bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical crystallography by serial femtosecond X-ray diffraction
Authors: Schriber Elyse A. , Paley Daniel W. , Bolotovsky Robert , Rosenberg Daniel J. , Sierra Raymond G. , Aquila Andrew , Mendez Derek , Poitevin Frédéric , Blaschke Johannes P. , Bhowmick Asmit , Kelly Ryan P. , Hunter Mark , Hayes Brandon , Popple Derek C. , Yeung Matthew , Pareja-Rivera Carina , Lisova Stella , Tono Kensuke , Sugahara Michihiro , Owada Shigeki , Kuykendall Tevye , Yao Kaiyuan , Schuck P. James , Solis-Ibarra Diego , Sauter Nicholas K. , Brewster Aaron S. , Hohman J. Nathan 
Published: January 2022

AbstractInorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties1. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction2,3 and electron microdiffraction4–11. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach14, the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data15–17. We describe the ab initio structure solutions of mithrene (AgSePh)18–20, thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties20. We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.
Global fine-scale changes in ambient NO2 during COVID-19 lockdowns
Authors: Cooper Matthew J. , Martin Randall V. , Hammer Melanie S. , Levelt Pieternel F. , Veefkind Pepijn , Lamsal Lok N. , Krotkov Nickolay A. , Brook Jeffrey R. , McLinden Chris A. 
Published: January 2022

AbstractNitrogen dioxide (NO2) is an important contributor to air pollution and can adversely affect human health1–9. A decrease in NO2 concentrations has been reported as a result of lockdown measures to reduce the spread of COVID-1910–20. Questions remain, however, regarding the relationship of satellite-derived atmospheric column NO2 data with health-relevant ambient ground-level concentrations, and the representativeness of limited ground-based monitoring data for global assessment. Here we derive spatially resolved, global ground-level NO2 concentrations from NO2 column densities observed by the TROPOMI satellite instrument at sufficiently fine resolution (approximately one kilometre) to allow assessment of individual cities during COVID-19 lockdowns in 2020 compared to 2019. We apply these estimates to quantify NO2 changes in more than 200 cities, including 65 cities without available ground monitoring, largely in lower-income regions. Mean country-level population-weighted NO2 concentrations are 29% ± 3% lower in countries with strict lockdown conditions than in those without. Relative to long-term trends, NO2 decreases during COVID-19 lockdowns exceed recent Ozone Monitoring Instrument (OMI)-derived year-to-year decreases from emission controls, comparable to 15 ± 4 years of reductions globally. Our case studies indicate that the sensitivity of NO2 to lockdowns varies by country and emissions sector, demonstrating the critical need for spatially resolved observational information provided by these satellite-derived surface concentration estimates.
Quantum logic with spin qubits crossing the surface code threshold
Authors: Xue Xiao , Russ Maximilian , Samkharadze Nodar , Undseth Brennan , Sammak Amir , Scappucci Giordano , Vandersypen Lieven M. K. 
Published: January 2022

AbstractHigh-fidelity control of quantum bits is paramount for the reliable execution of quantum algorithms and for achieving fault tolerance—the ability to correct errors faster than they occur1. The central requirement for fault tolerance is expressed in terms of an error threshold. Whereas the actual threshold depends on many details, a common target is the approximately 1% error threshold of the well-known surface code2,3. Reaching two-qubit gate fidelities above 99% has been a long-standing major goal for semiconductor spin qubits. These qubits are promising for scaling, as they can leverage advanced semiconductor technology4. Here we report a spin-based quantum processor in silicon with single-qubit and two-qubit gate fidelities, all of which are above 99.5%, extracted from gate-set tomography. The average single-qubit gate fidelities remain above 99% when including crosstalk and idling errors on the neighbouring qubit. Using this high-fidelity gate set, we execute the demanding task of calculating molecular ground-state energies using a variational quantum eigensolver algorithm5. Having surpassed the 99% barrier for the two-qubit gate fidelity, semiconductor qubits are well positioned on the path to fault tolerance and to possible applications in the era of noisy intermediate-scale quantum devices.
Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variants
Authors: Zhang Lianghui , Dutta Soumajit , Xiong Shiqin , Chan Matthew , Chan Kui K. , Fan Timothy M. , Bailey Keith L. , Lindeblad Matthew , Cooper Laura M. , Rong Lijun , Gugliuzza Anthony F. , Shukla Diwakar , Procko Erik , Rehman Jalees , Malik Asrar B. 
Published: January 2022

