bluuebunny/crossref_metadata_2025 huggingface dataset:
Could dietary restrictions affect periodontal disease? A systematic review
Authors: Mainas Giuseppe , Santamaria Pasquale , Ide Mark , Longo Valter , Vinciguerra Manlio , Nart Jose , Nibali Luigi
Published: May 2023

Objective

This review aimed at evaluating the possible benefits that caloric restriction (CR) may provide to periodontal disease progression and response to treatment.

Material and methods

Electronic search on Medline, Embase and Cochrane, and manual search were performed to identify pre-clinical and on human studies reporting the consequences of CR on clinical and inflammatory parameters related to periodontitis. Newcastle Ottawa System and SYRCLE scale were used to assess the risk of bias.

Results

Four thousand nine hundred eighty articles were initially screened, and a total of 6 articles were finally included, consisting of 4 animal studies and 2 studies in humans. Due to the limited number of studies and heterogeneity of the data, results were presented in descriptive analyses. All studies showed that, compared to the normal (ad libitum) diet, CR might have the potential to reduce the local and systemic hyper-inflammatory state as well as disease progression in periodontal patients.

Conclusions

Within the existing limitations, this review highlights that CR showed some improvements in the periodontal condition by reducing the local and systemic inflammation related to the periodontitis and by improving clinical parameters. However, the results should be interpreted with caution since robust research such as randomized clinical trials is still missing.

Clinical relevance

This review shows that some dietary/caloric restrictions approaches may have the potential to improve periodontal conditions and, in addition, highlights a need for human studies with a robust methodology in order to draw stronger evidence-based conclusions.
Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis
Authors: Meng Wei , Johnsen Kay-Martin , Fenton Christopher G. , Florholmen Jon , Paulssen Ruth H.
Published: May 2023

Due to the lack of clinical, immunologic, genetic, and laboratory markers to predict remission in ulcerative colitis (UC) without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission with active treatment-naïve UC and healthy control subjects underwent whole-transcriptome RNA-seq. Principal component analysis (PCA) and Cox proportional hazards regression analysis were applied to the remission data concerning duration and status of patients. A randomly chosen remission sample set was used for validation of the applied methods and results. The analyses distinguished two different UC remission patient groups with respect to remission duration and outcome (relapse). Both groups showed that altered states of UC with quiescent microscopic disease activity are still present. The patient group with the longest remission duration and no relapse revealed specific and increased expression of antiapoptotic factors belonging to the MTRNR2-like gene family and non-coding RNAs. In summary, the expression of anti-apoptotic factors and non-coding RNAs may contribute to personalized medicine approaches in UC by improving patient stratification for different treatment regimens.
Trust-Building in Peer-to-Peer Carsharing: Design Case Study for Algorithm-Based Reputation Systems
Authors: Neifer Thomas , Bossauer Paul , Pakusch Christina , Boehm Lukas , Lawo Dennis
Published: May 2023

Peer-to-peer sharing platforms become increasingly important in the platform economy. From an HCI-perspective, this development is of high interest, as those platforms mediate between different users. Such mediation entails dealing with various social issues, e.g., building trust between peers online without any physical presence. Peer ratings have proven to be an important mechanism in this regard. At the same time, scoring via car telematics become more common for risk assessment by car insurances. Since user ratings face crucial problems such as fake or biased ratings, we conducted a design case study to determine whether algorithm-based scoring has the potential to improve trust-building in P2P-carsharing. We started with 16 problem-centered interviews to examine how people understand algorithm-based scoring, we co-designed an app with scored profiles, and finally evaluated it with 12 participants. Our findings show that scoring systems can support trust-building in P2P-carsharing and give insights how they should be designed.
Virus-like particle-based delivery of Cas9/guide RNA ribonucleoprotein efficiently edits the brachyury gene and inhibits chordoma growth in vivo
Authors: Hu Yunping , Lu Baisong , Deng Zhiyong , Xing Fei , Hsu Wesley
Published: May 2023

Purpose

Chordoma is a rare and aggressive bone cancer driven by the developmental transcription factor brachyury. Efforts to target brachyury are hampered by the absence of ligand-accessible small-molecule binding pockets. Genome editing with CRISPR systems provides an unprecedented opportunity to modulate undruggable transcription factor targets. However, delivery of CRISPR remains a bottleneck for in vivo therapy development. The aim was to investigate the in vivo therapeutic efficiency of Cas9/guide RNA (gRNA) ribonucleoprotein (RNP) delivery through a novel virus-like particle (VLP) by fusing an aptamer-binding protein to the lentiviral nucleocapsid protein.

