bluuebunny/crossref_metadata_2025_split huggingface dataset:
rAAV-PHP.B escapes the mouse eye and causes lethality whereas rAAV9 can transduce aniridic corneal limbal stem cells without lethality
Authors: Mirjalili Mohanna Seyedeh Zeinab , Korecki Andrea J. , Simpson Elizabeth M. 
Published: April 2023

AbstractRecently safety concerns have been raised in connection with high doses of recombinant adeno-associated viruses (rAAV). Therefore, we undertook a series of experiments to test viral capsid (rAAV9 and rAAV-PHP.B), dose, and route of administration (intrastromal, intravitreal, and intravenous) focused on aniridia, a congenital blindness that currently has no cure. The success of gene therapy for aniridia may depend on the presence of functional limbal stem cells (LSCs) in the damaged aniridic corneas and whether rAAV can transduce them. Both these concerns were unknown, and thus were also addressed by our studies. For the first time, we report ataxia and lethality after intravitreal or intrastromal rAAV-PHP.B virus injections. We demonstrated virus escape from the eye and transduction of non-ocular tissues by rAAV9 and rAAV-PHP.B capsids. We have also shown that intrastromal and intravitreal delivery of rAAV9 can transduce functional LSCs, as well as all four PAX6-expressing retinal cell types in aniridic eye, respectively. Overall, lack of adverse events and successful transduction of LSCs and retinal cells makes it clear that rAAV9 is the capsid of choice for future aniridia gene therapy. Our finding of rAAV lethality after intraocular injections will be impactful for other researchers developing rAAV-based gene therapies.
Native qudit entanglement in a trapped ion quantum processor
Authors: Hrmo Pavel , Wilhelm Benjamin , Gerster Lukas , van Mourik Martin W. , Huber Marcus , Blatt Rainer , Schindler Philipp , Monz Thomas , Ringbauer Martin 
Published: April 2023

AbstractQuantum information carriers, just like most physical systems, naturally occupy high-dimensional Hilbert spaces. Instead of restricting them to a two-level subspace, these high-dimensional (qudit) quantum systems are emerging as a powerful resource for the next generation of quantum processors. Yet harnessing the potential of these systems requires efficient ways of generating the desired interaction between them. Here, we experimentally demonstrate an implementation of a native two-qudit entangling gate up to dimension 5 in a trapped-ion system. This is achieved by generalizing a recently proposed light-shift gate mechanism to generate genuine qudit entanglement in a single application of the gate. The gate seamlessly adapts to the local dimension of the system with a calibration overhead that is independent of the dimension.
Programmable mammalian translational modulators by CRISPR-associated proteins
Authors: Kawasaki Shunsuke , Ono Hiroki , Hirosawa Moe , Kuwabara Takeru , Sumi Shunsuke , Lee Suji , Woltjen Knut , Saito Hirohide 
Published: April 2023

AbstractTranslational modulation based on RNA-binding proteins can be used to construct artificial gene circuits, but RNA-binding proteins capable of regulating translation efficiently and orthogonally remain scarce. Here we report CARTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Gene control) to repurpose Cas proteins as translational modulators in mammalian cells. We demonstrate that a set of Cas proteins efficiently and orthogonally repress or activate the translation of designed mRNAs that contain a Cas-binding RNA motif in the 5’-UTR. By linking multiple Cas-mediated translational modulators, we designed and built artificial circuits like logic gates, cascades, and half-subtractor circuits. Moreover, we show that various CRISPR-related technologies like anti-CRISPR and split-Cas9 platforms could be similarly repurposed to control translation. Coupling Cas-mediated translational and transcriptional regulation enhanced the complexity of synthetic circuits built by only introducing a few additional elements. Collectively, CARTRIDGE has enormous potential as a versatile molecular toolkit for mammalian synthetic biology.
Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b
Authors: Kaspers Marietta S. , Pogenberg Vivian , Pett Christian , Ernst Stefan , Ecker Felix , Ochtrop Philipp , Groll Michael , Hedberg Christian , Itzen Aymelt 
Published: April 2023

AbstractBacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3’s catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.
How to characterize figures of merit of two-dimensional photodetectors
Authors: Wang Fang , Zhang Tao , Xie Runzhang , Wang Zhen , Hu Weida 
Published: April 2023

