bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear nanomechanical resonators approaching the quantum ground state
Authors: Samanta C. , De Bonis S. L. , Møller C. B. , Tormo-Queralt R. , Yang W. , Urgell C. , Stamenic B. , Thibeault B. , Jin Y. , Czaplewski D. A. , Pistolesi F. , Bachtold A. 
Published: June 2023

AbstractIt is an open question whether mechanical resonators can be made nonlinear with vibrations approaching the quantum ground state. This requires the engineering of a mechanical nonlinearity far beyond what has been realized so far. Here we discover a mechanism to boost the Duffing nonlinearity by coupling the vibrations of a nanotube resonator to single-electron tunnelling and by operating the system in the ultrastrong-coupling regime. We find that thermal vibrations become highly nonlinear when lowering the temperature. The average vibration amplitude at the lowest temperature is 13 times the zero-point motion, with approximately 42% of the thermal energy stored in the anharmonic part of the potential. Our work may enable the realization of mechanical Schrödinger cat states, mechanical qubits and quantum simulators emulating the electron–phonon coupling.
Hardwiring tissue-specific AAV transduction in mice through engineered receptor expression
Authors: Zengel James , Wang Yu Xin , Seo Jai Woong , Ning Ke , Hamilton James N. , Wu Bo , Raie Marina , Holbrook Colin , Su Shiqi , Clements Derek R. , Pillay Sirika , Puschnik Andreas S. , Winslow Monte M. , Idoyaga Juliana , Nagamine Claude M. , Sun Yang , Mahajan Vinit B. , Ferrara Katherine W. , Blau Helen M. , Carette Jan E. 
Published: June 2023

AbstractThe development of transgenic mouse models that express genes of interest in specific cell types has transformed our understanding of basic biology and disease. However, generating these models is time- and resource-intensive. Here we describe a model system, SELective Expression and Controlled Transduction In Vivo (SELECTIV), that enables efficient and specific expression of transgenes by coupling adeno-associated virus (AAV) vectors with Cre-inducible overexpression of the multi-serotype AAV receptor, AAVR. We demonstrate that transgenic AAVR overexpression greatly increases the efficiency of transduction of many diverse cell types, including muscle stem cells, which are normally refractory to AAV transduction. Superior specificity is achieved by combining Cre-mediated AAVR overexpression with whole-body knockout of endogenous Aavr, which is demonstrated in heart cardiomyocytes, liver hepatocytes and cholinergic neurons. The enhanced efficacy and exquisite specificity of SELECTIV has broad utility in development of new mouse model systems and expands the use of AAV for gene delivery in vivo.
RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization
Authors: Collombet Samuel , Rall Isabell , Dugast-Darzacq Claire , Heckert Alec , Halavatyi Aliaksandr , Le Saux Agnes , Dailey Gina , Darzacq Xavier , Heard Edith 
Published: June 2023

AbstractSubnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome in distinct physical and biochemical environments. During X chromosome inactivation (XCI), the noncoding Xist RNA coats the X chromosome, triggers gene silencing and forms a dense body of heterochromatin from which the transcription machinery appears to be excluded. Phase separation has been proposed to be involved in XCI, and might explain the exclusion of the transcription machinery by preventing its diffusion into the Xist-coated territory. Here, using quantitative fluorescence microscopy and single-particle tracking, we show that RNA polymerase II (RNAPII) freely accesses the Xist territory during the initiation of XCI. Instead, the apparent depletion of RNAPII is due to the loss of its chromatin stably bound fraction. These findings indicate that initial exclusion of RNAPII from the inactive X reflects the absence of actively transcribing RNAPII, rather than a consequence of putative physical compartmentalization of the inactive X heterochromatin domain.
A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling
Authors: Eché Camille , Iampietro Carole , Birbes Clément , Dréau Andreea , Kuchly Claire , Di Franco Arnaud , Klopp Christophe , Faraut Thomas , Djebali Sarah , Castinel Adrien , Zytnicki Matthias , Denis Erwan , Boussaha Mekki , Grohs Cécile , Boichard Didier , Gaspin Christine , Milan Denis , Donnadieu Cécile 
Published: June 2023

