bluuebunny/crossref_metadata_2025 huggingface dataset:
C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes
Authors: Mori Takahiro , Kumano Takuto , He Haibing , Watanabe Satomi , Senda Miki , Moriya Toshio , Adachi Naruhiko , Hori Sanae , Terashita Yuzu , Kawasaki Masato , Hashimoto Yoshiteru , Awakawa Takayoshi , Senda Toshiya , Abe Ikuro , Kobayashi Michihiko
Published: November 2021

C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.
Vibrationally excited molecular hydrogen production from the water photochemistry
Authors: Chang Yao , An Feng , Chen Zhichao , Luo Zijie , Zhao Yarui , Hu Xixi , Yang Jiayue , Zhang Weiqing , Wu Guorong , Xie Daiqian , Yuan Kaijun , Yang Xueming
Published: November 2021

Vibrationally excited molecular hydrogen has been commonly observed in the dense photo-dominated regions (PDRs). It plays an important role in understanding the chemical evolution in the interstellar medium. Until recently, it was widely accepted that vibrational excitation of interstellar H2 was achieved by shock wave or far-ultraviolet fluorescence pumping. Here we show a further pathway to produce vibrationally excited H2 via the water photochemistry. The results indicate that the H2 fragments identified in the O(1S) + H2(X1Σg+) channel following vacuum ultraviolet (VUV) photodissociation of H2O in the wavelength range of λ = ~100-112 nm are vibrationally excited. In particular, more than 90% of H2(X) fragments populate in a vibrational state v = 3 at λ~112.81 nm. The abundance of water and VUV photons in the interstellar space suggests that the contributions of these vibrationally excited H2 from the water photochemistry could be significant and should be recognized in appropriate interstellar chemistry models.
CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage
Authors: Conners Rebecca , McLaren Mathew , Łapińska Urszula , Sanders Kelly , Stone M. Rhia L. , Blaskovich Mark A. T. , Pagliara Stefano , Daum Bertram , Rakonjac Jasna , Gold Vicki A. M.
Published: November 2021

The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.
Endothelial deletion of SHP2 suppresses tumor angiogenesis and promotes vascular normalization
Authors: Xu Zhiyong , Guo Chunyi , Ye Qiaoli , Shi Yueli , Sun Yihui , Zhang Jie , Huang Jiaqi , Huang Yizhou , Zeng Chunlai , Zhang Xue , Ke Yuehai , Cheng Hongqiang
Published: November 2021

SHP2 mediates the activities of multiple receptor tyrosine kinase signaling and its function in endothelial processes has been explored extensively. However, genetic studies on the role of SHP2 in tumor angiogenesis have not been conducted. Here, we show that SHP2 is activated in tumor endothelia. Shp2 deletion and pharmacological inhibition reduce tumor growth and microvascular density in multiple mouse tumor models. Shp2 deletion also leads to tumor vascular normalization, indicated by increased pericyte coverage and vessel perfusion. SHP2 inefficiency impairs endothelial cell proliferation, migration, and tubulogenesis through downregulating the expression of proangiogenic SRY-Box transcription factor 7 (SOX7), whose re-expression restores endothelial function in SHP2-knockdown cells and tumor growth, angiogenesis, and vascular abnormalization in Shp2-deleted mice. SHP2 stabilizes apoptosis signal-regulating kinase 1 (ASK1), which regulates SOX7 expression mediated by c-Jun. Our studies suggest SHP2 in tumor associated endothelial cells is a promising anti-angiogenic target for cancer therapy.
A feasible route for the design and manufacture of customised respiratory protection through digital facial capture
Authors: Carter Luke N. , Reed Caroline A. , Morrell Alexander P. , Fong Anthony K. H. , Chowdhury Rayyan , Miller Ewan , Alberini Federico , Khambay Balvinder , Anand Shivana , Grover Liam M. , Coward Trevor , Addison Owen , Cox Sophie C.
Published: November 2021

The World Health Organisation has called for a 40% increase in personal protective equipment manufacturing worldwide, recognising that frontline workers need effective protection during the COVID-19 pandemic. Current devices suffer from high fit-failure rates leaving significant proportions of users exposed to risk of viral infection. Driven by non-contact, portable, and widely available 3D scanning technologies, a workflow is presented whereby a user’s face is rapidly categorised using relevant facial parameters. Device design is then directed down either a semi-customised or fully-customised route. Semi-customised designs use the extracted eye-to-chin distance to categorise users in to pre-determined size brackets established via a cohort of 200 participants encompassing 87.5% of the cohort. The user’s nasal profile is approximated to a Gaussian curve to further refine the selection in to one of three subsets. Flexible silicone provides the facial interface accommodating minor mismatches between true nasal profile and the approximation, maintaining a good seal in this challenging region. Critically, users with outlying facial parameters are flagged for the fully-customised route whereby the silicone interface is mapped to 3D scan data. These two approaches allow for large scale manufacture of a limited number of design variations, currently nine through the semi-customised approach, whilst ensuring effective device fit. Furthermore, labour-intensive fully-customised designs are targeted as those users who will most greatly benefit. By encompassing both approaches, the presented workflow balances manufacturing scale-up feasibility with the diverse range of users to provide well-fitting devices as widely as possible. Novel flow visualisation on a model face is presented alongside qualitative fit-testing of prototype devices to support the workflow methodology.
Photoplethysmography for demarcation of cutaneous squamous cell carcinoma
Authors: Rasmussen Simon Mylius , Nielsen Thomas , Hody Sofie , Hager Henrik , Schousboe Lars Peter
Published: November 2021

