bluuebunny/crossref_metadata_2025_split huggingface dataset:
Provably-secure quantum randomness expansion with uncharacterised homodyne detection
Authors: Wang Chao , Primaatmaja Ignatius William , Ng Hong Jie , Haw Jing Yan , Ho Raymond , Zhang Jianran , Zhang Gong , Lim Charles 
Published: January 2023

AbstractQuantum random number generators (QRNGs) are able to generate numbers that are certifiably random, even to an agent who holds some side information. Such systems typically require that the elements being used are precisely calibrated and validly certified for a credible security analysis. However, this can be experimentally challenging and result in potential side-channels which could compromise the security of the QRNG. In this work, we propose, design and experimentally demonstrate a QRNG protocol that completely removes the calibration requirement for the measurement device. Moreover, our protocol is secure against quantum side information. We also take into account the finite-size effects and remove the independent and identically distributed requirement for the measurement side. More importantly, our QRNG scheme features a simple implementation which uses only standard optical components and are readily implementable on integrated-photonic platforms. To validate the feasibility and practicability of the protocol, we set up a fibre-optical experimental system with a home-made homodyne detector with an effective efficiency of 91.7% at 1550 nm. The system works at a rate of 2.5 MHz, and obtains a net randomness expansion rate of 4.98 kbits/s at 1010 rounds. Our results pave the way for an integrated QRNG with self-testing feature and provable security.
Large scale phenotype imputation and in vivo functional validation implicate ADAMTS14 as an adiposity gene
Authors: Kentistou Katherine A. , Luan Jian’an , Wittemans Laura B. L. , Hambly Catherine , Klaric Lucija , Kutalik Zoltán , Speakman John R. , Wareham Nicholas J. , Kendall Timothy J. , Langenberg Claudia , Wilson James F. , Joshi Peter K. , Morton Nicholas M. 
Published: January 2023

AbstractObesity remains an unmet global health burden. Detrimental anatomical distribution of body fat is a major driver of obesity-mediated mortality risk and is demonstrably heritable. However, our understanding of the full genetic contribution to human adiposity is incomplete, as few studies measure adiposity directly. To address this, we impute whole-body imaging adiposity phenotypes in UK Biobank from the 4,366 directly measured participants onto the rest of the cohort, greatly increasing our discovery power. Using these imputed phenotypes in 392,535 participants yielded hundreds of genome-wide significant associations, six of which replicate in independent cohorts. The leading causal gene candidate, ADAMTS14, is further investigated in a mouse knockout model. Concordant with the human association data, the Adamts14−/− mice exhibit reduced adiposity and weight-gain under obesogenic conditions, alongside an improved metabolic rate and health. Thus, we show that phenotypic imputation at scale offers deeper biological insights into the genetics of human adiposity that could lead to therapeutic targets.
Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1
Authors: Conti Michelle M. , Li Rui , Narváez Ramos Michelle A. , Zhu Lihua Julie , Fazzio Thomas G. , Benanti Jennifer A. 
Published: January 2023

AbstractOrdered cell cycle progression is coordinated by cyclin dependent kinases (CDKs). CDKs often phosphorylate substrates at multiple sites clustered within disordered regions. However, for most substrates, it is not known which phosphosites are functionally important. We developed a high-throughput approach, Phosphosite Scanning, that tests the importance of each phosphosite within a multisite phosphorylated domain. We show that Phosphosite Scanning identifies multiple combinations of phosphosites that can regulate protein function and reveals specific phosphorylations that are required for phosphorylation at additional sites within a domain. We applied this approach to the yeast transcription factor Hcm1, a conserved regulator of mitotic genes that is critical for accurate chromosome segregation. Phosphosite Scanning revealed a complex CDK-regulatory circuit that mediates Cks1-dependent phosphorylation of key activating sites in vivo. These results illuminate the mechanism of Hcm1 activation by CDK and establish Phosphosite Scanning as a powerful tool for decoding multisite phosphorylated domains.
Time-dependent unloading effects on muscle and bone and involvement of FNDC5/irisin axis
Authors: Sanesi Lorenzo , Storlino Giuseppina , Dicarlo Manuela , Oranger Angela , Zerlotin Roberta , Pignataro Patrizia , Suriano Clelia , Guida Gabriella , Grano Maria , Colaianni Graziana , Colucci Silvia Concetta 
Published: January 2023