AbstractPhotodetectors based on two-dimensional (2D) materials have been the focus of intensive research and development over the past decade. However, a gap has long persisted between fundamental research and mature applications. One of the main reasons behind this gap has been the lack of a practical and unified approach for the characterization of their figures of merit, which should be compatible with the traditional performance evaluation system of photodetectors. This is essential to determine the degree of compatibility of laboratory prototypes with industrial technologies. Here we propose general guidelines for the characterization of the figures of merit of 2D photodetectors and analyze common situations when the specific detectivity, responsivity, dark current, and speed can be misestimated. Our guidelines should help improve the standardization and industrial compatibility of 2D photodetectors.
Health disparities among older adults following tropical cyclone exposure in Florida
Authors: Burrows K. , Anderson G. B. , Yan M. , Wilson A. , Sabath M. B. , Son J. Y. , Kim H. , Dominici F. , Bell M. L. 
Published: April 2023

AbstractTropical cyclones (TCs) pose a significant threat to human health, and research is needed to identify high-risk subpopulations. We investigated whether hospitalization risks from TCs in Florida (FL), United States, varied across individuals and communities. We modeled the associations between all storms in FL from 1999 to 2016 and over 3.5 million Medicare hospitalizations for respiratory (RD) and cardiovascular disease (CVD). We estimated the relative risk (RR), comparing hospitalizations during TC-periods (2 days before to 7 days after) to matched non-TC-periods. We then separately modeled the associations in relation to individual and community characteristics. TCs were associated with elevated risk of RD hospitalizations (RR: 4.37, 95% CI: 3.08, 6.19), but not CVD (RR: 1.04, 95% CI: 0.87, 1.24). There was limited evidence of modification by individual characteristics (age, sex, or Medicaid eligibility); however, risks were elevated in communities with higher poverty or lower homeownership (for CVD hospitalizations) and in denser or more urban communities (for RD hospitalizations). More research is needed to understand the potential mechanisms and causal pathways that might account for the observed differences in the association between tropical cyclones and hospitalizations across communities.
Spectroscopic visualization and phase manipulation of chiral charge density waves in 1T-TaS2
Authors: Zhao Yan , Nie Zhengwei , Hong Hao , Qiu Xia , Han Shiyi , Yu Yue , Liu Mengxi , Qiu Xiaohui , Liu Kaihui , Meng Sheng , Tong Lianming , Zhang Jin 
Published: April 2023

AbstractThe chiral charge density wave is a many-body collective phenomenon in condensed matter that may play a role in unconventional superconductivity and topological physics. Two-dimensional chiral charge density waves provide the building blocks for the fabrication of various stacking structures and chiral homostructures, in which physical properties such as chiral currents and the anomalous Hall effect may emerge. Here, we demonstrate the phase manipulation of two-dimensional chiral charge density waves and the design of in-plane chiral homostructures in 1T-TaS2. We use chiral Raman spectroscopy to directly monitor the chirality switching of the charge density wave—revealing a temperature-mediated reversible chirality switching. We find that interlayer stacking favours homochirality configurations, which is confirmed by first-principles calculations. By exploiting the interlayer chirality-locking effect, we realise in-plane chiral homostructures in 1T-TaS2. Our results provide a versatile way to manipulate chiral collective phases by interlayer coupling in layered van der Waals semiconductors.
Plasma degradation of contaminated PPE: an energy-efficient method to treat contaminated plastic waste
Authors: Marco Tobías Mariano , Åhlén Michelle , Cheung Ocean , Bucknall David G. , McCoustra Martin R. S. , Yiu Humphrey H. P. 
Published: April 2023

AbstractThe use of PPE has drastically increased because of the SARS-CoV-2 (COVID-19) pandemic as disposable surgical face masks made from non-biodegradable polypropylene (PP) polymers have generated a significant amount of waste. In this work, a low-power plasma method has been used to degrade surgical masks. Several analytical techniques (gravimetric analysis, scanning electron microscopy (SEM), attenuated total reflection-infra-red spectroscopy (ATR-IR), x-ray photoelectron spectroscopy (XPS), thermogravimetric analysis/differential scanning calorimetry (TGA/DSC) and wide-angle x-ray scattering (WAXS)) were used to evaluate the effects of plasma irradiation on mask samples. After 4 h of irradiation, an overall mass loss of 63 ± 8%, through oxidation followed by fragmentation, was observed on the non-woven 3-ply surgical mask, which is 20 times faster than degrading a bulk PP sample. Individual components of the mask also showed different degradation rates. Air plasma clearly represents an energy-efficient tool for treating contaminated PPE in an environmentally friendly approach.
COVID-19 amplified racial disparities in the US criminal legal system
Authors: Klein Brennan , Ogbunugafor C. Brandon , Schafer Benjamin J. , Bhadricha Zarana , Kori Preeti , Sheldon Jim , Kaza Nitish , Sharma Arush , Wang Emily A. , Eliassi-Rad Tina , Scarpino Samuel V. , Hinton Elizabeth 
Published: April 2023

