bluuebunny/crossref_metadata_2025 huggingface dataset:
Latent factor analysis and measurement on sustainable urban livability in Siliguri Municipal Corporation, West Bengal through EFA and CFA model
Authors: Adhikari Amit Kumar , Roy Tamal Basu
Published: October 2021

United Nations’ Sustainable Development Goal targets to make cities and human settlements inclusive, safe, resilient, and sustainable; as it is predicting 95% urban expansion in the next decades. Consequently, urban livability can serve as a useful conceptual and analytical framework to improve the quality of urban life by facilitating the evaluation of the person–environment relationship and leading the improvement without deteriorating the environmental conditions. This present paper aims to identify the dimensions and indicators of subjective and objective livability for Siliguri Municipal Corporation (SMC). The residents’ perception has been carried out using stratified random sampling technique. Samples have been collected from the residents from each core, semi-periphery and peripheral areas of SMC. Mainly, adaptation of Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) model involves four livability dimensions; under which the overall model explains 65% of the total variance indicating with the high reliability (α > 0.7) and the Goodness-of-fit index (GFI) about 0.90. The result indicates that, ‘Accessibility Factor’ bears the highest impact (24.91%) among the four latent variables and ‘Socio-Economic’ factor has the lower impact (8.39%) upon the urban livability.
Weather
Authors: Hakim Gregory J. , Patoux Jérôme
Published: October 2021

The second edition of this concise, affordable textbook is ideal for curious undergraduate majors and non-majors taking a first course in meteorology. The first two chapters introduce readers to the main concepts and tools used to analyze weather patterns. Chapters 3-8 provide a foundational understanding of the fundamental processes taking place in the atmosphere, and in Chapters 9-12 these physical concepts are applied to specific weather phenomena. Weather concepts are then used in Chapters 13-15 to explain weather forecasting, air pollution, and the impact of climate change on weather. Key concepts are illustrated through a running case study of a single mid-latitude cyclone, providing students with an opportunity to progressively develop their understanding of weather phenomena with a familiar example approached from multiple perspectives. This edition includes expanded and updated coverage of precipitation types and formation, satellite and radar technology, tornadoes, and more. It also features thought-provoking end-of-chapter review questions, new visual analysis exercises, an expanded test bank and nearly 100 new figures.
RUSSIA'S 2020 CONSTITUTIONAL AMENDMENTS: A COMPARATIVE ANALYSIS
Authors: PARTLETT William
Published: October 2021

This article will place the 2020 amendments to the Russian Constitution in comparative perspective. Although these amendments were officially justified as strengthening the Russian state in order to tackle emerging new problems, they constitutionalise already-existing legislative trends from the last twenty years. They therefore do little to overcome existing problems of Russian state building. What was the reform process about then? It was intended to project the image of reform by involving the people in a staged process of constitutional change while further entrenching the power of the current political elite. The constitutional reforms therefore demonstrate the symbolic role that constitutional law can play in seeking to ensure the survival of mature or later-stage forms of authoritarian populism. This kind of ‘theatrical constitution-making’ is a broader reminder of how the expressive aspects of constitutional change can be (ab)used by established authoritarian regimes.
Niacin supplementation impairs exercise performance
Authors: Davis Greggory R. , Nelson Arnold G.
Published: October 2021

Abstract: Several pre-workout supplements contain niacin, although the exercise performance effects of niacin are poorly understood. The purpose of the present study was to examine the performance effects of niacin versus caffeine as a pre-workout supplement. Twenty-five untrained males were recruited to complete three identical ramped aerobic cycling exercise trials. Participants were administered caffeine (CA) at 5 mg/kg body weight, 1000 mg niacin (NI), or a methylcelluloce placebo (PL) supplement prior to each trial. NI treatment induced significantly higher respiratory exchange ratio (RER) during exercise compared to the CA treatment, but not the PL treatment (PL=0.87±0.08, NI=0.91±0.08, CA=0.87±0.08; p=0.02). Similarly, exercise time to exhaustion (in minutes) was significantly different between the NI treatment and the CA treatment, but not the PL treatment (PL=27.45±4.47, NI=26.30±4.91, CA=28.76±4.86; p<0.01). Habitual caffeine use (p=0.16), habitual aerobic exercise (p=0.60), and habitual resistance exercise (p=0.10) did not significantly affect RER. Similarly, habitual caffeine use (p=0.72), habitual aerobic exercise (p=0.08), and habitual resistance exercise (p=0.39) did not significantly affect total work performed. The elevated RER and decreased time to exhaustion in the NI treatment suggests limited lipid availability during exercise and impaired exercise performance.
Measuring Sea Level Rise Along the Coast
Authors: Shultz David
Published: October 2021

Scientists created a global map of vertical land motion to show how the solid ground is moving relative to the planet’s rising seas.
Retrieving PmP Travel Times From a Persistent Localized Microseismic Source
Authors: Xie Jinyun , Luo Yinhe , Yang Yingjie
Published: October 2021

