bluuebunny/crossref_metadata_2025_split huggingface dataset:
Violence and repair: The practice and challenges of non-State armed groups engaging in reparations
Authors: Moffett Luke 
Published: August 2021

AbstractAtrocities by non-State armed groups (NSAGs) often capture international attention, but efforts to repair the harm they have caused are often overlooked. This article traces out some of the practices and tensions in NSAGs making reparations during wartime and in post-conflict transitions. It argues that engaging in reparations for acts committed by NSAGs can not only encourage greater compliance with international humanitarian law but also build support amongst civilian populations during armed conflict and facilitate ex-fighter reintegration at the end of hostilities. Drawing from interviews with a number of armed groups, the article also suggests that engaging with the armed group's organization rather than just individuals themselves can be an effective way to collectively mobilize a group's motivation and capacity to deliver on reparations, including recovery of disappeared persons, restitution of property and apologies. As such, this article seeks to contribute to a deeper understanding of reparation practices by NSAGs in order to see how reparations can be mediated and a hierarchy of reparation obligations developed.
Fighting Deforestation in Non-International Armed Conflicts: The Relevance of the Rome Statute for Rosewood Trafficking in Senegal
Authors: Martini Pauline , Sarliève Maud 
Published: August 2021

AbstractThis article examines rosewood trafficking in the Casamance region of Senegal to determine whether acts of massive deforestation committed in the context of a non-international armed conflict can be prosecuted before the International Criminal Court (ICC) as war crimes of pillage and destruction of property under Article 8(2)(e)(v) and (xii) of the Rome Statute, respectively. It examines two of the main challenges resulting from the application of these provisions to acts of massive deforestation in the light of the ICC Elements of Crimes. Firstly, the article addresses the delicate issue of the establishment of a nexus between these acts and the related non-international armed conflict. Secondly, it discusses whether natural resources may qualify as ‘property’ for the purpose of Article 8(2)(e)(v) and (xii). It then offers avenues of reflection regarding the determination of ownership of these resources to fulfil the requirements of the Rome Statute.
Exploring Negative Beliefs About Power
Authors: Wingen Tobias , Dohle Simone 
Published: August 2021

Abstract. “The powerful are immoral”! Across four preregistered studies (total N = 2,744), we explored the role of perceived autonomy (control over own resources) and perceived influence (control over others’ resources) for this belief. In Study 1, perceived autonomy and influence mediated the effect of power on expected immorality. Likewise, directly manipulating perceived autonomy and influence led to increased expected immorality, increased perceived intentionality of a transgression, and consequently to harsher punishment recommendations (Studies 3 and 4). Interestingly, Study 2 revealed an interaction between autonomy and influence, which we however could not replicate in Study 4. Overall, our findings suggest that both autonomy and influence are associated with immorality and thus likely drive the belief that the powerful are immoral.
The Plasma Environment Surrounding the Reiner Gamma Magnetic Anomaly
Authors: Deca J. , Poppe A. R. , Divin A. , Lembège B. 
Published: August 2021

AbstractReiner Gamma is a prime target for low‐orbiting spacecraft or even surface‐landed missions in the near future. The region hosts a prominent lunar swirl that is co‐located with a strong and well‐structured magnetic anomaly. We simulate and discuss Reiner Gamma's near‐surface plasma environment at different altitudes above the lunar surface using the fully kinetic particle‐in‐cell code iPIC3D. The input magnetic field model is based on orbital‐altitude observations from the Kaguya and Lunar Prospector missions. We develop eight simulation cases, representing the distinct plasma regimes. Reiner Gamma is exposed to along a typical orbit, including different solar wind incidence angles and the magnetosheath crossing. We show that the plasma environment is vastly different at different altitudes and depends critically on the upstream plasma parameters, consistent with the predictions of the solar wind standoff model. Our work helps to define measurement requirements for a possible future low‐orbiting or lander mission to the Reiner Gamma area or similarly magnetized regions of the lunar surface.
The Role of Flare‐Driven Ionospheric Electron Density Changes on the Doppler Flash Observed by SuperDARN HF Radars
Authors: Chakraborty S. , Qian L. , Ruohoniemi J. M. , Baker J. B. H. , Mclnerney J. M. , Nishitani N. 
Published: August 2021

