bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical inferences on nonconstant relative potency with quantal response data
Authors: Kerns Lucy X.
Published: January 2021

Relative potency is widely used in toxicological and pharmacological studies to characterize potency of chemicals. The relative potency of a test chemical compared to a standard chemical is defined as the ratio of equally effective doses (standard divided by test). This classical concept relies on the assumption that the two chemicals are toxicologically similar—that is, they have parallel dose–response curves on log‐dose scale—and thus have constant relative potency. Nevertheless, investigators are often faced with situations where the similarity assumption is deemed unreasonable, and hence the classical idea of constant relative potency fails to hold; in such cases, simply reporting a single constant value for relative potency can produce misleading conclusions. Relative potency functions, describing relative potency as a function of the mean response (or other quantities), is seen as a useful tool for handling nonconstant relative potency in the absence of similarity. Often, investigators are interested in assessing nonconstant relative potency at a finite set of some specific response levels for various regulatory concerns, rather than the entire relative potency function; this simultaneous assessment gives rise to multiplicity, which calls for efficient statistical inference procedures with multiplicity adjusted methods. In this paper, we discuss the estimation of relative potency at multiple response levels using the relative potency function, under the log‐logistic dose–response model. We further propose and evaluate three approaches to calculating multiplicity‐adjusted confidence limits as statistical inference procedures for assessing nonconstant relative potency. Monte Carlo simulations are conducted to evaluate the characteristics of the simultaneous limits.
Oligonucleotide abundance biases aid design of a type IIS synthetic genomics framework with plant virome capacity
Authors: Pasin Fabio
Published: January 2021

Synthetic genomics‐driven dematerialization of genetic resources facilitates flexible hypothesis testing and rapid product development. Biological sequences have compositional biases, which, I reasoned, could be exploited for engineering of enhanced synthetic genomics systems. In proof‐of‐concept assays reported herein, the abundance of random oligonucleotides in viral genomic components was analyzed and used for the rational design of a synthetic genomics framework with plant virome capacity (SynViP). Type IIS endonucleases with low abundance in the plant virome, as well as Golden Gate and No See'm principles were combined with DNA chemical synthesis for seamless viral clone assembly by one‐step digestion‐ligation. The framework described does not require subcloning steps, is insensitive to insert terminal sequences, and was used with linear and circular DNA molecules. Based on a digital template, DNA fragments were chemically synthesized and assembled by one‐step cloning to yield a scar‐free infectious clone of a plant virus suitable for Agrobacterium‐mediated delivery. SynViP allowed rescue of a genuine virus without biological material, and has the potential to greatly accelerate biological characterization and engineering of plant viruses as well as derived biotechnological tools. Finally, computational identification of compositional biases in biological sequences might become a common standard to aid scalable biosystems design and engineering.
Synthesis of Cyclopropyl Ester and Amide Substituted Pyrimidinediones as Protoporphyrinogen Oxidase‐Inhibiting Herbicides
Authors: Lee Won Hyung , Kwon Young Bin , Lee Kye Hwan , Choi Jong‐Soo , Seu Young‐Bae
Published: January 2021

The protoporphyrinogen oxidase (PPO) enzyme is involved in the biosynthesis of chlorophyll and is an important target in research for development of new herbicides. In this study, new pyrimidinedione compounds with thioester tail group containing cyclopropyl moiety are synthesized from the commercially available 2‐(1‐(mercaptomethyl)cyclopropyl)acetic acid. The herbicidal activity of the synthesized compounds is also evaluated. Most of the synthesized compounds exhibit herbicidal activities against both monocot and dicot weeds. In particular, 10a showed similar activity to the control material, Saflufenacil. And when against the monocot weeds, Echinochloa crusgalli and Digitaria sanguinalis, 10a shows superior activity to Saflufenacil.
Reduced hippocampal volumes and memory deficits in adolescents with single ventricle heart disease
Authors: Pike Nancy A. , Roy Bhaswati , Moye Stefanie , Cabrera‐Mino Cristina , Woo Mary A. , Halnon Nancy J. , Lewis Alan B. , Kumar Rajesh
Published: January 2021

Introduction

Adolescents with single ventricle congenital heart disease (SVHD) show functional deficits, particularly in memory and mood regulation. Hippocampi are key brain structures that regulate mood and memory; however, their tissue integrity in SVHD is unclear. Our study aim is to evaluate hippocampal volumes and their associations with memory, anxiety, and mood scores in adolescents with SVHD compared to healthy controls.

