bluuebunny/crossref_metadata_2025 huggingface dataset:
The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s
Authors: Tunbak Hale , Enriquez-Gasca Rocio , Tie Christopher H. C. , Gould Poppy A. , Mlcochova Petra , Gupta Ravindra K. , Fernandes Liane , Holt James , van der Veen Annemarthe G. , Giampazolias Evangelos , Burns Kathleen H. , Maillard Pierre V. , Rowe Helen M.
Published: November 2020

The Human Silencing Hub (HUSH) complex is necessary for epigenetic repression of LINE-1 elements. We show that HUSH-depletion in human cell lines and primary fibroblasts leads to induction of interferon-stimulated genes (ISGs) through JAK/STAT signaling. This effect is mainly attributed to MDA5 and RIG-I sensing of double-stranded RNAs (dsRNAs). This coincides with upregulation of primate-conserved LINE-1s, as well as increased expression of full-length hominid-specific LINE-1s that produce bidirectional RNAs, which may form dsRNA. Notably, LTRs nearby ISGs are derepressed likely rendering these genes more responsive to interferon. LINE-1 shRNAs can abrogate the HUSH-dependent response, while overexpression of an engineered LINE-1 construct activates interferon signaling. Finally, we show that the HUSH component, MPP8 is frequently downregulated in diverse cancers and that its depletion leads to DNA damage. These results suggest that LINE-1s may drive physiological or autoinflammatory responses through dsRNA sensing and gene-regulatory roles and are controlled by the HUSH complex.
Bulk valley transport and Berry curvature spreading at the edge of flat bands
Authors: Sinha Subhajit , Adak Pratap Chandra , Surya Kanthi R. S. , Chittari Bheema Lingam , Sangani L. D. Varma , Watanabe Kenji , Taniguchi Takashi , Jung Jeil , Deshmukh Mandar M.
Published: November 2020

2D materials based superlattices have emerged as a promising platform to modulate band structure and its symmetries. In particular, moiré periodicity in twisted graphene systems produces flat Chern bands. The recent observation of anomalous Hall effect (AHE) and orbital magnetism in twisted bilayer graphene has been associated with spontaneous symmetry breaking of such Chern bands. However, the valley Hall state as a precursor of AHE state, when time-reversal symmetry is still protected, has not been observed. Our work probes this precursor state using the valley Hall effect. We show that broken inversion symmetry in twisted double bilayer graphene (TDBG) facilitates the generation of bulk valley current by reporting experimental evidence of nonlocal transport in a nearly flat band system. Despite the spread of Berry curvature hotspots and reduced quasiparticle velocities of the carriers in these flat bands, we observe large nonlocal voltage several micrometers away from the charge current path — this persists when the Fermi energy lies inside a gap with large Berry curvature. The high sensitivity of the nonlocal voltage to gate tunable carrier density and gap modulating perpendicular electric field makes TDBG an attractive platform for valley-twistronics based on flat bands.
cAMP-dependent regulation of HCN4 controls the tonic entrainment process in sinoatrial node pacemaker cells
Authors: Fenske Stefanie , Hennis Konstantin , Rötzer René D. , Brox Verena F. , Becirovic Elvir , Scharr Andreas , Gruner Christian , Ziegler Tilman , Mehlfeld Verena , Brennan Jaclyn , Efimov Igor R. , Pauža Audrys G. , Moser Markus , Wotjak Carsten T. , Kupatt Christian , Gönner Rasmus , Zhang Rai , Zhang Henggui , Zong Xiangang , Biel Martin , Wahl-Schott Christian
Published: November 2020

It is highly debated how cyclic adenosine monophosphate-dependent regulation (CDR) of the major pacemaker channel HCN4 in the sinoatrial node (SAN) is involved in heart rate regulation by the autonomic nervous system. We addressed this question using a knockin mouse line expressing cyclic adenosine monophosphate-insensitive HCN4 channels. This mouse line displayed a complex cardiac phenotype characterized by sinus dysrhythmia, severe sinus bradycardia, sinus pauses and chronotropic incompetence. Furthermore, the absence of CDR leads to inappropriately enhanced heart rate responses of the SAN to vagal nerve activity in vivo. The mechanism underlying these symptoms can be explained by the presence of nonfiring pacemaker cells. We provide evidence that a tonic and mutual interaction process (tonic entrainment) between firing and nonfiring cells slows down the overall rhythm of the SAN. Most importantly, we show that the proportion of firing cells can be increased by CDR of HCN4 to efficiently oppose enhanced responses to vagal activity. In conclusion, we provide evidence for a novel role of CDR of HCN4 for the central pacemaker process in the sinoatrial node.
ArfB can displace mRNA to rescue stalled ribosomes
Authors: Carbone Christine E. , Demo Gabriel , Madireddy Rohini , Svidritskiy Egor , Korostelev Andrei A.
Published: November 2020

Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
Behavior control of membrane-less protein liquid condensates with metal ion-induced phase separation
Authors: Hong Kibeom , Song Daesun , Jung Yongwon
Published: November 2020

