bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis of ribosomal RNA transcription regulation
Authors: Shin Yeonoh , Qayyum M. Zuhaib , Pupov Danil , Esyunina Daria , Kulbachinskiy Andrey , Murakami Katsuhiko S. 
Published: January 2021

AbstractRibosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β’ lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.
A functional family of fluorescent nucleotide analogues to investigate actin dynamics and energetics
Authors: Colombo Jessica , Antkowiak Adrien , Kogan Konstantin , Kotila Tommi , Elliott Jenna , Guillotin Audrey , Lappalainen Pekka , Michelot Alphée 
Published: January 2021

AbstractActin polymerization provides force for vital processes of the eukaryotic cell, but our understanding of actin dynamics and energetics remains limited due to the lack of high-quality probes. Most current probes affect dynamics of actin or its interactions with actin-binding proteins (ABPs), and cannot track the bound nucleotide. Here, we identify a family of highly sensitive fluorescent nucleotide analogues structurally compatible with actin. We demonstrate that these fluorescent nucleotides bind to actin, maintain functional interactions with a number of essential ABPs, are hydrolyzed within actin filaments, and provide energy to power actin-based processes. These probes also enable monitoring actin assembly and nucleotide exchange with single-molecule microscopy and fluorescence anisotropy kinetics, therefore providing robust and highly versatile tools to study actin dynamics and functions of ABPs.
Spin blockade and phonon bottleneck for hot electron relaxation observed in n-doped colloidal quantum dots
Authors: Wang Junhui , Wang Lifeng , Yu Shuwen , Ding Tao , Xiang Dongmei , Wu Kaifeng 
Published: January 2021

AbstractUnderstanding and manipulating hot electron dynamics in semiconductors may enable disruptive energy conversion schemes. Hot electrons in bulk semiconductors usually relax via electron-phonon scattering on a sub-picosecond timescale. Quantum-confined semiconductors such as quantum dots offer a unique platform to prolong hot electron lifetime through their size-tunable electronic structures. Here, we study hot electron relaxation in electron-doped (n-doped) colloidal CdSe quantum dots. For lightly-doped dots we observe a slow 1Pe hot electron relaxation (~10 picosecond) resulting from a Pauli spin blockade of the preoccupying 1Se electron. For heavily-doped dots, a large number of electrons residing in the surface states introduce picosecond Auger recombination which annihilates the valance band hole, allowing us to observe 300-picosecond-long hot electrons as a manifestation of a phonon bottleneck effect. This brings the hot electron energy loss rate to a level of sub-meV per picosecond from a usual level of 1 eV per picosecond. These results offer exciting opportunities of hot electron harvesting by exploiting carrier-carrier, carrier-phonon and spin-spin interactions in doped quantum dots.
Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules
Authors: Szalai Alan M. , Siarry Bruno , Lukin Jerónimo , Williamson David J. , Unsain Nicolás , Cáceres Alfredo , Pilo-Pais Mauricio , Acuna Guillermo , Refojo Damián , Owen Dylan M. , Simoncelli Sabrina , Stefani Fernando D. 
Published: January 2021

AbstractSingle-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule’s image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope. SIMPLER requires no hardware modification whatsoever to a conventional total internal reflection fluorescence microscope and complements any 2D single-molecule localization microscopy method to deliver 3D images with nearly isotropic nanometric resolution. Performance examples include SIMPLER-direct stochastic optical reconstruction microscopy images of the nuclear pore complex with sub-20 nm axial localization precision and visualization of microtubule cross-sections through SIMPLER-DNA points accumulation for imaging in nanoscale topography with sub-10 nm axial localization precision.
Emr1 regulates the number of foci of the endoplasmic reticulum-mitochondria encounter structure complex
Authors: Rasul Faiz , Zheng Fan , Dong Fenfen , He Jiajia , Liu Ling , Liu Wenyue , Cheema Javairia Yousuf , Wei Wenfan , Fu Chuanhai 
Published: January 2021

AbstractThe endoplasmic reticulum-mitochondria encounter structure (ERMES) complex creates contact sites between the endoplasmic reticulum and mitochondria, playing crucial roles in interorganelle communication, mitochondrial fission, mtDNA inheritance, lipid transfer, and autophagy. The mechanism regulating the number of ERMES foci within the cell remains unclear. Here, we demonstrate that the mitochondrial membrane protein Emr1 contributes to regulating the number of ERMES foci. We show that the absence of Emr1 significantly decreases the number of ERMES foci. Moreover, we find that Emr1 interacts with the ERMES core component Mdm12 and colocalizes with Mdm12 on mitochondria. Similar to ERMES mutant cells, cells lacking Emr1 display defective mitochondrial morphology and impaired mitochondrial segregation, which can be rescued by an artificial tether capable of linking the endoplasmic reticulum and mitochondria. We further demonstrate that the cytoplasmic region of Emr1 is required for regulating the number of ERMES foci. This work thus reveals a crucial regulatory protein necessary for ERMES functions and provides mechanistic insights into understanding the dynamic regulation of endoplasmic reticulum-mitochondria communication.
Deterministic spin-photon entanglement from a trapped ion in a fiber Fabry–Perot cavity
Authors: Kobel Pascal , Breyer Moritz , Köhl Michael 
Published: January 2021

