bluuebunny/crossref_metadata_2025 huggingface dataset:
Chlorite oxidized oxyamylose differentially influences the microstructure of fibrin and self assembling peptide hydrogels as well as dental pulp stem cell behavior
Authors: EzEldeen Mostafa , Toprakhisar Burak , Murgia Denise , Smisdom Nick , Deschaume Olivier , Bartic Carmen , Van Oosterwyck Hans , Pereira Rafaela Vaz Sousa , Opdenakker Ghislain , Lambrichts Ivo , Bronckaers Annelies , Jacobs Reinhilde , Patterson Jennifer
Published: March 2021

Tailored hydrogels mimicking the native extracellular environment could help overcome the high variability in outcomes within regenerative endodontics. This study aimed to evaluate the effect of the chemokine-binding and antimicrobial polymer, chlorite-oxidized oxyamylose (COAM), on the microstructural properties of fibrin and self-assembling peptide (SAP) hydrogels. A further goal was to assess the influence of the microstructural differences between the hydrogels on the in vitro behavior of human dental pulp stem cells (hDPSCs). Structural and mechanical characterization of the hydrogels with and without COAM was performed by atomic force microscopy and scanning electron microscopy to characterize their microstructure (roughness and fiber length, diameter, straightness, and alignment) and by nanoindentation to measure their stiffness (elastic modulus). Then, hDPSCs were encapsulated in hydrogels with and without COAM. Cell viability and circularity were determined using confocal microscopy, and proliferation was determined using DNA quantification. Inclusion of COAM did not alter the microstructure of the fibrin hydrogels at the fiber level while affecting the SAP hydrogel microstructure (homogeneity), leading to fiber aggregation. The stiffness of the SAP hydrogels was sevenfold higher than the fibrin hydrogels. The viability and attachment of hDPSCs were significantly higher in fibrin hydrogels than in SAP hydrogels. The DNA content was significantly affected by the hydrogel type and the presence of COAM. The microstructural stability after COAM inclusion and the favorable hDPSCs' response observed in fibrin hydrogels suggest this system as a promising carrier for COAM and application in endodontic regeneration.
Market instability and the size-variance relationship
Authors: Buldyrev Sergey V. , Flori Andrea , Pammolli Fabio
Published: March 2021

We show that some key features of the behavior of mutual funds is accounted for by a stochastic model of proportional growth. We find that the negative dependence of the variance of funds’ growth rates on size is well described by an approximate power law. We discover that during periods of crisis the volatility of the largest funds’ growth rates increases with respect to mid-sized funds. Our result reveals that a lower and flatter slope provides relevant information on the structure of the system. We find that growth rates volatility poorly depends on the size of the funds, thus questioning the benefits of diversification achieved by larger funds. Our findings show that the slope of the size-variance relationship can be used as a synthetic indicator to monitor the intensity of instabilities and systemic risk in financial markets.
Decratonization by rifting enables orogenic reworking and transcurrent dispersal of old terranes in NE Brazil
Authors: Ganade Carlos E. , Weinberg Roberto F. , Caxito Fabricio A. , Lopes Leonardo B. L. , Tesser Lucas R. , Costa Iago S.
Published: March 2021

Dispersion and deformation of cratonic fragments within orogens require weakening of the craton margins in a process of decratonization. The orogenic Borborema Province, in NE Brazil, is one of several Brasiliano/Pan-African late Neoproterozoic orogens that led to the amalgamation of Gondwana. A common feature of these orogens is that a period of extension and opening of narrow oceans preceded inversion and collision. For the case of the Borborema Province, the São Francisco Craton was pulled away from its other half, the Benino-Nigerian Shield, during an intermittent extension event between 1.0–0.92 and 0.9–0.82 Ga. This was followed by inversion of an embryonic and confined oceanic basin at ca. 0.60 Ga and transpressional orogeny from ca. 0.59 Ga onwards. Here we investigate the boundary region between the north São Francisco Craton and the Borborema Province and demonstrate how cratonic blocks became physically involved in the orogeny. We combine these results with a wide compilation of U–Pb and Nd-isotopic model ages to show that the Borborema Province consists of up to 65% of strongly sheared ancient rocks affiliated with the São Francisco/Benino-Nigerian Craton, separated by major transcurrent shear zones, with only ≈ 15% addition of juvenile material during the Neoproterozoic orogeny. This evolution is repeated across a number of Brasiliano/Pan-African orogens, with significant local variations, and indicate that extension weakened cratonic regions in a process of decratonization that prepared them for involvement in the orogenies, that led to the amalgamation of Gondwana.
Admission serum potassium levels and prognosis of vasospastic angina
Authors: Seo Won-Woo , Jo Sang-Ho , Kim Sung Eun , Kim Hyun-Jin , Han Seung Hwan , Lee Kwan Yong , Her Sung Ho , Lee Min-Ho , Cho Seong-Sik , Kim Hack-Lyoung , Baek Sang Hong
Published: March 2021

