bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid generation of Shigella flexneri GMMA displaying natural or new and cross-reactive O-Antigens
Authors: Gasperini Gianmarco , Raso Maria Michelina , Schiavo Fabiola , Aruta Maria Grazia , Ravenscroft Neil , Bellich Barbara , Cescutti Paola , Necchi Francesca , Rappuoli Rino , Micoli Francesca 
Published: June 2022

AbstractGeneralized modules for membrane antigens (GMMA) are exosomes released from engineered Gram-negative bacteria and represent an attractive vaccine platform for the delivery of the O-Antigen (OAg), recognized as the key target for protective immunity against several pathogens such as Shigella. Shigella is a major cause of disease in Low- and Middle-Income countries and the development of a vaccine needs to deal with its large serotypic diversity. All S. flexneri serotypes, except serotype 6, share a conserved OAg backbone, corresponding to serotype Y. Here, a GMMA-producing S. flexneri scaffold strain displaying the OAg backbone was engineered with different OAg-modifying enzymes, either individually or in combinations. This strategy rapidly yielded GMMA displaying 12 natural serotypes and 16 novel serotypes expressing multiple epitopes combinations that do not occur in nature. Importantly, a candidate GMMA displaying a hybrid OAg elicited broadly cross-bactericidal antibodies against a large panel of S. flexneri serotypes.
Time-resolved terahertz–Raman spectroscopy reveals that cations and anions distinctly modify intermolecular interactions of water
Authors: Balos Vasileios , Kaliannan Naveen Kumar , Elgabarty Hossam , Wolf Martin , Kühne Thomas D. , Sajadi Mohsen 
Published: June 2022

AbstractThe solvation of ions changes the physical, chemical and thermodynamic properties of water, and the microscopic origin of this behaviour is believed to be ion-induced perturbation of water’s hydrogen-bonding network. Here we provide microscopic insights into this process by monitoring the dissipation of energy in salt solutions using time-resolved terahertz–Raman spectroscopy. We resonantly drive the low-frequency rotational dynamics of water molecules using intense terahertz pulses and probe the Raman response of their intermolecular translational motions. We find that the intermolecular rotational-to-translational energy transfer is enhanced by highly charged cations and is drastically reduced by highly charged anions, scaling with the ion surface charge density and ion concentration. Our molecular dynamics simulations reveal that the water–water hydrogen-bond strength between the first and second solvation shells of cations increases, while it decreases around anions. The opposite effects of cations and anions on the intermolecular interactions of water resemble the effects of ions on the stabilization and denaturation of proteins.
Vision and vocal communication guide three-dimensional spatial coordination of zebra finches during wind-tunnel flights
Authors: Arnold Fabian , Staniszewski Michael S. , Pelzl Lisa , Ramenda Claudia , Gahr Manfred , Hoffmann Susanne 
Published: June 2022

AbstractAnimal collective motion is a natural phenomenon readily observable in various taxa. Although theoretical models can predict the macroscopic pattern of group movements based on the relative spatial position of group members, it is poorly understood how group members exchange directional information, which enables the spatial coordination between individuals during collective motion. To test if vocalizations emitted during flocking flight are used by birds to transmit directional information between group members, we recorded vocal behaviour, head orientation and spatial position of each individual in a small flock of zebra finches (Taeniopygia guttata) flying in a wind tunnel. We found that the finches can use both visual and acoustic cues for three-dimensional flock coordination. When visual information is insufficient, birds can increasingly exploit active vocal communication to avoid collisions with flock mates. Our study furthers the mechanistic understanding of collective motion in birds and highlights the impact interindividual vocal interactions can have on group performances in these animals.
GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins
Authors: Arif Amena , Bailey Shannon , Izumi Natsuko , Anzelon Todd A. , Ozata Deniz M. , Andersson Cecilia , Gainetdinov Ildar , MacRae Ian J. , Tomari Yukihide , Zamore Phillip D. 
Published: June 2022

