bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological pathway expression complementation contributes to biomass heterosis in
Arabidopsis
Authors: Liu Wenwen , He Guangming , Deng Xing Wang
Published: April 2021

Significance

Heterosis, referring to the better performance of an F
1
hybrid compared with its parents, has been greatly exploited in agriculture to improve yield. Nevertheless, our understanding of its genetic and molecular mechanism has remained limited. We investigated the temporally dynamic phenotypes and transcriptomes during early seedling development in two
Arabidopsis
ecotypes together with their hybrid and unveiled differences in the transcriptional regulatory network between the hybrid and parents, orchestrating the hybrid growth vigor. Moreover, we found complementary high-parent expression in the hybrid between the network hub genes involved in photosynthesis and cell cycle. Our findings provide molecular-level evidence that dominant expression complementation between genes involved in two fundamental biological pathways contributes to heterosis.
Decoding allosteric regulation by the acyl carrier protein
Authors: Sztain Terra , Bartholow Thomas G. , Lee D. John , Casalino Lorenzo , Mitchell Andrew , Young Megan A. , Wang Jianing , McCammon J. Andrew , Burkart Michael D.
Published: April 2021

Significance

Acyl carrier proteins (ACPs) are involved in primary and secondary metabolic pathways, including the ubiquitous fatty acid biosynthesis, required for all domains of life. This single protein must deliver pathway intermediates to the appropriate enzyme, distinguishing between a myriad of possible intermediate-enzyme combinations. The intermediate is delivered to the active site of enzymes through a large conformational change termed “chain flipping.” Whether chain flipping is a stochastic or regulated process has remained a mystery. This study provides evidence for an allosteric regulatory mechanism—demonstrating that substrates sequestered within the interior side of the four-helical ACP bundle confer structural changes to the exterior which are recognized by enzymes via protein–protein interactions—presenting a unique paradigm for understanding these biosynthetic pathways.
Acacia hockii.
Authors: Pasiecznik Nick
Published: April 2021

A datasheet on Acacia hockii covering, as an economically important tree, its taxonomy, importance, silviculture, distribution, biology and ecology, uses, products and pests.
Rauvolfia caffra (quinine tree).
Authors: Rojas-Sandoval Julissa
Published: April 2021

A datasheet on Rauvolfia caffra covering, as an economically important tree, its taxonomy, importance, silviculture, distribution, biology and ecology, uses, products and pests.
Distribution of eight heavy metals in the inner shelf sediments of East China Sea: Risk assessments and sources analysis
Authors: Wang Chunjie , Wang Zhangwei , Zhang Xiaoshan
Published: April 2021

Although numerous studies on heavy metals (HMs) in sediments have been carried out in the East China Sea (ECS), the knowledge on the recent pollution levels of HMs in coastal region remains not well understood due to the rapid developments of urbanization in eastern China. In this study, 23 surface samples and 4 core samples are collected in the inner shelf of the ECS. The average dry-weight concentrations follow the descending order of Zn, Cr, Ni, Pb, Cu, As, Cd, and Hg (103.6 ± 26.0, 42.8 ± 12.4, 37.0 ± 9.1, 34.7 ± 11.1, 19.5 ± 10.3, 15.7 ± 11.6, 0.056 ± 0.017, and 0.041 ± 0.017 μg g
−1
, respectively). HMs concentrations share a similar spatial distribution pattern of TOC content with a decreasing trend from coastline to outer sea. Additionally, HMs concentrations exhibit a decreasing trend from top to bottom sediments, especially for Hg at the open sites due to the wet and dry deposition of atmospheric Hg besides the riverine inputs. The potential ecological risk indices (
PERI
) values in coastal sediments were about 2–4 times higher than those in open sea. Although the Hg and Cd concentrations were lower by 2–3 orders of magnitude than those of other six metals, the
PERI
values of Hg (65.5) and Cd (52.1) were 3–40 times higher than those of others. The hierarchical cluster result is consistent with the PCA result, suggesting that Hg, Cd, and As have similar sources and probably mainly originated from anthropogenic emissions.
RTKN-1/Rhotekin shields endosome-associated F-actin from disassembly to ensure endocytic recycling
Authors: Yan Yanling , Liu Shuai , Hu Can , Xie Chaoyi , Zhao Linyue , Wang Shimin , Zhang Wenjuan , Cheng Zihang , Gao Jinghu , Fu Xin , Yang Zhenrong , Wang Xianghong , Zhang Jing , Lin Long , Shi Anbing
Published: April 2021