A video processing algorithm designed to identify cancer suspicious skin areas is presented here. It is based on video recordings of squamous cell carcinoma in the skin. Squamous cell carcinoma is a common malignancy, normally treated by surgical removal. The surgeon should always balance sufficient tissue removal against unnecessary mutilation, and therefore methods for distinction of cancer boundaries are wanted. Squamous cell carcinoma has angiogenesis and increased blood supply. Remote photoplethysmography is an evolving technique for analysis of signal variations in video recordings in order to extract vital signs such as pulsation. We hypothesize that the remote photoplethysmography signal inside the area of a squamous cell carcinoma is significantly different from the surrounding healthy skin. Based on high speed video recordings of 13 patients with squamous cell carcinoma, we have examined temporal signal differences in cancer areas versus healthy skin areas. A significant difference in temporal signal changes between cancer areas and healthy areas was found. Our video processing algorithm showed promising results encouraging further investigation to clarify how detailed distinctions can be made.
Male-biased protein expression in primordial germ cells, identified through a comparative study of UAS vectors in Drosophila
Authors: Masukawa Masaki , Ishizaki Yuki , Miura Hiroki , Hayashi Makoto , Ota Ryoma , Kobayashi Satoru
Published: November 2021

In Drosophila, three types of UAS vectors (UASt, UASp, and UASz) are currently available for use with the Gal4-UAS system. They have been used successfully in somatic cells and germline cells from ovaries. However, it remains unclear whether they are functional in the germline cells of embryos, larvae, and adult testes. In this study, we found that all three types of UAS vectors were functional in the germline cells of embryos and larvae and that the UASt and UASz vectors were active in the germline of the distal tip region in adult testes. Moreover, we observed that protein expression from the UAS vectors was male-biased in germline cells of late embryos, whereas their respective mRNA expression levels were not. Furthermore, O-propargyl-puromycin (OPP) staining revealed that protein synthesis was male-biased in these germline cells. In addition, GO terms related to translation and ribosomal maturation were significantly enriched in the male germline. These observations show that translational activity is higher in male than in female germline cells. Therefore, we propose that male-biased protein synthesis may be responsible for the sex differences observed in the early germline.
Intraepineurial fat quantification and cross-sectional area analysis of the sciatic nerve using MRI in Charcot-Marie-Tooth disease type 1A patients
Authors: Kim Hyun Su , Lee Ji Hyun , Yoon Young Cheol , Cha Min Jae , Nam Soo Hyun , Kwon Hye Mi , Kim Seonwoo , Won Hojeong , Choi Byung-Ok
Published: November 2021

The objectives of this study were to assess the fat fraction (FF) and cross-sectional area (CSA) of the sciatic nerve in Charcot-Marie-Tooth disease type 1A (CMT1A) patients using Dixon-based proton density fat quantification MRI and to elucidate its potential association with clinical parameters. Thigh MRIs of 18 CMT1A patients and 18 age- and sex-matched volunteers enrolled for a previous study were reviewed. Analyses for FF and CSA of the sciatic nerve were performed at three levels (proximal to distal). CSA and FF were compared between the two groups and among the different levels within each group. The relationship between the MRI parameters and clinical data were assessed in the CMT1A patients. The CMT1A patients showed significantly higher FF at level 3 (p = 0.0217) and significantly larger CSA at all three levels compared with the control participants (p < 0.0001). Comparisons among levels showed significantly higher FF for levels 2 and 3 than for level 1 and significantly larger CSA for level 2 compared with level 1 in CMT1A patients. CSA at level 3 correlated positively with the CMT neuropathy score version 2 (CMTNSv2). In conclusion, the sciatic nerve FF of CMT1A patients was significantly higher on level 3 compared with both the controls and the measurements taken on more proximal levels, suggesting the possibility of increased intraepineurial fat within the sciatic nerves of CMT1A patients, with a possible distal tendency. Sciatic nerve CSA at level 3 correlated significantly and positively with CMTNSv2, suggesting its potential value as an imaging marker for clinical severity.
Composition of the Frenkel–Kontorova and Ising models for investigation the magnetic properties of a ferromagnetic monolayer on a stretching substrate
Authors: Belim Sergey V. , Tikhomirov Ilya V.
Published: November 2021

