bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment
Authors: Walczak Michal , Brady Ryan A. , Mancini Leonardo , Contini Claudia , Rubio-Sánchez Roger , Kaufhold William T. , Cicuta Pietro , Di Michele Lorenzo 
Published: August 2021

AbstractBiology has evolved a variety of agents capable of permeabilizing and disrupting lipid membranes, from amyloid aggregates, to antimicrobial peptides, to venom compounds. While often associated with disease or toxicity, these agents are also central to many biosensing and therapeutic technologies. Here, we introduce a class of synthetic, DNA-based particles capable of disrupting lipid membranes. The particles have finely programmable size, and self-assemble from all-DNA and cholesterol-DNA nanostructures, the latter forming a membrane-adhesive core and the former a protective hydrophilic corona. We show that the corona can be selectively displaced with a molecular cue, exposing the ‘sticky’ core. Unprotected particles adhere to synthetic lipid vesicles, which in turn enhances membrane permeability and leads to vesicle collapse. Furthermore, particle-particle coalescence leads to the formation of gel-like DNA aggregates that envelop surviving vesicles. This response is reminiscent of pathogen immobilisation through immune cells secretion of DNA networks, as we demonstrate by trappingE. colibacteria.
Dpb4 promotes resection of DNA double-strand breaks and checkpoint activation by acting in two different protein complexes
Authors: Casari Erika , Gobbini Elisa , Gnugnoli Marco , Mangiagalli Marco , Clerici Michela , Longhese Maria Pia 
Published: August 2021

AbstractBudding yeast Dpb4 (POLE3/CHRAC17 in mammals) is a highly conserved histone fold protein that is shared by two protein complexes: the chromatin remodeler ISW2/hCHRAC and the DNA polymerase ε (Pol ε) holoenzyme. In Saccharomyces cerevisiae, Dpb4 forms histone-like dimers with Dls1 in the ISW2 complex and with Dpb3 in the Pol ε complex. Here, we show that Dpb4 plays two functions in sensing and processing DNA double-strand breaks (DSBs). Dpb4 promotes histone removal and DSB resection by interacting with Dls1 to facilitate the association of the Isw2 ATPase to DSBs. Furthermore, it promotes checkpoint activation by interacting with Dpb3 to facilitate the association of the checkpoint protein Rad9 to DSBs. Persistence of both Isw2 and Rad9 at DSBs is enhanced by the A62S mutation that is located in the Dpb4 histone fold domain and increases Dpb4 association at DSBs. Thus, Dpb4 exerts two distinct functions at DSBs depending on its interactors.
An omics-based framework for assessing the health risk of antimicrobial resistance genes
Authors: Zhang An-Ni , Gaston Jeffry M. , Dai Chengzhen L. , Zhao Shijie , Poyet Mathilde , Groussin Mathieu , Yin Xiaole , Li Li-Guan , van Loosdrecht Mark C. M. , Topp Edward , Gillings Michael R. , Hanage William P. , Tiedje James M. , Moniz Katya , Alm Eric J. , Zhang Tong 
Published: August 2021

AbstractAntibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that are high-risk. Here, we developed an ‘omics-based’ framework to evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our framework classifies human-associated, mobile ARGs (3.6% of all ARGs) as the highest risk, which we further differentiate as ‘current threats’ (Rank I; 3%) - already present among pathogens - and ‘future threats’ (Rank II; 0.6%) - novel resistance emerging from non-pathogens. Our framework identified 73 ‘current threat’ ARG families. Of these, 35 were among the 37 high-risk ARGs proposed by the World Health Organization and other literature; the remaining 38 were significantly enriched in hospital plasmids. By evaluating all pathogen genomes released since framework construction, we confirmed that ARGs that recently transferred into pathogens were significantly enriched in Rank II (‘future threats’). Lastly, we applied the framework to gut microbiome genomes from fecal microbiota transplantation donors. We found that although ARGs were widespread (73% of genomes), only 8.9% of genomes contained high-risk ARGs. Our framework provides an easy-to-implement approach to identify current and future antimicrobial resistance threats, with potential clinical applications including reducing risk of microbiome-based interventions.
CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin
Authors: Zhao Yanyan , Schmid Michael F. , Frydman Judith , Chiu Wah 
Published: August 2021

AbstractChaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.
Reconfigurable artificial microswimmers with internal feedback
Authors: Alvarez L. , Fernandez-Rodriguez M. A. , Alegria A. , Arrese-Igor S. , Zhao K. , Kröger M. , Isa Lucio 
Published: August 2021

AbstractSelf-propelling microparticles are often proposed as synthetic models for biological microswimmers, yet they lack the internally regulated adaptation of their biological counterparts. Conversely, adaptation can be encoded in larger-scale soft-robotic devices but remains elusive to transfer to the colloidal scale. Here, we create responsive microswimmers, powered by electro-hydrodynamic flows, which can adapt their motility via internal reconfiguration. Using sequential capillary assembly, we fabricate deterministic colloidal clusters comprising soft thermo-responsive microgels and light-absorbing particles. Light absorption induces preferential local heating and triggers the volume phase transition of the microgels, leading to an adaptation of the clusters’ motility, which is orthogonal to their propulsion scheme. We rationalize this response via the coupling between self-propulsion and variations of particle shape and dielectric properties upon heating. Harnessing such coupling allows for strategies to achieve local dynamical control with simple illumination patterns, revealing exciting opportunities for developing tactic active materials.
The inherent community structure of hyperbolic networks
Authors: Kovács Bianka , Palla Gergely 
Published: August 2021

AbstractA remarkable approach for grasping the relevant statistical features of real networks with the help of random graphs is offered by hyperbolic models, centred around the idea of placing nodes in a low-dimensional hyperbolic space, and connecting node pairs with a probability depending on the hyperbolic distance. It is widely appreciated that these models can generate random graphs that are small-world, highly clustered and scale-free at the same time; thus, reproducing the most fundamental common features of real networks. In the present work, we focus on a less well-known property of the popularity-similarity optimisation model and the $${\mathbb {S}}^1/{\mathbb {H}}^2$$

S

1

/

H

2

model from this model family, namely that the networks generated by these approaches also contain communities for a wide range of the parameters, which was certainly not an intention at the design of the models. We extracted the communities from the studied networks using well-established community finding methods such as Louvain, Infomap and label propagation. The observed high modularity values indicate that the community structure can become very pronounced under certain conditions. In addition, the modules found by the different algorithms show good consistency, implying that these are indeed relevant and apparent structural units. Since the appearance of communities is rather common in networks representing real systems as well, this feature of hyperbolic models makes them even more suitable for describing real networks than thought before.
Interpretable deep recommender system model for prediction of kinase inhibitor efficacy across cancer cell lines
Authors: Koras Krzysztof , Kizling Ewa , Juraeva Dilafruz , Staub Eike , Szczurek Ewa 
Published: August 2021

AbstractComputational models for drug sensitivity prediction have the potential to significantly improve personalized cancer medicine. Drug sensitivity assays, combined with profiling of cancer cell lines and drugs become increasingly available for training such models. Multiple methods were proposed for predicting drug sensitivity from cancer cell line features, some in a multi-task fashion. So far, no such model leveraged drug inhibition profiles. Importantly, multi-task models require a tailored approach to model interpretability. In this work, we develop DEERS, a neural network recommender system for kinase inhibitor sensitivity prediction. The model utilizes molecular features of the cancer cell lines and kinase inhibition profiles of the drugs. DEERS incorporates two autoencoders to project cell line and drug features into 10-dimensional hidden representations and a feed-forward neural network to combine them into response prediction. We propose a novel interpretability approach, which in addition to the set of modeled features considers also the genes and processes outside of this set. Our approach outperforms simpler matrix factorization models, achieving R $$=$$
=
0.82 correlation between true and predicted response for the unseen cell lines. The interpretability analysis identifies 67 biological processes that drive the cell line sensitivity to particular compounds. Detailed case studies are shown for PHA-793887, XMD14-99 and Dabrafenib.
Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea
Authors: Lee Jeong Eun , Lee Soon Ok , Lee Shinwon , Park Sohee , Kim Hyung-Hoi , Shin Kyung-Hwa , Kang Jin Suk , Lee Sun Hee 
Published: August 2021