Phase separation of specific biomolecules into liquid droplet-like condensates is a key mechanism to form membrane-less organelles, which spatio-temporally organize diverse biochemical processes in cells. To investigate the working principles of these biomolecular condensates as dynamic reaction centers, precise control of diverse condensate properties is essential. Here, we design a strategy for metal ion-induced clustering of minimal protein modules to produce liquid protein condensates, the properties of which can be widely varied by simple manipulation of the protein clustering systems. The droplet forming-minimal module contains only a single receptor protein and a binding ligand peptide with a hexahistidine tag for divalent metal ion-mediated clustering. A wide range of protein condensate properties such as droplet forming tendency, droplet morphology, inside protein diffusivity, protein recruitment, and droplet density can be varied by adjusting the nature of receptor/ligand pairs or used metal ions, metal/protein ratios, incubation time, binding motif variation on recruited proteins, and even spacing between receptor/ligand pairs and the hexahistidine tag. We also demonstrate metal-ion-induced protein phase separation in cells. The present phase separation strategy provides highly versatile protein condensates, which will greatly facilitate investigation of molecular and structural codes of droplet-forming proteins and the monitoring of biomolecular behaviors inside diverse protein condensates.
Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients
Authors: Fernando Tharu M. , Piskol Robert , Bainer Russell , Sokol Ethan S. , Trabucco Sally E. , Zhang Qing , Trinh Huong , Maund Sophia , Kschonsak Marc , Chaudhuri Subhra , Modrusan Zora , Januario Thomas , Yauch Robert L.
Published: November 2020

Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.
Genealogy of the neurodegenerative diseases based on a meta-analysis of age-stratified incidence data
Authors: Gerovska Daniela , Irizar Haritz , Otaegi David , Ferrer Isidre , López de Munain Adolfo , Araúzo-Bravo Marcos J.
Published: November 2020

While the central common feature of the neurodegenerative diseases (NDs) is the accumulation of misfolded proteins, they share other pathogenic mechanisms. However, we miss an explanation for the onset of the NDs. The mechanisms through which genetic mutations, present from conception are expressed only after several decades of life are unknown. We aim to find clues on the complexity of the disease onset trigger of the different NDs expressed in the number of steps of factors related to a disease. We collected brain autopsies on diseased patients with NDs, and found a dynamic increase of the ND multimorbidity with the advance of age. Together with the observation that the NDs accumulate multiple misfolded proteins, and the same misfolded proteins are involved in more than one ND, motivated us to propose a model for a genealogical tree of the NDs. To collect the dynamic data needed to build the tree, we used a Big-data approach that searched automatically epidemiological datasets for age-stratified incidence of NDs. Based on meta-analysis of over 400 datasets, we developed an algorithm that checks whether a ND follows a multistep model, finds the number of steps necessary for the onset of each ND, finds the number of common steps with other NDs and the number of specific steps of each ND, and builds with these findings a parsimony tree of the genealogy of the NDs. The tree discloses three types of NDs: the stem NDs with less than 3 steps; the trunk NDs with 5 to 6 steps; and the crown NDs with more than 7 steps. The tree provides a comprehensive understanding of the relationship across the different NDs, as well as a mathematical framework for dynamic adjustment of the genealogical tree of the NDs with the appearance of new epidemiological studies and the addition of new NDs to the model, thus setting the basis for the search for the identity and order of these steps. Understanding the complexity, or number of steps, of factors related to disease onset trigger is important prior deciding to study single factors for a multiple steps disease.
Metabolic comparison of polycystic ovarian syndrome and control women in Middle Eastern and UK Caucasian populations
Authors: Butler Alexandra E. , Abouseif Ahmed , Dargham Soha R. , Sathyapalan Thozhukat , Atkin Stephen L.
Published: November 2020

To determine if metabolic characteristics differed in women with and without polycystic ovary syndrome (PCOS) between a Caucasian and Middle East population. Comparative cross-sectional analysis. Demographic and metabolic data from Middle Eastern women from Qatar Biobank (97 with PCOS, 622 controls) were compared to a Caucasian PCOS biobank in Hull UK (108 with PCOS, 69 controls). In both populations, PCOS women showed a worse cardiovascular risk profile of increased systolic and diastolic blood pressure, increased C-reactive protein (CRP), reduced HDL, insulin resistance as well as increased androgens compared to their respective controls without PCOS. UK women without PCOS had higher systolic and diastolic blood pressures, and increased testosterone results (p < 0.01) compared to Middle Eastern women without PCOS who had higher inflammatory markers (WBC and CRP), HDL and insulin resistance (p < 0.001). UK PCOS women had a higher body mass index, systolic and diastolic blood pressures, triglycerides (p < 0.01), whilst Middle Eastern PCOS women showed increased testosterone, free androgen index, HDL and CRP (P < 0.01). There was no difference in insulin or insulin resistance between the two PCOS cohorts. This study highlights ethnic population differences because, whilst cardiovascular risk indices were increased for both PCOS cohorts, this may be for different reasons: BMI, waist and hip measurements, systolic and diastolic blood pressure, and triglycerides were higher in the UK cohort whilst testosterone, HDL and CRP were higher in the Middle East population. Insulin resistance did not differ between the two PCOS populations despite differences in BMI.
Assessment of body composition in obese patients undergoing one anastomosis gastric bypass: cross-sectional study
Authors: Jimenez Jose-Maria , Ruiz-Tovar Jaime , López María , Marc-Hernandez Artur , Carbajo Miguel-Angel , Cao Maria-Jose , Garcia Sara , Castro Maria-Jose
Published: November 2020

