bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical genetics of regeneration: Contrasting temporal effects of CoCl2 on axolotl tail regeneration
Authors: Baddar Nour W. Al Haj , Dwaraka Varun B. , Ponomareva Larissa V. , Thorson Jon S. , Voss S. Randal 
Published: January 2021

AbstractBackgroundHistone deacetylases (HDACs) regulate transcriptional responses to injury stimuli that are critical for successful tissue regeneration. Previously we showed that HDAC inhibitor romidepsin potently inhibits axolotl tail regeneration when applied for only 1‐minute postamputation (MPA).ResultsHere we tested CoCl2, a chemical that induces hypoxia and cellular stress, for potential to reverse romidepsin inhibition of tail regeneration. Partial rescue of regeneration was observed among embryos co‐treated with romidepsin and CoCl2 for 1 MPA, however, extending the CoCl2 dosage window either inhibited regeneration (CoCl2:0 to 30 MPA) or was lethal (CoCl2:0 to 24 hours postamputation; HPA). CoCl2:0 to 30 MPA caused tissue damage, tissue loss, and cell death at the distal tail tip, while CoCl2 treatment of non‐amputated embryos or CoCl2:60 to 90 MPA treatment after re‐epithelialization did not inhibit tail regeneration. CoCl2‐romidepsin:1 MPA treatment partially restored expression of transcription factors that are typical of appendage regeneration, while CoCl2:0 to 30 MPA significantly increased expression of genes associated with cell stress and inflammation. Additional experiments showed that CoCl2:0 to 1 MPA and CoCl2:0 to 30 MPA significantly increased levels of glutathione and reactive oxygen species, respectively.ConclusionOur study identifies a temporal window from tail amputation to re‐epithelialization, within which injury activated cells are highly sensitive to CoCl2 perturbation of redox homeostasis.
Mechanism and restoration strategy of lysosomal abnormalities induced by urinary protein overload in proximal tubule epithelial cells
Authors: Li Xiaoyu , Zou Ting , Wang Shujun , Wu Hongluan , Wu Man , Liu Zejian , Liu Huafeng 
Published: January 2021

AbstractBackgroundPersistent elevated concentrations of urinary protein can destroy proximal tubule epithelial cells (PTECs) by inducing lysosomal abnormalities, thereby aggravating PTEC damage and renal fibrosis. However, the specific mechanisms of these serial biochemical events and methods for treating or preventing PTEC damage upon proteinuria need further investigation.ResultsIn this study, electron microscopy and dual‐labeled immunofluorescence analysis for identifying lysosome type revealed inadequate primary lysosome biogenesis and secondary lysosome accumulation in the PTECs of patients with minimal change nephrotic syndrome or membranous nephropathy who suffered from proteinuria. In vitro studies on HK‐2 cells indicated that this abnormality was associated with decreased expression of transcription factor EB (TFEB). In contrast, TFEB overexpressing HK‐2 cells under urinary protein overload exhibited significantly reduced accumulation of secondary lysosomes and increased proportion and quantity of primary lysosomes as indicated by dual‐labeled immunofluorescence. Further, these cells could upregulate lysosomal degradation functions, as determined using Cathepsin L activity assays and flow cytometry for dye quenched‐albumin.ConclusionsThese results indicate that abnormal TFEB expression is a key mechanism of lysosomal dyshomeostasis caused by protein overload in PTECs. TFEB is thus a potential therapeutic target for the treatment of urinary protein‐related kidney disease.
COVID‐19‐convalescence phase unmasks a silent myocardial infarction due to coronary plaque rupture
Authors: Tschöpe Carsten , Sherif Mohammad , Anker Markus S. , Geisel Dominik , Kuehne Titus , Kelle Sebastian 
Published: January 2021