AbstractThe identification of biomarkers and countermeasures to prevent the adverse effects on the musculoskeletal system caused by the absence of mechanical loading is the main goal of space biomedical research studies. In this study, we analyzed over 4 weeks of unloading, the modulation in the expression of key proteins in Vastus lateralis, Gastrocnemius and cortical bone in parallel with the modulation of irisin serum levels and its precursor FNDC5 in skeletal muscle of hind limb unloaded (HU) mice. Here we report that Atrogin-1 was up-regulated as early as 1- and 2-week of unloading, whereas Murf-1 at 2- and 3-weeks, along with a marked modulation in the expression of myosin heavy chain isoforms during unloading. Since HU mice showed reduced irisin serum levels at 4-weeks, as well as FNDC5 decrease at 3- and 4-weeks, we treated HU mice with recombinant irisin for 4 weeks, showing that unloading-dependent decline of myosin heavy chain isoforms, MyHCIIα and MyHCIIx, and the anti-apoptotic factor Bcl2, were prevented. In parallel, irisin treatment inhibited the increase of the senescence marker p53, and the pro-apoptotic factor Bax. Overall, these results suggest that the myokine irisin could be a possible therapy to counteract the musculoskeletal impairment caused by unloading.
Multi-omics microsampling for the profiling of lifestyle-associated changes in health
Authors: Shen Xiaotao , Kellogg Ryan , Panyard Daniel J. , Bararpour Nasim , Castillo Kevin Erazo , Lee-McMullen Brittany , Delfarah Alireza , Ubellacker Jessalyn , Ahadi Sara , Rosenberg-Hasson Yael , Ganz Ariel , Contrepois Kévin , Michael Basil , Simms Ian , Wang Chuchu , Hornburg Daniel , Snyder Michael P. 
Published: January 2023

AbstractCurrent healthcare practices are reactive and use limited physiological and clinical information, often collected months or years apart. Moreover, the discovery and profiling of blood biomarkers in clinical and research settings are constrained by geographical barriers, the cost and inconvenience of in-clinic venepuncture, low sampling frequency and the low depth of molecular measurements. Here we describe a strategy for the frequent capture and analysis of thousands of metabolites, lipids, cytokines and proteins in 10 μl of blood alongside physiological information from wearable sensors. We show the advantages of such frequent and dense multi-omics microsampling in two applications: the assessment of the reactions to a complex mixture of dietary interventions, to discover individualized inflammatory and metabolic responses; and deep individualized profiling, to reveal large-scale molecular fluctuations as well as thousands of molecular relationships associated with intra-day physiological variations (in heart rate, for example) and with the levels of clinical biomarkers (specifically, glucose and cortisol) and of physical activity. Combining wearables and multi-omics microsampling for frequent and scalable omics may facilitate dynamic health profiling and biomarker discovery.
Aerodynamic characterisation of porous fairings: pressure drop and Laser Doppler Velocimetry measurements
Authors: Méry Fabien , Sebbane Delphine 
Published: January 2023

AbstractWind tunnel measurements of pressure drop and steady and unsteady velocity field of a flow through fairing samples are described. 10 samples have been tested in pressure drop among which the velocity fields of 3 samples have been characterized by means of laser Doppler velocimetry. The samples are perforated plates, wiremesh plates or complex 3D geometries resulting from additive manufacturing methods. The Reynolds number of the experiments ranges from 55 000 to 117 000.
Bioclimatic atlas of the terrestrial Arctic
Authors: Rantanen Mika , Kämäräinen Matti , Niittynen Pekka , Phoenix Gareth K. , Lenoir Jonathan , Maclean Ilya , Luoto Miska , Aalto Juha 
Published: January 2023