AbstractRecent data on non-B subtypes’ epidemiology among patients infected with human immunodeficiency virus-1 (HIV-1) in Korea are lacking. We aimed to assess the changing trends in the epidemiology of non-B subtypes of HIV-1 in Korea using phyloepidemiological analyses. We analyzed the demographic records and sequencing data obtained from genotypic drug resistance tests between 2005 and 2019 from 517 patients infected with HIV attending a tertiary care hospital in Busan, Korea. Subtyping and phylogenetic analyses with reference sequences were performed. Additionally, transmission clusters were identified via maximum-likelihood trees. Non-B subtypes accounted for 21.3% of the 517 sequences. CRF01_AE (52.7%) was the most common non-B subtype, followed by CRF02_AG (16.4%), A1 (11.8%), and C (5.5%). The prevalence of non-B subtypes decreased from 36.4 to 13.4% by 2009, while it increased to 27.4% between 2015 and 2019. Among patients with non-B subtypes, the proportion of overseas sailors decreased from 66.7 to 7.5%; contrarily, the proportion of men-who-have-sex-with-men (MSM) increased from 0 to 46.9% over the study period. We identified 8 transmission clusters involving non-B subtypes, with sizes ranging from 2 to 4 patients, including 3 clusters containing MSM. Our results highlight the changes in the epidemiological trends of non-B subtypes of HIV-1 in Korea.
Identification of genes encoding a novel ABC transporter in Lactobacillus delbrueckii for inulin polymers uptake
Authors: Tsujikawa Yuji , Ishikawa Shu , Sakane Iwao , Yoshida Ken-ichi , Osawa Ro 
Published: August 2021

AbstractLactobacillus delbrueckii JCM 1002T grows on highly polymerized inulin-type fructans as its sole carbon source. When it was grown on inulin, a > 10 kb long gene cluster inuABCDEF (Ldb1381-1386) encoding a plausible ABC transporter was suggested to be induced, since a transcriptome analysis revealed that the fourth gene inuD (Ldb1384) was up-regulated most prominently. Although Bacillus subtilis 168 is originally unable to utilize inulin, it became to grow on inulin upon heterologous expression of inuABCDEF. When freshly cultured cells of the recombinant B. subtilis were then densely suspended in buffer containing inulin polymers and incubated, inulin gradually disappeared from the buffer and accumulated in the cells without being degraded, whereas levan-type fructans did not disappear. The results imply that inuABCDEF might encode a novel ABC transporter in L. delbrueckii to “monopolize” inulin polymers selectively, thereby, providing a possible advantage in competition with other concomitant inulin-utilizing bacteria.
Design and validation of fiber optic localized surface plasmon resonance sensor for thyroglobulin immunoassay with high sensitivity and rapid detection
Authors: Kim Hyeong-Min , Jeong Dae Hong , Lee Ho-Young , Park Jae-Hyoung , Lee Seung-Ki 
Published: August 2021

