julilili42/papers huggingface dataset:
A tyrosine phospho‐switch within the Longin domain of VAMP721 modulates SNARE functionality
2023-09-02

SUMMARY 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 short‐lived phosphorylation of Y57 serves as a regulatory step to control VAMP721 activity, favoring its open state and interaction with cognate partners to ultimately drive membrane fusion.
Language contact phenomena in multiword units: The code-switching–calquing continuum
2023-09-02

Aims and objectives: Code-switching and calquing are two widespread language contact phenomena in bilingual speech. While both phenomena have been discussed extensively in research on language contact in the past decades, only very few studies systematically investigate code-switching and calquing of and within multiword units or constructions. In our contribution, we aim at developing a more differentiated account of code-switching and calquing of and within multiword units and constructions, bringing together recent usage-based psycholinguistic and Construction Grammar theories and modeling with cognitively oriented approaches to language contact and bilingualism. Design: We analyze and discuss corpus data from the Corpus of Spanish in Southern Arizona (CESA) from first-, second-, and third-generation bilingual Spanish–English speakers in Arizona. Data and analysis: The corpus analysis focuses on code-switching and calquing of and within N Prep N, NN(N), and Adj N/N Adj patterns (N = noun, Prep = preposition, Adj = adjective). Findings/conclusions: The analysis highlights the importance of both lexically specific multiword units and partially and fully schematic constructions in code-switching and calquing as well as a continuum between constructions situated closer to the lexical or to the syntactic pole. Originality: Whereas multiword sequences have been found to play an important role in (mostly first language [L1]) acquisition, use, and processing, the role of multiword units and constructions in bilingual speech has been much less studied so far. Significance/implications: The study shows that both lexically specific constructions or multiword units as well as partially or fully schematic constructions play a central role in code-switching and calquing. The study argues that code-switching and calquing may ultimately be viewed as a continuum, since the speakers rely on similar, highly frequent, and productive constructions and their interlingual correspondences for both phenomena.
Like the swing of the pendulum: The history of government-sponsored rural settlements in São Paulo, Brazil (1820s–1920s)
2023-09-02

This paper studies the history of government-sponsored rural settlements in the province/state of São Paulo, Brazil, as a pendular movement, whose points of reversion depended on the interests of a landowning elite to obtain labour for newly expanding plantations from the 1820s to the 1920s. Faltering infrastructure and ill-defined property rights over public lands were persistent constraints to the development of such rural settlements. Part of this failure can be attributed to a lack of State capacity and part to the opposition of plantation owners to the settling of independent smallholdings. The paper complements this historical-institutional analysis with a quantitative description of such settlements in 1898–1920. These late government-sponsored rural settlements showed the potential to grow in demographic and economic terms and had an overall demographic and occupational composition well aligned with the goal of creating a family-based peasantry. However, there were enormous heterogeneities in ethno-linguistic composition, educational attainment, and economic prosperity between and within such rural settlements, which point to idiosyncratic features that should be taken into account in future research assessing the short- and long-run effects of immigration and settlement policies in Brazil.
Automated sample preparation with 6-Aminoquinolyl-N-hydroxysuccinimidyl carbamate and iodoacetamide derivatization reagents for enantioselective liquid chromatography tandem mass spectrometry amino acid analysis
2023-09-03

Enantioselective amino acid analysis is gaining increasing importance in pharmaceutical, biomedical and food sciences. While there are many methods available for enantiomer separation of amino acids, the simultaneous analysis of all chiral proteinogenic amino acids by a single method with one column and a single condition is still challenging. Herein, we report an enantioselective high-performance liquid chromatography-tandem mass spectrometry (LC-MS) assay using Chiralpak QN-AX as chiral column. With 6-aminoquinolyl-N-hydrosysuccinimidyl carbamate (AQC) as derivatization reagent, efficient enantioselective separation of D- and L-amino acids using HPLC has become possible. Thiol-containing amino acids like Cys are alkylated prior to AQC-labelling. A protocol for automated sample preparation including both derivatization step and calibrator preparation is presented. For compensating matrix effects, u-<sup>13</sup>C<sup>15</sup>N-labelled internal standards (IS) were employed. The method was validated and applied to the enantioselective analysis of amino acids in a bacterial fermentation broth.
From colonial exploitation to renewable transition: A critical analysis of Africa's energy paradigm
2023-09-03

