bluuebunny/crossref_metadata_2025_split 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

AbstractC-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

AbstractVibrationally 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

AbstractThe 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

AbstractSHP2 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

AbstractThe 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

AbstractA 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

AbstractIn 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

AbstractThe 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

AbstractIn 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

AbstractThe 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

AbstractThe 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

AbstractMethodological 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

AbstractIn 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.