bluuebunny/crossref_metadata_2025 huggingface dataset:
All-optical polarization and amplitude modulation of second-harmonic generation in atomically thin semiconductors
Authors: Klimmer Sebastian , Ghaebi Omid , Gan Ziyang , George Antony , Turchanin Andrey , Cerullo Giulio , Soavi Giancarlo
Published: September 2021

Second-harmonic generation is of paramount importance in several fields of science and technology, including frequency conversion, self-referencing of frequency combs, nonlinear spectroscopy and pulse characterization. Advanced functionalities are enabled by modulation of the harmonic generation efficiency, which can be achieved with electrical or all-optical triggers. Electrical control of the harmonic generation efficiency offers large modulation depth at the cost of low switching speed, by contrast to all-optical nonlinear devices, which provide high speed and low modulation depth. Here we demonstrate all-optical modulation of second-harmonic generation in MoS2 with a modulation depth of close to 100% and speed limited only by the fundamental pulse duration. This result arises from a combination of D3h crystal symmetry and the deep subwavelength thickness of the sample, it can therefore be extended to the whole family of transition metal dichalcogenides to provide great flexibility in the design of advanced nonlinear optical devices such as high-speed integrated frequency converters, broadband autocorrelators for ultrashort pulse characterization, and tunable nanoscale holograms.
The largest and earliest known sample of dental caries in an extinct mammal (Mammalia, Euarchonta, Microsyops latidens) and its ecological implications
Authors: Selig Keegan R. , Silcox Mary T.
Published: September 2021

Dental cavities or caries is a common disease among modern humans, affecting almost every adult. Caries frequency has been used to study dietary change in humans over time, based on an inferred tie between the incidence of caries and a carbohydrate-rich diet. However, the disease is not unique to our species. Among non-human primates, there is also variation in caries frequency associated with diet, suggesting that this metric may provide a mechanism for studying diet in broader contexts, and across geological time. To date, very few studies have examined caries among fossil mammals, and none have done so among Eocene mammals. Here, we present our analysis of the largest sample to date of fossil caries in a single extinct mammal species,Microsyops latidens, a stem primate from the early Eocene, which is known from over a thousand specimens from the Southern Bighorn Basin of Wyoming (n = 1030). Our results show thatMicrosyops latidensis characterized by a high prevalence of dental caries (7.48% of individuals), with notable variation through time, reaching 17.24% of individuals from a particular interval. This interval is also associated with a change in overall dental form, as quantified by dental topographic analysis, which measures functional aspects of the chewing surface of teeth. These observations suggest that this species experienced a shift in their diet to include more fruit or other sugar rich-foods for a short period. Our analysis, therefore, suggests that the diet ofM. latidensfluctuated over time, as well as providing a framework for assessing caries in other fossil taxa.
Effect of particle size on phytochemical composition and antioxidant properties of Sargassum cristaefolium ethanol extract
Authors: Prasedya E. S. , Frediansyah A. , Martyasari N. W. R. , Ilhami B. K. , Abidin A. S. , Padmi H. , Fahrurrozi  , Juanssilfero A. B. , Widyastuti S. , Sunarwidhi A. L.
Published: September 2021

Sample particle size is an important parameter in the solid–liquid extraction system of natural products for obtaining their bioactive compounds. This study evaluates the effect of sample particle size on the phytochemical composition and antioxidant activity of brown macroalgae Sargassum cristaefolium. The crude ethanol extract was extracted from dried powders of S.cristeafolium with various particle sizes (> 4000 µm, > 250 µm, > 125 µm, > 45 µm, and < 45 µm). The ethanolic extracts of S.cristaefolium were analysed for Total Phenolic Content (TPC), Total Flavonoid Content (TFC), phenolic compound concentration and antioxidant activities. The extract yield and phytochemical composition were more abundant in smaller particle sizes. Furthermore, the TPC (14.19 ± 2.08 mg GAE/g extract to 43.27 ± 2.56 mg GAE/g extract) and TFC (9.6 ± 1.8 mg QE/g extract to 70.27 ± 3.59 mg QE/g extract) values also significantly increased as particle sizes decreased. In addition, phenolic compounds epicatechin (EC), epicatechin gallate (ECG), epigallocatechin (EGC), and Epigallocatechin gallate (EGCG) concentration were frequently increased in samples of smaller particle sizes based on two-way ANOVA and Tukey’s multiple comparison analysis. These results correlate with the significantly stronger antioxidant activity in samples with smaller particle sizes. The smallest particle size (< 45 µm) demonstrated the strongest antioxidant activity based on DPPH, ABTS, hydroxyl assay and FRAP. In addition, ramp function graph evaluates the desired particle size for maximum phytochemical composition and antioxidant activity is 44 µm. In conclusion, current results show the importance of particle size reduction of macroalgae samples to increase the effectivity of its biological activity.
Agricultural impacts of sustainable water use in the United States
Authors: Graham Neal T. , Iyer Gokul , Hejazi Mohamad I. , Kim Son H. , Patel Pralit , Binsted Matthew
Published: September 2021