AbstractThe development of efficient network nodes is a key element for the realization of quantum networks which promise great capabilities as distributed quantum computing or provable secure communication. We report the realization of a quantum network node using a trapped ion inside a fiber-based Fabry–Perot cavity. We show the generation of deterministic entanglement at a high fidelity of 90.1(17)% between a trapped Yb ion and a photon emitted into the resonator mode. We achieve a success probability for generation and detection of entanglement for a single shot of 2.5 × 10−3 resulting in 62 Hz entanglement rate.
Factors affecting the onset and progression of rotator cuff tears in the general population
Authors: Ichinose Tsuyoshi , Shitara Hitoshi , Tajika Tsuyoshi , Kobayashi Tsutomu , Yamamoto Atsushi , Hamano Noritaka , Sasaki Tsuyoshi , Shimoyama Daisuke , Kamiyama Masataka , Miyamoto Ryosuke , Takagishi Kenji , Chikuda Hirotaka 
Published: January 2021

AbstractWhile previous studies have revealed factors affecting the progression of rotator cuff tear (RCT), none have yet described factors affecting its onset. The purpose of this longitudinal observational study was to analyze factors affecting the RCT onset and progression in the general population. The present study included 185 shoulders from 93 participants who completed all the examinations in both 2012 and 2017. Participants received a questionnaire with age, gender, arm dominance, and presence of pain at rest, in motion, and at night. The range of motion (ROM), simple shoulder test (SST) were also examined. Anteroposterior radiograph of the shoulder joint was performed to evaluate the degree of osteoarthritic changes by the Samilson-Prieto (S-P) classification. The degree of RCT was examined by ultrasonography. There were 132 shoulders without RCT and 53 with RCT in 2012. RCT occurred in 21 of 132 shoulders, and the factor affecting the RCT onset was S-P grade 2 osteoarthritic change in 2012 (odds ratio [OR] 10.10). RCT progressed in 22 of 53 shoulders, and the factor affecting RCT progression was the presence of motion pain in 2012 (OR 13.76). These results added new knowledge regarding the natural course of RCT onset and progression.
Septohippocampal transmission from parvalbumin-positive neurons features rapid recovery from synaptic depression
Authors: Yi Feng , Garrett Tavita , Deisseroth Karl , Haario Heikki , Stone Emily , Lawrence J. Josh 
Published: January 2021

AbstractParvalbumin-containing projection neurons of the medial-septum-diagonal band of Broca ($$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

) are essential for hippocampal rhythms and learning operations yet are poorly understood at cellular and synaptic levels. We combined electrophysiological, optogenetic, and modeling approaches to investigate $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

neuronal properties. $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

neurons had intrinsic membrane properties distinct from acetylcholine- and somatostatin-containing MS-DBB subtypes. Viral expression of the fast-kinetic channelrhodopsin ChETA-YFP elicited action potentials to brief (1–2 ms) 470 nm light pulses. To investigate $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

transmission, light pulses at 5–50 Hz frequencies generated trains of inhibitory postsynaptic currents (IPSCs) in CA1 stratum oriens interneurons. Using a similar approach, optogenetic activation of local hippocampal PV ($$\hbox {PV}_{\text{HC}}$$

PV
HC

) neurons generated trains of $$\hbox {PV}_{\text{HC}}$$

PV
HC

-mediated IPSCs in CA1 pyramidal neurons. Both synapse types exhibited short-term depression (STD) of IPSCs. However, relative to $$\hbox {PV}_{\text{HC}}$$

PV
HC

synapses, $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

synapses possessed lower initial release probability, transiently resisted STD at gamma (20–50 Hz) frequencies, and recovered more rapidly from synaptic depression. Experimentally-constrained mathematical synapse models explored mechanistic differences. Relative to the $$\hbox {PV}_{\text{HC}}$$

PV
HC

model, the $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

model exhibited higher sensitivity to calcium accumulation, permitting a faster rate of calcium-dependent recovery from STD. In conclusion, resistance of $$\hbox {PV}_{\text{MS-DBB}}$$

PV
MS-DBB

synapses to STD during short gamma bursts enables robust long-range GABAergic transmission from MS-DBB to hippocampus.
Far field superlensing inside biological media through a nanorod lens using spatiotemporal information
Authors: Hajiahmadi Mohamad J. , Faraji-Dana Reza , Skrivervik Anja K. 
Published: January 2021

