bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-dimensional mapping of surface scatterers on an optical fiber core using selective mode launching
Authors: Peng Lu , Nguyen Linh Viet , Li Jiawen , Riesen Nicolas , Otten Dale , Lancaster David G. , Ebendorff-Heidepriem Heike , Warren-Smith Stephen C.
Published: February 2021

The tracking of small particles is an important but challenging task for biological applications such as disease diagnostics and medical research. Current methods are limited to the use of bulky instruments such as flow cytometers and microscopes. Here, a novel technique for the detection and measurement of micron-scale optical scatterers using a few-mode exposed-core microstructured optical fiber is proposed. Through selective mode launching combined with optical frequency domain reflectometry, scatterers located on the fiber core surface can be simultaneously mapped with both longitudinal and transverse information. This technique is demonstrated by detecting the two-dimensional positions of several femtosecond-laser-inscribed micron-scale ablations written at different locations on the fiber core surface. Due to the compact nature of the optical fiber and its local sensitivity to scatterers that are in close proximity to it, this technique has the potential for the measurement and detection of micron-scale particles in difficult to reach biological environments for in vivo applications.
The dynamical creation/annihilation of a Dp-brane from D(p − 2) branes
Authors: Zhu Xiaoying
Published: February 2021

We discuss how to generate a dynamical Dp-brane with a topology of

R

p
−
2

×

S

2

from N D(p − 2)-branes with

R

p
−
2

topology with or without the presence of a constant RR (p + 2)-form flux. This extends the previous work (Chen and Lu 2004 arXiv:hep-th/0405265) of generating a dynamical spherical D2 brane from N D0 branes in a constant RR four-form flux to a general p. In particular, dynamically generating a higher dimensional brane from lower dimensional ones does not necessarily need the presence of a relevant RR background flux but needs excess energy, lending support to the spacetime uncertainty principle. The time evolution of the dynamical p-brane for a general p remains the same as for the p = 2 case, however there is a class of spatial dependent Dp configurations when p ≥ 3. Some of these spatial-dependent Dp brane configurations and their properties have been discussed previously which can also be obtained from the time-dependent one by euclideanizing the time. Properties of the spatial-dependent solutions and their relations to the corresponding brane-anti brane system are discussed.
Planning of Charging Facilities Considering Terrain Characteristics
Authors: Yi Long , Xianjun Zeng , Peng Kang , Ping Zhou , Chenxu Zhao , Fangxing Chen
Published: February 2021

The existing studies on the planning of charging facilities generally neglect the influence of terrain characteristics. First, this study quantifies the transportation characteristics based on the relative height to calculate the travel energy consumption of electric vehicles (EVs) users. Then, the charging demand of EVs is estimated and assigned according to urban traffic flow. Finally, a land purchasing coefficient is proposed based on a functional agglomeration phenomenon. The coefficient is integrated into formulating a planning model with the objective of minimising the total annual social costs. Numerical experiments are conducted to validate the novel planning method. The experimental results verify that the terrain characteristics increase users’ travel energy consumption and limit their driving range.
Construction of plug-and-play local protection system for smart substation
Authors: Chao Wujie , Tang Zhijun , Lin Guodong , Hu Wenwang , Zhuang Li , Xu Jie
Published: February 2021

This paper studies the application of plug-and-play location-based protection device in smart substation, introduces the hardware and software design scheme of smart substation plug-and-play location-based protection device, in order to improve the environmental adaptability and operation reliability of smart substation protection device, and reduce the operation cost of substation. In order to improve the protection performance and operation reliability of smart substation, the practicability and effectiveness of plug and play local-based protection device and intelligent management unit software are verified.
Optimal Design of Photovoltaic MPPT Disturbance Step Length in a Rapidly Changing Environment
Authors: Guo Kunli , Liu Luyu , Yan Dong
Published: February 2021

The traditional maximum power point tracking (MPPT) algorithm can not track the maximum power point (MPP) quickly and accurately in the environment of rapidly changing illumination amplitude. In this paper, based on the basic circuit model of solar cell, the small signal model between the disturbance step size of MPPT algorithm near the maximum power point and the intensity of light irradiance, ambient temperature, working voltage and working current is used, and then the MPPT duty cycle disturbance is modelled and analysed. The simulation results show that the model proposed in this paper clarifies the mechanism of the disturbance step size of MPPT algorithm in the environment of rapidly changing illumination amplitude. It also provides a theoretical basis for the design of subsequent disturbance step size.
Tie-line Power Adjustment Method Based on Proximal Policy Optimization Algorithm
Authors: Hou Jinxiu , Yu Zhihong , Zheng Qingping , Xu Huating , Li Shufang
Published: February 2021