Methods

We collected brain magnetic resonance imaging data from 25 SVHD (age 15.9 ± 1.2 years; 15 male) and 38 controls (16.0 ± 1.1 years; 19 male) and assessed memory (Wide Range Assessment of Memory and Learning 2, WRAML2), anxiety (Beck Anxiety Inventory, BAI), and mood (Patient Health Questionnaire 9, PHQ‐9) functions. Both left and right hippocampi were outlined and global volumes, as well as three‐dimensional surfaces were compared between groups using ANCOVA and associations with cognitive and behavioral scores with partial correlations (covariates: age and total brain volume).

Results

The SVHD group showed significantly higher BAI (p = .001) and PHQ‐9 (p < .001) scores, indicating anxiety and depression symptoms and significantly reduced WRAML2 scores (p < .001), suggesting memory deficits compared with controls. SVHD group had significantly reduced right global hippocampal volumes (p = .036) compared with controls, but not the left (p = .114). Right hippocampal volume reductions were localized in the CA1, CA4, subiculum, and dentate gyrus. Positive correlations emerged between WRAML2 scores and left (r = 0.32, p = .01) and right (r = 0.28, p = .03) hippocampal volumes, but BAI and PHQ‐9 did not show significant correlations.

Conclusion

Adolescents with SVHD show reduced hippocampal volumes, localized in several sites (CA1, CA4, subiculum, and dentate gyrus), which are associated with memory deficits. The findings indicate the need to explore ways to improve memory to optimize academic achievement and ability for self‐care in the condition.
Tripartite collaboration of blood‐derived endothelial cells, next generation RNA sequencing and bioengineered vessel‐chip may distinguish vasculopathy and thrombosis among sickle cell disease patients
Authors: Mathur Tanmay , Flanagan Jonathan M. , Jain Abhishek
Published: January 2021

Sickle cell disease (SCD) is the most prevalent inherited blood disorder in the world. But the clinical manifestations of the disease are highly variable. In particular, it is currently difficult to predict the adverse outcomes within patients with SCD, such as, vasculopathy, thrombosis, and stroke. Therefore, for most effective and timely interventions, a predictive analytic strategy is desirable. In this study, we evaluate the endothelial and prothrombotic characteristics of blood outgrowth endothelial cells (BOECs) generated from blood samples of SCD patients with known differences in clinical severity of the disease. We present a method to evaluate patient‐specific vaso‐occlusive risk by combining novel RNA‐seq and organ‐on‐chip approaches. Through differential gene expression (DGE) and pathway analysis we find that BOECs from SCD patients exhibit an activated state through cell adhesion molecule (CAM) and cytokine signaling pathways among many others. In agreement with clinical symptoms of patients, DGE analyses reveal that patient with severe SCD had a greater extent of endothelial activation compared to patient with milder symptoms. This difference is confirmed by performing qRT‐PCR of endothelial adhesion markers like E‐selectin, P‐selectin, tissue factor, and Von Willebrand factor. Finally, the differential regulation of the proinflammatory phenotype is confirmed through platelet adhesion readouts in our BOEC vessel‐chip. Taken together, we hypothesize that these easily blood‐derived endothelial cells evaluated through RNA‐seq and organ‐on‐chips may serve as a biotechnique to predict vaso‐occlusive episodes in SCD patients and will ultimately allow better therapeutic interventions.
Single Ir Atoms Anchored on Ordered Mesoporous WO3 Are Highly Efficient for the Selective Catalytic Reduction of NO with CO under Oxygen‐rich Conditions
Authors: Jiang Ruihuan , Liu Shaomian , Li Liang , Ji Yongjun , Li Huifang , Guo Xiangfeng , Jia Lihua , Zhong Ziyi , Su Fabing
Published: January 2021

