bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of effective young’s modulus based on 3-D finite element model with particle-matrix interface for metal matrix composites
Authors: Irfan Ahammed K P , Narayanan Aswathy A , Sudheesh R S
Published: April 2021

Effective Young’s Moduli of composite materials are estimated by variety of methods so far. This work attempts to estimate the Effective Young’s Modulus of aluminium356 with silicon carbide particle (SiCp) Metal Matrix Composite (MMC) with different particle aspect ratios using a simplified finite element model. Simplifications were made in terms of geometry of the particle. An improved model of the composite with an interface between the particle and the matrix was then developed and used to compare the results with the simplified model. The results were validated with experimental results, and the predicted values obtained from the Rule of Mixtures and the Halpin–Tsai (HT) model. The Young’s moduli estimated by considering the interface geometry in 3-D model is found to have better agreement with the experimental values than the simplified model at higher aspect ratios. The improvement in the results of the 3-D model with interface considerations is expected to make the model suitable for advanced studies.
A review on gas-generants for application in exploding fire extinguisher balls
Authors: Muhammed Afnas , Sreelakshmi Paruvayakode , Praseeda P N , Jishnu  , Shan S
Published: April 2021

Fire is a highly exothermic reaction caused due to the rapid oxidation of a flammable substance. The mechanism of fire can be explained well with the help of a Fire Triangle comprised of the Source, Heat and Oxygen. Fire is complete and active only when all these three components are present simultaneously. There are numerous methods employed to extinguish fire, by depriving the fire of one or more of the components of the fire triangle. Recent technologies have emerged which makes use of a solid chemical mixture, placedinside a shell, which explodes when the chemical decomposes on being thrown into a fire and floodsthe fire surface with an inert gas which is a product of the decomposition. The chemical decomposes by absorbing heat from fire. Nitrogen or other non-toxic gases gets released and puts out the fire by rapidly expanding and forming a blanket around the source of fire replacing Oxygen. The light weight, portability, easy and quick deployment and the release of non-toxic by-product are the advantages of the Fire Extinguishing Shells over the conventional ones. This paper presents a review of various chemicals that can be used can potentially be used in such fire extinguishing shells.
Comparative study on iron removal using chemically and greenly synthesised zero-valent iron nanoparticles
Authors: Jismy Antony , Meera V , RaphaelVinod P
Published: April 2021

As an adsorbent, the nano zero-valent iron (nZVI) has gained attention among researchers for the removal of pollutants like metallic ions from water. The high surface area and resulting high reactivity of nZVI make it a promising material for water/wastewater treatment. The uptake behaviour of iron on nZVI has not been investigated so far. The aim of the study is to compare greenly synthesised (GnZVI) and chemically synthesised (CnZVI) nano zero-valent iron in terms of size, functional groups and stability and to explore the feasibility of utilizing it for iron removal from water. In this study, the liquid-phase reduction technique was used to synthesis nZVI. Sodium borohydride as well as Amaranthus Dubius leaf extract were used as the reductants in this process. Characterization study of nZVI was performed using UV, FTIR, XRD and TEM. The peaks obtained at 312 nm and 316 nm in UV-Vis spectrum for chemically and greenly synthesised particles respectively, confirmed the formation of nanoparticles. The FTIR spectrum revealed the presence of C=O, C-O stretching and – CH bending vibrations of bonds. It was found that the CnZVI nanoparticles were largely spherical with size ranging from 80 nm-99 nm whereas GnZVI nanoparticles were in the range of 1nm-3nm. For an influent total iron concentration of 0.5ppm with Fe2+/Fe3+ ratio as 2.5:0.5, total iron removal efficiencies of 54.00% and 35.19% were achieved by CnZVI and GnZVI respectively, at pH of 6.85 and contact time of 3 hours.
Efficacy of nanochitosan impregnated polyurethane foam in removing phosphate from aqueous solutions
Authors: Anjali P Sasidharan , Meera V , Vinod P Raphael
Published: April 2021

A novel potential adsorbent was developed by impregnating chitosan nanoparticles on polyurethane foam (PFC) for the reduction of phosphate in aqueous solutions. The emergence of nanoparticles was first confirmed by the ultraviolet-visible (UV-Vis) spectroscopy. The mean size of chitosan nanoparticles between 56 nm and 112 nm was provided by the field emission scanning electron microscopy (FESEM). The presence of specific elements (C, O, P) in PFC before and after treatment was determined by energy dispersive X-ray (EDX) spectroscopy. The interplay between amino groups in PFC and phosphate ions during adsorption was identified by the Fourier transform infrared (FTIR) spectroscopy. X-ray diffraction (XRD) analysis of PFC showed nearly the same pattern before and after treatment, indicating the stability of sorbent. The point of zero charge experiment described the positive surface charge of PFC below pH 7.4. The experimental studies showed that phosphate removal efficiency by PFC increases from 35.04% to 69.78% with the decrease of influent phosphate concentration from 150 mg/L to 3 mg/L at contact time 6 h and pH 6.5. Hence PFC can be considered as an effective sorbent for removing phosphate at lower concentrations.
Modelling and simulation of SISO model prosthetic limb by Open Modelica an acausal and cyber physical modelling language
Authors: Reji Sachu , Sibichan Sanu K , Raju Vargheses Lejo , Venkatesh V , Madhukumar T K
Published: April 2021