AbstractVaccine hesitancy and emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) escaping vaccine-induced immune responses highlight the urgency for new COVID-19 therapeutics. Engineered angiotensin-converting enzyme 2 (ACE2) proteins with augmented binding affinities for SARS-CoV-2 spike (S) protein may prove to be especially efficacious against multiple variants. Using molecular dynamics simulations and functional assays, we show that three amino acid substitutions in an engineered soluble ACE2 protein markedly augmented the affinity for the S protein of the SARS-CoV-2 WA-1/2020 isolate and multiple VOCs: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta). In humanized K18-hACE2 mice infected with the SARS-CoV-2 WA-1/2020 or P.1 variant, prophylactic and therapeutic injections of soluble ACE22.v2.4-IgG1 prevented lung vascular injury and edema formation, essential features of CoV-2-induced SARS, and above all improved survival. These studies demonstrate broad efficacy in vivo of an engineered ACE2 decoy against SARS-CoV-2 variants in mice and point to its therapeutic potential.
Effectiveness of COVID-19 booster vaccines against COVID-19-related symptoms, hospitalization and death in England
Authors: Andrews Nick , Stowe Julia , Kirsebom Freja , Toffa Samuel , Sachdeva Ruchira , Gower Charlotte , Ramsay Mary , Lopez Bernal Jamie 
Published: January 2022

AbstractBooster vaccination with messenger RNA (mRNA) vaccines has been offered to adults in England starting on 14 September 2021. We used a test-negative case–control design to estimate the relative effectiveness of a booster dose of BNT162b2 (Pfizer-BioNTech) compared to only a two-dose primary course (at least 175 days after the second dose) or unvaccinated individuals from 13 September 2021 to 5 December 2021, when Delta variant was dominant in circulation. Outcomes were symptomatic coronavirus disease 2019 (COVID-19) and hospitalization. The relative effectiveness against symptomatic disease 14–34 days after a BNT162b2 or mRNA-1273 (Moderna) booster after a ChAdOx1-S (AstraZeneca) and BNT162b2 as a primary course ranged from around 85% to 95%. Absolute vaccine effectiveness ranged from 94% to 97% and was similar in all age groups. Limited waning was seen 10 or more weeks after the booster. Against hospitalization or death, absolute effectiveness of a BNT162b2 booster ranged from around 97% to 99% in all age groups irrespective of the primary course, with no evidence of waning up to 10 weeks. This study provides real-world evidence of substantially increased protection from the booster vaccine dose against mild and severe disease irrespective of the primary course.
Impact of measurement timing on reproducibility of testing among haemodialysis patients
Authors: Junqué Jiménez Anna , Tomás Bernabeu Ester , Andreu Périz Lola , Segura Ortí Eva 
Published: January 2022

AbstractAccurate evaluation of physical function in patients undergoing haemodialysis is crucial in the analysis of the impact of exercise programs in this population. The aim of this study was to evaluate the reproducibility of several physical functional tests, depending on the timing of their implementation (before the HD session vs. non-HD days). This is a prospective, non-experimental, descriptive study. Thirty patients in haemodialysis were evaluated twice, 1 week apart. The test session was performed before the haemodialysis session started and a retest was performed in non-dialysis day. The testing battery included the short physical performance battery, sit-to-stand tests, 6 min walk test, one-leg stand test, timed up and go, and handgrip strength with and without forearm support. The intra-rater reproducibility was determined by the intraclass correlation coefficients and the agreement was assessed by Bland–Altman analysis. The intraclass correlation coefficients values ranged from 0.86 to 0.96, so that all tests showed good to very good relative reliability. The mean differences between trials of sit to stand 10 and 60, timed up and go and all the handgrip tests were close to zero, indicating no systematic differences between trials. Large range of values between trials was observed for the 6 min walk test, gait speed, one-leg stand test and short physical performance battery, indicating a systematic bias for these four tests. In conclusion, the sit to stand 10 and 60, timed up and go and handgrip tests had good to excellent test–retest reliability in measuring physical function in different dialysis days of patients undertaking haemodialysis. The minimal detectable change values are provided for this population. Bias were found for the 6 min walk test, gait speed, Short physical performance battery or one-leg stand test when the testing day changed.
Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment
Authors: Yue Congbo , Zhao Tianyi , Zhang Shoucai , Liu Yingjie , Zheng Guixi , Zhang Yi 
Published: January 2022

