bluuebunny/crossref_metadata_2025_split huggingface dataset:
A distinct assembly pathway of the human 39S late pre-mitoribosome
Authors: Cheng Jingdong , Berninghausen Otto , Beckmann Roland 
Published: July 2021

AbstractAssembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
In-situ nanospectroscopic imaging of plasmon-induced two-dimensional [4+4]-cycloaddition polymerization on Au(111)
Authors: Shao Feng , Wang Wei , Yang Weimin , Yang Zhilin , Zhang Yao , Lan Jinggang , Dieter Schlüter A. , Zenobi Renato 
Published: July 2021

AbstractPlasmon-induced chemical reactions (PICRs) have recently become promising approaches for highly efficient light-chemical energy conversion. However, an in-depth understanding of their mechanisms at the nanoscale still remains challenging. Here, we present an in-situ investigation by tip-enhanced Raman spectroscopy (TERS) imaging of the plasmon-induced [4+4]-cycloaddition polymerization within anthracene-based monomer monolayers physisorbed on Au(111), and complement the experimental results with density functional theory (DFT) calculations. This two-dimensional (2D) polymerization can be flexibly triggered and manipulated by the hot carriers, and be monitored simultaneously by TERS in real time and space. TERS imaging provides direct evidence for covalent bond formation with ca. 3.7 nm spatial resolution under ambient conditions. Combined with DFT calculations, the TERS results demonstrate that the lateral polymerization on Au(111) occurs by a hot electron tunneling mechanism, and crosslinks form via a self-stimulating growth mechanism. We show that TERS is promising to be plasmon-induced nanolithography for organic 2D materials.
Unfolding the multiscale structure of networks with dynamical Ollivier-Ricci curvature
Authors: Gosztolai Adam , Arnaudon Alexis 
Published: July 2021

AbstractDescribing networks geometrically through low-dimensional latent metric spaces has helped design efficient learning algorithms, unveil network symmetries and study dynamical network processes. However, latent space embeddings are limited to specific classes of networks because incompatible metric spaces generally result in information loss. Here, we study arbitrary networks geometrically by defining a dynamic edge curvature measuring the similarity between pairs of dynamical network processes seeded at nearby nodes. We show that the evolution of the curvature distribution exhibits gaps at characteristic timescales indicating bottleneck-edges that limit information spreading. Importantly, curvature gaps are robust to large fluctuations in node degrees, encoding communities until the phase transition of detectability, where spectral and node-clustering methods fail. Using this insight, we derive geometric modularity to find multiscale communities based on deviations from constant network curvature in generative and real-world networks, significantly outperforming most previous methods. Our work suggests using network geometry for studying and controlling the structure of and information spreading on networks.
Vaccination as a preventative measure contributing to immune fitness
Authors: Laupèze Béatrice , Del Giudice Giuseppe , Doherty Mark T. , Van der Most Robbert 
Published: July 2021

AbstractThe primary goal of vaccination is the prevention of pathogen-specific infection. The indirect consequences may include maintenance of homeostasis through prevention of infection-induced complications; trained immunity that re-programs innate cells to respond more efficiently to later, unrelated threats; slowing or reversing immune senescence by altering the epigenetic clock, and leveraging the pool of memory B and T cells to improve responses to new infections. Vaccines may exploit the plasticity of the immune system to drive longer-term immune responses that promote health at a broader level than just the prevention of single, specific infections. In this perspective, we discuss the concept of “immune fitness” and how to potentially build a resilient immune system that could contribute to better health. We argue that vaccines may contribute positively to immune fitness in ways that are only beginning to be understood, and that life-course vaccination is a fundamental tool for achieving healthy aging.
Fast and scalable likelihood maximization for Exponential Random Graph Models with local constraints
Authors: Vallarano Nicolò , Bruno Matteo , Marchese Emiliano , Trapani Giuseppe , Saracco Fabio , Cimini Giulio , Zanon Mario , Squartini Tiziano 
Published: July 2021