Methods

The p24 based ELISA and transmission electron microscopy were used to determine the characterization of engineered VLP-packaged Cas9/gRNA RNP. The deletion efficiency of brachyury gene in chordoma cells and tissues was measured by genome cleavage detection assay. RT-PCR, Western blot, immunofluorescence staining, and IHC were employed to test the function of brachyury deletion. Cell growth and tumor volume were measured to evaluate the therapeutic efficiency of brachyury deletion by VLP-packaged Cas9/gRNA RNP.

Results

Our “all-in-one” VLP-based Cas9/gRNA RNP system allows for transient expression of Cas9 in chordoma cells, but maintains efficient editing capacity leading to approximately 85% knockdown of brachyury with subsequent inhibition of chordoma cell proliferation and tumor progression. In addition, this VLP-packaged brachyury-targeting Cas9 RNP avoids systemic toxicities in vivo.

Conclusion

Our preclinical studies demonstrate the potential of VLP-based Cas9/gRNA RNP gene therapy for the treatment of brachyury-dependent chordoma.
Findings in Danish long-term care facilities in the first year of the SARS-CoV-2 pandemic
Authors: Espenhain Laura , Funk Tjede , Kunøe Asja , Chaine Manon , Lauenborg Møller Karina , Kristensen Brian
Published: May 2023

Purpose

To describe the occurrence of SARS-CoV-2 infections, deaths and outbreaks among residents in Danish long-term care facilities (LTCFs) from February 2020 to February 2021.

Methods

Danish COVID-19 national register data from a newly implemented automated surveillance system was used to describe incidence rate and deaths (per 1000 residents’ years), number of tests, SARS-CoV-2 infections and outbreaks among LTCF residents. A case was defined as a LTCF resident with a positive SARS-CoV-2 PCR test. An outbreak was defined as two or more cases in one LTCF within a 14-day period, and considered closed if no new cases had occurred within 28 days. Death was defined as occurring within 30-days of a positive test.

Results

A total of 55,359 residents living in 948 LTCFs were included. The median age of the residents was 85 years and 63% were female. There was a total of 3712 cases found among residents across 43% of all LTCFs. Nearly all (94%) cases were linked to outbreaks. Higher numbers of cases and outbreaks were seen in Denmark’s Capital Region compared to other regions. Overall, 22 SARS-CoV-2 deaths and 359 deaths (non-SARS-CoV-2) per 1000 resident years were identified in the study period.

Conclusion

Less than half of LTCFs identified any cases. The majority of cases were linked to outbreaks, emphasizing the importance of preventing introductions of SARS-CoV-2 into the facilities. Furthermore, it highlights the need to invest efforts into infrastructures, routine procedures and monitoring of SARS-CoV-2 in LTCFs to limit the introduction and the spread of SARS-CoV-2.
Calcification of Joints and Arteries (CALJA) Is a Rare Cause of Arthritis and Lower Limb Ischemia: Case Report and Literature Review
Authors: Maffi Michele , De Mattia Giammarco , Mazzoni Maria Rosa , Michelucci Angela , Toschi Benedetta , Adelaide Caligo Maria , Mosca Marta , Mazzantini Maurizio
Published: May 2023

Calcification of Joints and Arteries (CALJA) is a rare disease that leads to chronic arthritis and lower limb claudication due to hydroxyapatite crystal deposition. The disease is caused by mutations in the 5-nucleotidase (NT5E) gene, which is responsible for pyrophosphate metabolism. Only 23 cases have been described so far. In this case report, we describe a new case of CALJA and provide a literature review. A 65-year-old woman was referred to the Rheumatology Unit with the diagnosis of seronegative oligo-arthritis. She complained of lower limb claudication, which was becoming progressively worse. Doppler ultrasound revealed bilateral obliteration of the popliteal and femoral arteries, and X-rays of the knees, hands, and feet showed extensive periarticular calcific deposits. The results of the NT5E gene analysis were positive for an inactivating variant, leading to the diagnosis of CALJA. The clinical features of CALJA are caused by hydroxyapatite crystal deposition at the periarticular and vascular levels due to abnormalities of pyrophosphate metabolism. Currently, no specific treatment is available, although a trial on the use of etidronate is ongoing. Patients with CALJA are often treated with immunosuppressant agents in the suspect of inflammatory rheumatologic diseases. Our case is the first in which clinical symptoms and a steady increase of inflammatory markers improved only after colchicine therapy initiation. It is crucial for the rheumatologist to recognize the features CALJA and keep it in mind in the differential diagnosis of patients with lower limb arterial insufficiency and arthritis or early osteoarthritis with joint calcification.
The importance of equally accessible genomic surveillance in the age of pandemics
Authors: Zeghbib Safia , Kemenesi Gábor , Jakab Ferenc
Published: May 2023

Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe.
How attractive is the participation in a Living Lab study? Experimental evidence and recommendations
Authors: Brohmer Hilmar , Munz Katinka , Röderer Kathrin , Anzengruber Christoph , Wendland Matthias , Corcoran Katja
Published: May 2023

Living Labs, which are urban sites that include households and workplaces and are used to study the real-time use of technological innovations and devices, have become increasingly popular among environmental scientists to gain insights into energy consumption in peoples’ everyday life. However, recruiting a viable number of participants for such studies can pose a challenge to researchers: Factors like month-long study durations and the requirements to handle smart technology proficiently or frequently exchange information with researchers and other users do not necessarily make participation attractive for everyone. To identify relevant factors for participation, we conducted three large preregistered surveys (total N = 1479) in Austria: two conjoint studies and one experimental study. We found that advertising a Living Lab with a shorter duration (less than a month), providing the option to participate from home, and—a crucial point—offering financial incentives should be considered when considering promotion strategies and conducting thorough study planning. However, we discuss the fact that there might be a risk of selection bias for technic-savvy and future-oriented people.
Automated prediction of wet-snow avalanche activity in the Swiss Alps
Authors: Hendrick Martin , Techel Frank , Volpi Michele , Olevski Tasko , Pérez-Guillén Cristina , Herwijnen Alec van , Schweizer Jürg
Published: May 2023

Wet-snow avalanches are triggered by the infiltration of liquid water which weakens the snowpack. Wet-snow avalanches are among the most destructive avalanches, yet their release mechanism is not sufficiently understood for a process-based prediction model. Therefore, we followed a data-driven approach and developed a random forest model, depending on slope aspect, to predict the local wet-snow avalanche activity at the locations of 124 automated weather stations distributed throughout the Swiss Alps. The input variables were the snow and weather data recorded by the stations over the past 20 years. The target variable was based on manual observations over the same 20-year period. To filter out erroneous reports, we defined the days with wet-snow avalanches in a stringent manner, selecting only the most extreme active or inactive days, which reduced the size of the dataset but increased the reliability of the target variable. The model was trained with weather variables and variables computed from simulated snow stratigraphy in 38$^\circ$ slopes facing the 4 cardinal directions. While model development and validation were done in nowcast mode, we also studied model performance in 24-hour forecast mode by using input variables computed from a numerical weather prediction (NWP) model. Overall, the performance was good in both nowcast and forecast mode (f1-score around 0.8). To assess model performance beyond the stringent definition of wet-snow avalanche days, we compared model predictions to wet-snow avalanche activity over the entire Swiss Alps, based on the raw data over 8 winters. We obtained a Spearman correlation coefficient of 0.71. Hence, our model represents a step toward the application of support tools in operational wet-snow avalanche forecasting.
Is the quality of evidence in health technology assessment deteriorating over time? A case study on cancer drugs in Australia
Authors: Gao Yuan , Laka Mah , Merlin Tracy
Published: May 2023

Objective

This study aimed to assess whether there have been changes in the quality of clinical evidence submitted for government subsidy decisions on cancer medicines over the past 15 years.

Methods

We reviewed public summary documents (PSDs) reporting on subsidy decisions made by the Pharmaceutical Benefits Advisory Committee (PBAC) from July 2005 to July 2020. Information was extracted on the study design, directness of comparison, sample size, and risk of bias (RoB). Changes in the quality of evidence were assessed using regression analysis.

Results

Overall, 214 PSDs were included in the analysis. Thirty-seven percent lacked direct comparative evidence. Thirteen percent presented observational or single-arm studies as the basis for decisions. Among PSDs presenting indirect comparisons, 78 percent reported transitivity issues. Nearly half (41 percent) of PSDs reporting on medicines supported by head-to-head studies noted there was a moderate/high/unclear RoB. PSDs reporting concerns with RoB increased by a third over the past 7 years, even after adjusting for disease rarity and trial data maturity (OR 1.30, 95% CI: 0.99, 1.70). No time trends were observed regarding the directness of clinical evidence, study design, transitivity issues, or sample size during any of the analyzed periods.

Conclusion

Our findings indicate that the clinical evidence supplied to inform funding decisions for cancer medicines is often of poor quality and has been deteriorating over time. This is concerning as it introduces greater uncertainty in decision making. This is particularly important as the evidence supplied to the PBAC is often the same as that supplied to other global decision-making bodies.
Extraverted innovators and conscientious laggards? Investigating effects of personality traits on language change
Authors: Steiner Carina , Jeszenszky Péter , Stebler Viviane , Leemann Adrian
Published: May 2023