In this article, we examine the intersection of energy and colonialism in Africa. Specifically, we argue that at the core, colonial projects are driven by the imperative to transform the potential energy stored in colonized (or colonizable) subjects into mechanical energy for the production of wealth. We cohere how the search for new forms of energy has engendered vociferous criticism of fossil fuel and other environmentally degrading sources of energy under energy colonialism. We critique this rationale and identify the (neo)colonial catalysts behind the decisions to switch from one energy form to another. We further argue that colonialism has the coloration of a search for new forms of energy and that the wave of the current push for the transition to renewable energy (RE) in Africa is subtly related to this imperial project. We conclude that although the transition to RE is assumed to be the next big and sustainable energy source for Africa, such a transition must only be deployed after stripping it from the vestiges of colonialism that characterized previous energy transitions. This article, as a contribution to knowledge, provides a framework for a fair and just RE transition in Africa.
Optimizing Predictive Metrics for Human Reading Behavior
2023-09-03

Abstract Expectation and memory have been found to play crucial roles in human language comprehension. Currently, the effects of both expectation and memory can be estimated using computational methods. Computational metrics of surprisal and semantic relevance, which represent expectation and memory respectively, have been developed to accurately predict and explain language comprehension and processing. However, their efficacy is hindered by their inadequate integration of contextual information. Drawing inspiration from the attention mechanism in transformers and human forgetting mechanism, this study introduces an attention-aware method that thoroughly incorporates contextual information, updating surprisal and semantic relevance into attention-aware metrics respectively. Furthermore, by employing the quantum superposition principle, the study proposes an enhanced approach for integrating and encoding diverse information sources based on the two attention-aware metrics. Metrics that are both attention-aware and enhanced can integrate information from expectation and memory, showing superior effectiveness compared to existing metrics. This leads to more accurate predictions of eye movements during the reading of naturalistic discourse in 13 languages. The proposed approaches are fairly capable of facilitating simulation and evaluation of existing reading models and language processing theories. The metrics computed by the proposed approaches are highly interpretable and exhibit cross-language generalizations in predicting language comprehension. The innovative computational methods proposed in this study hold the great potential to enhance our understanding of human working memory mechanisms, human reading behavior and cognitive modeling in language processing. Moreover, they have the capacity to revolutionize ongoing research in computational cognition for language processing, offering valuable insights for computational neuroscience, quantum cognition and optimizing the design of AI systems.
Fair and equitable AI in biomedical research and healthcare: Social science perspectives
2023-09-04

Artificial intelligence (AI) offers opportunities but also challenges for biomedical research and healthcare. This position paper shares the results of the international conference "Fair medicine and AI" (online 3-5 March 2021). Scholars from science and technology studies (STS), gender studies, and ethics of science and technology formulated opportunities, challenges, and research and development desiderata for AI in healthcare. AI systems and solutions, which are being rapidly developed and applied, may have undesirable and unintended consequences including the risk of perpetuating health inequalities for marginalized groups. Socially robust development and implications of AI in healthcare require urgent investigation. There is a particular dearth of studies in human-AI interaction and how this may best be configured to dependably deliver safe, effective and equitable healthcare. To address these challenges, we need to establish diverse and interdisciplinary teams equipped to develop and apply medical AI in a fair, accountable and transparent manner. We formulate the importance of including social science perspectives in the development of intersectionally beneficent and equitable AI for biomedical research and healthcare, in part by strengthening AI health evaluation.
Timing and drivers of exhumation and sedimentation in the eastern Peruvian Andes: Insights from thermokinematic modelling
2023-09-04

This study assesses the impact of fold-thrust belt driven deformation on the topographic evolution, bedrock exhumation and basin formation in the southeastern Peruvian Andes. We do this through a flexural and thermokinematically modelled balanced cross-section. In addition, published thermochronology samples from low-elevation (river canyons) and high-elevation (interfluves) and Cenozoic sedimentary basin datasets along the balanced cross-section were used to evaluate the age, location, and geometry of fault-driven uplift, as well as potential relationships to the timing of ∼2 km of canyon incision. The integrated structural, thermochronologic, and basin data were used to test the sensitivity of model results to various shortening rates and durations, a range of thermophysical parameters, and different magnitudes and timing of canyon incision. Results indicate that young apatite (U-Th)/He (AHe) canyon samples from ∼2 km in elevation or lower are consistent with river incision occurring between ∼8–2 Ma and are independent of the timing of ramp-driven uplift and accompanying erosion. In contrast, replicating the young AHe canyon samples located at &amp;gt;2.7 km elevation requires ongoing ramp-driven uplift. Replicating older interfluve cooling ages concurrent with young canyon ages necessitates slow shortening rates (0.25–0.6 mm/y) from ∼10 Ma to Present, potentially reflecting a decrease in upper plate compression during slab steepening. The best-fit model that reproduces basin ages and depositional contacts requires a background shortening rate of 3–4 mm/y with a marked decrease in rates to ≤0.5 mm/y at ∼10 Ma. Canyon incision occurred during this period of slow shortening, potentially enhanced by Pliocene climate change.
The genetic and physiological basis of Arabidopsis thaliana tolerance to Pseudomonas viridiflava
2023-09-04

