bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tradeoff between lag time and growth rate drives the plasmid acquisition cost
Authors: Ahmad Mehrose , Prensky Hannah , Balestrieri Jacqueline , ElNaggar Shahd , Gomez-Simmonds Angela , Uhlemann Anne-Catrin , Traxler Beth , Singh Abhyudai , Lopatkin Allison J. 
Published: April 2023

AbstractConjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.
Parity-encoding-based quantum computing with Bayesian error tracking
Authors: Lee Seok-Hyung , Omkar Srikrishna , Teo Yong Siah , Jeong Hyunseok 
Published: April 2023

AbstractMeasurement-based quantum computing (MBQC) in linear optical systems is promising for near-future quantum computing architecture. However, the nondeterministic nature of entangling operations and photon losses hinder the large-scale generation of graph states and introduce logical errors. In this work, we propose a linear optical topological MBQC protocol employing multiphoton qubits based on the parity encoding, which turns out to be highly photon-loss tolerant and resource-efficient even under the effects of nonideal entangling operations that unavoidably corrupt nearby qubits. For the realistic error analysis, we introduce a Bayesian methodology, in conjunction with the stabilizer formalism, to track errors caused by such detrimental effects. We additionally suggest a graph-theoretical optimization scheme for the process of constructing an arbitrary graph state, which greatly reduces its resource overhead. Notably, we show that our protocol is advantageous over several other existing approaches in terms of the fault-tolerance and resource overhead.
Adverse effects, perceptions and attitudes related to BNT162b2, mRNA-1273 or JNJ-78436735 SARS-CoV-2 vaccines: Population-based cohort
Authors: Bürzle Oliver , Menges Dominik , Maier Julian D. , Schams Daniel , Puhan Milo A. , Fehr Jan , Ballouz Tala , Frei Anja 
Published: April 2023

AbstractLong-term control of SARS-CoV-2 requires effective vaccination strategies. This has been challenged by public mistrust and the spread of misinformation regarding vaccine safety. Better understanding and communication of the longer-term and comparative experiences of individuals in the general population following vaccination are required. In this population-based longitudinal study, we included 575 adults, randomly selected from all individuals presenting to a Swiss reference vaccination center, for receipt of BNT162b2, mRNA1273, or JNJ-78436735. We assessed the prevalence, onset, duration, and severity of self-reported adverse effects over 12 weeks following vaccination. We additionally evaluated participants’ perceptions of vaccines, trust in public health authorities and pharmaceutical companies, and compliance with public health measures. Most participants reported at least one adverse effect within 12 weeks following vaccination. Adverse effects were mostly mild or moderate, resolved within three days, and rarely resulted in anaphylaxis or hospitalizations. Female sex, younger age, higher education, and receipt of mRNA-1273 were associated with reporting adverse effects. Compared to JNJ-78436735 recipients, a higher proportion of mRNA vaccine recipients agreed that vaccination is important, and trusted public health authorities. Our findings provide real-world estimates of the prevalence of adverse effects following SARS-CoV-2 vaccination and highlight the importance of transparent communication to ensure the success of current or future vaccination campaigns.
Three-Dimensional Motion Capture Data of a Movement Screen from 183 Athletes
Authors: Zhao Xiong , Ross Gwyneth , Dowling Brittany , Graham Ryan B. 
Published: April 2023

AbstractMovement screens are widely used to identify aberrant movement patterns in hopes of decreasing risk of injury, identifying talent, and/or improving performance. Motion capture data can provide quantitative, objective feedback regarding movement patterns. The dataset contains three-dimensional (3D) motion capture data of 183 athletes performing mobility tests (ankle, back bend, crossover adduction, crossover rotation, elbows, head, hip turn, scorpion, shoulder abduction, shoulder azimuth, shoulder rotation, side bends, side lunges and trunk rotation) and stability tests (drop jump, hop down, L-cut, lunge, rotary stability, step down and T-balance) bilaterally (where applicable), the athletes’ injury history, and demographics. All data were collected at 120 Hz or 480 Hz using an 8-camera Raptor-E motion capture system with 45 passive reflective markers. A total of 5,493 trials were pre-processed and included in .c3d and .mat formats. This dataset will enable researchers and end users to explore movement patterns of athletes of varying demographics from different sports and competition levels; develop objective movement assessment tools; and gain new insights into the relationships between movement patterns and injury.
Short-term effect of intravitreal brolucizumab injections in patients with neovascular age-related macular degeneration on retinal nerve fiber layer thickness
Authors: Jun Sung Yeon , Hwang Daniel Duck-Jin 
Published: April 2023