Although personality-related factors play a crucial role in sociolinguistics as conceivable sources of language variation and change, there is insufficient quantitative evidence on such relationships. Using a large and balanced sample (n= 1000), this study investigated effects of personality traits on the use of a Swiss German plural marker in its early stages of diffusion. Besides age and region, conscientiousness and extraversion emerged as the most important predictors: less conscientious and, to a certain extent, more extraverted speakers were more likely to contribute to the diffusion of the morphological innovations under investigation. Based on our results, we argue that less conscientious speakers might monitor their own speech and that of others less closely, thus adopting innovations earlier, whereas extraverted speakers may act as successful brokers in transmitting innovations from one social group to another.
A comparison of latent semantic analysis and correspondence analysis of document-term matrices
Authors: Qi Qianqian , Hessen David J. , Deoskar Tejaswini , van der Heijden Peter G. M.
Published: May 2023

Latent semantic analysis (LSA) and correspondence analysis (CA) are two techniques that use a singular value decomposition for dimensionality reduction. LSA has been extensively used to obtain low-dimensional representations that capture relationships among documents and terms. In this article, we present a theoretical analysis and comparison of the two techniques in the context of document-term matrices. We show that CA has some attractive properties as compared to LSA, for instance that effects of margins, that is, sums of row elements and column elements, arising from differing document lengths and term frequencies are effectively eliminated so that the CA solution is optimally suited to focus on relationships among documents and terms. A unifying framework is proposed that includes both CA and LSA as special cases. We empirically compare CA to various LSA-based methods on text categorization in English and authorship attribution on historical Dutch texts and find that CA performs significantly better. We also apply CA to a long-standing question regarding the authorship of the Dutch national anthem Wilhelmus and provide further support that it can be attributed to the author Datheen, among several contenders.
Community Practices and Getting Good at Bad Emotions
Authors: Olberding Amy
Published: May 2023

Early Confucian philosophy is remarkable in its attention to everyday social interactions and their power to steer our emotional lives. Their work on the social dimensions of our moral-emotional lives is enormously promising for thinking through our own context and struggles, particularly, I argue, the ways that public rhetoric and practices may steer us away from some emotions it can be important to have, especially negative emotions. Some of our emotions are bad – unpleasant to experience, reflective of dissatisfactions or even heartbreak – but nonetheless quite important to express and, more basically, to feel. Grief is like this, for example. So, too, is disappointment. In this essay, I explore how our current social practices may fail to support expressions of disappointment and thus suppress our ability to feel it well.
Vasubandhu on the First Person
Authors: Das Nilanjan
Published: May 2023

In classical South Asia, most philosophers thought that the self (if it exists at all) is what the first-person pronoun ‘I’ stands for. It is something that persists through time, undergoes conscious thoughts and experiences, and exercises control over actions. The Buddhists accepted the ‘no self’ thesis: they denied that such a self is substantially real. This gave rise to a puzzle for these Buddhists. If there is nothing substantially real that ‘I’ stands for, what are we talking about when we speak of ourselves? In this paper, I present one Buddhist answer to this question, an answer that emerges from the work of the Abhidharma thinker Vasubandhu (4th to 5th century CE).
Introduction: How Can and Should Philosophy Be Expanding its Horizons?
Authors: Baggini Julian
Published: May 2023

The Royal Institute of Philosophy volume of which this paper is an introduction is on the theme of ‘Expanding Horizons’. But what does it mean for philosophy to fruitfully expand its horizons? The contributions to the volume suggest at least five profitable ways. First, by looking to other philosophical traditions for new perspectives on familiar questions and alternative methods, questions, and ways of understanding. Second, by looking to what has been neglected or overlooked in our own histories of thought. Third, by developing novel methods, in addition to argument, for investigating philosophical issues. Fourth, by embracing different modalities for doing philology, such as the literary. Fifth, by reflecting on the practice of comparative philosophy to better understand the extent to which philosophy can and should be universal. Together, these approaches both increase the range of voices heard in philosophy and the scope and ambition of the discipline.
Computing Rates and Distributions of Rock Recovery in Subduction Zones
Authors: Kerswell Buchanan C. , Kohn Matthew J. , Gerya Taras V.
Published: May 2023