AbstractArgonaute proteins use nucleic acid guides to find and bind specific DNA or RNA target sequences. Argonaute proteins have diverse biological functions and many retain their ancestral endoribonuclease activity, cleaving the phosphodiester bond between target nucleotides t10 and t11. In animals, the PIWI proteins—a specialized class of Argonaute proteins—use 21–35 nucleotide PIWI-interacting RNAs (piRNAs) to direct transposon silencing, protect the germline genome, and regulate gene expression during gametogenesis1. The piRNA pathway is required for fertility in one or both sexes of nearly all animals. Both piRNA production and function require RNA cleavage catalysed by PIWI proteins. Spermatogenesis in mice and other placental mammals requires three distinct, developmentally regulated PIWI proteins: MIWI (PIWIL1), MILI (PIWIL2) and MIWI22–4 (PIWIL4). The piRNA-guided endoribonuclease activities of MIWI and MILI are essential for the production of functional sperm5,6. piRNA-directed silencing in mice and insects also requires GTSF1, a PIWI-associated protein of unknown function7–12. Here we report that GTSF1 potentiates the weak, intrinsic, piRNA-directed RNA cleavage activities of PIWI proteins, transforming them into efficient endoribonucleases. GTSF1 is thus an example of an auxiliary protein that potentiates the catalytic activity of an Argonaute protein.
Telomeric 8-oxo-guanine drives rapid premature senescence in the absence of telomere shortening
Authors: Barnes Ryan P. , de Rosa Mariarosaria , Thosar Sanjana A. , Detwiler Ariana C. , Roginskaya Vera , Van Houten Bennett , Bruchez Marcel P. , Stewart-Ornstein Jacob , Opresko Patricia L. 
Published: June 2022

AbstractOxidative stress is a primary cause of cellular senescence and contributes to the etiology of numerous human diseases. Oxidative damage to telomeric DNA has been proposed to cause premature senescence by accelerating telomere shortening. Here, we tested this model directly using a precision chemoptogenetic tool to produce the common lesion 8-oxo-guanine (8oxoG) exclusively at telomeres in human fibroblasts and epithelial cells. A single induction of telomeric 8oxoG is sufficient to trigger multiple hallmarks of p53-dependent senescence. Telomeric 8oxoG activates ATM and ATR signaling, and enriches for markers of telomere dysfunction in replicating, but not quiescent cells. Acute 8oxoG production fails to shorten telomeres, but rather generates fragile sites and mitotic DNA synthesis at telomeres, indicative of impaired replication. Based on our results, we propose that oxidative stress promotes rapid senescence by producing oxidative base lesions that drive replication-dependent telomere fragility and dysfunction in the absence of shortening and shelterin loss.
In-situ TD-GCMS measurements of oxidative products of monoterpenes at typical vaping temperatures: implications for inhalation exposure to vaping products
Authors: Zhu Jiping , Niu Jianjun , Das Dharani , Cabecinha Ashley , Abramovici Hanan 
Published: June 2022

AbstractVaping is gaining in popularity. However, there is still much that remains unknown about the potential risk and harms of vaping. Formation of oxidative products is one of such areas that are not well understood. In this study, we used an in-situ thermal desorption GC/MS method to investigate the formation of oxidative products of several monoterpenes at or below typical vaping temperatures. Among the five tested monoterpenes, the unchanged portion of the parent compound in the vapour varied from 97 to 98% for myrcene to 11–28% for terpinolene. The majority of formed oxidative products in the vapour have a molecular weight of 134 (loss of two hydrogens), 150 (insertion of one oxygen and loss of two hydrogen atoms) or 152 (insertion of one oxygen atom). Three products, likely to be p-(1-propenyl)-toluene, β-pinone and fenchol were also observed. This is the first in-situ thermal desorption GC/MS study to investigate the possible formation of oxidative products of monoterpenes, one of the major components in vaping liquids, at temperatures that are relevant to the vaping process. Although the toxicity of inhaling these oxidative products is not clear yet, allergic and irritation reactions associated with oxidized monoterpene oils are well documented. Therefore, potential adverse effects of inhaling these oxidative products during vaping could be investigated to help support human risk assessment.
Quantum decision making in automatic driving
Authors: Song Qingyuan , Fu Weiping , Wang Wen , Sun Yuan , Wang Denggui , Zhou Jincao 
Published: June 2022