Hypokalemia is a common electrolyte disturbance and is related to poor prognosis in patients with cardiovascular disease. However, the role of hypokalemia in patients with vasospastic angina (VSA) has not yet been studied. The present study enrolled 1454 patients diagnosed with VSA according to ergonovine provocation test results and available admission serum potassium data. The primary outcome was a composite of cardiac death, acute coronary syndrome, and new-onset life-threatening arrhythmia. Based on a hypokalemia definition as serum potassium concentration ≤ 3.5 mEq/L, the hypokalaemia group included 70 patients (4.8%). The median potassium levels were 3.4 mEq/L [interquartile range (IQR) 3.3–3.5] in the hypokalemia group and 4.1 mEq/L (IQR 3.9–4.3) in the no-hypokalemia group. The median follow-up duration was 764 days. Primary outcomes occurred in seven patients (10.0%) in the hypokalemia group and 51 patients (3.7%) in the no-hypokalemia group. The Kaplan–Meier analysis showed a higher cumulative incidence of primary outcomes in the hypokalemia group compared to that in the no-hypokalemia group (log-rank P = 0.014). Multivariate Cox regression analysis also showed that hypokalemia was an independent predictor of primary outcomes. In conclusion, hypokalemia at admission was associated with adverse clinical outcomes in VSA.
On the modulation and maintenance of hibernation in captive dwarf lemurs
Authors: Blanco Marina B. , Greene Lydia K. , Schopler Robert , Williams Cathy V. , Lynch Danielle , Browning Jenna , Welser Kay , Simmons Melanie , Klopfer Peter H. , Ehmke Erin E.
Published: March 2021

In nature, photoperiod signals environmental seasonality and is a strong selective “zeitgeber” that synchronizes biological rhythms. For animals facing seasonal environmental challenges and energetic bottlenecks, daily torpor and hibernation are two metabolic strategies that can save energy. In the wild, the dwarf lemurs of Madagascar are obligate hibernators, hibernating between 3 and 7 months a year. In captivity, however, dwarf lemurs generally express torpor for periods far shorter than the hibernation season in Madagascar. We investigated whether fat-tailed dwarf lemurs (Cheirogaleus medius) housed at the Duke Lemur Center (DLC) could hibernate, by subjecting 8 individuals to husbandry conditions more in accord with those in Madagascar, including alternating photoperiods, low ambient temperatures, and food restriction. All dwarf lemurs displayed daily and multiday torpor bouts, including bouts lasting ~ 11 days. Ambient temperature was the greatest predictor of torpor bout duration, and food ingestion and night length also played a role. Unlike their wild counterparts, who rarely leave their hibernacula and do not feed during hibernation, DLC dwarf lemurs sporadically moved and ate. While demonstrating that captive dwarf lemurs are physiologically capable of hibernation, we argue that facilitating their hibernation serves both husbandry and research goals: first, it enables lemurs to express the biphasic phenotypes (fattening and fat depletion) that are characteristic of their wild conspecifics; second, by “renaturalizing” dwarf lemurs in captivity, they will emerge a better model for understanding both metabolic extremes in primates generally and metabolic disorders in humans specifically.
A parameter adaptive method for state of charge estimation of lithium-ion batteries with an improved extended Kalman filter
Authors: Yang Shichun , Zhou Sida , Hua Yang , Zhou Xinan , Liu Xinhua , Pan Yuwei , Ling Heping , Wu Billy
Published: March 2021

An accurate state of charge (SOC) estimation in battery management systems (BMS) is of crucial importance to guarantee the safe and effective operation of automotive batteries. However, the BMS consistently suffers from inaccuracy of SOC estimation. Herein, we propose a SOC estimation approach with both high accuracy and robustness based on an improved extended Kalman filter (IEKF). An equivalent circuit model is established, and the simulated annealing-particle swarm optimization (SA-PSO) algorithm is used for offline parameter identification. Furthermore, improvements have been made with noise adaptation, a fading filter and a linear-nonlinear filtering based on the traditional EKF method, and rigorous mathematical proof has been carried out accordingly. To deal with model mismatch, online parameter identification is achieved by a dual Kalman filter. Finally, various experiments are performed to validate the proposed IEKF. Experimental results show that the IEKF algorithm can reduce the error to 2.94% under dynamic stress test conditions, and robustness analysis is verified with noise interference, hence demonstrating its practicability for extending to state estimation of battery packs applied in real-world operating conditions.
APTES monolayer coverage on self-assembled magnetic nanospheres for controlled release of anticancer drug Nintedanib
Authors: Karade V. C. , Sharma A. , Dhavale R. P. , Dhavale R. P. , Shingte S. R. , Patil P. S. , Kim J. H. , Zahn D. R. T. , Chougale A. D. , Salvan G. , Patil P. B.
Published: March 2021