The tie-line power adjustment is an essential part of the power system operation state calculation. Various existing algorithms to solve the tie-line power adjustment problem are mainly implemented by introducing tie-line power equation constraints into conventional power flow calculations. Such methods have low calculation efficiency, not enough automation, and are prone to non-convergence in the power flow calculation. In this paper, the tie-line power adjustment problem is formulated as a Markov decision process, and the proximal policy optimization algorithm is introduced to optimize the decision policy. In order to enhance the effectiveness of the proposed method, a new deep neural network structure suitable for the proximal policy optimization algorithm is designed. The proposed method is verified with the IEEE 39-bus system.
Data Driven Remaining Life Prediction of Electrolytic Capacitor in DC/DC Converter
Authors: Zhang Chenguang , Ni Junkang , Zhang Xiaobin , Lei Tao
Published: February 2021

A remaining useful life prediction model for electrolytic capacitor in DC-DC converter is presented in this paper based on Neural Network method. First, the degradation data of electrolytic capacitor is acquired from mathematical models. Next, the neural network prediction model is established by processing the degradation data of the electrolytic capacitor. Finally, the effectiveness of the developed life prediction model is verified using Matlab/Simulink. This paper provides the basis for the overall life prediction of dc/dc converter.
Research on improving ERT reconstruction precision based on combined algorithm
Authors: Li Shihan , Yan Hua
Published: February 2021

Among the traditional image reconstruction algorithm for ERT (Electrical Resistance Tomography) system, the Landweber algorithm is the most commonly used iterative algorithm, with moderate computation and good reconstruction quality. However, because "soft field" error is usually ignored in reconstruction, there is still much room for improvement in the quality of reconstructed images. Aiming this problem, a combined algorithm is proposed. The Landweber reconstruction results were taken as the initial population position of the particle swarm optimization (PSO). Through the random forest regression model, the "soft field" error prior condition is obtained, and used in the construction of the PSO objective function to eliminate the influence of ignoring the "soft field" error. The simulation experiment results show that the proposed algorithm effectively improves the accuracy of the reconstructed image.
Indonesian sugarcane seed system performance: an assessment from the perspective of institutional and technological innovation support
Authors: Ardana I K , Hartati R S , Wulandari S , Saefudin  , Suhesti S
Published: February 2021

Provision of plant seeds involves various stakeholders in a relatively complex supply chain, starting from tracing the source of superior seeds, producing, storing, and distributing to the end user. Research on the performance of the Indonesian sugarcane seed system from the perspective of institutional and technological innovation was conducted from March to October 2018. The survey method with snowball sampling and the multidimensional scaling analysis was used in this study. The results showed that the performance of the Indonesian sugarcane seed system was categorized as “pretty good” with a range of performance indexes in each dimension 54.23 - 73.13 and an average index of 65.89. The highest performance is achieved in the organizational dimension, while the lowest is in the dissemination dimension. The lever for improving the performance of seed institutions is the regulation of tariffs and the carrying capacity of tissue culture laboratory infrastructure, while technology licensing partnerships and training for seed producers are levers from the perspective of supporting technological innovation.
Effect of vanadium on Fe-rich phase, mechanical properties and thermal conductivity of hypoeutectic Al–Si alloy
Authors: Qin Rong , Yan Rui-Fang , Guan Zhi-Ping , Zhang Guang-Qi , Song Jia-Wang , Ren Ming-Wen , Wang Jin-Guo
Published: February 2021

In this paper, the effects of element V addition (0, 0.2, 0.4, 0.6, 0.8 and 1.0 wt%) on microstructures, mechanical properties and thermal conductivity of Al–8Si–0.1Cu–0.6Mg–0.7Fe hypoeutectic alloy in gravity die casting process were investigated. Microstructure analysis indicates that the size of Fe-rich phase in the Al–Si alloy is greatly affected by the contents of element V addition. The modification of element V could decrease the length of needle-like β-Fe phase which has the adverse impact to mechanical properties, and promote the formation of short rod-like α-Fe phase which has the favorable effect on mechanical properties and thermal conductivity. Then, the dependencies of mechanical properties and thermal conductivity on the size of Fe-rich phase of the alloy is revealed. When the content of element V is 0.6%, the length of Fe-rich phase in the alloy reaches the minimum, and correspondingly both the mechanical properties and the thermal conductivity could achieve the optimal level, as comparison with other contents of element V addition. However, excessive V addition would form VSi2 phase and Fe-rich phase with large size, resulting in poor properties of the alloy.
Synthesis of barium hexaferrite templated by nanocrystalline cellulose extracted from luffa acutangula fiber
Authors: Nuruddin Ahmad , Habibullah Achmadun , Adipratama Maria Johana , Purwasasmita Bambang Sunendar
Published: February 2021