Governance measures such as restrictions on groundwater pumping and adjustments to sectoral water pricing have been suggested as response strategies to curtail recent increases in groundwater pumping and enhance sustainable water use. However, little is known about the impacts of such sustainability strategies. We investigate the implications of such measures, with the United States (U.S.) as an example. Using the Global Change Analysis Model (GCAM) with state-level details in the U.S., we find that the combination of these two governance measures can drastically alter agricultural production in the U.S. The Southwest stands to lose upwards of 25% of their total agricultural production, much of which is compensated for by production increases in river basins on the east coast of the U.S. The implementation of future sustainable water governance measures will require additional investments that allow farmers to maximize production while minimizing water withdrawals to avoid potentially detrimental revenue losses.
Interaction of MS prevalence, radon gas concentration, and patient nutrition: a case–control study
Authors: Yakhdani Monire Fallah , Jalili Mahrokh , Salehi-Abargouei Amin , Mirzaei Masuod , Rahimdel Abolghasem , Ebrahimi Ali Asghar
Published: September 2021

In general, ecological findings indicate a positive correlation between MS and the intake of certain foods. This study aimed to investigate the relationship between radon (Rn) gas concentration and nutrition of patients in food groups with MS. Demographic information, diet, and building characteristics were collected by a questionnaire. Indoors Rn gas was measured using CR-39 detectors. Three models were used in the study of food intake. The interaction analysis between MS prevalence, diet, residential building characteristics, and Rn gas content was performed using SPSS 2020. The total Rn was significantly associated with cooling devices (P = 0.021). Buildings > 20 years had higher Rn concentrations than buildings < 20 years (P = 0.038). Also, no significant relationship was found between Rn-total and MS concentrations, but the total Rn concentration was higher in people homes with MS. Case group used more processed meat than the control (P < 0.001). The case group consumed more butter than the control, which was significant in Model III (P < 0.04). Tomato consumption in the case group was significantly higher than the control (P < 0.03). According to the results there was no interaction between Rn gas concentration in any of the food groups in each cases. However, future studies with larger sample sizes will be needed prospectively.
Second-generation cryoballoon versus contact force radiofrequency ablation for atrial fibrillation: an updated meta-analysis of evidence from randomized controlled trials
Authors: Wu Chenxia , Li Xinyi , Lv Zhengtian , Chen Qian , Lou Yang , Mao Wei , Zhou Xinbin
Published: September 2021

Catheter ablation has been recommended for patients with symptomatic atrial fibrillation (AF), with pulmonary vein isolation being the cornerstone of the ablation procedure. Newly developed technologies, such as cryoballoon ablation with a second-generation cryoballoon (CB2) and the contact force radiofrequency (CF-RF) ablation, have been introduced in recent years to overcome the shortcomings of the widely used RF ablation approach. However, high-quality results comparing CB2 and CF-RF remain controversial. Thus, we conducted this meta-analysis to assess the efficacy and safety between CB2 and CF-RF using evidence from randomized controlled trials (RCTs). Databases including Embase, PubMed, the Cochrane Library, and ClinicalTrials.gov were systematically searched from their date of inception to January 2021. Only RCTs that met the inclusion criteria were included for analysis. The primary outcome of interest was freedom from atrial tachyarrhythmia (AT) during follow-up. Secondary outcomes included procedure-related complications, procedure time and fluoroscopy time. Six RCTs with a total of 987 patients were finally enrolled. No significant differences were found between CB2 and CF-RF in terms of freedom from AT (relative risk [RR] = 1.03, 95% confidence interval [CI] 0.92–1.14,p = 0.616) or total procedural-related complications (RR = 1.25, 95% CI 0.69–2.27,p = 0.457). CB2 treatment was associated with a significantly higher risk of phrenic nerve palsy (PNP) than CF-RF (RR = 4.93, 95% CI 1.12–21.73,p = 0.035). The occurrences of pericardial effusion/tamponade and vascular complications were comparable between the CB2 and CF-RF treatments (RR = 0.41,p = 0.398; RR = 0.82,p = 0.632). In addition, CB2 treatment had a significantly shorter procedure time than CF-RF (weighted mean difference [WMD] = − 20.75 min, 95% CI − 25.44 ~ − 16.05 min,P < 0.001), whereas no difference was found in terms of fluoroscopy time (WMD = 4.63 min,p = 0.179). CB2 and CF-RF treatment are comparable for AF patients regarding freedom from AT and procedure-related complications. Compared to CF-RF, CB2 treatment was associated with a shorter procedure time but a higher incidence of PNP. Further large-scale studies are warranted to compare these two techniques and provide an up-to-date recommendation.
Probiotics combined with rifaximin influence the neurometabolic changes in a rat model of type C HE
Authors: Flatt Emmanuelle , McLin Valérie A. , Braissant Olivier , Pierzchala Katarzyna , Mastromarino Paola , Mitrea Stefanita-Octavian , Sessa Dario , Gruetter Rolf , Cudalbu Cristina
Published: September 2021