Bodies of rock that are detached (recovered) from subducting oceanic plates, and exhumed to Earth's surface, become invaluable records of the mechanical and chemical processing of rock along subduction interfaces. Exposures of interface rocks with high‐pressure (HP) mineral assemblages provide insights into the nature of rock recovery, yet various inconsistencies arise when directly comparing the rock record with numerical simulations of subduction. Constraining recovery rates and depths from the rock record presents a major challenge because small sample sizes of HP rocks reduce statistical power. As an alternative approach, this study implements a classification algorithm to identify rock recovery in numerical simulations of oceanic‐continental convergence. Over one million markers are classified from 64 simulations representing a large range of subduction zones. Recovery pressures (depths) correlate strongly with convergence velocity and moderately with oceanic plate age, while slab‐top thermal gradients correlate strongly with oceanic plate age and upper‐plate thickness. Recovery rates strongly correlate with upper‐plate thickness, yet show no correlation with convergence velocity or oceanic plate age. Likewise, pressure‐temperature (PT) distributions of recovered markers vary among numerical experiments and generally show deviations from the rock record that cannot be explained by petrologic uncertainties alone. For example, a significant gap in marker recovery is found near 2 GPa and 550°C, coinciding with the highest frequencies of exhumed HP rocks. Explanations for such a gap in marker recovery include numerical modeling uncertainties, selective sampling of exhumed HP rocks, or natural geodynamic factors not accounted for in numerical experiments.
Greenland Subglacial Discharge as a Driver of Hotspots of Increasing Coastal Chlorophyll Since the Early 2000s
Authors: Oliver Hilde , Slater Donald , Carroll Dustin , Wood Michael , Morlighem Mathieu , Hopwood Mark J.
Published: May 2023

Subglacial discharge emerging from the base of Greenland's marine‐terminating glaciers drives upwelling of nutrient‐rich bottom waters to the euphotic zone, which can fuel nitrate‐limited phytoplankton growth. Here, we use buoyant plume theory to quantify this subglacial discharge‐driven nutrient supply on a pan‐Greenland scale. The modeled nitrate fluxes were concentrated in a few critical systems, with half of the total modeled nitrate flux anomaly occurring at just 14% of marine‐terminating glaciers. Increasing subglacial discharge fluxes results in elevated nitrate fluxes, with the largest flux occurring at Jakobshavn Isbræ in Disko Bay, where subglacial discharge is largest. Subglacial discharge and nitrate flux anomaly also account for significant temporal variability in summer satellite chlorophyll a (Chl) within 50 km of Greenland's coast, particularly in some regions in central west and northwest Greenland.
Using InSight Data to Calibrate Seismicity From Remote Observations of Surface Faulting
Authors: Sabbeth L. , Smrekar S. E. , Stock J. M.
Published: May 2023

We use a scaling relationship between fault length and scalar moment to predict seismicity from the Cerberus Fossae graben using shear modulus and fault lengths. Cerberus Fossae is 20–40° (1,200–2,300 km) from the InSight lander and matches the location of 21 recorded seismic events withMw ≥ 3. These unique seismic observations make an ideal laboratory to test our method of predicting seismicity on another planet using surface fault observations. Terrestrial faults have observed patterns of rupture depth distributions and segmentation. We use these patterns and magnitudes of detected marsquakes to predict moment release of events in Cerberus Fossae over a range of plausible Martian rupture vertical slip extents (VSEs) of 2, 20, and 40 km, which are rooted in estimates of crustal thickness, elastic thickness, and seismicity depth. We sum individual events for each case to determine cumulative moment release and use deformation duration to determine annual moment release. Predicted seismicity rates are dependent on the duration of deformation, which in this case is well constrained to 2–10 Ma. We compare our results to events recorded at Cerberus Fossae by InSight and find that seismicity rates for the cases with a 40 km maximum VSE or no limit on VSE are within an order of magnitude of observed seismicity. Faults with maximum VSEs of 2 km best match observed magnitudes. Our approach, using only observed fault lengths, segmentation, seismogenic thickness estimates, and deformation duration, produces seismicity estimates that are as accurate as methods that take rupture offset into account.
Modeling Ring Current Proton Fluxes Using Artificial Neural Network and Van Allen Probe Measurements
Authors: Li Jinxing , Bortnik Jacob , Chu Xiangning , Ma Donglai , Tian Sheng , Wang Chih‐Ping , Manweiler Jerry W. , Lanzerotti Louis J.
Published: May 2023

Terrestrial ring current dynamics are a critical part of the near‐space environment, in that they directly drive geomagnetic field variations that control particle drifts, and define geomagnetic storms. The present study aims to specify a global and time‐varying distribution of ring current proton using geomagnetic indices and solar wind parameters with their history as input. We train an artificial neural network (ANN) model to reproduce proton fluxes measured by the Radiation Belt Storm Probes Ion Composition Experiment instrument onboard Van Allen Probes. By choosing optimal feature parameters and their history length, the model results show a high correlation and a small error between model specifications and satellite measurements. The modeled results well capture energy‐dependent proton dynamics in association with geomagnetic storms, including inward radial diffusion, acceleration and decay. Our ANN model produces proton fluxes with their corresponding 3D spatiotemporal variations, capturing the latitudinal distribution and local time asymmetry that are consistent with observations and that can further inform theory.
Contrasting Responses of Atlantic and Pacific Tropical Cyclone Activity to Atlantic Multidecadal Variability
Authors: Huang Huanping , Collins William D. , Patricola Christina M. , Ruprich‐Robert Yohan , Ullrich Paul A. , Baker Alexander J.
Published: May 2023