Cargo sorting and the subsequent membrane carrier formation require a properly organized endosomal actin network. To better understand the actin dynamics during endocytic recycling, we performed a genetic screen in C. elegans and identified RTKN-1/Rhotekin as a requisite to sustain endosome-associated actin integrity. Loss of RTKN-1 led to a prominent decrease in actin structures and basolateral recycling defects. Furthermore, we showed that the presence of RTKN-1 thwarts the actin disassembly competence of UNC-60A/cofilin. Consistently, in RTKN-1–deficient cells, UNC-60A knockdown replenished actin structures and alleviated the recycling defects. Notably, an intramolecular interaction within RTKN-1 could mediate the formation of oligomers. Overexpression of an RTKN-1 mutant form that lacks self-binding capacity failed to restore actin structures and recycling flow in rtkn-1 mutants. Finally, we demonstrated that SDPN-1/Syndapin acts to direct the recycling endosomal dwelling of RTKN-1 and promotes actin integrity there. Taken together, these findings consolidated the role of SDPN-1 in organizing the endosomal actin network architecture and introduced RTKN-1 as a novel regulatory protein involved in this process.
Moral Orders of Multinationals: Registers of Value in Corporate Food Production
Authors: Yount-André Chelsie
Published: April 2021

This article analyzes moral registers about and within one of the world’s largest food corporations. Based on fieldwork at a French multinational corporation, I trace how speech registers surrounding food circulate across institutional arenas, reconfiguring material connections between the company and consumers. I examine the emergence of a “Big Food” register, critical of the food industry, and analyze the discourses it has triggered within one corporation, comparing talk of ethics and economics among employees in Paris and Johannesburg. Corporate efforts to produce value through food result from struggles between value projects of diverse employees who are positioned differently relative to corporate hierarchies and global inequalities. I argue that moral language in and around the food industry can elucidate current transformations in global capitalism, revealing multinationals’ struggles to credibly voice registers aligned with consumers’ values in their search for competitive advantage.
Opportunities and challenges of inorganic perovskites in high-performance photodetectors
Authors: Cai Wensi , Li Haiyun , Li Mengchao , Wang Meng , Wang Huaxin , Chen Jiangzhao , Zang Zhigang
Published: April 2021

Compared with organic–inorganic hybrid perovskites, fully inorganic perovskites show an increased stability and are therefore attracting considerable attention, especially in recent years. Such materials are not only being extensively used in applications such as solar cells and light-emitting diodes, but also show great potential as photodetectors due to their exceptional optoelectronic properties. In this review, the recent progress on emerging photodetectors based on inorganic perovskites is comprehensively summarized, focusing on the versatile compositions and morphologies of constituent materials and diverse device architectures, and covering the sensing regions from UV–visible–NIR to x-ray and even gamma-ray. A brief outlook that highlights the current challenges impeding the commercialization of inorganic perovskite-based photodetectors is also included, and possible solutions to these problems are provided.
Low-noise, high-detectivity, polarization-sensitive, room-temperature infrared photodetectors based on Ge quantum dot-decorated Si-on-insulator nanowire field-effect transistors
Authors: John John Wellington , Dhyani Veerendra , Singh Sudarshan , Jakhar Alka , Sarkar Arijit , Das Samaresh , Ray Samit K
Published: April 2021

A CMOS-compatible infrared (IR; 1200–1700 nm) detector based on Ge quantum dots (QDs) decorated on a single Si-nanowire channel on a silicon-on-insulator (SOI) platform with a superior detectivity at room temperature is presented. The spectral response of a single nanowire device measured in a back-gated field-effect transistor geometry displays a very high value of peak detectivity ∼9.33 × 1011 Jones at ∼1500 nm with a relatively low dark current (∼20 pA), which is attributed to the fully depleted Si nanowire channel on SOI substrates. The noise power spectrum of the devices exhibits a