AbstractThe behavior intention estimation and interaction between Autonomous Vehicles (AV) and human traffic participants are the key problems in Automatic Driving System (ADS). When the classical decision theory studies implicitly assume that the behavior of human traffic participants is completely rational. However, according to the booming quantum decision theory in recent years and actual traffic cases, traffic behaviors and other human behaviors are often irrational and violate the assumptions of classical cognitive and decision theory. This paper explores the decision-making problem in the two-car game scene based on quantum decision theory and compares it with the current mainstream method of studying irrational behavior-Cumulative Prospect Theory (CPT) model. The comparative analysis proved that the Quantum Game Theory (QGT) model can explain the separation effect which the classical probability model can’t reveal, and it has more advantages than CPT model in dealing with game scene decision-making. When two cars interact with each other, the QGT model can consider the interests of both sides from the perspective of the other car. Compared with the classical probability model and CPT model, the QGT is more realistic in the behavior decision-making of ADS.
American dog ticks along their expanding range edge in Ontario, Canada
Authors: Nelder Mark P. , Russell Curtis B. , Johnson Steven , Li Ye , Cronin Kirby , Cawston Tania , Patel Samir N. 
Published: June 2022

AbstractThe American dog tick,Dermacentorvariabilis, is a tick of public and veterinary health importance in North America. Using passive tick surveillance data, we document distribution changes for the American dog tick in Ontario, Canada, from 2010 through 2018.Dermacentorvariabilissubmissions from the public were geocoded and aggregated—from large to small administrative geographies—by health region, public health unit (PHU) and Forward Sortation Area (FSA). PHU hot spots with high rates ofD.variabilissubmissions were (1) Brant County, Haldimand-Norfolk and Niagara Regional in the Central West region and (2) Lambton and Winsor-Essex County in the South West region. The number of establishedD.variabilispopulations with ≥ 6 submissions per year increased significantly during the study at regional (PHUs: 22 to 31) and local (FSAs: 27 to 91) scales. The range ofD.variabilisincreased similarly to the positive control (Ixodesscapularis) during the study and in contrast to the static range of the negative control (Ixodescookei). Submission hot spots were in warmer, low elevation areas with poorly drained soils, compared to the province’s low submission areas.Dermacentorvariabilisis spreading in Ontario and continued research into their vector ecology is required to assess medicoveterinary health risks.
Detecting overlapping communities in complex networks using non-cooperative games
Authors: Ferdowsi Farhad , Aghababaei Samani Keivan 
Published: June 2022

AbstractDetecting communities in complex networks is of paramount importance, and its wide range of real-life applications in various areas has caused a lot of attention to be paid to it, and many efforts have been made to have efficient and accurate algorithms for this purpose. In this paper, we proposed a non-cooperative game theoretic-based algorithm that is able to detect overlapping communities. In this algorithm, nodes are regarded as players, and communities are assumed to be groups of players with similar strategies. Our two-phase algorithm detects communities and the overlapping nodes in separate phases that, while increasing the accuracy, especially in detecting overlapping nodes, brings about higher algorithm speed. Moreover, there is no need for setting parameters regarding the size or number of communities, and the absence of any stochastic process caused this algorithm to be stable. By appropriately adjusting stop criteria, our algorithm can be categorized among those with linear time complexity, making it highly scalable for large networks. Experiments on synthetic and real-world networks demonstrate our algorithm’s good performance compared to similar algorithms in terms of detected overlapping nodes, detected communities size distribution, modularity, and normalized mutual information.
Effect of body position on the redistribution of regional lung aeration during invasive and non-invasive ventilation of COVID-19 patients
Authors: Dos Santos Rocha André , Diaper John , Balogh Adam L. , Marti Christophe , Grosgurin Olivier , Habre Walid , Peták Ferenc , Südy Roberta 
Published: June 2022