Design of cost effective transradial prosthesis has been in the research field for some time. Instead of complex systems with less dexterity, we put forth a design considering solely the wrist movement of the prosthetic hand, driven by a flex sensor-Arduino system which translates the motion of natural hand to the prosthetic one. Objective of this paper is to conduct a simulation experiment of this design, using Open Modelica, by creating a virtual lab environment. This paper describes the present state of the research, simulation along with the results obtained and the conclusions we could reach at this period in comparison with the initial hypothesis.
Physical, optical and structural characterizations of Dy3+-doped lead borate glasses
Authors: Chopra Neetu , Kaur Sandeep , Pandey O P , Sharma Gopi , Sharma Surbhi
Published: April 2021

In the current studies optical, physical and structural properties of rare-earth doped borate glasses have been reported. Bulk samples were prepared by using melt quenching technique with nominal composition 70B2O3-(17-x)ZnO-10PbF2-3Na2O-xDyF3 and 60B2O3-(27-x)ZnO-10PbF2-3Na2O-xDyF3, where (x=0,1). XRD analysis was used to confirm the amorphous nature of prepared samples. Optical and structural properties of as prepared samples were studied using UV-Visible and FTIR absorption spectra. The undoped and doped glasses exhibit characteristic absorption bands due to the presence of rare earth ion. A decrease in the band gap has been observed with the addition of rare earth ion. Variations in density have been observed with the addition of rare earth ion.
Multiplexing physical stimulation on single human induced pluripotent stem cell-derived cardiomyocytes for phenotype modulation
Authors: Kit-Anan Worrapong , Mazo Manuel M , Wang Brian X , Leonardo Vincent , Pence Isaac J , Gopal Sahana , Gelmi Amy , Nagelkerke Anika , Becce Michele , Chiappini Ciro , Harding Sian E , Terracciano Cesare M , Stevens Molly M
Published: April 2021

Traditional in vitro bioengineering approaches whereby only individual biophysical cues are manipulated at any one time are highly inefficient, falling short when recapitulating the complexity of the cardiac environment. Multiple biophysical cues are present in the native myocardial niche and are essential during development, as well as in maintenance of adult cardiomyocyte (CM) phenotype in both health and disease. This study establishes a novel biofabrication workflow to study and manipulate hiPSC-CMs and to understand how these cells respond to a multiplexed biophysical environment, namely 3D shape and substrate stiffness, at a single cell level. Silicon masters were fabricated and developed to generate inverse patterns of the desired 3D shapes in bas relief, which then were used to mold the designed microwell arrays into a hydrogel. Polyacrylamide (PAAm) was modified with the incorporation of acrylic acid to provide a carboxylic group conjugation site for adhesion motifs, without compromising capacity to modulate stiffness. In this manner, two individual parameters can be finely tuned independently within the hydrogel: the shape of the 3D microwell and its stiffness. The design allows the platform to isolate single hiPSC-CMs to study solely biophysical cues in the absence of cell-cell physical interaction. Under physiologic-like physical conditions (3D shape resembling that of adult CM and 9.83 kPa substrate stiffness that mimics muscle stiffness), isolated single hiPSC-CMs exhibit increased Cx-43 density, cell membrane stiffness and calcium transient amplitude; co-expression of the subpopulation-related MYL2-MYL7 proteins; and higher anisotropism than cells in pathologic-like conditions (flat surface and 112 kPa substrate stiffness). This demonstrates that supplying a physiologic or pathologic microenvironment to an isolated single hiPSC-CM in the absence of any physical cell-to-cell communication in this biofabricated platform leads to a significantly different set of cellular features, thus presenting a differential phenotype. Importantly, this demonstrates the high plasticity of hiPSC-CMs even in isolation. The ability of multiple biophysical cues to significantly influence isolated single hiPSC-CM phenotype and functionality highlights the importance of fine-tuning such cues for specific applications. This has the potential to produce more fit-for-purpose hiPSC-CMs. Further understanding of human cardiac development is enabled by the robust, versatile and reproducible biofabrication techniques applied here. We envision that this system could be easily applied to other tissues and cell types where the influence of cellular shape and stiffness of the surrounding environment is hypothesized to play an important role in physiology.
Role of charge doping and strain in the stabilization of in-plane ferromagnetism in monolayer

VSe2

at room temperature
Authors: Memarzadeh S , Roknabadi M Rezaee , Modarresi M , Mogulkoc A , Rudenko A N
Published: April 2021