AbstractThe Arctic is the region on Earth that is warming at the fastest rate. In addition to rising means of temperature-related variables, Arctic ecosystems are affected by increasingly frequent extreme weather events causing disturbance to Arctic ecosystems. Here, we introduce a new dataset of bioclimatic indices relevant for investigating the changes of Arctic terrestrial ecosystems. The dataset, called ARCLIM, consists of several climate and event-type indices for the northern high-latitude land areas > 45°N. The indices are calculated from the hourly ERA5-Land reanalysis data for 1950–2021 in a spatial grid of 0.1 degree (~9 km) resolution. The indices are provided in three subsets: (1) the annual values during 1950–2021; (2) the average conditions for the 1991–2020 climatology; and (3) temporal trends over 1951–2021. The 72-year time series of various climate and event-type indices draws a comprehensive picture of the occurrence and recurrence of extreme weather events and climate variability of the changing Arctic bioclimate.
The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism
Authors: Silva Felipe André , Souza Érica M. S. , Ramos Elisa , Freitas Lucas , Nery Mariana F. 
Published: January 2023

AbstractCetaceans are a group of aquatic mammals with the largest body sizes among living animals, including giant representatives such as blue and fin whales. To understand the genetic bases of gigantism in cetaceans, we performed molecular evolutionary analyses on five genes (GHSR, IGF2, IGFBP2, IGFBP7, and EGF) from the growth hormone/insulin-like growth factor axis, and four genes (ZFAT, EGF, LCORL, and PLAG1) previously described as related to the size of species evolutionarily close to cetaceans, such as pigs, cows, and sheep. Our dataset comprised 19 species of cetaceans, seven of which are classified as giants because they exceed 10 m in length. Our results revealed signs of positive selection in genes from the growth hormone/insulin-like growth factor axis and also in those related to body increase in cetacean-related species. In addition, pseudogenization of the EGF gene was detected in the lineage of toothless cetaceans, Mysticeti. Our results suggest the action of positive selection on gigantism in genes that act both in body augmentation and in mitigating its consequences, such as cancer suppression when involved in processes such as division, migration, and cell development control.
Full genome sequence for the African swine fever virus outbreak in the Dominican Republic in 1980
Authors: Spinard Edward , O’Donnell Vivian , Vuono Elizabeth , Rai Ayushi , Davis Charronne , Ramirez-Medina Elizabeth , Espinoza Nallely , Valladares Alyssa , Borca Manuel V. , Gladue Douglas P. 
Published: January 2023

AbstractAfrican swine fever is a lethal disease of domestic pigs, geographically expanding as a pandemic, that is affecting countries across Eurasia and severely damaging their swine production industry. After more than 40 years of being absent in the Western hemisphere, in 2020 ASF reappeared in the Dominican Republic and Haiti. The recent outbreak strain in the Dominican Republic has been identified as a genotype II ASFV a derivative of the ASF strain circulating in Asia and Europe. However, to date no full-length genome sequence from either the 1978–1980 Here we report the complete genome sequence of an African swine fever virus (ASFV) (DR-1980) that was previously isolated from blood collected in 1980 from the Dominican Republic at the end of the last outbreak, before culling of all swine on the island of Hispaniola and stored in the Plum Island Animal Disease Center ASFV repository. A contig representing the full-length genome (183,687 base pairs) was de novo assembled into a single contig using both Nanopore and Illumina sequences. DR-1980 was determined to belong to genotype I and, as determined by full genome comparison, a close relative to the sequenced Sardinia viruses that were causing outbreaks at this time.
Video-based formative and summative assessment of surgical tasks using deep learning
Authors: Yanik Erim , Kruger Uwe , Intes Xavier , Rahul Rahul , De Suvranu 
Published: January 2023

AbstractTo ensure satisfactory clinical outcomes, surgical skill assessment must be objective, time-efficient, and preferentially automated—none of which is currently achievable. Video-based assessment (VBA) is being deployed in intraoperative and simulation settings to evaluate technical skill execution. However, VBA is manual, time-intensive, and prone to subjective interpretation and poor inter-rater reliability. Herein, we propose a deep learning (DL) model that can automatically and objectively provide a high-stakes summative assessment of surgical skill execution based on video feeds and low-stakes formative assessment to guide surgical skill acquisition. Formative assessment is generated using heatmaps of visual features that correlate with surgical performance. Hence, the DL model paves the way for the quantitative and reproducible evaluation of surgical tasks from videos with the potential for broad dissemination in surgical training, certification, and credentialing.
Early detection of variants of concern via funnel plots of regional reproduction numbers
Authors: Milanesi Simone , Rosset Francesca , Colaneri Marta , Giordano Giulia , Pesenti Kenneth , Blanchini Franco , Bolzern Paolo , Colaneri Patrizio , Sacchi Paolo , De Nicolao Giuseppe , Bruno Raffaele 
Published: January 2023