In the article, computer simulation on the behavior of a ferromagnetic thin film on a non-magnetic substrate by computer simulation is performed. The substrate is described by the two-dimensional Frenkel–Kontorova potential. The Ising model is used to describe the magnetic properties of a two-dimensional ferromagnetic film. The Wolf cluster algorithm is used to model the magnetic behavior of the film. A square lattice is considered for an unperturbed ferromagnetic film. Computer simulations show that mismatch of film and substrate periods results in film splitting into regions with different atomic structures. Magnetic properties for the obtained structure have been investigated. The hysteresis loop is calculated using the Metropolis algorithm. Deformations of the substrate lead to a decrease in the phase transition temperature. The Curie temperature decreases both when the substrate is compressed and when stretched. The change in phase transition temperature depends on the decreasing rate of exchange interaction with distance and the amplitude of interaction with the substrate. When the substrate is compressed, an increase in the amplitude of the interaction between the film and the substrate results in an increase in the phase transition temperature. The opposite effect occurs when the substrate is stretched. The hysteresis loop changes its shape and parameters when the substrate is deformed. Compression and stretching of the substrate results in a decrease in coercive force. The reduction in coercive force when compressing the substrate is greater than when stretching. The magnetization of the film is reduced by deformations at a fixed temperature.
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation
Authors: Yazar Volkan , Kang Sung-Ung , Ha Shinwon , Dawson Valina L. , Dawson Ted M.
Published: November 2021

The transcriptional repressor called parkin interacting substrate (PARIS; ZNF746) was initially identified as a novel co-substrate of parkin and PINK1 that leads to Parkinson’s disease (PD) by disrupting mitochondrial biogenesis through peroxisome proliferator-activated receptor gamma (PPARγ) coactivator -1α (PGC-1α) suppression. Since its initial discovery, growing evidence has linked PARIS to defective mitochondrial biogenesis observed in PD pathogenesis. Yet, dopaminergic (DA) neuron-specific mechanistic underpinnings and genome-wide PARIS binding landscape has not been explored. We employed conditional translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines expressing human PARIS wild type (WT) or mutant (C571A). We also generated genome-wide maps of PARIS occupancy using ChIP-seq in human SH-SY5Y cells. The results demonstrated that PPARγ functions as a master regulator of PARIS-induced molecular changes at the transcriptome level, confirming that PARIS acts primarily on PGC-1α to lead to neurodegeneration in PD. Moreover, we identified that PARIS actively modulates expression of PPARγ target genes by physically binding to the promoter regions. Together, our work revealed how PARIS drives adverse effects on modulation of PPAR-γ associated gene clusters in DA neurons.
Nano-photoluminescence of natural anyon molecules and topological quantum computation
Authors: Mintairov Alexander M. , Lebedev Dmitrii V. , Vlasov Alexei S. , Orlov Alexei O. , Snider Gregory L. , Blundell Steven A.
Published: November 2021

The proposal of fault-tolerant quantum computations, which promise to dramatically improve the operation of quantum computers and to accelerate the development of the compact hardware for them, is based on topological quantum field theories, which rely on the existence in Nature of physical systems described by a Lagrangian containing a non-Abelian (NA) topological term. These are solid-state systems having two-dimensional electrons, which are coupled to magnetic-flux-quanta vortexes, forming complex particles, known as anyons. Topological quantum computing (TQC) operations thus represent a physical realization of the mathematical operations involving NA representations of a braid group Bn, generated by a set of n localized anyons, which can be braided and fused using a “tweezer” and controlled by a detector. For most of the potential TQC material systems known so far, which are 2D-electron–gas semiconductor structure at high magnetic field and a variety of hybrid superconductor/topological-material heterostructures, the realization of anyon localization versus tweezing and detecting meets serious obstacles, chief among which are the necessity of using current control, i.e., mobile particles, of the TQC operations and high density electron puddles (containing thousands of electrons) to generate a single vortex. Here we demonstrate a novel system, in which these obstacles can be overcome, and in which vortexes are generated by a single electron. This is a ~ 150 nm size many electron InP/GaInP2 self-organized quantum dot, in which molecules, consisting of a few localized anyons, are naturally formed and exist at zero external magnetic field. We used high-spatial-resolution scanning magneto-photoluminescence spectroscopy measurements of a set of the dots having five and six electrons, together with many-body quantum mechanical calculations to demonstrate spontaneous formation of the anyon magneto-electron particles (eν) having fractional charge ν = n/k, where n = 1–4 and k = 3–15 are the number of electrons and vortexes, respectively, arranged in molecular structures having a built-in (internal) magnetic field of 6–12 T. Using direct imaging of the molecular configurations we observed fusion and braiding of eν-anyons under photo-excitation and revealed the possibility of using charge sensing for their control. Our investigations show that InP/GaInP2 anyon-molecule QDs, which have intrinsic transformations of localized eν-anyons compatible with TQC operations and capable of being probed by charge sensing, are very promising for the realization of TQC.
Multichannel anodal tDCS over the left dorsolateral prefrontal cortex in a paediatric population
Authors: Splittgerber Maike , Borzikowsky Christoph , Salvador Ricardo , Puonti Oula , Papadimitriou Kiriaki , Merschformann Christoph , Biagi Maria Chiara , Stenner Tristan , Brauer Hannah , Breitling-Ziegler Carolin , Prehn-Kristensen Alexander , Krauel Kerstin , Ruffini Giulio , Pedersen Anya , Nees Frauke , Thielscher Axel , Dempfle Astrid , Siniatchkin Michael , Moliadze Vera
Published: November 2021

