bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parameter and Model Recovery of Reinforcement Learning Models for Restless Bandit Problems
Authors: Danwitz Ludwig , Mathar David , Smith Elke , Tuzsus Deniz , Peters Jan 
Published: June 2022

AbstractMulti-armed restless bandit tasks are regularly applied in psychology and cognitive neuroscience to assess exploration and exploitation behavior in structured environments. These models are also readily applied to examine effects of (virtual) brain lesions on performance, and to infer neurocomputational mechanisms using neuroimaging or pharmacological approaches. However, to infer individual, psychologically meaningful parameters from such data, computational cognitive modeling is typically applied. Recent studies indicate that softmax (SM) decision rule models that include a representation of environmental dynamics (e.g. the Kalman Filter) and additional parameters for modeling exploration and perseveration (Kalman SMEP) fit human bandit task data better than competing models. Parameter and model recovery are two central requirements for computational models: parameter recovery refers to the ability to recover true data-generating parameters; model recovery refers to the ability to correctly identify the true data generating model using model comparison techniques. Here we comprehensively examined parameter and model recovery of the Kalman SMEP model as well as nested model versions, i.e. models without the additional parameters, using simulation and Bayesian inference. Parameter recovery improved with increasing trial numbers, from around .8 for 100 trials to around .93 for 300 trials. Model recovery analyses likewise confirmed acceptable recovery of the Kalman SMEP model. Model recovery was lower for nested Kalman filter models as well as delta rule models with fixed learning rates. Exploratory analyses examined associations of model parameters with model-agnostic performance metrics. Random exploration, captured by the inverse softmax temperature, was associated with lower accuracy and more switches. For the exploration bonus parameter modeling directed exploration, we confirmed an inverse- U-shaped association with accuracy, such that both an excess and a lack of directed exploration reduced accuracy. Taken together, these analyses underline that the Kalman SMEP model fulfills two basic requirements of a cognitive model.
Spatio-temporal stratified associations between urban human activities and crime patterns: a case study in San Francisco around the COVID-19 stay-at-home mandate
Authors: Chen Tongxin , Bowers Kate , Zhu Di , Gao Xiaowei , Cheng Tao 
Published: June 2022

AbstractCrime changes have been reported as a result of human routine activity shifting due to containment policies, such as stay-at-home (SAH) mandates during the COVID-19 pandemic. However, the way in which the manifestation of crime in both space and time is affected by dynamic human activities has not been explored in depth in empirical studies. Here, we aim to quantitatively measure the spatio-temporal stratified associations between crime patterns and human activities in the context of an unstable period of the ever-changing socio-demographic backcloth. We propose an analytical framework to detect the stratified associations between dynamic human activities and crimes in urban areas. In a case study of San Francisco, United States, we first identify human activity zones (HAZs) based on the similarity of daily footfall signatures on census block groups (CBGs). Then, we examine the spatial associations between crime spatial distributions at the CBG-level and the HAZs using spatial stratified heterogeneity statistical measurements. Thirdly, we use different temporal observation scales around the effective date of the SAH mandate during the COVID-19 pandemic to investigate the dynamic nature of the associations. The results reveal that the spatial patterns of most crime types are statistically significantly associated with that of human activities zones. Property crime exhibits a higher stratified association than violent crime across all temporal scales. Further, the strongest association is obtained with the eight-week time span centred around the SAH order. These findings not only enhance our understanding of the relationships between urban crime and human activities, but also offer insights into that tailored crime intervention strategies need to consider human activity variables.
Evolution and Electoral Implications of Congressional Gun Control Issue Framing: “From Crime Control to Mass Shootings”
Authors: QUINN GENEVIEVE 
Published: June 2022

AbstractThis paper traces the political development of Congressional gun control issue framing (with a specific focus from the early 1990s to the present), demonstrating that there have been two primary contexts in which gun control policy has been debated over this time frame: as a component of general crime control and as a specific response to mass shooting events. It identifies the primary historical, political, and electoral forces shaping the gun control debate in a given period while distinguishing the critical changes that drove the evolution from a crime control to a mass shooting focus. It assesses the degree of policy coherence and electoral salience specific to each context, illuminating why “gun control as crime control” had bipartisan Congressional support in the early 1990s and identifying what comparative disadvantages hinder the mass shooting focus of the present while also recognizing that the latter unfolded against a backdrop of heighted partisan polarization. The paper concludes that although one cannot compare the crime control and mass shooting framing contexts in a political vacuum, the electoral implications particular to each are relevant for understanding legislative action or inaction in Congress over the past thirty years, if more so in some periods than others.
Images of the East African Rift System by Global Adaptive‐Resolution Surface‐Wave Tomography
Authors: Korostelev Félicie , Lu Yang , Magrini Fabrizio , Boschi Lapo , Leroy Sylvie , Vétel William 
Published: June 2022

