bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engaging community in the translational process: Environmental scan of adaptive capacity and preparedness of Clinical and Translational Science Award Program hubs
Authors: Volkov Boris B. , Hoyo Verónica , Hunt Joe 
Published: June 2022

AbstractThis paper is part of the Environmental Scan of Adaptive Capacity and Preparedness of Clinical and Translational Science Award (CTSA) hubs, illuminating challenges, practices, and lessons learned related to CTSA hubs’ efforts of engaging community partners to reduce the spread of the virus, address barriers to COVID-19 testing, identify treatments to improve health outcomes, and advance community participation in research. CTSA researchers, staff, and community partners collaborated to develop evidence-based, inclusive, accessible, and culturally appropriate strategies and resources helping community members stay healthy, informed, and connected during the pandemic. CTSA institutions have used various mechanisms to advance co-learning and co-sharing of knowledge, resources, tools, and experiences between academic professionals, patients, community partners, and other stakeholders. Forward-looking and adaptive decision-making structures are those that prioritize sustained relationships, mutual trust and commitment, ongoing communication, proactive identification of community concerns and needs, shared goals and decision making, as well as ample appreciation of community members and their contributions to translational research. There is a strong need for further community-engaged research and workforce training on how to build our collective and individual adaptive capacity to sustain and improve processes and outcomes of engagement with and by communities—in all aspects of translational science.
Artificial Intelligence Risks and Algorithmic Regulation
Authors: Fortes Pedro Rubim Borges , Baquero Pablo Marcello , Amariles David Restrepo 
Published: June 2022

AbstractIn this editorial article, we aim to map out the central features of algorithmic regulation and its conceptual basis – seeking to bring together different strands of the literature relating to the topic that have often remained apart. We then reflect on the ways through which algorithmic law could evolve to address the challenges of artificial intelligence in the legal domain, particularly by examining the potential of applying a “prudential” test in order to determine whether automated decision-making systems are suitable to adequately support legal decision-making.
Theoretical analysis of close-contact melting on superhydrophobic surfaces
Authors: Kozak Yoram 
Published: June 2022

The present study deals with close-contact melting of a vertical cylinder on a horizontal isothermal superhydrophobic surface with an array of circular posts. A new numerical model for this phenomenon is formulated under several simplifying assumptions. For the limiting case of perfect slip and thermal contact, based on the model assumptions, it is demonstrated that superhydrophobic surfaces can enhance the melting time by no more than 30 %. Numerical solution of the new model reveals that the effect of superhydrophobic hydrodynamic slip can decrease the molten layer thickness. However, due to the dominant effect of thermal slip, the heat transfer rate can be decreased significantly, and the melting time can be roughly doubled. An approximate analytical model is developed for understanding the problem dynamics better. The analytical model predictions are compared extensively against the numerical model results. For sufficiently low surface volume fractions, the analytical model provides excellent estimations of the numerical model predictions. Dimensional analysis reveals that according to the analytical model, the ratio between the melting times for superhydrophobic and regular surfaces is governed by a single dimensionless group. Moreover, according to the analytical model, the melting time on a superhydrophobic surface is always longer than on a regular surface, which agrees qualitatively with the numerical model results. Based on this analysis, a dimensionless condition for the analytical model range of validity is formulated. Finally, a conservative criterion for the liquid–gas interface stability under a close-contact melting process is established.
Episodes of liberalization in autocracies: a new approach to quantitatively studying democratization
Authors: Wilson Matthew C. , Medzihorsky Juraj , Maerz Seraphine F. , Lindenfors Patrik , Edgell Amanda B. , Boese Vanessa A. , Lindberg Staffan I. 
Published: June 2022