Methodological studies investigating transcranial direct current stimulation (tDCS) over the left dorsolateral prefrontal cortex (lDLPFC) in paediatric populations are limited. Therefore, we investigated in a paediatric population whether stimulation success of multichannel tDCS over the lDLPFC depends on concurrent task performance and individual head anatomy. In a randomised, sham-controlled, double-blind crossover study 22 healthy participants (10–17 years) received 2 mA multichannel anodal tDCS (atDCS) over the lDLPFC with and without a 2-back working memory (WM) task. After stimulation, the 2-back task and a Flanker task were performed. Resting state and task-related EEG were recorded. In 16 participants we calculated the individual electric field (E-field) distribution. Performance and neurophysiological activity in the 2-back task were not affected by atDCS. atDCS reduced reaction times in the Flanker task, independent of whether atDCS had been combined with the 2-back task. Flanker task related beta oscillation increased following stimulation without 2-back task performance. atDCS effects were not correlated with the E-field. We found no effect of multichannel atDCS over the lDLPFC on WM in children/adolescents but a transfer effect on interference control. While this effect on behaviour was independent of concurrent task performance, neurophysiological activity might be more sensitive to cognitive activation during stimulation. However, our results are limited by the small sample size, the lack of an active control group and variations in WM performance.
Accurate interpretation of genetic variants in sudden unexpected death in infancy by trio-targeted gene-sequencing panel analysis
Authors: Shingu Keita , Murase Takehiko , Yamamoto Takuma , Abe Yuki , Shinba Yoriko , Mitsuma Masahide , Umehara Takahiro , Yamashita Hiromi , Ikematsu Kazuya
Published: November 2021

In sudden unexpected death in infancy cases, postmortem genetic analysis with next-generation sequencing potentially can extract candidate genes associated with sudden death. However, it is difficult to accurately interpret the clinically significant genetic variants. The study aim was to conduct trio analysis of cases of sudden unexpected death in infancy and their parents to more accurately interpret the clinically significant disease-associated gene variants associated with cause of death. From the TruSight One panel targeting 4813 genes we extracted candidate genetic variants of 66 arrhythmia-, 63 inherited metabolic disease-, 81 mitochondrial disease-, and 6 salt-losing tubulopathy-related genes in 7 cases and determined if they were de novo or parental-derived variants. Thirty-four parental-derived variants and no de novo variants were found, but none appeared to be related to the cause of death. Using trio analysis and an in silico algorithm to analyze all 4813 genes, we identified OBSCN of compound heterozygous and HCCS of hemizygous variants as new candidate genetic variants related to cause of death. Genetic analysis of these deceased infants and their living parents can provide more accurate interpretation of the clinically significant genetic variants than previously possible and help confirm the cause of death.
Expression of truncated Kir6.2 promotes insertion of functionally inverted ATP-sensitive K+ channels
Authors: Heitz Benjamin A. , Bränström Robert , Yang Wei , Huang Yiding , Moede Tilo , Leibiger Ingo B. , Leibiger Barbara , Chen Liu Qi , Yu Jia , Yang Shao-Nian , Larsson Olof , Saavedra S. Scott , Berggren Per-Olof , Aspinwall Craig A.
Published: November 2021

ATP-sensitive K+ (KATP) channels couple cellular metabolism to electrical activity in many cell types. Wild-type KATP channels are comprised of four pore forming (Kir6.x) and four regulatory (sulfonylurea receptor, SURx) subunits that each contain RKR endoplasmic reticulum retention sequences that serve to properly translocate the channel to the plasma membrane. Truncated Kir6.x variants lacking RKR sequences facilitate plasma membrane expression of functional Kir6.x in the absence of SURx; however, the effects of channel truncation on plasma membrane orientation have not been explored. To investigate the role of truncation on plasma membrane orientation of ATP sensitive K+ channels, three truncated variants of Kir6.2 were used (Kir6.2ΔC26, 6xHis-Kir6.2ΔC26, and 6xHis-EGFP-Kir6.2ΔC26). Oocyte expression of Kir6.2ΔC26 shows the presence of a population of inverted inserted channels in the plasma membrane, which is not present when co-expressed with SUR1. Immunocytochemical staining of intact and permeabilized HEK293 cells revealed that the N-terminus of 6xHis-Kir6.2ΔC26 was accessible on both sides of the plasma membrane at roughly equivalent ratios, whereas the N-terminus of 6xHis-EGFP-Kir6.2Δ26 was only accessible on the intracellular face. In HEK293 cells, whole-cell electrophysiological recordings showed a ca. 50% reduction in K+ current upon addition of ATP to the extracellular solution for 6xHis-Kir6.2ΔC26, though sensitivity to extracellular ATP was not observed in 6xHis-EGFP-Kir6.2ΔC26. Importantly, the population of channels that is inverted exhibited similar function to properly inserted channels within the plasma membrane. Taken together, these data suggest that in the absence of SURx, inverted channels can be formed from truncated Kir6.x subunits that are functionally active which may provide a new model for testing pharmacological modulators of Kir6.x, but also indicates the need for added caution when using truncated Kir6.2 mutants.
Biomarkers of subclinical atherosclerosis in patients with psoriasis
Authors: Kaiser Hannah , Wang Xing , Kvist-Hansen Amanda , Krakauer Martin , Gørtz Peter Michael , McCauley Benjamin D. , Skov Lone , Becker Christine , Hansen Peter Riis
Published: November 2021

