bluuebunny/crossref_metadata_2025_split huggingface dataset:
PEG-stabilized coaxial stacking of two-dimensional covalent organic frameworks for enhanced photocatalytic hydrogen evolution
Authors: Zhou Ting , Wang Lei , Huang Xingye , Unruangsri Junjuda , Zhang Hualei , Wang Rong , Song Qingliang , Yang Qingyuan , Li Weihua , Wang Changchun , Takahashi Kaito , Xu Hangxun , Guo Jia 
Published: June 2021

AbstractTwo-dimensional covalent organic frameworks (2D COFs) featuring periodic frameworks, extended π-conjugation and layered stacking structures, have emerged as a promising class of materials for photocatalytic hydrogen evolution. Nevertheless, the layer-by-layer assembly in 2D COFs is not stable during the photocatalytic cycling in water, causing disordered stacking and declined activity. Here, we report an innovative strategy to stabilize the ordered arrangement of layered structures in 2D COFs for hydrogen evolution. Polyethylene glycol is filled up in the mesopore channels of a β-ketoenamine-linked COF containing benzothiadiazole moiety. This unique feature suppresses the dislocation of neighbouring layers and retains the columnar π-orbital arrays to facilitate free charge transport. The hydrogen evolution rate is therefore remarkably promoted under visible irradiation compared with that of the pristine COF. This study provides a general post-functionalization strategy for 2D COFs to enhance photocatalytic performances.
Thbs1 induces lethal cardiac atrophy through PERK-ATF4 regulated autophagy
Authors: Vanhoutte Davy , Schips Tobias G. , Vo Alexander , Grimes Kelly M. , Baldwin Tanya A. , Brody Matthew J. , Accornero Federica , Sargent Michelle A. , Molkentin Jeffery D. 
Published: June 2021

AbstractThe thrombospondin (Thbs) family of secreted matricellular proteins are stress- and injury-induced mediators of cellular attachment dynamics and extracellular matrix protein production. Here we show that Thbs1, but not Thbs2, Thbs3 or Thbs4, induces lethal cardiac atrophy when overexpressed. Mechanistically, Thbs1 binds and activates the endoplasmic reticulum stress effector PERK, inducing its downstream transcription factor ATF4 and causing lethal autophagy-mediated cardiac atrophy. Antithetically, Thbs1−/− mice develop greater cardiac hypertrophy with pressure overload stimulation and show reduced fasting-induced atrophy. Deletion of Thbs1 effectors/receptors, including ATF6α, CD36 or CD47 does not diminish Thbs1-dependent cardiac atrophy. However, deletion of the gene encoding PERK in Thbs1 transgenic mice blunts the induction of ATF4 and autophagy, and largely corrects the lethal cardiac atrophy. Finally, overexpression of PERK or ATF4 using AAV9 gene-transfer similarly promotes cardiac atrophy and lethality. Hence, we identified Thbs1-mediated PERK-eIF2α-ATF4-induced autophagy as a critical regulator of cardiomyocyte size in the stressed heart.
The human nucleoporin Tpr protects cells from RNA-mediated replication stress
Authors: Kosar Martin , Giannattasio Michele , Piccini Daniele , Maya-Mendoza Apolinar , García-Benítez Francisco , Bartkova Jirina , Barroso Sonia I. , Gaillard Hélène , Martini Emanuele , Restuccia Umberto , Ramirez-Otero Miguel Angel , Garre Massimiliano , Verga Eleonora , Andújar-Sánchez Miguel , Maynard Scott , Hodny Zdenek , Costanzo Vincenzo , Kumar Amit , Bachi Angela , Aguilera Andrés , Bartek Jiri , Foiani Marco 
Published: June 2021