Nanocrystalline cellulose templated barium hexaferrite has been prepared by sol-gel auto combustion and calcination method. Nanocrystalline cellulose template of 0, 0.5%, 1.0%, and 1.5% (w/v) were used to synthesize barium hexaferrite. The XRD pattern and TEM observation reveal the crystalline phase formation of hexagonal barium ferrite. Cellulose template changes the microstructure and properties of barium hexaferrite. Adding cellulose template of 0.5% (w/v) produce well-defined hexagonal platelet barium ferrite without impurity while adding more template result in barium hexaferrite containing hematite and excess cellulose template causing the decrease in magnetic properties. The crystallite size reduces with the addition of the cellulose template. The saturation magnetization and magnetocrystalline anisotropy are estimated using the Law of Approach to Saturation magnetization. The maximum values of saturation magnetization and magnetocrystalline anisotropy are 57.43 ± 0.25 emu g−1 and (4.64 ± 0.1) × 105 erg cm−3.
Effect of a cooling method on the structural and mechanical properties of friction stir spot welding with a 2524 aluminum alloy
Authors: Hu Yi-Jie , Sun You-Ping , Zhou Shi-Peng , He Jiang-Mei , Yang Chun-Yang
Published: February 2021

Friction stir spot welding (FSSW) is a clean, environmentally-friendly and cost-effective welding technology. To weld joints with improved mechanical properties, an FSSW experiment with a 2 mm-thick 2524 aluminum alloy sheet was performed to explore the influence of ambient cooling (AC), forced air cooling (FAC), waterflow cooling (WC), and an increasing rotational speed under WC, and to evaluate the welding method with regard to the resulting structural and tensile properties of the joint. The results showed that cooling-assisted welding reduced the width of the heat-affected zone (HAZ) and marginally increased the microhardness of the welding nugget zone (WNZ). The maximum tensile shear load (L) and effective width (W) values were 4673 N and 1958 μm at FAC, respectively, which were higher than the values of 4296 N and 1763 μm found with AC, respectively; in addition, the minimum values were 2946 N and 948 μm with WC, respectively. These results are not consistent with the idea that the joint strength can typically be improved with WC, because water absorbs a large amount of welding heat and reduces the plastic deformation capacity of the structure, thereby decreasing the W and L of the joint. Increasing the rotation speed of the welding tool can increase the heat input, which requires increasing the rotation speed along with WC. L and W reach their maximum values of 7652 N and 3320 μm, respectively, at 2500 r·min−1. As the rotation speed increases, L and W decrease. All joints underwent ductile fracturing, and the dispersion distribution of the second-phase particles at the bottom of the dimple exhibited good performance.
Difference in communication systems explained by balance between edge and node activations
Authors: Takano Masanori , Nakazato Kenichi
Published: February 2021

The trade-off between the number of friendships and the closeness of friendships of humans arises due to the limitations of time and cognitive capacities for communication. This trade-off distinguishes asynchronous text communication through the internet (lightweight communication) from face-to-face communication and the social grooming of primates (elaborate communication). This study modelled communication as messaging flows driven by edge and node activations to investigate micro-mechanisms that realise the trade-off law and the differences between the two types of communications. We observed the emergence of five patterns of social structures depending on the strengths of the two types of activations, namely, edge and node activations. The two patterns that show known statistics on empirical studies, such as the trade-off and power-law distributions of closeness, emerged around a threshold between elaborate and lightweight communications, where network structures qualitatively changed. A balance between edge and node activations shifts one pattern (elaborate communication) to another pattern (lightweight communication). Consequently, relation networks that communicate through lightweight communication become less clustered. These results suggest how communication systems construct different social structures, e.g., the impact of popularising the internet.
Anomalous stepped-hysteresis and T-induced unit-cell-volume reduction in carbon nanotubes continuously filled with faceted Fe3C nanowires
Authors: Xia JiaChen , Guo Jian , Zhang Xi , Lan Mu , Wen Jiqiu , Wang Shanling , He Yi , Xiang Gang , Corrias Anna , Boi Filippo S
Published: February 2021

Ferromagnetically-filled carbon nanotubes have been recently considered important candidates for application into data recording quantum disk devices. Achievement of high filling rates of the ferromagnetic materials is particularly desirable for applications. Here we report the novel observation of carbon nanotubes continuously filled along the capillary with unusual μm-long faceted Fe3C nanowires. Anomalous magnetic features possibly due to strain effects of the crystal facets are reported. Magnetization measurements revealed unusual stepped magnetic hysteresis-loops at 300 K and at 2 K together with an anomalous decrease in the coercivity at low temperature. The observed unusual shape of the hysteresis is ascribed to the existence of an antiferromagnetic transition within or at the boundary of the ferromagnetic facets. The collapse in the coercivity value as the temperature decreases and the characteristic width-enhancement of the hysteresis with the field increasing appear to indicate the existence of layered antiferromagnetic phases, possibly in the strain-rich regions of the nanowire facets. Zero field cooled (ZFC) and field cooled (FC) magnetic curves evidenced presence of magnetic irreversibilities, an indicator of a possible spin-glass-like behavior induced by competing antiferromagnetic and ferromagnetic interactions. Characterization performed with low temperature XRD measurements, further revealed a slight variation in the average Fe3C unit cell parameters, suggesting the absence of additional unit-cell volume induced ferromagnetic transitions at low temperature.
IsoTV: processing and visualizing functional features of translated transcript isoforms
Authors: Annaldasula Siddharth , Gajos Martyna , Mayer Andreas
Published: February 2021

Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure. To address this issue and enable researchers to assess potential functional consequences of transcript isoform variation on the proteome, we developed IsoTV. IsoTV is a versatile pipeline to process, predict and visualize the functional features of translated transcript isoforms. Attributes such as gene and isoform expression, transcript composition and functional features are summarized in an easy-to-interpret visualization. IsoTV is able to analyze a variety of data types from all eukaryotic organisms, including short- and long-read RNA-seq data. Using Oxford Nanopore long read data, we demonstrate that IsoTV facilitates the understanding of potential protein isoform function in different cancer cell types.

Availability and implementation

IsoTV is available at https://github.molgen.mpg.de/MayerGroup/IsoTV, with the corresponding documentation at https://isotv.readthedocs.io/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Negative intersexual genetic correlation for colour pattern in a variable aposematic insect
Authors: Burdfield-Steel Emily , Kemp Darrell J
Published: February 2021

Despite the fact their coloration functions as an aposematic signal, and is thus expected to be under stabilizing selection, hibiscus harlequin bugs (Tectocoris diophthalmus) show an impressive level of variation in their iridescent coloration both within and between populations. To date the heritability of coloration in this species remains unknown. Here we focus on a single population in New South Wales (the southern part of this species’ Australian range), with the greatest colour variation. We reared full-sib families of known pedigree in the laboratory and analysed the extent of iridescent coloration at adulthood. We then looked for evidence of heritability, condition dependence and antagonistic sexual selection acting on colour in this species. We found significant heritability in the extent of iridescent coloration for both sexes, as well as in development time and body size, but no evidence that condition dependence played a role in the determination of adult coloration. There was, however, a sex by genotype interaction for iridescent cover, in the form of a negative intersexual genetic correlation: in families where sons had high iridescent cover the daughters had low, and vice versa. Our results suggest that different selective pressures may act on coloration in males and females of this species.
Complications and survival after hybrid and fully minimally invasive oesophagectomy
Authors: Veenstra M M K , Smithers B M , Visser E , Edholm D , Brosda S , Thomas J M , Gotley D C , Thomson I G , Wijnhoven B P L , Barbour A P
Published: February 2021

Background

Minimally invasive oesophagectomy (MIO) is reported to produce fewer respiratory complications than open oesophagectomy. This study assessed differences in postoperative complications between MIO and hybrid MIO (HMIO) employing thoracoscopy and laparotomy, along with the influence of co-morbidities on postoperative outcomes.

Methods

Patients with oesophageal cancer undergoing three-stage MIO or three-stage HMIO between 1999 and 2018 were identified from a prospectively developed database, which included patient demographics, co-morbidities, preoperative therapies, and cancer stage. The primary outcome was postoperative complications in the two groups. Secondary outcomes included duration of operation, blood transfusion requirement, duration of hospital stay, and overall survival.

Results

There were 828 patients, of whom 722 had HMIO and 106 MIO, without significant baseline differences. Median duration of operation was longer for MIO (325 versus 289 min; P < 0.001), but with less blood loss (median 250 versus 300 ml; P < 0.001) and a shorter hospital stay (median 12 versus 13 days; P = 0.006). Respiratory complications were not associated with operative approach (31.1 versus 35.2 per cent for MIO and HMIO respectively; P = 0.426). Anastomotic leak rates (10.4 versus 10.2 per cent) and 90-day mortality (1.0 versus 1.7 per cent) did not differ. Cardiac co-morbidity was associated with more medical and surgical complications. Overall survival was associated with AJCC stage and co-morbidities, but not operative approach.

Conclusion

MIO had a small benefit in terms of blood loss and hospital stay, but not in operating time. Oncological outcomes were similar in the two groups. Postoperative complications were associated with pre-existing cardiorespiratory co-morbidities rather than operative approach.
Proteinuria in COVID-19
Authors: Mohamed Muner M B , Velez Juan Carlos Q
Published: February 2021

