bluuebunny/crossref_metadata_2025_split huggingface dataset:
A redox switch regulates the assembly and anti-CRISPR activity of AcrIIC1
Authors: Zhao Yanan , Hu Jiaojiao , Yang Shan-Shan , Zhong Jing , Liu Jianping , Wang Shuo , Jiao Yuzhuo , Jiang Fang , Zhai Ruiyang , Ren Bingnan , Cong Hua , Zhu Yuwei , Han Fengtong , Zhang Jixian , Xu Yue , Huang Zhiwei , Zhang Shengnan , Yang Fan 
Published: November 2022

AbstractAnti-CRISPRs (Acrs) are natural inhibitors of bacteria’s CRISPR-Cas systems, and have been developed as a safeguard to reduce the off-target effects of CRISPR gene-editing technology. Acrs can directly bind to CRISPR-Cas complexes and inhibit their activities. However, whether this process is under regulation in diverse eukaryotic cellular environments is poorly understood. In this work, we report the discovery of a redox switch for NmeAcrIIC1, which regulates NmeAcrIIC1’s monomer-dimer interconversion and inhibitory activity on Cas9. Further structural studies reveal that a pair of conserved cysteines mediates the formation of inactive NmeAcrIIC1 dimer and directs the redox cycle. The redox switch also applies to the other two AcrIIC1 orthologs. Moreover, by replacing the redox-sensitive cysteines, we generated a robust AcrIIC1 variant that maintains potent inhibitory activity under various redox conditions. Our results reveal a redox-dependent regulation mechanism of Acr, and shed light on the design of superior Acr for CRISPR-Cas systems.
A widespread group of large plasmids in methanotrophic Methanoperedens archaea
Authors: Schoelmerich Marie C. , Ouboter Heleen T. , Sachdeva Rohan , Penev Petar I. , Amano Yuki , West-Roberts Jacob , Welte Cornelia U. , Banfield Jillian F. 
Published: November 2022

AbstractAnaerobic methanotrophic (ANME) archaea obtain energy from the breakdown of methane, yet their extrachromosomal genetic elements are little understood. Here we describe large plasmids associated with ANME archaea of the Methanoperedens genus in enrichment cultures and other natural anoxic environments. By manual curation we show that two of the plasmids are large (155,605 bp and 191,912 bp), circular, and may replicate bidirectionally. The plasmids occur in the same copy number as the main chromosome, and plasmid genes are actively transcribed. One of the plasmids encodes three tRNAs, ribosomal protein uL16 and elongation factor eEF2; these genes appear to be missing in the host Methanoperedens genome, suggesting an obligate interdependence between plasmid and host. Our work opens the way for the development of genetic vectors to shed light on the physiology and biochemistry of Methanoperedens, and potentially genetically edit them to enhance growth and accelerate methane oxidation rates.
Cancer cell survival depends on collagen uptake into tumor-associated stroma
Authors: Hsu Kuo-Sheng , Dunleavey James M. , Szot Christopher , Yang Liping , Hilton Mary Beth , Morris Karen , Seaman Steven , Feng Yang , Lutz Emily M. , Koogle Robert , Tomassoni-Ardori Francesco , Saha Saurabh , Zhang Xiaoyan M. , Zudaire Enrique , Bajgain Pradip , Rose Joshua , Zhu Zhongyu , Dimitrov Dimiter S. , Cuttitta Frank , Emenaker Nancy J. , Tessarollo Lino , St. Croix Brad 
Published: November 2022

AbstractCollagen I, the most abundant protein in humans, is ubiquitous in solid tumors where it provides a rich source of exploitable metabolic fuel for cancer cells. While tumor cells were unable to exploit collagen directly, here we show they can usurp metabolic byproducts of collagen-consuming tumor-associated stroma. Using genetically engineered mouse models, we discovered that solid tumor growth depends upon collagen binding and uptake mediated by the TEM8/ANTXR1 cell surface protein in tumor-associated stroma. Tumor-associated stromal cells processed collagen into glutamine, which was then released and internalized by cancer cells. Under chronic nutrient starvation, a condition driven by the high metabolic demand of tumors, cancer cells exploited glutamine to survive, an effect that could be reversed by blocking collagen uptake with TEM8 neutralizing antibodies. These studies reveal that cancer cells exploit collagen-consuming stromal cells for survival, exposing an important vulnerability across solid tumors with implications for developing improved anticancer therapy.
Impact of pulmonary African trypanosomes on the immunology and function of the lung
Authors: Mabille Dorien , Dirkx Laura , Thys Sofie , Vermeersch Marjorie , Montenye Daniel , Govaerts Matthias , Hendrickx Sarah , Takac Peter , Van Weyenbergh Johan , Pintelon Isabel , Delputte Peter , Maes Louis , Pérez-Morga David , Timmermans Jean-Pierre , Caljon Guy 
Published: November 2022