Ocean swells or storms can generate persistent localized microseismic sources in deep oceans, which emanate body wave energy traveling through the Earth’s interior, carrying abundant information about subsurface structures as earthquake waves do. However, body waves from localized microseismic sources have not been fully exploited to map the internal structures of the Earth. Here, we report that the travel times of body wave reflections from the Moho can be obtained from body waves generated by localized microseismic sources. We further demonstrate that body waves from these sources can be utilized to constrain the Moho morphology through synthetic experiments and comparisons with earthquake receiver function results. Our work suggests that localized microseismic sources can be exploited to map the internal structure of the Earth without relying on earthquake data.
Three‐Dimensional Global Hybrid Simulations of High Latitude Magnetopause Reconnection and Flux Ropes During the Northward IMF
Authors: Guo Jin , Lu San , Lu Quanming , Lin Yu , Wang Xueyi , Zhang Qinghe , Xing Zanyang , Huang Kai , Wang Rongsheng , Wang Shui
Published: October 2021

When the interplanetary magnetic field (IMF) is northward, magnetic reconnection between the IMF and the geomagnetic field can occur at the high latitude magnetopause, which allows energy transfer from the solar wind into Earth's magnetosphere. In this letter, by using three‐dimensional global hybrid simulations, we find that during the northward IMF, high latitude magnetic reconnection both poleward and equatorward of the cusp can occur almost simultaneously. High latitude magnetopause flux ropes (HLMFRs) with four topologies of magnetic field lines can be formed by multiple X‐line reconnection. At the center of the HLMFRs, there is a decrease in the surrounding magnetic field magnitude (weak core field) and an increase in parallel temperature. When the IMF is purely northward, the HLMFRs are located at the noon‐midnight meridian plane. When the IMF has a positive component, the HLMFRs in the northern hemisphere shift duskward.
The Role of Along‐Fault Dilatancy in Fault Slip Behavior
Authors: Caniven Yannick , Morgan Julia K. , Blank David G.
Published: October 2021

Earthquakes result from fast slip that occurs along a fault surface. Interestingly, numerous dense geodetic observations over the last two decades indicate that such dynamic slip may start by a gradual unlocking of the fault surface and related progressive slip acceleration. This first slow stage is of great interest, because it could define an early indicator of a devastating earthquake. However, not all slow slip turns into fast slip, and sometimes it may simply stop. In this study, we use a numerical model based on the discrete element method to simulate crustal strike‐slip faults of 50 km length that generate a wide variety of slip‐modes, from stable‐slip, to slow earthquakes, to fast earthquakes, all of which show similar characteristics to natural cases. The main goal of this work is to understand the conditions that allow slow events to turn into earthquakes, in contrast to those that cause slow earthquakes to stop. Our results suggest that fault surface geometry and related dilation/contraction patterns along strike play a key role. Slow earthquakes that initiate in large dilated regions bounded by neutral or low contracted domains, might turn into earthquakes. Slow events occurring in regions dominated by closely spaced, alternating, small magnitude dilational and contractional zones tend not to accelerate and may simply stop as isolated slow earthquakes.
Long-term cognitive outcomes in term newborns with watershed injury caused by neonatal encephalopathy
Authors: Lee Bo Lyun , Gano Dawn , Rogers Elizabeth E. , Xu Duan , Cox Stephany , James Barkovich A. , Li Yi , Ferriero Donna M. , Glass Hannah C.
Published: October 2021

Background

We previously reported that increasing severity of watershed (WS) injury in neonatal magnetic resonance imaging (MRI) is associated with worse language outcomes in early childhood. In the present study, we investigated the relationship between neonatal injury patterns and cognitive profile in adolescents with neonatal encephalopathy.

Methods

Term neonates with encephalopathy were prospectively enrolled and imaged using brain MRI from 1999 to 2008. Neonatal brain injury was scored according to the degree of injury in WS and basal ganglia/thalamus (BG/T) areas. The children underwent a neurocognitive assessment and follow-up brain MRI at the age of 10–16 years. The relationship between neonatal brain injury patterns and adolescent cognitive outcomes was assessed.

Results

In a cohort of 16 children, neonatal MRI showed WS injury in 7, BG/T injury in 2, and normal imaging in 7. Children with WS injury had lower estimated overall cognitive ability than those with normal imaging. Increasing WS injury score was associated with decreasing estimated overall cognitive ability, Perceptual Reasoning Index, and digit span score.

Conclusions

Children with the WS injury are at an increased risk of having problems in long-term intellectual ability. These cognitive outcomes may underlie early language difficulties seen in children with neonatal WS injury.

Impact

Adolescents with a history of neonatal encephalopathy and watershed pattern of injury on neonatal brain magnetic resonance imaging (MRI) had lower overall cognitive ability, perceptual reasoning skills, and auditory working memory than those with normal neonatal imaging.

Children with post-neonatal epilepsy and cerebral palsy had the worst cognitive outcomes.

Watershed pattern of injury confers high long-term differences in intellectual ability.
Comprehensive investigations revealed consistent pathophysiological alterations after vaccination with COVID-19 vaccines
Authors: Liu Jiping , Wang Junbang , Xu Jinfang , Xia Han , Wang Yue , Zhang Chunxue , Chen Wei , Zhang Huina , Liu Qi , Zhu Rong , Shi Yiqi , Shen Zihao , Xing Zhonggang , Gao Wenxia , Zhou Liqiang , Shao Jinliang , Shi Jiayu , Yang Xuejiao , Deng Yaxuan , Wu Li , Lin Quan , Zheng Changhong , Zhu Wenmin , Wang Congrong , Sun Yi E. , Liu Zhongmin
Published: October 2021