Bariatric surgery is the most effective long-term treatment to obesity, and it is necessary to assess changes in body composition and to be able to establish better follow-up of patients. Cross-sectional, observational study in patients undergoing One Anastomosis Gastric Bypass (OAGB) bariatric surgery. We analysed changes in weight and body composition during the first postoperative year. 405 patients (68.9% women. 31.1% men), mean age 44 years, mean weight 110.02 kg, Body Mass Index (BMI) 39.76 kg/m2, height 1.66 m. The variables analyzed were substantially decreased compared to the preoperative values one year after surgery in every case: weight (110.02 ± 22.03 kg vs. 69.36 ± 13.60 kg), BMI (39.76 ± 6.65 vs. 24.52 ± 3. 76), fat free mass (61.12 ± 12.43 kg vs. 53.61 ± 11.61 kg), fat mass (50.44 ± 14.36 kg vs. 15.74 ± 6.74 kg), bone mass (58.06 ± 11.85 kg vs. 50.92 ± 11.06 kg) and water (45.08 ± 9.99 kg vs. 37.39 ± 9.23 kg), P < 0.001. The results show noticeable improvements in weight reduction and changes in body composition, and will contribute to develop a thorough understanding of both of them, contributing also to perform a better patients’ follow-up.
Deep learning method for comet segmentation and comet assay image analysis
Authors: Hong Yiyu , Han Hyo-Jeong , Lee Hannah , Lee Donghwan , Ko Junsu , Hong Zhen-yu , Lee Ji-Young , Seok Ju-Hyung , Lim Hee Seon , Son Woo-Chan , Sohn Insuk
Published: November 2020

Comet assay is a widely used method, especially in the field of genotoxicity, to quantify and measure DNA damage visually at the level of individual cells with high sensitivity and efficiency. Generally, computer programs are used to analyze comet assay output images following two main steps. First, each comet region must be located and segmented, and next, it is scored using common metrics (e.g., tail length and tail moment). Currently, most studies on comet assay image analysis have adopted hand-crafted features rather than the recent and effective deep learning (DL) methods. In this paper, however, we propose a DL-based baseline method, called DeepComet, for comet segmentation. Furthermore, we created a trainable and testable comet assay image dataset that contains 1037 comet assay images with 8271 manually annotated comet objects. From the comet segmentation test results with the proposed dataset, the DeepComet achieves high average precision (AP), which is an essential metric in image segmentation and detection tasks. A comparative analysis was performed between the DeepComet and the state-of-the-arts automatic comet segmentation programs on the dataset. Besides, we found that the DeepComet records high correlations with a commercial comet analysis tool, which suggests that the DeepComet is suitable for practical application.
Assessment of hemodynamic responses to exercise in aortic coarctation using MRI-ergometry in combination with computational fluid dynamics
Authors: Schubert Charlotte , Brüning Jan , Goubergrits Leonid , Hennemuth Anja , Berger Felix , Kühne Titus , Kelm Marcus
Published: November 2020

In patients with aortic coarctation it would be desirable to assess pressure gradients as well as information about blood flow profiles at rest and during exercise. We aimed to assess the hemodynamic responses to physical exercise by combining MRI-ergometry with computational fluid dynamics (CFD). MRI was performed on 20 patients with aortic coarctation (13 men, 7 women, mean age 21.5 ± 13.7 years) at rest and during ergometry. Peak systolic pressure gradients, wall shear stress (WSS), secondary flow degree (SFD) and normalized flow displacement (NFD) were calculated using CFD. Stroke volume was determined based on MRI. On average, the pressure gradient was 18.0 ± 16.6 mmHg at rest and increased to 28.5 ± 22.6 mmHg (p < 0.001) during exercise. A significant increase in cardiac index was observed (p < 0.001), which was mainly driven by an increase in heart rate (p < 0.001). WSS significantly increased during exercise (p = 0.006), whereas SFD and NFD remained unchanged. The combination of MRI-ergometry with CFD allows assessing pressure gradients as well as flow profiles during physical exercise. This concept has the potential to serve as an alternative to cardiac catheterization with pharmacological stress testing and provides hemodynamic information valuable for studying the pathophysiology of aortic coarctation.
Positron annihilation spectroscopy study of radiation-induced defects in W and Fe irradiated with neutrons with different spectra
Authors: Ogorodnikova O. V. , Majerle M. , Čížek J. , Simakov S. , Gann V. V. , Hruška P. , Kameník J. , Pospíšil J. , Štefánik M. , Vinš M.
Published: November 2020