Summary The opportunistic pathogen Pseudomonas viridiflava colonizes &gt; 50 agricultural crop species and is the most common Pseudomonas in the phyllosphere of European Arabidopsis thaliana populations. Belonging to the P. syringae complex, it is genetically and phenotypically distinct from well‐characterized P. syringae sensu stricto . Despite its prevalence, we lack knowledge of how A. thaliana responds to its native isolates at the molecular level. Here, we characterize the host response in an A. thaliana – P. viridiflava pathosystem. We measured host and pathogen growth in axenic infections and used immune mutants, transcriptomics, and metabolomics to determine defense pathways influencing susceptibility to P. viridiflava infection. Infection with P. viridiflava increased jasmonic acid (JA) levels and the expression of ethylene defense pathway marker genes. The immune response in a susceptible host accession was delayed compared with a tolerant one. Mechanical injury rescued susceptibility, consistent with an involvement of JA. The JA/ethylene pathway is important for suppression of P. viridiflava , yet suppression capacity varies between accessions. Our results shed light on how A. thaliana can suppress the ever‐present P. viridiflava , but further studies are needed to understand how P. viridiflava evades this suppression to spread broadly across A. thaliana populations.
Search for tri-nucleon decays of $$^{76}$$Ge in GERDA
2023-09-04

Abstract We search for tri-nucleon decays of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>76</mml:mn> </mml:msup> </mml:math> Ge in the dataset from the GERmanium Detector Array (GERDA) experiment. Decays that populate excited levels of the daughter nucleus above the threshold for particle emission lead to disintegration and are not considered. The ppp-, ppn-, and pnn-decays lead to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Cu, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Zn, and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Ga nuclei, respectively. These nuclei are unstable and eventually proceed by the beta decay of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Ga to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Ge (stable). We search for the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>73</mml:mn> </mml:msup> </mml:math> Ga decay exploiting the fact that it dominantly populates the 66.7 keV <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mrow> <mml:mn>73</mml:mn> <mml:mi>m</mml:mi> </mml:mrow> </mml:msup> </mml:math> Ga state with half-life of 0.5 s. The nnn-decays of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>76</mml:mn> </mml:msup> </mml:math> Ge that proceed via <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mrow> <mml:mn>73</mml:mn> <mml:mi>m</mml:mi> </mml:mrow> </mml:msup> </mml:math> Ge are also included in our analysis. We find no signal candidate and place a limit on the sum of the decay widths of the inclusive tri-nucleon decays that corresponds to a lower lifetime limit of 1.2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mo>×</mml:mo> </mml:math> 10 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mn>26</mml:mn> </mml:msup> </mml:math> yr (90% credible interval). This result improves previous limits for tri-nucleon decays by one to three orders of magnitude.
The Importance of the Piperazine Ring for the Development of Trypanomicide Compounds
2023-09-04

Abstract Chagas disease (CD) is one of extremely Neglected Tropical Diseases (NTD) that have been challenging the health of billions of people in the world. Despite being a threat worldwide many of these diseases have a scarce chemotherapeutic armamentarium and the drugs currently used are not effective because of several reason, such as drug resistance, serious side‐effects, among others. Only two drugs are currently available for CD therapeutics, and they are not active in the chronic phase of the diseases. Considering the huge necessity of drugs for this parasitosis, the search for either new or better drugs than those used, many research groups have been involved in this investigation. New scaffolds can be used with this purpose and piperazine is one of them. Since it has many chemical, pharmacological and pharmacokinetics advantages, including multitarget activity, this group has been often used in CD. In this review, which the role of piperazine group in the structure‐activity of some important targets for T. cruzi , as cruzain, trypanothione reductase, Fe‐superoxide dismutase, and nitroreductase as well, is comprehended, several examples have been given to inspire researchers to optimize either hit or lead compounds against T. cruzi .
Stable Yaw Estimation of Boats from the Viewpoint of UAVs and USVs
2023-09-04