AbstractInspired by the production of reference data sets in the Genome in a Bottle project, we sequenced one Charolais heifer with different technologies: Illumina paired-end, Oxford Nanopore, Pacific Biosciences (HiFi and CLR), 10X Genomics linked-reads, and Hi-C. In order to generate haplotypic assemblies, we also sequenced both parents with short reads. From these data, we built two haplotyped trio high quality reference genomes and a consensus assembly, using up-to-date software packages. The assemblies obtained using PacBio HiFi reaches a size of 3.2 Gb, which is significantly larger than the 2.7 Gb ARS-UCD1.2 reference. The BUSCO score of the consensus assembly reaches a completeness of 95.8%, among highly conserved mammal genes. We also identified 35,866 structural variants larger than 50 base pairs. This assembly is a contribution to the bovine pangenome for the “Charolais” breed. These datasets will prove to be useful resources enabling the community to gain additional insight on sequencing technologies for applications such as SNP, indel or structural variant calling, and de novo assembly.
MER and increased operative time are not risk factors for the formation of pneumocephalus during DBS
Authors: Iess Guglielmo , Bonomo Giulio , Levi Vincenzo , Aquino Domenico , Zekaj Edvin , Mezza Federica , Servello Domenico 
Published: June 2023

AbstractAlthough only recently directional leads have proven their potential to compensate for sub-optimally placed electrodes, optimal lead positioning remains the most critical factor in determining Deep Brain Stimulation (DBS) outcome. Pneumocephalus is a recognized source of error, but the factors that contribute to its formation are still a matter of debate. Among these, operative time is one of the most controversial. Because cases of DBS performed with Microelectrode Recordings (MER) are affected by an increase in surgical length, it is useful to analyze whether MER places patients at risk for increased intracranial air entry. Data of 94 patients from two different institutes who underwent DBS for different neurologic and psychiatric conditions were analyzed for the presence of postoperative pneumocephalus. Operative time and use of MER, as well as other potential risk factors for pneumocephalus (age, awake vs. asleep surgery, number of MER passages, burr hole size, target and unilateral vs. bilateral implants) were examined. Mann-Whitney U and Kruskal-Wallis tests were utilized to compare intracranial air distributions across groups of categorical variables. Partial correlations were used to assess the association between time and volume. A generalized linear model was created to predict the effects of time and MER on the volume of intracranial air, controlling for other potential risk factors identified: age, number of MER passages, awake vs. asleep surgery, burr hole size, target, unilateral vs. bilateral surgery. Significantly different distributions of air volume were noted between different targets, unilateral vs. bilateral implants, and number of MER trajectories. Patients undergoing DBS with MER did not present a significant increase in pneumocephalus compared to patients operated without (p = 0.067). No significant correlation was found between pneumocephalus and time. Using multivariate analysis, unilateral implants exhibited lower volumes of pneumocephalus (p = 0.002). Two specific targets exhibited significantly different volumes of pneumocephalus: the bed nucleus of the stria terminalis with lower volumes (p < 0.001) and the posterior hypothalamus with higher volumes (p = 0.011). MER, time, and other parameters analyzed failed to reach statistical significance. Operative time and use of intraoperative MER are not significant predictors of pneumocephalus during DBS. Air entry is greater for bilateral surgeries and may be also influenced by the specific stimulated target.
Impact of the COVID-19 pandemic on liver transplant waitlist outcome in France
Authors: Legeai Camille , Antoine Corinne , Jasseron Carine , Kerbaul François , Dumortier Jérôme 
Published: June 2023

AbstractThe objective of this study was to investigate the impact of the COVID-19 pandemic on the outcome of patients on the liver transplantation (LT) waitlist in 2020 in France, in particular, the incidence of deaths and delisting for worsening condition, depending on the allocation score component. The 2020 cohort of patients on the waiting list was compared with the 2018/2019 cohorts. 2020 saw fewer LTs than in either 2019 or 2018 (1128, 1356, and 1325, respectively), together with fewer actual brain dead donors (1355, 1729, and 1743). In 2020, deaths or delisting for worsening condition increased significantly versus 2018/2019 (subdistribution hazard ratio 1.4, 95% confidence interval [CI] 1.2–1.7), after adjustment for age, place of care, diabetes, blood type, and score component, although COVID-19-related mortality was low. This increased risk mainly concerned patients with hepatocellular carcinoma (1.52, 95% CI 1.22–1.90), with 650 MELD exception points (2.19, 95% CI 1.08–4.43), and especially those without HCC and MELD scores from 25 to 30 (3.36 [95% CI 1.82–6.18]). In conclusion, by significantly decreasing LT activity in 2020, the COVID-19 pandemic increased the number of waitlist deaths and delisting for worsening condition, and significantly more for particular components of the score, including intermediate severity cirrhosis.
Tailoring recommendation algorithms to ideal preferences makes users better off
Authors: Khambatta Poruz , Mariadassou Shwetha , Morris Joshua , Wheeler S. Christian 
Published: June 2023