The use of an appropriate delivery system capable of protecting, translocating, and selectively releasing therapeutic moieties to desired sites can promote the efficacy of an active compound. In this work, we have developed a nanoformulation which preserves its magnetization to load a model anticancerous drug and to explore the controlled release of the drug in a cancerous environment. For the preparation of the nanoformulation, self-assembled magnetic nanospheres (MNS) made of superparamagnetic iron oxide nanoparticles were grafted with a monolayer of (3-aminopropyl)triethoxysilane (APTES). A direct functionalization strategy was used to avoid the loss of the MNS magnetization. The successful preparation of the nanoformulation was validated by structural, microstructural, and magnetic investigations. X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) were used to establish the presence of APTES on the MNS surface. The amine content quantified by a ninhydrin assay revealed the monolayer coverage of APTES over MNS. The monolayer coverage of APTES reduced only negligibly the saturation magnetization from 77 emu/g (for MNS) to 74 emu/g (for MNS-APTES). Detailed investigations of the thermoremanent magnetization were carried out to assess the superparamagnetism in the MNS. To make the nanoformulation pH-responsive, the anticancerous drug Nintedanib (NTD) was conjugated with MNS-APTES through the acid liable imine bond. At pH 5.5, which mimics a cancerous environment, a controlled release of 85% in 48 h was observed. On the other hand, prolonged release of NTD was found at physiological conditions (i.e., pH 7.4). In vitro cytotoxicity study showed dose-dependent activity of MNS-APTES-NTD for human lung cancer cells L-132. About 75% reduction in cellular viability for a 100 μg/mL concentration of nanoformulation was observed. The nanoformulation designed using MNS and monolayer coverage of APTES has potential in cancer therapy as well as in other nanobiological applications.
Many-impurity scattering on the surface of a topological insulator
Authors: Hernando José Luis , Baba Yuriko , Díaz Elena , Domínguez-Adame Francisco
Published: March 2021

We theoretically address the impact of a random distribution of non-magnetic impurities on the electron states formed at the surface of a topological insulator. The interaction of electrons with the impurities is accounted for by a separable pseudo-potential method that allows us to obtain closed expressions for the density of states. Spectral properties of surface states are assessed by means of the Green’s function averaged over disorder realisations. For comparison purposes, the configurationally averaged Green’s function is calculated by means of two different self-consistent methods, namely the self-consistent Born approximation (SCBA) and the coherent potential approximation (CPA). The latter is often regarded as the best single-site theory for the study of the spectral properties of disordered systems. However, although a large number of works employ the SCBA for the analysis of many-impurity scattering on the surface of a topological insulator, CPA studies of the same problem are scarce in the literature. In this work, we find that the SCBA overestimates the impact of the random distribution of impurities on the spectral properties of surface states compared to the CPA predictions. The difference is more pronounced when increasing the magnitude of the disorder.
The effect of ABO blood group and antibody class on the risk of COVID-19 infection and severity of clinical outcomes
Authors: Almadhi Marwa Ali , Abdulrahman Abdulkarim , Alawadhi Abdulla , Rabaan Ali A. , Atkin Stephen , AlQahtani Manaf
Published: March 2021

The COVID-19 pandemic has affected more than 100 million cases and caused immense burdens on governments and healthcare systems worldwide. Since its emergence in December 2019, research has been focused on treating the infected, identifying those at risk and preventing spread. There is currently no known biological biomarker that predicts the risk of infection. Several studies emerged suggesting an association between ABO blood group and the risk of COVID-19 infection. In this study, we used retrospective observational data in Bahrain to investigate the association between ABO blood group and risk of infection, as well as susceptibility to severe ICU-requiring infection. We found a higher risk associated with blood group B, and a lower risk with blood group AB. No association was observed between blood group and the risk of a severe ICU-requiring infection. We extended the analysis to study the association by antibodies; anti-a (blood groups B and O) and anti-b (blood groups A and O). No association between antibodies and both risk of infection or susceptibility to severe infection was found. The current study, along with the variation in blood group association results, indicates that blood group may not be an ideal biomarker to predict risk of COVID-19 infection.
A novel role for bone marrow-derived cells to recover damaged keratinocytes from radiation-induced injury
Authors: Okano Junko , Nakae Yuki , Nakagawa Takahiko , Katagi Miwako , Terashima Tomoya , Nagakubo Daisuke , Nakayama Takashi , Yoshie Osamu , Suzuki Yoshihisa , Kojima Hideto
Published: March 2021

Exposure to moderate doses of ionizing radiation (IR), which is sufficient for causing skin injury, can occur during radiation therapy as well as in radiation accidents. Radiation-induced skin injury occasionally recovers, although its underlying mechanism remains unclear. Moderate-dose IR is frequently utilized for bone marrow transplantation in mice; therefore, this mouse model can help understand the mechanism. We had previously reported that bone marrow-derived cells (BMDCs) migrate to the epidermis-dermis junction in response to IR, although their role remains unknown. Here, we investigated the role of BMDCs in radiation-induced skin injury in BMT mice and observed that BMDCs contributed to skin recovery after IR-induced barrier dysfunction. One of the important mechanisms involved the action of CCL17 secreted by BMDCs on irradiated basal cells, leading to accelerated proliferation and recovery of apoptosis caused by IR. Our findings suggest that BMDCs are key players in IR-induced skin injury recovery.
Oscillatory pattern of glycemic control in patients with diabetes mellitus
Authors: Vasquez-Muñoz Manuel , Arce-Alvarez Alexis , von Igel Magdalena , Veliz Carlos , Ruiz-Esquide Gonzalo , Ramirez-Campillo Rodrigo , Alvarez Cristian , Ramirez-Velez Robinson , Crespo Fernando A. , Izquierdo Mikel , Del Rio Rodrigo , Andrade David C.
Published: March 2021