We study the origin of in-plane ferromagnetism in monolayer VSe2 focusing on the effect of charge doping and mechanical strain. We start from an anisotropic spin Hamiltonian, estimate its parameters from density functional calculations, and determine the spectrum of spin-wave excitations. We show that 1T-VSe2 is characterized by relatively strong on-site Coulomb repulsion (U ≃ 5 eV), favoring an antiferromagnetic ground state, which contradicts experimental observations. We calculate the magnetic phase diagram as a function of charge doping and strain, and find a transition to the ferromagnetic state with in-plane easy axis under moderate hole doping (∼1014 cm−2). Analysis of spin-wave excitations in doped monolayer VSe2 reveals a gap due to the in-plane anisotropy, giving rise to long-range magnetic order well above 300 K, in agreement with recent experiments. Our findings suggest that experimentally available 1T-VSe2 monolayer samples might be intrinsically or extrinsically doped, which opens up the possibility for a controllable manipulation of their magnetic properties.
Wideband dielectric properties of silicon and glass substrates for terahertz integrated circuits and microsystems
Authors: Chudpooti Nonchanutt , Duangrit Nattapong , Burnett Andrew D , Freeman Joshua R , Gill Thomas B , Phongcharoenpanich Chuwong , Imberg Ulrik , Torrungrueng Danai , Akkaraekthalin Prayoot , Robertson Ian D , Somjit Nutapong
Published: April 2021

This paper presents a comprehensive study of the optical and electrical dielectric material properties of six commonly-used silicon and glass substrates at terahertz (THz) frequencies, including refractive index, absorption coefficient, dielectric constant and loss factor. The material characterization techniques used in this paper feature THz time-domain transmission and reflection spectroscopy with the measurement frequencies from 0.5 THz up to a maximum of 6.5 THz. Of the six selected dielectric and semiconductor substrates, two are silicon wafers with resistivities ranging from 0.001 to 0.02 Ω-cm. From the measurement results, loss tangents of the selected silicon wafers range from 0.680 to 5.455 and the dielectric constants are from 1.079 to 17.735. The four other wafers are all glass-based substrates: D263 glass, Borofloat 33 glass, fused silica and Sapphire. From the measurements, it is found that the THz dielectric properties vary considerably between the substrate samples e.g. dielectric constants range from 1.925 to 3.207 while loss tangents are from 0.042 × 10−3 to 0.127. Most of the selected silicon and glass-based substrates are quite useful for many THz applications, e.g., THz integrated circuits (THz ICs), THz microsystem technologies (THz MSTs) and THz system-on-a-chip (THz SoC) and system-on-substrate (SiP).
Microwave breakdown in an overmoded relativistic backward wave oscillator operating at low magnetic field
Authors: Xiao Renzhen , Gui Youyou , Zhang Guangshuai , Shi Yanchao , Wang Huida , Chen Kun
Published: April 2021

Microwave breakdown has always been a huge challenge to the development of high-power microwave (HPM) sources. Some unique breakdown phenomena in a novel and powerful overmoded relativistic backward wave oscillator (RBWO) operating at low magnetic field are demonstrated. Three different breakdown mechanisms are utilized to explain these phenomena through detailed electromagnetic field calculation and particle-in-cell demonstration and effective methods are applied or suggested to mitigate the breakdown. The breakdown in the slow wave structure (SWS) mainly results from bombardment by the main electron beam under the intense radial electric field. Increasing the span between the main electron beam and the SWS or applying a coaxial extraction structure operating at coaxial TM01 mode might decrease the radial electric field and lessen the bombardment. The breakdown in the internal reflector originates with the field-induced emission in the inner ring under the intense axial electric field of the TM01 and TM02 mode and the subsequent electron-triggered emission in the outer ring. Removing the central part or constructing a complex reflector surface can suppress the emission. The breakdown in the slot retained for the Rogowski coil results from low pressure gas discharge initiated by microwave leakage from the RBWO into the diode region. Pasting microwave absorbing material into the coaxial diode region helps to obtain normal beam current waveforms measured by the Rogowski coil.
How different power plant types contribute to electric grid reliability, resilience, and vulnerability: a comparative analytical framework
Authors: Ramirez-Meyers K , Neal Mann W , Deetjen T A , Johnson S C , Rhodes J D , Webber M E
Published: April 2021