Psoriasis is linked with increased risk of cardiovascular disease (CVD) that is underestimated by traditional risk stratification. We conducted a large-scale plasma proteomic analysis by use of a proximity extension assay in 85 patients with a history of moderate-to-severe psoriasis with or without established atherosclerotic CVD. Differentially expressed proteins associated with CVD were correlated with subclinical atherosclerotic markers including vascular inflammation determined by18F-fluorodeoxyglucose positron emission tomography/computed tomography, carotid intima-media thickness (CIMT), carotid artery plaques, and coronary artery calcium score (CCS) in the patients without CVD and statin treatment. We also examined the association between the neutrophil-to-lymphocyte ratio (NLR) and subclinical atherosclerosis. In unadjusted analyses, growth differentiation factor-15 (GDF-15) levels and NLR were increased, while tumor necrosis factor (TNF)-related activation-inducing ligand (TRANCE) and TNF-related apoptosis-induced ligand (TRAIL) levels were decreased in patients with established CVD compared to those without CVD. Among patients with psoriasis without CVD and statin treatment, GDF-15 levels were negatively associated with vascular inflammation in the ascending aorta and entire aorta, and positively associated with CIMT and CCS. NLR was positively associated with vascular inflammation in the carotid arteries. Our data suggest that circulating GDF-15 levels and NLR might serve as biomarkers of subclinical atherosclerosis in patients with psoriasis.
Peptide barcoding for one-pot evaluation of sequence–function relationships of nanobodies
Authors: Matsuzaki Yusei , Aoki Wataru , Miyazaki Takumi , Aburaya Shunsuke , Ohtani Yuta , Kajiwara Kaho , Koike Naoki , Minakuchi Hiroyoshi , Miura Natsuko , Kadonosono Tetsuya , Ueda Mitsuyoshi
Published: November 2021

Optimisation of protein binders relies on laborious screening processes. Investigation of sequence–function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence–function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody–antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence–function relationships.
Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown
Authors: Munis Altar M. , Andersson Monique , Mobbs Alexander , Hyde Stephen C. , Gill Deborah R.
Published: November 2021

Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.
Genomic surveillance of enterovirus associated with aseptic meningitis cases in southern Spain, 2015–2018
Authors: Gámbaro Fabiana , Pérez Ana Belén , Agüera Eduardo , Prot Matthieu , Martínez-Martínez Luis , Cabrerizo María , Simon-Loriere Etienne , Fernandez-Garcia Maria Dolores
Published: November 2021

New circulating Enterovirus (EV) strains often emerge through recombination. Upsurges of recombinant non-polio enteroviruses (NPEVs) associated with neurologic manifestations such as EVA71 or Echovirus 30 (E30) are a growing public health concern in Europe. Only a few complete genomes of EVs circulating in Spain are available in public databases, making it difficult to address the emergence of recombinant EVs, understand their evolutionary relatedness and the possible implication in human disease. We have used metagenomic (untargeted) NGS to generate full-length EV genomes from CSF samples of EV-positive aseptic meningitis cases in Southern Spain between 2015 and 2018. Our analyses reveal the co-circulation of multiple Enterovirus B (EV-B) types (E6, E11, E13 and E30), including a novel E13 recombinant form. We observed a genetic turnover where emergent lineages (C1 for E6 and I [tentatively proposed in this study] for E30) replaced previous lineages circulating in Spain, some concomitant with outbreaks in other parts of Europe. Metagenomic sequencing provides an effective approach for the analysis of EV genomes directly from PCR-positive CSF samples. The detection of a novel, disease-associated, recombinant form emphasizes the importance of genomic surveillance to monitor spread and evolution of EVs.
Quantitative analysis of binary and ternary organo-mineral solid dispersions by Raman spectroscopy for robotic planetary exploration missions on Mars
Authors: Demaret L. , Hutchinson I. B. , Eppe G. , Malherbe C.
Published: November 2021