Type C hepatic encephalopathy (HE) is a neuropsychiatric disease caused by chronic liver disease. Management of type C HE remains an important challenge because treatment options are limited. Both the antibiotic rifaximin and probiotics have been reported to reduce the symptoms of HE, but longitudinal studies assessing their effects on brain metabolism are lacking and the molecular mechanisms underpinning their effects are not fully understood. Therefore, we evaluated in detail the effects of these different treatments on the neurometabolic changes associated with type C HE using a multimodal approach including ultra-high field in vivo 1H MRS. We analyzed longitudinally the effect of rifaximin alone or in combination with the probiotic Vivomixx on the brain metabolic profile in the hippocampus and cerebellum of bile duct ligated (BDL) rats, an established model of type C HE. Overall, while rifaximin alone appeared to induce no significant effect on the neurometabolic profile of BDL rats, its association with the probiotic resulted in more attenuated neurometabolic alterations in BDL rats followed longitudinally (i.e. a smaller increase in Gln and milder decrease in Glu and Cr levels). Given that both rifaximin and some probiotics are used in the treatment of HE, the implications of these findings may be clinically relevant.
Light entrainment of the SCN circadian clock and implications for personalized alterations of corticosterone rhythms in shift work and jet lag
Authors: Li Yannuo , Androulakis Ioannis P.
Published: September 2021

The suprachiasmatic nucleus (SCN) functions as the central pacemaker aligning physiological and behavioral oscillations to day/night (activity/inactivity) transitions. The light signal entrains the molecular clock of the photo-sensitive ventrolateral (VL) core of the SCN which in turn entrains the dorsomedial (DM) shell via the neurotransmitter vasoactive intestinal polypeptide (VIP). The shell converts the VIP rhythmic signals to circadian oscillations of arginine vasopressin (AVP), which eventually act as a neurotransmitter signal entraining the hypothalamic–pituitary–adrenal (HPA) axis, leading to robust circadian secretion of glucocorticoids. In this work, we discuss a semi-mechanistic mathematical model that reflects the essential hierarchical structure of the photic signal transduction from the SCN to the HPA axis. By incorporating the interactions across the core, the shell, and the HPA axis, we investigate how these coupled systems synchronize leading to robust circadian oscillations. Our model predicts the existence of personalized synchronization strategies that enable the maintenance of homeostatic rhythms while allowing for differential responses to transient and permanent light schedule changes. We simulated different behavioral situations leading to perturbed rhythmicity, performed a detailed computational analysis of the dynamic response of the system under varying light schedules, and determined that (1) significant interindividual diversity and flexibility characterize adaptation to varying light schedules; (2) an individual’s tolerances to jet lag and alternating shift work are positively correlated, while the tolerances to jet lag and transient shift work are negatively correlated, which indicates trade-offs in an individual’s ability to maintain physiological rhythmicity; (3) weak light sensitivity leads to the reduction of circadian flexibility, implying that light therapy can be a potential approach to address shift work and jet lag related disorders. Finally, we developed a map of the impact of the synchronization within the SCN and between the SCN and the HPA axis as it relates to the emergence of circadian flexibility.
Reinforcement learning derived chemotherapeutic schedules for robust patient-specific therapy
Authors: Eastman Brydon , Przedborski Michelle , Kohandel Mohammad
Published: September 2021

The in-silico development of a chemotherapeutic dosing schedule for treating cancer relies upon a parameterization of a particular tumour growth model to describe the dynamics of the cancer in response to the dose of the drug. In practice, it is often prohibitively difficult to ensure the validity of patient-specific parameterizations of these models for any particular patient. As a result, sensitivities to these particular parameters can result in therapeutic dosing schedules that are optimal in principle not performing well on particular patients. In this study, we demonstrate that chemotherapeutic dosing strategies learned via reinforcement learning methods are more robust to perturbations in patient-specific parameter values than those learned via classical optimal control methods. By training a reinforcement learning agent on mean-value parameters and allowing the agent periodic access to a more easily measurable metric, relative bone marrow density, for the purpose of optimizing dose schedule while reducing drug toxicity, we are able to develop drug dosing schedules that outperform schedules learned via classical optimal control methods, even when such methods are allowed to leverage the same bone marrow measurements.
Prolonged warm ischemia time leads to severe renal dysfunction of donation-after-cardiac death kidney grafts
Authors: Urbanellis Peter , Mazilescu Laura , Kollmann Dagmar , Linares-Cervantes Ivan , Kaths J. Moritz , Ganesh Sujani , Oquendo Fabiola , Sharma Manraj , Goto Toru , Noguchi Yuki , John Rohan , Konvalinka Ana , Mucsi Istvan , Ghanekar Anand , Bagli Darius , Robinson Lisa A. , Selzner Markus
Published: September 2021