This work explores the dependability tradeoffs provided by the most common types of central power plants in the United States. Historically, the electricity sector has lacked consensus on how reliability, resilience, and vulnerability differ and how those metrics change depending on the power plant fleet composition. We propose distinct definitions for these metrics and an analytical framework to evaluate power plant fleet dependability. Using data analysis and literature review, we identify fifteen dependability attributes across which we rank eleven power plant types relative to natural gas combined-cycle (NGCC) plants. We use NGCC as the benchmark because it is common to many locations and is of relatively recent vintage. The framework shows that each power plant type has unique dependability benefits and drawbacks. We provide examples of how researchers may use the framework to evaluate grid dependability qualitatively under different scenarios. We find that assuming all attributes that contribute to grid dependability are equally important and additive, electric grid dependability is best supported when power plant fleets include a mixture of power generation technologies. Then, we discuss scenario characteristics that could alter the prioritization and relationships of attributes. We also find that if current capacity installation trends continue to favor low- and zero-carbon power plants, US power grids may benefit from increased resilience and reduced vulnerability at the cost of decreased reliability. We conclude by recommending methods for adapting the framework and quantifying relationships between attributes in individual scenarios.
Smart concrete: an illustration through a smart concrete chess game of potential applications in construction 4.0
Authors: Amghar Bilal , Mansoutre Sandrine , Colin Johan , Florence Celine , Brito Artur De Morais
Published: April 2021

The global performance of a structure or a system can be improved during the process of its construction or operation or end of life, with multifunction and connected elements. Concrete presents several benefits for being used in this way, in particular with integrated electronic systems. This paper deals with smart concrete through a small size example, a chess game, i.e. board and pawns, to illustrate the potential applications on a larger scale in the field of construction. Different kind of sensors can be used in concrete construction. After comparing the advantages and disadvantages of each, magnetic sensors have been chosen to equip the concrete chessboard, handcrafted in the present work. The concrete used is UHPC (Ultra high performance concrete fiber reinforced or not), a new type of concrete with special properties, for the benefits of its mechanical strength and deformation, self-levelling workability and aesthetic surface rendering. Chess pawns and chess board have been cast with a specific protocol to embed the magnets and the sensor inside the concrete, by taking into account both its flocculation and setting times. Results of the tests show the feasibility to use magnetic sensors in concrete systems and show a good transmission of the magnetic signal through the concrete, which is very promising for further development of new concrete smart systems, that are easy and rentable to implement. The permeability of concrete to magnetic fields, robustness and sensitivity of sensor are the advantages of this application.
Fundamental gene network rewiring at the second order within and across mammalian systems
Authors: Sharma Ruby , Kumar Sajal , Song Mingzhou
Published: April 2021

Motivation

Genetic or epigenetic events can rewire molecular networks to induce extraordinary phenotypical divergences. Among the many network rewiring approaches, no model-free statistical methods can differentiate gene–gene pattern changes not attributed to marginal changes. This may obscure fundamental rewiring from superficial changes.

Results

Here we introduce a model-free Sharma–Song test to determine if patterns differ in the second order, meaning that the deviation of the joint distribution from the product of marginal distributions is unequal across conditions. We prove an asymptotic chi-squared null distribution for the test statistic. Simulation studies demonstrate its advantage over alternative methods in detecting second-order differential patterns. Applying the test on three independent mammalian developmental transcriptome datasets, we report a lower frequency of co-expression network rewiring between human and mouse for the same tissue group than the frequency of rewiring between tissue groups within the same species. We also find second-order differential patterns between microRNA promoters and genes contrasting cerebellum and liver development in mice. These patterns are enriched in the spliceosome pathway regulating tissue specificity. Complementary to previous mammalian comparative studies mostly driven by first-order effects, our findings contribute an understanding of system-wide second-order gene network rewiring within and across mammalian systems. Second-order differential patterns constitute evidence for fundamentally rewired biological circuitry due to evolution, environment or disease.

Availability and implementation

The generic Sharma–Song test is available from the R package ‘DiffXTables’ at https://cran.r-project.org/package=DiffXTables. Other code and data are described in Section 2.

Supplementary information

Supplementary data are available at Bioinformatics online.
Axillary evaluation in ductal cancer in situ of the breast: challenging the diagnostic accuracy of clinical practice guidelines
Authors: Karakatsanis Andreas , Charalampoudis Petros , Pistioli Lida , Di Micco Rosa , Foukakis Theodoros , Valachis Antonios ,   the SentiNot Trialists Group, Wärnberg F , Bagge Roger Olofsson , Eriksson Staffan , Nagy Guyla , Mohammed Imad , Sundqvist Marie , Kwong Ava , Stålberg Peter
Published: April 2021

Background

Staging of the axilla is not routine in ductal cancer in situ (DCIS) although invasive cancer is observed in 20–25 per cent of patients at final pathology. Upfront sentinel lymph node dissection (SLND) is advocated in clinical practice guidelines in certain situations. These include expected challenges in subsequent SLN detection and when the risk for invasion is high. Clinical practice guidelines are, however, inconsistent and lead to considerable practice variability.

Methods

Clinical practice guidelines for upfront SLND in DCIS were identified and applied to patients included in the prospective SentiNot study. These patients were evaluated by six independent, blinded raters. Agreement statistics were performed to assess agreement and concordance. Receiver operating characteristic curves were constructed, to assess guideline accuracy in identifying patients with underlying invasion.