AbstractThis paper introduces a new approach to the quantitative study of democratization. Building on the comparative case-study and large-N literature, it outlines an episode approach that identifies the discrete beginning of a period of political liberalization, traces its progression, and classifies episodes as successful versus different types of failing outcomes, thus avoiding potentially fallacious assumptions of unit homogeneity. We provide a description and analysis of all 383 liberalization episodes from 1900 to 2019, offering new insights on democratic “waves”. We also demonstrate the value of this approach by showing that while several established covariates are valuable for predicting the ultimate outcomes, none explain the onset of a period of liberalization.
Global biogeography of estuary-associated fishes
Authors: Harrison Trevor D. , Whitfield Alan K. 
Published: June 2022

AbstractThis study examines global zoogeographic patterns of estuary-associated fishes using meta-assemblages compiled at the marine ecoregion scale. The classification of biogeographic regions based on estuary-associated fish species is assessed in relation to marine and freshwater zoogeographic patterns. Historical (palaeobiogeographic) and contemporary environmental factors that contribute to the establishment and maintenance of these regions are also discussed. Global patterns in estuary-associated fish species richness demonstrated that tropical ecoregions are more diverse and richer in species than temperate ecoregions; the tropical Indo-Pacific and the tropical western Atlantic were two major centres of high global species richness. Multivariate analyses identified several ecoregion groupings that broadly corresponded with both freshwater and marine biogeographic regions. These groupings could also be related to global marine palaeobiogeographic processes such as the closure of the Tethys Sea linkage during the Cenozoic as well as contemporary factors such ocean currents, upwelling areas and climatic factors, particularly rainfall and runoff.
THE TECHNOLOGY OF PUBLIC SHAMING
Authors: Frye Harrison 
Published: June 2022

AbstractThis essay argues that online public shaming can be productively understood as a problem of technology. In particular, the technology of public shaming is ambiguous between two senses. On the one hand, public shaming depends on various technologies, such as social media posts or, more historically, pillories. These are the artifacts of shame. On the other hand, public shaming itself is a social technology. In particular, public shaming is a way for communities to promote cooperation. Ultimately, I claim there is a mismatch between the artifacts of shame and this important social technology of shame. Social media drifts toward disintegrative shame, which tends to corrode cooperation. This suggests that we must either realign the technology of public shame or reject shame as a legitimate option.
URBAN PLANNING AND URBAN VALUES: A JACOBSIAN ANALYSIS
Authors: Ikeda Sanford 
Published: June 2022

AbstractThe great urbanist Jane Jacobs details how urban planning impacts the social interactions and social networks responsible for the economic death or life of a city. How might urban planning impinge on the moral values that underlie that development? I draw on Jacobs’s work on the moral foundations of commercial society to identify two “urban values” (tolerance and innovation). I then examine how these values support the social networks and processes that facilitate urban-based innovation and how urban planning can strengthen or undermine those values. I use the examples of urban planning in the 15th Ward of Syracuse, New York and of city building in the private development of Cayalá in Guatemala City to illustrate these points.
A Numerical Investigation of the Effect of Wave‐Induced Mixing on Tropical Cyclones Using a Coupled Ocean‐Atmosphere‐Wave Model
Authors: Zhang Wenqing , Zhao Dongliang , Zhu Donglin , Li Jingkai , Guan Changlong , Sun Jian 
Published: June 2022

AbstractOcean surface waves play a significant role in regulating the sea surface temperature and mixed layer depth, which are essential for accurate prediction of tropical cyclone (TC) intensity. The effects of wave breaking and wave orbital motion induced mixing on the TC intensity and size are investigated using a coupled ocean‐atmosphere‐wave model for both idealized and real TC cases. The results show that both wave breaking and wave orbital motion lead to greater sea surface temperature cooling and mixed layer deepening, resulting in decreases in TC intensity and size owing to the reduction of air‐sea heat fluxes. Wave orbital motion has a slightly greater effect than wave breaking on the TC intensity and size when the mixed layer is shallow, whereas it has a much greater effect when the mixed layer is deep. In addition, including wave orbital motion induced mixing in models can effectively reduce the error in simulated TC size.
Alcohol use disorder is associated with DNA methylation-based shortening of telomere length and regulated by TESPA1: implications for aging
Authors: Jung Jeesun , McCartney Daniel L. , Wagner Josephin , Rosoff Daniel B. , Schwandt Melanie , Sun Hui , Wiers Corinde E. , de Carvalho Luana Martins , Volkow Nora D. , Walker Rosie M. , Campbell Archie , Porteous David J. , McIntosh Andrew M. , Marioni Riccardo E. , Horvath Steve , Evans Kathryn L. , Lohoff Falk W. 
Published: June 2022

