selective 2e−oxygen reduction reaction surface-active sites. Particularly, an electronic coupling interaction between O2and surface, which boosts the population and prolongs the lifetime of the active shallow-trapped electrons, is experimentally substantiated.
Bicyclo[2.2.0]hexene derivatives as a proaromatic platform for group transfer and chemical sensing
Authors: Wu Bin , Wang Jianing , Liu Xingchen , Zhu Rong
Published: June 2021

Here we report the design, preparation, synthetic utility, and sensing application of a class of proaromatic structures, namely bicyclo[2.2.0]hexene (BCH) derivatives. Building on a valence isomerism concept, they feature modular and easy synthesis as well as high thermal stability, and can be oxidatively activated under mild conditions. New alkyl transfer reactions using BCHs as a radical donor have been developed to showcase the utility of their proaromaticity. Moreover, the redox-triggered valence isomerization of a quinoline-derived BCH led to colorimetric and fluorescent responses toward vapors of electrophilic reagents in solution and solid phase, respectively. This optical response was shown to involve a 1,3-cyclohexadiene structure that possesses an intramolecular charge transfer excited state with interesting aggregation induced emission (AIE) character. Thus, the potential of BCHs has been demonstrated as a versatile platform for the development of new reagents and functional materials.
Halide perovskite memristors as flexible and reconfigurable physical unclonable functions
Authors: John Rohit Abraham , Shah Nimesh , Vishwanath Sujaya Kumar , Ng Si En , Febriansyah Benny , Jagadeeswararao Metikoti , Chang Chip-Hong , Basu Arindam , Mathews Nripan
Published: June 2021

Physical Unclonable Functions (PUFs) address the inherent limitations of conventional hardware security solutions in edge-computing devices. Despite impressive demonstrations with silicon circuits and crossbars of oxide memristors, realizing efficient roots of trust for resource-constrained hardware remains a significant challenge. Hybrid organic electronic materials with a rich reservoir of exotic switching physics offer an attractive, inexpensive alternative to design efficient cryptographic hardware, but have not been investigated till date. Here, we report a breakthrough security primitive exploiting the switching physics of one dimensional halide perovskite memristors as excellent sources of entropy for secure key generation and device authentication. Measurements of a prototypical 1 kb propyl pyridinium lead iodide (PrPyr[PbI3]) weak memristor PUF with a differential write-back strategy reveals near ideal uniformity, uniqueness and reliability without additional area and power overheads. Cycle-to-cycle write variability enables reconfigurability, while in-memory computing empowers a strong recurrent PUF construction to thwart machine learning attacks.
Neighborhood-level disparities and subway utilization during the COVID-19 pandemic in New York City
Authors: Carrión Daniel , Colicino Elena , Pedretti Nicolo Foppa , Arfer Kodi B. , Rush Johnathan , DeFelice Nicholas , Just Allan C.
Published: June 2021

The COVID-19 pandemic has yielded disproportionate impacts on communities of color in New York City (NYC). Researchers have noted that social disadvantage may result in limited capacity to socially distance, and consequent disparities. We investigate the association between neighborhood social disadvantage and the ability to socially distance, infections, and mortality in Spring 2020. We combine Census Bureau and NYC open data with SARS-CoV-2 testing data using supervised dimensionality-reduction with Bayesian Weighted Quantile Sums regression. The result is a ZIP code-level index with weighted social factors associated with infection risk. We find a positive association between neighborhood social disadvantage and infections, adjusting for the number of tests administered. Neighborhood disadvantage is also associated with a proxy of the capacity to socially isolate, NYC subway usage data. Finally, our index is associated with COVID-19-related mortality.
Nonlinearity-induced nanoparticle circumgyration at sub-diffraction scale
Authors: Qin Yaqiang , Zhou Lei-Ming , Huang Lu , Jin Yunfeng , Shi Hao , Shi Shali , Guo Honglian , Xiao Liantuan , Yang Yuanjie , Qiu Cheng-Wei , Jiang Yuqiang
Published: June 2021