Kidney transplantation with grafts procured after donation-after-cardiac death (DCD) has led to an increase in incidence of delayed graft function (DGF). It is thought that the warm ischemic (WI) insult encountered during DCD procurement is the cause of this finding, although few studies have been designed to definitely demonstrate this causation in a transplantation setting. Here, we use a large animal renal transplantation model to study the effects of prolonged WI during procurement on post-transplantation renal function. Kidneys from 30 kg-Yorkshire pigs were procured following increasing WI times of 0 min (Heart-Beating Donor), 30 min, 60 min, 90 min, and 120 min (n = 3–6 per group) to mimic DCD. Following 8 h of static cold storage and autotransplantation, animals were followed for 7-days. Significant renal dysfunction (SRD), resembling clinical DGF, was defined as the development of oliguria < 500 mL in 24 h from POD3-4 along with POD4 serum potassium > 6.0 mmol/L. Increasing WI times resulted in incremental elevation of post-operative serum creatinine that peaked later. DCD120min grafts had the highest and latest elevation of serum creatinine compared to all groups (POD5: 19.0 ± 1.1 mg/dL, p < 0.05). All surviving animals in this group had POD4 24 h urine output < 500 cc (mean 235 ± 172 mL) and elevated serum potassium (7.2 ± 1.1 mmol/L). Only animals in the DCD120min group fulfilled our criteria of SRD (p = 0.003), and their renal function improved by POD7 with 24 h urine output > 500 mL and POD7 serum potassium < 6.0 mmol/L distinguishing this state from primary non-function. In a transplantation survival model, this work demonstrates that prolonging WI time similar to that which occurs in DCD conditions contributes to the development of SRD that resembles clinical DGF.
Predicting severe outcomes using national early warning score (NEWS) in patients identified by a rapid response system: a retrospective cohort study
Authors: Kim Sang Hyuk , Choi Hye Suk , Jin Eun Suk , Choi Hayoung , Lee Hyun , Lee Sang-Hwa , Lee Chang Youl , Lee Myung Goo , Kim Youlim
Published: September 2021

There are insufficient data in managing patients at high risk of deterioration. We aimed to investigate that national early warning score (NEWS) could predict severe outcomes in patients identified by a rapid response system (RRS), focusing on the patient’s age. We conducted a retrospective cohort study from June 2019 to December 2020. Outcomes were unplanned intensive care unit (ICU) admission, ICU mortality, and in-hospital mortality. We analyzed the predictive ability of NEWS using receiver operating characteristics (ROC) curve and the effect of NEWS parameters using multivariable logistic regression. A total of 2,814 RRS activations were obtained. The predictive ability of NEWS for unplanned ICU admission and in-hospital mortality was fair but was poor for ICU mortality. The predictive ability of NEWS showed no differences between patients aged 80 years or older and under 80 years. However, body temperature affected in-hospital mortality for patients aged 80 years or older, and the inverse effect on unplanned ICU admission was observed. The NEWS showed fair predictive ability for unplanned ICU admission and in-hospital mortality among patients identified by the RRS. The different presentations of patients 80 years or older should be considered in implementing the RRS.
Mean-field model of melting in superheated crystals based on a single experimentally measurable order parameter
Authors: Kryuchkov Nikita P. , Dmitryuk Nikita A. , Li Wei , Ovcharov Pavel V. , Han Yilong , Sapelkin Andrei V. , Yurchenko Stanislav O.
Published: September 2021

Melting is one of the most studied phase transitions important for atomic, molecular, colloidal, and protein systems. However, there is currently no microscopic experimentally accessible criteria that can be used to reliably track a system evolution across the transition, while providing insights into melting nucleation and melting front evolution. To address this, we developed a theoretical mean-field framework with the normalised mean-square displacement between particles in neighbouring Voronoi cells serving as the local order parameter, measurable experimentally. We tested the framework in a number of colloidal and in silico particle-resolved experiments against systems with significantly different (Brownian and Newtonian) dynamic regimes and found that it provides excellent description of system evolution across melting point. This new approach suggests a broad scope for application in diverse areas of science from materials through to biology and beyond. Consequently, the results of this work provide a new guidance for nucleation theory of melting and are of broad interest in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.
Modeling hydrogen solubility in hydrocarbons using extreme gradient boosting and equations of state
Authors: Mohammadi Mohammad-Reza , Hadavimoghaddam Fahime , Pourmahdi Maryam , Atashrouz Saeid , Munir Muhammad Tajammal , Hemmati-Sarapardeh Abdolhossein , Mosavi Amir H. , Mohaddespour Ahmad
Published: September 2021