AbstractChronic heavy alcohol consumption is associated with increased mortality and morbidity and often leads to premature aging; however, the mechanisms of alcohol-associated cellular aging are not well understood. In this study, we used DNA methylation derived telomere length (DNAmTL) as a novel approach to investigate the role of alcohol use on the aging process. DNAmTL was estimated by 140 cytosine phosphate guanines (CpG) sites in 372 individuals with alcohol use disorder (AUD) and 243 healthy controls (HC) and assessed using various endophenotypes and clinical biomarkers. Validation in an independent sample of DNAmTL on alcohol consumption was performed (N = 4219). Exploratory genome-wide association studies (GWAS) on DNAmTL were also performed to identify genetic variants contributing to DNAmTL shortening. Top GWAS findings were analyzed usingin-silicoexpression quantitative trait loci analyses and related to structural MRI hippocampus volumes of individuals with AUD. DNAmTL was 0.11-kilobases shorter per year in AUD compared to HC after adjustment for age, sex, race, and blood cell composition (p = 4.0 × 10−12). This association was partially attenuated but remained significant after additionally adjusting for BMI, and smoking status (0.06 kilobases shorter per year,p = 0.002). DNAmTL shortening was strongly associated with chronic heavy alcohol use (ps < 0.001), elevated gamma-glutamyl transferase (GGT), and aspartate aminotransferase (AST) (ps < 0.004). Comparison of DNAmTL with PCR-based methods of assessing TL revealed positive correlations (R = 0.3,p = 2.2 × 10−5), highlighting the accuracy of DNAmTL as a biomarker. The GWAS meta-analysis identified a single nucleotide polymorphism (SNP), rs4374022 and 18 imputed ones in Thymocyte Expressed, Positive Selection Associated 1(TESPA1), at the genome-wide level (p = 3.75 × 10−8). The allele C of rs4374022 was associated with DNAmTL shortening, lower hippocampus volume (p < 0.01), and decreased mRNA expression in hippocampus tissue (p = 0.04). Our study demonstrates DNAmTL-related aging acceleration in AUD and suggests a functional role forTESPA1in regulating DNAmTL length, possibly via the immune system with subsequent biological effects on brain regions negatively affected by alcohol and implicated in aging.
Signal pathways and precision therapy of small-cell lung cancer
Authors: Yuan Min , Zhao Yu , Arkenau Hendrik-Tobias , Lao Tongnei , Chu Li , Xu Qing 
Published: June 2022

AbstractSmall-cell lung cancer (SCLC) encounters up 15% of all lung cancers, and is characterized by a high rate of proliferation, a tendency for early metastasis and generally poor prognosis. Most of the patients present with distant metastatic disease at the time of clinical diagnosis, and only one-third are eligible for potentially curative treatment. Recently, investigations into the genomic make-up of SCLC show extensive chromosomal rearrangements, high mutational burden and loss-of-function mutations of several tumor suppressor genes. Although the clinical development of new treatments for SCLC has been limited in recent years, a better understanding of oncogenic driver alterations has found potential novel targets that might be suitable for therapeutic approaches. Currently, there are six types of potential treatable signaling pathways in SCLC, including signaling pathways targeting the cell cycle and DNA repair, tumor development, cell metabolism, epigenetic regulation, tumor immunity and angiogenesis. At this point, however, there is still a lack of understanding of their role in SCLC tumor biology and the promotion of cancer growth. Importantly optimizing drug targets, improving drug pharmacology, and identifying potential biomarkers are the main focus and further efforts are required to recognize patients who benefit most from novel therapies in development. This review will focus on the current learning on the signaling pathways, the status of immunotherapy, and targeted therapy in SCLC.
Australian arm of the International Spinal Cord Injury (Aus-InSCI) Community Survey: 2. Understanding the lived experience in people with spinal cord injury
Authors: Middleton James W. , Arora Mohit , Kifley Annette , Clark Jillian , Borg Samantha J. , Tran Yvonne , Atresh Sridhar , Kaur Jasbeer , Shetty Sachin , Nunn Andrew , Marshall Ruth , Geraghty Timothy 
Published: June 2022