Results

Eight guidelines with relevant recommendations were identified. Interobserver agreement varied greatly (kappa: 0.23–0.9) and the interpretation as to whether SLND should be performed ranged from 40–90 per cent and with varying concordance (32–88 per cent). The diagnostic accuracy was low with area under the curve ranging from 0.45 to 0.55. Fifty to 90 per cent of patients with pure DCIS would undergo unnecessary SLNB, whereas 10–50 per cent of patients with invasion were not identified as ‘high risk’. Agreement across guidelines was low (kappa = 0.24), meaning that different patients had a similar risk of being treated inaccurately.

Conclusion

Available guidelines are inaccurate in identifying patients with DCIS who would benefit from upfront SLNB. Guideline refinement with detailed preoperative work-up and novel techniques for SLND identification could address this challenge and avoid overtreatment.
Changes in Seasonal Respiratory Illnesses in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic
Authors: Rodgers Loren , Sheppard Michael , Smith Amanda , Dietz Stephanie , Jayanthi Praveena , Yuan Yan , Bull Lara , Wotiz Samantha , Schwarze Tessa , Azondekon Roseric , Hartnett Kathleen , Adjemian Jennifer , Kirking Hannah L , Kite-Powell Aaron
Published: April 2021

Background

Respiratory tract infections are common, often seasonal, and caused by multiple pathogens. We assessed whether seasonal respiratory illness patterns changed during the COVID-19 pandemic.

Methods

We categorized emergency department (ED) visits reported to the National Syndromic Surveillance Program according to chief complaints and diagnosis codes, excluding visits with diagnosed SARS-CoV-2 infections. For each week during 1 March 2020 through 26 December 2020 (“pandemic period”), we compared the proportion of ED visits in each respiratory category with the proportion of visits in that category during the corresponding weeks of 2017–2019 (“pre–pandemic period”). We analyzed positivity of respiratory viral tests from 2 independent clinical laboratories.

Results

During March 2020, cough, shortness of breath, and influenza-like illness accounted for twice as many ED visits compared with the pre–pandemic period. During the last 4 months of 2020, all respiratory conditions, except shortness of breath, accounted for a smaller proportion of ED visits than during the pre–pandemic period. Percent positivity for influenza virus, respiratory syncytial virus, human parainfluenza virus, adenoviruses, and human metapneumovirus was lower in 2020 than 2019. Although test volume decreased, percent positivity was higher for rhinovirus/enterovirus during the final weeks of 2020 compared with 2019, with ED visits similar to the pre–pandemic period.

Conclusions

Broad reductions in respiratory test positivity and respiratory ED visits (excluding COVID-19) occurred during 2020. Interventions for mitigating spread of SARS-CoV-2 likely also reduced transmission of other pathogens. Timely surveillance is needed to understand community health threats, particularly when current trends deviate from seasonal norms.
Multimorbidity and the risk of major adverse kidney events: findings from the UK Biobank cohort
Authors: Sullivan Michael K , Jani Bhautesh Dinesh , Lees Jennifer S , Welsh Claire E , McConnachie Alex , Stanley Bethany , Welsh Paul , Nicholl Barbara I , Lyall Donald M , Carrero Juan-Jesus , Nitsch Dorothea , Sattar Naveed , Mair Frances S , Mark Patrick B
Published: April 2021

Background

Multimorbidity [the presence of two or more long-term conditions (LTCs)] is associated with a heightened risk of mortality, but little is known about its relationship with the risk of kidney events.

Methods

Associations between multimorbidity and major adverse kidney events [MAKE: the need for long-term kidney replacement therapy, doubling of serum creatinine, fall of estimated glomerular filtration rate (eGFR) to <15 mL/min/1.73 m2 or 30% decline in eGFR] were studied in 68 505 participants from the UK Biobank cohort. Participants were enrolled in the study between 2006 and 2010. Associations between LTC counts and MAKE were tested using survival analyses accounting for the competing risk of death.

Results

Over a median follow-up period of 12.0 years, 2963 participants had MAKE. There were associations between LTC count categories and the risk of MAKE [one LTC adjusted subhazard ratio (sHR) = 1.29, 95% confidence interval (CI) 1.15–1.45; two LTCs sHR = 1.74 (95% CI 1.55–1.96); and three or more LTCs sHR = 2.41 (95% CI 2.14–2.71)]. This finding was more pronounced when only cardiometabolic LTCs were considered [one LTC sHR = 1.58 (95% CI 1.45–1.73); two LTCs sHR = 3.17 (95% CI 2.80–3.59); and three or more LTCs sHR = 5.24 (95% CI 4.34–6.33)]. Combinations of LTCs associated with MAKE were identified. Diabetes, hypertension and coronary heart disease featured most commonly in high-risk combinations.