Upper respiratory and pulmonary diseases are the primary manifestations of coronavirus disease 2019 (COVID-19). However, kidney involvement has also been recognized and extensively described. A large percentage of affected patients present with acute kidney injury (AKI). However, specific phenotypic aspects of AKI or other renal manifestations of COVID-19 remain sparsely characterized. Many reports indicate that proteinuria can be detected in AKI associated with COVID-19 (CoV-AKI) despite CoV-AKI being largely described as a form of acute tubular injury. On the other hand, individuals of African ancestry with the high-risk APOL1 genotype are uniquely at risk of developing collapsing glomerulopathy when they are infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the entity now known as COVID-19-associated nephropathy (COVAN). Patients with COVAN typically present with nephrotic-range proteinuria. The exact incidence of proteinuria in COVID-19 is unclear due to heterogeneity in the frequency with which proteinuria has been assessed in cases of COVID-19, as well as methodological differences in the way proteinuria is measured and/or reported. In this review we discuss the current evidence of proteinuria as a manifestation of COVID-19 and elaborate on potential pathophysiological mechanisms associated with it.
Cuticular hydrocarbon profiles differ between ant body parts: implications for communication and our understanding of CHC diffusion
Authors: Sprenger Philipp P , Gerbes Lisa J , Sahm Jacqueline , Menzel Florian
Published: February 2021

Insect cuticular hydrocarbons (CHCs) serve as communication signals and protect against desiccation. They form complex blends of up to 150 different compounds. Due to differences in molecular packing, CHC classes differ in melting point. Communication is especially important in social insects like ants, which use CHCs to communicate within the colony and to recognize nestmates. Nestmate recognition models often assume a homogenous colony odor, where CHCs are collected, mixed, and redistributed in the postpharyngeal gland (PPG). Via diffusion, recognition cues should evenly spread over the body surface. Hence, CHC composition should be similar across body parts and in the PPG. To test this, we compared CHC composition among whole-body extracts, PPG, legs, thorax, and gaster, across 17 ant species from 3 genera. Quantitative CHC composition differed between body parts, with consistent patterns across species and CHC classes. Early-melting CHC classes were most abundant in the PPG. In contrast, whole body, gaster, thorax, and legs had increasing proportions of CHC classes with higher melting points. Intraindividual CHC variation was highest for rather solid, late-melting CHC classes, suggesting that CHCs differ in their diffusion rates across the body surface. Our results show that body parts strongly differ in CHC composition, either being rich in rather solid, late-melting, or rather liquid, early-melting CHCs. This implies that recognition cues are not homogenously present across the insect body. However, the unequal diffusion of different CHCs represents a biophysical mechanism that enables caste differences despite continuous CHC exchange among colony members.
Successful resuscitation of acute cardiogenic shock presenting as ventricular fibrillation via Bipella approach: a case report
Authors: Zoltowska Dominika M , Agrawal Yashwant , Nazroo Jean-Yves R , Patel Kirit
Published: February 2021

Background

The use of mechanical circulatory support (MCS) in acute myocardial infarction and cardiogenic shock (AMICS) complicated by biventricular failure is poorly discussed in the literature.

Case summary

We present successful treatment of a 52-year-old old man presenting with AMICS following cardiac arrest and prolonged CPR via a Bipella approach for biventricular support and restoration of haemodynamic stability.

Discussion

This case demonstrates the importance of understanding the role of MCS in the management of cardiogenic shock; the value of the cardiac power output and pulmonary artery pulsatility index as haemodynamic metrics to assess the cardiac function of a patient with cardiogenic shock; and the importance of a Bipella MCS approach in high inpatient morbidity and mortality AMICS with biventricular failure.
Regena (Rga), a Drosophila Homolog of the Global Negative Transcriptional Regulator CDC36 (NOT2) from Yeast, Modifies Gene Expression and Suppresses Position Effect Variegation
Authors: Frolov Maxim V , Benevolenskaya Elizaveta V , Birchler James A
Published: February 2021

A mutation in Regena (Rga) was isolated in screens for modifiers of white eye color gene expression. The reduction in the level of the Rga product results in a complex modulation of white mRNA both positively and negatively, depending on the developmental stage. In addition to white, Rga also affects the expression of several other tested genes, with one of them, Vinculin, being regulated in a strong sex-specific manner. Rga was cloned by transposon tagging. Its predicted product lacks any recognized nucleic acid–binding motif but is homologous to a global negative transcriptional regulator, CDC36 (NOT2), from yeast. Rga also acts as a suppressor of position effect variegation, suggesting that a possible function of Rga could be mediation of an interaction between chromatin proteins and the transcriptional complex.
The Murine Misty Mutation: Phenotypic Effects on Melanocytes, Platelets and Brown Fat
Authors: Sviderskaya Elena V , Novak Edward K , Swank Richard T , Bennett Dorothy C
Published: February 2021