This research assesses the influences of Atlantic Multidecadal Variability (AMV) on global tropical cyclones (TCs) using two large ensembles of idealized global climate model simulations with opposite signs of AMV forcings superimposed (i.e., AMV+ and AMV–). We first detect TCs and then compare TC activity by basin in the two AMV experiments. We find contrasting responses of Atlantic and Pacific TC frequency to the AMV anomalies. Compared to AMV–, AMV+ significantly increases TC frequency in the North Atlantic, including those making landfalls. The increase is explained by warmer sea surface temperature, higher relative humidity, increased relative vorticity, and weaker vertical wind shear under AMV+. By contrast, AMV+ decreases TC occurrence over the western North Pacific and South Pacific, which is tied to stronger vertical wind shear and lower relative humidity. The opposite responses of TC activity to AMV+ are attributed to strengthened Walker Circulation between the Atlantic and Pacific.
Extreme Flood Sediment Production and Export Controlled by Reach‐Scale Morphology
Authors: Baynes E. R. C. , Kincey M. E. , Warburton J.
Published: May 2023

Rapid earth surface evolution is discrete in nature, with short‐duration extreme events having a widespread impact on landscapes despite occurring relatively infrequently. Here, we exploit a unique opportunity to identify the broad, process‐based, controls on sediment production and export during extreme rainfall‐runoff events through a multi‐catchment analysis. A 3 hr extreme rainfall event generated significantly different impacts across three catchments, ranging from (a) sediment export exceeding two orders of magnitude more than the typical long term average to (b) a minimal impact, with this variability primarily controlled by catchment steepness and the presence of reach‐scale morphological transitions caused by postglacial landscape adjustment. In any catchment worldwide where populations are at risk, we highlight the importance of combining topographic analysis with detailed mapping of channel bed material (e.g., presence of transitions between process domains) and identification of sediment sources within morphological transition zones for accurately predicting the impact of extreme events.
Distributing task-related neural activity across a cortical network through task-independent connections
Authors: Kim Christopher M. , Finkelstein Arseny , Chow Carson C. , Svoboda Karel , Darshan Ran
Published: May 2023

Task-related neural activity is widespread across populations of neurons during goal-directed behaviors. However, little is known about the synaptic reorganization and circuit mechanisms that lead to broad activity changes. Here we trained a subset of neurons in a spiking network with strong synaptic interactions to reproduce the activity of neurons in the motor cortex during a decision-making task. Task-related activity, resembling the neural data, emerged across the network, even in the untrained neurons. Analysis of trained networks showed that strong untrained synapses, which were independent of the task and determined the dynamical state of the network, mediated the spread of task-related activity. Optogenetic perturbations suggest that the motor cortex is strongly-coupled, supporting the applicability of the mechanism to cortical networks. Our results reveal a cortical mechanism that facilitates distributed representations of task-variables by spreading the activity from a subset of plastic neurons to the entire network through task-independent strong synapses.
Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows
Authors: Bonacci Miki , Qiao Junfeng , Spallanzani Nicola , Marrazzo Antimo , Pizzi Giovanni , Molinari Elisa , Varsano Daniele , Ferretti Andrea , Prezzi Deborah
Published: May 2023

The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and implementations that are relevant to extend this approach beyond density functional theory (DFT), in order to automate many-body perturbation theory (MBPT) calculations. Notably, an algorithm pursuing the goal of an efficient and robust convergence procedure for GW and BSE simulations is provided, together with its implementation in a fully automated framework. This is accompanied by an automatic GW band interpolation scheme based on maximally localized Wannier functions, aiming at a reduction of the computational burden of quasiparticle band structures while preserving high accuracy. The proposed developments are validated on a set of representative semiconductor and metallic systems.
Empirical distributions of traffic loads from one year of weigh-in-motion data
Authors: Iervolino Iunio , Baltzopoulos Georgios , Vitale Antonio , Grella Antonio , Bonini Giovanni , Iannaccone Antonio
Published: May 2023

In the state-of-the-art of structural engineering the actions for design or assessment of bridges should derive from a probabilistic (i.e., frequentist) characterization of the loads. Data from weigh-in-motion (WIM) systems can inform stochastic models for traffic loads. However, WIM is not widespread, and data of this kind are scarce in the literature and often not recent. Due to structural safety reasons, the 52 km long A3 highway in Italy, connecting the cities of Naples and Salerno, has been equipped with a WIM system which has been operational since the beginning of 2021. The system’s measurements of each vehicle transiting over the WIM devices, impede overloads on the many bridges featured in the transportation infrastructure. By the time of this writing the WIM system has seen one year of uninterrupted operation, collecting more than thirty-six million datapoints in the meantime. This short paper presents and discusses these WIM measurements, deriving the empirical distributions of traffic loads and making the original data available for further research and applications.
Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data
Authors: Shooshtari Parisa , Feng Samantha , Nelakuditi Viswateja , Asakereh Reza , Hosseini Naghavi Nader , Foong Justin , Brudno Michael , Cotsapas Chris
Published: May 2023