AbstractAlternative splicing (AS) events play a crucial role in the tumorigenesis and progression of cancer. Transcriptome data and Percent Spliced In (PSI) values of ovarian cancer patients were downloaded from TCGA database and TCGA SpliceSeq. Totally we identified 1472 AS events that were associated with survival of ovarian serous cystadenocarcinoma (OC) and exon skipping (ES) was the most important type. Univariate and multivariate Cox regression analysis were performed to identify survival-associated AS events and developed the prognostic model based on 11-AS events. The immune cells and different response to cytotoxic T lymphocyte associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) blockers in low-risk and high-risk group of OC patients were analyzed. Ten kinds of immune cells were found up-regulated in low-risk group. Activated B cell, natural killer T cell, natural killer cell and regulatory T cell were associated with survival of OC. The patients in low-risk group had good response to CTLA-4 and PD-1 blockers treatment. Moreover, a regulatory network was established according to the correlation between AS events and splicing factors (SFs). The present study provided valuable insights into the underlying mechanisms of OC. AS events that were correlated with the immune system might be potential therapeutic targets.
Creating electronic oscillator-based Ising machines without external injection locking
Authors: Vaidya Jaykumar , Surya Kanthi R. S. , Shukla Nikhil 
Published: January 2022

AbstractCoupled electronic oscillators have recently been explored as a compact, integrated circuit- and room temperature operation-compatible hardware platform to design Ising machines. However, such implementations presently require the injection of an externally generated second-harmonic signal to impose the phase bipartition among the oscillators. In this work, we experimentally demonstrate a new electronic autaptic oscillator (EAO) that uses engineered feedback to eliminate the need for the generation and injection of the external second harmonic signal to minimize the Ising Hamiltonian. Unlike conventional relaxation oscillators that typically decay with a single time constant, the feedback in the EAO is engineered to generate two decay time constants which effectively helps generate the second harmonic signal internally. Using this oscillator design, we show experimentally, that a system of capacitively coupled EAOs exhibits the desired bipartition in the oscillator phases without the need for any external second harmonic injection, and subsequently, demonstrate its application in solving the computationally hard Maximum Cut (MaxCut) problem. Our work not only establishes a new oscillator design aligned to the needs of the oscillator Ising machine but also advances the efforts to creating application specific analog computing platforms.
The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail
Authors: Clavijo Viviana , Morales Tatiana , Vives-Flores Martha Josefina , Reyes Muñoz Alejandro 
Published: January 2022

AbstractThe microbiota in broiler chicken intestines affects the animals’ health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers’ drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota’s structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.
A model for cascading failures with the probability of failure described as a logistic function
Authors: Kim Minjung , Kim Jun Soo 
Published: January 2022

AbstractIn most cascading failure models in networks, overloaded nodes are assumed to fail and are removed from the network. However, this is not always the case due to network mitigation measures. Considering the effects of these mitigating measures, we propose a new cascading failure model that describes the probability that an overloaded node fails as a logistic function. By performing numerical simulations of cascading failures on Barabási and Albert (BA) scale-free networks and a real airport network, we compare the results of our model and the established model describing the probability of failure as a linear function. The simulation results show that the difference in the robustness of the two models depends on the initial load distribution and the redistribution of load. We further investigate the conditions of our new model under which the network exhibits the strongest robustness in terms of the load distribution and the network topology. We find the optimal value for the parameter of the load distribution and demonstrate that the robustness of the network improves as the average degree increases. The results regarding the optimal load distribution are verified by theoretical analysis. This work can be used to develop effective mitigation measures and design networks that are robust to cascading failure phenomena.
High speed, long range, deep penetration swept source OCT for structural and angiographic imaging of the anterior eye
Authors: Chen Siyu , Potsaid Benjamin , Li Yan , Lin Junhong , Hwang Yunchan , Moult Eric M. , Zhang Jason , Huang David , Fujimoto James G. 
Published: January 2022