Although the recessive murine mutation misty (m) is well known, its phenotype has never been reported beyond brief descriptions of a dilution of coat color and white spotting of the belly and extremities, suggesting a developmental mutation. A report in abstract has also suggested effects on white fat and body weight. Here, we report effects of the homozygous misty mutation on an unusual combination of three cell types: melanocytes, platelets, and brown fat. Brown fat appeared to be completely absent from all expected locations in neonatal m/m mice. A prolonged bleeding time was observed; platelet count and platelet serotonin and ATP levels were normal, but the level of ADP in m/m platelets was low. Primary cultures and immortal lines of melanocytes from m/m mice showed several abnormalities. There was a marked deficiency in net proliferation, suggesting that the color dilution and spotting in vivo may result from reduced numbers of melanocytes and their precursors. m/m melanocytes were also hyperdendritic in morphology, overproduced melanin, and had deficient responses to the cAMP agonists cholera toxin and melanocyte-stimulating hormone, which normally promote melanin production. The misty gene product may be involved in adenine nucleotide metabolism or signaling.
A Mixture Model Approach to the Mapping of Quantitative Trait Loci in Complex Populations With an Application to Multiple Cattle Families
Authors: Jansen Ritsert C , Johnson David L , Van Arendonk Johan A M
Published: February 2021

A mixture model approach is presented for the mapping of one or more quantitative trait loci (QTLs) in complex populations. In order to exploit the full power of complete linkage maps the simultaneous likelihood of phenotype and a multilocus (all markers and putative QTLs) genotype is computed. Maximum likelihood estimation in our mixture models is implemented via an Expectation-Maximization algorithm: exact, stochastic or Monte Carlo EM by using a simple and flexible Gibbs sampler. Parameters include allele frequencies of markers and QTLs, discrete or normal effects of biallelic or multiallelic QTLs, and homogeneous or heterogeneous residual variances. As an illustration a dairy cattle data set consisting of twenty half-sib families has been reanalyzed. We discuss the potential which our and other approaches have for realistic multiple-QTL analyses in complex populations.
Restriction Fragment Length Polymorphism and Divergence in the Genomic Regions of High and Low Recombination in Self-Fertilizing and Cross-Fertilizing Aegilops Species
Authors: Dvorřák Jan , Luo Ming-Cheng , Yang Zu-Li
Published: February 2021

RFLP was investigated at 52 single-copy gene loci among six species of Aegilops, including both cross-fertilizing and self-fertilizing species. Average gene diversity (H) was found to correlate with the level of outcrossing. No relationship was found between H and the phylogenetic status of a species. In all six species, the level of RFLP at a locus was a function of the position of the locus on the chromosome and the recombination rate in the neighborhood of the locus. Loci in the proximal chromosome regions, which show greatly reduced recombination rates relative to the distal regions, were significantly less variable than loci in the distal chromosome regions in all six species. Variation in recombination rates was also reflected in the haplotype divergence between closely related species; loci in the chromosome regions with low recombination rates were found to be diverged less than those in the chromosome regions with high recombination rates. This relationship was not found among the more distantly related species.
Translation of Some Maize Small Heat Shock Proteins Is Initiated From Internal In-Frame AUGs
Authors: Frappier J Roger H , Walden David B , Atkinson Burr G
Published: February 2021

Etiolated maize radicles (inbred Oh43) subjected to a brief heat shock synthesize a family of small heat shock proteins (≃18 kD) that is composed of at least 12 members. We previously described the cDNA-derived sequence of three maize shsp mRNAs (cMHSP18-1, cMHSP18-3, and cMHSP18-9). In this report, we demonstrate that the mRNA transcribed in vitro from one of these cDNAs (cMHSP 18-9) is responsible for the synthesis of three members of the shsp family, and we suggest that cMHSP18-3 may be responsible for the synthesis of three additional members and cMHSP18-1 for the synthesis of two other members of this family. The fact that these genes do not contain introns, coupled with the observations reported herein, suggest that maize may have established another method of using a single gene to produce a number of different proteins.
Genetic Interaction With vps8-200 Allows Partial Suppression of the Vestigial Vacuole Phenotype Caused by a pep5 Mutation in Saccharomyces cerevisiae
Authors: Woolford Carol A , Bounoutas George S , Frew Sarah E , Jones Elizabeth W
Published: February 2021

pep5 mutants of Saccharomyces cerevisiae accumulate inactive precursors to the vacuolar hydrolases. In addition, they show a vestigial vacuole morphology and a sensitivity to growth on media containing excess divalent cations. This pleiotropic phenotype observed for pep5::TRP1 mutants is partially suppressed by the vps8-200 allele. pep5::TRP1 vps8-200 mutants show near wild-type levels of mature-sized soluble vacuolar hydrolases, growth on zinc-containing medium, and a more “wild-type” vacuolar morphology; however, aminopeptidase I and alkaline phosphatase accumulate as precursors. These data suggest that Pep5p is a bifunctional protein and that the TRP1 insertion does not eliminate function, but results in a shorter peptide that can interact with Vps8-200p, allowing for partial function. vps8 deletion/disruption mutants contain a single enlarged vacuole. This genetic interaction was unexpected, since Pep5p was thought to interact more directly with the vacuole, and Vps8p is thought to play a role in transport between the Golgi complex and the prevacuolar compartment. The data are consistent with Pep5p functioning both at the site of Vps8p function and more closely proximal to the vacuole. They also provide evidence that the three transport pathways to the vacuole either converge or share gene products at late step(s) in the pathway(s).
Characterization of mat A-2, mat A-3 and ΔmatA Mating-Type Mutants of Neurospora crassa
Authors: Ferreira Adlane V-B , An Zhiqiang , Metzenberg Robert L , Glass N Louise
Published: February 2021