AbstractFar field superlensing of light has generated great attention in optical focusing and imaging applications. The capability of metamaterials to convert evanescent waves to propagative waves has led to numerous proposals in this regard. The common drawback of these approaches is their poor performance inside strongly scattering media like biological samples. Here, we use a metamaterial structure made out of aluminum nanorods in conjunction with time-reversal technique to exploit all temporal and spatial degrees of freedom for superlensing. Using broadband optics, we numerically show that this structure can perform focusing inside biological tissues with a resolution of λ/10. Moreover, for the imaging scheme we propose the entropy criterion for the image reconstruction step to reduce the number of required optical transducers. We propose an imaging scenario to reconstruct the spreading pattern of a diffusive material inside a tissue. In this way super-resolution images are obtained.
Tribo-mechanical properties evaluation of HA/TiO2/CNT nanocomposite
Authors: Zalnezhad Erfan , Musharavati F. , Chen Tianyi , Jaber Fadi , Uzun Kaan , Chowdhury Muhammad E. H. , Khandakar Amith , Liu Junxing , Bae S. 
Published: January 2021

AbstractIn this study, a combination of reverse microemulsion and hydrothermal techniques were used to synthesize HA. A hydrothermal method was used to synthesize HA/TiO2/CNT nanocomposite powders. Cold and hot isostatic pressing techniques were used to fabricate tablet-shaped samples. To investigate the biocompatibility and tribo-mechanical properties of HA/TiO2 and HA/TiO2/CNTs, four samples were prepared with different percentages of CNTs, namely, HA/TiO2 (S0), HA/TiO2/CNT (S1.0), HA/TiO2/CNT (S2.0), and HA/TiO2/CNT (S3.0). The microstructure and morphology of the HA/TiO2/CNTs were characterized by transmission electron microscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray diffraction. Hardness test results show that S3.0 displayed the highest surface hardness (285 HV) compared to other samples. The wear rate of HA/TiO2/CNT with the highest CNT content showed a decrease compared with those of the other samples. The results from nanoindentation tests showed that Young’s modulus of the S3.0 sample was 58.1% greater than that of the S0 sample. Furthermore, the human MDA-MB-231 cell line demonstrated good binding to the surface of the samples in the in-vitro biocompatibility evaluation of the HA/TiO2/CNT composites.
Deep learning-based detection of dental prostheses and restorations
Authors: Takahashi Toshihito , Nozaki Kazunori , Gonda Tomoya , Mameno Tomoaki , Ikebe Kazunori 
Published: January 2021

AbstractThe purpose of this study is to develop a method for recognizing dental prostheses and restorations of teeth using a deep learning. A dataset of 1904 oral photographic images of dental arches (maxilla: 1084 images; mandible: 820 images) was used in the study. A deep-learning method to recognize the 11 types of dental prostheses and restorations was developed using TensorFlow and Keras deep learning libraries. After completion of the learning procedure, the average precision of each prosthesis, mean average precision, and mean intersection over union were used to evaluate learning performance. The average precision of each prosthesis varies from 0.59 to 0.93. The mean average precision and mean intersection over union of this system were 0.80 and 0.76, respectively. More than 80% of metallic dental prostheses were detected correctly, but only 60% of tooth-colored prostheses were detected. The results of this study suggest that dental prostheses and restorations that are metallic in color can be recognized and predicted with high accuracy using deep learning; however, those with tooth color are recognized with moderate accuracy.
SHANK2 mutations impair apoptosis, proliferation and neurite outgrowth during early neuronal differentiation in SH-SY5Y cells
Authors: Unsicker Christine , Cristian Flavia-Bianca , von Hahn Manja , Eckstein Volker , Rappold Gudrun A. , Berkel Simone 
Published: January 2021

AbstractSHANK2 mutations have been identified in individuals with neurodevelopmental disorders, including intellectual disability and autism spectrum disorders (ASD). Using CRISPR/Cas9 genome editing, we obtained SH-SY5Y cell lines with frameshift mutations on one or both SHANK2 alleles. We investigated the effects of the different SHANK2 mutations on cell morphology, cell proliferation and differentiation potential during early neuronal differentiation. All mutant cell lines showed impaired neuronal differentiation marker expression. Cells with bi-allelic SHANK2 mutations revealed diminished apoptosis and increased proliferation, as well as decreased neurite outgrowth during early neuronal differentiation. Bi-allelic SHANK2 mutations resulted in an increase in p-AKT levels, suggesting that SHANK2 mutations impair downstream signaling of tyrosine kinase receptors. Additionally, cells with bi-allelic SHANK2 mutations had lower amyloid precursor protein (APP) expression compared to controls, suggesting a molecular link between SHANK2 and APP. Together, we can show that frameshift mutations on one or both SHANK2 alleles lead to an alteration of neuronal differentiation in SH-SY5Y cells, characterized by changes in cell growth and pre- and postsynaptic protein expression. We also provide first evidence that downstream signaling of tyrosine kinase receptors and amyloid precursor protein expression are affected.
Perceptual insensitivity to the modulation of interoceptive signals in depression, anxiety, and substance use disorders
Authors: Smith Ryan , Feinstein Justin S. , Kuplicki Rayus , Forthman Katherine L. , Stewart Jennifer L. , Paulus Martin P. ,   Tulsa 1000 Investigators, Aupperle Robin L. , Bodurka Jerzy , Savitz Jonathan B. , Victor Teresa A. , Khalsa Sahib S. 
Published: January 2021