The ability of light beams to rotate nano-objects has important applications in optical micromachines and biotechnology. However, due to the diffraction limit, it is challenging to rotate nanoparticles at subwavelength scale. Here, we propose a method to obtain controlled fast orbital rotation (i.e., circumgyration) at deep subwavelength scale, based on the nonlinear optical effect rather than sub-diffraction focusing. We experimentally demonstrate rotation of metallic nanoparticles with orbital radius of 71 nm, to our knowledge, the smallest orbital radius obtained by optical trapping thus far. The circumgyration frequency of particles in water can be more than 1 kHz. In addition, we use a femtosecond pulsed Gaussian beam rather than vortex beams in the experiment. Our study provides paradigms for nanoparticle manipulation beyond the diffraction limit, which will not only push toward possible applications in optically driven nanomachines, but also spur more fascinating research in nano-rheology, micro-fluid mechanics and biological applications at the nanoscale.
Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases
Authors: Deng Cheng-Cheng , Hu Yong-Fei , Zhu Ding-Heng , Cheng Qing , Gu Jing-Jing , Feng Qing-Lan , Zhang Li-Xue , Xu Ying-Ping , Wang Dong , Rong Zhili , Yang Bin
Published: June 2021

Fibrotic skin disease represents a major global healthcare burden, characterized by fibroblast hyperproliferation and excessive accumulation of extracellular matrix. Fibroblasts are found to be heterogeneous in multiple fibrotic diseases, but fibroblast heterogeneity in fibrotic skin diseases is not well characterized. In this study, we explore fibroblast heterogeneity in keloid, a paradigm of fibrotic skin diseases, by using single-cell RNA-seq. Our results indicate that keloid fibroblasts can be divided into 4 subpopulations: secretory-papillary, secretory-reticular, mesenchymal and pro-inflammatory. Interestingly, the percentage of mesenchymal fibroblast subpopulation is significantly increased in keloid compared to normal scar. Functional studies indicate that mesenchymal fibroblasts are crucial for collagen overexpression in keloid. Increased mesenchymal fibroblast subpopulation is also found in another fibrotic skin disease, scleroderma, suggesting this is a broad mechanism for skin fibrosis. These findings will help us better understand skin fibrotic pathogenesis, and provide potential targets for fibrotic disease therapies.
A method for measuring the molecular ratio of inhalation to exhalation and effect of inspired oxygen levels on oxygen consumption
Authors: Shinozaki Koichiro , Okuma Yu , Saeki Kota , Miyara Santiago J. , Aoki Tomoaki , Molmenti Ernesto P. , Yin Tai , Kim Junhwan , Lampe Joshua W. , Becker Lance B.
Published: June 2021

Using a new method for measuring the molecular ratio (R) of inhalation to exhalation, we investigated the effect of high fraction of inspired oxygen (FIO2) on oxygen consumption (VO2), carbon dioxide generation (VCO2), and respiratory quotient (RQ) in mechanically ventilated rats. Twelve rats were equally assigned into two groups by anesthetics: intravenous midazolam/fentanyl vs. inhaled isoflurane. R, VO2, VCO2, and RQ were measured at FIO2 0.3 or 1.0. R error was ± 0.003. R was 1.0099 ± 0.0023 with isoflurane and 1.0074 ± 0.0018 with midazolam/fentanyl. R was 1.0081 ± 0.0017 at an FIO2 of 0.3 and 1.0092 ± 0.0029 at an FIO2 of 1.0. There were no differences in VCO2 among the groups. VO2 increased at FIO2 1.0, which was more notable when midazolam/fentanyl was used (isoflurane-FIO2 0.3: 15.4 ± 1.1; isoflurane-FIO2 1.0: 17.2 ± 1.8; midazolam/fentanyl-FIO2 0.3: 15.4 ± 1.1; midazolam/fentanyl-FIO2 1.0: 21.0 ± 2.2 mL/kg/min at STP). The RQ was lower at FIO2 1.0 than FIO2 0.3 (isoflurane-FIO2 0.3: 0.80 ± 0.07; isoflurane-FIO2 1.0: 0.71 ± 0.05; midazolam/fentanyl-FIO2 0.3: 0.79 ± 0.03; midazolam/fentanyl-FIO2 1.0: 0.59 ± 0.04). R was not affected by either anesthetics or FIO2. Inspired 100% O2 increased VO2 and decreased RQ, which might be more remarkable when midazolam/fentanyl was used.
Functional and genetic diversity of native rhizobial isolates nodulating cowpea (Vigna unguiculata L. Walp.) in Mozambican soils
Authors: Simbine Margarida G. , Mohammed Mustapha , Jaiswal Sanjay K. , Dakora Felix D.
Published: June 2021