Due to industrial development, designing and optimal operation of processes in chemical and petroleum processing plants require accurate estimation of the hydrogen solubility in various hydrocarbons. Equations of state (EOSs) are limited in accurately predicting hydrogen solubility, especially at high-pressure or/and high-temperature conditions, which may lead to energy waste and a potential safety hazard in plants. In this paper, five robust machine learning models including extreme gradient boosting (XGBoost), adaptive boosting support vector regression (AdaBoost-SVR), gradient boosting with categorical features support (CatBoost), light gradient boosting machine (LightGBM), and multi-layer perceptron (MLP) optimized by Levenberg–Marquardt (LM) algorithm were implemented for estimating the hydrogen solubility in hydrocarbons. To this end, a databank including 919 experimental data points of hydrogen solubility in 26 various hydrocarbons was gathered from 48 different systems in a broad range of operating temperatures (213–623 K) and pressures (0.1–25.5 MPa). The hydrocarbons are from six different families including alkane, alkene, cycloalkane, aromatic, polycyclic aromatic, and terpene. The carbon number of hydrocarbons is ranging from 4 to 46 corresponding to a molecular weight range of 58.12–647.2 g/mol. Molecular weight, critical pressure, and critical temperature of solvents along with pressure and temperature operating conditions were selected as input parameters to the models. The XGBoost model best fits all the experimental solubility data with a root mean square error (RMSE) of 0.0007 and an average absolute percent relative error (AAPRE) of 1.81%. Also, the proposed models for estimating the solubility of hydrogen in hydrocarbons were compared with five EOSs including Soave–Redlich–Kwong (SRK), Peng–Robinson (PR), Redlich–Kwong (RK), Zudkevitch–Joffe (ZJ), and perturbed-chain statistical associating fluid theory (PC-SAFT). The XGBoost model introduced in this study is a promising model that can be applied as an efficient estimator for hydrogen solubility in various hydrocarbons and is capable of being utilized in the chemical and petroleum industries.
Acoustic tweezing of microparticles in microchannels with sinusoidal cross sections
Authors: Jannesar Elnaz Attar , Hamzehpour Hossein
Published: September 2021

Acoustic tweezing of bioparticles has distinct advantages over other manipulation methods such as electrophoresis or magnetophoresis in biotechnological applications. This manipulation method guarantees the viability of the bio-particles during and after the process. In this paper, the effects of sinusoidal boundaries of a microchannel on acoustophoretic manipulation of microparticles are studied. Our results show that while top and bottom walls are vertically actuated at the horizontal half-wave resonance frequency, a large mono-vortex appears, which is never achievable in a rectangular geometry with flat walls and one-dimensional oscillations. The drag force caused by such a vortex in combination with the tilted acoustic radiation force leads to trapping and micromixing of microparticles with diameters larger and smaller than the critical size, respectively. Simulation results in this paper show that efficient particle trapping occurs at the intermediate sinusoidal boundary amplitudes. It is also indicated that in a square-sinusoidal geometry there are two strong vortices, instead of one vortex. Sub-micrometer particles tend to be trapped dramatically faster in such a geometry than in the rectangular-sinusoidal ones.
Fixation probabilities in network structured meta-populations
Authors: Yagoobi Sedigheh , Traulsen Arne
Published: September 2021

The effect of population structure on evolutionary dynamics is a long-lasting research topic in evolutionary ecology and population genetics. Evolutionary graph theory is a popular approach to this problem, where individuals are located on the nodes of a network and can replace each other via the links. We study the effect of complex network structure on the fixation probability, but instead of networks of individuals, we model a network of sub-populations with a probability of migration between them. We ask how the structure of such a meta-population and the rate of migration affect the fixation probability. Many of the known results for networks of individuals carry over to meta-populations, in particular for regular networks or low symmetric migration probabilities. However, when patch sizes differ we find interesting deviations between structured meta-populations and networks of individuals. For example, a two patch structure with unequal population size suppresses selection for low migration probabilities.
Flow estimation solely from image data through persistent homology analysis
Authors: Suzuki Anna , Miyazawa Miyuki , Minto James M. , Tsuji Takeshi , Obayashi Ippei , Hiraoka Yasuaki , Ito Takatoshi
Published: September 2021

Topological data analysis is an emerging concept of data analysis for characterizing shapes. A state-of-the-art tool in topological data analysis is persistent homology, which is expected to summarize quantified topological and geometric features. Although persistent homology is useful for revealing the topological and geometric information, it is difficult to interpret the parameters of persistent homology themselves and difficult to directly relate the parameters to physical properties. In this study, we focus on connectivity and apertures of flow channels detected from persistent homology analysis. We propose a method to estimate permeability in fracture networks from parameters of persistent homology. Synthetic 3D fracture network patterns and their direct flow simulations are used for the validation. The results suggest that the persistent homology can estimate fluid flow in fracture network based on the image data. This method can easily derive the flow phenomena based on the information of the structure.
Development of an automated system to measure ion channel currents using a surface-modified gold probe
Authors: Hirano Minako , Tomita Masahisa , Takahashi Chikako , Kawashima Nobuyuki , Ide Toru
Published: September 2021