AbstractPeople often struggle to do what they ideally want because of a conflict between their actual and ideal preferences. ​​​By focusing on maximizing engagement, recommendation algorithms appear to be exacerbating this struggle. However, this need not be the case. Here we show that tailoring recommendation algorithms to ideal (vs. actual) preferences would provide meaningful benefits to both users and companies. To examine this, we built algorithmic recommendation systems that generated real-time, personalized recommendations tailored to either a person’s actual or ideal preferences. Then, in a high-powered, pre-registered experiment (n = 6488), we measured the effects of these recommendation algorithms. We found that targeting ideal rather than actual preferences resulted in somewhat fewer clicks, but it also increased the extent to which people felt better off and that their time was well spent. Moreover, of note to companies, targeting ideal preferences increased users' willingness to pay for the service, the extent to which they felt the company had their best interest at heart, and their likelihood of using the service again. Our results suggest that users and companies would be better off if recommendation algorithms learned what each person was striving for and nudged individuals toward their own unique ideals.
Assessing the cytotoxicity of aerosolized carbon black and benzo[a]pyrene with controlled physical and chemical properties on human lung epithelial cells
Authors: Ryu Youngri , Roh Soonjong , Joung Young Soo 
Published: June 2023

AbstractAtmospheric particulate matter (PM) is a complex mixture of hazardous particles containing hundreds of inorganic and organic species. Organic components, such as carbon black (CB) and benzo[a]pyrene (BaP), are known to exhibit diverse genotoxic and carcinogenic effects. The toxicity of CB and polycyclic aromatic hydrocarbons has been well studied, however the combined toxicity is much less understood. A spray-drying system was used to control the size and chemical composition of PMs. PMs were prepared by loading BaP on three different sized CBs (0.1 μm, 2.5 μm, and 10 μm) to obtain BaP-unloaded CB (CB0.1, CB2.5, and CB10) and BaP-loaded CB (CB0.1–BaP, CB2.5–BaP, and CB10–BaP). We analyzed cell viability, levels of oxidative stress, and pro-inflammatory cytokines using human lung cells (A549 epithelial cells). Cell viability decreased when exposed to all PMs (PM0.1, PM2.5, and PM10), regardless of the presence of BaP. The increase in PM size due to BaP-adsorption to CB resulted in insufficient toxic effects on human lung cells compared to CB alone. Smaller CBs reduced cell viability, leading to reactive oxygen species formation, which can cause damage to cellular structures deliver more harmful substances. Additionally, small CBs were predominant in inducing the expression of pro-inflammatory cytokines in A549 epithelial cells. These results indicate that the size of CB is a key factor that immediately affects the inflammation of lung cells, compared to the presence of BaP.
Biomechanical performance of a novel light-curable bone fixation technique
Authors: Schwarzenberg Peter , Colding-Rasmussen Thomas , Hutchinson Daniel J. , Mischler Dominic , Horstmann Peter , Petersen Michael Mørk , Jacobsen Stine , Pastor Tatjana , Malkoch Michael , Wong Christian , Varga Peter 
Published: June 2023