Daily glucose variability is higher in diabetic mellitus (DM) patients which has been related to the severity of the disease. However, it is unclear whether glycemic variability displays a specific pattern oscillation or if it is completely random. Thus, to determine glycemic variability pattern, we measured and analyzed continuous glucose monitoring (CGM) data, in control subjects and patients with DM type-1 (T1D). CGM data was assessed for 6 days (day: 08:00–20:00-h; and night: 20:00–08:00-h). Participants (n = 172; age = 18–80 years) were assigned to T1D (n = 144, females = 65) and Control (i.e., healthy; n = 28, females = 22) groups. Anthropometry, pharmacologic treatments, glycosylated hemoglobin (HbA1c) and years of evolution were determined. T1D females displayed a higher glycemia at 10:00–14:00-h vs. T1D males and Control females. DM patients displays mainly stationary oscillations (deterministic), with circadian rhythm characteristics. The glycemia oscillated between 2 and 6 days. The predictive model of glycemia showed that it is possible to predict hyper and hypoglycemia (R2 = 0.94 and 0.98, respectively) in DM patients independent of their etiology. Our data showed that glycemic variability had a specific oscillation pattern with circadian characteristics, with episodes of hypoglycemia and hyperglycemia at day phases, which could help therapeutic action for this population.
An ex vivo model of medical device-mediated bacterial skin translocation
Authors: Wang Hao , Agrawal Anant , Wang Yi , Crawford David W. , Siler Zachary D. , Peterson Marnie L. , Woofter Ricky T. , Labib Mohamed , Shin Hainsworth Y. , Baumann Andrew P. , Phillips K. Scott
Published: March 2021

The skin is a barrier and part of the immune system that protects us from harmful bacteria. Because indwelling medical devices break this barrier, they greatly increase the risk of infection by microbial pathogens. To study how these infections can be prevented through improved clinical practices and medical device technology, it is important to have preclinical models that replicate the early stages of microbial contamination, ingress, and colonization leading up to infection. At present, there are no preclinical ex vivo models specifically developed to simulate conditions for indwelling medical devices. Translocation of pathogens from outside the body across broken skin to normally sterile internal compartments is a rate-limiting step in infectious pathogenesis. In this work, we report a sensitive and reproducible ex vivo porcine skin–catheter model to test how long antimicrobial interventions can delay translocation. Skin preparation was first optimized to minimize tissue damage. The presence of skin dramatically decreased bacterial migration time across the polyurethane catheter interface from > 96 h to 12 h. Using visual colony detection, fluorescence, a luminescent in vitro imaging system, and confocal microscopy, the model was used to quantify time-dependent differences in translocation for eluting and non-eluting antimicrobial catheters. The results show the importance of including tissue in preclinical biofilm models and help to explain current gaps between in vitro testing and clinical outcomes for antimicrobial devices.
A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs
Authors: Cicchese Joseph M. , Sambarey Awanti , Kirschner Denise , Linderman Jennifer J. , Chandrasekaran Sriram
Published: March 2021

Tuberculosis (TB) is the deadliest infectious disease worldwide. The design of new treatments for TB is hindered by the large number of candidate drugs, drug combinations, dosing choices, and complex pharmaco-kinetics/dynamics (PK/PD). Here we study the interplay of these factors in designing combination therapies by linking a machine-learning model, INDIGO-MTB, which predicts in vitro drug interactions using drug transcriptomics, with a multi-scale model of drug PK/PD and pathogen-immune interactions called GranSim. We calculate an in vivo drug interaction score (iDIS) from dynamics of drug diffusion, spatial distribution, and activity within lesions against various pathogen sub-populations. The iDIS of drug regimens evaluated against non-replicating bacteria significantly correlates with efficacy metrics from clinical trials. Our approach identifies mechanisms that can amplify synergistic or mitigate antagonistic drug interactions in vivo by modulating the relative distribution of drugs. Our mechanistic framework enables efficient evaluation of in vivo drug interactions and optimization of combination therapies.
Bioinformatics-based prediction of conformational epitopes for Enterovirus A71 and Coxsackievirus A16
Authors: Wang Liping , Zhu Miao , Fang Yulu , Rong Hao , Gao Liuying , Liao Qi , Zhang Lina , Dong Changzheng
Published: March 2021

Enterovirus A71 (EV-A71), Coxsackievirus A16 (CV-A16) and CV-A10 are the major causative agents of hand, foot and mouth disease (HFMD). The conformational epitopes play a vital role in monitoring the antigenic evolution, predicting dominant strains and preparing vaccines. In this study, we employed a Bioinformatics-based algorithm to predict the conformational epitopes of EV-A71 and CV-A16 and compared with that of CV-A10. Prediction results revealed that the distribution patterns of conformational epitopes of EV-A71 and CV-A16 were similar to that of CV-A10 and their epitopes likewise consisted of three sites: site 1 (on the “north rim” of the canyon around the fivefold vertex), site 2 (on the “puff”) and site 3 (one part was in the “knob” and the other was near the threefold vertex). The reported epitopes highly overlapped with our predicted epitopes indicating the predicted results were reliable. These data suggested that three-site distribution pattern may be the basic distribution role of epitopes on the enteroviruses capsids. Our prediction results of EV-A71 and CV-A16 can provide essential information for monitoring the antigenic evolution of enterovirus.
Systemic deletion of Atp7b modifies the hepatocytes’ response to copper overload in the mouse models of Wilson disease
Authors: Muchenditsi Abigael , Talbot C. Conover , Gottlieb Aline , Yang Haojun , Kang Byunghak , Boronina Tatiana , Cole Robert , Wang Li , Dev Som , Hamilton James P. , Lutsenko Svetlana
Published: March 2021