AbstractExponential Random Graph Models (ERGMs) have gained increasing popularity over the years. Rooted into statistical physics, the ERGMs framework has been successfully employed for reconstructing networks, detecting statistically significant patterns in graphs, counting networked configurations with given properties. From a technical point of view, the ERGMs workflow is defined by two subsequent optimization steps: the first one concerns the maximization of Shannon entropy and leads to identify the functional form of the ensemble probability distribution that is maximally non-committal with respect to the missing information; the second one concerns the maximization of the likelihood function induced by this probability distribution and leads to its numerical determination. This second step translates into the resolution of a system of O(N) non-linear, coupled equations (with N being the total number of nodes of the network under analysis), a problem that is affected by three main issues, i.e. accuracy, speed and scalability. The present paper aims at addressing these problems by comparing the performance of three algorithms (i.e. Newton’s method, a quasi-Newton method and a recently-proposed fixed-point recipe) in solving several ERGMs, defined by binary and weighted constraints in both a directed and an undirected fashion. While Newton’s method performs best for relatively little networks, the fixed-point recipe is to be preferred when large configurations are considered, as it ensures convergence to the solution within seconds for networks with hundreds of thousands of nodes (e.g. the Internet, Bitcoin). We attach to the paper a Python code implementing the three aforementioned algorithms on all the ERGMs considered in the present work.
Anisotropic chemical expansion due to oxygen vacancies in perovskite films
Authors: Tyunina M. , Pacherova O. , Kocourek T. , Dejneka A. 
Published: July 2021

AbstractIn scientifically intriguing and technologically important multifunctional ABO3 perovskite oxides, oxygen vacancies are most common defects. They cause lattice expansion and can alter the key functional properties. Here, it is demonstrated that contrary to weak isotropic expansion in bulk samples, oxygen vacancies produce strong anisotropic strain in epitaxial thin films. This anisotropic chemical strain is explained by preferential orientation of elastic dipoles of the vacancies. Elastic interaction of the dipoles with substrate-imposed misfit strain is suggested to define the dipolar orientation. Such elastic behavior of oxygen vacancies is anticipated to be general for perovskite films and have critical impacts on the film synthesis and response functions.
Structure and dynamics of small-scale turbulence in vaporizing two-phase flows
Authors: Boukharfane Radouan , Er-raiy Aimad , Parsani Matteo , Chakraborty Nilanjan 
Published: July 2021

AbstractImproving our fundamental understanding of multiphase turbulent flows will be beneficial for analyses of a wide range of industrial and geophysical processes. Herein, we investigate the topology of the local flow in vaporizing forced homogeneous isotropic turbulent two-phase flows. The invariants of the velocity-gradient, rate-of-strain, rate-of-rotation tensors, and scalar gradient were computed and conditioned for different distances from the liquid–gas surface. A Schur decomposition of the velocity gradient tensor into a normal and non-normal parts was undertaken to supplement the classical double decomposition into rotation and strain tensors. Using direct numerical simulations results, we show that the joint probability density functions of the second and third invariants have classical shapes in all carrier-gas regions but gradually change as they approach the carrier-liquid interface. Near the carrier-liquid interface, the distributions of the invariants are remarkably similar to those found in the viscous sublayer of turbulent wall-bounded flows. Furthermore, the alignment of both vorticity and scalar gradient with the strain-rate field changes spatially such that its universal behaviour occurs far from the liquid–gas interface. We found also that the non-normal effects of the velocity gradient tensor play a crucial role in explaining the preferred alignment.
Phonon-assisted relaxation between triplet and singlet states in a self-assembled double quantum dot
Authors: Gawarecki Krzysztof , Machnikowski Paweł 
Published: July 2021

