julilili42/papers huggingface dataset:
The Case for an EIC Theory Alliance
2023-03-19

This documents outlines the case for the creation of an EIC Theory Alliance. The EIC will be a unique and versatile facility that will enable the understanding of some of the most compelling questions in the physics of the strong nuclear force. To fully exploit the potential of the EIC, a focused theory effort will be required. The goal of the EIC Theory Alliance is to provide support and stewardship of the theory effort in EIC physics, broadly defined, over the lifetime of the facility. It will promote EIC theory and contribute to workforce development through: support of graduate students; EIC Theory Fellowships for postdocs; bridge positions at universities; and short and long term visitor programs to enhance collaboration between groups. In addition, the alliance will organize topical schools and workshops. The EIC Theory Alliance will be a decentralized organization, open to participation by anyone in the community who is interested in EIC physics, i.e., it will be a membership organization, where members elect an executive board which will effectively run the alliance. The executive board will determine the major scientific thrusts of the theory alliance, make decisions regarding at which universities bridge faculty positions will be created, and serve as a search committee for EIC-related positions. Furthermore, the executive board will coordinate the organization of workshops and schools related to the research activities of the alliance. In addition, the EIC theory alliance will seek out and nurture international cooperation to maximally leverage the available funding. The EIC theory alliance has a wider range of physics goals and longer lifetime, commensurate with that of the EIC research program, than individual nuclear theory topical collaborations. The structure of the EIC Theory Alliance will build on previous examples of successful alliances in nuclear theory.
Slab tearing in non-collisional settings: Insights from thermo-mechanical modelling of oblique subduction
2023-03-20

The propagation of slab break-off (slab tearing) is usually attributed to laterally variable plate convergence systems with a spatial transition between simultaneous oceanic subduction and continental collision. To study the process of slab tearing in a non-collisional geodynamic context, here we use a 3D thermo-mechanical numerical approach to model the oblique subduction of a homogeneous oceanic plate. We investigate the effects of the following parameters: (1) subduction obliquity angle, (2) age of oceanic slab, and (3) partitioning of boundary velocities (i.e., the ratio between the subduction component and the advance of the overriding plate in the total convergence). In our simulations, the retreat of the subduction zone leads to a thinning of the fore-arc and back-arc lithosphere, which are decoupled from the subducting slab by the rise of the hot asthenosphere from the underlying mantle wedge. As a consequence of the initial obliquity of the active plate margin, slab roll-back velocities are subject to progressive along-trench variations. Consistent with the gradual rotation of the trench, the front of the decoupling between the overriding and downgoing plates (together with predicted magmatic activity and topographic uplift) migrates in a horizontal direction. In the experiments with low angles of subduction obliquity (&lt; 15°), relatively old subducting plates (&gt; 50 Ma), and in the absence of the subduction component in the overall shortening, slab detachment either develops simultaneously along the entire length of the subduction zone or does not occur at all. In contrast, with higher subduction obliquity (≥ 15°), younger slabs (≤ 50 Ma) and in the presence of a boundary push on the oceanic side, the initial slab break-off is followed by the gradual growth of the “tear” window in the direction opposite to the migration path of the previously established plates decoupling. The sharp contrast in trench retreat rates between subduction zone segments affected and unaffected by slab detachment results in the arcuate shape of the trench. Furthermore, the direction of slab tearing may change from horizontal to vertical, eventually leading to the formation of a transform fault on the subducting plate. Our results show striking similarities with several features – such as trench curvature, subduction zone segmentation, magmatic production, lithospheric stress/deformation fields, and associated topographic changes – observed in many subduction zones (e.g., Marianas, New Hebrides, Mexico, Calabrian).
Intermittent Exposure to a 16 Hz Extremely Low Frequency Pulsed Electromagnetic Field Promotes Osteogenesis In Vitro through Activating Piezo 1-Induced Ca2+ Influx in Osteoprogenitor Cells
2023-03-20

Exposure to extremely low frequency pulsed electromagnetic fields (ELF-PEMF) is supposed to simulate local EMF generated during mechanical stimulation of bone and may therefore be used to improve bone regeneration. This study aimed at optimizing the exposure strategy and investigating the underlying mechanisms of a 16 Hz ELF-PEMF, previously reported to boost osteoblast function. Comparing influences of daily continuous (30 min every 24 h) and intermittent (10 min every 8 h) exposure to the 16 Hz ELF-PEMF on osteoprogenitor cells revealed that the intermittent exposure strategy enhanced the 16 Hz ELF-PEMF effects regarding cell numbers and osteogenic function. Gene expression of piezo 1 and related Ca2+ influx were significantly increased in SCP-1 cells with the daily intermittent exposure. Pharmacological inhibition of piezo 1 with Dooku 1 largely abolished the positive effect of the 16 Hz ELF-PEMF exposure on osteogenic maturation of SCP-1 cells. In summary, the intermittent exposure strategy enhanced the positive effects of 16 Hz continuous ELF-PEMF exposure in terms of cell viability and osteogenesis. This effect was shown to be mediated by an increased expression of piezo 1 and related Ca2+ influx. Thus, the intermittent exposure strategy is a promising way to further optimize the therapeutic effects of the 16 Hz ELF-PEMF regarding fracture healing or osteoporosis.
Evaluation of Data Dependent MS/MS Acquisition Parameters for Non-targeted Metabolomics and Molecular Networking of Environmental Samples - Focus on the Q Exactive Platform
2023-03-20