Wilson disease (WD) is caused by inactivation of the copper transporter Atp7b and copper overload in tissues. Mice with Atp7b deleted either globally (systemic inactivation) or only in hepatocyte recapitulate various aspects of human disease. However, their phenotypes vary, and neither the common response to copper overload nor factors contributing to variability are well defined. Using metabolic, histologic, and proteome analyses in three Atp7b-deficient mouse strains, we show that global inactivation of Atp7b enhances and specifically modifies the hepatocyte response to Cu overload. The loss of Atp7b only in hepatocytes dysregulates lipid and nucleic acid metabolisms and increases the abundance of respiratory chain components and redox balancing enzymes. In global knockouts, independently of their background, the metabolism of lipid, nucleic acid, and amino acids is inhibited, respiratory chain components are down-regulated, inflammatory response and regulation of chromosomal replication are enhanced. Decrease in glucokinase and lathosterol oxidase and elevation of mucin-13 and S100A10 are observed in all Atp7b mutant strains and reflect the extent of liver injury. The magnitude of proteomic changes in Atp7b−/− animals inversely correlates with the metallothioneins levels rather than liver Cu content. These findings facilitate identification of WD-specific metabolic and proteomic changes for diagnostic and treatment.
ABA signalling and metabolism are not essential for dark-induced stomatal closure but affect response speed
Authors: Pridgeon Ashley J. , Hetherington Alistair M.
Published: March 2021

Stomata are microscopic pores that open and close, acting to balance CO2 uptake with water loss. Stomata close in response to various signals including the drought hormone abscisic acid (ABA), microbe-associated-molecular-patterns, high CO2 levels, and darkness. The signalling pathways underlying ABA-induced stomatal closure are well known, however, the mechanism for dark-induced stomatal closure is less clear. ABA signalling has been suggested to play a role in dark-induced stomatal closure, but it is unclear how this occurs. Here we investigate the role of ABA in promoting dark-induced stomatal closure. Tracking stomatal movements on the surface of leaf discs we find, although steady state stomatal apertures are affected by mutations in ABA signalling and metabolism genes, all mutants investigated close in response to darkness. However, we observed a delayed response to darkness for certain ABA signalling and metabolism mutants. Investigating this further in the quadruple ABA receptor mutant (pyr1pyl1pyl2pyl4), compared with wild-type, we found reduced stomatal conductance kinetics. Although our results suggest a non-essential role for ABA in dark-induced stomatal closure, we show that ABA modulates the speed of the dark-induced closure response. These results highlight the role of ABA signalling and metabolic pathways as potential targets for enhancing stomatal movement kinetics.
Hyperparameter optimisation and validation of registration algorithms for measuring regional ventricular deformation using retrospective gated computed tomography images
Authors: Razeghi Orod , Heinrich Mattias , Fastl Thomas E. , Corrado Cesare , Karim Rashed , De Vecchi Adelaide , Banks Tom , Donnelly Patrick , Behar Jonathan M. , Gould Justin , Rajani Ronak , Rinaldi Christopher A. , Niederer Steven
Published: March 2021

Recent dose reduction techniques have made retrospective computed tomography (CT) scans more applicable and extracting myocardial function from cardiac computed tomography (CCT) images feasible. However, hyperparameters of generic image intensity-based registration techniques, which are used for tracking motion, have not been systematically optimised for this modality. There is limited work on their validation for measuring regional strains from retrospective gated CCT images and open-source software for motion analysis is not widely available. We calculated strain using our open-source platform by applying an image registration warping field to a triangulated mesh of the left ventricular endocardium. We optimised hyperparameters of two registration methods to track the wall motion. Both methods required a single semi-automated segmentation of the left ventricle cavity at end-diastolic phase. The motion was characterised by the circumferential and longitudinal strains, as well as local area change throughout the cardiac cycle from a dataset of 24 patients. The derived motion was validated against manually annotated anatomical landmarks and the calculation of strains were verified using idealised problems. Optimising hyperparameters of registration methods allowed tracking of anatomical measurements with a mean error of 6.63% across frames, landmarks, and patients, comparable to an intra-observer error of 7.98%. Both registration methods differentiated between normal and dyssynchronous contraction patterns based on circumferential strain ($$p_1=0.0065$$

p
1

=
0.0065

, $$p_2=0.0011$$

p
2

=
0.0011

). To test whether a typical 10 temporal frames sampling of retrospective gated CCT datasets affects measuring cardiac mechanics, we compared motion tracking results from 10 and 20 frames datasets and found a maximum error of $$8.51\pm 0.8\%$$