AbstractA simple optical fiber sensor based on localized surface plasmon resonance was constructed for direct and rapid measurement of thyroglobulin (Tg). Specific tests for Tg in patients that have undergone thyroidectomy are limited because of insufficient sensitivity, complicated procedures, and in some cases, a long time to yield a result. A sensitive, fast, and simple method is necessary to relieve the psychological and physical burden of the patient. Various concentrations of Tg were measured in a microfluidic channel using an optical fiber sensor with gold nanoparticles. The sensor chip has a detection limit of 93.11 fg/mL with no specificity for other antigens. The potential applicability of the Tg sensing system was evaluated using arbitrary samples containing specific concentrations of Tg. Finally, the sensor can be employed to detect Tg in the patient’s serum, with a good correlation when compared with the commercial kit.
Design of industrial wastewater demulsifier by HLD-NAC model
Authors: Ghasemi Hassan , Eslami Fatemeh 
Published: August 2021

AbstractThe chemical method is one of the treatment techniques for the separation of oil–water emulsion systems. The selection of appropriate demulsifiers for each emulsion system is the most challenging issue. Hydrophilic-lipophilic-deviation (HLD) is a powerful semi-empirical model, providing predictive tools to formulate the emulsion and microemulsion systems. This work aims to apply HLD to obtain an optimal condition for demulsification of oil-in-water emulsion system—real industrial wastewater—with different water in oil ratios (WOR). Therefore, the oil parameter of the contaminant oil and surfactant parameter for three types of commercial surfactants were calculated by performing salinity scans. Furthermore, the net-average-curvature (NAC) framework coupled with HLD was used to predict the phase behavior of the synthetic microemulsion systems, incorporating solubilization properties, the shape of droplets, and quality of optimum formulation. The geometrical sizes of non-spherical droplets (Ld, Rd)—as an indicator of how droplet sizes are changing with HLD—were consistent with the separation results. Correlating Ld/Rd at phase transition points with bottle test results validates the hypothesis that NAC-predicted geometries and demulsification behavior are interconnected. Finally, the effect of sec-butanol was examined on both synthetic and real systems, providing reliable insights in terms of the effect of alcohol for WOR ≠ 1.
On the interpretation of annual oscillations in 32Si and 36Cl decay rate measurements
Authors: Pommé S. , Pelczar K. , Kossert K. , Kajan I. 
Published: August 2021

AbstractThe 32Si decay rate measurement data of Alburger et al. obtained in 1982–1986 at Brookhaven National Laboratory have been presented repeatedly as evidence for solar neutrino-induced beta decay. The count rates show an annual sinusoidal oscillation of about 0.1% amplitude and maximum at February–March. Several authors have claimed that the annual oscillations could not be explained by environmental influences on the set-up, and they questioned the invariability of the decay constant. They hypothesised a correlation with changes in the solar neutrino flux due to annual variations in the Earth-Sun distance, in spite of an obvious mismatch in amplitude and phase. In this work, environmental conditions at the time of the experiment are presented. The 32Si decay rate measurements appear to be inversely correlated with the dew point in a nearby weather station. Susceptibility of the detection set-up to local temperature and humidity conditions is a likely cause of the observed instabilities in the measured decay rates. Similar conclusions apply to 36Cl decay rates measured at Ohio State University in 2005–2012.
Securing genetic integrity in freshwater pearl mussel propagation and captive breeding
Authors: Geist Juergen , Bayerl Helmut , Stoeckle Bernhard C. , Kuehn Ralph 
Published: August 2021

AbstractSecuring genetic integrity is of key importance in conservation-oriented captive breeding programs releasing juveniles into the wild. This is particularly true for species such as the endangered freshwater pearl mussel (Margaritifera margaritifera) for which a number of captive breeding facilities has been established in Europe. The core objective of this study was to compare the genetic constitution of 29 cohorts of captive-bred freshwater pearl mussels from five different breeding facilities in Austria, France, Luxembourg and Germany, with their original 14 source populations from nine major European drainages, based on microsatellite markers. Captive-bred mussels represented 11 different genetic clusters, suggesting an important contribution of the breeding stations to securing the genetic diversity of the species. In almost all cases, the cultured offspring closely resembled the genetic constitution of the source mussels as revealed from the STRUCTURE analysis and the generally high assignment of offspring to the original source populations. The majority of captive-bred cohorts had an increased inbreeding coefficient and decreased genetic variability compared to their source populations as measured by AR and HO. Highest numbers of deformed juveniles coincided with very low levels of HO < 0.05. Since erosion of genetic diversity in captive breeding was mostly evident in individual year-cohorts, long-term breeding over multiple years can minimize such effects. The systematic selection of priority populations for conservation, effective breeding strategies avoiding effects of in- and outbreeding by genetically informed selection of parent individuals, and a network of collaboration among the different breeding facilities would be very useful to increase resilience and effectiveness.
Impact of peripheral muscle strength on prognosis after extubation and functional outcomes in critically ill patients: a feasibility study
Authors: Wang Tsung-Hsien , Wu Chin-Pyng , Wang Li-Ying 
Published: August 2021