Abstract
Study design
Cross-sectional survey.

Objectives
To identify common problems across key domains of functioning, health and wellbeing, as well as evaluate self-reported quality of life (QoL) by people with SCI, examining differences by age, gender, injury characteristics and level of mobility.

Setting
Data from four state-wide SCI clinical services, one government insurance agency and three not-for-profit consumer organisations.

Methods
Participants were 18 years or over with SCI and at least 12 months post-injury, recruited between Mar’18 and Jan’19. The Aus-InSCI questionnaire comprised 193 questions, including socio-demographics, SCI characteristics, body functions and structures, activities and participation, environmental and personal factors, and appraisal of health and well-being. General linear model was used to examine differences in functioning and QoL.

Results
Participants (mean age 57 years, range 19–94 years) with tetraplegia and/or complete injuries had more health problems, activity/participation problems and environmental barriers. However, self-rated overall QoL did not differ for injury level or completeness. Participants with more recent injuries exhibited lower independence levels, more mental health problems and poorer satisfaction with self and their living conditions. Major activity/participation problems related to intimate relationships and accessing public transportation. Less than half of the working age population were engaged in paid work. The top two environmental barriers frequently related to accessing public places or homes and unfavourable climatic conditions.

Conclusions
This large, comprehensive community survey draws a detailed picture of the lived experience of people with SCI in Australia, identifying priority needs, gaps in services and barriers to achieving a full and satisfying life.
Ethical, legal and social/societal implications (ELSI) of recall-by-genotype (RbG) and genotype-driven-research (GDR) approaches: a scoping review
Authors: Tschigg Katharina , Consoli Luca , Biasiotto Roberta , Mascalzoni Deborah 
Published: June 2022

AbstractRecall by Genotype (RbG), Genotype-driven-recall (GDR), and Genotype-based-recall (GBR) strategies are increasingly used to conduct genomic or biobanking sub-studies that single out participants as eligible because of their specific individual genotypic information. However, existing regulatory and governance frameworks do not apply to all aspects of genotype-driven research approaches. The recall strategies disclose or withhold personal genotypic information with uncertain clinical utility. Accordingly, this scoping review aims to identify peculiar, explicit and implicit ethical, legal, and societal/social implications (ELSI) of RbG study designs. We conducted a systematic literature search of three electronic databases from November 2020 to February 2021. We investigated qualitative and quantitative research methods used to report ELSI aspects in RbG research. Congruent with other research findings, we identified a lack of qualitative research investigating the particular ELSI challenges with RbG. We included and analysed the content of twenty-five publications. We found a consensus on RbG posing significant ethical issues, dilemmas, barriers, concerns and societal challenges. However, we found that the approaches to disclosure and study-specific recall and communication strategies employed consent models and Return of Research Results (RoRR) policies varied considerably. Furthermore, we identified a high heterogeneity in perspectives of participants and experts about ELSI of study-specific RbG policies. Therefore, further fine-mapping through qualitative and empirical research is needed to draw conclusions and re-fine ELSI frameworks.
Signatures of copy number alterations in human cancer
Authors: Steele Christopher D. , Abbasi Ammal , Islam S. M. Ashiqul , Bowes Amy L. , Khandekar Azhar , Haase Kerstin , Hames-Fathi Shadi , Ajayi Dolapo , Verfaillie Annelien , Dhami Pawan , McLatchie Alex , Lechner Matt , Light Nicholas , Shlien Adam , Malkin David , Feber Andrew , Proszek Paula , Lesluyes Tom , Mertens Fredrik , Flanagan Adrienne M. , Tarabichi Maxime , Van Loo Peter , Alexandrov Ludmil B. , Pillay Nischalan 
Published: June 2022