AbstractIn this study we map the entire East African Rift System (EARS) within a global surface‐wave velocity model to better constrain the structure of the underlying mantle, as well as patterns that might be associated with its continuation in the Mozambique Channel. We use all publicly available seismograms from the African continent, amounting to 1296 stations and more than 30 years of recordings. From these data, we obtain dispersion curves using both ambient noise and teleseismic earthquakes. To our measurements, we add global counterparts and jointly invert them for phase‐velocity maps. We exploit a linearized inversion based on the ray theory, with an adaptive parameterization that allows for maximizing the resolution of the final maps based on the density of data coverage. We thus image the main African cratons and also some of the Archean blocks within them. We highlight the discontinuous nature of magmatic activity along the EARS and also display low‐velocity anomalies beneath the Comores Archipelago, Madagascar and Bassas da India volcanic islands and seamounts. This last low‐velocity anomaly is in the direct continuation of the EARS and could unveil an important magmatic system in the Mozambique Channel.
Sulfur Biogeochemical Cycling and Redox Dynamics in a Shale‐Dominated Mountainous Watershed
Authors: Fox Patricia M. , Carrero Sergio , Anderson Cam , Dewey Christian , Keiluweit Marco , Conrad Mark , Naughton Hannah R. , Fendorf Scott , Carroll Rosemary , Dafflon Baptiste , Malenda‐Lawrence Helen , Dwivedi Dipankar , Gilbert Benjamin , Christensen John N. , Boye Kristin , Beutler Curtis , Brown Wendy , Newman Alexander , Versteeg Roelof , Williams Kenneth H. , Nico Peter S. 
Published: June 2022

AbstractSulfur (S) is an essential macronutrient and important component of the earth’s crust, and its cycling has critical impacts on trace metal mobility, water quality, and human health. Pyrite weathering is the primary pathway by which sulfur enters surface waters. However, biogeochemical cycling of sulfur in soils and the river corridor mediates sulfate exports. In this study, we identified the major forms of sulfur across multiple compartments and scales in a pristine mountainous watershed, including shale bedrock weathering profiles, hillslope soils, and alluvial floodplain sediments, in order to provide insight into biogeochemical sulfur cycling in a hydrologically variable alpine system. X‐ray absorption near‐edge spectroscopy (XANES) analysis of shale weathering profiles showed clear evidence of pyrite oxidation to sulfate, with large accumulations of intermediate S(0) (20%–53%). Micro‐scale XANES showed evidence of reprecipitation of pyrite at fracture surfaces within the permanently saturated zone. Organic sulfur dominated S speciation in shallow hillslope soil and floodplain sediment, with little evidence of reduced inorganic S. However, mackinawite formation, representing active sulfate reduction, was observed in saturated oxbow sediments and saturated weathered shale underlying floodplain sediments. Further evidence of sulfate reduction from aqueous sulfur isotopic analysis was observed in shallow groundwater transects across an Fe‐reducing meander, whereas increases in pore water sulfate concentrations implied sulfur oxidation at other locations. The data present an integrated picture of sulfur cycling in a shale‐dominated watershed, where riverine sulfate exports are mediated by biological cycling, particularly in redox‐stratified and temporally dynamic hyporheic zone sediments.
Chemical Mohometry: Assessing Crustal Thickness of Ancient Orogens Using Geochemical and Isotopic Data
Authors: Luffi P. , Ducea M. N. 
Published: June 2022