The mating-type locus of Neurospora crassa regulates mating identity and entry into the sexual cycle. The mat A idiomorph encodes three genes, mat A-1, mat A-2, and mat A-3. Mutations in mat A-1 result in strains that have lost mating identity and vegetative incompatibility with mat a strains. A strain containing mutations in both mat A-2 and mat A-3 is able to mate, but forms few ascospores. In this study, we describe the isolation and characterization of a mutant deleted for mat (ΔmatA), as well as mutants in either mat A-2 or mat A-3. The ΔmatA strain is morphologically wild type during vegetative growth, but it is sterile and heterokaryon compatible with both mat A and mat a strains. The mat A-2 and mat A-3 mutants are also normal during vegetative growth, mate as a mat A strain, and produce abundant biparental asci in crosses with mat a, and are thus indistinguishable from a wild-type mat A strain. These data and the fact that the mat A-2 mat A-3 double mutant makes few asci with ascospores indicate that MAT A-2 and MAT A-3 are redundant and may function in the same pathway. Analysis of the expression of two genes (sdv-1 and sdv-4) in the various mat mutants suggests that the mat A polypeptides function in concert to regulate the expression of some sexual development genes.
Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data
Authors: Sillanpää Mikko J , Arjas Elja
Published: February 2021

A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL-intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the location wise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/~mjs.
The Roles of the Bacteriophage T4 r Genes in Lysis Inhibition and Fine-Structure Genetics: A New Perspective
Authors: Paddison Patrick , Abedon Stephen T , Dressman Holly Kloos , Gailbreath Katherine , Tracy Julia , Mosser Eric , Neitzel James , Guttman Burton , Kutter Elizabeth
Published: February 2021

Seldom has the study of a set of genes contributed more to our understanding of molecular genetics than has the characterization of the rapid-lysis genes of bacteriophage T4. For example, T4 rII mutants were used to define gene structure and mutagen effects at the molecular level and to help unravel the genetic code. The large-plaque morphology of these mutants reflects a block in expressing lysis inhibition (LIN), the ability to delay lysis for several hours in response to sensing external related phages attacking the cell, which is a unique and highly adaptive attribute of the T4 family of phages. However, surprisingly little is known about the mechanism of LIN, or how the various r genes affect its expression. Here, we review the extensive old literature about the r genes and the lysis process and try to sort out the major players affecting lysis inhibition. We confirm that superinfection can induce lysis inhibition even while infected cells are lysing, suggesting that the signal response is virtually instantaneous and thus probably the result of post-translational regulation. We identify the rI gene as ORF tk.–2, based on sequence analysis of canonical rI mutants. The rI gene encodes a peptide of 97 amino acids (Mr = 11.1 kD; pI = 4.8) that probably is secreted into the periplasmic space. This gene is widely conserved among T-even phage. We then present a model for LIN, postulating that rI is largely responsible for regulating the gpt holin protein in response to superinfection. The evidence suggests that the rIIA and B genes are not directly involved in lysis inhibition; rather, when they are absent, an alternate pathway for lysis develops which depends on the presence of genes from any of several possible prophages and is not sensitive to lysis inhibition.
Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation
Authors: Walker Elsbeth L
Published: February 2021

In paramutation two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. The large (220 kbp) multigenic complex R-r is paramutable: its level of expression is changed during paramutation. R-r was found to exhibit increases in its level of cytosine methylation (C-methylation) following paramutation. These C-methylation changes are localized to the 5′ portions of the two genes in the complex that are most sensitive to paramutation. These methylation changes flank a small region called σ that is thought to have been derived from a transposon named doppia. A mutant derivative of R-r that has a deletion of the σ region fails to become methylated under conditions in which R-r is heavily methylated. This suggests that the presence of σ sequences at the locus is required for the methylation changes that are observed following paramutation.
How Optimized Is the Translational Machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?
Authors: Xia Xuhua
Published: February 2021

The optimization of the translational machinery in cells requires the mutual adaptation of codon usage and tRNA concentration, and the adaptation of tRNA concentration to amino acid usage. Two predictions were derived based on a simple deterministic model of translation which assumes that elongation of the peptide chain is rate-limiting. The highest translational efficiency is achieved when the codon recognized by the most abundant tRNA reaches the maximum frequency. For each codon family, the tRNA concentration is optimally adapted to codon usage when the concentration of different tRNA species matches the square-root of the frequency of their corresponding synonymous codons. When tRNA concentration and codon usage are well adapted to each other, the optimal content of all tRNA species carrying the same amino acid should match the square-root of the frequency of the amino acid. These predictions are examined against empirical data from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae.
Quantitative Trait Locus (QTL) Mapping Using Different Testers and Independent Population Samples in Maize Reveals Low Power of QTL Detection and Large Bias in Estimates of QTL Effects
Authors: Melchinger Albrecht E , Utz H Friedrich , Schön Chris C
Published: February 2021