AbstractTrans‐ionospheric high frequency (HF: 3–30 MHz) signals experience strong attenuation following a solar flare‐driven sudden ionospheric disturbance (SID). Solar flare‐driven HF absorption, referred to as short‐wave fadeout, is a well‐known impact of SIDs, but the initial Doppler frequency shift phenomena, also known as “Doppler flash” in the traveling radio wave is not well understood. This study seeks to advance our understanding of the initial impacts of solar flare‐driven SID using a physics‐based whole atmosphere model for a specific solar flare event. First, we demonstrate that the Doppler flash phenomenon observed by Super Dual Auroral Radar Network (SuperDARN) radars can be successfully reproduced using first‐principles based modeling. The output from the simulation is validated against SuperDARN line‐of‐sight Doppler velocity measurements. We then examine which region of the ionosphere, D, E, or F, makes the largest contribution to the Doppler flash. We also consider the relative contribution of change in refractive index through the ionospheric layers versus lowered reflection height. We find: (a) the model is able to reproduce radar observations with an root‐median‐squared‐error and a mean percentage error (δ) of 3.72 m/s and 0.67%, respectively; (b) the F‐region is the most significant contributor to the total Doppler flash (∼48%), 30% of which is contributed by the change in F‐region's refractive index, while the other ∼18% is due to change in ray reflection height. Our analysis shows lowering of the F‐region's ray reflection point is a secondary driver compared to the change in refractive index.
Oxidation of Proteinaceous Matter by Ozone and Nitrogen Dioxide in PM2.5: Reaction Mechanisms and Atmospheric Implications
Authors: Zhu Ren‐Guo , Xiao Hua‐Yun , Wen Zequn , Zhu Yuwen , Fang Xiaozheng , Pan Yuanyuan , Chen Zhenping , Xiao Hongwei 
Published: August 2021

AbstractInteractions between proteinaceous matter and atmospheric oxidants can affect amino acids (AAs) bioavailability, the climate, and human health. However, atmospheric reactions of proteinaceous matter remain poorly understood. PM2.5 samples were collected during spring (2019) and winter (2020) sampling campaigns conducted in Nanchang, China. Concentrations of combined and free AAs, and the δ15N values of combined and free glycine (C‐Gly and F‐Gly) in PM2.5 samples were analyzed. Concentrations of TFAA under different O3 and NO2 levels, and correlations of specific FAA species with ambient O3 and NO2 concentrations suggest that the ability of O3 to release TFAA from proteinaceous matter is greater than that of NO2. Furthermore, O3 may trend to release neutral and hydrophilic FAA species, whereas NO2 tends to generate hydrophobic FAA species. With aerosol aging, the slope of the fitted line between [TFAA] and [TSAA] [O3 + NO2] increased, indicating that FAAs yield from protein degradation in PM2.5 was affected greatly by aerosol aging. The TCAAs concentration observed in spring was substantially higher than that in winter. Moreover, the δ15NF‐Gly and δ15NC‐Gly values in PM2.5 exhibited negative correlations with atmospheric O3 concentration. These results suggest that increased levels of proteinaceous matter in spring were derived from natural sources related to biological activities rather than biomass burning sources. Our study confirms that the reaction of degradation of proteinaceous matter to FAAs could be influenced by aerosol aging, which is a finding that enhances current understanding regarding atmospheric processes of aerosol proteinaceous matter under different ambient O3 and NO2 levels.
Chemical Response of the Upper Atmosphere Due to Lightning‐Induced Electron Precipitation
Authors: Xu Wei , Marshall Robert A. , Kero Antti , Sousa Austin 
Published: August 2021

AbstractTerrestrial lightning frequently serves as a loss mechanism for energetic electrons in the Van Allen radiation belts, leading to lightning‐induced electron precipitation (LEP). Regardless of the specific causes, energetic electron precipitation from the radiation belts in general has a significant influence on the ozone concentration in the stratosphere and mesosphere. The atmospheric chemical effects induced by LEP have been previously investigated using subionospheric VLF measurements at Faraday station, Antarctica (65.25°S, 64.27°W, L = 2.45). However, there exist large variations in the precipitation flux, ionization production, and occurrence rate of LEP events depending on the peak current of the parent lightning discharge, as well as the season, location, and intensity of the thunderstorm activity. These uncertainties motivate us to revisit the calculation of atmospheric chemical changes produced by LEP. In this study, we combine a well‐validated LEP model and first‐principles atmospheric chemical simulation, and investigate three intense storms in the year of 2013, 2015, and 2017 at the magnetic latitude of 50., 32., and 35., respectively. Modeling results show that the LEP events in these storms can cumulatively drive significant changes in the , , and concentration in the mesosphere. These changes are as high as , , and at 75–85 km altitude, respectively, and comparable to the effects typically induced by other types of radiation belt electron precipitation events. Considering the high occurrence rate of thunderstorms around the globe, the long‐term global chemical effects produced by LEP events need to be properly quantified.
Importance of Bcl-2-family proteins in murine hematopoietic progenitor and early B cells
Authors: Kurschat Constanze , Metz Arlena , Kirschnek Susanne , Häcker Georg 
Published: August 2021