Artificial lipid bilayer single-channel recording technique has been employed to determine the biophysical and pharmacological properties of various ion channels. However, its measurement efficiency is very low, as it requires two time-consuming processes: preparation of lipid bilayer membranes and incorporation of ion channels into the membranes. In order to address these problems, we previously developed a technique based on hydrophilically modified gold probes on which are immobilized ion channels that can be promptly incorporated into the bilayer membrane at the same time as the membrane is formed on the probes’ hydrophilic area. Here, we improved further this technique by optimizing the gold probe and developed an automated channel current measurement system. We found that use of probes with rounded tips enhanced the efficiency of channel current measurements, and introducing a hydrophobic area on the probe surface, beside the hydrophilic one, further increased measurement efficiency by boosting membrane stability. Moreover, we developed an automated measurement system using the optimized probes; it enabled us to automatically measure channel currents and analyze the effects of a blocker on channel activity. Our study will contribute to the development of high-throughput devices to identify drug candidates affecting ion channel activity.
Atomic-resolution STEM-EDS studies of cation ordering in Ti-Nb oxide crystals
Authors: Iijima Sumio , Ohnishi Ichiro , Liu Zheng
Published: September 2021

Ternary metal oxide compounds, such as Ti-Nb and Nb-W oxides, have renewed research interest in energy storage materials because these oxides contain multivalent metal ions that may be able to control the ion transport in solid lithium batteries. One of these oxides is Ti2Nb10O29, which is composed of metal–oxygen octahedra connected through corner-sharing and edge-sharing to form “block structures”. In the early 1970s Von Dreele and Cheetham proposed a metal-atoms ordering in this oxide crystal using Rietveld refined neutron powder diffraction method. Most recent studies on these oxides, however, have not considered cation ordering in evaluating the battery electrode materials. In this paper, by utilizing the latest scanning transmission electron microscopy combined with energy dispersive X-ray spectroscopy imaging technology, the cation chemical ordering in those oxide crystals was directly revealed at atomic resolution.
The gastric microbiota in patients with Crohn’s disease; a preliminary study
Authors: Ostrowski Jerzy , Kulecka Maria , Zawada Iwona , Żeber-Lubecka Natalia , Paziewska Agnieszka , Graca-Pakulska Katarzyna , Dąbkowski Krzysztof , Skubisz Karolina , Cybula Patrycja , Ambrożkiewicz Filip , Urasińska Elżbieta , Mikula Michał , Starzyńska Teresa
Published: September 2021

The gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.
TLR4-interactor with leucine-rich repeats (TRIL) is involved in diet-induced hypothalamic inflammation
Authors: Moura-Assis Alexandre , Nogueira Pedro A. S. , de-Lima-Junior Jose C. , Simabuco Fernando M. , Gaspar Joana M. , Donato Jr Jose , Velloso Licio A.
Published: September 2021

Obesity and high-fat diet (HFD) consumption result in hypothalamic inflammation and metabolic dysfunction. While the TLR4 activation by dietary fats is a well-characterized pathway involved in the neuronal and glial inflammation, the role of its accessory proteins in diet-induced hypothalamic inflammation remains unknown. Here, we demonstrate that the knockdown of TLR4-interactor with leucine-rich repeats (Tril), a functional component of TLR4, resulted in reduced hypothalamic inflammation, increased whole-body energy expenditure, improved the systemic glucose tolerance and protection from diet-induced obesity. The POMC-specific knockdown of Tril resulted in decreased body fat, decreased white adipose tissue inflammation and a trend toward increased leptin signaling in POMC neurons. Thus, Tril was identified as a new component of the complex mechanisms that promote hypothalamic dysfunction in experimental obesity and its inhibition in the hypothalamus may represent a novel target for obesity treatment.
Pleiotropic effects between cardiovascular disease risk factors and measures of cognitive and physical function in long-lived adults
Authors: Yudkovicz Julia J. , Minster Ryan L. , Barinas-Mitchell Emma , Christensen Kaare , Feitosa Mary , Barker Megan S. , Newman Anne B. , Kuipers Allison L.
Published: September 2021