AbstractTraumatic bone fractures are often debilitating injuries that may require surgical fixation to ensure sufficient healing. Currently, the most frequently used osteosynthesis materials are metal-based; however, in certain cases, such as complex comminuted osteoporotic fractures, they may not provide the best solution due to their rigid and non-customizable nature. In phalanx fractures in particular, metal plates have been shown to induce joint stiffness and soft tissue adhesions. A new osteosynthesis method using a light curable polymer composite has been developed. This method has demonstrated itself to be a versatile solution that can be shaped by surgeons in situ and has been shown to induce no soft tissue adhesions. In this study, the biomechanical performance of AdhFix was compared to conventional metal plates. The osteosyntheses were tested in seven different groups with varying loading modality (bending and torsion), osteotomy gap size, and fixation type and size in a sheep phalanx model. AdhFix demonstrated statistically higher stiffnesses in torsion (64.64 ± 9.27 and 114.08 ± 20.98 Nmm/° vs. 33.88 ± 3.10 Nmm/°) and in reduced fractures in bending (13.70 ± 2.75 Nm/mm vs. 8.69 ± 1.16 Nmm/°), while the metal plates were stiffer in unreduced fractures (7.44 ± 1.75 Nm/mm vs. 2.70 ± 0.72 Nmm/°). The metal plates withstood equivalent or significantly higher torques in torsion (534.28 ± 25.74 Nmm vs. 614.10 ± 118.44 and 414.82 ± 70.98 Nmm) and significantly higher bending moments (19.51 ± 2.24 and 22.72 ± 2.68 Nm vs. 5.38 ± 0.73 and 1.22 ± 0.30 Nm). This study illustrated that the AdhFix platform is a viable, customizable solution that is comparable to the mechanical properties of traditional metal plates within the range of physiological loading values reported in literature.
Tumor-educated platelet blood tests for Non-Small Cell Lung Cancer detection and management
Authors: Antunes-Ferreira Mafalda , D’Ambrosi Silvia , Arkani Mohammad , Post Edward , In ‘t Veld Sjors G. J. G. , Ramaker Jip , Zwaan Kenn , Kucukguzel Ece Demirel , Wedekind Laurine E. , Griffioen Arjan W. , Oude Egbrink Mirjam , Kuijpers Marijke J. E. , van den Broek Daan , Noske David P. , Hartemink Koen J. , Sabrkhany Siamack , Bahce Idris , Sol Nik , Bogaard Harm-Jan , Koppers-Lalic Danijela , Best Myron G. , Wurdinger Thomas 
Published: June 2023

AbstractLiquid biopsy approaches offer a promising technology for early and minimally invasive cancer detection. Tumor-educated platelets (TEPs) have emerged as a promising liquid biopsy biosource for the detection of various cancer types. In this study, we processed and analyzed the TEPs collected from 466 Non-small Cell Lung Carcinoma (NSCLC) patients and 410 asymptomatic individuals (controls) using the previously established thromboSeq protocol. We developed a novel particle-swarm optimization machine learning algorithm which enabled the selection of an 881 RNA biomarker panel (AUC 0.88). Herein we propose and validate in an independent cohort of samples (n = 558) two approaches for blood samples testing: one with high sensitivity (95% NSCLC detected) and another with high specificity (94% controls detected). Our data explain how TEP-derived spliced RNAs may serve as a biomarker for minimally-invasive clinical blood tests, complement existing imaging tests, and assist the detection and management of lung cancer patients.
Study on the driving mechanism of lagged effects based on different time scales in a karst drainage basin in South China
Authors: He Zhonghua , Pan Shan , Gu Xiaolin , Xu Mingjin , Wang Maoqiang 
Published: June 2023

AbstractCompared to earthquakes and volcanoes, drought is one of the most damaging natural disasters and is mainly affected by rainfall losses, especially by the runoff regulation ability of the underlying watershed surface. Based on monthly rainfall runoff data recorded from 1980 to 2020, in this study, the distributed lag regression model is used to simulate the rainfall-runoff process in the karst distribution region of South China, and a time series of watershed lagged-flow volumes is calculated. The watershed lagged effect is analyzed by four distribution models, and the joint probability between the lagged intensity and frequency is simulated by the copula function family. The results show that (1) the watershed lagged effects simulated by the normal, log-normal, P-III and log-logistic distribution models in the karst drainage basin are particularly significant, with small mean square errors (MSEs) and significant time-scale characteristics. (2) Affected by spatiotemporal distribution differences in rainfall and the impacts of different basin media and structures, the lag response of runoff to rainfall differs significantly among different time scales. Especially at the 1-, 3- and 12-month scales, the coefficient of variation (Cv) of the watershed lagged intensity is greater than 1, while it is less than 1 at the 6- and 9-month scales. (3) The lagged frequencies simulated by the log-normal, P-III and log-logistic distribution models are relatively high (with medium, medium–high and high frequencies, respectively), while that simulated by the normal distribution is relatively low (medium–low and low frequencies). (4) There is a significant negative correlation (R < − 0.8, Sig. < 0.01) between the watershed lagged intensity and frequency. For the joint probability simulation, the fitting effect of the gumbel Copula is the best, followed by the Clayton and Frank-1 copulas, and while that of the Frank-2 copula is relatively weak. Consequently, the propagation mechanism from meteorological drought to agricultural or hydrological drought and the conversion mechanism between agricultural and hydrological drought are effectively revealed in this study, thereby providing a scientific basis for the rational utilization of water resources and drought resistance and disaster relief in karst areas.
Impact of the South Atlantic Anomaly on radiation exposure at flight altitudes during solar minimum
Authors: Meier Matthias M. , Berger Thomas , Jahn Thomas , Matthiä Daniel , Plettenberg Mona C. , Scheibinger Markus , Schennetten Kai , Wirtz Michael 
Published: June 2023