AbstractAlthough human nucleoporin Tpr is frequently deregulated in cancer, its roles are poorly understood. Here we show that Tpr depletion generates transcription-dependent replication stress, DNA breaks, and genomic instability. DNA fiber assays and electron microscopy visualization of replication intermediates show that Tpr deficient cells exhibit slow and asymmetric replication forks under replication stress. Tpr deficiency evokes enhanced levels of DNA-RNA hybrids. Additionally, complementary proteomic strategies identify a network of Tpr-interacting proteins mediating RNA processing, such as MATR3 and SUGP2, and functional experiments confirm that their depletion trigger cellular phenotypes shared with Tpr deficiency. Mechanistic studies reveal the interplay of Tpr with GANP, a component of the TREX-2 complex. The Tpr-GANP interaction is supported by their shared protein level alterations in a cohort of ovarian carcinomas. Our results reveal links between nucleoporins, DNA transcription and replication, and the existence of a network physically connecting replication forks with transcription, splicing, and mRNA export machinery.
Nuclear ADP-ribosylation drives IFNγ-dependent STAT1α enhancer formation in macrophages
Authors: Gupte Rebecca , Nandu Tulip , Kraus W. Lee 
Published: June 2021

AbstractSTAT1α is a key transcription factor driving pro-inflammatory responses in macrophages. We found that the interferon gamma (IFNγ)-regulated transcriptional program in macrophages is controlled by ADP-ribosylation (ADPRylation) of STAT1α, a post-translational modification resulting in the site-specific covalent attachment of ADP-ribose moieties. PARP-1, the major nuclear poly(ADP-ribose) polymerase (PARP), supports IFNγ-stimulated enhancer formation by regulating the genome-wide binding and IFNγ-dependent transcriptional activation of STAT1α. It does so by ADPRylating STAT1α on specific residues in its DNA-binding domain (DBD) and transcription activation (TA) domain. ADPRylation of the DBD controls STAT1α binding to its cognate DNA elements, whereas ADPRylation of the TA domain regulates enhancer activation by modulating STAT1α phosphorylation and p300 acetyltransferase activity. Loss of ADPRylation at either site leads to diminished IFNγ-dependent transcription and downstream pro-inflammatory responses. We conclude that PARP-1-mediated ADPRylation of STAT1α drives distinct enhancer activation mechanisms and is a critical regulator of inflammatory responses in macrophages.
Diversity-oriented synthesis of nanographenes enabled by dearomative annulative π-extension
Authors: Matsuoka Wataru , Ito Hideto , Sarlah David , Itami Kenichiro 
Published: June 2021

AbstractNanographenes and polycyclic aromatic hydrocarbons (PAHs) are among the most important classes of compounds, with potential applications in nearly all areas of science and technology. While the theoretically possible number of nanographene structures is extraordinary, most of these molecules remain synthetically out of reach due to a lack of programmable and diversity-oriented synthetic methods, and their potentially huge structure-property diversity has not been fully exploited. Herein we report a diversity-oriented, growth-from-template synthesis of nanographenes enabled by iterative annulative π-extension (APEX) reactions from small PAH starting materials. The developed dearomative annulative π-extension (DAPEX) reaction enables π-elongation at the less-reactive M-regions of PAHs, and is successfully combined with complementary APEX reactions that occur at K- and bay-regions to access a variety of previously untapped nanographenes.
Damage mechanism identification in composites via machine learning and acoustic emission
Authors: Muir C. , Swaminathan B. , Almansour A. S. , Sevener K. , Smith C. , Presby M. , Kiser J. D. , Pollock T. M. , Daly S. 
Published: June 2021

AbstractDamage mechanism identification has scientific and practical ramifications for the structural health monitoring, design, and application of composite systems. Recent advances in machine learning uncover pathways to identify the waveform-damage mechanism relationship in higher-dimensional spaces for a comprehensive understanding of damage evolution. This review evaluates the state of the field, beginning with a physics-based understanding of acoustic emission waveform feature extraction, followed by a detailed overview of waveform clustering, labeling, and error analysis strategies. Fundamental requirements for damage mechanism identification in any machine learning framework, including those currently in use, under development, and yet to be explored, are discussed.
Adaptive quantum state tomography with neural networks
Authors: Quek Yihui , Fort Stanislav , Ng Hui Khoon 
Published: June 2021