AbstractEarly detection of the emergence of a new variant of concern (VoC) is essential to develop strategies that contain epidemic outbreaks. For example, knowing in which region a VoC starts spreading enables prompt actions to circumscribe the geographical area where the new variant can spread, by containing it locally. This paper presents ‘funnel plots’ as a statistical process control method that, unlike tools whose purpose is to identify rises of the reproduction number ($${R}_{t}$$

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t

), detects when a regional $${R}_{t}$$

R
t

departs from the national average and thus represents an anomaly. The name of the method refers to the funnel-like shape of the scatter plot that the data take on. Control limits with prescribed false alarm rate are derived from the observation that regional $${R}_{t}$$

R
t

's are normally distributed with variance inversely proportional to the number of infectious cases. The method is validated on public COVID-19 data demonstrating its efficacy in the early detection of SARS-CoV-2 variants in India, South Africa, England, and Italy, as well as of a malfunctioning episode of the diagnostic infrastructure in England, during which the Immensa lab in Wolverhampton gave 43,000 incorrect negative tests relative to South West and West Midlands territories.
Evolution of oxidative stress markers in livers of ducks during force-feeding
Authors: Remignon Herve , Burgues Pierre 
Published: January 2023

AbstractMule ducks have been force-fed to develop a hepatic steatosis, also called “foie gras”, which is similar to the non-alcoholic fatty liver disease (NAFLD) described in humans and mammals. However, in hepatic steatosis resulting from force-feeding of ducks, very little is known about the fine biochemical events that occur due to the enormous and very rapid increase in total lipids that mainly accumulate in hepatocytes. To begin to reduce this lack of knowledge associated with the development of this specific hepatic steatosis, liver samples were taken at different times to follow the overall biochemical transformation of the liver as well as different markers of oxidative stress, hypoxia and apoptosis. The results indicate that the lipid content increases rapidly in the liver throughout the force-feeding period while the protein content decreases. The amount of hydroxyproline remains constant indicating that no liver fibrosis develops during the force-feeding period. On the contrary, all the tested biomarkers of cellular oxidative stress increase rapidly but without any visible disorder in the coordination of paired activities. At the same time, hypoxia-inducible factors also increase indicating that a hypoxia situation is gradually occurring in hepatocytes. This leads, in addition to the lipotoxicity induced by the accumulation of lipids, to an increased number of liver cells to enter into apoptosis. A relative variability in the level of these cellular responses was also observed indicating that, probably, certain animals support the development of this steatosis differently. This leads us to imagine that the physiological status of these birds may differ widely for reasons that remain to be clarified.
Children and adults rely on different heuristics for estimation of durations
Authors: Stojić Sandra , Topić Vanja , Nadasdy Zoltan 
Published: January 2023

AbstractTime is a uniquely human yet culturally ubiquitous concept acquired over childhood and provides an underlying dimension for episodic memory and estimating durations. Because time, unlike distance, lacks a sensory representation, we hypothesized that subjects at different ages attribute different meanings to it when comparing durations; pre-kindergarten children compare the density of events, while adults use the concept of observer-independent absolute time. We asked groups of pre-kindergarteners, school-age children, and adults to compare the durations of an "eventful" and "uneventful" video, both 1-minute long but durations unknown to subjects. In addition, participants were asked to express the durations of both videos non-verbally with simple hand gestures. Statistical analysis has revealed highly polarized temporal biases in each group, where pre-kindergarteners estimated the duration of the eventful video as "longer." In contrast, the school-age group of children and adults claimed the same about the uneventful video. The tendency to represent temporal durations with a horizontal hand gesture was evident among all three groups, with an increasing prevalence with age. These results support the hypothesis that pre-kindergarten-age children use heuristics to estimate time, and they convert from availability to sampling heuristics between pre-kindergarten and school age.
Evolutionary analysis of resident groups’ intention to participate in green retrofit PPP projects of traditional apartment complexes
Authors: Yang Yaohong , Sun Ruicong , Wang Yonghao , Zhu Mengjuan , Yang Peishu 
Published: January 2023