Non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) is a widely used tool for the detection and annotation of small molecules in complex environmental samples. Data Dependent Acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with Classical and Feature-based Molecular Networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality related metrics such as annotation and singleton rates, MS/MS placement and coverage. Our results show that Automatic Gain Control, Microscans, Mass Resolution, and Dynamic Exclusion are the most critical parameters, whereas Collision Energy, TopN, and Isolation Width had moderate and Apex Trigger, Monoisotopic Selection, and Isotopic Exclusion minor effects. The insights into the data acquisition ergonomics of the Orbitrap platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.
Resonant contributions to polarized proton structure functions
2023-03-20

Nucleon resonance contributions to the polarized proton g1 and g2 structure functions are computed from resonance electroexcitation amplitudes extracted from CLAS exclusive meson electroproduction data. Including resonances in the mass range up to 1.75 GeV, and taking into account the interference between excited states, we compare the resonant contributions with the polarized proton structure function and polarization asymmetry data from Jefferson Lab 6 GeV measurements. All resonance-like structure observed in the polarized structure functions and asymmetries can be attributed to the resonant contributions, confirming their essential role in the behavior of g1 and g2 in the resonant region over the entire range Q2&lt;7.5GeV2 covered by the measurements. Comparing the resonance contributions with the g1 and g2 structure functions computed from parton distribution functions extrapolated from the deep-inelastic region, we also quantify the degree to which quark-hadron duality holds for g1 and g2 and their moments.
Insights from the first winter weather observations near Mount Everest's summit
2023-03-20

The highest reaches of our planet experience some of the most extreme weather on Earth and hold very significant supplies of freshwater for communities downstream. However, we know very little of the meteorological detail about this high-altitude frontier. We address this here with new winter weather observations from the upper reaches of Mt. Everest (2019-2021). We show that substantial sublimation rates are possible, with losses up to 2.5 mm/d. Wind chill plunging to -83°C, and frostbite possible in less than one minute also attest to the severe cold stress facing mountaineers attempting winter ascents of this most iconic peak.
TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
2023-03-20

Abstract Background The reactivation of genetic programs from early development is a common mechanism for injury-induced organ regeneration. T-box 3 (TBX3) is a member of the T-box family of transcription factors previously shown to regulate pluripotency and subsequent lineage commitment in a number of tissues, including limb and lung. TBX3 is also involved in lung and heart organogenesis. Here, we provide a comprehensive and thorough characterization of TBX3 and its role during pancreatic organogenesis and regeneration. Results We interrogated the level and cell specificity of TBX3 in the developing and adult pancreas at mRNA and protein levels at multiple developmental stages in mouse and human pancreas. We employed conditional mutagenesis to determine its role in murine pancreatic development and in regeneration after the induction of acute pancreatitis. We found that Tbx3 is dynamically expressed in the pancreatic mesenchyme and epithelium. While Tbx3 is expressed in the developing pancreas, its absence is likely compensated by other factors after ablation from either the mesenchymal or epithelial compartments. In an adult model of acute pancreatitis, we found that a lack of Tbx3 resulted in increased proliferation and fibrosis as well as an enhanced inflammatory gene programs, indicating that Tbx3 has a role in tissue homeostasis and regeneration. Conclusions TBX3 demonstrates dynamic expression patterns in the pancreas. Although TBX3 is dispensable for proper pancreatic development, its absence leads to altered organ regeneration after induction of acute pancreatitis.
A Tyrosine Phospho-switch within the Longin Domain of VAMP721 modulates SNARE functionality
2023-03-20