AbstractSevere COVID-19-related acute respiratory distress syndrome (C-ARDS) requires mechanical ventilation. While this intervention is often performed in the prone position to improve oxygenation, the underlying mechanisms responsible for the improvement in respiratory function during invasive ventilation and awake prone positioning in C-ARDS have not yet been elucidated. In this prospective observational trial, we evaluated the respiratory function of C-ARDS patients while in the supine and prone positions during invasive (n = 13) or non-invasive ventilation (n = 15). The primary endpoint was the positional change in lung regional aeration, assessed with electrical impedance tomography. Secondary endpoints included parameters of ventilation and oxygenation, volumetric capnography, respiratory system mechanics and intrapulmonary shunt fraction. In comparison to the supine position, the prone position significantly increased ventilation distribution in dorsal lung zones for patients under invasive ventilation (53.3 ± 18.3% vs. 43.8 ± 12.3%, percentage of dorsal lung aeration ± standard deviation in prone and supine positions, respectively; p = 0.014); whereas, regional aeration in both positions did not change during non-invasive ventilation (36.4 ± 11.4% vs. 33.7 ± 10.1%; p = 0.43). Prone positioning significantly improved the oxygenation both during invasive and non-invasive ventilation. For invasively ventilated patients reduced intrapulmonary shunt fraction, ventilation dead space and respiratory resistance were observed in the prone position. Oxygenation is improved during non-invasive and invasive ventilation with prone positioning in patients with C-ARDS. Different mechanisms may underly this benefit during these two ventilation modalities, driven by improved distribution of lung regional aeration, intrapulmonary shunt fraction and ventilation-perfusion matching. However, the differences in the severity of C-ARDS may have biased the sensitivity of electrical impedance tomography when comparing positional changes between the protocol groups.Trial registration: ClinicalTrials.gov (NCT04359407) and Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359407.
The influence of meteorological factors and terrain on air pollution concentration and migration: a geostatistical case study from Krakow, Poland
Authors: Danek Tomasz , Weglinska Elzbieta , Zareba Mateusz 
Published: June 2022

AbstractDespite the very restrictive laws, Krakow is known as the city with the highest level of air pollution in Europe. It has been proven that, due to its location, air pollutants are transported to this city from neighboring municipalities. In this study, a complex geostatistical approach for spatio-temporal analysis of particulate matter (PM) concentrations was applied. For background noise reduction, data were recorded during the COVID-19 lockdown using 100 low-cost sensors and were validated based on indications from reference stations. Standardized Geographically Weighted Regression, local Moran’s I spatial autocorrelation analysis, and Getis–Ord Gi* statistic for hot-spot detection with Kernel Density Estimation maps were used. The results indicate the relation between the topography, meteorological variables, and PM concentrations. The main factors are wind speed (even if relatively low) and terrain elevation. The study of the PM2.5/PM10 ratio allowed for a detailed analysis of spatial pollution migration, including source differentiation. This research indicates that Krakow’s unfavorable location makes it prone to accumulating pollutants from its neighborhood. The main source of air pollution in the investigated period is solid fuel heating outside the city. The study shows the importance and variability of the analyzed factors’ influence on air pollution inflow and outflow from the city.
The close interaction between hypoxia-related proteins and metastasis in pancarcinomas
Authors: López-Cortés Andrés , Prathap Lavanya , Ortiz-Prado Esteban , Kyriakidis Nikolaos C. , León Cáceres Ángela , Armendáriz-Castillo Isaac , Vera-Guapi Antonella , Yumiceba Verónica , Simbaña-Rivera Katherine , Echeverría-Garcés Gabriela , García-Cárdenas Jennyfer M. , Pérez-Villa Andy , Guevara-Ramírez Patricia , Abad-Sojos Andrea , Bautista Jhommara , Puig San Andrés Lourdes , Varela Nelson , Guerrero Santiago 
Published: June 2022

AbstractMany primary-tumor subregions exhibit low levels of molecular oxygen and restricted access to nutrients due to poor vascularization in the tissue, phenomenon known as hypoxia. Hypoxic tumors are able to regulate the expression of certain genes and signaling molecules in the microenvironment that shift it towards a more aggressive phenotype. The transcriptional landscape of the tumor favors malignant transformation of neighboring cells and their migration to distant sites. Herein, we focused on identifying key proteins that participate in the signaling crossroads between hypoxic environment and metastasis progression that remain poorly defined. To shed light on these mechanisms, we performed an integrated multi-omics analysis encompassing genomic/transcriptomic alterations of hypoxia-related genes and Buffa hypoxia scores across 17 pancarcinomas taken from the PanCancer Atlas project from The Cancer Genome Atlas consortium, protein–protein interactome network, shortest paths from hypoxia-related proteins to metastatic and angiogenic phenotypes, and drugs involved in current clinical trials to treat the metastatic disease. As results, we identified 30 hypoxia-related proteins highly involved in metastasis and angiogenesis. This set of proteins, validated with the MSK-MET Project, could represent key targets for developing therapies. The upregulation of mRNA was the most prevalent alteration in all cancer types. The highest frequencies of genomic/transcriptomic alterations and hypoxia score belonged to tumor stage 4 and positive metastatic status in all pancarcinomas. The most significantly associated signaling pathways were HIF-1, PI3K-Akt, thyroid hormone, ErbB, FoxO, mTOR, insulin, MAPK, Ras, AMPK, and VEGF. The interactome network revealed high-confidence interactions among hypoxic and metastatic proteins. The analysis of shortest paths revealed several ways to spread metastasis and angiogenesis from hypoxic proteins. Lastly, we identified 23 drugs enrolled in clinical trials focused on metastatic disease treatment. Six of them were involved in advanced-stage clinical trials: aflibercept, bevacizumab, cetuximab, erlotinib, ipatasertib, and panitumumab.
Effects of seawater sulfur starvation and enrichment on Gracilaria gracilis growth and biochemical composition
Authors: Mensi Fethi , Ben Ghedifa Aziz , Rajhi Hayfa 
Published: June 2022