AbstractThis study reported the short-term effects of intravitreal brolucizumab (IVB) on peripapillary retinal nerve fiber layer (RNFL) thickness in patients with neovascular age-related macular degeneration (nAMD). This retrospective observational case series included patients with nAMD treated with other anti-vascular endothelial growth factor (anti-VEGF) agents and subsequently switched to IVB because of poor response to those other agents on spectral domain optical coherence tomography (SD-OCT). Best-corrected visual acuity (BCVA), intraocular pressure, funduscopy, and SD-OCT were assessed at baseline, 2 weeks, 1 month, and 3 months after injection. Twenty-two patients were included in the study. In the IVB group, BCVA significantly improved 3 months after injection compared with baseline (0.45 ± 0.25 vs. 0.38 ± 0.25, p = 0.012). During the 3-month follow-up, compared with baseline, RNFL thicknesses of the global, superior temporal, inferior temporal, inferior nasal, nasal, and superior nasal sectors did not change substantially in the IVB group. However, temporal RNFL thickness significantly decreased at 1 month (p = 0.045), and the significance was lost at 3 months (p = 0.378). The central macular thickness of treated eyes significantly decreased compared with the baseline at every follow-up visit. IVB in patients with nAMD had morphological and functional visual gain effects without RNFL thinning during the short-term follow-up.
Morphological analysis of ventricular septal defect by echocardiography for prediction of aortic regurgitation in pediatric population
Authors: El Louali Fedoua , Soler Floriane , Fouilloux Virginie , Evin Morgane , Ovaert Caroline 
Published: April 2023

AbstractVentricular septal defects (VSD) are the most common congenital heart diseases in children. Among them, perimembranous VSD (pm-VSD) have a higher risk of complications, including aortic valve prolapse and aortic regurgitation (AR). The aim of our study was to assess echocardiographic criteria associated with AR during follow-up of pm-VSD. Forty children with restrictive pm-VSD, followed-up in our unit and who underwent a workable echocardiographic evaluation between 2015 and 2019 were included and retrospectively analyzed. The propensity score was used to match 15 patients with AR to 15 patients without AR. Median age was 2.2 year [1.4–5.7]. Median weight was 14 kg [9.9–20.3]. Aortic annulus z-score, Valsalva sinus z-score, sinotubular junction z-score, valve prolapse and commissure commitment were significantly different between the two groups (p = 0.047, p = 0.001, p = 0.010, p = 0.007, p < 0.001 respectively). Aortic root dilatation, aortic valve prolapse and commissure commitment to a perimembranous VSD are associated to aortic regurgitation.
Performance analysis of DNA crossbar arrays for high-density memory storage applications
Authors: De Arpan , Mohammad Hashem , Wang Yiren , Kubendran Rajkumar , Das Arindam K. , Anantram M. P. 
Published: April 2023