The paper presents new knowledge on primary defect formation in tungsten (W) and iron (Fe) irradiated by fission and high-energy neutrons at near-room temperature. Using a well-established method of positron-annihilation lifetime-spectroscopy (PALS), it was found that irradiation of W in the fission reactor and by high-energy neutrons from the p(35 MeV)-Be generator leads to the formation of small radiation-induced vacancy clusters with comparable mean size. In the case of Fe, smaller mean size of primary radiation-induced vacancy clusters was measured after irradiation with fission neutrons compared to irradiation with high-energy neutrons from the p(35 MeV)-Be generator. It was found that one of the reasons of the formation of the larger size of the defects with lower density in Fe is lower flux in the case of irradiation with high-energy neutrons from the p(35 MeV)-Be source. The second reason is enhanced defect agglomeration and recombination within the energetic displacement cascade at high energy primary knock-on-atoms (PKAs). This is consistent with the concept of the athermal recombination corrected (arc-dpa) model, although the measured dpa cross-section of both fission neutrons and wide-spectrum high-energy neutrons in W is between the conventional Norgett–Robinson–Torrens (NRT-dpa) and arc-dpa predictions. This means that the physics of the primary radiation effects in materials is still not fully known and requires further study through a combination of modeling and experimental efforts. The present data serve as a basis for the development of an improved concept of the displacement process.
Desacetyl-α-MSH and α-MSH have sex specific interactions with diet to influence mouse gut morphology, metabolites and microbiota
Authors: Sun Bo , Vatanen Tommi , Jayasinghe Thilini N. , McKenzie Elizabeth , Murphy Rinki , O’Sullivan Justin M.
Published: November 2020

The melanocortin peptides have an important role in regulating body weight and appetite. Mice that lack the desacetyl-α-MSH and α-MSH peptides (Pomctm1/tm1) develop obesity. This effect is exacerbated by a high fat diet (HFD). However, development of obesity in femalePomctm1/tm1mice during chronic HFD conditions is not fully accounted for by the increased energy intake. We hypothesized that the protection against chronic HFD-induced obesity imparted by MSH peptides in females is mediated by sex-specific alterations in the gut structure and gut microbiota. We determined that female WT mice had reduced jejunum villus length and increased crypt depth in response to chronic HFD. WT males andPomctm1/tm1mice lacked this adaptation to a chronic HFD. BothPomctm1/tm1genotype and chronic HFD were significantly associated with gut microbiota composition. Sex-specific associations betweenPomctm1/tm1genotype and gut microbiota were observed in the presence of a chronic HFD.Pomctm1/tm1females had significantly reduced fecal acetate and propionate concentrations when compared to WT females. We conclude that MSH peptides influence jejunum villus length, crypt depth and the structure of the gut microbiota. These effects favor reduced nutrient absorption and occur in addition to the recognized roles of desacetyl-α-MSH and α-MSH peptides in appetite control.
Integrating large mammal behaviour and traffic flow to determine traversability of roads with heterogeneous traffic on a Central Indian Highway
Authors: Saxena Akanksha , Chatterjee Nilanjan , Rajvanshi Asha , Habib Bilal
Published: November 2020

Roads impact wildlife in multiple ways, most conspicuous amongst which are animal-vehicle collisions (AVCs). Mitigation measures to reduce AVCs at the local scale are often centred on species-specific crossing zones and collision hotspots. However, at the road network scale, consideration of interactions among road, species and traffic characteristics influencing AVC occurrence is required to design effective mitigation strategies. We modelled traversability—the probability of an animal successfully crossing a road- across an Indian highway for six large mammal species under different scenarios of road and traffic characteristics. Among the study species, group-living and slow-moving animals had higher AVC probabilities that increased significantly with increasing traffic volume and proportions of heavy vehicles in the traffic flow. The risk of AVC was higher for species that were active near roadside habitat during peak traffic hours. Our approach could help identify roads that pose potential mortality risks to animals using empirical data on animal and traffic characteristics. Results suggest that regulating traffic volume and heterogeneity on existing road stretches could potentially reduce animal mortality and barrier effect. Mitigation on roads expected to carry heavy traffic loads passing through ecologically-sensitive areas should be prioritised to ensure traversability for animal communities.
Muometric positioning system (μPS) with cosmic muons as a new underwater and underground positioning technique
Authors: Tanaka Hiroyuki K. M.
Published: November 2020

Thus far, underwater and underground positioning techniques have been limited to those using classical waves (sound waves, electromagnetic waves or their combination). However, the positioning accuracy is strongly affected by the conditions of media they propagate (temperature, salinity, density, elastic constants, opacity, etc.). In this work, we developed a precise and entirely new three-dimensional positioning technique with cosmic muons. This muonic technique is totally unaffected by the media condition and can be universally implemented anywhere on the globe without a signal transmitter. Results of our laboratory-based experiments and simulations showed that, for example, plate-tectonics-driven seafloor motion and magma-driven seamount deformation can be detected with the μPS.
Explaining among-country variation in COVID-19 case fatality rate
Authors: Sorci Gabriele , Faivre Bruno , Morand Serge
Published: November 2020

While the epidemic of SARS-CoV-2 has spread worldwide, there is much concern over the mortality rate that the infection induces. Available data suggest that COVID-19 case fatality rate had varied temporally (as the epidemic has progressed) and spatially (among countries). Here, we attempted to identify key factors possibly explaining the variability in case fatality rate across countries. We used data on the temporal trajectory of case fatality rate provided by the European Center for Disease Prevention and Control, and country-specific data on different metrics describing the incidence of known comorbidity factors associated with an increased risk of COVID-19 mortality at the individual level. We also compiled data on demography, economy and political regimes for each country. We found that temporal trajectories of case fatality rate greatly vary among countries. We found several factors associated with temporal changes in case fatality rate both among variables describing comorbidity risk and demographic, economic and political variables. In particular, countries with the highest values of DALYs lost to cardiovascular, cancer and chronic respiratory diseases had the highest values of COVID-19 CFR. CFR was also positively associated with the death rate due to smoking in people over 70 years. Interestingly, CFR was negatively associated with share of death due to lower respiratory infections. Among the demographic, economic and political variables, CFR was positively associated with share of the population over 70, GDP per capita, and level of democracy, while it was negatively associated with number of hospital beds ×1000. Overall, these results emphasize the role of comorbidity and socio-economic factors as possible drivers of COVID-19 case fatality rate at the population level.
Antibiofilm activity of flavonoids on staphylococcal biofilms through targeting BAP amyloids
Authors: Matilla-Cuenca Leticia , Gil Carmen , Cuesta Sergio , Rapún-Araiz Beatriz , Žiemytė Miglė , Mira Alex , Lasa Iñigo , Valle Jaione
Published: November 2020