8.51
±
0.8
%

. Our findings show that intensity-based registration techniques with optimal hyperparameters are able to accurately measure regional strains from CCT in a very short amount of time. Furthermore, sufficient sensitivity can be achieved to identify heart failure patients and left ventricle mechanics can be quantified with 10 reconstructed temporal frames. Our open-source platform will support increased use of CCT for quantifying cardiac mechanics.
Synthesis of silver nanostructure on gold nanoparticle using near field assisted second harmonic generation
Authors: Yatsui Takashi , Brandenburg Felix , Leuschel Benjamin , Soppera Olivier
Published: March 2021

By using gold (Au) nanoparticles (NPs) as an optical near-field source under far-field illumination in combination with a silver (Ag) ion solution containing a photoinitiator, we coated Ag on Au NPs using a near-field (NF)-assisted process. We evaluated the change in the size of the NPs using transmission electron microscopy. Evaluation of the synthesized Ag volume over illumination power confirmed the squared power dependence of the NP volume with illumination using 808 nm light, i.e., a wavelength longer than the absorption edge wavelength of the photoinitiator molecules. The rate of volume increase was much lower than the plasmonic field enhancement effect. Therefore, the squared power dependency of the volume increase using a wavelength longer than the absorption edge wavelength originated from NF-assisted second-harmonic generation and the resulting excitation.
Global multi-method analysis of interaction parameters for reversibly self-associating macromolecules at high concentrations
Authors: Parupudi Arun , Chaturvedi Sumit K. , Adão Regina , Harkness Robert W. , Dragulin-Otto Sonia , Kay Lewis E. , Esfandiary Reza , Zhao Huaying , Schuck Peter
Published: March 2021

Weak macromolecular interactions assume a dominant role in the behavior of highly concentrated solutions, and are at the center of a variety of fields ranging from colloidal chemistry to cell biology, neurodegenerative diseases, and manufacturing of protein drugs. They are frequently measured in different biophysical techniques in the form of second virial coefficients, and nonideality coefficients of sedimentation and diffusion, which may be related mechanistically to macromolecular distance distributions in solution and interparticle potentials. A problem arises for proteins where reversible self-association often complicates the concentration-dependent behavior, such that grossly inconsistent coefficients are measured in experiments based on different techniques, confounding quantitative conclusions. Here we present a global multi-method analysis that synergistically bridges gaps in resolution and sensitivity of orthogonal techniques. We demonstrate the method with a panel of monoclonal antibodies exhibiting different degrees of self-association. We show how their concentration-dependent behavior, examined by static and dynamic light scattering and sedimentation velocity, can be jointly described in a self-consistent framework that separates nonideality coefficients from self-association properties, and thereby extends the quantitative interpretation of nonideality coefficients to probe dynamics in highly concentrated protein solutions.
Precision medicine and machine learning towards the prediction of the outcome of potential celiac disease
Authors: Piccialli Francesco , Calabrò Francesco , Crisci Danilo , Cuomo Salvatore , Prezioso Edoardo , Mandile Roberta , Troncone Riccardo , Greco Luigi , Auricchio Renata
Published: March 2021

Potential Celiac Patients (PCD) bear the Celiac Disease (CD) genetic predisposition, a significant production of antihuman transglutaminase antibodies, but no morphological changes in the small bowel mucosa. A minority of patients (17%) showed clinical symptoms and need a gluten free diet at time of diagnosis, while the majority progress over several years (up to a decade) without any clinical problem neither a progression of the small intestine mucosal damage even when they continued to assume gluten in their diet. Recently we developed a traditional multivariate approach to predict the natural history, on the base of the information at enrolment (time 0) by a discriminant analysis model. Still, the traditional multivariate model requires stringent assumptions that may not be answered in the clinical setting. Starting from a follow-up dataset available for PCD, we propose the application of Machine Learning (ML) methodologies to extend the analysis on available clinical data and to detect most influent features predicting the outcome. These features, collected at time of diagnosis, should be capable to classify patients who will develop duodenal atrophy from those who will remain potential. Four ML methods were adopted to select features predictive of the outcome; the feature selection procedure was indeed capable to reduce the number of overall features from 85 to 19. ML methodologies (Random Forests, Extremely Randomized Trees, and Boosted Trees, Logistic Regression) were adopted, obtaining high values of accuracy: all report an accuracy above 75%. The specificity score was always more than 75% also, with two of the considered methods over 98%, while the best performance of sensitivity was 60%. The best model, optimized Boosted Trees, was able to classify PCD starting from the selected 19 features with an accuracy of 0.80, sensitivity of 0.58 and specificity of 0.84. Finally, with this work, we are able to categorize PCD patients that can more likely develop overt CD using ML. ML techniques appear to be an innovative approach to predict the outcome of PCD, since they provide a step forward in the direction of precision medicine aimed to customize healthcare, medical therapies, decisions, and practices tailoring the clinical management of PCD children.
Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni
Authors: Neal-McKinney Jason M. , Liu Kun C. , Lock Christopher M. , Wu Wen-Hsin , Hu Jinxin
Published: March 2021