Identification and symbiotic characterization of indigenous rhizobial isolates are the basis for inoculant formulations needed for sustainable grain legume production. This study screened for morpho-genetic diversity of indigenous cowpea nodulating rhizobia in farmers’ fields across two contrasting agroecological zones of Northern Mozambique. The photosynthetic function induced by the isolates in their homologous cowpea was assessed. The results showed high genetic variability among the isolates based on morphology and ERIC-PCR fingerprinting. The trap cowpea genotype did not influence the diversity of isolates collected from the two different agroecologies, suggesting that the cowpea-rhizobia compatibility may be conserved at species level. Phylogenetic analysis of the 16S rRNA gene assigned representative rhizobial isolates to species in the Bradyrhizobium and Rhizobium genera, with some isolates showing high divergence from the known reference type strains. The isolates from both agroecologies highly varied in the number and biomass of nodules induced in the homologous cowpea, resulting in variable plant growth and photosynthetic activities. A total of 72% and 83% of the isolates collected from the agroecological zones 7 and 8 were respectively classified as highly effective candidates with > 80% relative effectiveness compared to plants fertilized with nitrate, indicating that elite native strains populated the studied soils. Moreover, the top 25% of high N2-fixing isolates from the two agroecologies recorded relative effectiveness ranging from 115 to 154%, values higher than the effectiveness induced by the commercial Bradyrhizobium sp. strain CB756. These strains are considered as having potential for use in inoculant formulations. However, future studies should be done to assess the ecologically adaptive traits and symbiotic performance under field conditions.
Quality of life and therapeutic regimen management in onychomycosis patients and in vitro study of antiseptic solutions
Authors: Silva-Neves Vasco , Hugo Vitor , Alves Paulo , Amado João Costa , Pais-Vieira Carla , Sousa Fátima , Cerqueira Fátima , Pinto Eugénia , Pais-Vieira Miguel
Published: June 2021

Onychomycosis or tinea unguium (EE12.1) and Onychomycosis due to non-dermatophyte moulds (1F2D.5) (OM) is a fungal infection of the nail plates with a high prevalence that often affects vulnerable people with co-existing health problems. Gold standard pharmacological treatments for onychomycosis have been associated with low success rates and increasing antifungal resistance, suggesting that treatment outcome is dependent on multiple variables. Here, the prevalence of OM and quality of life were characterized in two vulnerable populations—Hospital patients and Homeless people. Comparing both groups, the most prevalent fungal species were identified in Hospital patients. Then, the in vitro fungicidal properties of the antiseptics povidone-iodine, polyhexamethylene biguanide-betaine, octenidine dihydrochloride, and a super-oxidized solution against two ATCC strains (Candida albicans and Aspergillus niger) and three clinical fungal isolates from Hospital patients (Candida parapsilosis, Trichophyton interdigitale, and Trichophyton rubrum) were tested. OM prevalence was high in both patient groups studied, who also reported a reduction in quality of life and concerns about the state of their feet. In addition, Hospital patients had a non-negligent therapeutic regimen management style. Antiseptics tested in vitro revealed antifungal properties. As antiseptics are low-cost and easy to apply and have few iatrogenic effects, the demonstration of fungicidal properties of these solutions suggests that they may constitute potential supportive therapeutics for OM.
Global assessment of innovative solutions to tackle marine litter
Authors: Bellou Nikoleta , Gambardella Chiara , Karantzalos Konstantinos , Monteiro João Gama , Canning-Clode João , Kemna Stephanie , Arrieta-Giron Camilo A. , Lemmen Carsten
Published: June 2021