AbstractWe study theoretically phonon-induced spin dynamics of two electrons confined in a self-assembled double quantum dot. We calculate the transition rates and time evolution of occupations for the spin-triplet and spin-singlet states. We characterize the relative importance of various relaxation channels, including two-phonon processes, as a function of the electric and magnetic fields. The simulations are based on a model combining the eight-band $$\varvec{k}\!\cdot \!\varvec{p}$$

k

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p

method and configuration-interaction approach. We show that the electron g-factor mismatch between the Zeeman doublets localized on different dots opens a relatively fast triplet-singlet phonon-assisted relaxation channel. We also demonstrate, that the relaxation near the triplet-singlet anticrossing is slowed down up to several orders of magnitude due to vanishing of some relaxation channels.
Target position and avoidance margin effects on path planning in obstacle avoidance
Authors: Saeedpour-Parizi Mohammad R. , Hassan Shirin E. , Azad Ariful , Baute Kelly J. , Baniasadi Tayebeh , Shea John B. 
Published: July 2021

AbstractThis study examined how people choose their path to a target, and the visual information they use for path planning. Participants avoided stepping outside an avoidance margin between a stationary obstacle and the edge of a walkway as they walked to a bookcase and picked up a target from different locations on a shelf. We provided an integrated explanation for path selection by combining avoidance margin, deviation angle, and distance to the obstacle. We found that the combination of right and left avoidance margins accounted for 26%, deviation angle accounted for 39%, and distance to the obstacle accounted for 35% of the variability in decisions about the direction taken to circumvent an obstacle on the way to a target. Gaze analysis findings showed that participants directed their gaze to minimize the uncertainty involved in successful task performance and that gaze sequence changed with obstacle location. In some cases, participants chose to circumvent the obstacle on a side for which the gaze time was shorter, and the path was longer than for the opposite side. Our results of a path selection judgment test showed that the threshold for participants abandoning their preferred side for circumventing the obstacle was a target location of 15 cm to the left of the bookcase shelf center.
Funneliformis mosseae inoculation under water deficit stress improves the yield and phytochemical characteristics of thyme in intercropping with soybean
Authors: Amani Machiani Mostafa , Javanmard Abdollah , Morshedloo Mohammad Reza , Aghaee Ahmad , Maggi Filippo 
Published: July 2021

AbstractIntercropping of medicinal plants/legumes along with bio-fertilizer application is a relatively new sustainable practice for improving the yield and secondary metabolites production. Here, a 2-years field experiment was performed to evaluate the effects of water deficit stress and arbuscular mycorrhizal fungi (AMF) application (as bio-fertilizer) on nutrients concentration, dry matter yield, essential oil quantity and quality of thyme in intercropping with soybean. Three irrigation levels, including (i) irrigation after depletion of 20% (I20) as non-stressed, 50% (I50) as moderate water deficit and 80% (I80) available water as severe water deficit were applied as the main factor. The sub-factor was represented by different cropping patterns including thyme sole culture, replacement intercrop ratio of 50:50 and 66:34 (soybean: thyme) and the third factor was non-usage (control) and usage of AMF. According to our results, the thyme dry yield under moderate and severe water deficit stress decreased by 35 and 44% in the first year, and by 27 and 40% in the second year compared with non-stressed (I20) plants, respectively. Also, the macro- and micro-nutrients of thyme leaves increased significantly in intercropping patterns after application of AMF. The maximum essential oil percentage of thyme was achieved in 50:50 intercropping ratio treated with AMF. Under moderate and severe water deficits, the major constituents of thyme essential oil including thymol, p-cymene and γ-terpinene were increased in intercropping patterns treated with AMF. Generally, AMF application in intercropping ratio of 50:50 may be proposed to farmers as an eco-friendly approach to achieve desirable essential oil quality and quantity in thyme under water deficit stress conditions.
Biodistribution and internal radiation dosimetry of a companion diagnostic radiopharmaceutical, [68Ga]PSMA-11, in subcutaneous prostate cancer xenograft model mice
Authors: Kim Su Bin , Song In Ho , Song Yoo Sung , Lee Byung Chul , Gupta Arun , Lee Jae Sung , Park Hyun Soo , Kim Sang Eun 
Published: July 2021