1
/

f

γ

,

with the exponent, γ showing two different values of 0.9 and 1.8 owing to mobility fluctuations and generation-recombination of carriers, respectively. Ge QD-decorated nanowire devices exhibit a novel polarization anisotropy with a remarkably high photoconductive gain of ∼104. The superior performance of a Ge QDs/Si nanowire phototransistor in IR wavelengths is potentially attractive to integrate electro-optical devices into Si for on-chip optical communications.
High mobility field-effect transistors based on MoS2 crystals grown by the flux method
Authors: Patil Vilas , Kim Jihyun , Agrawal Khushabu , Park Tuson , Yi Junsin , Aoki Nobuyuki , Watanabe Kenji , Taniguchi Takashi , Kim Gil-Ho
Published: April 2021

Two-dimensional (2D) molybdenum disulphide (MoS2) transition metal dichalcogenides (TMDs) have great potential for use in optical and electronic device applications; however, the performance of MoS2 is limited by its crystal quality, which serves as a measure of the defects and grain boundaries in the grown material. Therefore, the high-quality growth of MoS2 crystals continues to be a critical issue. In this context, we propose the formation of high-quality MoS2 crystals via the flux method. The resulting electrical properties demonstrate the significant impact of crystal morphology on the performance of MoS2 field-effect transistors. MoS2 made with a relatively higher concentration of sulphur (a molar ratio of 2.2) and at a cooling rate of 2.5 °C h−1 yielded good quality and optimally sized crystals. The room-temperature and low-temperature (77 K) electrical transport properties of MoS2 field-effect transistors (FETs) were studied in detail, with and without the use of a hexagonal boron nitride (h-BN) dielectric to address the mobility degradation issue due to scattering at the SiO2/2D material interface. A maximum field-effect mobility of 113 cm2 V−1 s−1 was achieved at 77 K for the MoS2/h-BN FET following high-quality crystal formation by the flux method. Our results confirm the achievement of large-scale high-quality crystal growth with reduced defect density using the flux method and are key to achieving higher mobility in MoS2 FET devices in parallel with commercially accessible MoS2 crystals.
A comparison of insertion methods for surgical placement of penetrating neural interfaces
Authors: Thielen Brianna , Meng Ellis
Published: April 2021

Many implantable electrode arrays exist for the purpose of stimulating or recording electrical activity in brain, spinal, or peripheral nerve tissue, however most of these devices are constructed from materials that are mechanically rigid. A growing body of evidence suggests that the chronic presence of these rigid probes in the neural tissue causes a significant immune response and glial encapsulation of the probes, which in turn leads to gradual increase in distance between the electrodes and surrounding neurons. In recording electrodes, the consequence is the loss of signal quality and, therefore, the inability to collect electrophysiological recordings long term. In stimulation electrodes, higher current injection is required to achieve a comparable response which can lead to tissue and electrode damage. To minimize the impact of the immune response, flexible neural probes constructed with softer materials have been developed. These flexible probes, however, are often not strong enough to be inserted on their own into the tissue, and instead fail via mechanical buckling of the shank under the force of insertion. Several strategies have been developed to allow the insertion of flexible probes while minimizing tissue damage. It is critical to keep these strategies in mind during probe design in order to ensure successful surgical placement. In this review, existing insertion strategies will be presented and evaluated with respect to surgical difficulty, immune response, ability to reach the target tissue, and overall limitations of the technique. Overall, the majority of these insertion techniques have only been evaluated for the insertion of a single probe and do not quantify the accuracy of probe placement. More work needs to be performed to evaluate and optimize insertion methods for accurate placement of devices and for devices with multiple probes.
Superior thermoelectric performance of α-Se2Te monolayer
Authors: Zhong Xuanhong , Huang Yuhong , Yang Xiaoyue , Chen Hong
Published: April 2021