Marine litter is one of the most relevant pollution problems that our oceans are facing today. Marine litter in our oceans is a major threat to a sustainable planet. Here, we provide a comprehensive analysis of cutting-edge solutions developed globally to prevent, monitor and clean marine litter. Prevention in this research includes only innovative solutions to prevent litter entering oceans and seas rather than interventions such as waste reduction and recycling. On the basis of extensive search and data compilation, our analysis reveals that information is dispersed across platforms and is not easily accessible. In total, 177 solutions—the equivalent to <0.9% of the search hits—fulfilled our validation criteria and were evaluated. Most solutions (n = 106, 60%) primarily address monitoring and were developed during the past 3 years, with the scientific community being the key driver. Few solutions reached mature technical readiness and market availability, while none were validated for efficiency and environmental impact. Looking ahead, we elaborate on the limitations of the existing solutions, the challenges of developing new solutions, and provide recommendations for funding schemes and policy instruments to prevent, monitor and clean marine litter globally. In doing so, we encourage researchers, innovators and policy-makers worldwide to act towards achieving and sustaining a cleaner ocean for future generations.
An Oligocene giant rhino provides insights into Paraceratherium evolution
Authors: Deng Tao , Lu Xiaokang , Wang Shiqi , Flynn Lawrence J. , Sun Danhui , He Wen , Chen Shanqin
Published: June 2021

As one of the largest land mammals, the origin and evolution of the giant rhino Paraceratherium bugtiense in Pakistan have been unclear. We report a new species Paraceratherium linxiaense sp. nov. from northwestern China with an age of 26.5 Ma. Morphology and phylogeny reveal that P. linxiaense is the highly derived species of the genus Paraceratherium, and its clade with P. lepidum has a tight relationship to P. bugtiense. Based on the paleogeographical literature, P. bugtiense represents a range expansion of Paraceratherium from Central Asia via the Tibetan region. By the late Oligocene, P. lepidum and P. linxiaense were found in the north side of the Tibetan Plateau. The Tibetan region likely hosted some areas with low elevation, possibly under 2000 m during Oligocene, and the lineage of giant rhinos could have dispersed freely along the eastern coast of the Tethys Ocean and perhaps through some lowlands of this region.
Building a stem cell-based primate uterus
Authors: Bergmann Sophie , Schindler Magdalena , Munger Clara , Penfold Christopher A. , Boroviak Thorsten E.
Published: June 2021

The uterus is the organ for embryo implantation and fetal development. Most current models of the uterus are centred around capturing its function during later stages of pregnancy to increase the survival in pre-term births. However, in vitro models focusing on the uterine tissue itself would allow modelling of pathologies including endometriosis and uterine cancers, and open new avenues to investigate embryo implantation and human development. Motivated by these key questions, we discuss how stem cell-based uteri may be engineered from constituent cell parts, either as advanced self-organising cultures, or by controlled assembly through microfluidic and print-based technologies.
Normal cells repel WWOX-negative or -dysfunctional cancer cells via WWOX cell surface epitope 286-299
Authors: Chen Yu-An , Sie Yong-Da , Liu Tsung-Yun , Kuo Hsiang-Ling , Chou Pei-Yi , Chen Yu-Jie , Lee Kuan-Ting , Chen Pin-Jun , Chen Shur-Tzu , Chang Nan-Shan
Published: June 2021

Metastatic cancer cells are frequently deficient in WWOX protein or express dysfunctional WWOX (designated WWOXd). Here, we determined that functional WWOX-expressing (WWOXf) cells migrate collectively and expel the individually migrating WWOXd cells. For return, WWOXd cells induces apoptosis of WWOXf cells from a remote distance. Survival of WWOXd from the cell-to-cell encounter is due to activation of the survival IκBα/ERK/WWOX signaling. Mechanistically, cell surface epitope WWOX286-299 (repl) in WWOXf repels the invading WWOXd to undergo retrograde migration. However, when epitope WWOX7-21 (gre) is exposed, WWOXf greets WWOXd to migrate forward for merge. WWOX binds membrane type II TGFβ receptor (TβRII), and TβRII IgG-pretreated WWOXf greet WWOXd to migrate forward and merge with each other. In contrast, TβRII IgG-pretreated WWOXd loses recognition by WWOXf, and WWOXf mediates apoptosis of WWOXd. The observatons suggest that normal cells can be activated to attack metastatic cancer cells. WWOXd cells are less efficient in generating Ca2+ influx and undergo non-apoptotic explosion in response to UV irradiation in room temperature. WWOXf cells exhibit bubbling cell death and Ca2+ influx effectively caused by UV or apoptotic stress. Together, membrane WWOX/TβRII complex is needed for cell-to-cell recognition, maintaining the efficacy of Ca2+ influx, and control of cell invasiveness.
Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin
Authors: Zhao Rui , Biddle Jennifer F
Published: June 2021

Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.
Dealing with Quadrupolar Nuclei in Paramagnetic Systems
Authors: Hu Bingwen , Amoureux Jean-Paul
Published: June 2021

Quadrupolar nuclei with spin quantum number I > 1/2, e.g. 7Li, 23Na and 17O, are frequently encountered in lithium-ion batteries and sodium-ion batteries. This chapter describes: (i) the basic theory, (ii) the powder sample line-shapes with first- and second-order quadrupolar broadening observed under static or MAS conditions, (iii) some important experimental techniques such as MQMAS, and finally (iv) the developments of correlation NMR experiments. In recent years, solid-state nuclear magnetic resonance spectroscopy (SS-NMR) has become a vital analytical method that provides atomic-level structural information of materials used for Li-ion and Na-ion batteries.1 In these materials, 7Li, 23Na and 17O isotopes are frequently encountered, which are typical quadrupolar nuclei with spin quantum number I > 1/2. In fact, quadrupolar nuclei account for ca. 75% of all NMR-active nuclei in the periodic table, and they are very important for SS-NMR structural analyses. This chapter describes: (i) the basic theory, (ii) the powder sample line-shapes with first- and second-order quadrupolar broadening observed under static or MAS conditions, (iii) some important experimental techniques such as MQMAS, and finally (iv) the developments of correlation NMR experiments.
Stray Field Imaging for High Resolution In Situ Analysis of Lithium-ion Batteries
Authors: Tang Joel A.
Published: June 2021

Stray field (STRAFI) imaging is an alternative imaging method to produce high resolution images using extremely strong magnetic field gradients. This chapter will cover the basic theory of STRAFI imaging, how to implement the technique using existing NMR magnets, probe design, and experimental considerations. The application of STRAFI imaging to study lithium-ion batteries will be reviewed.
Effects of psyllium seed husk powder, methylcellulose, pregelatinised starch, and cold water swelling starch on the production of gluten free crackers
Authors: Ren Yi , Linter Bruce R. , Foster Tim J.
Published: June 2021

Psyllium seed husk powder and pregelatinised starch crackers had comparable textural properties and sound release to wheat crackers, while the functionality of methylcellulose was limited due to low moisture addition.
Determination of fluorine in copper concentrate via CaF molecules using laser-induced breakdown spectroscopy
Authors: Tang Zhiyang , Zhou Ran , Liu Ke , Hao Zhongqi , Liu Kun , Zhang Wen , Li Qingzhou , Zhu Chenwei , Li Xiangyou
Published: June 2021

CaF molecular emission as an alternative to F atomic emission was proposed to detect the fluorine element in copper concentrate.
Atomic Spectrometry Update: review of advances in elemental speciation
Authors: Clough Robert , Harrington Chris F. , Hill Steve J. , Madrid Yolanda , Tyson Julian F.
Published: June 2021

This review covers advances in elemental speciation by a range of coupled techniques, including HPLC-ICP-MS, HPLC-HG-AFS and GC-ICP-MS.
Just add water: hydratable, morphologically diverse nanocarrier powders for targeted delivery
Authors: Bobbala Sharan , Vincent Michael P. , Scott Evan A.
Published: June 2021

We present a storage-stable carbohydrate-based powder technology that forms monodisperse polymeric nanocarriers of diverse morphology upon simple hydration. This platform loads a wide range of cargoes and is capable of targeted delivery.
Shining a new light on the structure of polyurea/polyurethane materials
Authors: Phoungtawee Piangtawan , Crespy Daniel
Published: June 2021

Polyurea and polyurethane are widely used in coatings, foams, and micro- and nanocapsules. Investigations of the polymers structure indicate that a significant amount of hydrolyzed isocyanate is incorporated in the macromolecular backbone.
Genetically-encoded discovery of proteolytically stable bicyclic inhibitors for morphogen NODAL
Authors: Wong Jeffrey Y.-K. , Mukherjee Raja , Miao Jiayuan , Bilyk Olena , Triana Vivian , Miskolzie Mark , Henninot Antoine , Dwyer John J. , Kharchenko Serhii , Iampolska Anna , Volochnyuk Dmitriy M. , Lin Yu-Shan , Postovit Lynne-Marie , Derda Ratmir
Published: June 2021