AbstractThis study reports the development of prototype swept-source optical coherence tomography (SS-OCT) technology for imaging the anterior eye. Advances in vertical-cavity surface-emitting laser (VCSEL) light sources, signal processing, optics and mechanical designs, enable a unique combination of high speed, long range, and deep penetration that addresses the challenges of anterior eye imaging. We demonstrate SS-OCT with a 325 kHz A-scan rate, 12.2 µm axial resolution (in air), and 15.5 mm depth range (in air) at 1310 nm wavelength. The ultrahigh 325 kHz A-scan rate not only facilitates biometry measurements by minimizing acquisition time and thus reducing motion, but also enables volumetric OCT for comprehensive structural analysis and OCT angiography (OCTA) for visualizing vasculature. The 15.5 mm (~ 11.6 mm in tissue) depth range spans all optical surfaces from the anterior cornea to the posterior lens capsule. The 1310 nm wavelength range enables structural OCT and OCTA deep in the sclera and through the iris. Achieving high speed and long range requires linearizing the VCSEL wavenumber sweep to efficiently utilize analog-to-digital conversion bandwidth. Dual channel recording of the OCT and calibration interferometer fringe signals, as well as sweep to sweep wavenumber compensation, is used to achieve invariant 12.2 µm (~ 9.1 µm in tissue) axial resolution and optimum point spread function throughout the depth range. Dynamic focusing using a tunable liquid lens extends the effective depth of field while preserving the lateral resolution. Improved optical and mechanical design, including parallax “split view” iris cameras and stable, ergonomic patient interface, facilitates accurate instrument positioning, reduces patient motion, and leads to improved imaging data yield and measurement accuracy. We present structural and angiographic OCT images of the anterior eye, demonstrating the unique imaging capabilities using representative scanning protocols which may be relevant to future research and clinical applications.
Phenolic compound profile of probiotic (Lacticaseibacillus rhamnosus LR5) fortified vegetable tablet and probiotic survival in the simulated gastrointestinal tract
Authors: Jafari Saeid , Thongmat Krongkan , Kijpatanasilp Isaya , Kerdsup Paramaporn , Naknaen Phisut , Taweechotipatr Malai , Assatarakul Kitipong 
Published: January 2022

AbstractThe objectives of this research were to study the changes of phenolic compounds in vegetable (yellow VS green) tablets with/without probiotics (Lacticaseibacillus rhamnosus LR5) supplementation by using high performance liquid chromatography and probiotic survivability through the simulated gastrointestinal tract. The green vegetable tablets with/without probiotics had a greater (p ≤ 0.05) phenolic content compared to the yellow ones. There were no significant differences of most phenolic compound contents between probiotic-supplemented vegetable tablets and non-probiotic supplemented ones (p > 0.05). The contents of ferulic acid, epicatechin, tannic acid and rutin for both vegetable tablets tended to decrease through passing the stomach (1 and 2 h) and small intestine (2 and 4 h), however, the content of catechin in the yellow vegetable tablets tended to increase. The results also showed that the survival of Lacticaseibacillus rhamnosus LR5 slightly decreased through the simulated gastrointestinal tract. The vibrations from FTIR appeared in the wave length of 4000–3100, 3000–2800 and 1652–1545 cm−1, which accounted for the change in the N–H bonds of the amine group, changes in the structure of fatty acids and the change of carbonyl groups, respectively. This work highlighted the opportunity of application of probiotics in food products; especially non-dairy foods for consumer with dairy allergy.
Genome and transcriptome profiling of spontaneous preterm birth phenotypes
Authors: Gupta Juhi K. , Care Angharad , Goodfellow Laura , Alfirevic Zarko , Müller-Myhsok Bertram , Alfirevic Ana 
Published: January 2022

AbstractPreterm birth (PTB) occurs before 37 weeks of gestation. Risk factors include genetics and infection/inflammation. Different mechanisms have been reported for spontaneous preterm birth (SPTB) and preterm birth following preterm premature rupture of membranes (PPROM). This study aimed to identify early pregnancy biomarkers of SPTB and PPROM from the maternal genome and transcriptome. Pregnant women were recruited at the Liverpool Women’s Hospital. Pregnancy outcomes were categorised as SPTB, PPROM (≤ 34 weeks gestation, n = 53), high-risk term (HTERM, ≥ 37 weeks, n = 126) or low-risk (no history of SPTB/PPROM) term (LTERM, ≥ 39 weeks, n = 188). Blood samples were collected at 16 and 20 weeks gestation from which, genome (UK Biobank Axiom array) and transcriptome (Clariom D Human assay) data were acquired. PLINK and R were used to perform genetic association and differential expression analyses and expression quantitative trait loci (eQTL) mapping. Several significant molecular signatures were identified across the analyses in preterm cases. Genome-wide significant SNP rs14675645 (ASTN1) was associated with SPTB whereas microRNA-142 transcript and PPARG1-FOXP3 gene set were associated with PPROM at week 20 of gestation and is related to inflammation and immune response. This study has determined genomic and transcriptomic candidate biomarkers of SPTB and PPROM that require validation in diverse populations.