AbstractConvergent plate boundaries are key sites for continental crustal formation and recycling. Quantifying the evolution of crustal thickness and paleoelevation along ancient convergent margins represents a major goal in orogenic system analyses. Chemical and in some cases isotopic compositions of igneous rocks formed in modern supra‐subduction arcs and collisional belts are sensitive to Moho depths at the location of magmatism, implying that igneous suites from fossil orogens carry information about crustal thickness from the time they formed. Several whole‐rock chemical parameters correlate with crustal thickness, some of which were calibrated to serve as “mohometers,” that is, quantitative proxies of paleo‐Moho depths. Based on mineral‐melt partition coefficients, this concept has been extended to detrital zircons, such that combined chemical and geochronological information extracted from these minerals allows us to reconstruct the crustal thickness evolution using the detrital archive. We discuss here the mohometric potential of a variety of chemical and isotopic parameters and show that their combined usage improves paleocrustal thickness estimates. Using a MATLAB® app developed for the underlying computations, we present examples from the modern and the deeper time geologic record to illustrate the promises and pitfalls of the technique. Since arcs are in isostatic equilibrium, mohometers are useful in reconstructing orogenic paleoelevation as well. Our analysis suggests that many global‐scale correlations between magma composition and crustal thickness used in mohometry originate in the sub‐arc mantle; additional effects resulting from intracrustal igneous differentiation depend on the compatible or incompatible behavior of the involved parameters.
Inception and Evolution of La Corona Lava Tube System (Lanzarote, Canary Islands, Spain)
Authors: Tomasi I. , Massironi M. , Meyzen C. M. , Pozzobon R. , Sauro F. , Penasa L. , Santagata T. , Tonello M. , Santana Gomez G. D. , Martinez‐Frìas J. 
Published: June 2022

AbstractGrowing interest in studying large terrestrial lava tubes is motivated in part by their analogy with their extra‐terrestrial counterparts. However, on Earth, the formation of such structures is still poorly understood. Here, the lava tube system of La Corona (Lanzarote, Canary Islands, Spain) is studied to identify how pre‐existing stratigraphy can govern a lava tube's evolution. Combining terrestrial laser scanner technology with field observations and geochemical analyses of the pre‐existing lava enabled us to reconstruct the three‐dimensional geometry of the lava tube system, the paleo‐surface trough which it developed, and the volcanic series into which it carved its path. We show that a pyroclastic layer played a key role in the development of the lava tube. The layer—Derived from late Quaternary Strombolian activity—Is traceable along almost the full length of the tube path and defines the paleo‐topography. The excavation process mostly happens because of the mechanical strength of the substrate, that controls the widening of the growing lava tube. Other influential parameters controlling erosion include slope variations of the paleo‐surface (i.e., knickpoints), and the lava physical properties. Since weak layers such as regolith are a common feature of extra‐terrestrial lava flows, the processes seen at La Corona to the may be highly relevant to the development of planetary lava tube systems.
Addressing bias and knowledge gaps regarding race and ethnicity in neonatology manuscript review
Authors: Karvonen Kayla L. , Bonachea Elizabeth M. , Burris Heather H. , Fraiman Yarden S. , Lee Henry C. , Proaño Alvaro , Walker Valencia P. , Parker Margaret G. 
Published: June 2022

AbstractA recent shift in public attention to racism, racial disparities, and health equity have resulted in an abundance of calls for relevant papers and publications in academic journals. Peer-review for such articles may be susceptible to bias, as subject matter expertise in the evaluation of social constructs, like race, is variable. From the perspective of researchers focused on neonatal health equity, we share our positive and negative experiences in peer-review, provide relevant publicly available data regarding addressing bias in peer-review from 12 neonatology-focused journals, and give recommendations to address bias and knowledge gaps in the peer review process of health equity research.
Immunogenicity and safety of NVSI-06-07 as a heterologous booster after priming with BBIBP-CorV: a phase 2 trial
Authors: Kaabi Nawal Al , Yang Yun Kai , Zhang Jing , Xu Ke , Liang Yu , Kang Yun , Su Ji Guo , Yang Tian , Hussein Salah , ElDein Mohamed Saif , Shao Shuai , Yang Sen Sen , Lei Wenwen , Gao Xue Jun , Jiang Zhiwei , Wang Hui , Li Meng , Mekki Hanadi Mekki , Zaher Walid , Mahmoud Sally , Zhang Xue , Qu Chang , Liu Dan Ying , Zhang Jing , Yang Mengjie , Eltantawy Islam , Xiao Peng , Wang Zhao Nian , Yin Jin Liang , Mao Xiao Yan , Zhang Jin , Liu Ning , Shen Fu Jie , Qu Liang , Zhang Yun Tao , Yang Xiao Ming , Wu Guizhen , Li Qi Ming 
Published: June 2022