AbstractApproximately 20% of sleeping sickness patients exhibit respiratory complications, however, with a largely unknown role of the parasite. Here we show that tsetse fly-transmitted Trypanosoma brucei parasites rapidly and permanently colonize the lungs and occupy the extravascular spaces surrounding the blood vessels of the alveoli and bronchi. They are present as nests of multiplying parasites exhibiting close interactions with collagen and active secretion of extracellular vesicles. The local immune response shows a substantial increase of monocytes, macrophages, dendritic cells and γδ and activated αβ T cells and a later influx of neutrophils. Interestingly, parasite presence results in a significant reduction of B cells, eosinophils and natural killer cells. T. brucei infected mice show no infection-associated pulmonary dysfunction, mirroring the limited pulmonary clinical complications during sleeping sickness. However, the substantial reduction of the various immune cells may render individuals more susceptible to opportunistic infections, as evident by a co-infection experiment with respiratory syncytial virus. Collectively, these observations provide insights into a largely overlooked target organ, and may trigger new diagnostic and supportive therapeutic approaches for sleeping sickness.
Cesium-mediated electron redistribution and electron-electron interaction in high-pressure metallic CsPbI3
Authors: Ke Feng , Yan Jiejuan , Niu Shanyuan , Wen Jiajia , Yin Ketao , Yang Hong , Wolf Nathan R. , Tzeng Yan-Kai , Karunadasa Hemamala I. , Lee Young S. , Mao Wendy L. , Lin Yu 
Published: November 2022

AbstractElectron-phonon coupling was believed to govern the carrier transport in halide perovskites and related phases. Here we demonstrate that electron-electron interaction enhanced by Cs-involved electron redistribution plays a direct and prominent role in the low-temperature electrical transport of compressed CsPbI3 and renders Fermi liquid (FL)-like behavior. By compressing δ-CsPbI3 to 80 GPa, an insulator-semimetal-metal transition occurs, concomitant with the completion of a slow structural transition from the one-dimensional Pnma (δ) phase to a three-dimensional Pmn21 (ε) phase. Deviation from FL behavior is observed upon CsPbI3 entering the metallic ε phase, which progressively evolves into a FL-like state at 186 GPa. First-principles density functional theory calculations reveal that the enhanced electron-electron coupling results from the sudden increase of the 5d state occupation in Cs and I atoms. Our study presents a promising strategy of cationic manipulation for tuning the electronic structure and carrier scattering of halide perovskites at high pressure.
Fine-tuned local coordination environment of Pt single atoms on ceria controls catalytic reactivity
Authors: Tan Wei , Xie Shaohua , Le Duy , Diao Weijian , Wang Meiyu , Low Ke-Bin , Austin Dave , Hong Sampyo , Gao Fei , Dong Lin , Ma Lu , Ehrlich Steven N. , Rahman Talat S. , Liu Fudong 
Published: November 2022

AbstractConstructing single atom catalysts with fine-tuned coordination environments can be a promising strategy to achieve satisfactory catalytic performance. Herein, via a simple calcination temperature-control strategy, CeO2 supported Pt single atom catalysts with precisely controlled coordination environments are successfully fabricated. The joint experimental and theoretical analysis reveals that the Pt single atoms on Pt1/CeO2 prepared at 550 °C (Pt/CeO2-550) are mainly located at the edge sites of CeO2 with a Pt–O coordination number of ca. 5, while those prepared at 800 °C (Pt/CeO2-800) are predominantly located at distorted Ce substitution sites on CeO2 terrace with a Pt–O coordination number of ca. 4. Pt/CeO2-550 and Pt/CeO2-800 with different Pt1-CeO2 coordination environments exhibit a reversal of activity trend in CO oxidation and NH3 oxidation due to their different privileges in reactants activation and H2O desorption, suggesting that the catalytic performance of Pt single atom catalysts in different target reactions can be maximized by optimizing their local coordination structures.
Decarboxylative oxidation-enabled consecutive C-C bond cleavage
Authors: Li Ruining , Dong Ya , Khan Shah Nawaz , Zaman Muhammad Kashif , Zhou Junliang , Miao Pannan , Hu Lifu , Sun Zhankui 
Published: November 2022