AbstractMitochondrial apoptosis regulates survival and development of hematopoietic cells. Prominent roles of some Bcl-2-family members in this regulation have been established, for instance for pro-apoptotic Bim and anti-apoptotic Mcl-1. Additional, mostly smaller roles are known for other Bcl-2-members but it has been extremely difficult to obtain a comprehensive picture of the regulation of mitochondrial apoptosis in hematopoietic cells by Bcl-2-family proteins. We here use a system of mouse ‘conditionally immortalized’ lymphoid-primed hematopoietic progenitor (LMPP) cells that can be differentiated in vitro to pro-B cells, to analyze the importance of these proteins in cell survival. We established cells deficient in Bim, Noxa, Bim/Noxa, Bim/Puma, Bim/Bmf, Bax, Bak or Bax/Bak and use specific inhibitors of Bcl-2, Bcl-XL and Mcl-1 to assess their importance. In progenitor (LMPP) cells, we found an important role of Noxa, alone and together with Bim. Cell death induced by inhibition of Bcl-2 and Bcl-XL entirely depended on Bim and could be implemented by Bax and by Bak. Inhibition of Mcl-1 caused apoptosis that was independent of Bim but strongly depended on Noxa and was completely prevented by the absence of Bax; small amounts of anti-apoptotic proteins were co-immunoprecipitated with Bim. During differentiation to pro-B cells, substantial changes in the expression of Bcl-2-family proteins were seen, and Bcl-2, Bcl-XL and Mcl-1 were all partially in complexes with Bim. In differentiated cells, Noxa appeared to have lost all importance while the loss of Bim and Puma provided protection. The results strongly suggest that the main role of Bim in these hematopoietic cells is the neutralization of Mcl-1, identify a number of likely molecular events during the maintenance of survival and the induction of apoptosis in mouse hematopoietic progenitor cells, and provide data on the regulation of expression and importance of these proteins during differentiation along the B cell lineage.
Teaching a neural network to attach and detach electrons from molecules
Authors: Zubatyuk Roman , Smith Justin S. , Nebgen Benjamin T. , Tretiak Sergei , Isayev Olexandr 
Published: August 2021

AbstractInteratomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2–3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions.
A last-in first-out stack data structure implemented in DNA
Authors: Lopiccolo Annunziata , Shirt-Ediss Ben , Torelli Emanuela , Olulana Abimbola Feyisara Adedeji , Castronovo Matteo , Fellermann Harold , Krasnogor Natalio 
Published: August 2021

AbstractDNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, and able to be interfaced with external nucleic acid computing circuits, have so far received little attention. Here we present an in vitro implementation of a stack data structure using DNA polymers. The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. We derive how the performance of the stack increases with the efficiency of washing steps between successive reaction stages, and report how stack performance depends on the history of stack operations under inefficient washing. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure.
Locomotion dependent neuron-glia interactions control neurogenesis and regeneration in the adult zebrafish spinal cord
Authors: Chang Weipang , Pedroni Andrea , Bertuzzi Maria , Kizil Caghan , Simon András , Ampatzis Konstantinos 
Published: August 2021

AbstractPhysical exercise stimulates adult neurogenesis, yet the underlying mechanisms remain poorly understood. A fundamental component of the innate neuroregenerative capacity of zebrafish is the proliferative and neurogenic ability of the neural stem/progenitor cells. Here, we show that in the intact spinal cord, this plasticity response can be activated by physical exercise by demonstrating that the cholinergic neurotransmission from spinal locomotor neurons activates spinal neural stem/progenitor cells, leading to neurogenesis in the adult zebrafish. We also show that GABA acts in a non-synaptic fashion to maintain neural stem/progenitor cell quiescence in the spinal cord and that training-induced activation of neurogenesis requires a reduction of GABAA receptors. Furthermore, both pharmacological stimulation of cholinergic receptors, as well as interference with GABAergic signaling, promote functional recovery after spinal cord injury. Our findings provide a model for locomotor networks’ activity-dependent neurogenesis during homeostasis and regeneration in the adult zebrafish spinal cord.
Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase
Authors: Newman Joseph A. , Douangamath Alice , Yadzani Setayesh , Yosaatmadja Yuliana , Aimon Antony , Brandão-Neto José , Dunnett Louise , Gorrie-stone Tyler , Skyner Rachael , Fearon Daren , Schapira Matthieu , von Delft Frank , Gileadi Opher 
Published: August 2021