The opportunistic pathogen Staphylococcus aureus is responsible for causing infections related to indwelling medical devices, where this pathogen is able to attach and form biofilms. The intrinsic properties given by the self-produced extracellular biofilm matrix confer high resistance to antibiotics, triggering infections difficult to treat. Therefore, novel antibiofilm strategies targeting matrix components are urgently needed. The Biofilm Associated Protein, Bap, expressed by staphylococcal species adopts functional amyloid-like structures as scaffolds of the biofilm matrix. In this work we have focused on identifying agents targeting Bap-related amyloid-like aggregates as a strategy to combat S. aureus biofilm-related infections. We identified that the flavonoids, quercetin, myricetin and scutellarein specifically inhibited Bap-mediated biofilm formation of S. aureus and other staphylococcal species. By using in vitro aggregation assays and the cell-based methodology for generation of amyloid aggregates based on the Curli-Dependent Amyloid Generator system (C-DAG), we demonstrated that these polyphenols prevented the assembly of Bap-related amyloid-like structures. Finally, using an in vivo catheter infection model, we showed that quercetin and myricetin significantly reduced catheter colonization by S. aureus. These results support the use of polyphenols as anti-amyloids molecules that can be used to treat biofilm-related infections.
Machine learning approach for elucidating and predicting the role of synthesis parameters on the shape and size of TiO2 nanoparticles
Authors: Pellegrino Francesco , Isopescu Raluca , Pellutiè Letizia , Sordello Fabrizio , Rossi Andrea M. , Ortel Erik , Martra Gianmario , Hodoroaba Vasile-Dan , Maurino Valter
Published: November 2020

In the present work a series of design rules are developed in order to tune the morphology of TiO2 nanoparticles through hydrothermal process. Through a careful experimental design, the influence of relevant process parameters on the synthesis outcome are studied, reaching to the develop predictive models by using Machine Learning methods. The models, after the validation and training, are able to predict with high accuracy the synthesis outcome in terms of nanoparticle size, polydispersity and aspect ratio. Furthermore, they are implemented by reverse engineering approach to do the inverse process, i.e. obtain the optimal synthesis parameters given a specific product characteristic. For the first time, it is presented a synthesis method that allows continuous and precise control of NPs morphology with the possibility to tune the aspect ratio over a large range from 1.4 (perfect truncated bipyramids) to 6 (elongated nanoparticles) and the length from 20 to 140 nm.
The influence of the pore shape on the bulk modulus and the Biot coefficient of fluid-saturated porous rocks
Authors: Selvadurai A. P. S. , Suvorov A. P.
Published: November 2020

Fluid-saturated rocks are multi-phasic materials and the mechanics of partitioning the externally applied stresses between the porous skeleton of the rock and the interstitial fluids has to take into consideration the mechanical behaviour of the phases. In these studies the porosity of the multi-phasic material is important for estimating the multi-phasic properties and most studies treat the porosity as a scalar measure without addressing the influence of pore shape and pore geometry. This paper shows that both the overall bulk modulus of a porous medium and the Biot coefficient depend on the shape of the pores. Pores with shapes resembling either thin oblate spheroids or spheres are considered. The Mori–Tanaka and the self-consistent methods are used to estimate the overall properties and the results are compared with experimental data. The pore density and the aspect ratio of the spheroidal pores influence the porosity of the geomaterials. For partially saturated rocks, the equivalent bulk modulus of the fluid–gas mixture occupying the pore space can also be obtained. The paper also examines the influence of the pore shape in estimating the Biot coefficient that controls the stress partitioning in fluid-saturated poroelastic materials.
Catalytic liquefaction of sewage sludge to small molecular weight chemicals
Authors: Wang Yuehu , Tian Feihong , Guo Peimei , Fu Dazhen , Heeres Hero Jan , Tang Taotao , Yuan Huayu , Wang Bing , Li Jiang
Published: November 2020

The catalytic hydrotreatment of sewage sludge, the wet solid byproducts from wastewater treatment plants, using supported Ir, Pt, Pd, Ru catalysts had been investigated with different solvent conditions. Reactions were carried out in a batch set-up at elevated temperatures (400 °C) using a hydrogen donor (formic acid (FA) in isopropanol (IPA) or hydrogen gas), with sewage sludge obtained from different sampling places. Sewage sludge conversions of up to 83.72% were achieved using Pt/C, whereas the performance for the others catalysts is different and solvent had a strong effect on the conversion rate and product constitution. The sewage sludge oils were characterised using a range of analytical techniques (GC, GC–MS, GCxGC, GPC) and were shown to consist of monomers, mainly alkanes and higher oligomers.
Chitosan overlaid Fe3O4/rGO nanocomposite for targeted drug delivery, imaging, and biomedical applications
Authors: Karthika Viswanathan , AlSalhi Mohamad S. , Devanesan Sandhanasamy , Gopinath Kasi , Arumugam Ayyakannu , Govindarajan Marimuthu
Published: November 2020