Conclusions

Multimorbidity, and in particular cardiometabolic multimorbidity, is a risk factor for MAKE. Future research should study groups of patients who are at high risk of progressive kidney disease based on the number and type of LTCs.
Thermoinducible expression system for producing recombinant proteins in Escherichia coli: advances and insights
Authors: Restrepo-Pineda Sara , O. Pérez Néstor , Valdez-Cruz Norma A , Trujillo-Roldán Mauricio A
Published: April 2021

Recombinant protein (RP) production from Escherichia coli has been extensively studied to find strategies for increasing product yields. The thermoinducible expression system is commonly employed at the industrial level to produce various RPs, which avoids the addition of chemical inducers, thus minimizing contamination risks. Multiple aspects of the molecular origin and biotechnological uses of its regulatory elements (pL/pR promoters and cI857 thermolabile repressor) derived from bacteriophage λ provide knowledge to improve the bioprocesses using this system. Here, we discuss the main aspects of the potential use of the λpL/pR-cI857 thermoinducible system for RP production in E. coli, focusing on the approaches of investigations that have contributed to the advancement of this expression system. Metabolic and physiological changes that occur in the host cells caused by heat stress and RP overproduction are also described. Therefore, the current scenario and the future applications of systems that use heat to induce RP production are discussed to understand the relationship between the activation of the bacterial heat shock response, RP accumulation and its possible aggregation to form inclusion bodies.
Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting
Authors: Sizova Irina , Kelterborn Simon , Verbenko Valeriy , Kateriya Suneel , Hegemann Peter
Published: April 2021

The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection in Drosophila
Authors: Sheffield Lakbira , Sciambra Noah , Evans Alysa , Hagedorn Eli , Goltz Casey , Delfeld Megan , Kuhns Haley , Fierst Janna L , Chtarbanova Stanislava
Published: April 2021

Advanced age in humans is associated with greater susceptibility to and higher mortality rates from infections, including infections with some RNA viruses. The underlying innate immune mechanisms, which represent the first line of defense against pathogens, remain incompletely understood. Drosophila melanogaster is able to mount potent and evolutionarily conserved innate immune defenses against a variety of microorganisms including viruses and serves as an excellent model organism for studying host–pathogen interactions. With its relatively short lifespan, Drosophila also is an organism of choice for aging studies. Despite numerous advantages that this model offers, Drosophila has not been used to its full potential to investigate the response of the aged host to viral infection. Here, we show that, in comparison to younger flies, aged Drosophila succumb more rapidly to infection with the RNA-containing Flock House virus due to an age-dependent defect in disease tolerance. Relative to younger individuals, we find that older Drosophila mount transcriptional responses characterized by differential regulation of more genes and genes regulated to a greater extent. We show that loss of disease tolerance to Flock House virus with age associates with a stronger regulation of genes involved in apoptosis, some genes of the Drosophila immune deficiency NF-kB pathway, and genes whose products function in mitochondria and mitochondrial respiration. Our work shows that Drosophila can serve as a model to investigate host–virus interactions during aging and furthermore sets the stage for future analysis of the age-dependent mechanisms that govern survival and control of virus infections at older age.
Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus
Authors: Dong Zhixue , Alam Muhammad Khorshed , Xie Meili , Yang Li , Liu Jie , Helal M M U , Huang Junyan , Cheng Xiaohui , Liu Yueying , Tong Chaobo , Zhao Chuanji , Liu Shengyi
Published: April 2021

Plant height is a crucial element related to plant architecture that influences the seed yield of oilseed rape (Brassica napus L.). In this study, we isolated a natural B. napus mutant, namely a semi-dwarf mutant (sdw-e), which exhibits a 30% reduction in plant height compared with Zhongshuang 11-HP (ZS11-HP). Quantitative trait locus sequencing (QTL-seq) was conducted using two extreme DNA bulks in F2 populations in Wuchang-2017 derived from ZS11-HP × sdw-e to identify QTLs associated with plant height. The result suggested that two QTL intervals were located on chromosome A10. The F2 population consisting of 200 individuals in Yangluo-2018 derived from ZS11-HP × sdw-e was used to construct a high-density linkage map using whole-genome resequencing. The high-density linkage map harbored 4323 bin markers and covered a total distance of 2026.52 cM with an average marker interval of 0.47 cM. The major QTL for plant height named qPHA10 was identified on linkage group A10 by interval mapping and composite interval mapping methods. The major QTL qPHA10 was highly consistent with the QTL-seq results. And then, we integrated the variation sites and expression levels of genes in the major QTL interval to predict the candidate genes. Thus, the identified QTL and candidate genes could be used in marker-assisted selection for B. napus breeding in the future.
EUPLOID DERIVATIVES OF DUPLICATIONS FROM A TRANSLOCATION IN NEUROSPORA
Authors: Turner Barbara C
Published: April 2021