Large-scale COVID-19 vaccinations are currently underway in many countries in response to the COVID-19 pandemic. Here, we report, besides generation of neutralizing antibodies, consistent alterations in hemoglobin A1c, serum sodium and potassium levels, coagulation profiles, and renal functions in healthy volunteers after vaccination with an inactivated SARS-CoV-2 vaccine. Similar changes had also been reported in COVID-19 patients, suggesting that vaccination mimicked an infection. Single-cell mRNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) before and 28 days after the first inoculation also revealed consistent alterations in gene expression of many different immune cell types. Reduction of CD8+ T cells and increase in classic monocyte contents were exemplary. Moreover, scRNA-seq revealed increased NF-κB signaling and reduced type I interferon responses, which were confirmed by biological assays and also had been reported to occur after SARS-CoV-2 infection with aggravating symptoms. Altogether, our study recommends additional caution when vaccinating people with pre-existing clinical conditions, including diabetes, electrolyte imbalances, renal dysfunction, and coagulation disorders.
Mesenchymal stem cell treatment improves outcome of COVID-19 patients via multiple immunomodulatory mechanisms
Authors: Zhu Rongjia , Yan Tingdong , Feng Yingmei , Liu Yan , Cao Hongcui , Peng Gongxin , Yang Yanlei , Xu Zhen , Liu Jingqi , Hou Wei , Wang Xiaoyue , Li Zhe , Deng Luchan , Wang Shihua , Li Jing , Han Qin , Li Hongling , Shan Guangliang , Cao Yinghao , An Xingyan , Yan Jianshe , Zhang Zhonghui , Li Huafei , Qu Xuebin , Zhu Jiaqi , Zhou Shumin , Wang Jiao , Zhang Fengchun , Gao Jinming , Jin Ronghua , Xu Dayong , Ma Yan-Qing , Huang Tao , Peng Shuang , Zheng Zhi , Stambler Ilia , Gilson Eric , Lim Lee Wei , Moskalev Alexey , Cano Antonio , Chakrabarti Sasanka , Ulfhake Brun , Su Huanxing , Xu Haoying , Xu Sihuan , Wei Feng , Brown-Borg Holly M. , Min Kyung-Jin , Ellison-Hughes Georgina , Caruso Calogero , Jin Kunlin , Zhao Robert Chunhua
Published: October 2021

The infusion of coronavirus disease 2019 (COVID-19) patients with mesenchymal stem cells (MSCs) potentially improves clinical symptoms, but the underlying mechanism remains unclear. We conducted a randomized, single-blind, placebo-controlled (29 patients/group) phase II clinical trial to validate previous findings and explore the potential mechanisms. Patients treated with umbilical cord-derived MSCs exhibited a shorter hospital stay (P = 0.0198) and less time required for symptoms remission (P = 0.0194) than those who received placebo. Based on chest images, both severe and critical patients treated with MSCs showed improvement by day 7 (P = 0.0099) and day 21 (P = 0.0084). MSC-treated patients had fewer adverse events. MSC infusion reduced the levels of C-reactive protein, proinflammatory cytokines, and neutrophil extracellular traps (NETs) and promoted the maintenance of SARS-CoV-2-specific antibodies. To explore how MSCs modulate the immune system, we employed single-cell RNA sequencing analysis on peripheral blood. Our analysis identified a novel subpopulation of VNN2+ hematopoietic stem/progenitor-like (HSPC-like) cells expressing CSF3R and PTPRE that were mobilized following MSC infusion. Genes encoding chemotaxis factors — CX3CR1 and L-selectin — were upregulated in various immune cells. MSC treatment also regulated B cell subsets and increased the expression of costimulatory CD28 in T cells in vivo and in vitro. In addition, an in vivo mouse study confirmed that MSCs suppressed NET release and reduced venous thrombosis by upregulating kindlin-3 signaling. Together, our results underscore the role of MSCs in improving COVID-19 patient outcomes via maintenance of immune homeostasis.
Topology-transformable block copolymers based on a rotaxane structure: change in bulk properties with same composition
Authors: Sato Hiroki , Aoki Daisuke , Marubayashi Hironori , Uchida Satoshi , Sogawa Hiromitsu , Nojima Shuichi , Liang Xiaobin , Nakajima Ken , Hayakawa Teruaki , Takata Toshikazu
Published: October 2021

The topology of polymers affects their characteristic features, i.e., their microscopic structure and macroscopic properties. However, the topology of a polymer is usually fixed during the construction of the polymer chain and cannot be transformed after its determination during the synthesis. In this study, topology-transformable block copolymers that are connected via rotaxane linkages are introduced. We will present systems in which the topology transformation of block copolymers changes their 1) microphase-separated structures and 2) macroscopic mechanical properties. The combination of a rotaxane structure at the junction point and block copolymers that spontaneously form microphase-separated structures in the bulk provides access to systems that cannot be attained using conventional covalent bonds.
Synchronization between peripheral circadian clock and feeding-fasting cycles in microfluidic device sustains oscillatory pattern of transcriptome
Authors: Gagliano Onelia , Luni Camilla , Li Yan , Angiolillo Silvia , Qin Wei , Panariello Francesco , Cacchiarelli Davide , Takahashi Joseph S. , Elvassore Nicola
Published: October 2021