AbstractThe South Atlantic Anomaly (SAA) is a geographical region over the South Atlantic Ocean where the inner Van Allen radiation belt extends down particularly close to Earth. This leads to highly increased levels of ionizing radiation and related impacts on spacecraft in Low Earth Orbits, e.g., correspondingly increased radiation exposure of astronauts and electronic components on the International Space Station. According to an urban legend, the SAA is also supposed to affect the radiation field in the atmosphere even down to the altitudes of civil aviation. In order to identify and quantify any additional contributions to the omnipresent radiation exposure due to the Galactic Cosmic Radiation at flight altitudes, comprehensive measurements were performed crossing the geographical region of the SAA at an altitude of 13 km in a unique flight mission—Atlantic Kiss. No indication of increased radiation exposure was found.
Foot morphology as a predictor of hallux valgus development in children
Authors: Martín-Casado Laura , Aldana-Caballero Alberto , Barquín Christian , Criado-Álvarez Juan José , Polonio-López Begoña , Marcos-Tejedor Félix 
Published: June 2023

AbstractAn excess of body weight can produce morphological changes in the feet of children. The aim of this study was to assess the morphological differences of the foot in children based on their body mass index and to determine the risk factors for the development of a hallux valgus in childhood and adolescence. One Thousand Six Hundred Seventy-Eight children (5–17 years) were classified as group with obesity, overweight, and normal weight. Lengths, widths, heights and angles of both feet was measured with a 3D scanner. The risk of developing hallux valgus was calculated. Group with overweight and obesity presented longer feet (p = 0.00), wider metatarsals (p = 0.00) and wider heels (p = 0.00). Arch height was lower (p > 0.01) in the group with obesity, and the hallux angle was greater in the group with normal weight (p < 0.05). The relative risk of a lateral hallux deviation increases with age, foot length and heel width (Exp (B) > 1). Children with overweight and obesity had longer and wider feet. The arch height was higher in children with overweight, and lower in children with obesity. Age, foot length, and heel width could be risk factors for the development of hallux valgus, while metatarsal width and arch height could be protective factors. Monitorization of the development and characterization of the foot in childhood as a clinical tool could help professionals to early identify the patients presenting risk factors and prevent future deformities and other biomechanical conditions in adulthood by implementing protecting measures.
Temperature contributes to host specialization of coffee wilt disease (Fusarium xylarioides) on arabica and robusta coffee crops
Authors: Zhang Xiuhan , Peck Lily D. , Flood Julie , Ryan Matthew J. , Barraclough Timothy G. 
Published: June 2023

AbstractCoffee wilt disease, caused by the fungusFusarium xylarioides, is a vascular wilt disease that has affected coffee production in sub-Saharan Africa over the past century. Today, the disease has two host-specific populations specialising on arabica and robusta coffee crops, which grow at high and low altitude, respectively. Here we test whether adaptation to different temperatures contributes to specialisation of the fungi on each crop. Firstly, climate models show that the severity of the arabica and robusta populations of coffee wilt disease correlates with temperature. The robusta population shows higher peak severity than the arabica population overall, but the latter has greater cold tolerance. Secondly, growth assays of thermal performance of fungal strains in vitro show that, while robusta strains grow faster than arabicas at intermediate temperatures, the arabica strains have higher sporulation and spore germination rates at temperatures below 15ºC. The match between environmental patterns of severity in nature with thermal performance of fungal cultures in the laboratory supports a role for temperature adaptation in specialisation on arabica and robusta coffee. Extrapolating our temperature-models to future climate change predicts that disease severity could decline on average due to increased temperature but could increase in some coffee-growing regions.