Under oxygen‐rich conditions, achieving a selective and efficient reduction of NO by CO is always challenging. Here, we report the synthesis of the catalyst consisting of single Ir atoms anchored on mesoporous WO3 (denoted as Ir1/m‐WO3) using a facile template method followed by wet impregnation. X‐ray diffraction and transmission electron microscope studies indicated that the Ir atoms were distributed uniformly on the internal surface of m‐WO3. When tested for the reduction of NO by CO, the Ir1/m‐WO3 catalyst with a low Ir loading of 0.28 wt % exhibited excellent catalytic performance in the presence of 2 vol % O2 (volume ratio of CO to O2 being 1 : 10), achieving a NO conversion of 73 % and N2 selectivity of 100 % at 350 °C. In particular, its turnover frequency (TOF) value reached 0.30 s−1 at 200 °C, which is six times higher than that of the catalyst with Ir nanoparticles supported on mesoporous WO3 (0.05 s−1). The superior catalytic performance of Ir1/m‐WO3 is attributed to the formation of the isolated Ir atoms and the more newly generated Ir‐WO3 interfaces that can promote the adsorption and activation of NO, and the presence of accessible mesopores in m‐WO3 that facilitates the mass transfer of NO and CO. This study brings a new fundamental understanding of active sites in Ir‐based catalysts for the CO+NO reaction and provides a new way to the design and synthesis of single‐atom catalysts, especially precious metal catalysts for emissions control.
Palladium‐Catalyzed Allylation of Vinylethylene Carbonates with β‐Ketophosphonates: Stereoselective Synthesis of (Z)‐Homoallylic Phosphonates
Authors: Liu Zhigang , Ke Miaolin , Zhang Ke , Wang Zexu , Ye Baijun , Chen Fener
Published: January 2021

A first simple palladium catalyzed allylation of vinylethylene carbonates with β‐ketophosphonates has been developed. This method provides access to (Z)‐tri‐ and tetrasubstituted homoallylic phosphonates with exclusive regioselectivity, chemoselectivity and (Z)‐stereoselectivity. The reaction tolerates a wide substrate scope of vinylethylene carbonates and β‐ketophosphonates with electron‐donating and electron‐withdrawing groups and works well on the gram scale.
How Americans used their COVID‐19 economic impact payments
Authors: Asebedo Sarah D. , Liu Yi , Gray Blake , Quadria Taufiq Hasan
Published: January 2021

This study investigates how Americans used their CARES Act Economic Impact Payments (EIP) for their spending needs, spending wants, and financial transactions. The results from a sample of 1,172 Amazon MTurk users collected in July 2020 suggest that EIP use varied across spending and financial transaction categories. Those with job instability, less financial resources, and more people to care for received essential support. A smaller proportion of the population spent at least some of their EIP on their wants. Americans' primarily focused their EIP spending on housing, food, and hobbies. In addition, people were able to improve their financial situation through investing and debt reduction. Decisions to save the EIP were related to economic recovery concerns; a broad policy package and public messaging strategy that offers assurance of economic recovery and stability might enhance policy effectiveness for boosting immediate economic growth through EIP spending.
Advanced petroleum coke oxy‐combustion power generation with carbon capture and sequestration: Part II—Environmental assessment and cost of CO2 avoided
Authors: Okeke Ikenna J. , Adams Thomas A.
Published: January 2021

The life‐cycle environmental impact assessment and cost of the CO2 avoided (CCA) of a petroleum coke oxy‐combustion electric power generation technology operated with and without carbon capture and sequestration (CCS) are discussed. In an extension of our work on the design and economics presented in Part I, the environmental assessment was carried out for three candidate petroleum coke oxy‐combustion designs: petcoke oxy‐combustion operated without carbon capture and sequestration (CCS); petcoke oxy‐combustion operated with CCS; and petcoke oxy‐combustion with CO2 purification by distillation and CCS. The environmental life‐cycle assessment of the designs was computed using both TRACI 2.1 midpoint and ReCiPe 2016 midpoint and endpoint methods. Using a levelized cost of electricity, the CCA was also employed as a performance metric for each of the designs. The results showed a life‐cycle GWP of 1089 kgCO2eq/MWh, 17.32 kgCO2eq/MWh, and 75.65 kgCO2eq/MWh for the petcoke oxy‐combustion design operated without CCS, petcoke oxy‐combustion design operated with CCS, and petcoke oxy‐combustion with CO2 purification by distillation and CCS, respectively. It was also found that acidification potential and particulate matter emissions were higher for the petcoke oxy‐combustion design operated without CCS due to the venting of SO2 to the atmosphere. With a levelized cost of electricity between $90.94/MWh and $102.8/MWh, the CCA of the CCS‐enabled designs were between $10.43/tCO2eq and $24.35/tCO2eq, which is competitive with most other carbon capture options for large‐scale fossil‐based power plants. When the cost parameters were varied at the worst‐case scenario, the highest CCA observed was $115.9/tCO2eq.
Airflow characterization within the pleat channel of HEPA filters with mini pleats
Authors: Alilou Youssef , Bourrous Soleiman , Gélain Thomas , Bardin‐Monnier Nathalie , Thomas Dominique
Published: January 2021