AbstractThe criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features1–3. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%—the largest, fastest reduction in prison population in American history4. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people5. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo6.
Optimization of the multivariate polynomial public key for quantum safe digital signature
Authors: Kuang Randy , Perepechaenko Maria 
Published: April 2023

AbstractKuang, Perepechaenko, and Barbeau recently proposed a novel quantum-safe digital signature algorithm called Multivariate Polynomial Public Key or MPPK/DS. The key construction originated with two univariate polynomials and one base multivariate polynomial defined over a ring. The variable in the univariate polynomials represents a plain message. All but one variable in the multivariate polynomial refer to noise used to obscure private information. These polynomials are then used to produce two multivariate product polynomials, while excluding the constant term and highest order term with respect to the message variable. The excluded terms are used to create two noise functions. Then four produced polynomials, masked with two randomly chosen even numbers over the ring, form the Public Key. The two univariate polynomials and two randomly chosen numbers, behaving as an encryption key to obscure public polynomials, form the Private Key. The verification equation is derived from multiplying all of the original polynomials together. MPPK/DS uses a special safe prime to prevent private key recovery attacks over the ring, forcing adversaries to solve for private values over a sub-prime field and lift the solutions to the original ring. Lifting entire solutions from the sub-prime field to the ring is designed to be difficult based on security requirements. This paper intends to optimize MPPK/DS to reduce the signature size by a fifth. We added extra two private elements to further increase the complexity of the private key recovery attack. However, we show in our newly identified optimal attack that these extra private elements do not have any effect on the complexity of the private recovery attack due to the intrinsic feature of MPPK/DS. The optimal key-recovery attack reduces to a Modular Diophantine Equation Problem or MDEP with more than one unknown variables for a single equation. MDEP is a well-known NP-complete problem, producing a set with many equally-likely solutions, so the attacker would have to make a decision to choose the correct solution from the entire list. By purposely choosing the field size and the order of the univariate polynomials, we can achieve the desired security level. We also identified a new deterministic attack on the coefficients of two univariate private polynomials using intercepted signatures, which forms a overdetermined set of homogeneous cubic equations. To the best of our knowledge, the solution to such a problem is to brute force search all unknown variables and verify the obtained solutions. With those optimizations, MPPK/DS can offer extra security of 384 bit entropy at 128 bit field with a public key size being 256 bytes and signature size 128 or 256 bytes using SHA256 or SHA512 as the hash function respectively.
More than unfamiliar environmental connection to super typhoon climatology
Authors: Kang Namyoung , Jang Chan Joo , Elsner James B. 
Published: April 2023

AbstractThis study employs a refined geometric variability model to look at the environmental relationship to super typhoon climatology, which is one of the major concerns about climate change and disasters. It is noted that adding only several recent years leads to a remarkable weakening of the environmental explanatory power on super typhoon climatology. Looking into the annual covariance elements, we find that the recent observations showing a group of outlying events with a particular drift are more than unfamiliar compared to the former stable relationship from 1985 through 2012. Greater uncertainty thereby amplifies concerns about the looming climate crisis.
Label-free autofluorescence lifetime reveals the structural dynamics of ataxin-3 inside droplets formed via liquid–liquid phase separation
Authors: Matsuura Uchu , Tahara Shinya , Kajimoto Shinji , Nakabayashi Takakazu 
Published: April 2023

AbstractLiquid–liquid phase separation is a phenomenon that features the formation of liquid droplets containing concentrated solutes. The droplets of neurodegeneration-associated proteins are prone to generate aggregates and cause diseases. To uncover the aggregation process from the droplets, it is necessary to analyze the protein structure with keeping the droplet state in a label-free manner, but there was no suitable method. In this study, we observed the structural changes of ataxin-3, a protein associated with Machado–Joseph disease, inside the droplets, using autofluorescence lifetime microscopy. Each droplet showed autofluorescence due to tryptophan (Trp) residues, and its lifetime increased with time, reflecting structural changes toward aggregation. We used Trp mutants to reveal the structural changes around each Trp and showed that the structural change consists of several steps on different timescales. We demonstrated that the present method visualizes the protein dynamics inside a droplet in a label-free manner. Further investigations revealed that the aggregate structure formed in the droplets differs from that formed in dispersed solutions and that a polyglutamine repeat extension in ataxin-3 hardly modulates the aggregation dynamics in the droplets. These findings highlight that the droplet environment facilitates unique protein dynamics different from those in solutions.
In vivo imaging of renal microvasculature in a murine ischemia–reperfusion injury model using optical coherence tomography angiography
Authors: Lee ByungKun , Kang Woojae , Oh Se-Hyun , Cho Seungwan , Shin Inho , Oh Eun-Joo , Kim You-Jin , Ahn Ji-Sun , Yook Ju-Min , Jung Soo-Jung , Lim Jeong-Hoon , Kim Yong-Lim , Cho Jang-Hee , Oh Wang-Yuhl 
Published: April 2023