AbstractCurrent algorithms for quantum state tomography (QST) are costly both on the experimental front, requiring measurement of many copies of the state, and on the classical computational front, needing a long time to analyze the gathered data. Here, we introduce neural adaptive quantum state tomography (NAQT), a fast, flexible machine-learning-based algorithm for QST that adapts measurements and provides orders of magnitude faster processing while retaining state-of-the-art reconstruction accuracy. As in other adaptive QST schemes, measurement adaptation makes use of the information gathered from previous measured copies of the state to perform a targeted sensing of the next copy, maximizing the information gathered from that next copy. Our NAQT approach allows for a rapid and seamless integration of measurement adaptation and statistical inference, using a neural-network replacement of the standard Bayes’ update, to obtain the best estimate of the state. Our algorithm, which falls into the machine learning subfield of “meta-learning” (in effect “learning to learn” about quantum states), does not require any ansatz about the form of the state to be estimated. Despite this generality, it can be retrained within hours on a single laptop for a two-qubit situation, which suggests a feasible time-cost when extended to larger systems and potential speed-ups if provided with additional structure, such as a state ansatz.
Guiding urban water management towards 1.5 °C
Authors: Parkinson Simon 
Published: June 2021

AbstractReliable access to clean and affordable water is prerequisite for human well being, but its provision in cities generates environmental externalities including greenhouse gas (GHG) emissions. As policy-makers target opportunities to mitigate GHGs in line with the Paris Agreement, it remains vague how urban water management can contribute to the goal of limiting climate warming to 1.5 °C. This perspective guides policy-makers in the selection of innovative technologies and strategies for leveraging urban water management as a climate change mitigation solution. Recent literature, data and scenarios are reviewed to shine a light on the GHG mitigation potential and the key areas requiring future research. Increasing urban water demands in emerging economies and over-consumption in developed regions pose mitigation challenges due to energy and material requirements that can be partly offset through end-use water conservation and expansion of decentralized, nature-based solutions. Policies that integrate urban water and energy flows, or reconfigure urban water allocation at the river basin-level remain untapped mitigation solutions with large gaps in our understanding of potentials.
Study on the average speed of particles from a particle swarm derived from a stationary particle swarm
Authors: Guo Tao 
Published: June 2021

AbstractIt has been more than 100 years since the advent of special relativity, but the reasons behind the related phenomena are still unknown. This article aims to inspire people to think about such problems. With the help of Mathematica software, I have proven the following problem by means of statistics: In 3-dimensional Euclidean space, for point particles whose speeds are c and whose directions are uniformly distributed in space (assuming these particles’ reference system is $$\mathcal {R}_{0}$$

R
0

, if their average velocity is 0), when some particles (assuming their reference system is $$\mathcal {R}_{u}$$

R
u

), as a particle swarm, move in a certain direction with a group speed u (i.e., the norm of the average velocity) relative to $$\mathcal {R}_{0}$$

R
0

, their (or the sub-particle swarm’s) average speed relative to $$\mathcal {R}_{u}$$

R
u

is slower than that of particles (or the same scale sub-particle swarm) in $$\mathcal {R}_{0}$$

R
0

relative to $$\mathcal {R}_{0}$$

R
0

. The degree of slowing depends on the speed u of $$\mathcal {R}_{u}$$

R
u

and accords with the quantitative relationship described by the Lorentz factor $$\frac{c}{\sqrt{c^2-u^2}}$$

c

c
2

-

u
2

. Base on this conclusion, I have deduced the speed distribution of particles in $$\mathcal {R}_{u}$$

R
u

when observing from $$\mathcal {R}_{0}$$

R
0

.
Chimeric vaccine designs against Acinetobacter baumannii using pan genome and reverse vaccinology approaches
Authors: Shahid Fatima , Zaheer Tahreem , Ashraf Shifa Tariq , Shehroz Muhammad , Anwer Farha , Naz Anam , Ali Amjad 
Published: June 2021