Nontandem terminal chromosome duplications derived from N. crassa translocation T(I→VI)NM103 give rise mitotically to some daughter nuclei which have become euploid by loss of one or the other of the two duplicated segments. Loss of the segment in normal sequence occurs as often as loss of the translocated segment. This is in contrast to all of several other Neurospora duplications that have been studied, where loss of the segment in normal sequence is absent or rare.—T(NM103) has the distal two thirds of linkage group IR exchanged with the right tip of VI. Crosses to normal sequence produce a class of morphologically distinct progeny with IR chromosome duplications. For a few days after germination, test crosses of these progeny are barren (make perithecia but few or no spores, as observed commonly with Neurospora duplications). Growing duplication cultures become fertile by accumulating nuclei which have been reduced to either normal sequence (by loss of the segment in translocation sequence) or translocation sequence (by loss of the segment in normal sequence). Both types usually appear within the first week of growth. Naturally formed mixtures or heterokaryons of NM103 duplication nuclei and their reduced euploid products have been studied by plating and by progeny testing. Determination of nuclear type is based on culture morphology, expression of genetic markers, and crossing behavior. Within the limits of testing, loss is found to begin precisely at the interchange points. The unique finding of frequent breakdown of normal-sequence linkage group I chromosomes is not dependent on the strain from which the chromosome was derived. Many different strains were tested, and for each one evidence was found that nuclei reduced to translocation sequence had been produced from duplication nuclei by loss of the segment in normal sequence.
CHARACTERIZATION OF DOMINANT RESISTANCE TO COBALT CHLORIDE IN DICTYOSTELIUM DISCOIDEUM AND ITS USE IN PARASEXUAL GENETIC ANALYSIS
Authors: Williams Keith L
Published: April 2021

Strains of Dictyostelium discoideum resistant to cobaltous chloride have been isolated at a frequency of approximately 10-6. The resistant strains have one of three phenotypes, recessive to wild type, dominant to wild type and dominant to wild type but requiring the presence of cobaltous chloride to maintain resistance. Strains carrying a dominant cobaltous chloride resistance mutation and a recessive growth temperature-sensitive mutation can be mixed with wild-type haploid lines and then subjected to selection so that only diploid lines survive. Differential sensitivity to cycloheximide has also been observed. Hypersensitivity to cycloheximide in combination with dominant cobaltous chloride resistance provides a means of selecting diploids without the use of temperature-sensitive mutations.
ISOLATION AND CHARACTERIZATION OF pso MUTANTS SENSITIVE TO PHOTO-ADDITION OF PSORALEN DERIVATIVES IN SACCHAROMYCES CEREVISIAE
Authors: Henriques J A P , Moustacchi E
Published: April 2021

We have isolated mutants sensitive to photo-addition of bi-functional and mono-functional derivatives of psoralen in Saccharomyces cerevisiae. Three of these pso mutants were analyzed in detail. They segregate in meiosis like Mendelian genes and complement each other, as well as existing radiationsensitive (rad and rev) mutants. The study of heterozygous diploid strains (PSO+/pso) indicates that the three pso genes are recessive. The mutant psol-1 demonstrates a cross-sensitivity to UV and γ-rays, whereas mutants pso2-1 and pso3-1 are specifically sensitive to photo-addition of psoralen derivatives. The comparison of exponentially growing cells to stationary-phase cells demonstrates that for the three mutants the defect in repair capacity of DNA cross-links and monoadducts concerns G1 and early S-phase cells. The pso2-1 mutant is, however, also defective in G2 repair and loses diploid resistance when it is in the homozygous state.——The block in repair capacity in these novel mutants is discussed in relation to the three other repair pathways known to be involved in the repair of furocoumarins photo-induced lesions in yeast DNA.
NEW MUTATIONAL VARIANTS OF NEUROSPORA NADP-SPECIFIC GLUTAMATE DEHYDROGENASE
Authors: Kinsey John A , Fincham J R S , Siddig M A M , Keighren Margaret
Published: April 2021

The am locus of Neurospora codes for NADP-dependent glutamate dehydrogenase (GDH). Four new am mutants that produced mutationally altered GDH have been characterized. Mutant am  119 is a CRM-negative, complementing mutant that maps between am  2 and am  1. The other three mutants are CRM formers that produce varieties of GDH that can be activated by glutamate or succinate. The GDH of am  130 and am  l31 is similar in terms of activation properties to that of am  3. The GDH of am  l22, requires very high concentrations of dicarboxylate for activity. The mutation in am  l30 maps between am  l4 and am  2 and resulted in a replacement at residue 75 of the GDH (pro→ser). The mutation in am  l22 maps near am  ll and apparently resulted in the replacement of the tryptophan residue at position 389 with an unknown amino acid. The mutation in am  l31 maps between am  2 and am  1.
EFFECT OF MATING STRUCTURE ON VARIATION IN LINKAGE DISEQUILIBRIUM
Authors: Weir B S , Hill W G
Published: April 2021

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (Ne) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium. ——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of Ne, mating structure, n, and linkage or recombination parameter.—The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.
CORRIGENDUM
Authors: Golding G B , Strobeck C
Published: April 2021