Based on the first-principles of density functional theory and Boltzmann transport theory, we report two-dimensional (2D) α-Se2Te monolayer to be a high-performance medium temperature p-type thermoelectric material with low lattice thermal conductivity (κ

l
), high power factor (PF) and high dimensionless figure of merit (ZT). At the temperature of 700 K, PF is up to 3.77 and 11.5 mW m−1 K−2, ZT is up to 0.55 and 1.91 in appropriate doping level for n- and p-types, respectively, and k

l
is as low as 2.09 W m−1 K−1. We also examine the effect of spin-orbital coupling (SOC) on the carrier transport and find that with SOC, PF and hence ZT will be reduced significantly due to the reduced band gap. The higher PF of p-type than that of n-type is evidently due to the flatter valence band edge than conduction band edge. Low k

l
is inevitably attributed to the strong lattice anharmonicity.
Impact of V substitution on the physical properties of Ni–Zn–Co ferrites: structural, magnetic, dielectric and electrical properties
Authors: Hossain M D , Jamil A T M K , Hasan M R , Ali M A , Esha I N , Hossain Md Sarowar , Hakim M A , Khan M N I
Published: April 2021

We have investigated the Vanadium- (V) substituted Ni–Zn–Co ferrites where the samples are prepared using the solid-state reaction technique. The impact of V5+ substitution on the structural, magnetic, dielectric and electrical properties of Ni–Zn–Co ferrites has been studied. The XRD analysis confirms the formation of a single-phase cubic spinel structure. The lattice constants have been calculated both theoretically and experimentally along with other structural parameters such as bulk density, x-ray density and porosity. The FESEM images are studied for analyzing the surface morphology. FTIR measurement confirms spinel structure formation. The saturation magnetization (M
s), coercive field (H
c) and Bohr magnet on (μ
B) are calculated from the obtained M-H loops. The temperature-dependent permeability is studied to obtain the Curie temperature. The frequency and the composition dependence of permeability are also analyzed. Frequency dependent dielectric behavior and ac resistivity are also investigated. An inverse relationship is observed between the composition dependent dielectric constant and ac resistivity. The obtained results such as the electrical resistivity, dielectric constants and magnetic properties suggest the appropriateness of the studied ferrites in microwave device applications.
Graphitization of carbon-based catalyst for improving the performance of negative electrode in vanadium redox flow battery
Authors: Hou Bingxue , Tang Rui , Zhang Qi , Cui Xumei , Chen Yungui
Published: April 2021

Carbon-based materials were prepared to catalyze the V3+/V2+ couple of vanadium redox flow battery using chitosan as the preliminary material and FeCl3 as activating agent. Graphite microcrystals were the main structures of the obtained catalyst (CTS-Fe-900) activated by FeCl3, and they contained a large number of curled and overlapped carbon nanosheets. Compared with CTS-D-900 (without FeCl3 as an activating agent), CTS-Fe-900 exhibits a better structure, higher graphitization degree, stronger current response, and smaller charge transfer resistance. The charge/discharge measurements indicates that the performances of the cell are improved by using the CTS-Fe-900-modified negative electrode in terms of increased discharge capacity and energy efficiency. Compared with pristine cell, the capacity retention for the CTS-Fe-900 modified cell maintains 82.2% at 50 mA cm−2 after 50 cycles, increased by 5.2%, and the corresponding energy efficiency reaches 81.3%, enhanced by 5.1%. This work reveals that CTS-Fe-900 catalyst can improve the comprehensive energy storage performance. The excellent electrocatalytic properties are mainly attribute to the effect of the FeCl3 template and the increase in the degree of graphitization.
Hydrophobic and optical properties of silica antireflective coating prepared via sol-gel method
Authors: Zhang Qianying , Liu Hui , Zhao Siyuan , Dong Wanmeng
Published: April 2021

A simple and low-cost process for the preparing of multifunctional coating is essential in practical applications. Here, alkali-catalyzed SiO2 antireflection coating was first prepared by using the sol-gel method, the tetraethyl orthosilicate (TEOS) and ammonia (NH3·H2O) were used as a raw material and catalyst, respectively. Then, a layer of dimethyl silicone was sprayed on the surface of the as-prepared primary coating to obtain a bifunctional coating of antireflection and hydrophobicity simultaneously. The experimental results shown that the peak transmittance of the as-prepared bifunctional coating was 98.11% in the wavelength range of 300–1500 nm, while the water contact angle of the prepared coating was 140°, which was caused by the introduction of hydrophobic methyl groups of dimethyl silicone. Besides, the tape adhesion test and pencil scratch test results shown that the coatings have excellent mechanical robustness. Therefore, this work provides a practical strategy for the preparation of bifunctional coatings with antireflective and hydrophobic properties.
Electrochemical detection of choline at f-MWCNT/Fe3O4nanocomposite modified glassy carbon electrode
Authors: Uwaya Gloria E , Fayemi Omolola E
Published: April 2021