AbstractThe selective cleavage of C-C bonds is of fundamental interest because it provides an alternative approach to traditional chemical synthesis, which is focused primarily on building up molecular complexity. However, current C-C cleavage methods provide only limited opportunities. For example, selective C(sp3)-C(sp3) bond cleavage generally relies on the use of transition-metal to open strained ring systems or iminyl and alkoxy radicals to induce β-fragmentation. Here we show that by merging photoredox catalysis with copper catalysis, we are able to employ α-trisubstituted carboxylic acids as substrates and achieve consecutive C-C bond cleavage, resulting in the scission of the inert β-CH2 group. The key transformation relies on the decarboxylative oxidation process, which could selectively generate in-situ formed alkoxy radicals and trigger consecutive C-C bond cleavage. This complicated yet interesting reaction might help the development of other methods for inert C(sp3)-C(sp3) bond cleavage.
A predictable prospect of the South Asian summer monsoon
Authors: Zhang Tuantuan , Jiang Xingwen , Yang Song , Chen Junwen , Li Zhenning 
Published: November 2022

AbstractPrediction of the South Asian summer monsoon (SASM) has remained a challenge for both scientific research and operational climate prediction for decades. By identifying two dominant modes of the SASM, here we show that the unsatisfactory prediction may be due to the fact that the existing SASM indices are mostly related to the less predictable second mode. The first mode, in fact, is highly predictable. It is physically linked to the variation of the Indian monsoon trough coupled with large rainfall anomalies over core monsoon zone and the northern Bay of Bengal. An index is constructed as a physical proxy of this first mode, which can be well predicted one season in advance, with an overall skill of 0.698 for 1979–2020. This result suggests a predictable prospect of the SASM, and we recommend the new index for real-time monitoring and prediction of the SASM.
Theory of non-Hermitian topological whispering gallery
Authors: Pernas-Salomón René , Zheng Li-Yang , Zhang Zhiwang , Gao Penglin , Liu Xiaojun , Cheng Ying , Christensen Johan 
Published: November 2022

AbstractTopological insulators have taken the condensed matter physics scenery by storm and captivated the interest among scientists and materials engineers alike. Surprisingly, this arena which was initially established and profoundly studied in electronic systems and crystals, has sparked a drive among classical physicists to pursue a wave-based analogy for sound, light and vibrations. In the latest efforts combining valley-contrasting topological sound with non-Hermitian ingredients, B. Hu et al. [Nature 597, 655 (2021)] employed thermoacoustic coupling in sonic lattices whose elementary building blocks are coated with electrically biased carbon nanotube films. In this contribution, we take a theoretical and numerical route towards understanding the complex acoustic interplay between geometry and added acoustic gain as inspired by the aforesaid publication. Besides complex bulk and edge states predictions and computations of mode-split resonances using whispering gallery configurations, we also predict an acoustic amplitude saturation in dependence on the activated coated elements. We foresee that our computational advances may assist future efforts in exploring thermoacoustic topological properties.
SARS-CoV-2 RNA levels in Scotland’s wastewater
Authors: Scorza Livia C. T. , Cameron Graeme J. , Murray-Williams Roisin , Findlay David , Bolland Julie , Cerghizan Brindusa , Campbell Kirsty , Thomson David , Corbishley Alexander , Gally David , Fitzgerald Stephen , Low Alison , McAteer Sean , Roberts Adrian M. I. , Fang Zhou , Mayer Claus-Dieter , Frantsuzova Anastasia , Baby Sumy V. , Zieliński Tomasz , Millar Andrew J. 
Published: November 2022

AbstractNationwide, wastewater-based monitoring was newly established in Scotland to track the levels of SARS-CoV-2 viral RNA shed into the sewage network, during the COVID-19 pandemic. We present a curated, reference dataset produced by this national programme, from May 2020 to February 2022. Viral levels were analysed by RT-qPCR assays of the N1 gene, on RNA extracted from wastewater sampled at 162 locations. Locations were sampled up to four times per week, typically once or twice per week, and in response to local needs. We report sampling site locations with geographical coordinates, the total population in the catchment for each site, and the information necessary for data normalisation, such as the incoming wastewater flow values and ammonia concentration, when these were available. The methodology for viral quantification and data analysis is briefly described, with links to detailed protocols online. These wastewater data are contributing to estimates of disease prevalence and the viral reproduction number (R) in Scotland and in the UK.
Variability of microcirculatory measurements in healthy volunteers
Authors: Bol M. E. , Broddin B. E. K. , Delhaas T. , Sels J. E. M. , van de Poll M. C. G. 
Published: November 2022