Abstract The final step in secretion is membrane fusion facilitated by SNARE proteins that reside in opposite membranes. The formation of a trans-SNARE complex between one R and three Q coiled-coiled SNARE domains drives the final approach of the membranes providing the mechanical energy for fusion. Biological control of this mechanism is exerted by additional domains within some SNAREs. For example, the N-terminal Longin domain (LD) of R-SNAREs (also called Vesicle-associated membrane proteins, VAMPs) can fold back onto the SNARE domain blocking interaction with other cognate SNAREs. The LD may also determine the subcellular localization via interaction with other trafficking related proteins. Here, we provide cell-biological and genetic evidence that phosphorylation of the Tyrosine57 residue regulates the functionality of VAMP721. We found that an aspartate mutation mimics phosphorylation, leading to protein instability and subsequent degradation in lytic vacuoles. The mutant SNARE also fails to rescue the defects of vamp721vamp722 loss-of-function lines in spite of its wildtype-like localization within the secretory pathway and the ability to interact with cognate SNARE partners. Most importantly, it imposes a dominant negative phenotype interfering with root growth, normal secretion and cytokinesis in wildtype plants generating large aggregates that mainly contain secretory vesicles. Non-phosphorylatable VAMP721 Y57F needs higher gene dosage to rescue double mutants in comparison to native VAMP721 underpinning that phosphorylation modulates SNARE function. We propose a model where a short-lived phosphorylation of Y57 serves as a regulatory step to control VAMP721 activity, favouring its open state and interaction with cognate partners to ultimately drive membrane fusion.
A flexible implant towards acute intrapancreatic electrophysiology
2023-03-20

Abstract Microelectrode arrays (MEAs) have proven to be a powerful tool to study electrophysiological processes over the last decades with most technology developed for investigation of the heart or brain. Other targets in the field of bioelectronic medicine are the peripheral nervous system and its innervation of various organs. Beyond the heart and nervous systems, the beta cells of the pancreatic islets of Langerhans generate action potentials during the production of insulin. In vitro experiments have demonstrated that their activity is a biomarker for blood glucose levels, suggesting that recording their activity in vivo could support patients suffering from diabetes mellitus with long-term automated read-out of blood glucose concentrations. Here, we present a flexible polymer-based implant having 64 low impedance microelectrodes designed to be implanted to a depth of 10 mm into the pancreas. As a first step, the implant will be used in acute experiments in pigs to explore the electrophysiological processes of the pancreas in vivo. Beyond use in the pancreas, our flexible implant and simple implantation method may also be used in other organs such as the brain.
Direct and indirect evidence of compression of word lengths. Zipf's law of abbreviation revisited
2023-03-20

Zipf's law of abbreviation, the tendency of more frequent words to be shorter, is one of the most solid candidates for a linguistic universal, in the sense that it has the potential for being exceptionless or with a number of exceptions that is vanishingly small compared to the number of languages on Earth. Since Zipf's pioneering research, this law has been viewed as a manifestation of a universal principle of communication, i.e. the minimization of word lengths, to reduce the effort of communication. Here we revisit the concordance of written language with the law of abbreviation. Crucially, we provide wider evidence that the law holds also in speech (when word length is measured in time), in particular in 46 languages from 14 linguistic families. Agreement with the law of abbreviation provides indirect evidence of compression of languages via the theoretical argument that the law of abbreviation is a prediction of optimal coding. Motivated by the need of direct evidence of compression, we derive a simple formula for a random baseline indicating that word lengths are systematically below chance, across linguistic families and writing systems, and independently of the unit of measurement (length in characters or duration in time). Our work paves the way to measure and compare the degree of optimality of word lengths in languages.
The Applicability of Photovoice in Pseudo-total Institutions – Methodological Insights From an Exploratory Study on Physical Activity in Nursing Homes
2023-03-20

Photovoice helps participants express their perspectives through photography. As a setting for Photovoice, nursing homes represent challenging, yet promising, contexts partly characterized by elements of Goffman’s concept of “total institutions” and more fully characterized as Heinzelmann’s “pseudo-total institutions.” We analyzed Photovoice’s applicability in nursing homes within the context of physical activity promotion research. Our results indicate Photovoice (1) helps overcome fear and builds trust between researchers and participants, (2) requires certain ethical considerations, (3) addresses technical alienation, (4) determines what is relevant from participants’ point of view, and (5) points out the invisibility of significant others. Further, we provide insights for (6) making Photovoice research a priority in organizational routines, (7) contextualizing photographs, and (8) adjusting for COVID19-related methodological challenges. We also discuss our insights for potential adaptations to ensure participant privacy and safety when using Photovoice in pseudo-total institutions, such as nursing homes. Photovoice reveals activity-promoting and activity-impeding factors possibly unrecognized with other research methods, as well as differences in stakeholder perspectives about physical activity.
Data and analysis code for "Rapid Assessment of Landslide and Rockslide Scale using an Enhanced Probabilistic Neural Network”
2023-03-20