AbstractIncreased risk of cardiovascular complications during and post‐COVID‐19 infection is more and more recognized—including myocarditis, arrhythmias, and myocardial infarctions (MIs). The mechanisms leading to these complications are direct virus‐induced injuries, as well as potential thrombotic and inflammatory‐induced mechanisms. To the latter, inflammatory plaque instability and plaque rupture are discussed entities contributing to MI‐induced post‐COVID‐19 complications. Our case report describes the first time, when a temporary impairment of LVEF in the COVID‐19‐convalescence phase unmasks a silent MI due to coronary plaque rupture by using invasive (OCT) and non‐invasive (CMR) modalities. Myocardial infarction might be an important differential diagnosis to consider in deteriorating patients with COVID‐19, especially if dyspnoea persists after acute infection.
Monitoring cell productivity for the production of recombinant proteins by flow cytometry: An effective application using the cold capture assay
Authors: Meyer Katharina V. , Siller Ina G. , Schellenberg Jana , Gonzalez Salcedo Alina , Solle Dörte , Matuszczyk Jens , Scheper Thomas , Bahnemann Janina 
Published: January 2021

AbstractDue to the increasing economic and social relevance of biotherapeutics, their production processes are continually being reconsidered and reoptimized in an effort to secure higher product concentrations and qualities. Monitoring the productivity of cultured cells is therefore a critically important part of the cultivation process. Traditionally, this is achieved by determining the overall product titer by high performance liquid chromatography (HPLC), and then calculating the specific cell productivity based on this titer and an associated viable cell density. Unfortunately, this process is typically time‐consuming and laborious. In this study, the productivity of Chinese Hamster Ovary (CHO) cells expressing a monoclonal antibody was analyzed over the course of the cultivation process. In addition to calculating the specific cell productivity based on the traditional product titer determined by HPLC analysis, culture productivity of single cells was also analyzed via flow cytometry using a cold capture assay. The cold capture assay is a cell surface labelling technique described by Brezinsky et al., which allows for the visualization of a product on the surface of the producing cell. The cell productivity results obtained via HPLC and the results of cold capture assay remained in great accordance over the whole cultivation process. Accordingly, our study demonstrates that the cold capture assay offers an interesting, comparatively time‐effective, and potentially cheaper alternative for monitoring the productivity of a cell culture.
pyFOOMB: Python framework for object oriented modeling of bioprocesses
Authors: Hemmerich Johannes , Tenhaef Niklas , Wiechert Wolfgang , Noack Stephan 
Published: January 2021

AbstractQuantitative characterization of biotechnological production processes requires the determination of different key performance indicators (KPIs) such as titer, rate and yield. Classically, these KPIs can be derived by combining black‐box bioprocess modeling with non‐linear regression for model parameter estimation. The presented pyFOOMB package enables a guided and flexible implementation of bioprocess models in the form of ordinary differential equation systems (ODEs). By building on Python as powerful and multi‐purpose programing language, ODEs can be formulated in an object‐oriented manner, which facilitates their modular design, reusability, and extensibility. Once the model is implemented, seamless integration and analysis of the experimental data is supported by various Python packages that are already available. In particular, for the iterative workflow of experimental data generation and subsequent model parameter estimation we employed the concept of replicate model instances, which are linked by common sets of parameters with global or local properties. For the description of multi‐stage processes, discontinuities in the right‐hand sides of the differential equations are supported via event handling using the freely available assimulo package. Optimization problems can be solved by making use of a parallelized version of the generalized island approach provided by the pygmo package. Furthermore, pyFOOMB in combination with Jupyter notebooks also supports education in bioprocess engineering and the applied learning of Python as scientific programing language. Finally, the applicability and strengths of pyFOOMB will be demonstrated by a comprehensive collection of notebook examples.
Enhancing potential of hydrofracturing in mylonitic coal by biocementation
Authors: Song Chenpeng , Zhi Sheng , Feng Gan , Lin Junzhi 
Published: January 2021

AbstractMylonite coal is a representative of tectonically deformed coal and is a result of crushing original coal into fine coal grains under strong shear or long‐low tectonic stress. Because of its granular nature and the resultant inferior mechanical property, it is difficult to initiate fluid‐driven fractures within mylonitic coal reservoirs for enhancing coalbed methane recovery. The following explores a biomineralization method of microbially mediated calcium carbonate precipitation (MICP) to enhance the structural integrity and mechanical strength of mylonitic coal, enabling potential success for hydrofracturing. The experimental results indicate that the mechanical properties of mylonite coal are significantly enhanced after a short period of MICP treatment with ten cycles of treatments yielding a maximum uniaxial compressive strength (UCS) of 8.7 MPa and a maximum brittleness index of 0.218 approaching that of the hard coal. The increments in UCS and brittleness of biocemented mylonite coal show a positive correlation with the generated calcium carbonate content. Scanning electron microscopy (SEM) imaging indicates that the generated calcium carbonate precipitates first randomly occur on the particle surfaces, and then occupies the interstitial space until particle‐particle bonds are developed. The irregular morphology of coal particles results in two contact relations between particles, point contact and planar contact, causing a significant difference in biocementation effectiveness. Two microfailure patterns of biocemented coal with uniaxial compression are observed. One is that the coal particles are crushed, and the other occurs at the biocemented interface between the coal particles and calcium carbonate crystals.
Developing Hazard Rating Calculation Methodologies for Per- and Polyfluoroalkyl Substances
Authors: McDougall Mandy R.R. , Kalinovich Indra 
Published: January 2021