AbstractThe increased coronavirus disease 2019 (COVID-19) breakthrough cases pose the need of booster vaccination. We conducted a randomised, double-blinded, controlled, phase 2 trial to assess the immunogenicity and safety of the heterologous prime-boost vaccination with an inactivated COVID-19 vaccine (BBIBP-CorV) followed by a recombinant protein-based vaccine (NVSI-06-07), using homologous boost with BBIBP-CorV as control. Three groups of healthy adults (600 individuals per group) who had completed two-dose BBIBP-CorV vaccinations 1–3 months, 4–6 months and ≥6 months earlier, respectively, were randomly assigned in a 1:1 ratio to receive either NVSI-06-07 or BBIBP-CorV boost. Immunogenicity assays showed that in NVSI-06-07 groups, neutralizing antibody geometric mean titers (GMTs) against the prototype SARS-CoV-2 increased by 21.01–63.85 folds on day 28 after vaccination, whereas only 4.20–16.78 folds of increases were observed in control groups. For Omicron variant, the neutralizing antibody GMT elicited by homologous boost was 37.91 on day 14, however, a significantly higher neutralizing GMT of 292.53 was induced by heterologous booster. Similar results were obtained for other SARS-CoV-2 variants of concerns (VOCs), including Alpha, Beta and Delta. Both heterologous and homologous boosters have a good safety profile. Local and systemic adverse reactions were absent, mild or moderate in most participants, and the overall safety was quite similar between two booster schemes. Our findings indicated that NVSI-06-07 is safe and immunogenic as a heterologous booster in BBIBP-CorV recipients and was immunogenically superior to the homologous booster against not only SARS-CoV-2 prototype strain but also VOCs, including Omicron.
SMYD2 aggravates gastrointestinal stromal tumor via upregulation of EZH2 and downregulation of TET1
Authors: Ji Yong , Xu Xiaofeng , Long Cong , Wang Jianjiang , Ding Li , Zheng Zhizhong , Wu Huiping , Yang Liu , Tao Lan , Gao Feng 
Published: June 2022

AbstractSMYD2, as an oncogene, has been involved in multiple types of cancer, but the potential role of SMYD2 in gastrointestinal stromal tumors (GIST) remains enigmatic and requires further investigation. Hence, this study was conducted with the main objective of analyzing the effect of SMYD2 on GIST. GIST and adjacent normal tissues were collected from 46 patients with GIST where the expression of EZH2, SMYD2, and TET1 was determined, followed by the analysis of their interactions. The functional role of SMYD2 in cell biological functions was determined using a loss-of-function assay in GIST-T1 cells. Nude mouse xenograft experiments were performed to verify the role of the SMYD2/EZH2/TET1 axis in GIST in vivo. EZH2 was upregulated in GIST tissues and cell lines, which was positively correlated with SMYD2 expression and inversely correlated with TET1 expression in GIST tissues. EZH2 silencing due to SMYD2 inhibition reduced GIST-T1 cell proliferation and accelerated cell senescence. EZH2 repressed TET1 expression by promoting H3K27me3 methylation in the TET1 promoter region. TET1 inhibition reversed the effect of EZH2 silencing on the biological functions of GIST-T1 cells. In vivo data further revealed the promoting effect of SMYD2 on the progression of GIST by regulating the EZH2/TET1 axis. Overall, this study demonstrates that SMYD2 can increase EZH2 expression while suppressing TET1 expression, thus accelerating GIST, and creating new treatment opportunities for GIST.
Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies
Authors: Zhao Miao-Miao , Zhu Yun , Zhang Li , Zhong Gongxun , Tai Linhua , Liu Shuo , Yin Guoliang , Lu Jing , He Qiong , Li Ming-Jia , Zhao Ru-Xuan , Wang Hao , Huang Weijin , Fan Changfa , Shuai Lei , Wen Zhiyuan , Wang Chong , He Xijun , Chen Qiuluan , Liu Banghui , Xiong Xiaoli , Bu Zhigao , Wang Youchun , Sun Fei , Yang Jin-Kui 
Published: June 2022