High efficiency particulate air (HEPA) pleated filters are used to ensure the containment of airborne contamination within nuclear facilities. These filters are often the last barrier before a potential release of radioactive substances into the environment. The present article focuses on the characterization of air velocity fields within mini‐pleats HEPA filters at the elementary pleat scale. Numerical simulations of the velocity fields in a pleat using two different codes, ANSYS CFX and GeoDict, based on two different simulation strategies have been performed. Computed velocity profiles within the pleat have then been compared to measurements performed using an experimental setup based on a μ‐PIV measurement technique. Results show that both codes are able to reproduce the measured profiles with a satisfying accuracy. However, GeoDict requires a much finer meshing than ANSYS CFX because the voxel size is constant for the whole domain. Simulation and experimental results confirm a self‐similarity profile along the pleat assessed as a hypothesis by other authors working on this topic.
Outcomes after readmission at the index or nonindex hospital following acute myocardial infarction complicated by cardiogenic shock
Authors: Lin Zhen , Han Hedong , Qin Yingyi , Zhang Yuan , Yin Daqing , Wu Cheng , Wei Xin , Cao Yang , He Jia
Published: January 2021

Little is known about the prevalence and outcomes of readmission to nonindex hospitals after an admission for acute myocardial infarction complicated by cardiogenic shock (AMI‐CS). We aimed to determine the rate of nonindex readmissions following AMI‐CS and to evaluate its association with clinical factors, hospitalization cost, length of stay (LOS), and in‐hospital mortality rates.

Hypothesis

Nonindex readmission may lead to worse in‐hospital outcomes.

Methods

We reviewed the data of inpatients with AMI‐CS between 2010 and 2017 using the National Readmission Database. The survey analytical methods recommended by the Healthcare Cost and Utilization Project were used for national estimates. Multiple regression models were used to evaluate the predictors of nonindex readmission, and its association with hospitalization cost, LOS, and in‐hospital mortality rates.

Results

Of 238 349 patients with AMI‐CS, 28028 (11.76%) had an unplanned readmission within 30 days. Of these patients, 7423 (26.48%) were readmitted to nonindex hospitals. Compared with index readmission, nonindex readmission was associated with higher hospitalization costs (p < .0001), longer LOS (p < .0001), and increased in‐hospital mortality rates (p = .0016). Patients who had a history of percutaneous coronary intervention, received intubation/mechanical ventilation, or left against medical advice during the initial admission had greater odds of a nonindex readmission.

Conclusions

Over one‐fourth of readmissions following AMI‐CS were to nonindex hospitals. These admissions were associated with higher hospitalization costs, longer LOS, and higher in‐hospital mortality rates. Further studies are needed to evaluate whether a continuity of care plan in the acute hospital setting can improve outcomes after AMI‐CS.
Numerical Modeling of Heat Transfer and Thermal Stress at the Czochralski Growth of Neodymium Scandate Single Crystals
Authors: Böttcher Klaus , Miller Wolfram , Ganschow Steffen
Published: January 2021

The Czochralski growth of NdScO3 single crystals along the [110]‐direction is numerically analyzed with the focus on the influence of the optical thickness on the shape of the crystal–melt interface and on the generation of thermal stresses. Due to lack of data, the optical thickness (i.e., the absorption coefficient) is varied over the entire interval between optically thin and thick. While the thermal calculation in the entire furnace is treated as axisymmetric, the stress calculation of the crystal is done three‐dimensionally in order to meet the spatial anisotropy of thermal expansion and elastic coefficients. The numerically obtained values of the deflection of the crystal/melt interface meet the experimental ones for absorption coefficients in the range between 40 and 200 m−1. The maximum values of the von Mises stress appear for the case of absorption coefficient between 20 and 40 m−1. Applying absorption coefficients in the range between 3 and 100 m−1 leads to local peaks of high temperature in the shoulder region and the tail region near the end of the cylindrical part.
Soybean Gall Midge: How Do You Solve a Problem You Know Little About?
Authors: Sever Megan
Published: January 2021

The soybean gall midge, identified as a new species in 2018, has already affected growers in Iowa, Minnesota, Missouri, Nebraska, and South Dakota. And it’s threatening the $41 billion soybean industry in the U.S. Scientists studying the pest have far more questions than answers. This article will discuss what we know and don’t know about soybean gall midge. Earn 1 CEU in Integrated Pest Management by reading this article and taking the quiz at www.certifiedcropadviser.org/education/classroom/classes/916.
TMA: Tera‐MACs/W neural hardware inference accelerator with a multiplier‐less massive parallel processor
Authors: Park Hyunbin , Kim Dohyun , Kim Shiho
Published: January 2021