Cardiovacular disease (CVD) is the leading cause of death among older adults and is often accompanied by functional decline. It is unclear what is driving this co-occurrence, but it may be behavioral, environmental and/or genetic. We used a family-based study to estimate the phenotypic and shared genetic correlation between CVD risk factors and physical and cognitive functional measures. Participants (n = 1,881) were from the Long Life Family Study, which enrolled families based on their exceptional longevity (sample mean age = 69.4 years, 44% female). Cardiovascular disease risk factors included carotid vessel measures [intima-media thickness and inter-adventitial diameter], obesity [body mass index (BMI) and waist circumference], and hypertension [systolic and diastolic blood pressures]. Function was measured in the physical [gait speed, grip strength, chair stand] and cognitive [digital symbol substitution test, retained and working memory, semantic fluency, and trail making tests] domains. We used SOLAR to estimate the genetic, environmental, and phenotypic correlation between each pair adjusting for age, age2, sex, field center, smoking, height, and weight. There were significant phenotypic correlations (range |0.05–0.22|) between CVD risk factors and physical and cognitive function (all P < 0.05). Most significant genetic correlations (range |0.21–0.62|) were between CVD risk factorsand cognitive function, although BMI and waist circumference had significant genetic correlation with gait speed and chair stand time (range |0.29–0.53|; all P < 0.05). These results suggest that CVD risk factors may share a common genetic-and thus, biologic-basis with both cognitive and physical function. This is particularly informative for research into the genetic determinants of chronic disease.
Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Authors: Hul Ludmila Mudri , Ibelli Adriana Mércia Guaratini , Savoldi Igor Ricardo , Marcelino Débora Ester Petry , Fernandes Lana Teixeira , Peixoto Jane Oliveira , Cantão Maurício Egídio , Higa Roberto Hiroshi , Giachetto Poliana Fernanda , Coutinho Luiz Lehmann , Ledur Mônica Corrêa
Published: September 2021

Locomotor problems are among one of the main concerns in the current poultry industry, causing major economic losses and affecting animal welfare. The most common bone anomalies in the femur are dyschondroplasia, femoral head separation (FHS), and bacterial chondronecrosis with osteomyelitis (BCO), also known as femoral head necrosis (FHN). The present study aimed to identify differentially expressed (DE) genes in the articular cartilage (AC) of normal and FHS-affected broilers by RNA-Seq analysis. In the transcriptome analysis, 12,169 genes were expressed in the femur AC. Of those, 107 genes were DE (FDR < 0.05) between normal and affected chickens, of which 9 were downregulated and 98 were upregulated in the affected broilers. In the gene-set enrichment analysis using the DE genes, 79 biological processes (BP) were identified and were grouped into 12 superclusters. The main BP found were involved in the response to biotic stimulus, gas transport, cellular activation, carbohydrate-derived catabolism, multi-organism regulation, immune system, muscle contraction, multi-organism process, cytolysis, leukocytes and cell adhesion. In this study, the first transcriptome analysis of the broilers femur articular cartilage was performed, and a set of candidate genes (AvBD1,AvBD2,ANK1,EPX,ADA,RHAG) that could trigger changes in the broiler´s femoral growth plate was identified. Moreover, these results could be helpful to better understand FHN in chickens and possibly in humans.
Global analysis of lysine acetylation in soybean leaves
Authors: Li Geng , Zheng Bin , Zhao Wei , Ren Tinghu , Zhang Xinghui , Ning Tangyuan , Liu Peng
Published: September 2021

Protein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.
Tracking of the biochemical changes upon pleomorphic adenoma progression using vibrational microspectroscopy
Authors: Paluszkiewicz Czesława , Roman Maciej , Piergies Natalia , Pięta Ewa , Woźniak Monika , Guidi Mariangela Cestelli , Miśkiewicz-Orczyk Katarzyna , Marków Magdalena , Ścierski Wojciech , Misiołek Maciej , Drozdzowska Bogna , Kwiatek Wojciech M.
Published: September 2021

Head and neck tumors can be very challenging to treat because of the risk of problems or complications after surgery. Therefore, prompt and accurate diagnosis is extremely important to drive appropriate treatment decisions, which may reduce the chance of recurrence. This paper presents the original research exploring the feasibility of Fourier transform infrared (FT-IR) and Raman spectroscopy (RS) methods to investigate biochemical alterations upon the development of the pleomorphic adenoma. Principal component analysis (PCA) was used for a detailed assessment of the observed changes and to determine the spectroscopic basis for salivary gland neoplastic pathogenesis. It is implied that within the healthy margin, as opposed to the tumoral tissue, there are parts that differ significantly in lipid content. This observation shed new light on the crucial role of lipids in tissue physiology and tumorigenesis. Thus, a novel approach that eliminates the influence of lipids on the elucidation of biochemical changes is proposed. The performed analysis suggests that the highly heterogeneous healthy margin contains more unsaturated triacylglycerols, while the tumoral section is rich in proteins. The difference in protein content was also observed for these two tissue types, i.e. the healthy tissue possesses more proteins in the anti-parallel β-sheet conformation, whereas the tumoral tissue is dominated by proteins rich in unordered random coils. Furthermore, the pathogenic tissue shows a higher content of carbohydrates and reveals noticeable differences in nucleic acid content. Finally, FT-IR and Raman spectroscopy methods were proposed as very promising methods in the discrimination of tumoral and healthy tissues of the salivary gland.
Occupational exposure and markers of genetic damage, systemic inflammation and lung function: a Danish cross-sectional study among air force personnel
Authors: Andersen Maria Helena Guerra , Saber Anne Thoustrup , Frederiksen Marie , Clausen Per Axel , Sejbaek Camilla Sandal , Hemmingsen Caroline Hallas , Ebbehøj Niels E. , Catalán Julia , Aimonen Kukka , Koivisto Joonas , Loft Steffen , Møller Peter , Vogel Ulla
Published: September 2021