A hybrid and straightforward nanosystem that can be used simultaneously for cancer-targeted fluorescence imaging and targeted drug delivery in vitro was reported in this study. A chitosan (CS) polymer coated with reduced graphene oxide (rGO) and implanted with Fe3O4 nanoparticles was fabricated. The fundamental physicochemical properties were confirmed via FT-IR, XRD, FE-SEM, HR-TEM, XPS, and VSM analysis. The in vivo toxicity study in zebrafish showed that the nanocomposite was not toxic. The in vitro drug loading amount was 0.448 mg/mL−1 for doxorubicin, an anticancer therapeutic, in the rGO/Fe3O4/CS nanocomposite. Furthermore, the pH-regulated release was observed using folic acid. Cellular uptake and multimodal imaging revealed the benefit of the folic acid-conjugated nanocomposite as a drug carrier, which remarkably improves the doxorubicin accumulation inside the cancer cells over-express folate receptors. The rGO/Fe3O4/CS nanocomposite showed enhanced antibiofilm and antioxidant properties compared to other materials. This study's outcomes support the use of the nanocomposite in targeted chemotherapy and the potential applications in the polymer, cosmetic, biomedical, and food industries.
Short-term comparison of preoperative and postoperative pain after indirect decompression surgery and direct decompression surgery in patients with degenerative spondylolisthesis
Authors: Hiyama Akihiko , Katoh Hiroyuki , Sakai Daisuke , Tanaka Masahiro , Sato Masato , Watanabe Masahiko
Published: November 2020

The purpose of this study was to compare the short-term clinical outcomes between extreme lateral interbody fusion (XLIF) and minimally invasive surgery (MIS)–transforaminal interbody fusion (TLIF) in patients with degenerative spondylolisthesis with stenosis. One hundred-six patients were enrolled; 44 were treated with MIS–TLIF (direct decompression group; DP), and 62 were treated with XLIF (indirect decompression group; IDP). Perioperative indexes included operation time and intraoperative bleeding. Perioperative indexes preoperative and postoperative numeric rating scale (NRS) scores for low back pain (NRS-BP), leg pain (NRS-LP), and leg numbness (NRS-LN), and the preoperative score on the Japanese version of the painDETECT questionnaire (PDQ-J) were also assessed. The average follow-up period for the collection of NRS scores was 12.6 months. The operation time was significantly shorter in the IDP than in the DP group (109.9 ± 35.4 vs. 153.3 ± 50.9 min; p < 0.001). Intraoperative blood loss was also significantly less in the IDP group than in the DP group (85.4 ± 125.4 vs. 258.3 ± 220.4 mL; p < 0.001). The PDQ-J score and preoperative NRS scores (NRS-BP, NRS-LP, and NRS-LN) did not differ significantly between groups. Less improvement in the NRS-BP (ΔNRS-BP) was observed in the DP group than in the IDP group (p < 0.05). Although pain improved after surgery in both groups, IDP surgery was advantageous in minimizing bleeding and preserving posterior support elements such as the facet joints, lamina, and paraspinal muscles. These findings suggest that this may have contributed to the higher rate of improvement in low back pain compared with DP surgery.
The POLD1R689W variant increases the sensitivity of colorectal cancer cells to ATR and CHK1 inhibitors
Authors: Job Albert , Tatura Marina , Schäfer Cora , Lutz Veronika , Schneider Hanna , Lankat-Buttgereit Brigitte , Zielinski Alexandra , Borgmann Kerstin , Bauer Christian , Gress Thomas M. , Buchholz Malte , Gallmeier Eike
Published: November 2020

Inhibition of the kinase ATR, a central regulator of the DNA damage response, eliminates subsets of cancer cells in certain tumors. As previously shown, this is at least partly attributable to synthetic lethal interactions between ATR and POLD1, the catalytic subunit of the polymerase δ. Various POLD1 variants have been found in colorectal cancer, but their significance as therapeutic targets for ATR pathway inhibition remains unknown. Using CRISPR/Cas9 in the colorectal cancer cell line DLD-1, which harbors four POLD1 variants, we established heterozygous POLD1-knockout clones with exclusive expression of distinct variants to determine the functional relevance of these variants individually by assessing their impact on ATR pathway activation, DNA replication, and cellular sensitivity to inhibition of ATR or its effector kinase CHK1. Of the four variants analyzed, only POLD1R689W affected POLD1 function, as demonstrated by compensatory ATR pathway activation and impaired DNA replication. Upon treatment with ATR or CHK1 inhibitors, POLD1R689W strongly decreased cell survival in vitro, which was attributable at least partly to S phase impairment and apoptosis. Similarly, treatment with the ATR inhibitor AZD6738 inhibited growth of murine xenograft tumors, harboring the POLD1R689W variant, in vivo. Our POLD1-knockout model thus complements algorithm-based models to predict the pathogenicity of tumor-specific variants of unknown significance and illustrates a novel and potentially clinically relevant therapeutic approach using ATR/CHK1 inhibitors in POLD1-deficient tumors.
Pooling RT-qPCR testing for SARS-CoV-2 in 1000 individuals of healthy and infection-suspected patients
Authors: Hirotsu Yosuke , Maejima Makoto , Shibusawa Masahiro , Nagakubo Yuki , Hosaka Kazuhiro , Amemiya Kenji , Sueki Hitomi , Hayakawa Miyoko , Mochizuki Hitoshi , Tsutsui Toshiharu , Kakizaki Yumiko , Miyashita Yoshihiro , Omata Masao
Published: November 2020