Yaw estimation of boats from the viewpoint of unmanned aerial vehicles (UAVs) and unmanned surface vehicles (USVs) or boats is a crucial task in various applications such as 3D scene rendering, trajectory prediction, and navigation. However, the lack of literature on yaw estimation of objects from the viewpoint of UAVs has motivated us to address this domain. In this paper, we propose a method based on HyperPosePDF for predicting the orientation of boats in the 6D space. For that, we use existing datasets, such as PASCAL3D+ and our own datasets, SeaDronesSee-3D and BOArienT, which we annotated manually. We extend HyperPosePDF to work in video-based scenarios, such that it yields robust orientation predictions across time. Naively applying HyperPosePDF on video data yields single-point predictions, resulting in far-off predictions and often incorrect symmetric orientations due to unseen or visually different data. To alleviate this issue, we propose aggregating the probability distributions of pose predictions, resulting in significantly improved performance, as shown in our experimental evaluation. Our proposed method could significantly benefit downstream tasks in marine robotics.
A QGIS -plugin for gully erosion modeling
2023-09-04

Abstract Gully erosion affects the landscape and human life in many ways, including the destruction of agricultural land and infrastructures, altering the hydraulic potential of soils, as well as water availability. Due to climate change, more areas are expected to be affected by gully erosion in the future, threatening especially low-income agricultural regions. In the past decades, quantitative methods have been proposed to simulate and predict gully erosion at different scales. However, gully erosion is still underrepresented in modern GIS-based modeling and simulation approaches. Therefore, this study aims to develop a QGIS plugin using Python to assess gully erosion dynamics. We explain the preparation of the input data, the modeling procedure based on Sidorchuk’s (Sidorchuk A (1999) Dynamic and static models of gully erosion. CATENA 37:401–414.) gully simulation model, and perform a detailed sensitivity analysis of model parameters. The plugin uses topographical data, soil characteristics and discharge information as gully model input. The plugin was tested on a gully network in KwaThunzi, KwaZulu-Natal, South Africa. The results and sensitivity analyses confirm Sidorchuck’s earlier observations that the critical runoff velocity is a main controlling parameter in gully erosion evolution, alongside with the slope stability threshold and the soil erodibility coefficient. The implemented QGIS plugin simplifies the gully model setup, the input parameter preparation as well as the post-processing and visualization of modelling results. The results are provided in different data formats to be visualized with different 3D visualization software tools. This enables a comprehensive gully assessment and the derivation of respective coping and mitigation strategies.
Older adults’ coping strategies during the COVID-19 pandemic – a longitudinal mixed-methods study
2023-09-04

Introduction Older age is a main risk factor for severe COVID-19. In 2020, a broad political debate was initiated as to what extent older adults need special protection and isolation to minimize their risk for SARS-CoV-2 infection. However, isolation might also have indirect negative psychological (e.g., loneliness, stress, fear, anxiety, depression) or physical (e.g., lack of exercise, missing medical visits) consequences depending on individual strategies and personality traits to cope longitudinally with this crisis. Methods To examine the impact of individuals’ coping with the pandemic on mental health, a large sample of 880 older adults of the prospective longitudinal cohort TREND study were surveyed six times about their individual coping strategies in the COVID-19 pandemic between May 2020 (05/2020: M age = 72.1, SD age = 6.4, Range: 58–91 years) and November 2022 in an open response format. The relevant survey question was: “What was helpful for you to get through the last months despite the COVID-19 pandemic? E.g. , phone calls, going for a walk, or others.” Results and Discussion In total, we obtained 4,561 records containing 20,578 text passages that were coded and assigned to 427 distinct categories on seven levels based on qualitative content analysis using MAXQDA. The results allow new insights into the impact of personal prerequisites (e.g., value beliefs, living conditions), the general evaluation of the pandemic (e.g., positive, irrelevant, stressful) as well as the applied coping strategies (e.g., cognitive, emotional- or problem-focused) to deal with the COVID-19 pandemic by using an adapted Lazarus stress model. Throughout the pandemic emotional-focused as well as problem-focused strategies were the main coping strategies, whereas general beliefs, general living conditions and the evaluation were mentioned less frequently.