AbstractThe genus Gracilaria, largest biomass producer in coastal regions, encompasses a wide range of species includingGracilaria gracilis. Nowadays, there is a spate of interest in its culture in lagoon where the water sulfate concentration is variable. A laboratory culture was carried out to determine the sulfate concentration effect on their growth as well as their biochemical composition, which were 2.5, 27 or 50 mM, referred to as SSS (sulfur starved seawater), SW (seawater) and SES (sulfur enriched seawater).We found that the sulfate content of the surrounding medium is a key parameter influencing both the alga growth and its composition. However, seawater proved to be the most suitable environment to sustain alga growth, proteins, R-phycoerythrin and agar yields, but sulfur enrichment and starvation affects them. The sulfate degree of agar and therefore its quality is related to the medium sulfate concentration. We conclude that sulfur starvation (2.5 mM) for three weeks, led to severe growth retardation, lower agar yield and quality and indicated the limit potential ofG. gracilisfor mariculture under these conditions. These results demonstrated that the success ofG. gracilisculture in the lagoon is feasible if sulfate concentration is closer to that of seawater.
Prediction of all-cause and cardiovascular mortality using ankle-brachial index and brachial-ankle pulse wave velocity in patients with type 2 diabetes
Authors: Lin Cheng-Chieh , Li Chia-Ing , Liu Chiu-Shong , Lin Chih-Hsueh , Yang Shing-Yu , Li Tsai-Chung 
Published: June 2022

AbstractAnkle-brachial index (ABI) and brachial-ankle pulse wave velocity (baPWV) are used as non-invasive indicators for detecting atherosclerosis and arterial stiffness, two well-known predictors of mortality in patients with type 2 diabetes mellitus (T2DM). ABI and baPWV have independent associations with mortality; however, their joint and interactive effects on mortality have not been assessed in patients with T2DM. This work aims to evaluate the independent, joint, and interactive associations of ABI and baPWV with all-cause and expanded cardiovascular disease (CVD) mortality in patients with T2DM. This observational study included 2160 patients with T2DM enlisted in the Diabetes Care Management Program database of China Medical University Hospital from 2001 to 2016 and then followed their death status until August 2021. Cox proportional hazard models were used to evaluate the independent, joint, and interactive effects of ABI and baPWV on the risk of all-cause and expanded CVD mortality. A total of 474 patient deaths occurred after a mean follow-up of 8.4 years, and 268 of which were attributed to cardiovascular events. Abnormal ABI (≤ 0.9) and highest baPWV quartile were independently associated with increased risks of all-cause [ABI: hazard ratio (HR) 1.67, 95% confidence interval (CI) 1.30–2.11; baPWV: 1.63, 1.16–2.27] and expanded CVD mortality (ABI: 2.21, 1.62–3.02; baPWV: 1.75, 1.09–2.83). The combination of abnormal ABI (≤ 0.9) and highest baPWV quartile was associated with a significantly higher risk of all-cause (4.51, 2.50–8.11) and expanded CVD mortality (9.74, 4.21–22.51) compared with that of the combination of normal ABI and lowest baPWV quartile. Significant interactions were observed between ABI and baPWV in relation to all-cause and expand CVD mortality (both p for interaction < 0.001). Through their independent, joint, and interactive effects, ABI and baPWV are significant parameters that can improve the prediction of all-cause and expanded CVD mortality in patients with T2DM and help identify high-risk patients who may benefit from diabetes care.