Severe acute respiratory coronavirus 2 (SARS-CoV-2) testing reagents are expected to become scarce worldwide. However, little is known regarding whether pooling of samples accurately detects SARS-CoV-2. To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiments were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2-positive and -negative patients. Furthermore, we studied 1000 individuals, 667 of whom were “healthy” individuals (195 healthcare workers and 472 hospitalized patients with disorders other than COVID-19 infection), and 333 infection-suspected patients with cough and fever. Serial dilution analysis showed a limit of detection of around 10–100 viral genome copies according to the protocol of the National Institute of Infectious Diseases, Japan. Spike-in experiments demonstrated that RT-qPCR detected positive signals in pooled samples with SARS-CoV-2-negative and -positive patients at 5-, 10-, 20-fold dilutions. By screening with this pooling strategy, by the end of April 2020 there were 12 SARS-CoV-2-positive patients in 333 infection-suspected patients (3.6%) and zero in 667 “healthy” controls. We obtained these results with a total of 538 runs using the pooling strategy, compared with 1000 standard runs. In a prospective study, we successfully detected SARS-CoV-2 using 10- to 20-fold diluted samples of nasopharyngeal swabs from eighteen COVID-19 patients with wide ranges of viral load. Pooling sample is feasible for conserving test reagents and detecting SARS-CoV-2 in clinical settings. This strategy will help us to research the prevalence infected individuals and provide infected-status information to prevent the spread of the virus and nosocomial transmission.
Bidirectional, non-necrotizing glomerular crescents are the critical pathology in X-linked Alport syndrome mouse model harboring nonsense mutation of human COL4A5
Authors: Song Jiang Ying , Saga Nobuyuki , Kawanishi Kunio , Hashikami Kentaro , Takeyama Michiyasu , Nagata Michio
Published: November 2020

X-linked Alport syndrome (XLAS) is a progressive kidney disease caused by genetic abnormalities of COL4A5. Lack of collagen IV α5 chain staining and “basket-weave” by electron microscopy (EM) in glomerular basement membrane (GBM) are its typical pathology. However, the causal relationship between GBM defects and progressive nephropathy is unknown. We analyzed sequential pathology in a mouse model of XLAS harboring a human nonsense mutation of COL4A5. In mutant mice, nephropathy commenced from focal GBM irregularity by EM at 6 weeks of age, prior to exclusive crescents at 13 weeks of age. Low-vacuum scanning EM demonstrated substantial ragged features in GBM, and crescents were closely associated with fibrinoid exudate, despite lack of GBM break and podocyte depletion at 13 weeks of age. Crescents were derived from two sites by different cellular components. One was CD44 + cells, often with fibrinoid exudate in the urinary space, and the other was accumulation of α-SMA + cells in the thickened Bowman’s capsule. These changes finally coalesced, leading to global obliteration. In conclusion, vulnerability of glomerular and capsular barriers to the structural defect in collagen IV may cause non-necrotizing crescents via activation of PECs and migration of interstitial fibroblasts, promoting kidney disease in this model.
Three-dimensional reconstruction of laryngeal cancer with whole organ serial immunohistochemical sections
Authors: Tian Jun , Qian Bo , Zhang Sanmei , Guo Rui , Zhang Hui , Jeannon J.-P. , Jin Rongxiu , Feng Xiang , Zhan Yangni , Liu Jie , He Pengfei , Guo Jue , Li Le , Jia Yue , Huang Fuhui , Wang Binquan
Published: November 2020

Three-dimensional (3D) image reconstruction of tumors based on serial histological sectioning is one of the most powerful methods for accurate high-resolution visualization of tumor structures. However, 3D histological reconstruction of whole tumor has not yet been achieved. We established a high-resolution 3D model of molecular marked whole laryngeal cancer by optimizing the currently available techniques. A series of 5,388 HE stained or immunohistochemically stained whole light microscopic images (200 ×) were acquired (15.61 TB).The data set of block-face images (96.2 GB) was also captured. Direct volume rendering of serial 6.25 × light microscopy images did not demonstrate the major characteristics of the laryngeal cancer as expected. Based on fusion of two datasets, the accurate boundary of laryngeal tumor bulk was visualized in an anatomically realistic context. In the regions of interest, micro tumor structure, budding, cell proliferation and tumor lymph vessels were well represented in 3D after segmentation, which highlighted the advantages of 3D reconstruction of light microscopy images. In conclusion, generating 3D digital histopathological images of a whole solid tumor based on current technology is feasible. However, data mining strategy should be developed for complete utilization of the large amount of data generated.
Identification of mesenchymal stromal cell survival responses to antimicrobial silver ion concentrations released from orthopaedic implants
Authors: Souter Paul , Vaughan John , Butcher Kerry , Dowle Adam , Cunningham Jim , Dodd James , Hall Michael , Wilson Darren , Horner Alan , Genever Paul
Published: November 2020