The circadian system cyclically regulates many physiological and behavioral processes within the day. Desynchronization between physiological and behavioral rhythms increases the risk of developing some, including metabolic, disorders. Here we investigate how the oscillatory nature of metabolic signals, resembling feeding-fasting cycles, sustains the cell-autonomous clock in peripheral tissues. By controlling the timing, period and frequency of glucose and insulin signals via microfluidics, we find a strong effect on Per2::Luc fibroblasts entrainment. We show that the circadian Per2 expression is better sustained via a 24 h period and 12 h:12 h frequency-encoded metabolic stimulation applied for 3 daily cycles, aligned to the cell-autonomous clock, entraining the expression of hundreds of genes mostly belonging to circadian rhythms and cell cycle pathways. On the contrary misaligned feeding-fasting cycles synchronize and amplify the expression of extracellular matrix-associated genes, aligned during the light phase. This study underlines the role of the synchronicity between life-style-associated metabolic signals and peripheral clocks on the circadian entrainment.
The impact of physiological metabolite levels on serine uptake, synthesis and utilization in cancer cells
Authors: Hennequart Marc , Labuschagne Christiaan F. , Tajan Mylène , Pilley Steven E. , Cheung Eric C. , Legrave Nathalie M. , Driscoll Paul C. , Vousden Karen H.
Published: October 2021

Serine is a non-essential amino acid that is critical for tumour proliferation and depletion of circulating serine results in reduced tumour growth and increased survival in various cancer models. While many cancer cells cultured in a standard tissue culture medium depend on exogenous serine for optimal growth, here we report that these cells are less sensitive to serine/glycine depletion in medium containing physiological levels of metabolites. The lower requirement for exogenous serine under these culture conditions reflects both increased de novo serine synthesis and the use of hypoxanthine (not present in the standard medium) to support purine synthesis. Limiting serine availability leads to increased uptake of extracellular hypoxanthine, sparing available serine for other pathways such as glutathione synthesis. Taken together these results improve our understanding of serine metabolism in physiologically relevant nutrient conditions and allow us to predict interventions that may enhance the therapeutic response to dietary serine/glycine limitation.
The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag
Authors: Sahu Indrajit , Mali Sachitanand M. , Sulkshane Prasad , Xu Cong , Rozenberg Andrey , Morag Roni , Sahoo Manisha Priyadarsini , Singh Sumeet K. , Ding Zhanyu , Wang Yifan , Day Sharleen , Cong Yao , Kleifeld Oded , Brik Ashraf , Glickman Michael H.
Published: October 2021

The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.
Structural basis for protein glutamylation by the Legionella pseudokinase SidJ
Authors: Adams Michael , Sharma Rahul , Colby Thomas , Weis Felix , Matic Ivan , Bhogaraju Sagar
Published: October 2021

Legionella pneumophila (LP) avoids phagocytosis by secreting nearly 300 effector proteins into the host cytosol. SidE family of effectors (SdeA, SdeB, SdeC and SidE) employ phosphoribosyl ubiquitination to target multiple host Rab GTPases and innate immune factors. To suppress the deleterious toxicity of SidE enzymes in a timely manner, LP employs a metaeffector named SidJ. Upon activation by host Calmodulin (CaM), SidJ executes an ATP-dependent glutamylation to modify the catalytic residue Glu860 in the mono-ADP-ribosyl transferase (mART) domain of SdeA. SidJ is a unique glutamylase that adopts a kinase-like fold but contains two nucleotide-binding pockets. There is a lack of consensus about the substrate recognition and catalytic mechanism of SidJ. Here, we determined the cryo-EM structure of SidJ in complex with its substrate SdeA in two different states of catalysis. Our structures reveal that both phosphodiesterase (PDE) and mART domains of SdeA make extensive contacts with SidJ. In the pre-glutamylation state structure of the SidJ-SdeA complex, adenylylated E860 of SdeA is inserted into the non-canonical (migrated) nucleotide-binding pocket of SidJ. Structure-based mutational analysis indicates that SidJ employs its migrated pocket for the glutamylation of SdeA. Finally, using mass spectrometry, we identified several transient autoAMPylation sites close to both the catalytic pockets of SidJ. Our data provide unique insights into the substrate recognition and the mechanism of protein glutamylation by the pseudokinase SidJ.
Clonal hematopoiesis with JAK2V617F promotes pulmonary hypertension with ALK1 upregulation in lung neutrophils
Authors: Kimishima Yusuke , Misaka Tomofumi , Yokokawa Tetsuro , Wada Kento , Ueda Koki , Sugimoto Koichi , Minakawa Keiji , Nakazato Kazuhiko , Ishida Takafumi , Oshima Motohiko , Koide Shuhei , Shide Kotaro , Shimoda Kazuya , Iwama Atsushi , Ikeda Kazuhiko , Takeishi Yasuchika
Published: October 2021