A two-fold symmetric linchpin (TSL) converts readily available phage-displayed disulfide peptide libraries to proteolytically stable bicyclic peptides. The bicyclic phage library was screened to discover an antagonist of NODAL morphogen.
The Relationship Between Tinnitus Pitch, Audiogram Edge Frequency, and Auditory Stream Segregation Abilities in Individuals With Tinnitus
Authors: Jain Saransh , Cherian Riya , Nataraja Nuggehalli P. , Narne Vijaya Kumar
Published: June 2021

Purpose

Around 80%–93% of the individuals with tinnitus have hearing loss. Researchers have found that tinnitus pitch was related to the frequencies of hearing loss, but unclear about the relationship between tinnitus pitch and audiometry edge frequency. The comorbidity of tinnitus and speech perception in noise problems had also been reported, but the relationship between tinnitus pitch and speech perception in noise had seldom been investigated. This study was designed to estimate the relationship between tinnitus pitch, audiogram edge frequency, and speech perception in noise. The speech perception in noise was measured using auditory stream segregation paradigm.

Method

Thirteen individuals with bilateral mild-to-severe tonal tinnitus and minimal-to-mild cochlear hearing loss were selected. Thirteen individuals with hearing loss without tinnitus were also selected. The audiogram of each participant with tinnitus was matched with that of the participant without tinnitus. Tinnitus pitch of the participants with tinnitus was measured and compared with audiogram edge frequency. The stream segregation thresholds were calculated at the participants' admitted tinnitus pitch and one octave below the tinnitus pitch. The stream segregation thresholds were estimated at fission and fusion boundary using pure-tone stimuli in ABA paradigm.

Results

High correlation between tinnitus pitch and audiogram edge frequency was noted. Overall stream segregation thresholds were higher for individuals with tinnitus. Higher thresholds indicated poorer stream segregation abilities. Within tinnitus participants, the thresholds were significantly lesser at frequency corresponding to admitted tinnitus pitch than at one octave below the tinnitus pitch.

Conclusions

The information from this study may be helpful in educating the patients about the relationship between hearing loss and tinnitus. The findings may also account for speech-perception-in-noise difficulties often reported by the individuals with tinnitus.
CVaR‐based generation expansion planning of cascaded hydro‐photovoltaic‐pumped storage system with uncertain solar power considering flexibility constraints
Authors: Du Mingkun , Huang Yuan , Liu Junyong , Wu Gang , Jawad Shafqat
Published: June 2021

The development of a high solar energy penetrated power system requires considerable flexibility to hedge the risk of solar power curtailment and power shortage. This paper explores how the generation portfolio of cascaded hydro‐photovoltaic‐pumped storage (CH‐PV‐PS) generation system will be appropriately designed to balance the overall planning costs and operational flexibility constraints. The proposed study relies on the generation expansion planning (GEP) model of the CH‐PV‐PS system, considering a full set of flexibility constraints. An index designated ramp‐capability reserve shortage (RCRS) based on the conditional value at risk (CVaR) method is introduced to quantify the risk of solar power and load uncertainty. The piecewise linearization method and triangle method are developed to accommodate the non‐linear terms in the proposed model. Finally, the case studies are conducted to demonstrate the applicability and effectiveness of the proposed model.
Multistage reaction‐diffusion equation network for image super‐resolution
Authors: Pu Xiaofeng , Wang Zengmao
Published: June 2021

Deep learning‐based models have progressed considerably in single‐image super‐resolution. A high‐resolution pattern generation task is performed at the end of convolution neural networks (CNNs) with some convolution‐based operations in these models. However, this process may be difficult because all the work is done through the remarkable learning ability of CNN without any specific learning target. Reaction‐diffusion equation (RDE) is a mechanism involved in the pattern generation process that can serve as a guide for super‐resolution. It is proposed to embed RDE into a super‐resolution network by designing a reaction‐diffusion process block (RDPB) in this study. The proposed RDPB uses Euler method for iteratively solving one particular RDE, which is determined by the parameter generated through CNN. Accordingly, this module guides and leads the CNN in generating patterns for image super‐resolution. Moreover, a multistage framework is constructed to guide each network module further. On the basis of these two designs, the multistage reaction‐diffusion equation network is proposed for image super‐resolution. Experimental results demonstrated that the proposed model can obtain findings consistent with the conclusions of state‐of‐the‐art methods with a relatively shallow structure and small model size.
Vector co‐occurrence morphological edge detection for colour image
Authors: Lu Ying , He Chunming , Yu Yu‐Feng , Xu Guoxia , Zhu Hu , Deng Lizhen
Published: June 2021