International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.
Application of non-degradable waste as building material for low-cost housing
Authors: Zuraida Siswanti , Dewancker Bart , Margono Romi Bramantyo
Published: May 2023

Building material is one of the essential aspects in accommodating the supply and demand of low-cost housing in Indonesia. Recently, several researchers have devoted much time and effort to developing waste recycling for building materials since it is more ecologically benign, particularly for non-degradable waste. This article focuses on recycling disposable diaper waste as composite material for a structural and architectural component of the building based on Indonesian building standards. In addition to offering a broad perspective on the implementation of experimental findings, the design scenario comprised the construction of low-cost housing with a floorplan area of 36 m2. The experimental results indicate that disposable diapers waste to use as composite materials of the building has a maximum capacity of 10% for structural components and 40% for nonstructural and architectural components. The prototype housing also reveals that 1.73 m3 of disposable diaper waste can be decreased and utilised for a housing area of 36 m2.
A new spinosaurid dinosaur species from the Early Cretaceous of Cinctorres (Spain)
Authors: Santos-Cubedo Andrés , de Santisteban Carlos , Poza Begoña , Meseguer Sergi
Published: May 2023

A new spinosaurid genus and species is described based on the right maxilla and five caudal vertebrae of a single specimen from the Arcillas de Morella Formation (Early Cretaceous) at the locality of Cinctorres (Castellón, Spain). Protathlitis cinctorrensis gen. et sp. nov. is diagnosed by one autapomorphic feature as well as by a unique combination of characters. The autapomorphy includes a subcircular depression in the anterior corner of the antorbital fossa in the maxilla. The new Iberian species is recovered as a basal baryonychine. The recognition of Protathlitis cinctorrensis gen. et sp. nov. as the first baryonychine dinosaur species identified from the Arcillas de Morella Formation (late Barremian) from the same time as Vallibonavenatrix cani, the first spinosaurine dinosaur from the same formation in the Morella subbasin (Maestrat Basin, eastern Spain), indicates that the Iberian Peninsula was home to a highly diverse assemblage of medium-to-large bodied spinosaurid dinosaurs. It seems that spinosaurids appeared during the Early Cretaceous in Laurasia, with the two subfamilies occupying the western part of Europe during this period. Later, during the Barremian–Aptian, they migrated to Africa and Asia, where they would diversify. In Europe, baryonychines were dominant, while in Africa, spinosaurines were most abundant.
Embedding responsibility in intelligent systems: from AI ethics to responsible AI ecosystems
Authors: Stahl Bernd Carsten
Published: May 2023

Intelligent systems that are capable of making autonomous decisions based on input from their environment have great potential to do good, but they also raise significant social and ethical concerns. The discourse on ethics and artificial intelligence (AI) has covered these concerns in depth and developed an array of possible ways of addressing them. This article argues that a shortcoming of this discourse is that it concentrates on specific issues and their mitigation but neglects the nature of intelligent systems as socio-technical systems of systems that are often described as ecosystems. Building on the discussion of ethics and AI, the article suggests that it would be beneficial to come to an understanding of what would constitute responsible AI ecosystems. By introducing the concept of meta-responsibility or higher-level responsibility, the article proposes characteristics that an ecosystem would have to fulfil, in order to be considered a responsible ecosystem. This perspective is theoretically interesting because it extends the current AI ethics discourse. It furthermore offers a novel perspective for researchers and developers of intelligent system and helps them reflect on the way they relate to ethical issues.
A global conservation basic income to safeguard biodiversity
Authors: de Lange Emiel , Sze Jocelyne S. , Allan James , Atkinson Scott , Booth Hollie , Fletcher Robert , Khanyari Munib , Saif Omar
Published: May 2023

Biodiversity conservation supporting a global sustainability transformation must be inclusive, equitable, just and embrace plural values. The conservation basic income (CBI), a proposed unconditional cash transfer to individuals residing in important conservation areas, is a potentially powerful mechanism for facilitating this radical shift in conservation. This analysis provides comprehensive projections for potential gross costs of global CBI using spatial analyses of three plausible future conservation scenarios. Gross costs vary widely, depending on the areas and populations included, from US$351 billion to US$6.73 trillion annually. A US$5.50 per day CBI in existing protected areas in low- and middle-income countries would cost US$478 billion annually. These costs are large compared with current government conservation spending (~US$133 billion in 2020) but represent a potentially sensible investment in safeguarding incalculable social and natural values and the estimated US$44 trillion in global economic production dependent on nature.
Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries
Authors: Huggett Megan J. , Hobbs Jean-Paul A. , Vitelli Federico , Stat Michael , Sinclair-Taylor Tane H. , Bunce Michael , DiBattista Joseph D.
Published: May 2023

Hybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genusCentropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species.
Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals
Authors: Lai Xiaoqian , Li Rong , Wang Panpan , Li Meng , Xiao Chenxi , Cao Qiang , Li Xin , Zhao Wenxue
Published: May 2023

PD-1 has become a common target for cancer treatment. However, the molecular regulation of PD-1 expression homeostasis remains unclear. Here we report the PD-1 3’ UTR can dramatically repress gene expression via promoting mRNA decay. Deletion of the PD-1 3’ UTR inhibits T cell activity and promotes T-ALL cell proliferation. Interestingly, the robust repression is attributable to cumulative effects of many weak regulatory regions, which we show together are better able to maintain PD-1 expression homeostasis. We further identify several RNA binding proteins (RBPs) that modulate PD-1 expression via the 3’ UTR, including IGF2BP2, RBM38, SRSF7, and SRSF4. Moreover, despite rapid evolution, PD-1 3’ UTRs are functionally conserved and strongly repress gene expression through many common RBP binding sites. These findings reveal a previously unrecognized mechanism of maintaining PD-1 expression homeostasis and might represent a general model for how small regulatory effects play big roles in regulation of gene expression and biology.
Ultrastrong magnetic light-matter interaction with cavity mode engineering
Authors: Choi Hyeongrak , Englund Dirk
Published: May 2023

Magnetic interaction between photons and dipoles is essential in electronics, sensing, spectroscopy, and quantum computing. However, its weak strength often requires resonators to confine and store the photons. Here, we present mode engineering techniques to create resonators with ultrasmall mode volume and ultrahigh quality factor. In particular, we show that it is possible to achieve an arbitrarily small mode volume only limited by materials or fabrication with minimal quality-factor degradation. We compare mode-engineered cavities in a trade-off space and show that the magnetic interaction can be strengthened more than 1016 times compared to free space. Proof-of-principles experiments using an ensemble of diamond nitrogen-vacancy spins show good agreement with our theoretical predictions. These methods enable new applications from high-cooperativity microwave-spin coupling in quantum computing or compact electron paramagnetic resonance sensors to fundamental science such as dark matter searches.
A marvel of chiral squaraine aggregates: chiroptical spectra beyond the exciton model
Authors: Giavazzi Davide , Schumacher Marvin F. , Grisanti Luca , Anzola Mattia , Di Maiolo Francesco , Zablocki Jennifer , Lützen Arne , Schiek Manuela , Painelli Anna
Published: May 2023

An extensive experimental study of a family of chiral aggregates of proline derived squaraines is presented and discussed with reference to two theoretical models and to MD simulations to shed light on the chiroptical properties of these systems.
Virus-like silica nanoparticles enhance macromolecule permeationin vivo
Authors: Cao Yuxue , Janjua Taskeen Iqbal , Qu Zhi , Draphoen Bastian , Bai Yunfan , Linden Mika , Moniruzzaman Md , Hasnain Sumaira Z. , Kumeria Tushar , Popat Amirali
Published: May 2023

Silica nanoparticle based permeation enhancers have the potential to improve the oral delivery of biologics.
Heteroleptic copper(i) complexes [Cu(dmp)(N^P)]BF4 for photoinduced atom-transfer radical addition reactions
Authors: Zhao You-Hui , Li Hai-Yan , Young David James , Cao Xiangqian , Zhu Da-Liang , Ren Zhi-Gang , Li Hong-Xi
Published: May 2023

Reactions of Cu(MeCN)4BF4 with an imine-phosphine and a diimine afforded mononuclear complexes [Cu(N^P)(N^N)]BF4, which serve as visible-light photosensitizers to facilitate intermolecular atom-transfer radical addition reactions.
Efficient hydrodeoxygenation of methyl levulinate into pentanoic biofuels over Ru/USY catalysts
Authors: Wang Shaohua , Cui Wenhao , Miao Caixia , Tang Nanfang , Lin Lu , Wu Zhijie , An Qingda , Tian Peng , Pang Jifeng , Luo Wenhao
Published: May 2023

Ru/USY-15 with an optimal site ratio of ∼1 : 5 between metal and strong acid sites is illustrated for the efficient production of pentanoic biofuels in the hydrodeoxygenation of methyl levulinate.