Pulmonary hypertension (PH) is a progressive cardiopulmonary disease characterized by pulmonary arterial remodeling. Clonal somatic mutations including JAK2V617F, the most frequent driver mutation among myeloproliferative neoplasms, have recently been identified in healthy individuals without hematological disorders. Here, we reveal that clonal hematopoiesis with JAK2V617F exacerbates PH and pulmonary arterial remodeling in mice. JAK2V617F-expressing neutrophils specifically accumulate in pulmonary arterial regions, accompanied by increases in neutrophil-derived elastase activity and chemokines in chronic hypoxia-exposed JAK2V617F transgenic (JAK2V617F) mice, as well as recipient mice transplanted with JAK2V617F bone marrow cells. JAK2V617F progressively upregulates Acvrl1 (encoding ALK1) during the differentiation from bone marrow stem/progenitor cells peripherally into mature neutrophils of pulmonary arterial regions. JAK2V617F-mediated STAT3 phosphorylation upregulates ALK1-Smad1/5/8 signaling. ALK1/2 inhibition completely prevents the development of PH in JAK2V617F mice. Finally, our prospective clinical study identified JAK2V617F-positive clonal hematopoiesis is more common in PH patients than in healthy subjects. These findings indicate that clonal hematopoiesis with JAK2V617F causally leads to PH development associated with ALK1 upregulation.
Hot exciplexes in U-shaped TADF molecules with emission from locally excited states
Authors: Schleper A. Lennart , Goushi Kenichi , Bannwarth Christoph , Haehnle Bastian , Welscher Philipp J. , Adachi Chihaya , Kuehne Alexander J. C.
Published: October 2021

Fast emission and high color purity are essential characteristics of modern opto-electronic devices, such as organic light emitting diodes (OLEDs). These properties are currently not met by the latest generation of thermally activated delayed fluorescence (TADF) emitters. Here, we present an approach, called “hot exciplexes” that enables access to both attributes at the same time. Hot exciplexes are produced by coupling facing donor and acceptor moieties to an anthracene bridge, yielding an exciplex with large T1 to T2 spacing. The hot exciplex model is investigated using optical spectroscopy and quantum chemical simulations. Reverse intersystem crossing is found to occur preferentially from the T3 to the S1 state within only a few nanoseconds. Application and practicality of the model are shown by fabrication of organic light-emitting diodes with up to 32 % hot exciplex contribution and low efficiency roll-off.
Precise measurements of chromatin diffusion dynamics by modeling using Gaussian processes
Authors: Oliveira Guilherme M. , Oravecz Attila , Kobi Dominique , Maroquenne Manon , Bystricky Kerstin , Sexton Tom , Molina Nacho
Published: October 2021

The spatiotemporal organization of chromatin influences many nuclear processes: from chromosome segregation to transcriptional regulation. To get a deeper understanding of these processes, it is essential to go beyond static viewpoints of chromosome structures, to accurately characterize chromatin’s diffusion properties. We present GP-FBM: a computational framework based on Gaussian processes and fractional Brownian motion to extract diffusion properties from stochastic trajectories of labeled chromatin loci. GP-FBM uses higher-order temporal correlations present in the data, therefore, outperforming existing methods. Furthermore, GP-FBM allows to interpolate incomplete trajectories and account for substrate movement when two or more particles are present. Using our method, we show that average chromatin diffusion properties are surprisingly similar in interphase and mitosis in mouse embryonic stem cells. We observe surprising heterogeneity in local chromatin dynamics, correlating with potential regulatory activity. We also present GP-Tool, a user-friendly graphical interface to facilitate usage of GP-FBM by the research community.
Alpine-style nappes thrust over ancient North China continental margin demonstrate large Archean horizontal plate motions
Authors: Zhong Yating , Kusky Timothy , Wang Lu , Polat Ali , Liu Xuanyu , Peng Yaying , Luan Zhikang , Wang Chuanhai , Wang Junpeng , Deng Hao
Published: October 2021

Whether modern-style plate tectonics operated on early Earth is debated due to a paucity of definitive records of large-scale plate convergence, subduction, and collision in the Archean geological record. Archean Alpine-style sub-horizontal fold/thrust nappes in the Precambrian basement of China contain a Mariana-type subduction-initiation sequence of mid-ocean ridge basalt blocks in a 1600-kilometer-long mélange belt, overthrusting picritic-boninitic and island-arc tholeiite bearing nappes, in turn emplaced over a passive margin capping an ancient Archean continental fragment. Picrite-boninite and tholeiite units are 2698 ± 30 million years old marking the age of subduction initiation, with nappes emplaced over the passive margin at 2520 million years ago. Here, we show the life cycle of the subduction zone and ocean spanned circa 178 million years; conservative plate velocities of 2 centimeters per year yield a lateral transport distance of subducted oceanic crust of 3560 kilometers, providing direct positive evidence for horizontal plate tectonics in the Archean.
Full shell coating or cation exchange enhances luminescence
Authors: Zhang Yi , Lei Pengpeng , Zhu Xiaohui , Zhang Yong
Published: October 2021

Core-shell structure is routinely used for enhancing luminescence of optical nanoparticles, where the luminescent core is passivated by an inert shell. It has been intuitively accepted that the luminescence would gradually enhance with the coverage of inert shell. Here we report an “off-on” effect at the interface of core-shell upconversion nanoparticles, i.e., regardless of the shell coverage, the luminescence is not much enhanced unless the core is completely encapsulated. This effect indicates that full shell coating on the luminescent core is critical to significantly enhance luminescence, which is usually neglected. Inspired by this observation, a cation exchange approach is used to block the energy transfer between core nanoparticle and surface quenchers. We find that the luminescent core exhibits enhanced luminescence after cation exchange creates an effective shell region. These findings are believed to provide a better understanding of the interfacial energy dynamics and subsequent luminescence changes.
Rhesus macaques self-curing from a schistosome infection can display complete immunity to challenge
Authors: Amaral Murilo Sena , Santos Daisy Woellner , Pereira Adriana S. A. , Tahira Ana Carolina , Malvezzi João V. M. , Miyasato Patrícia Aoki , Freitas Rafaela de Paula , Kalil Jorge , Tjon Kon Fat Elisa M. , de Dood Claudia J. , Corstjens Paul L. A. M. , van Dam Govert J. , Nakano Eliana , Castro Simone de Oliveira , Mattaraia Vânia Gomes de Moura , Augusto Ronaldo de Carvalho , Grunau Christoph , Wilson R. Alan , Verjovski-Almeida Sergio
Published: October 2021