Choline is employed as cholinergic activity marker in brain tissue in the field of clinical detection of diseases. Although, chromatographic methods and biosensors are the most commonly used techniques for choline detection, there is also an interest in exploring the efficacy of a cost effective non-enzyme based sensor for choline detection. Here, electrochemical sensors based on green synthesized metal oxides (iron (III) oxide nanoparticles) fromCallistemon viminalisleaves and flowers extract (Fe3O4NPL and Fe3O4NPF) in combination of functionalized multi-walled carbon nanotube (f-MWCNT) supported on glassy carbon electrodes (GCE/f-MWCNT/Fe3O4NPL and GCE/f-MWCNT/Fe3O4NPF) were fabricated for choline detection. Morphological, structural and optical analysis of the nanocomposites were studied using scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD) and ultra violet-visible (UV–vis) spectroscopy accordingly. In contrast, electron transport properties on bare glassy carbon electrode (GCE) and nanocomposite modified electrodes (GCE/f-MWCNT/Fe3O4NPL and GCE/f-MWCNT/Fe3O4NPF) was examined through electrochemical characterization using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Electrochemical oxidation of choline was also studied through CV, EIS, square wave voltammetry (SWV) and chronoamperometry (CA). The result proved that f-MWCNT enhanced the reactivity of Fe3O4NP towards choline oxidation with voltammetric limit of detection (0.83 and 0.36μM) for choline at GCE/f-MWCNT/Fe3O4NPL and GCE/f-MWCNT/Fe3O4NPF electrodes respectively. Designed sensors proved selective, reproducible, stable and applicable for real sample sensing in choline dietary supplements.
Optimal calibration of gates in trapped-ion quantum computers
Authors: Maksymov Andrii , Niroula Pradeep , Nam Yunseong
Published: April 2021

To harness the power of quantum computing, it is essential that a quantum computer provide maximal possible fidelity for a quantum circuit. To this end, much work has been done in the context of qubit routing or embedding, i.e., mapping circuit qubits to physical qubits based on gate performance metrics to optimize the fidelity of execution. Here, we take an alternative approach that leverages a unique capability of a trapped-ion quantum computer, i.e., the all-to-all qubit connectivity. We develop a method to determine a fixed number (budget) of quantum gates that, when calibrated, will maximize the fidelity of a batch of input quantum programs. This dynamic allocation of calibration resources on randomly accessible gates, determined using our heuristics, increases, for a wide range of calibration budget, the average fidelity from 70% or lower to 90% or higher for a typical batch of jobs on an 11-qubit device, in which the fidelity of calibrated and uncalibrated gates are taken to be 99% and 90%, respectively. Our heuristics are scalable, more than 2.5 orders of magnitude faster than a randomized method for synthetic benchmark circuits generated based on real-world use cases.
Recent progress in 2D metal-organic framework photocatalysts: synthesis, photocatalytic mechanism and applications
Authors: Pan Yangdan , Abazari Reza , Yao Juming , Gao Junkuo
Published: April 2021

2D metal-organic framework (2D MOF) nanosheets and their derived nanocomposites have been widely studied in recent years due to their ultrathin atomic-level thickness, large surface area and adjustable structure. This review is thus aimed at summarizing the recent studies on synthesis methods and the photocatalytic mechanism of 2D MOF nanosheets. The synthesis methods can be concretely divided into top-down and bottom-up methods, including physical and chemical exfoliation, interfacial synthesis, three-layer synthesis and surfactant-assisted synthesis. The photocatalytic mechanisms can also be categorized into three classes: photo-absorption, photo-generated carrier separation and transport, and surface redox reaction. Moreover, the applications of 2D MOF nanosheets in the field of photocatalysis, including photocatalytic hydrogen evolution, photocatalytic CO2 reduction, photocatalytic degradation and organic chemical photosynthesis, were also briefly discussed. Finally, some challenges and expectations with regard to 2D MOF nanosheets in photocatalysis will be addressed.
Peering into few-layer black phosphorus nanosheets: from preparation to battery applications
Authors: Shao Lianyi , Guan Jieduo , Wang Shige , Yu Lu , Shi Xiaoyan , Sun Zhipeng , Cheng Fangyi
Published: April 2021