Antimicrobial silver (Ag+) coatings on orthopaedic implants may reduce infection rates, but should not be to the detriment of regenerative cell populations, primarily mesenchymal stem/stromal cells (MSCs). We determined intramedullary silver release profiles in vivo, which were used to test relevant Ag+ concentrations on MSC function in vitro. We measured a rapid elution of Ag+ from intramedullary pins in a rat femoral implantation model, delivering a maximum potential concentration of 7.8 µM, which was below toxic levels determined for MSCs in vitro (EC50, 33 µM). Additionally, we present in vitro data of the reduced colonisation of implants by Staphylococcus aureus. MSCs exposed to Ag+ prior to/during osteogenic differentiation were not statistically affected. Notably, at clonal density, the colony-forming capacity of MSCs was significantly reduced in the presence of 10 µM Ag+, suggesting that a subpopulation of clonal MSCs was sensitive to Ag+ exposure. At a molecular level, surviving colony-forming MSCs treated with Ag+ demonstrated a significant upregulation of components of the peroxiredoxin/thioredoxin pathway and processes involved in glutathione metabolism compared to untreated controls. Inhibition of glutathione synthesis using l-buthionine sulfoxamine eliminated MSC clonogenicity in the presence of Ag+, which was rescued by exogenous glutathione.
Anti-herpes virus activity of the carnivorous botanical, Sarracenia purpurea
Authors: Kannan Latha , Kumar Ashok , Kumar Aradhana , Jacobs Bertram , Langland Jeffrey
Published: November 2020

Herpes simplex virus type-1 (HSV-1), one of the most widely spread human viruses in the Herpesviridae family, causes herpes labialis (cold sores) and keratitis (inflammation of the cornea). Conventional treatment for HSV-1 infection includes pharmaceutical drugs, such as acyclovir and docosonal, which are efficacious but maintain the potential for the development of viral drug resistance. Extracts from the carnivorous pitcher plant,Sarracenia purpurea,have previously been shown to inhibit the replication of HSV-1. In this study, we demonstrate thatS. purpureaextracts can inhibit the replication of HSV-1 by two distinct mechanisms of action. These extracts directly inhibit extracellular virions or viral attachment to the human host cell as well as inhibiting the expression of viral immediate-early, early and late genes when added at various times post-infection. This botanical has previously been shown to inhibit the replication of poxviruses through the inhibition of early viral gene transcription. These results support a broader anti-viral activity ofS. purpureaextracts against both pox and herpes viruses.
Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse
Authors: Mu Tianhao , Xu Liqin , Zhong Yu , Liu Xinyu , Zhao Zhikun , Huang Chaoben , Lan Xiaofeng , Lufei Chengchen , Zhou Yi , Su Yixun , Xu Luang , Jiang Miaomiao , Zhou Hongpo , Lin Xinxin , Wu Liang , Peng Siqi , Liu Shiping , Brix Susanne , Dean Michael , Dunn Norris R. , Zaret Kenneth S. , Fu Xin-Yuan , Hou Yong
Published: November 2020

The liver and gallbladder are among the most important internal organs derived from the endoderm, yet the development of the liver and gallbladder in the early embryonic stages is not fully understood. Using a transgenic Foxa2eGFP reporter mouse line, we performed single-cell full-length mRNA sequencing on endodermal and hepatic cells isolated from ten embryonic stages, ranging from E7.5 to E15.5. We identified the embryonic liver developmental trajectory from gut endoderm to hepatoblasts and characterized the transcriptome of the hepatic lineage. More importantly, we identified liver primordium as the nascent hepatic progenitors with both gut and liver features and documented dynamic gene expression during the epithelial-hepatic transition (EHT) at the stage of liver specification during E9.5–11.5. We found six groups of genes switched on or off in the EHT process, including diverse transcripitional regulators that had not been previously known to be expressed during EHT. Moreover, we identified and revealed transcriptional profiling of gallbladder primordium at E9.5. The present data provides a high-resolution resource and critical insights for understanding the liver and gallbladder development.
Rapid poxvirus engineering using CRISPR/Cas9 as a selection tool
Authors: Gowripalan Anjali , Smith Stewart , Stefanovic Tijana , Tscharke David C.
Published: November 2020

In standard uses of CRISPR/Cas9 technology, the cutting of genomes and their efficient repair are considered to go hand-in-hand to achieve desired genetic changes. This includes the current approach for engineering genomes of large dsDNA viruses. However, for poxviruses we show that Cas9-guide RNA complexes cut viral genomes soon after their entry into cells, but repair of these breaks is inefficient. As a result, Cas9 targeting makes only modest, if any, improvements to basal rates of homologous recombination between repair constructs and poxvirus genomes. Instead, Cas9 cleavage leads to inhibition of poxvirus DNA replication thereby suppressing virus spread in culture. This unexpected outcome allows Cas9 to be used as a powerful tool for selecting conventionally generated poxvirus recombinants, which are otherwise impossible to separate from a large background of parental virus without the use of marker genes. This application of CRISPR/Cas9 greatly speeds up the generation of poxvirus-based vaccines, making this platform considerably more attractive in the context of personalised cancer vaccines and emerging disease outbreaks.