Computationally intensive inference tasks of deep neural networks have brought about a revolution in accelerator architecture, aiming to reduce power consumption as well as latency. The key figure‐of‐merit in hardware inference accelerators is the number of multiply‐and‐accumulation operations per watt (MACs/W); the state‐of‐ the‐art MACs/W, so far, has been several hundreds Giga‐MACs/W. We propose a Tera‐ MACS/W neural hardware inference accelerator (TMA) with 8‐bit activations and scalable integer weights less than 1‐byte. The architecture's main feature is a configurable neural processing element for matrix‐vector operations. The proposed neural processing element uses a multiplier‐less massive parallel processor that works without multipliers, which makes it attractive for energy efficient high‐performance neural network applications. We benchmark our system's latency, power, and performance using Alexnet trained on ImageNet. Finally, we compared our accelerator's throughput and power consumption to that of the prior works. The proposed accelerator outperforms the state‐of‐the‐art counterparts, in terms of the energy and area efficiency, achieving 2.3 TMACs/W@1.0 V on a 28‐nm Virtex‐7 FPGA chip.
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

Background

Histone 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).

Results

Here 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.

Conclusion

Our 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

Background

Persistent 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.

Results

In 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.

Conclusions

These 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

Increased 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

Due 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

Quantitative 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

Mylonite 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

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

While 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

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

It 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

To 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

Urinary 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

The 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.
Corticosterone does not have a role in temperature sex reversal in the central bearded dragon (Pogona vitticeps)
Authors: Castelli Meghan , Georges Arthur , Holleley Clare E.
Published: January 2021

Environmental sex determination (ESD) is common among ectothermic vertebrates. The stress axis and production of stress hormones (corticosteroids) regulates ESD in fish, but evidence of a similar influence in reptiles is sparse and conflicting. The central bearded dragon (Pogona vitticeps) has a system of sex determination involving the interplay between sex chromosomes (ZZ/ZW female heterogamety) and the thermal environment. High egg incubation temperatures induce sex reversal of the ZZ genotype, feminizing chromosomally male individuals. Here we show that corticosterone elevation is not associated with sex reversal in the central bearded dragon, either during embryonic development or adulthood. We also demonstrate experimentally that sex determination is not affected by corticosterone injection into the yolk. This strongly suggests that stress axis upregulation by high temperature during incubation does not cause sex reversal in P. vitticeps. Our work is in general agreement with other research in reptiles, which suggests that the stress axis does not mediate sex in reptiles with ESD. Alternative biological systems may be responsible for capturing environmental conditions during reptile development, such as cellular calcium and redox regulation or the action of temperature‐sensitive splicing factors.
Comparison of in‐source collision‐induced dissociation and beam‐type collision‐induced dissociation of emerging synthetic drugs using a high‐resolution quadrupole time‐of‐flight mass spectrometer
Authors: Davidson J. Tyler , Sasiene Zachary J. , Jackson Glen P.
Published: January 2021

In‐source collision‐induced dissociation (CID) is commonly used with single‐stage high‐resolution mass spectrometers to gather both a molecular formula and structural information through the collisional activation of analytes with residual background gas in the source region of the mass spectrometer. However, unlike tandem mass spectrometry, in‐source CID does not involve an isolation step prior to collisional activation leading to a product ion spectrum composed of fragment ions from any analyte present during the activation event. This work provides the first comparison of in‐source CID and beam‐type CID spectra of emerging synthetic drugs on the same instrument to understand the fragmentation differences between the two techniques and to contribute to the scientific foundations of in‐source CID. Electrospray ionization–quadrupole time‐of‐flight (ESI‐Q‐TOF) mass spectrometry was used to generate product ion spectra from in‐source CID and beam‐type CID for a series of well‐characterized fentanyl analogs and synthetic cathinones. A comparison between the fragmentation patterns and relative ion abundances for each technique was performed over a range of fragmentor offset voltages for in‐source CID and a range of collision energies for beam‐type CID. The results indicate that large fragmentor potentials for in‐source CID tend to favor higher energy fragmentation pathways that result in both kinetically favored pathways and consecutive neutral losses, both of which produce more abundant lower mass product ions relative to beam‐type CID. Although conditions can be found in which in‐source CID and beam‐type CID provide similar overall spectra, the in‐source CID spectra tend to contain elevated noise and additional chemical background peaks relative to beam‐type CID.