AbstractGreen retrofit PPP projects of traditional apartment complexes play an important role in promoting the green and low-carbon transformation of the construction industry and achieving China's "double carbon" goals. The integrated retrofit of apartment complexes presupposes that the resident groups agree to the retrofit. Therefore, it is necessary to study the evolutionary mechanism of residents' intention to green retrofit and the transformation process of their behavior, and to explore how to enhance residents' intention to participate. First, the dissemination model of residents' intention to green retrofit is constructed. Then, the strategic interaction among government, social capitals and residents under the PPP model is introduced into the dissemination model to define the state transformation probability of resident groups. Finally, the evolution laws of residents' intention to green retrofit are analyzed. The results show that: (1) the behavior of government regulation and social capitals' effort to retrofit can motivate the number of the resident agreeing to green retrofit to meet the proportional limit, (2) the faster the government chooses the strategy of regulation and the social capitals choose the strategy of effort to retrofit, the faster the number of residents agreeing to green retrofit reaches a steady state, (3) when the level of government publicity and education is too low, the cost of government regulation or the subsidy given to residents is too high, the green retrofit of traditional apartment complexes cannot be achieved. The research conclusions can provide a reference for the government to formulate green retrofit policies.
Semantic wikis as flexible database interfaces for biomedical applications
Authors: Falda Marco , Atzori Manfredo , Corbetta Maurizio 
Published: January 2023

AbstractSeveral challenges prevent extracting knowledge from biomedical resources, including data heterogeneity and the difficulty to obtain and collaborate on data and annotations by medical doctors. Therefore, flexibility in their representation and interconnection is required; it is also essential to be able to interact easily with such data. In recent years, semantic tools have been developed: semantic wikis are collections of wiki pages that can be annotated with properties and so combine flexibility and expressiveness, two desirable aspects when modeling databases, especially in the dynamic biomedical domain. However, semantics and collaborative analysis of biomedical data is still an unsolved challenge. The aim of this work is to create a tool for easing the design and the setup of semantic databases and to give the possibility to enrich them with biostatistical applications. As a side effect, this will also make them reproducible, fostering their application by other research groups. A command-line software has been developed for creating all structures required by Semantic MediaWiki. Besides, a way to expose statistical analyses as R Shiny applications in the interface is provided, along with a facility to export Prolog predicates for reasoning with external tools. The developed software allowed to create a set of biomedical databases for the Neuroscience Department of the University of Padova in a more automated way. They can be extended with additional qualitative and statistical analyses of data, including for instance regressions, geographical distribution of diseases, and clustering. The software is released as open source-code and published under the GPL-3 license athttps://github.com/mfalda/tsv2swm.
Association of 24-h urinary sodium excretion with microalbuminuria in a Chinese population
Authors: Xu Chunxiao , Du Xiaofu , Fang Le , Zhong Jieming , Lu Feng 
Published: January 2023

AbstractTo assess the relationship of sodium, potassium and the ratio of sodium to potassium (Na/K) with albuminuria, a cross-sectional study was carried out in China in 2017. Sodium, potassium and albumin excretions were examined in a 24-h (h) urine sample collected from 1486 participants. Microalbuminuria was defined as 24-h urinary albumin excretion between 30 and 300 mg/24 h. The participants had an average age of 46.2 ± 14.1 years old, and 48.9% were men. The proportion of patients with microalbuminuria was 9.0%. As illustrated by the adjusted generalized linear mixed model, sodium concentration increased significantly with the increase in 24-h urinary albumin (β = 1.16, 95% confidence interval (CI) 0.38–1.93; P = 0.003). Multivariable-adjusted logistic regression analyses demonstrated that the odds ratio (OR) of microalbuminuria increased with the quartiles of sodium [OR = 2.20, 95% CI 1.26–3.84 (the maximum quartile vs. the minimum quartile), Pfor trend = 0.006]. Potassium and the Na/K ratio did not have any association with outcome indicators. A high amount of sodium intake was potentially correlated with early renal function impairment.