AbstractDeoxyribonucleic acid (DNA) has emerged as a promising building block for next-generation ultra-high density storage devices. Although DNA has high durability and extremely high density in nature, its potential as the basis of storage devices is currently hindered by limitations such as expensive and complex fabrication processes and time-consuming read–write operations. In this article, we propose the use of a DNA crossbar array architecture for an electrically readable read-only memory (DNA-ROM). While information can be ‘written’ error-free to a DNA-ROM array using appropriate sequence encodings its read accuracy can be affected by several factors such as array size, interconnect resistance, and Fermi energy deviations from HOMO levels of DNA strands employed in the crossbar. We study the impact of array size and interconnect resistance on the bit error rate of a DNA-ROM array through extensive Monte Carlo simulations. We have also analyzed the performance of our proposed DNA crossbar array for an image storage application, as a function of array size and interconnect resistance. While we expect that future advances in bioengineering and materials science will address some of the fabrication challenges associated with DNA crossbar arrays, we believe that the comprehensive body of results we present in this paper establishes the technical viability of DNA crossbar arrays as low power, high-density storage devices. Finally, our analysis of array performance vis-à-vis interconnect resistance should provide valuable insights into aspects of the fabrication process such as proper choice of interconnects necessary for ensuring high read accuracies.
The illusion of the mind–body divide is attenuated in males
Authors: Berent Iris 
Published: April 2023

AbstractA large literature suggests that people are intuitive Dualists—they tend to perceive the mind as ethereal, distinct from the body. Here, we ask whether Dualism emanates from within the human psyche, guided, in part, by theory of mind (ToM). Past research has shown that males are poorer mind-readers than females. If ToM begets Dualism, then males should exhibit weaker Dualism, and instead, lean towards Physicalism (i.e., they should view bodies and minds alike). Experiments 1–2 show that males indeed perceive the psyche as more embodied—as more likely to emerge in a replica of one’s body, and less likely to persist in its absence (after life). Experiment 3 further shows that males are less inclined towards Empiricism—a putative byproduct of Dualism. A final analysis confirms that males’ ToM scores are lower, and ToM scores further correlate with embodiment intuitions (in Experiments 1–2). These observations (from Western participants) cannot establish universality, but the association of Dualism with ToM suggests its roots are psychological. Thus, the illusory mind–body divide may arise from the very workings of the human mind.
Evaluation of bone growth around bioactive glass S53P4 by scanning acoustic microscopy co-registered with optical interferometry and elemental analysis
Authors: Holmström Axi , Meriläinen Antti , Hyvönen Jere , Nolvi Anton , Ylitalo Tuomo , Steffen Kari , Björkenheim Robert , Strömberg Gustav , Nieminen Heikki J. , Kassamakov Ivan , Pajarinen Jukka , Hupa Leena , Salmi Ari , Hæggström Edward , Lindfors Nina C. 
Published: April 2023

AbstractBioactive glass (BAG) is a bone substitute that can be used in orthopaedic surgery. Following implantation, the BAG is expected to be replaced by bone via bone growth and gradual degradation of the BAG. However, the hydroxyapatite mineral forming on BAG resembles bone mineral, not providing sufficient contrast to distinguish the two in X-ray images. In this study, we co-registered coded-excitation scanning acoustic microscopy (CESAM), scanning white light interferometry (SWLI), and scanning electron microscopy with elemental analysis (Energy Dispersive X-ray Spectroscopy) (SEM–EDX) to investigate the bone growth and BAG reactions on a micron scale in a rabbit bone ex vivo. The acoustic impedance map recorded by the CESAM provides high elasticity-associated contrast to study materials and their combinations, while simultaneously producing a topography map of the sample. The acoustic impedance map correlated with the elemental analysis from SEM–EDX. SWLI also produces a topography map, but with higher resolution than CESAM. The two topography maps (CESAM and SWLI) were in good agreement. Furthermore, using information from both maps simultaneously produced by the CESAM (acoustic impedance and topography) allowed determining regions-of-interest related to bone formation around the BAG with greater ease than from either map alone. CESAM is therefore a promising tool for evaluating the degradation of bone substitutes and the bone healing process ex vivo.
Classification models for assessing coronary artery disease instances using clinical and biometric data: an explainable man-in-the-loop approach
Authors: Samaras Agorastos-Dimitrios , Moustakidis Serafeim , Apostolopoulos Ioannis D. , Papandrianos Nikolaos , Papageorgiou Elpiniki 
Published: April 2023