AbstractReliable assessment of the microcirculation is important to investigate microcirculatory properties in various disease states. The GlycoCheck system automatically analyzes sublingual sidestream dark field images to determine the perfused boundary region (PBR; a measure of glycocalyx thickness), red blood cell filling percentage, and microvascular vessel density. Although GlycoCheck has been used to study the microcirculation in patients, little is known about the reproducibility of measurements in healthy volunteers. We assessed intra- and interobserver agreement by having two experienced observers perform three consecutive microcirculation measurements with the GlycoCheck system in 49 healthy volunteers. Intraobserver agreement of single measurements were poor (intraclass correlation coefficients (ICCs) < 0.4) for PBR, red blood cell filling percentage and microvascular vessel density. ICCs increased to values > 0.6 (indicating good reproducibility) for all parameters when performing and averaging three consecutive measurements. No systematic differences were observed between observers for any parameter. Interobserver variability was fair for PBR (ICC = 0.53) and red blood cell filling percentage (ICC = 0.58) and poor for perfused vessel density (ICC = 0.20). In conclusion, GlycoCheck software can be used with acceptable reliability and reproducibility for microcirculation measurements on a population level when averaging three consecutive measurements. Repeated measurements are preferably performed by the same observer.
The effect of intravitreal brolucizumab on choroidal thickness in patients with neovascular age-related macular degeneration
Authors: Bae Ki Woong , Kim Dong Ik , Hwang Daniel Duck-Jin 
Published: November 2022

AbstractIn this study we evaluated the effect of intravitreal brolucizumab injections on choroidal thickness in patients with neovascular age-related macular degeneration (nAMD) who previously showed an incomplete response to anti-vascular endothelial growth factor treatment. A total of thirty-four eyes from 34 patients were included in this study. The patients received an average of 2.4 ± 1.1 brolucizumab injections with the mean follow-up period of 4.9 ± 2.0 months. After their first brolucizumab treatment, the central foveal thickness (CFT) and subfoveal choroidal thickness (SFCT) were significantly decreased from 431.6 ± 190.0 μm and 193.9 ± 75.1 μm to 274.6 ± 109.4 μm (P < 0.001) and 169.4 ± 71.1 μm (P < 0.001), respectively. However, there were no improvements in visual acuity. Patients were divided into three subgroups according to the number of brolucizumab treatments: one, two, and three or more injections. In all three subgroups, the CFT and SFCT were significantly reduced compared to baseline at all time points of brolucizumab injections. In conclusion, choroidal thickness was significantly reduced after intravitreal brolucizumab injections as a switching treatment in patients with nAMD.
Hydrogen at symmetric tilt grain boundaries in aluminum: segregation energies and structural features
Authors: Lousada Cláudio M. , Korzhavyi Pavel A. 
Published: November 2022

AbstractAluminum is envisioned to be an important material in future hydrogen-based energy systems. Here we report an ab initio investigation on the interactions between H-atoms and common grain boundaries (GBs) of fcc Al: Σ9, Σ5, Σ11 and Σ3. We found that upon segregation to the GBs, single H-atoms can cause displacement of Al-atoms. Increasing their concentration revealed large cooperative effects between H-atoms that favor the segregation when other H-atoms are bound at neighboring sites. This makes these GBs able to accommodate high concentrations of H-atoms with considerable segregation energies per atom. Structural analyses derived from Laguerre–Voronoi tessellations show that these GBs have many interstitial sites with higher symmetry than the bulk tetrahedral interstitial site. Many of those sites have also large volumes and higher coordination numbers than the bulk sites. These factors are the increased driving force for H-atom segregation at the studied GBs in Al when compared to other metals. These GBs can accommodate a higher concentration of H-atoms which indicates a likely uniform distribution of H-atoms at GBs in the real material. This suggests that attempting to mitigate hydrogen uptake solely by controlling the occurrence of certain GBs may not be the most efficient strategy for Al.
Visual outcomes and subjective experience with three intraocular lenses based presbyopia correcting strategies in cataract patients
Authors: Zhu Meiyi , Fan Wei , Zhang Guangbin 
Published: November 2022