The sequencing, assembly, and analysis of bacterial genomes is central to tracking and characterizing foodborne pathogens. The bulk of bacterial genome sequencing at the US Food and Drug Administration is performed using short-read Illumina MiSeq technology, resulting in highly accurate but fragmented genomic sequences. The MinION sequencer from Oxford Nanopore is an evolving technology that produces long-read sequencing data with low equipment cost. The goal of this study was to compare Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. Two reference strains and two field isolates of C. jejuni were sequenced using MiSeq and MinION, and the sequence data were assembled using the software programs SPAdes and Canu, respectively. Hybrid genome assembly was performed using the program Unicycler. Comparison of the C. jejuni 81-176 and RM1221 genome assemblies to the PacBio reference genomes revealed that the SPAdes assemblies had the most accurate nucleotide identity, while the hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate, containing many indels and substitutions that affected downstream analyses. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements such as rRNA and tRNA genes. The full genomes of both C. jejuni field isolates were completed and circularized using hybrid sequencing, and a plasmid was detected in one isolate. Continued development of nanopore sequencing technologies will likely enhance the accuracy of hybrid genome assemblies and enable public health laboratories to routinely generate complete circularized bacterial genome sequences.
Characterization of an active LINE-1 in the naked mole-rat genome
Authors: Yamaguchi Shunichi , Nohara Shizuka , Nishikawa Yuki , Suzuki Yusuke , Kawamura Yoshimi , Miura Kyoko , Tomonaga Keizo , Ueda Keiji , Honda Tomoyuki
Published: March 2021

Naked mole-rats (NMRs, Heterocephalus glaber) are the longest-living rodent species. A reason for their long lifespan is pronounced cancer resistance. Therefore, researchers believe that NMRs have unknown secrets of cancer resistance and seek to find them. Here, to reveal the secrets, we noticed a retrotransposon, long interspersed nuclear element 1 (L1). L1s can amplify themselves and are considered endogenous oncogenic mutagens. Since the NMR genome contains fewer L1-derived sequences than other mammalian genomes, we reasoned that the retrotransposition activity of L1s in the NMR genome is lower than those in other mammalian genomes. In this study, we successfully cloned an intact L1 from the NMR genome and named it NMR-L1. An L1 retrotransposition assay using the NMR-L1 reporter revealed that NMR-L1 was active retrotransposon, but its activity was lower than that of human and mouse L1s. Despite lower retrotrasposition activity, NMR-L1 was still capable of inducing cell senescence, a tumor-protective system. NMR-L1 required the 3′ untranslated region (UTR) for retrotransposition, suggesting that NMR-L1 is a stringent-type of L1. We also confirmed the 5′ UTR promoter activity of NMR-L1. Finally, we identified the G-quadruplex structure of the 3′ UTR, which modulated the retrotransposition activity of NMR-L1. Taken together, the data indicate that NMR-L1 retrotranspose less efficiently, which may contribute to the cancer resistance of NMRs.
Band structure engineering of NiS2 monolayer by transition metal doping
Authors: Khalatbari H. , Vishkayi S. Izadi , Oskouian M. , Soleimani H. Rahimpour
Published: March 2021

By using density functional theory calculations, we have studied the effects of V-, Cr-, Mn-, Fe- and Co-doped on the electronic and magnetic properties of the 1T-NiS2 monolayer. The results show that pure 1T-NiS2 monolayer is a non-magnetic semiconductor. Whereas depending on the species of transition metal atom, the substituted 1T-NiS2 monolayer can become a magnetic semiconductor (Mn-doped), half-metal (V- and Fe-doped) and magnetic (Cr-doped) or non-magnetic (Co-doped) metal. The results indicate that the magnetism can be controlled by the doping of 3d transition metal atoms on the monolayer. In this paper, the engineering of the electric and magnetic properties of 1T-NiS2 monolayer is revealed. It is clear that it could have a promising application in new nanoelectronic and spintronic devices.
In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
Authors: Sikkema Hendrik R. , Poolman Bert
Published: March 2021

Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Here we present an in silico approach that makes use of two or more structures (or structure models) to filter suitable residue pairs for FRET or EPR from all possible pairs within the protein. We apply the method for the study of the conformational dynamics of the substrate-binding domain of the osmoregulatory ATP-Binding Cassette transporter OpuA. This method speeds up the process of designing mutants, and because of its systematic nature, the chances of missing promising candidates are reduced.
Red meat intake is associated with early onset of rheumatoid arthritis: a cross-sectional study
Authors: Jin Jiayang , Li Jing , Gan Yuzhou , Liu Jiajia , Zhao Xiaozhen , Chen Jiali , Zhang Ruijun , Zhong Yan , Chen Xiaomei , Wu Lijun , Xiang Xiaohong , Zhou Yunshan , He Jing , Guo Jianping , Liu Xu , Li Zhanguo
Published: March 2021