AbstractThe influence of peripheral muscle strength on prognosis after extubation and subsequent functional outcomes is not evident. The objectives of this study were to determine (1) whether peripheral muscle strength can be used as a predictor for patients’ prognoses after extubation, and (2) whether the peripheral muscle strength before extubation is correlated with patients’ subsequent ambulation ability and in-hospital mortality. This study was a prospective observational cohort study. A hand-held dynamometer was used for evaluated the muscle strength of the biceps and quadriceps right before extubation. Besides, after the patients had been transferred from the ICU to the general ward, a 2-minute walk test was performed. A total of 52 patients were enrolled in this study, and the rate of extubation failure was 15%. The muscle strength of the quadriceps was significantly correlated with the prognosis after extubation, 48% of the patients were able to ambulate after being transferred to the general ward. The overall mortality rate was 11%, and there was a significant correlation between the biceps muscle strength and in-hospital mortality. Peripheral muscle strength may serve as an important predictor of a patients’ prognoses after extubation. Poor peripheral muscle strength is indicative of not only a higher risk of re-intubation but also higher in-hospital mortality and poorer functional outcomes.Trial registration: ISRCTN16370134. Registered 30 May 2019, prospectively registered.https://www.isrctn.com/ISRCTN16370134.
Effect of Chaihu-jia-Longgu-Muli decoction on withdrawal symptoms in rats with methamphetamine-induced conditioned place preference
Authors: Li Zifa , Qi Yuchen , Liu Kun , Cao Yiming , Zhang Hao , Song Chunhong , Deng Hualiang 
Published: August 2021

Abstract
Traditional Chinese medicine detoxification prescription Chaihu-jia-Longgu-Muli decoction (CLMD) relieves depressive symptoms in patients withdrawing from methamphetamine. In the present study, we assessed the effects of CLMD on methamphetamine withdrawal in rats. A methamphetamine-intoxicated rat model was established. Rats were randomly divided into the control, model, high-dosage, medium-dosage, and low-dosage groups, receiving high, medium, and low doses of CLMD, respectively. Weekly body weight measurements revealed that rats treated with methamphetamine had the lowest body weight. The conditioned place preference (CPP) experiment revealed that methamphetamine-intoxicated rats stayed significantly longer in the drug-paired chamber than the control rats. However, after administering high-dosage CLMD, the amount of time the rats spent in the drug-paired chamber was significantly less than that of the model rats. Our open-field test revealed that the model group had lower crossing and rearing scores than the control group. Additionally, rats that received CLMD treatment exhibited higher crossing and rearing scores than the model rats. Striatal dopamine (DA), 5-hydroxytryptamine (5-HT), and endorphins (β-EP) and serum interleukin (IL)-1α and IL-2 concentrations were estimated. Rats in the model group had lower striatal DA, 5-HT, and β-EP and higher serum IL-1α and IL-2 concentrations than those in the control group. High-dosage CLMD administration significantly changed the concentrations of these molecules, such that they approached normal concentrations. In general, CLMD could prevent the development of methamphetamine-induced withdrawal symptoms in rats by increasing the DA, 5-HT, and β-EP and lowering the IL-1α and IL-2 concentrations.