AbstractTo compare the visual outcomes and subjective experience of three intraocular lenses (IOL) implant strategies. Retrospective comparative study. This study comprised patients who underwent phacoemulsification and bilateral implantation of extended depth of focus (EDOF) IOL (ZXR00; EDOF group), blended implantation of EDOF and bifocal IOL (ZXR00/ZLB00; blended group), and bilateral implantation of trifocal IOL (AT LISA tri 839MP; trifocal group). The outcomes included visual acuity (VA), visual defocus curve, contrast sensitivity, visual quality, quality of life, spectacle independence, and patient satisfaction. Follow-up was performed 3 months after the surgery. This study included 114 eyes of 57 patients (20 in EDOF group; 16 in blended group; 21 in trifocal group). Patients in the three groups had high quality of life, patient satisfaction, and good contrast sensitivity. The EDOF group had the worst near VA, but the visual quality was the best. The blended group had good VA and slight photic disturbance. The trifocal group obtained the best whole range of VA, but the photic disturbance was significantly severe than the EDOF group. Both the blended and trifocal groups achieved high spectacle independence, but some patients in the EDOF group need spectacle when dealing with close-range tasks.
COVID-19 vaccine acceptance rates and predictors among the Egyptian general population and Healthcare workers, the intersectionality of age and other factors
Authors: El-Ghitany Engy Mohamed , Ashour Ayat , Omran Eman A. , Farghaly Azza Galal , Hassaan Mahmoud A. , Azzam Nashwa Fawzy Abd El-Moez 
Published: November 2022

AbstractThe promise of COVID-19 vaccines in ending the pandemic can only be achieved by overcoming the challenge of vaccine refusal. Healthcare workers (HCWs) are the trusted advisors of vaccination decisions. Recommendations for vaccinating children against COVID-19 are recently gaining more public health attention due to the role of children in disease transmission and associated morbidities. Vaccination is one of the first medical decisions parents or guardians make on behalf of their children. To investigate the determinants associated with vaccine acceptability among the general population through a direct interview questionnaire and assess guardians’ views towards childhood COVID-19 vaccinations. This cross-sectional study included 2919 participants A pre-designed structured questionnaire about COVID-19 vaccination acceptability was completed by trained interviewers and interviewing the participants or their guardians (for those below 18 years old). Nearly two-thirds of participants (66.5%) accepted vaccination, 20.2% were refusing and 13.3% were hesitant. Most participants who were guardians of children below 12 years and from 13 to 17 years reported that they would accept vaccination of their children (72.5% and 70.5%, respectively). The acceptance rate among HCWs was 58.2%. The main reasons beyond vaccine refusal were mistrust of vaccine efficacy (39.5%) and having concerns regarding vaccine safety (38.8%). In a multivariable regression model, being male (OR 1.362, 95% CI 1.082–1.714, p = 0.008) resident in rural area (OR 1.796, 95% CI 1.435–2.247, p = 0.000), and lower education (OR 1.245, 95% CI 1.018–1.523, p = 0.033) were associated with an increased acceptance to be vaccinated. The acceptance rate for vaccinating children reported among their guardians was higher than adults for themselves. Extremes of age showed higher vaccine acceptance compared to young adults. Upper Egypt governorates (Faiyum and Giza) were outpacing Lower Egypt governorates in vaccination acceptance rates.
Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment
Authors: Miyata Kaede , Inoue Yasuaki , Amano Yuto , Nishioka Tohru , Nagaike Tomohisa , Kawaguchi Takamitsu , Morita Osamu , Yamane Masayuki , Honda Hiroshi 
Published: November 2022

AbstractEnvironmental DNA (eDNA) metabarcoding is widely used for species analysis, while the use of environmental RNA (eRNA) metabarcoding is more limited. We conducted comparative eDNA/eRNA metabarcoding of the algae and arthropods (aquatic insects) in water samples from Naka River, Japan, to evaluate their potential for biological monitoring and water quality assessment. Both methods detected various algae and arthropod species; however, their compositions were remarkably different from those in traditional field surveys (TFSs), indicating low sensitivity. For algae, the species composition derived from eDNA and eRNA metabarcoding was equivalent. While TFSs focus on attached algae, metabarcoding analysis theoretically detects both planktonic and attached algae. A recently expanded genomic database for aquatic insects significantly contributed to the sensitivity and positive predictivity for arthropods. While the sensitivity of eRNA was lower than that of eDNA, the positive predictivity of eRNA was higher. The eRNA of terrestrial arthropods indicated extremely high or low read numbers when compared with eDNA, suggesting that eRNA could be an effective indicator of false positives. Arthropod and algae eDNA/eRNA metabarcoding analysis enabled water quality estimates from TFSs. The eRNA of algae and arthropods could thus be used to evaluate biodiversity and water quality and provide insights from ecological surveys.