Abstract[68Ga]PSMA-11 is a prostate-specific membrane antigen (PSMA)-targeting radiopharmaceutical for diagnostic PET imaging. Its application can be extended to targeted radionuclide therapy (TRT). In this study, we characterize the biodistribution and pharmacokinetics of [68Ga]PSMA-11 in PSMA-positive and negative (22Rv1 and PC3, respectively) tumor-bearing mice and subsequently estimated its internal radiation dosimetry via voxel-level dosimetry using a dedicated Monte Carlo simulation to evaluate the absorbed dose in the tumor directly. Consequently, this approach overcomes the drawbacks of the conventional organ-level (or phantom-based) method. The kidneys and urinary bladder both showed substantial accumulation of [68Ga]PSMA-11 without exhibiting a washout phase during the study. For the tumor, a peak concentration of 4.5 ± 0.7 %ID/g occurred 90 min after [68Ga]PSMA-11 injection. The voxel- and organ-level methods both determined that the highest absorbed dose occurred in the kidneys (0.209 ± 0.005 Gy/MBq and 0.492 ± 0.059 Gy/MBq, respectively). Using voxel-level dosimetry, the absorbed dose in the tumor was estimated as 0.024 ± 0.003 Gy/MBq. The biodistribution and pharmacokinetics of [68Ga]PSMA-11 in various organs of subcutaneous prostate cancer xenograft model mice were consistent with reported data for prostate cancer patients. Therefore, our data supports the use of voxel-level dosimetry in TRT to deliver personalized dosimetry considering patient-specific heterogeneous tissue compositions and activity distributions.
Swelling behaviours of compacted lime-softening sludge for application in landfill liners
Authors: Dąbska Agnieszka , Léthel Agata 
Published: July 2021

AbstractThe objective of this study was to investigate the swelling potential of compacted lime-softening sludge for application in landfill liners. The study involved the assessment of the effect of compaction and moulding moisture content (30–40%), corresponding to the Proctor standard compaction test. One-dimensional oedometer swell tests were conducted using distilled water, tap water, and municipal landfill leachate, resulting in the determination of the expansion indices. Moreover, changes in the moisture content and dry density during the swelling process were investigated. The expansion index was significantly influenced by the initial moisture content and liquid chemistry. Subsequently, these factors also affected the sludge dry density decrease, and its moisture content increase, whereas the impact of the initial dry density on expansion was of low importance. An increase in the sludge moulding moisture content, limited swelling in all liquids used. The highest expansion, dry density, and moisture content changes due to swelling were identified for leachate at w < wopt. It should be underlined that the effect of liquid on the swelling potential faded away along with a further increase in the moisture content w > wopt. The novelty of the work lies in identifying a significant plunge of the expansion index at w ≈ wopt for the leachate swelling test. The lime-softening sludge non-swelling moisture content was defined as wnon ≈ (wopt + 4.0%) − (wopt + 4.5%). For practical engineering implications, the moisture content between (wopt + 2.0%) and (wopt + 4.0%) was provided for the most suitable sludge application in landfill liners.
Geodiversity impacts plant community structure in a semi-arid region
Authors: De Falco Natalie , Tal-Berger Reut , Hjazin Amgad , Yizhaq Hezi , Stavi Ilan , Rachmilevitch Shimon 
Published: July 2021