Simultaneous quantification of organics and minerals in crushed rock mixtures relevant to Mars exploration using Raman spectroscopy considering experimental constraints associated with the ExoMars mission.
Two-photon fluorogenic probe for visualizing PGP-1 activity in inflammatory tissues and serum from patients
Authors: Bai Hua , Fang Bin , Wang Xujie , Qin Wenjing , Chen Yuhe , Zhang Dongliang , Li Yan , Peng Bo , Yang Xuekang , Fu Li , Li Lin
Published: November 2021

Picking PGP-1: a novel TP fluorogenic probe (BH1) was used to successfully detect the activities of endogenous PGP-1 in serum/skin tissues from clinical patients.
The mutual interactions of RNA, counterions and water – quantifying the electrostatics at the phosphate–water interface
Authors: Fingerhut Benjamin Philipp
Published: November 2021

Recent progress in the understanding of the electrostatics at the biological phosphate–water interface establishes the interaction strength with water molecules and counterions, the relevant fluctuation timescales and the spatial reach of interactions.
Tuning the structure of cerium phosphate nanorods
Authors: Allen Lisa , Davies-Jones Josh A. , Davies Philip R. , King Sarah , O'Reilly Padraic
Published: November 2021

The one-pot, shape selective synthesis of cerium phosphate nanorods has been explored and developed to give nanoparticles with aspect ratios between 3–24.8.
In situ SERS monitoring of photocatalysts by Au-decorated Fe3O4@TiO2 nanocomposites: novel perspectives and insights
Authors: Jin Sila , Park Eungyeong , Guo Shuang , Park Yeonju , Chen Lei , Jung Young Mee
Published: November 2021

The design and preparation of multifunctional nanomaterials are very important for photocatalytic research.
Vibrational energy relaxation of a diatomic molecule in a superfluid helium nanodroplet: influence of the nanodroplet size, interaction energy and energy gap
Authors: Blancafort-Jorquera Miquel , González Miguel
Published: November 2021

The influence of the nanodroplet size, interaction potential energy and vibrational energy gap on the vibrational energy relaxation of a diatomic molecule in a superfluid helium nanodroplet has been studied theoretically for the first time.
Haeckelite phosphorus: an emerging 2D allotrope of phosphorus for potential use in LIBs/SIBs
Authors: Barik Gayatree , Pal Sourav
Published: November 2021

A large surface-to-volume ratio is an essential feature of 2D materials used in many potential electronic applications.
Second harmonic generation-based nonlinear plasmonic RI-sensing in solution: the pivotal role of the particle size
Authors: Verma Mrigank Singh , Chandra Manabendra
Published: November 2021

Here, we demonstrate the utility of the second harmonic generation (SHG) for refractometric sensing in the solution phase.
Protein confinement fine-tunes aggregation-induced emission in human serum albumin
Authors: Liang Ruibin , Das Debojyoti , Bakhtiiari Amirhossein
Published: November 2021

Human serum albumin impedes the isomerization but speeds up the cyclization of TPE-4TA, leading to aggregation-induced emission.
Recent developments in germanium containing clusters in intermetallics and nanocrystals
Authors: Kauzlarich Susan M. , Ju Zheng , Tseng Emily , Lundervold Jesse
Published: November 2021

This review connects seemingly disparate fields of intermetallics and Zintl phases with nanocluster (nanocrystal) chemistry to inform on multimetallic bonding within nanoclusters through advances in structural characterization.
Towards cost-competitive middle distillate fuels from ethanol within a market-flexible biorefinery concept
Authors: Zhang Junyan , Yoo Eunji , Davison Brian H. , Liu Dongxia , Schaidle Joshua A. , Tao Ling , Li Zhenglong
Published: November 2021

Cost-competitive middle distillate production from ethanol can be achievedviaa pathway that relies on one-step ethanol to butene-rich olefins. 1,3-Butadiene can be flexibly produced by varying the reaction atmosphere from hydrogen to inert.
Acidic metal–organic framework empowered precise hydrodeoxygenation of bio-based furan compounds and cyclic ethers for sustainable fuels
Authors: Liu Dong-Huang , He Hai-Long , Wang Jun-Jie , Zhou Si-Yu , Zeng Tengwu , Gao Xiang-Yu , Xiao Yao , Yi Xianfeng , Zheng Anmin , Zhang Yue-Biao , Li Zhi
Published: November 2021

Mechanical mixture of Pd/C and a metal–organic framework-based nanoporous solid acid enables the precise hydrodeoxygenation of bio-based furan compounds and cyclic ethers towards sustainable, low carbon-footprint, and low pollution aviation fuels.
Photo-induced direct alkynylation of methane and other light alkanes by iron catalysis
Authors: Jin Yunhe , Wang Lifang , Zhang Qingqing , Zhang Yongqiang , Liao Qian , Duan Chunying
Published: November 2021

An iron-catalysed photoredox alkynylation of methane, ethane, and other light alkanes is developed as a concise and efficient approach to valuable internal alkyne synthesis.
Enzymatic degradation of synthetic polyisoprenes via surfactant-free polymer emulsification
Authors: Adjedje Vico K. B. , Schell Eugen , Wolf Yannick L. , Laub Annegret , Weissenborn Martin J. , Binder Wolfgang H.
Published: November 2021