The rhesus macaque provides a unique model of acquired immunity against schistosomes, which afflict >200 million people worldwide. By monitoring bloodstream levels of parasite-gut-derived antigen, we show that from week 10 onwards an established infection withSchistosoma mansoniis cleared in an exponential manner, eliciting resistance to reinfection. Secondary challenge at week 42 demonstrates that protection is strong in all animals and complete in some. Antibody profiles suggest that antigens mediating protection are the released products of developing schistosomula. In culture they are killed by addition of rhesus plasma, collected from week 8 post-infection onwards, and even more efficiently with post-challenge plasma. Furthermore, cultured schistosomula lose chromatin activating marks at the transcription start site of genes related to worm development and show decreased expression of genes related to lysosomes and lytic vacuoles involved with autophagy. Overall, our results indicate that enhanced antibody responses against the challenge migrating larvae mediate the naturally acquired protective immunity and will inform the route to an effective vaccine.
The cell envelope of Staphylococcus aureus selectively controls the sorting of virulence factors
Authors: Zheng Xuhui , Marsman Gerben , Lacey Keenan A. , Chapman Jessica R. , Goosmann Christian , Ueberheide Beatrix M. , Torres Victor J.
Published: October 2021

Staphylococcus aureus bi-component pore-forming leukocidins are secreted toxins that directly target and lyse immune cells. Intriguingly, one of the leukocidins, Leukocidin AB (LukAB), is found associated with the bacterial cell envelope in addition to secreted into the extracellular milieu. Here, we report that retention of LukAB on the bacterial cells provides S. aureus with a pre-synthesized active toxin that kills immune cells. On the bacteria, LukAB is distributed as discrete foci in two distinct compartments: membrane-proximal and surface-exposed. Through genetic screens, we show that a membrane lipid, lysyl-phosphatidylglycerol (LPG), and lipoteichoic acid (LTA) contribute to LukAB deposition and release. Furthermore, by studying non-covalently surface-bound proteins we discovered that the sorting of additional exoproteins, such as IsaB, Hel, ScaH, and Geh, are also controlled by LPG and LTA. Collectively, our study reveals a multistep secretion system that controls exoprotein storage and protein translocation across the S. aureus cell wall.
Tuning the selectivity of catalytic nitriles hydrogenation by structure regulation in atomically dispersed Pd catalysts
Authors: Liu Zhibo , Huang Fei , Peng Mi , Chen Yunlei , Cai Xiangbin , Wang Linlin , Hu Zenan , Wen Xiaodong , Wang Ning , Xiao Dequan , Jiang Hong , Sun Hongbin , Liu Hongyang , Ma Ding
Published: October 2021

The product selectivity in catalytic hydrogenation of nitriles is strongly correlated with the structure of the catalyst. In this work, two types of atomically dispersed Pd species stabilized on the defect-rich nanodiamond-graphene (ND@G) hybrid support: single Pd atoms (Pd1/ND@G) and fully exposed Pd clusters with average three Pd atoms (Pdn/ND@G), were fabricated. The two catalysts show distinct difference in the catalytic transfer hydrogenation of nitriles. The Pd1/ND@G catalyst preferentially generates secondary amines (Turnover frequency (TOF@333 K 709 h−1, selectivity >98%), while the Pdn/ND@G catalyst exhibits high selectivity towards primary amines (TOF@313 K 543 h−1, selectivity >98%) under mild reaction conditions. Detailed characterizations and density functional theory (DFT) calculations show that the structure of atomically dispersed Pd catalysts governs the dissociative adsorption pattern of H2 and also the hydrogenation pathway of the benzylideneimine (BI) intermediate, resulting in different product selectivity over Pd1/ND@G and Pdn/ND@G, respectively. The structure-performance relationship established over atomically dispersed Pd catalysts provides valuable insights for designing catalysts with tunable selectivity.
MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes
Authors: Maggiori Catherine , Raymond-Bouchard Isabelle , Brennan Laura , Touchette David , Whyte Lyle
Published: October 2021

Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites—HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)—where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species ofOctadecabacteris among the hybrid MAGs produced, containing the genus’s only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.
Characterizing non-critically ill COVID-19 survivors with and without in-hospital rehabilitation
Authors: Musheyev Benjamin , Janowicz Rebeca , Borg Lara , Matarlo Michael , Boyle Hayle , Hou Wei , Duong Tim Q.
Published: October 2021