AbstractGeodiversity refers to the variety of geological and physical elements as well as to geomorphological processes of the earth surface. Heterogeneity of the physical environment has an impact on plant diversity. In recent years, the relations between geodiversity and biodiversity has gained attention in conservation biology, especially in the context of climate change. In this study, we assessed the spatial and temporal change in plant’s community structure in a semi-arid region, Sayeret Shaked Long Term Ecosystem Research (LTER) station, Israel. Vegetation surveys were conducted on different hillslopes, either with or without rock covers in order to study the spatial trends of hillslope geodiversity. The surveys were conducted for two consecutive years (2016 and 2017), of which the second year was drier and hotter and therefore permitted to investigate the temporal change of plant’s community structure. The results of the spatial trends show that (1) geodiversity increases vegetation biodiversity and promotes perennial plants and those of the temporal change show that (2) the positive effect of geodiversity on plants’ community structure and species richness is greater in the drier year than that in a wetter year. The main insight is that in these drylands, hillslopes with higher geodiversity appear to buffer the effect of drier years, and supported a more diverse plant community than lower geodiversity hillslopes.
Tranexamic acid in non-traumatic intracranial bleeding: a systematic review and meta-analysis
Authors: Bouillon-Minois Jean-Baptiste , Croizier Carolyne , Baker Julien S. , Pereira Bruno , Moustafa Farès , Outrey Justin , Schmidt Jeannot , Peschanski Nicolas , Dutheil Frédéric 
Published: July 2021

AbstractNon-traumatic intracranial bleeding (NTIB), comprising subarachnoid hemorrhage (SAH) and intra-cranial bleeding (ICH) is a significant public health concern. Tranexamic acid (TXA) is a promising treatment with benefits yet to be fully demonstrated. We conducted a systematic review and meta-analysis on the impact of TXA on mortality in NTIB. We searched the PubMed, Cochrane Library, Google Scholar and ScienceDirect databases for studies reporting mortality data following the use of TXA in NTIB for comparisons with a control group. We computed random-effect meta-analysis on estimates of risk and sensitivity analyses. We computed meta-regression to examine the putative effects of the severity of NTIB, sociodemographic data (age, sex), and publication date. Among potentially 10,008 articles, we included 15 studies representing a total of 4883 patients: 2455 receiving TXA and 2428 controls; 1110 died (23%) during the follow-up. The meta-analysis demonstrated a potential of 22% decrease in mortality for patients treated by TXA (RR = 0.78, 95%CI 0.58–0.98, p = 0.002). Meta-regression did not demonstrate any influence of the severity of NTIB, age, sex, length of treatment or date of publication. Sensitivity analyses confirmed benefits of TXA on mortality. TXA appears to be a therapeutic option to reduce non-traumatic intracranial bleeding mortality, particularly in patients with SAH.
Associations of apparent temperature with acute cardiac events and subtypes of acute coronary syndromes in Beijing, China
Authors: Li Na , Ma Junxiong , Liu Fangjing , Zhang Yan , Ma Pengkun , Jin Yinzi , Zheng Zhi-Jie 
Published: July 2021

AbstractLimited evidence is available on apparent temperature (AT) and hospital admissions for acute cardiac events. We examined the associations of AT with admissions for acute cardiac events and acute coronary syndrome (ACS), and explored the effect difference between ST-elevation myocardial infarction (STEMI) and non-ST-elevation myocardial infarction ACS (NSTE-ACS). Poisson regression with distributed lag non-linear model was applied to examine the temperature-lag-admission associations. Stratified analyses were performed by gender and age-groups for acute cardiac events. A total of 11,657 acute cardiac events admissions were collected from hospital-based chest pain centers in Beijing, during 2017–2019. The single day effect of low AT (− 11 °C, 2.5th percentile) appeared on the 2nd day and persisted until the 11th day, with estimated relative risk (RR) ranging from 1.44 (95% CI: 1.159, 1.790) to 1.084 (95% CI: 1.022, 1.150) for acute cardiac events and from 1.034 (95% CI: 1.010, 1.059) to 1.006 (95% CI: 1.000, 1.011) for ACS. The single day effect of high AT (34 °C, 97.5th percentile) was only observed on the current day. The cold effect on acute cardiac events was more pronounced among female and older patients. The cumulative effect of high AT on STEMI admissions and low AT on NSTE-ACS reached a peak RR peak of 2.545 (95% CI: 1.016, 6.375) and 3.71 (95% CI: 1.315, 10.469) on lag 0–6 days, respectively. Both high and low ATs were associated with increased risk of acute cardiac events and ACS admissions. STEMI admissions may be more sensitive to high AT while NSTE-ACS to low AT.