Abstract
Historical and present-day use of per- and polyfluoroalkyl substances (PFAS) have been linked to environmental and human health impacts that prove challenging to address. Therefore, prioritization of PFAS management based on observed or predicted toxicological properties and environmental fate is critical in the development of effective risk management practices. Hazard rating calculations use a range of literature-derived quantitative data to identify and rank the potential risk posed by a contaminant of concern associated with an activity or land use. The present study describes the use of hazard rating calculation methodologies to evaluate PFAS at federally owned properties across Canada. The hazard rating calculations assess potential site impacts from the use of PFAS, including application of PFAS-containing aqueous film-forming foam (AFFF) at fire-fighting training areas (FFTAs). Eleven PFAS were evaluated based on their prevalence or use in AFFFs and the availability of established chemical data. The hazard rating evaluated 4 properties: human health, environmental fate, deleterious quantity, and release and impact modifier. In the present study, hazard ratings calculated for perfluorohexane sulfonate, perfluoroheptanoate, and 8:2 fluorotelomer sulfonate were greater than for the remaining evaluated PFAS. This hazard rating system is beneficial for selecting and/or developing site management or remediation strategies. The methodology supports a comprehensive, site-scale approach for prioritizing PFAS management, and can be integrated into future regulatory framework and contaminant prioritization. Environ Toxicol Chem 2021;40:937–946. © 2021 SETAC
Increasing farm size to improve energy use efficiency and sustainability in maize production
Authors: Zhang Wushuai , Qian Chunrong , Carlson Kimberly M. , Ge Xuanliang , Wang Xingbang , Chen Xinping 
Published: January 2021

AbstractWhile the relationship between crop yields and the environmental impacts of crop agriculture has been well‐documented, research on the relationship between farm size and the sustainability of cereal production is limited. Using survey data on 120 farms with both small‐ and large‐scale fields in Northeast China, this paper combines a life cycle assessment and the carbon‐based sustainability index (SI) algorithm to examine how maize productivity and agricultural inputs vary with farm size and to clarify how increasing farm size is correlated with energy use efficiency (EUE) and the SI. The results indicate that maize grain yield did not vary with farm size. Increasing farm size was shown to lead to reductions in the areal (per ha) rates of agro‐chemical inputs, energy depletion, and greenhouse gas emissions and increased in EUE and SI. Fertilizer‐ and fuel‐related agricultural inputs dominated the variations of EUE and SI. A scenario analysis indicates that, if farmers adopt a comprehensive management strategy (i.e., machines appropriate to farm size and recommended fertilizer application rates and crop management strategies), EUE and SI would increase by 68.5% (from 4.45 to 7.50) and 74.3% (from 10.1 to 17.6), respectively. Although increasing farm size could benefit maize sustainable production when matched with technical innovation and machinery coordination, supporting smallholder farmers to increase their resource use efficiency and sustainability is also key in China and other regions where smallholder farms comprise a large portion of the cropland area.
Application of an environmental multimedia modeling system for health risk assessment: Key influencing factors and uncertainties research
Authors: Yuan Jing , Chen Zhi , Ding Shimin , Zhang Qianfeng , Jia Yong 
Published: January 2021