AbstractThe main goal driving this work is to develop computer-aided classification models relying on clinical data to identify coronary artery disease (CAD) instances with high accuracy while incorporating the expert’s opinion as input, making it a "man-in-the-loop" approach. CAD is traditionally diagnosed in a definite manner by Invasive Coronary Angiography (ICA). A dataset was created using biometric and clinical data from 571 patients (21 total features, 43% ICA-confirmed CAD instances) along with the expert’s diagnostic yield. Five machine learning classification algorithms were applied to the dataset. For the selection of the best feature set for each algorithm, three different parameter selection algorithms were used. Each ML model’s performance was evaluated using common metrics, and the best resulting feature set for each is presented. A stratified ten-fold validation was used for the performance evaluation. This procedure was run both using the assessments of experts/doctors as input and without them. The significance of this paper lies in its innovative approach of incorporating the expert's opinion as input in the classification process, making it a "man-in-the-loop" approach. This approach not only increases the accuracy of the models but also provides an added layer of explainability and transparency, allowing for greater trust and confidence in the results. Maximum achievable accuracy, sensitivity, and specificity are 83.02%, 90.32%, and 85.49% when using the expert's diagnosis as input, compared to 78.29%, 76.61%, and 86.07% without the expert's diagnosis. The results of this study demonstrate the potential for this approach to improve the diagnosis of CAD and highlight the importance of considering the role of human expertise in the development of computer-aided classification models.
An apicomplexan parasite drives the collapse of the bay scallop population in New York
Authors: Pales Espinosa Emmanuelle , Bouallegui Younes , Grouzdev Denis , Brianik Christopher , Czaja Raymond , Geraci-Yee Sabrina , Kristmundsson Arni , Muehl Madison , Schwaner Caroline , Tettelbach Stephen T. , Tobi Harrison , Allam Bassem 
Published: April 2023

AbstractThe bay scallop, Argopecten irradians, represents a commercially, culturally and ecologically important species found along the United States’ Atlantic and Gulf coasts. Since 2019, scallop populations in New York have been suffering large-scale summer mortalities resulting in 90–99% reduction in biomass of adult scallops. Preliminary investigations of these mortality events showed 100% prevalence of an apicomplexan parasite infecting kidney tissues. This study was designed to provide histological, ultrastructural and molecular characteristics of a non-described parasite, member of the newly established Marosporida clade (Apicomplexa) and provisionally named BSM (Bay Scallop Marosporida). Molecular diagnostics tools (quantitative PCR, in situ hybridization) were developed and used to monitor disease development. Results showed that BSM disrupts multiple scallop tissues including kidney, adductor muscle, gill, and gonad. Microscopy observations allowed the identification of both intracellular and extracellular stages of the parasite. Field surveys demonstrated a strong seasonal signature in disease prevalence and intensity, as severe cases and mortality increase as summer progresses. These results strongly suggest that BSM infection plays a major role in the collapse of bay scallop populations in New York. In this framework, BSM may synergistically interact with stressful environmental conditions to impair the host and lead to mortality.
The burden of incidental SARS-CoV-2 infections in hospitalized patients across pandemic waves in Canada
Authors: McAlister Finlay A. , Hau Jeffrey P. , Atzema Clare , McRae Andrew D. , Morrison Laurie J. , Grant Lars , Cheng Ivy , Rosychuk Rhonda J. , Hohl Corinne M. ,   The Canadian COVID-19 Emergency Department Rapid Response Network (CCEDRRN) Investigators, Wiemer Hana , Fok Patrick , Campbell Samuel , Arsenault Kory , Dahn Tara , DeMone Corinne , Chandra Kavish , Fraser Jacqueline , Archambault Patrick , Turner Joel , Mercier Éric , Clark Greg , Mercier Éric , Robert Sébastien , Robert Sébastien , Audet Martyne , Nadeau Alexandra , Nolet Audrey , Xue Xiaoqing , Iannuzzi David , Lanthier Chantal , Morrison Laurie , Cheng Ivy , Brooks Steven , Taylor Connie , Perry Jeffrey , Welsford Michelle , Ohle Rob , Yan Justin , Mohindra Rohit , Landes Megan , Nirmalanathan Konika , Latiu Vlad , Yeung Joanna , Clayton Natasha , Chen Tom , Nichols Jenna , Jelic Tomislav , Mackenzie Kate , Davis Phil , Goss Aimee , McRae Andrew , Rowe Brian , Lin Katie , VandenBerg Stephanie , Hayward Jake , Khangura Jaspreet , Lobos Stacey , Ruddell Stacy , Runham Natalie , Su Karlin , Hohl Corinne , Scheuermeyer Frank , Ting Daniel , Stachura Maja , Braar Balijeet , Taylor John , Martin Ian , Wormsbecker Sean , Graham Lee , Kanu Josie , Bootsma Taylor , Huynh Bernice , Swirhun Amanda , Taylor Tracy , Hayashi Mai , Cheyne Mackenzie , Williams Neenah , Lam Katherine , Compagna Kelsey , Hau Jeffrey , Ho Vi , Small Serena , Cragg Amber , Xu Vicky 
Published: April 2023