In the paper by Golding and Strobek (Genetics 94: 777-789), several errors appeared. On page 780, the last three equations of (4a), (in small print) should appear at the top of page 781 as equations (4b), while the top two equations on page 781 are part of (4a). At the top of page 781, Φ(A/A)(B/B) should be  (A/A)(B/B), and a right parentheses should appear after  (B)(B). Still on page 781, "V= N(l-½S)μ =Nev" should be "V=N(l-½S  v = Nev". The equation for on page 782 has an error in the numerator; "[2(U+V)+]" should be "[2(U+V)+l]". In the APPENDIX at the top of page 787, the first "S" should be "S  2" in the equation for Φ′(A/A)(B/B). On page 789, the equation for Φ′(AB)(AB) should read "[½+½ Ψ(AB/AB)]", not " [½Ψ(AB/AB)]" and the equation for ∆′(A)(B)(A)(B) should read "[½Φ(A)(A)+…", not "[½+½Φ(A)(A)+…".
THE DISTRIBUTION OF MUTANT ALLELES IN A SUBDIVIDED POPULATION
Authors: Slatkin Montgomery
Published: April 2021

The results are presented from a simulation study of the spatial distribution of mutant alleles in a subdivided population. Statistical measures of the spatial pattern are defined in such a way that the same quantities could be measured in a geographic survey of allele frequencies in natural populations. Two types of quantities are discussed in this paper: (1)the occupancy distribution provides information on the presence or absence of the mutant in different numbers of demes; and (2) the conditional frequency distribution provides information about the extent of local differentiation when the mutant is present in different numbers of demes. Properties of these distributions are found for different types of natural selection acting on the mutant. Some results are presented for the same statistical measures based on samples of individuals from a fraction of the total number of demes. The simulation results for intermediate levels of the migration rates are compared with analytic results obtained on the limits of high and low migration rates. The main conclusion is that these measures of the spatial distribution of mutants in a subdivided population have simple properties that could provide a new perspective on data from natural populations.
PROBABILITY DISTRIBUTIONS AND COMPARTMENT BOUNDARIES IN THE DEVELOPMENT OF DROSOPHILA
Authors: Flanagan James R
Published: April 2021

Clone analysis and fate mapping probe several properties of development. Here it is shown that data on fate mapping support a probabilistic model of cell commitment in Drosophila blastoderms. Adult cells have a distribution of possible ancestors, as W. Baker (1978b) inferred from the theory of compartment-boundary development (Garcia-Bellido, Ripoll and Morata 1973). Fate-map data are used here to describe quantitatively the ancestry distributions on the blastoderm fate map. The properties of the distributions are sensitive to, and probes of, developmental events, such as relative time of cellularization and time of commitment. The theory of this analysis shows first how the meaningful interpretation of the stage represented by a fate map depends on the assumptions made in mapping. A general mapping model described below makes it possible to evaluate several interpretations. Interestingly, the data require a 3-dimensional map, and it is argued that this must be due to an effect of the preblastoderm nuclear synctial stage. Second, the theory shows how compartment boundaries affect ancestry distribution and why they have no observable effect on mapping. Third, the variability implied by ancestry variance does not create too much "noise" to make meaningful maps of small areas; rather, oddly enough, it tends to magnify the apparent distances within small areas to make them more resolvable. Empirical results include probabilistic maps of the Drosophila blastoderm. These results argue that time of commitment varies even for cells in the same compartment, demonstrating the need for a more complex model of early development than that proposed in the compartment model. The results also help to evaluate the significance of compartment boundaries in respect to developmental commitment.
NATURAL SELECTION OPPOSING ARTIFICIAL SELECTION: A TWO-LOCUS DETERMINISTIC SIMULATION
Authors: Minvielle Francis
Published: April 2021

A two-locus, two-allele metric trait was submitted to artificial truncation selection and to three types of opposing natural selection (two-locus extensions of directional selection, overdominance and underdominance) by numerical simulation in a large random-mating population. Limits to selection were generally reached by generation 100. Intermediate selection plateaus were found, with minor genes, for all three modes of opposing natural selection, but they were least frequent with underdominance. Multiple outcomes were common. In particular, fixation of the genotype favored by artificial selection was often associated with fixation of another genotype and/or with a central equilibrium; the end point actually reached depended on the genetic starting point of the simulation. In general, when the alleles favored by truncation selection were combined (positive linkage disequilibrium) in the base population, or when the trait was determined by major genes, artificial selection would prevail. Limitations inherent to this type of work are discussed, and possible avenues for further work on the antagonism between artificial and natural selection are proposed.
High-precision geochronological constraints on the duration of ‘Dinosaur Pompeii’ and the Yixian Formation
Authors: Zhong Yuting , Huyskens Magdalena H , Yin Qing-Zhu , Wang Yaqiong , Ma Qiang , Xu Yi-Gang
Published: April 2021

High-precision U-Pb zircon ages of 125.755 ± 0.061 Ma and 124.122 ± 0.048 Ma, respectively, represent the onset and termination of Yixian Formation in the Jin-Yang basin, bracketing its duration to 1.633 ± 0.078 Myr.