Air force ground crew personnel are potentially exposed to fuels and lubricants, as raw materials, vapours and combustion exhaust emissions, during operation and maintenance of aircrafts. This study investigated exposure levels and biomarkers of effects for employees at a Danish air force military base. We enrolled self-reported healthy and non-smoking employees (n = 79) and grouped them by exposure based on job function, considered to be potentially exposed (aircraft engineers, crew chiefs, fuel operators and munition specialists) or as reference group with minimal occupational exposure (avionics and office workers). We measured exposure levels to polycyclic aromatic hydrocarbons (PAHs) and organophosphate esters (OPEs) by silicone bands and skin wipes (PAHs only) as well as urinary excretion of PAH metabolites (OH-PAHs). Additionally, we assessed exposure levels of ultrafine particles (UFPs) in the breathing zone for specific job functions. As biomarkers of effect, we assessed lung function, plasma levels of acute phase inflammatory markers, and genetic damage levels in peripheral blood cells. Exposure levels of total PAHs, OPEs and OH-PAHs did not differ between exposure groups or job functions, with low correlations between PAHs in different matrices. Among the measured job functions, the UFP levels were higher for the crew chiefs. The exposure level of the PAH fluorene was significantly higher for the exposed group than the reference group (15.9 ± 23.7 ng/g per 24 h vs 5.28 ± 7.87 ng/g per 24 h, p = 0.007), as was the OPE triphenyl phosphate (305 ± 606 vs 19.7 ± 33.8 ng/g per 24 h, p = 0.011). The OPE tris(1,3-dichlor-2-propyl)phosphate had a higher mean in the exposed group (60.7 ± 135 ng/g per 24 h) compared to the reference group (8.89 ± 15.7 ng/g per 24 h) but did not reach significance. No evidence of effects for biomarkers of systemic inflammation, genetic damage or lung function was found. Overall, our biomonitoring study show limited evidence of occupational exposure of air force ground crew personnel to UFPs, PAHs and OPEs. Furthermore, the OH-PAHs and the assessed biomarkers of early biological effects did not differ between exposed and reference groups.
Association between telomere length and hepatic fibrosis in non-alcoholic fatty liver disease
Authors: Shin Hee Kyung , Park Jeong Hwan , Yu Jung Hwan , Jin Young-Joo , Suh Young Ju , Lee Jin-Woo , Kim Won ,   The Korean Nonalcoholic Fatty Liver Study Group (KNSG)
Published: September 2021

Telomere length has been linked to the prevalence and progression of metabolic disease. However, clinical implications of telomere length in biopsy-proven non-alcoholic fatty liver disease (NAFLD) patients remain unclear. Therefore, this study aimed to investigate the association of telomere length with the histological severity of NAFLD. The cross-sectional data derived from the prospectively enrolled Boramae NAFLD registry (n = 91) were analyzed. The liver tissues and clinical information were obtained from both NAFLD patients and non-NAFLD subjects. Binary logistic regression was performed to identify the independent association between telomere length and the histological severity of NAFLD. A total of 83 subjects with or without biopsy-proven NAFLD were included for analysis: non-NAFLD in 23 (27.7%), non-alcoholic fatty liver in 15 (18.1%), and non-alcoholic steatohepatitis (NASH) in 45 (54.2%). Telomere length measured from liver tissues showed a strong negative correlation (p < 0.001) with age, regardless of NAFLD status. Therefore, telomere length was corrected for age. Age-adjusted telomere length than decreased gradually with an increasing severity of fibrosis in patients with NAFLD (p < 0.028). In multivariate analysis, age-adjusted telomere length (odds ratio [OR] 0.59; 95% CI 0.37–0.92; p = 0.019) and high-density lipoprotein cholesterol (OR 0.94; 95% CI 0.80–0.99; p = 0.039) were independently associated with significant fibrosis. The age-adjusted telomere length tends to decrease along with the fibrosis stage of NAFLD. In particular, among the histological components of NAFLD, fibrosis severity seems to be related to telomere length in the liver.
Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains
Authors: Urzi Felicita , Šprem Nikica , Potočnik Hubert , Sindičić Magda , Konjević Dean , Ćirović Duško , Rezić Andrea , Duniš Luka , Melovski Dime , Buzan Elena
Published: September 2021

Habitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056–0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.