This study investigated pre-COVID-19 admission dependency, discharge assistive equipment, discharge medical follow-up recommendation, and functional status at hospital discharge of non-critically ill COVID-19 survivors, stratified by those with (N = 155) and without (N = 162) in-hospital rehabilitation. “Mental Status”, intensive-care-unit (ICU) Mobility, and modified Barthel Index scores were assessed at hospital discharge. Relative to the non-rehabilitation patients, rehabilitation patients were older, had more comorbidities, worse pre-admission dependency, were discharged with more assistive equipment and supplemental oxygen, spent more days in the hospital, and had more hospital-acquired acute kidney injury, acute respiratory failure, and more follow-up referrals (p < 0.05 for all). Cardiology, vascular medicine, urology, and endocrinology were amongst the top referrals. Functional scores of many non-critically ill COVID-19 survivors were abnormal at discharge (p < 0.05) and were associated with pre-admission dependency (p < 0.05). Some functional scores were negatively correlated with age, hypertension, coronary artery disease, chronic kidney disease, psychiatric disease, anemia, and neurological disorders (p < 0.05). In-hospital rehabilitation providing restorative therapies and assisting discharge planning were challenging in COVID-19 circumstances. Knowledge of the functional status, discharge assistive equipment, and follow-up medical recommendations at discharge could enable appropriate and timely post-discharge care. Follow-up studies of COVID-19 survivors are warranted as many will likely have significant post-acute COVID-19 sequela.
Triazolopyrimidine herbicides are potent inhibitors of Aspergillus fumigatus acetohydroxyacid synthase and potential antifungal drug leads
Authors: Low Y. S. , Garcia M. D. , Lonhienne T. , Fraser J. A. , Schenk G. , Guddat L. W.
Published: October 2021

Aspergillus fumigatus is a fungal pathogen whose effects can be debilitating and potentially fatal in immunocompromised patients. Current drug treatment options for this infectious disease are limited to just a few choices (e.g. voriconazole and amphotericin B) and these themselves have limitations due to potentially adverse side effects. Furthermore, the likelihood of the development of resistance to these current drugs is ever present. Thus, new treatment options are needed for this infection. A new potential antifungal drug target is acetohydroxyacid synthase (AHAS; EC 2.2.1.6), the first enzyme in the branched chain amino acid biosynthesis pathway, and a target for many commercial herbicides. In this study, we have expressed, purified and characterised the catalytic subunit of AHAS from A. fumigatus and determined the inhibition constants for several known herbicides. The most potent of these, penoxsulam and metosulam, have Ki values of 1.8 ± 0.9 nM and 1.4 ± 0.2 nM, respectively. Molecular modelling shows that these compounds are likely to bind into the herbicide binding pocket in a mode similar to Candida albicans AHAS. We have also shown that these two compounds inhibit A. fumigatus growth at a concentration of 25 µg/mL. Thus, AHAS inhibitors are promising leads for the development of new anti-aspergillosis therapeutics.
The new SRS/FSRT technique HyperArc for benign brain lesions: a dosimetric analysis
Authors: Ho Hsiu-Wen , Yang Ching-Chieh , Lin Hsiu-Man , Chen Hsiao-Yun , Huang Chun-Chiao , Wang Shih-Chang , Lin Yu-Wei
Published: October 2021

To evaluate the potential benefit of HyperArc (HA) fractionated stereotactic radiotherapy (FSRT) for the benign brain lesion. Sixteen patients with a single deep-seated, centrally located benign brain lesion treated by CyberKnife (CK, G4 cone-based model) were enrolled. Treatment plans for HA with two different optimization algorithms (SRS NTO and ALDO) and coplanar RapidArc (RA) were generated for each patient to meet the corresponding treatment plan criteria. These four FSRT treatment plans were divided into two groups—the homogeneous delivery group (HA-SRS NTO and coplanar RA) and the inhomogeneous delivery group (HA-ALDO and cone-based CK)—to compare for dosimetric outcomes. For homogeneous delivery, the brain V5, V12, and V24 and the mean brainstem dose were significantly lower with the HA-SRS NTO plans than with the coplanar RA plans. The conformity index, high and intermediate dose spillage, and gradient radius were significantly better with the HA-SRS NTO plans than with the coplanar RA plans. For inhomogeneous delivery, the HA-ALDO exhibited superior PTV coverage levels to the cone-based CK plans. Almost all the doses delivered to organs at risk and dose distribution metrics were significantly better with the HA-ALDO plans than with the cone-based CK plans. Good dosimetric distribution makes HA an attractive FSRT technique for the treatment of benign brain lesions.
Indocyanine green lymphangiography is superior to clinical staging in breast cancer-related lymphedema
Authors: Jørgensen Mads Gustaf , Hermann Anne Pernille , Madsen Anette Riis , Christensen Steffanie , Sørensen Jens Ahm
Published: October 2021