Abstract
In this paper, an environmental multimedia modeling system (EMMS) that combines a risk assessment with a Monte Carlo method (MCM) was used to explore the interaction between groundwater and surface water with respect to chemical exposure and risk. The EMMS-MCM simulations incorporated several key influencing factors that are inherent in traditional predictions of subsurface and surface-water interactions, including soil permeability coefficients and parameters such as hydraulic conductivity, density, recharge, layers, and depth. These influencing factors are generally associated with the largest sources of uncertainty in modeling and pose significant challenges to water management and to the optimal allocation of water resources. A case study involving benzene at the Trail Road landfill site located in the Ottawa–Carlton area of Canada is presented to illustrate the use of the EMMS-MCM approach. The model results are verified by comparisons to the results of groundwater and surface-water investigations in the landfill. The EMMS-MCM results are evaluated using a risk quotient (RQ) risk assessment method to quantify environmental risk. The EMMS-MCM simulations can be used to support hazardous field work and contribute to environmental management by predicting the possible consequences of hazardous chemical contaminations in surface waters and groundwater. The integration of the EMMS-MCM and RQ approaches represents an appropriate tool for the accurate assessment of long-term pollutant risks and environmental management of surface- and groundwater resources. Integr Environ Assess Manag 2021;17:877–886. © 2021 SETAC
KEY POINTS
An environmental multimedia modeling system (EMMS) considering water allocation factors is discussed. How different types of pollutants pose varying health and ecological risks when different water allocation parameters (such as hydraulic conductivity, density, recharge, layer number, and depth) are applied. The EMMS-MCM model, combined with the risk quotient risk assessment methodology, provides an effective basis for pollution control decisions in interconnected groundwater and surface water systems.
In vitro comparison of physical, chemical, and mechanical properties of graphene nanoplatelet added Angelus mineral trioxide aggregate to pure Angelus mineral trioxide aggregate and calcium hydroxide
Authors: Kucukyildiz Elif Nihan , Dayi Burak , Altin Serdar , Yigit Oktay 
Published: January 2021

AbstractIt is important to cover the pulp surface with a biocompatible material that is physically, mechanically, and chemically adequate. Graphene has the potential to form hard tissue, but at high doses, it shows toxic effects. It can be added to biocompatible materials at low doses to enhance their hard tissue forming potential. The aim of this study was to compare the physical, chemical, and mechanical properties of graphene nanoplatelet (GNP) added Angelus mineral trioxide aggregate (A‐MTA) to pure A‐MTA and calcium hydroxide. Homogeneous mixtures (created by adding +0.1 weight[wt]% and 0.3 wt% GNP to A‐MTA), pure A‐MTA, and Dycal were used. Three disc‐shaped samples of each material were prepared using Teflon mold. Scanning electron microscope–energy dispersive X‐ray (SEM–EDX), particle size, microhardness, and Fourier transform infrared spectroscopy (FTIR) analysis of the materials were performed in vitro. Data were analyzed using Kruskal–Wallis test followed by Conover test (p < .001). A‐MTA and GNP added samples showed similar peaks in FTIR analysis. In the EDX analysis, the amount of carbon was observed with a higher increase at A‐MTA + 0.3 wt% GNP than A‐MTA + 0.1 wt% GNP. In the SEM image, hollow structure and particle size decreased as the amount of GNP increased; particle size was smaller at A‐MTA + 0.3 wt% GNP than A‐MTA + 0.1 wt% GNP (p < .001). A‐MTA + 0.3 wt% GNP showed the highest microhardness while Dycal showed the lowest microhardness. The addition of GNP, a material with high potential for forming hard tissue, to the structure of capping materials can also positively contribute to the microhardness of the capping materials.
Did the COVID‐19 lockdown in Delhi and Kolkata improve the ambient air quality of the two cities?
Authors: Datta Arindam , Rahman Md. Hafizur , Suresh R. 
Published: January 2021