AbstractGains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage–fusion–bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3–5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.
Measurement of the bound-electron g-factor difference in coupled ions
Authors: Sailer Tim , Debierre Vincent , Harman Zoltán , Heiße Fabian , König Charlotte , Morgner Jonathan , Tu Bingsheng , Volotka Andrey V. , Keitel Christoph H. , Blaum Klaus , Sturm Sven 
Published: June 2022

AbstractQuantum electrodynamics (QED) is one of the most fundamental theories of physics and has been shown to be in excellent agreement with experimental results1–5. In particular, measurements of the electron’s magnetic moment (or g factor) of highly charged ions in Penning traps provide a stringent probe for QED, which allows testing of the standard model in the strongest electromagnetic fields6. When studying the differences between isotopes, many common QED contributions cancel owing to the identical electron configuration, making it possible to resolve the intricate effects stemming from the nuclear differences. Experimentally, however, this quickly becomes limited, particularly by the precision of the ion masses or the magnetic field stability7. Here we report on a measurement technique that overcomes these limitations by co-trapping two highly charged ions and measuring the difference in their g factors directly. We apply a dual Ramsey-type measurement scheme with the ions locked on a common magnetron orbit8, separated by only a few hundred micrometres, to coherently extract the spin precession frequency difference. We have measured the isotopic shift of the bound-electron g factor of the isotopes 20Ne9+ and 22Ne9+ to 0.56-parts-per-trillion (5.6 × 10−13) precision relative to their g factors, an improvement of about two orders of magnitude compared with state-of-the-art techniques7. This resolves the QED contribution to the nuclear recoil, accurately validates the corresponding theory and offers an alternative approach to set constraints on new physics.
Mechanism of replication origin melting nucleated by CMG helicase assembly
Authors: Lewis Jacob S. , Gross Marta H. , Sousa Joana , Henrikus Sarah S. , Greiwe Julia F. , Nans Andrea , Diffley John F. X. , Costa Alessandro 
Published: June 2022

AbstractThe activation of eukaryotic origins of replication occurs in temporally separated steps to ensure that chromosomes are copied only once per cell cycle. First, the MCM helicase is loaded onto duplex DNA as an inactive double hexamer. Activation occurs after the recruitment of a set of firing factors that assemble two Cdc45–MCM–GINS (CMG) holo-helicases. CMG formation leads to the underwinding of DNA on the path to the establishment of the replication fork, but whether DNA becomes melted at this stage is unknown1. Here we use cryo-electron microscopy to image ATP-dependent CMG assembly on a chromatinized origin, reconstituted in vitro with purified yeast proteins. We find that CMG formation disrupts the double hexamer interface and thereby exposes duplex DNA in between the two CMGs. The two helicases remain tethered, which gives rise to a splayed dimer, with implications for origin activation and replisome integrity. Inside each MCM ring, the double helix becomes untwisted and base pairing is broken. This comes as the result of ATP-triggered conformational changes in MCM that involve DNA stretching and protein-mediated stabilization of three orphan bases. Mcm2 pore-loop residues that engage DNA in our structure are dispensable for double hexamer loading and CMG formation, but are essential to untwist the DNA and promote replication. Our results explain how ATP binding nucleates origin DNA melting by the CMG and maintains replisome stability at initiation.