A bioinspired emulsification strategy resulted in substantially increased enzymatic activities in the degradation of synthetic polyisoprene with the latex clearing protein LcpK30, even with cis : trans ratios of 56 : 27.
Ruthenium nanoparticles supported on S-doped graphene as an efficient HER electrocatalyst
Authors: Jia Hai-Lang , Guo Cheng-Lin , Chen Rui-Xin , Zhao Jiao , Liu Rui , Guan Ming-Yun
Published: November 2021

An efficient HER catalyst was prepared by doping graphene and wrapping ruthenium nanoparticles, and its performance is comparable to that of commercial Pt/C.
Diboron-controlled product selectivity switch in copper-catalyzed decarboxylative substitutions of alkynyl cyclic carbonates
Authors: Pei Guojing , Chen Hui , Xu Wan , Chen Tao , Li Juan
Published: November 2021

DFT calculations were performed to explore the mechanisms, origins of diboron-controlled divergent product selectivity and stereoselectivity in the copper-catalyzed decarboxylative substitution of alkynyl cyclic carbonates.
Condensation of pyrylium salts with mixed anhydrides: aryl ethers, aryl amines and sterically congested aromatics
Authors: Grabowski Daniel , Alef Susanne , Becker Steven , Müller Ute , Schnakenburg Gregor , Höger Sigurd
Published: November 2021

Condensation of 2,4,6-triaryl pyrylium salts with mixed anhydrides, formed in situ from α-functionalized sodium acetates and an anhydride solvent, leads in good yields to the corresponding 2,4,6-triaryl benzenes functionalized at their 1-position.
Hydroamination of ethylene with NH3 induced by non-thermal atmospheric plasma
Authors: Dieu Julien , Jérôme François , Batiot-Dupeyrat Catherine
Published: November 2021

We show here that non-thermal atmospheric plasma induces the cleavage of the N–H bond of NH3 to form aminium radicals, which then add onto ethylene to form ethylamine in 17% yield.
Uncommon carbene insertion reactions
Authors: Huang Ming-Yao , Zhu Shou-Fei
Published: November 2021

Transition-metal-catalysed carbene insertion reaction is a straightforward and efficient protocol for the construction of carbon–carbon or carbon–heteroatom bonds.
Carbon–carbon bond activation by B(OMe)3/B2pin2-mediated fragmentation borylation
Authors: Wang Li , Zhong Qi , Zou Youliang , Yin Youzhi , Wu Aizhen , Chen Quan , Zhang Ke , Jiang Jiachen , Zhao Mengzhen , Zhang Hua
Published: November 2021

Non-polar unstrained Csp2–Csp3and Csp2–Csp2bond activation was achievedviaB(OMe)3/B2pin2-mediated fragmentation borylation, in which C–C bond activation occurred regioselectively at the C2-position in various substituted indoles.
Engineering structural defects into a covalent organic framework for enhanced photocatalytic activity
Authors: Wang Jixian , Tian Xin-Xin , Yu Lei , Young David J. , Wang Wen-Bao , Li Hai-Yan , Li Hong-Xi
Published: November 2021

Defect engineering of a β-ketoenamine-linked COF enhances its photocatalytic hydrogen evolution performance by enhancing charge separation efficiency and improving transport of electrons.
Revealing the crystal structures and relative dielectric constants of fluorinated silicon oxides
Authors: Xue Pengyan , Feng Junwei , Xie Congwei , Wang Lan , Tudi Abudukadi , Tikhonov Evgenii V. , Butler Keith T.
Published: November 2021

In this work, we show that the levels of fluorine doped into silica are high enough and we have predicted some hitherto unknown fluorinated silica with expected properties.
Extended π-conjugated cores on arylamine derivative-based hole-transporting materials for perovskite solar cells: theoretical design and experimental research
Authors: Chen Qian , Liu Hongyuan , Cheng Puhang , Liu Xiaorui
Published: November 2021

A potential theoretical model was provided for designing three triphenylamine derivative-based hole-transporting materials with different conjugated π-bridge cores, and the promising CQ4 was synthesized for perovskite solar cell applications.
Recent advances in PTP1B signaling in metabolism and cancer
Authors: Villamar-Cruz Olga , Loza-Mejía Marco A. , Arias-Romero Luis E. , Camacho-Arroyo Ignacio
Published: November 2021

Protein tyrosine phosphorylation is one of the major post-translational modifications in eukaryotic cells and represents a critical regulatory mechanism of a wide variety of signaling pathways. Aberrant protein tyrosine phosphorylation has been linked to various diseases, including metabolic disorders and cancer. Few years ago, protein tyrosine phosphatases (PTPs) were considered as tumor suppressors, able to block the signals emanating from receptor tyrosine kinases. However, recent evidence demonstrates that misregulation of PTPs activity plays a critical role in cancer development and progression. Here, we will focus on PTP1B, an enzyme that has been linked to the development of type 2 diabetes and obesity through the regulation of insulin and leptin signaling, and with a promoting role in the development of different types of cancer through the activation of several pro-survival signaling pathways. In this review, we discuss the molecular aspects that support the crucial role of PTP1B in different cellular processes underlying diabetes, obesity and cancer progression, and its visualization as a promising therapeutic target.
Hierarchical optimization: A hybrid processing for downlink massive MU‐MIMO mmWave systems
Authors: Ortega Alvaro Javier
Published: November 2021