The file includes all codes, landslide and rockslide seismic signal datasets for the establishment of ENPP method and case analysis in paper "Rapid Assessment of Landslide and Rockslide Scale using an Enhanced Probabilistic Neural Network"
Data and analysis code for "Rapid Assessment of Landslide and Rockslide Scale using an Enhanced Probabilistic Neural Network”
2023-03-20

The file includes all codes and landslide seismic signal datasets for the establishment of ENPP method and case analysis in paper "Rapid Assessment of Landslide and Rockslide Scale using an Enhanced Probabilistic Neural Network"
Data and analysis code for "Rapid Identification and Scale Assessment of Landslide using an Enhanced Probabilistic Neural Network”
2023-03-20

The file includes all codes, landslide and rockslide seismic signal datasets for the establishment of ENPP method and case analysis in paper "Rapid Identification and Scale Assessment of Landslide using an Enhanced Probabilistic Neural Network"
Addressing chemical pollution in biodiversity research
2023-03-21

Abstract Climate change, biodiversity loss, and chemical pollution are planetary‐scale emergencies requiring urgent mitigation actions. As these “triple crises” are deeply interlinked, they need to be tackled in an integrative manner. However, while climate change and biodiversity are often studied together, chemical pollution as a global change factor contributing to worldwide biodiversity loss has received much less attention in biodiversity research so far. Here, we review evidence showing that the multifaceted effects of anthropogenic chemicals in the environment are posing a growing threat to biodiversity and ecosystems. Therefore, failure to account for pollution effects may significantly undermine the success of biodiversity protection efforts. We argue that progress in understanding and counteracting the negative impact of chemical pollution on biodiversity requires collective efforts of scientists from different disciplines, including but not limited to ecology, ecotoxicology, and environmental chemistry. Importantly, recent developments in these fields have now enabled comprehensive studies that could efficiently address the manifold interactions between chemicals and ecosystems. Based on their experience with intricate studies of biodiversity, ecologists are well equipped to embrace the additional challenge of chemical complexity through interdisciplinary collaborations. This offers a unique opportunity to jointly advance a seminal frontier in pollution ecology and facilitate the development of innovative solutions for environmental protection.
Biomimetic S‐Adenosylmethionine Regeneration Starting from Multiple Byproducts Enables Biocatalytic Alkylation with Radical SAM Enzymes**
2023-03-21

Abstract S ‐Adenosylmethionine (SAM) is an enzyme cofactor involved in methylation, aminopropyl transfer, and radical reactions. This versatility renders SAM‐dependent enzymes of great interest in biocatalysis. The usage of SAM analogues adds to this diversity. However, high cost and instability of the cofactor impedes the investigation and usage of these enzymes. While SAM regeneration protocols from the methyltransferase (MT) byproduct S ‐adenosylhomocysteine are available, aminopropyl transferases and radical SAM enzymes are not covered. Here, we report a set of efficient one‐pot systems to supply or regenerate SAM and SAM analogues for all three enzyme classes. The systems’ flexibility is showcased by the transfer of an ethyl group with a cobalamin‐dependent radical SAM MT using S ‐adenosylethionine as a cofactor. This shows the potential of SAM (analogue) supply and regeneration for the application of diverse chemistry, as well as for mechanistic studies using cofactor analogues.
Cortical processing during robot and functional electrical stimulation
2023-03-21

Introduction Like alpha rhythm, the somatosensory mu rhythm is suppressed in the presence of somatosensory inputs by implying cortical excitation. Sensorimotor rhythm (SMR) can be classified into two oscillatory frequency components: mu rhythm (8–13 Hz) and beta rhythm (14–25 Hz). The suppressed/enhanced SMR is a neural correlate of cortical activation related to efferent and afferent movement information. Therefore, it would be necessary to understand cortical information processing in diverse movement situations for clinical applications. Methods In this work, the EEG of 10 healthy volunteers was recorded while fingers were moved passively under different kinetic and kinematic conditions for proprioceptive stimulation. For the kinetics aspect, afferent brain activity (no simultaneous volition) was compared under two conditions of finger extension: (1) generated by an orthosis and (2) generated by the orthosis simultaneously combined and assisted with functional electrical stimulation (FES) applied at the forearm muscles related to finger extension. For the kinematic aspect, the finger extension was divided into two phases: (1) dynamic extension and (2) static extension (holding the extended position). Results In the kinematic aspect, both mu and beta rhythms were more suppressed during a dynamic than a static condition. However, only the mu rhythm showed a significant difference between kinetic conditions (with and without FES) affected by attention to proprioception after transitioning from dynamic to static state, but the beta rhythm was not. Discussion Our results indicate that mu rhythm was influenced considerably by muscle kinetics during finger movement produced by external devices, which has relevant implications for the design of neuromodulation and neurorehabilitation interventions.