AbstractTo control the spread of COVID‐19, the government of India imposed a nationwide lockdown on all nonessential activities from 22 Mar. to 3 May 2020. Daily ambient particulate matter ≤10 μm in diameter (PM10), particulate matter ≤2.5 μm in diameter (PM2.5), NO, NO2, and O3 concentrations in Delhi and Kolkata from 1 March to 3 May in both 2019 and 2020 were collected from different monitoring stations along with meteorological data to study the impact of the COVID‐19 lockdown on ambient pollutant concentrations. In 2020, average ambient concentrations of PM10 and PM2.5 were significantly decreased (Delhi: 59 and 43%, respectively; Kolkata: 49 and 50%, respectively) during the lockdown period compared with the same period during 2019 in both cities. Average ambient O3 concentration in Delhi was significantly lower in 2020 (38.5 μg m–3) compared with 2019 (44.7 μg m–3) during the study period. However, average ambient O3 concentration was significantly higher during 2020 (46.9 μg m–3) compared with 2019 (31.4 μg m–3) in Kolkata. Effect size analysis of different predictive variables reveals that the lockdown period explains maximum variation in ambient concentrations of PM10 and PM2.5 during 2020 in both cities. However, maximum variation in ambient O3 concentrations in both cities was explained primarily by spatial variation rather than by the lockdown period. This study suggests that major policy implementation related to the transport and industrial sectors that aims to address the ambient air pollution problem in India may reduce the ambient particulate matter concentrations, although it may not have a significant effect on other ambient air pollutants such as O3 in major Indian cities.
Comparison of urinary extracellular vesicle isolation methods for transcriptomic biomarker research in diabetic kidney disease
Authors: Barreiro Karina , Dwivedi Om Prakash , Leparc German , Rolser Marcel , Delic Denis , Forsblom Carol , Groop Per‐Henrik , Groop Leif , Huber Tobias B. , Puhka Maija , Holthofer Harry 
Published: January 2021

AbstractUrinary Extracellular Vesicles (uEV) have emerged as a source for biomarkers of kidney damage, holding potential to replace the conventional invasive techniques including kidney biopsy. However, comprehensive studies characterizing uEV isolation methods with patient samples are rare. Here we compared performance of three established uEV isolation workflows for their subsequent use in transcriptomics analysis for biomarker discovery in diabetic kidney disease. We collected urine samples from individuals with type 1 diabetes with macroalbuminuria and healthy controls. We isolated uEV by Hydrostatic Filtration Dialysis (HFD), ultracentrifugation (UC), and a commercial kit‐ based isolation method (NG), each with different established urine clearing steps. Purified EVs were analysed by electron microscopy, nanoparticle tracking analysis, and Western blotting. Isolated RNAs were subjected to miRNA and RNA sequencing. HFD and UC samples showed close similarities based on mRNA sequencing data. NG samples had a lower number of reads and different mRNA content compared to HFD or UC. For miRNA sequencing data, satisfactory miRNA counts were obtained by all methods, but miRNA contents differed slightly. This suggests that the isolation workflows enrich specific subpopulations of miRNA‐rich uEV preparation components. Our data shows that HFD,UC and the kit‐based method are suitable methods to isolate uEV for miRNA‐seq. However, only HFD and UC were suitable for mRNA‐seq in our settings.
Relationship between exploratory activity and adrenocortical activity in the black rat (Rattus rattus)
Authors: Vobrubová Barbora , Fraňková Marcela , Štolhoferová Iveta , Kaftanová Barbora , Rudolfová Veronika , Chomik Aleksandra , Chumová Petra , Stejskal Václav , Palme Rupert , Frynta Daniel 
Published: January 2021

AbstractThe relationship between physiological and behavioral stress markers is documented in several rodent species. However, there is no information regarding the role of adrenocortical activity in behavior of the black rat (Rattus rattus). Therefore, we hypothesize that the adrenocortical activity of black rats varies between individuals and is related to some of the behaviors in a novel environment. To test this hypothesis, we (i) validated a method for quantifying glucocorticoid metabolites from feces (fGCMs) with an enzyme immunoassay (EIA); (ii) examined variation and diurnal rhythms of feces and GCM production; and (iii) examined the relationship between GCM levels and exploratory behavioral traits. We fulfilled the first aim (i) by successfully performing an ACTH challenge test to validate the use of a 5α‐pregnane‐3β,11β,21‐triol‐20‐one EIA for measuring fGCMs. Second (ii) we detected considerable consistent interindividual variability in production of both feces and glucocorticoids. The peak production of feces occurred in the first hour of the dark cycle, the peak of fGCMs occurred approximately 3 h later. Lastly, (iii) there was no clear relationship between behavior in the hole board test and GCMs. Grooming, a typical behavioral stress marker, was negatively associated with stress reactivity, while head‐dipping in the hole‐board test (traditionally considered an exploratory behavior independent of stress) was not correlated with the GCMs. This study offers a first look at GCMs in the black rat, successfully validates a method for their measurement and opens possibilities for future research of the relationship between glucocorticoids and exploratory behavior in this species.