Communications using the millimeter wave (mmWave) spectrum are a mainstream technology of the next generation systems due to their huge available bandwidth. However, the mmWave band will experience much more propagation loss than a low‐frequency band. Conventional precoding techniques are impractical in mmWave scenarios due to manufacturing costs and power consumption. Hybrid alternatives have been considered as a promising technology to provide a compromise between hardware complexity and system performance by reducing the number of radio‐frequency (RF) chains. In this paper, a hybrid processing design for downlink in mmWave scenarios is proposed, where the number of RF chains is reduced to the number of data streams. The precodification process is made by a three‐stage‐based hybrid precoder, whereas in the terminals, the equalization process only requires a low complex analog combiner. The three stages of the hybrid precoder are designed by a hierarchical strategy. The first stage addresses the phase shifters aiming to maximize the sum‐rate system, whereas the second and third stages are dedicated to mitigating the inter‐user interference effects. The proposed methodology gets a robust signal processing that can greatly mitigate the side effects of hardware reduction. Numerical results in terms of bit error rate (BER) and sum‐rate evidence that the proposed method not only overcomes other hybrid precoders/combiners but also reaches the same performance as a fully digital technique in some scenarios.
Feature fusion for inverse synthetic aperture radar image classification via learning shared hidden space
Authors: Lin Wenhao , Gao Xunzhang
Published: November 2021

Multi‐sensor fusion recognition is a meaningful task in ISAR image recognition. Compared with a single sensor, multi‐sensor fusion can provide richer target information, which is conducive to more accurate and robust identification. However, previous deep learning‐based fusion methods do not effectively deal with the redundancy and complementarity of information between different sources. In this letter, we construct a shared hidden space to align features from different sources. Accordingly, we design an end‐to‐end deep fusion framework to fuse dual ISAR images at the feature level. For combining the multi‐source information, deep generalised canonical correlation analysis (DGCCA) is used as the loss item to map features extracted from dual input onto the shared hidden space. Moreover, we propose an efficient and lightweight spatial attention module, named united attention module, which can be embedded between dual‐stream convolutional neural networks (CNNs) to promote DGCCA optimisation by information interaction. Compared with other deep fusion frameworks, our model obtains the competitive performance in ISAR image fusion for classification.
Probabilistic classification of X-ray sources applied to Swift-XRT and XMM-Newton catalogs
Authors: Tranin Hugo , Godet Olivier , Webb Natalie , Primorac Daria
Published: November 2021

Context. Serendipitous X-ray surveys have proven to be an efficient way to find rare objects, for example tidal disruption events, changing-look active galactic nuclei (AGN), binary quasars, ultraluminous X-ray sources, and intermediate mass black holes. With the advent of very large X-ray surveys, an automated classification of X-ray sources becomes increasingly valuable.

Aims. This work proposes a revisited naive Bayes classification of the X-ray sources in the Swift-XRT and XMM-Newton catalogs into four classes – AGN, stars, X-ray binaries (XRBs), and cataclysmic variables (CVs) – based on their spatial, spectral, and timing properties and their multiwavelength counterparts. An outlier measure is used to identify objects of other natures. The classifier is optimized to maximize the classification performance of a chosen class (here XRBs), and it is adapted to data mining purposes.

Methods. We augmented the X-ray catalogs with multiwavelength data, source class, and variability properties. We then built a reference sample of about 25 000 X-ray sources of known nature. From this sample, the distribution of each property was carefully estimated and taken as reference to assign probabilities of belonging to each class. The classification was then performed on the whole catalog, combining the information from each property.

Results. Using the algorithm on the Swift reference sample, we retrieved 99%, 98%, 92%, and 34% of AGN, stars, XRBs, and CVs, respectively, and the false positive rates are 3%, 1%, 9%, and 15%. Similar results are obtained on XMM sources. When applied to a carefully selected test sample, representing 55% of the X-ray catalog, the classification gives consistent results in terms of distributions of source properties. A substantial fraction of sources not belonging to any class is efficiently retrieved using the outlier measure, as well as AGN and stars with properties deviating from the bulk of their class. Our algorithm is then compared to a random forest method; the two showed similar performances, but the algorithm presented in this paper improved insight into the grounds of each classification.

Conclusions. This robust classification method can be tailored to include additional or different source classes and can be applied to other X-ray catalogs. The transparency of the classification compared to other methods makes it a useful tool in the search for homogeneous populations or rare source types, including multi-messenger events. Such a tool will be increasingly valuable with the development of surveys of unprecedented size, such as LSST, SKA, and Athena, and the search for counterparts of multi-messenger events.