Precise staging of breast cancer-related lymphedema (BCRL) is important to guide treatment-decision making. Recent studies have suggested staging of BCRL using indocyanine green lymphangiography (ICG-L) based on the extent of lymphatic injury and dermal backflow patterns. Currently, the benefits of ICG-L compared to conventional clinical staging are unknown. For this study, we included 200 patients with unilateral BCRL. All BCRL patients were staged using ICG-L and clinical exam. The amounts of excess arm volume, fat mass and lean mass were compared between stages using Dual Energy X-Ray Absorptiometry. Multivariate regression models were used to adjust for confounders. For each increase in the patient's ICG-L stage, the excess arm volume, fat mass and lean mass was increased by 8, 12 and 6.5 percentage points respectively (P < 0.001). For each increase in the patient's clinical ISL stage, the volume was increased by 3.5 percentage points (P < 0.05), however no statistically significant difference in the lean and fat mass content of the arm was observed for ascending stages. However, the residual plots showed a high degree of variance for both ICG-L and clinical staging. This study found that ICG-L staging of BCRL was superior to clinical staging in forecasting BCRL excess arm volume, fat mass, and lean mass. However, there was a high degree of variance in excess arm volume, fat mass, and lean mass within each staging system, and neither the ICG-L nor clinical staging forecasted perfectly.
The effect of population inversion saturation on the transverse mode instability threshold in high power fiber laser oscillators
Authors: Roohforouz Ali , Eyni Chenar Reza , Rezaei-Nasirabad Reza , Azizi Saeed , Hejaz Kamran , Hamedani Golshan Ali , Abedinajafi Ali , Vatani Vahid , Nabavi Seyed Hassan
Published: October 2021

To achieve a 3.02 kW Yb-doped fiber laser oscillator, the behavior of transverse mode instability (TMI) is experimentally studied in different pumping configurations; co, hybrid, counter, and bidirectional. A comparative analysis showed that population inversion saturation has a substantial impact on TMI threshold enhancement in high power fiber oscillators. Monitoring the dynamic power exchange of fundamental mode and higher-order mode of laser output beam indicates that in a hybrid pumping scheme, simultaneous pumping with two different wavelengths enhances the TMI threshold to a great stand. Moreover, injecting a few watts of pumping light in the counter direction mitigates the TMI caused by pumping in the co-direction. Calculation of population inversion in different pumping configurations using simulation shows that higher population inversion saturation leads to increasing the TMI threshold.
Data-driven analysis of amino acid change dynamics timely reveals SARS-CoV-2 variant emergence
Authors: Bernasconi Anna , Mari Lorenzo , Casagrandi Renato , Ceri Stefano
Published: October 2021

Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome. The co-occurrence of specific amino acid changes, collectively named ‘virus variant’, requires scrutiny (as variants may hugely impact the agent’s transmission, pathogenesis, or antigenicity); variant evolution is studied using phylogenetics. Yet, never has this problem been tackled by digging into data with ad hoc analysis techniques. Here we show that the emergence of variants can in fact be traced through data-driven methods, further capitalizing on the value of large collections of SARS-CoV-2 sequences. For all countries with sufficient data, we compute weekly counts of amino acid changes, unveil time-varying clusters of changes with similar—rapidly growing—dynamics, and then follow their evolution. Our method succeeds in timely associating clusters to variants of interest/concern, provided their change composition is well characterized. This allows us to detect variants’ emergence, rise, peak, and eventual decline under competitive pressure of another variant. Our early warning system, exclusively relying on deposited sequences, shows the power of big data in this context, and concurs to calling for the wide spreading of public SARS-CoV-2 genome sequencing for improved surveillance and control of the COVID-19 pandemic.
Antibacterial activity and characteristics of silver nanoparticles biosynthesized from Carduus crispus
Authors: Urnukhsaikhan Enerelt , Bold Bum-Erdene , Gunbileg Aminaa , Sukhbaatar Nominchimeg , Mishig-Ochir Tsogbadrakh
Published: October 2021

In recent years’ synthesis of metal nanoparticle using plants has been extensively studied and recognized as a non-toxic and efficient method applicable in biomedical field. The aim of this study is to investigate the role of different parts of medical plant Carduus crispus on synthesizing silver nanoparticles and characterize the produced nanoparticle. Our study showed that silver nanoparticles (AgNP) synthesized via whole plant extract exhibited a blue shift in absorption spectra with increased optical density, which correlates to a high yield and small size. Also, the results of zeta potential, X-ray diffraction, photon cross-correlation spectroscopy analysis showed the surface charge of − 54.29 ± 4.96 mV (AgNP-S), − 42.64 ± 3.762 mV (AgNP-F), − 46.02 ± 4.17 mV (AgNP-W), the crystallite size of 36 nm (AgNP-S), 13 nm (AgNP-F), 14 nm (AgNP-W) with face-centered cubic structure and average grain sizes of 145.1 nm, 22.5 nm and 99.6 nm. Another important characteristic, such as elemental composition and constituent capping agent has been determined by energy-dispersive X-ray spectroscopy and Fourier transform infrared. The silver nanoparticles were composed of ~ 80% Ag, ~ 15% K, and ~ 7.5% Ca (or ~ 2.8% P) elements. Moreover, the results of the FTIR measurement suggested that the distinct functional groups present in both AgNP-S and AgNP-F were found in AgNP-W. The atomic force microscopy analysis revealed that AgNP-S, AgNP-F and AgNP-W had sizes of 131 nm, 33 nm and 70 nm respectively. In addition, the biosynthesized silver nanoparticles were evaluated for their cytotoxicity and antibacterial activity. At 17 µg/ml concentration, AgNP-S, AgNP-F and AgNP-W showed very low toxicity on HepG2 cell line but also high antibacterial activity. The silver nanoparticles showed antibacterial activity on both gram-negative bacterium Escherichia coli (5.5 ± 0.2 mm to 6.5 ± 0.3 mm) and gram-positive bacterium Micrococcus luteus (7 ± 0.4 mm to 7.7 ± 0.5 mm). Our study is meaningful as a first observation indicating the possibility of using special plant organs to control the characteristics of nanoparticles.