Accumulating evidence has implicated dietary factors as important risks for rheumatoid arthritis (RA) development, but analyses of the effects of red meat consumption on RA have yielded diverging results. The aim of this study was to explore the association between red meat and RA in a large-scale, cross-sectional study. From June to December 2016, a total of 733 patients were investigated, from which 707 participants were included in the analysis. These patients were divided into two groups according to their consumption of red meat (< 100 g/day; ≥ 100 g/day). The intake of red meat was assessed via physician-administered questionnaire. Generalized linear models were used to analyze relationships between the red meat intake and RA, adjusting for potential confounders including demographic, clinical, laboratory, and other dietary factors. Compared with low-intake red meat RA patients, high-intake red meat patients had an earlier onset age (p = 0.02) and had higher BMI (p = 0.003). The age at disease onset for the high-intake patients was 6.46 years earlier than for low-intake patients, after adjustment for demographic and other possible confounders (β = − 6.46, 95% CI − 9.77, − 3.15; p = 0.0001). Further, stratified analyses showed that this inverse association of red meat intake with RA onset age was especially evident in smokers and overweight patients (BMI ≥ 24 kg/m2). In conclusion, high-intake red meat is associated with early onset of RA, especially in smokers or overweight patients. The findings indicate that eating less red meat could be a recommendation given to patients at risk for RA development.
Thrombomodulin is upregulated in the kidneys of women with pre-eclampsia
Authors: van Aanhold Cleo C. L. , Bos Manon , Mirabito Colafella Katrina M. , van der Hoorn Marie-Louise P. , Wolterbeek Ron , Bruijn Jan A. , Bloemenkamp Kitty W. M. , van den Meiracker Anton H. , Danser A. H. Jan , Baelde Hans J.
Published: March 2021

The endothelial glycoprotein thrombomodulin regulates coagulation, vascular inflammation and apoptosis. In the kidney, thrombomodulin protects the glomerular filtration barrier by eliciting crosstalk between the glomerular endothelium and podocytes. Several glomerular pathologies are characterized by a loss of glomerular thrombomodulin. In women with pre-eclampsia, serum levels of soluble thrombomodulin are increased, possibly reflecting a loss from the glomerular endothelium. We set out to investigate whether thrombomodulin expression is decreased in the kidneys of women with pre-eclampsia and rats exposed to an angiogenesis inhibitor. Thrombomodulin expression was examined using immunohistochemistry and qPCR in renal autopsy tissues collected from 11 pre-eclamptic women, 22 pregnant controls and 11 hypertensive non-pregnant women. Further, kidneys from rats treated with increasing doses of sunitinib or sunitinib in combination with endothelin receptor antagonists were studied. Glomerular thrombomodulin protein levels were increased in the kidneys of women with pre-eclampsia. In parallel, in rats exposed to sunitinib, glomerular thrombomodulin was upregulated in a dose-dependent manner, and the upregulation of glomerular thrombomodulin preceded the onset of histopathological changes. Selective ETAR blockade, but not dual ETA/BR blockade, normalised the sunitinib-induced increase in thrombomodulin expression and albuminuria. We propose that glomerular thrombomodulin expression increases at an early stage of renal damage induced by antiangiogenic conditions. The upregulation of this nephroprotective protein in glomerular endothelial cells might serve as a mechanism to protect the glomerular filtration barrier in pre-eclampsia.
Analysis of dynamic networks based on the Ising model for the case of study of co-authorship of scientific articles
Authors: Hurtado-Marín V. Andrea , Agudelo-Giraldo J. Dario , Robledo Sebastian , Restrepo-Parra Elisabeth
Published: March 2021

Two computational methods based on the Ising model were implemented for studying temporal dynamic in co-authorship networks: an interpretative for real networks and another for simulation via Monte Carlo. The objective of simulation networks is to evaluate if the Ising model describes in similar way the dynamic of the network and of the magnetic system, so that it can be found a generalized explanation to the behaviours observed in real networks. The scientific papers used for building the real networks were acquired from WoS core collection. The variables for each record took into account bibliographic references. The search equation for each network considered specific topics trying to obtain an advanced temporal evolution in terms of the addition of new nodes; that means 3 steps, a time to reach the interest of the scientific community, a gradual increase until reaching a peak and finally, a decreasing trend by losing of novelty. It is possible to conclude that both methods are consistent with each other, showing that the Ising model can predict behaviours such as the number and size of communities (or domains) according to the temporal distribution of new nodes.
Phylogeography and genetic diversity of the microbivalve Kidderia subquadrata, reveals new data from West Antarctic Peninsula
Authors: Levicoy Daniela , Flores Kamilla , Rosenfeld Sebastián , Cárdenas Leyla
Published: March 2021

It is well established that Antarctic biodiversity has been strongly influenced by rapid climatic fluctuations during the Quaternary. Marine invertebrates from Antarctica constitute an interesting lens through which to study the impacts of the last glacial periods as glaciation impacted the distribution and intraspecific genetic variation of these animals. However, the impact on the spatial genetic distribution and historical demography of local processes in areas adjacent to the West Antarctic Peninsula (WAP) is less clear. Here we present new genetic information on the bivalve Kidderia subquadrata, a small mollusk that inhabits intertidal rocky island ecosystems throughout the WAP. Using a phylogeographical approach, we examined the spatial patterns of genetic diversity in this brooder species to test the hypothesis of strong genetic structure in incubating organisms and the hypothesis of glacial refugia in organisms with limited dispersion. We found evidence of strong genetic structure among populations of the WAP and a recent expansion in the South Shetland Islands. Our findings are concordant with the predictions that incubating organisms, abundant in Antarctica, present a strong genetic structure among their populations and also support the hypothesis of glacial refugia in organisms with limited dispersion. The effect of the coastal current pattern in the WAP is suggested as a driver to the local spatial dynamics of the genetic diversity distribution. Although genetic information about this microbivalve is still scarce, the knowledge reported here has increased our understanding of the evolutionary patterns of this organism that is endemic to the Southern Ocean.