The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples (N = 344 and 107) of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL × environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS.
Top four types of sentinel events in Saudi Arabia during the period 2016–19
Authors: Altalhi Nasser , Alnaimi Haifa , Chaouali Mafaten , Alahmari Falaa , Alabdulkareem Noor , Alaama Tareef
Published: February 2021

Background

This study discusses the summary, investigation and root causes of the top four sentinel events (SEs) in Saudi Arabia (SA) that occurred between January 2016 and December 2019, as reported by the Ministry of Health (MOH) and private hospitals through the MOH SE reporting system (SERS). It is intended for use by legislators, health-care facilities and the public to shed light on areas that still need improvement to preserve patient safety.

Objectives

The purpose of this study is to review the most common SEs reported by the MOH and private hospitals between the years 2016 and 2019 to assess the patterns and identify risk areas and the common root causes of these events in order to promote country-wide learning and support services that can improve patient safety.

Methods

In this retrospective descriptive study, the data were retrieved from the SERS, which routinely collects records from both MOH and private hospitals in SA. SEs were analyzed by type of event, location, time, patient demographics, outcome and root causes.

Results

There were 727 SEs during this period, 38.4% of which were under the category of unexpected patient death, 19.4% under maternal death, 11.7% under unexpected loss of limb or function and 9.9% under retained instruments or sponge. Common root causes were related to policies and procedures, guidelines, miscommunication between health-care facilities, shortage of staff and lack of competencies.

Conclusion

Given these results, efforts should focus on improving the care of deteriorating patients in general wards, ICU (Intensive Care Units) admission/discharge criteria and maternal, child and surgical safety. The results also highlighted the problem of underreporting of SEs, which needs to be addressed and improved. Linking data sources such as claims and patient complaints databases and electronic medical records to the national reporting system must also be considered to ensure an optimal estimation of the number of events.
The Performance of Friendship: Paschal de L’estocart and His Circle at the University of Basel, 1581–1583
Authors: Latour Melinda
Published: February 2021

In this article, I present new research on the composer Paschal de L’Estocart during his peak years of activity at the University of Basel (1581–3). In addition to discussing two fresh pieces of archival evidence related to L’Estocart found in the Basel archives, I offer new research on the identities of his laudatory contributors. Considering how little biographical information has survived on the composer beyond his published music, the identities of these poetic contributors are a critical piece of evidence that fills in our skeletal knowledge of L’Estocart’s network and the social context of his music. Taken together, this new evidence sheds light on L’Estocart’s active participation in the most elite academic circles in Basel and Geneva, which makes his return to the Catholic world at the end of his life all the more difficult to explain. L’Estocart’s 1583 letter to Zwinger, however, offers a clue that might explain his break from the Reformed faith.
The Retroauricular Incision as an Effective and Safe Alternative Incision for Decompressive Hemicraniectomy
Authors: Dowlati Ehsan , Mortazavi Armin , Keating Gregory , Jha Ribhu Tushar , Felbaum Daniel R , Chang Jason J , Nair Mani N , Mason Robert B , Aulisi Edward F , Armonda Rocco A , Mai Jeffrey C
Published: February 2021

BACKGROUND

The reverse question mark (RQM) incision has been traditionally utilized to perform decompressive hemicraniectomies (DHC) to relieve refractory intracranial hypertension. Alternative incisions have been proposed in the literature but have not been compared directly.

OBJECTIVE

To present the retroauricular (RA) incision as an alternative incision that we hypothesize will increase calvarium exposure to maximize the removal of the hemicranium and will decrease wound-related complications compared to the RQM incision.

METHODS

This study is a retrospective review of all DHCs performed at our institution over a span of 34 mo, stratified based on the type of scalp incision. The surface areas of the cranial defects were calculated, normalizing to their respective skull diameters. For those patients surviving beyond 1 wk, complications were examined from both cohorts.

RESULTS

A total of 63 patients in the RQM group and 43 patients in the RA group were included. The average surface area for the RA and RQM incisions was 117.0 and 107.8 cm2 (P = .0009), respectively. The ratio of average defect size to skull size for RA incision was 0.81 compared to 0.77 for the RQM group (P = .0163). Of those who survived beyond 1 wk, the absolute risk for surgical site complications was 14.0% and 8.3% for RQM and RA group (P = .5201), respectively.

CONCLUSION

The RA incision provides a safe and effective alternative incision to the traditional RQM incision used for DHC. This incision affords a potentially larger craniectomy while mitigating postoperative wound complications.