AbstractAcinetobacter baumannii (A. baumannii), an opportunistic, gram-negative pathogen, has evoked the interest of the medical community throughout the world because of its ability to cause nosocomial infections, majorly infecting those in intensive care units. It has also drawn the attention of researchers due to its evolving immune evasion strategies and increased drug resistance. The emergence of multi-drug-resistant-strains has urged the need to explore novel therapeutic options as an alternative to antibiotics. Due to the upsurge in antibiotic resistance mechanisms exhibited by A. baumannii, the current therapeutic strategies are rendered less effective. The aim of this study is to explore novel therapeutic alternatives against A. baumannii to control the ailed infection. In this study, a computational framework is employed involving, pan genomics, subtractive proteomics and reverse vaccinology strategies to identify core promiscuous vaccine candidates. Two chimeric vaccine constructs having B-cell derived T-cell epitopes from prioritized vaccine candidates; APN, AdeK and AdeI have been designed and checked for their possible interactions with host BCR, TLRs and HLA Class I and II Superfamily alleles. These vaccine candidates can be experimentally validated and thus contribute to vaccine development against A. baumannii infections.
Atmospheric reaction of hydrazine plus hydroxyl radical
Authors: Douroudgari Hamed , Vahedpour Morteza , Khouini Fahime 
Published: June 2021

AbstractUnderstanding the mechanism of hydrazine oxidation reaction by OH radical along with the rate constants of all possible pathways leads to explain the fate of hydrazine in the atmosphere. In this article, the comprehensive mechanisms and kinetics of the hydrazine plus hydroxyl radical reaction have been investigated theoretically at different temperatures and pressures. To achieve the main goals, a series of high levels of quantum chemical calculations have been widely implemented in reliable channels of the H-abstraction, SN2, and addition/elimination reactions. The energy profile of all pathways accompanied by the molecular properties of the involved stationary points has been characterized at the MP2, M06-2X, and CCSD(T)/CBS levels. To estimate accurate barrier energies of the H-abstraction channels, large numbers of the CCSD (T) calculations in conjunction with various augmented basis sets have been implemented. The direct dynamic calculations have been carried out using the validated M06-2X/maug-cc-pVTZ level, and also by the CCSD(T) (energies) + MP2 (partition functions) level. The pressure-dependent rate constants of the barrierless pathways have been investigated by the strong collision approach. Therefore, the main behaviors of the N2H4 + OH reaction have been explored according to the influences of temperature and pressure on the computed rate coefficients within the well-behaved theoretical frameworks of the TST, VTST, and RRKM theories. It has been found that the H-abstraction mechanism (to form N2H3) is dominant relative to the SN2 reaction and OH-addition to the N center of N2H4moiety (to form H2NOH + NH2). The computed high pressure limit rate constant of the main reaction pathway, k(298.15) = 7.31 × 10–11 cm3molecule−1 s−1, has an excellent agreement with the experimental value (k (298.15) = (6.50 ± 1.3) × 10–11 cm3molecule−1 s−1) recommended by Vaghjiani. Also, the atmospheric lifetime of hydrazine degradation by OH radicals has been demonstrated to be 32.80 to 1161.11 h at the altitudes of 0–50 km. Finally, the disagreement in the calculated rate constants between the previous theoretical study and experimental results has been rectified.
Desmoglein-2 harnesses a PDZ-GEF2/Rap1 signaling axis to control cell spreading and focal adhesions independent of cell–cell adhesion
Authors: Shelton W. Tucker , Thomas S. Madison , Alexander Hunter R. , Thomes C. Evan , Conway Daniel E. , Dubash Adi D. 
Published: June 2021

AbstractDesmosomes have a central role in mediating extracellular adhesion between cells, but they also coordinate other biological processes such as proliferation, differentiation, apoptosis and migration. In particular, several lines of evidence have implicated desmosomal proteins in regulating the actin cytoskeleton and attachment to the extracellular matrix, indicating signaling crosstalk between cell–cell junctions and cell–matrix adhesions. In our study, we found that cells lacking the desmosomal cadherin Desmoglein-2 (Dsg2) displayed a significant increase in spreading area on both fibronectin and collagen, compared to control A431 cells. Intriguingly, this effect was observed in single spreading cells, indicating that Dsg2 can exert its effects on cell spreading independent of cell–cell adhesion. We hypothesized that Dsg2 may mediate cell–matrix adhesion via control of Rap1 GTPase, which is well known as a central regulator of cell spreading dynamics. We show that Rap1 activity is elevated in Dsg2 knockout cells, and that Dsg2 harnesses Rap1 and downstream TGFβ signaling to influence both cell spreading and focal adhesion protein phosphorylation. Further analysis implicated the Rap GEF PDZ-GEF2 in mediating Dsg2-dependent cell spreading. These data have identified a novel role for Dsg2 in controlling cell spreading, providing insight into the mechanisms via which cadherins exert non-canonical junction-independent effects.
Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities
Authors: de Melo Pacífico Dvison , Costa Cecília Leite , Moura Hercules , Barr John R. , Maia Guilherme Augusto , Filho Vilmar Benetti , Moreira Renato Simões , Wagner Glauber , Domingues Regina Maria Cavalcanti Pilotto , Quesada-Gómez Carlos , de Oliveira Ferreira Eliane , de Castro Brito Gerly Anne 
Published: June 2021

AbstractClostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. Data are available via ProteomeXchange with identifier PXD026218. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.
A link between pH homeostasis and colistin resistance in bacteria
Authors: Panta Pradip R. , Doerrler William T. 
Published: June 2021

AbstractColistin resistance is complex and multifactorial. DbcA is an inner membrane protein belonging to the DedA superfamily required for maintaining extreme colistin resistance of Burkholderia thailandensis. The molecular mechanisms behind this remain unclear. Here, we report that ∆dbcA displays alkaline pH/bicarbonate sensitivity and propose a role of DbcA in extreme colistin resistance of B. thailandensis by maintaining cytoplasmic pH homeostasis. We found that alkaline pH or presence of sodium bicarbonate displays a synergistic effect with colistin against not only extremely colistin resistant species like B. thailandensis and Serratia marcescens, but also a majority of Gram-negative and Gram-positive bacteria tested, suggesting a link between cytoplasmic pH homeostasis and colistin resistance across species. We found that lowering the level of oxygen in the growth media or supplementation of fermentable sugars such as glucose not only alleviated alkaline pH stress, but also increased colistin resistance in most bacteria tested, likely by avoiding cytoplasmic alkalinization. Our observations suggest a previously unreported link between pH, oxygen, and colistin resistance. We propose that maintaining optimal cytoplasmic pH is required for colistin resistance in a majority of bacterial species, consistent with the emerging link between cytoplasmic pH homeostasis and antibiotic resistance.
Considerations for quality assurance of multiplex malaria antigen detection assays with large sample sets
Authors: Alvarado Rachel , van den Hoogen Lotus L. , Iriemenam Nnaemeka C. , Akinmulero Oluwaseun O. , Thomas Andrew N. , Tamunonengiyeofori Israel , Erasogie Evbuomwan , Chimaoge Achugbu C. , Dawurung Ayuba B. , Esiekpe Mudiaga K. , Okoli Mary U. , Mba Nwando , Ogunniyi Abiodun , Abimiku Alash’le , Maire Mark , Bassey Orji O. , Okoye McPaul , Swaminathan Mahesh , Greby Stacie M. , Ndodo Nnaemeka , Ihekweazu Chikwe , Abubakar Ado , Steinhardt Laura , Rogier Eric 
Published: June 2021

AbstractMultiplex assays for malaria antigen detection can gather data from large sample sets, but considerations for the consistency and quality assurance (QA) of mass testing lack evaluation. We present a QA framework for a study occurring November 2019 to March 2020 involving 504 assay plates detecting four Plasmodium antigens: pan-Plasmodium aldolase and lactate dehydrogenase (LDH), histidine-rich protein 2 (HRP2), P. vivax LDH (PvLDH). Controls on each plate included buffer blank, antigen negative blood, and 4-point positive dilution curve. The blank and negative blood provided consistently low signal for all targets except for pAldolase, which showed variability. Positive curve signals decreased throughout the 5-month study duration but retained a coefficient of variation (CV) of < 5%, with the exception of HRP2 in month 5 (CV of 11%). Regression fittings for inter-plate control signals provided mean and standard deviations (SDs), and of 504 assay plates, 6 (1.2%) violated the acceptable deviation limits and were repeated. For the 40,272 human blood samples assayed in this study, of 161,088 potential data points (each sample × 4 antigens), 160,641 (99.7%) successfully passed quality checks. The QA framework presented here can be utilized to ensure quality of laboratory antigen detection for large sample sets.