AbstractThis study employed a series of heartbeat perception tasks to assess the hypothesis that cardiac interoceptive processing in individuals with depression/anxiety (N = 221), and substance use disorders (N = 136) is less flexible than that of healthy individuals (N = 53) in the context of physiological perturbation. Cardiac interoception was assessed via heartbeat tapping when: (1) guessing was allowed; (2) guessing was not allowed; and (3) experiencing an interoceptive perturbation (inspiratory breath hold) expected to amplify cardiac sensation. Healthy participants showed performance improvements across the three conditions, whereas those with depression/anxiety and/or substance use disorder showed minimal improvement. Machine learning analyses suggested that individual differences in these improvements were negatively related to anxiety sensitivity, but explained relatively little variance in performance. These results reveal a perceptual insensitivity to the modulation of interoceptive signals that was evident across several common psychiatric disorders, suggesting that interoceptive deficits in the realm of psychopathology manifest most prominently during states of homeostatic perturbation.
Biosynthesis of CuO nanoparticles using aqueous extract of herbal tea (Stachys Lavandulifolia) flowers and evaluation of its catalytic activity
Authors: Veisi Hojat , Karmakar Bikash , Tamoradi Taiebeh , Hemmati Saba , Hekmati Malak , Hamelian Mona 
Published: January 2021

AbstractPlant derived biogenic synthesis of nanoparticles (NP) has been the recent trend in material science as featured sustainable catalysts. A great deal of the current nanocatalytic research has been oriented on the bio-inspired green catalysts based on their wide applicability. In this context, CuO NPs are synthesized following a green approach using an herbal tea (Stachys Lavandulifolia) flower extract. The phytochemicals contained in it were used asthe internal reductant without applying harsh chemicals or strong heat. The derived nanoparticles also got stabilized by the biomolecular capping. The as-synthesized CuO NPs was characterized over FT-IR, FE-SEM, EDS, TEM, XRD, TGA and UV–Vis spectroscopy. These NPs were exploited as a competent catalyst in the aryl and heteroaryl C–heteroatom (N, O, S) cross coupling reactions affording outstanding yields. The nanocatalyst was isolated and recycled in 8 consecutive runs with reproducible catalytic activity. Rigidity of the CuO/S. Lavandulifolia nanocomposite was further justified by leaching test and heterogeneity test.
Strong texture tuning along different crystalline directions in glass-supported CeO2 thin films by ultrasonic spray pyrolysis
Authors: Zumeta-Dubé Inti , García Rangel José Manuel , Roque Jorge , Romero-Ibarra Issis Claudette , García Sánchez Mario Fidel 
Published: January 2021

AbstractThe strong facet-dependent performance of glass-supported CeO2 thin films in different applications (catalysis, smart windows, etc.) has been the target of diverse fundamental and technological approaches. However, the design of accurate, cost-effective and scalable methods with the potential for large-area coverage that produce highly textured glass-supported CeO2 thin films remains a technological challenge. In the present work, it is demonstrated that under proper tuning conditions, the ultrasonic spray pyrolysis technique enables one to obtain glass-supported polycrystalline CeO2 films with noticeable texture along both the (100) and (111) directions, as well as with randomly oriented crystallites (no texture). The influence of flow rates, solution molarity, and substrate temperature on the texture and morphological characteristics, as well as optical absorption and Raman response of the deposited films, is evaluated. The obtained results are discussed on the basis of the combined dependence of the CeO2-exposed surfaces on the thermodynamic stability of the corresponding facets and the reaction kinetics, which modulate the crystallite growth direction.
Mild synthesis of isoxazoline derivatives via an efficient [4 + 1] annulation reaction of transient nitrosoalkenes and sulfur ylides
Authors: Hua Ting-Bi , Liu Cheng-Xiong , Hu Wei-Min , Wang Long , Yang Qing-Qing 
Published: January 2021

AbstractAn efficient [4 + 1] annulation between α-bromooximes and sulfur ylides via in situ generation of nitrosoalkenes under mild basic reaction conditions has been developed, providing an expeditious and scalable approach to synthesize biologically interesting isoxazoline derivatives with good to excellent yields.