Morphological edge detection is a principal component in pattern recognition and machine vision. Traditional edge detection operators only take pixel mutual into consideration. However, the edges are influenced not only by pixel mutual but also by the boundary characteristics. Here, the vector co‐occurrence morphological edge detection operator is proposed, which takes the pixel and boundary information both into consideration. The vector co‐occurrence algorithm is exploited to resist the influence of the noise points and detect the edges from the colour image rather than the grey image. And, we lead to define a precise definition of the manner of sorting high‐dimensional data for the colour image. The experiment results always illustrate the advancement and practicability of our methods against the baseline method. In terms of experiments, the BSDS500 dataset is introduced to compare and analyse with other algorithms. Based on the standard benchmark index evaluation in the BSDS500 dataset, the ODS and AP of various algorithms are compared and analysed.
QProv: A provenance system for quantum computing
Authors: Weder Benjamin , Barzen Johanna , Leymann Frank , Salm Marie , Wild Karoline
Published: June 2021

Quantum computing promises breakthroughs in various application areas, such as machine learning, chemistry, or simulations. However, today’s quantum computers are error‐prone and have limited capabilities. This leads to various challenges when developing and executing quantum algorithms, for example, the mitigation of occurring errors or the selection of a suitable quantum computer to execute a certain quantum circuit. To address these challenges, detailed information about the quantum circuit to be executed as well as past executions, and the up‐to‐date information about the available quantum computers are required. Thus, this data must be continuously collected and stored in the long‐term, which is currently not supported. To overcome this problem, a provenance approach is introduced for quantum computing. Therefore, relevant provenance attributes that should be gathered in the area of quantum computing are identified. Furthermore, QProv, a provenance system that automatically collects the identified provenance attributes and provides them in a uniform manner to the user is introduced. Finally, a case study with the collected provenance data and corresponding use cases that can benefit from this provenance data are presented here.
On the improvement of accommodation to non-individual HRTFs via VR active learning and inclusion of a 3D room response
Authors: Poirier-Quinot David , Katz Brian F.G.
Published: June 2021

This study examines the efficiency of a training protocol using a virtual reality application designed to accelerate individual’s selection of, and accommodation to, non-individualized HRTF profiles. This training introduces three elements to hasten audio localization performance improvement: an interactive HRTF selection method, a parametric training program based on active learning, and a relatively dry room acoustic simulation designed to increase the quantity of spatial cues presented. Participants rapidly selected an HRTF (≈5 min) followed by training over three sessions of 12 min distributed over 5 days. To study the impact of the room acoustic component on localization performance evolution, participants were divided into two groups: one acting as control reference, training with only anechoic renderings, the other training in reverberant conditions. The efficiency of the training program was assessed across groups and the entire protocol was assessed through direct comparisons with results reported in previous studies. Results indicate that the proposed training program led to improved learning rates compared to that of previous studies, and that the included room response accelerated the learning process.
Analyses of multi-size particle mixing behavior in an ore pre-reduction rotary kiln by discrete element method
Authors: Liu Chenghong , Ding Xueyong
Published: June 2021

The particle distribution in pre-reduction rotary kiln directly affects the reduction process of iron ore, and in-depth understanding of the mixing behavior is helpful to improve the product quality and productivity. The present work focused on the mixed dynamics of multi-component and multi-size systems in rotary kiln using discrete element method (DEM). We first confirmed that the final particle distribution and mixing degree are independent of the initial particle distribution, and then further discussed the influence of the key operating parameters such as rotating speed, average size ratio and filling degree on mixing behavior. The size segregation pattern of three components shows that the large particles segregated to the outer region, while the small particles were concentrated in the core region, forming an annular distribution with different particle sizes. Furthermore, the results also indicate that the rotational speed and fill degree show strong influence on the mixing time and have little influence on the mixing quality. Conversely, the average size ratio significantly affects on the mixing quality. The particle segregation is suppressed and the coal and iron ore particles are well mixed together for the whole bed when the average size of coal particles is smaller than that of iron ore particle. The findings of this work provide a reference for controlling and optimizing the particle mixing process in pre-reduction rotary kiln.