AbstractThere is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two “druggable” pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.
ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer
Authors: Taftaf Rokana , Liu Xia , Singh Salendra , Jia Yuzhi , Dashzeveg Nurmaa K. , Hoffmann Andrew D. , El-Shennawy Lamiaa , Ramos Erika K. , Adorno-Cruz Valery , Schuster Emma J. , Scholten David , Patel Dhwani , Zhang Youbin , Davis Andrew A. , Reduzzi Carolina , Cao Yue , D’Amico Paolo , Shen Yang , Cristofanilli Massimo , Muller William A. , Varadan Vinay , Liu Huiping 
Published: August 2021

AbstractCirculating tumor cell (CTC) clusters mediate metastasis at a higher efficiency and are associated with lower overall survival in breast cancer compared to single cells. Combining single-cell RNA sequencing and protein analyses, here we report the profiles of primary tumor cells and lung metastases of triple-negative breast cancer (TNBC). ICAM1 expression increases by 200-fold in the lung metastases of three TNBC patient-derived xenografts (PDXs). Depletion of ICAM1 abrogates lung colonization of TNBC cells by inhibiting homotypic tumor cell-tumor cell cluster formation. Machine learning-based algorithms and mutagenesis analyses identify ICAM1 regions responsible for homophilic ICAM1-ICAM1 interactions, thereby directing homotypic tumor cell clustering, as well as heterotypic tumor-endothelial adhesion for trans-endothelial migration. Moreover, ICAM1 promotes metastasis by activating cellular pathways related to cell cycle and stemness. Finally, blocking ICAM1 interactions significantly inhibits CTC cluster formation, tumor cell transendothelial migration, and lung metastasis. Therefore, ICAM1 can serve as a novel therapeutic target for metastasis initiation of TNBC.
Genetic and environmental factors in Alzheimer’s and Parkinson’s diseases and promising therapeutic intervention via fecal microbiota transplantation
Authors: Wang Hui , Yang Feng , Zhang Shidong , Xin Ruihua , Sun Yan 
Published: August 2021

AbstractNeurodegenerative diseases are characterized by neuronal impairment and loss of function, and with the major shared histopathological hallmarks of misfolding and aggregation of specific proteins inside or outside cells. Some genetic and environmental factors contribute to the promotion of the development and progression of neurodegenerative diseases. Currently, there are no effective treatments for neurodegenerative diseases. It has been revealed that bidirectional communication exists between the brain and the gut. The gut microbiota is a changeable and experience-dependent ecosystem and can be modified by genetic and environmental factors. The gut microbiota provides potential therapeutic targets that can be regulated as new interventions for neurodegenerative diseases. In this review, we discuss genetic and environmental risk factors for neurodegenerative diseases, summarize the communication among the components of the microbiota-gut-brain axis, and discuss the treatment strategy of fecal microbiota transplantation (FMT). FMT is a promising treatment for neurodegenerative diseases, and restoration of the gut microbiota to a premorbid state is a novel goal for prevention and treatment strategies.
Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing
Authors: Schumacher A. , Rookmaaker M. B. , Joles J. A. , Kramann R. , Nguyen T. Q. , van Griensven M. , LaPointe V. L. S. 
Published: August 2021

AbstractThe kidney is among the most complex organs in terms of the variety of cell types. The cellular complexity of human kidneys is not fully unraveled and this challenge is further complicated by the existence of multiple progenitor pools and differentiation pathways. Researchers disagree on the variety of renal cell types due to a lack of research providing a comprehensive picture and the challenge to translate findings between species. To find an answer to the number of human renal cell types, we discuss research that used single-cell RNA sequencing on developing and adult human kidney tissue and compares these findings to the literature of the pre-single-cell RNA sequencing era. We find that these publications show major steps towards the discovery of novel cell types and intermediate cell stages as well as complex molecular signatures and lineage pathways throughout development. The variety of cell types remains variable in the single-cell literature, which is due to the limitations of the technique. Nevertheless, our analysis approaches an accumulated number of 41 identified cell populations of renal lineage and 32 of non-renal lineage in the adult kidney, and there is certainly much more to discover. There is still a need for a consensus on a variety of definitions and standards in single-cell RNA sequencing research, such as the definition of what is a cell type. Nevertheless, this early-stage research already proves to be of significant impact for both clinical and regenerative medicine, and shows potential to enhance the generation of sophisticated in vitro kidney tissue.