AbstractOptical coherence tomography angiography (OCTA) provides three-dimensional structural and semiquantitative imaging of microvasculature in vivo. We developed an OCTA imaging protocol for a murine kidney ischemia–reperfusion injury (IRI) model to investigate the correlation between renal microvascular changes and ischemic damage. Mice were divided into mild and moderate IRI groups according to the duration of ischemia (10 and 35 mins, respectively). Each animal was imaged at baseline; during ischemia; and at 1, 15, 30, 45, and 60 mins after ischemia. Amplitude decorrelation OCTA images were constructed with 1.5-, 3.0-, and 5.8-ms interscan times, to calculate the semiquantitative flow index in the superficial (50–70 μm) and the deep (220–340 μm) capillaries of the renal cortex. The mild IRI group showed no significant flow index change in both the superfial and the deep layers. The moderate IRI group showed a significantly decreased flow index from 15 and 45 mins in the superficial and deep layers, respectively. Seven weeks after IRI induction, the moderate IRI group showed lower kidney function and higher collagen deposition than the mild IRI group. OCTA imaging of the murine IRI model revealed changes in superficial blood flow after ischemic injury. A more pronounced decrease in superficial blood flow than in deep blood flow was associated with sustained dysfunction after IRI. Further investigation on post-IRI renal microvascular response using OCTA may improve our understanding of the relationship between the degree of ischemic insult and kidney function.
Red induces hyperalgesia and white induces hypoalgesia regardless of pain modality
Authors: Wiercioch-Kuzianik Karolina , Brączyk Justyna , Bieniek Helena , Bąbel Przemysław 
Published: April 2023

AbstractColors are an important factor that influences different aspects of people's lives. However, little is known about the effects of colors on pain. This preregistered study aimed to investigate whether the type of pain affects the impact of colors on pain intensity. 74 participants were randomly divided into 2 groups according to the type of pain: electrical or thermal. In both groups, pain stimuli of the same intensity were preceded by different colors. Participants rated the pain intensity induced by each pain stimulus. Additionally, pain expectations related to each color were rated at the beginning and the end of the procedure. A significant effect of color on pain intensity ratings was found. Pain was most intense in both groups after red, whereas the lowest ratings were given after white. A similar pattern of results was observed for pain expectations. Expectations also correlated with and were found to be a predictor of experienced pain for white, blue, and green. The study shows that white can reduce, while red can alter the experienced pain. Moreover, it shows that the effect of colors is affected to a greater extent by the pain expectations rather than the pain modality. We conclude that the way colors influence pain broadens the current knowledge on effects of colors on human behavior and could help in the future both patients and practitioners.
Prognostic model development for classification of colorectal adenocarcinoma by using machine learning model based on feature selection technique boruta
Authors: Maurya Neha Shree , Kushwah Shikha , Kushwaha Sandeep , Chawade Aakash , Mani Ashutosh 
Published: April 2023

AbstractColorectal cancer (CRC) is the third most prevalent cancer type and accounts for nearly one million deaths worldwide. The CRC mRNA gene expression datasets from TCGA and GEO (GSE144259, GSE50760, and GSE87096) were analyzed to find the significant differentially expressed genes (DEGs). These significant genes were further processed for feature selection through boruta and the confirmed features of importance (genes) were subsequently used for ML-based prognostic classification model development. These genes were analyzed for survival and correlation analysis between final genes and infiltrated immunocytes. A total of 770 CRC samples were included having 78 normal and 692 tumor tissue samples. 170 significant DEGs were identified after DESeq2 analysis along with the topconfects R package. The 33 confirmed features of importance-based RF prognostic classification model have given accuracy, precision, recall, and f1-score of 100% with 0% standard deviation. The overall survival analysis had finalized GLP2R and VSTM2A genes that were significantly downregulated in tumor samples and had a strong correlation with immunocyte infiltration. The involvement of these genes in CRC prognosis was further confirmed on the basis of their biological function and literature analysis. The current findings indicate that GLP2R and VSTM2A may play a significant role in CRC progression and immune response suppression.