AbstractThe spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important target for vaccine and drug development. However, the rapid emergence of variant strains with mutated S proteins has rendered many treatments ineffective. Cleavage of the S protein by host proteases is essential for viral infection. Here, we discovered that the S protein contains two previously unidentified Cathepsin L (CTSL) cleavage sites (CS-1 and CS-2). Both sites are highly conserved among all known SARS-CoV-2 variants. Our structural studies revealed that CTSL cleavage promoted S to adopt receptor-binding domain (RBD) “up” activated conformations, facilitating receptor-binding and membrane fusion. We confirmed that CTSL cleavage is essential during infection of all emerged SARS-CoV-2 variants (including the recently emerged Omicron variant) by pseudovirus (PsV) infection experiment. Furthermore, we found CTSL-specific inhibitors not only blocked infection of PsV/live virus in cells but also reduced live virus infection of ex vivo lung tissues of both human donors and human ACE2-transgenic mice. Finally, we showed that two CTSL-specific inhibitors exhibited excellent In vivo effects to prevent live virus infection in human ACE2-transgenic mice. Our work demonstrated that inhibition of CTSL cleavage of SARS-CoV-2 S protein is a promising approach for the development of future mutation-resistant therapy.
Online tools for efficient paper writing
Authors: Yamamoto Yasunori , Fujiwara Toyofumi 
Published: June 2022

AbstractFor researchers, writing a paper is an essential task, and it is crucial for them to have an environment to facilitate the paper writing process. In addition, writing in English is more difficult for many non-native English speakers. The Database Center for Life Science (DBCLS) provides researchers in the life sciences with several text-mining related services, such as Allie and inMeXes, which were developed to facilitate paper writing. Allie is an abbreviation database that shows researchers expanded forms and several relevant data, such as the papers that contain the abbreviations and their corresponding expanded forms. Since a large amount of abbreviations are coined, remembering their meanings is difficult, even in one’s research field. Therefore, Allie helps one lookup abbreviations. inMeXes is an incremental search service for English phrases appearing in PubMed. Researchers can learn English phrases used in life science papers, such as the use of prepositions or widely used phrases that contain a specific word. Allie and inMeXes are updated monthly and yearly, respectively, to provide the latest information.
Free-living wrist and hip accelerometry forecast cognitive decline among older adults without dementia over 1- or 5-years in two distinct observational cohorts
Authors: Shi Chengjian , Babiker Niser , Urbanek Jacek K. , Grossman Robert L. , Huisingh-Scheetz Megan , Rzhetsky Andrey 
Published: June 2022

AbstractThe prevalence of major neurocognitive disorders is expected to rise over the next 3 decades as the number of adults ≥65 years old increases. Noninvasive screening capable of flagging individuals most at risk of subsequent cognitive decline could trigger closer monitoring and preventive strategies. In this study, we used free-living accelerometry data to forecast cognitive decline within 1- or 5-years in older adults without dementia using two cohorts. The first cohort, recruited in the south side of Chicago, wore hip accelerometers for 7 continuous days. The second cohort, nationally recruited, wore wrist accelerometers continuously for 72 h. Separate classifier models forecasted 1-year cognitive decline with over 85% accuracy using hip data and forecasted 5-year cognitive decline with nearly 70% accuracy using wrist data, significant improvements compared to demographics and comorbidities alone. The proposed models are readily translatable to clinical practices serving ageing populations.
Machine learning in concrete science: applications, challenges, and best practices
Authors: Li Zhanzhao , Yoon Jinyoung , Zhang Rui , Rajabipour Farshad , Srubar III Wil V. , Dabo Ismaila , Radlińska Aleksandra 
Published: June 2022

AbstractConcrete, as the most widely used construction material, is inextricably connected with human development. Despite conceptual and methodological progress in concrete science, concrete formulation for target properties remains a challenging task due to the ever-increasing complexity of cementitious systems. With the ability to tackle complex tasks autonomously, machine learning (ML) has demonstrated its transformative potential in concrete research. Given the rapid adoption of ML for concrete mixture design, there is a need to understand methodological limitations and formulate best practices in this emerging computational field. Here, we review the areas in which ML has positively impacted concrete science, followed by a comprehensive discussion of the implementation, application, and interpretation of ML algorithms. We conclude by outlining future directions for the concrete community to fully exploit the capabilities of ML models.