AbstractMany health authorities differentiate hospitalizations in patients infected with SARS-CoV-2 as being “for COVID-19” (due to direct manifestations of SARS-CoV-2 infection) versus being an “incidental” finding in someone admitted for an unrelated condition. We conducted a retrospective cohort study of all SARS-CoV-2 infected patients hospitalized via 47 Canadian emergency departments, March 2020-July 2022 to determine whether hospitalizations with “incidental” SARS-CoV-2 infection are less of a burden to patients and the healthcare system. Using a priori standardized definitions applied to hospital discharge diagnoses in 14,290 patients, we characterized COVID-19 as (i) the “Direct” cause for the hospitalization (70%), (ii) a potential “Contributing” factor for the hospitalization (4%), or (iii) an “Incidental” finding that did not influence the need for admission (26%). The proportion of incidental SARS-CoV-2 infections rose from 10% in Wave 1 to 41% during the Omicron wave. Patients with COVID-19 as the direct cause of hospitalization exhibited significantly longer LOS (mean 13.8 versus 12.1 days), were more likely to require critical care (22% versus 11%), receive COVID-19-specific therapies (55% versus 19%), and die (17% versus 9%) compared to patients with Incidental SARS-CoV-2 infections. However, patients hospitalized with incidental SARS-CoV-2 infection still exhibited substantial morbidity/mortality and hospital resource use.
Synthesis of CuxO/Ag nanoparticles on exfoliated graphene: application for enhanced electrochemical detection of H2O2 in milk
Authors: Song Jie , Wan Yating , Yang Chen , Deng Qiuju , Cui Yingde , Yan Zhihong , Liu Yi 
Published: April 2023

AbstractIn this paper, a novel composite is constructed as a non-enzymatic hydrogen peroxide (H2O2) sensor by liquid-phase exfoliation method, which is composed of copper oxide, cuprous oxide and silver nanoparticles doped few-layer-graphene (CuxO/Ag@FLG). Its surface morphology and composition were characterized by scanning electron microscopy (SEM) and X-ray photo spectroscopy (XPS), and its H2O2 sensing performances include catalytic reduction and quantitative detection were studied with electrochemical methods. Our sensor had a high sensitivity of 174.5 μA mM−1 cm−2 (R2 = 0.9978) in an extremely wide range of concentrations from 10 μM to 100 mM, a fast response (about 5 s) and a low limit of detection (S/N = 3) of 2.13 μM. The sensor exhibits outstanding selectivity in the presence of various biological interference, such as dopamine, ascorbic acid, uric acid, citric acid, etc. In addition, the constructed sensor continued 95% current responsiveness after 1 month of storage further points to its long-term stability. Last but not least, it has a good recovery rate (90.12–102.00%) in milk sold on the open market, indicating that it has broad application possibilities in the food industry and biological medicine.