Few-layer black phosphorus (FLBP) nanosheets feature high charge storage capacity, large surface area, considerable mechanical flexibility, high carrier mobility and adjustable intrinsic band gap, allowing wide applications in electrochemical storage and conversion. This article presents a review on the preparation of FLBP materials and their applications in rechargeable batteries, including alkali metal batteries. Top-down and bottom-up synthetic strategies of FLBP are overviewed with examples of mechanical, liquid-phase and electrochemical exfoliation routes and chemical vapour and pulsed laser deposition. The electrochemical properties, structure-performance relationship and electrode mechanisms of FLBP are demonstrated as anode materials for storage of lithium, sodium and potassium ions. Issues including huge volume expansion and structural instability are discussed, along with solving strategies such as composing with nanostructured carbon, MXene, conductive polymer and transition metal oxides. Furthermore, the remaining challenges and future perspectives for the electrochemical use of FLBP are highlighted.
Analytical and Clinical Considerations in Implementing the Roche Elecsys Troponin T Gen 5 STAT Assay
Authors: Donato Leslie J , Wockenfus Amy M , Katzman Brooke M , Baumann Nikola A , Jaffe Allan S , Karon Brad S
Published: April 2021

Objectives

To evaluate the analytical and clinical performance characteristics of the fifth-generation troponin T reagent.

Methods

Troponin T was measured in 2,332 paired serum and plasma samples from emergency department and hospital patients using the fourth- and fifth-generation reagents. Testing was repeated after recentrifugation to determine the frequency of analytical outliers and percentage of patients with elevated values for each assay. We conducted separate experiments to determine the effects of biotin and hemolysis interference, as well as measure interinstrument variability, for fifth-generation troponin T.

Results

Analytic outliers occurred more frequently using the fifth-generation reagent (3.4%) compared with the fourth-generation reagent (1.0%). The frequency of elevated troponin T above the 99th percentile upper reference limit was 26% for the fourth-generation reagent and 52% for the fifth-generation reagent. Clinically significant assay interference by biotin was observed at 20 ng/mL, but hemolysis interference was not observed until an H index of 150. Instrument-to-instrument variability between e411 and e601/602 instrument platforms is predicted to confound clinical interpretation of troponin changes.

Conclusions

Analytical outliers and instrument-to-instrument variability are the two analytical variables most likely to confound interpretation of changes in fifth-generation troponin T results over time.
Forgetting to Remember: The Impact of Post-traumatic Stress Disorder on Prospective and Retrospective Memory Performance
Authors: Korinek Dale , Resch Zachary J , Soble Jason R , Aase Darrin M , Schroth Christopher , Phan K Luan
Published: April 2021

Objective

We examined the impact of post-traumatic stress disorder (PTSD) on both prospective (PM) and retrospective (RM) memory performance among a cross-sectional veteran sample.

Method

Data from tests of PM/RM memory and PTSD, anxiety, depression and sleep disturbance symptoms were examined among a prospectively recruited sample of 26 veterans with confirmed PTSD (PTSD+) and 26 well-matched, combat-exposed controls who did not meet criteria for PTSD (PTSD−).

Results

Small-to-moderate negative correlations emerged between PTSD symptom severity, visuospatial RM and some aspects of PM; general anxiety correlated more strongly with memory. The PTSD+ group demonstrated significantly worse, but still average visuospatial RM; differences in PM were nonsignificant between groups. Regression analyses implicated generalized anxiety, but not other psychiatric symptomology, as significant contributors to all memory performances.

Conclusions

Minimal memory differences were found between veterans with and without PTSD. PM/RM memory performance was better explained by generalized anxiety rather that PTSD-specific symptoms.
Machine learning approach to gene essentiality prediction: a review
Authors: Aromolaran Olufemi , Aromolaran Damilare , Isewon Itunuoluwa , Oyelade Jelili
Published: April 2021

Essential genes are critical for the growth and survival of any organism. The machine learning approach complements the experimental methods to minimize the resources required for essentiality assays. Previous studies revealed the need to discover relevant features that significantly classify essential genes, improve on the generalizability of prediction models across organisms, and construct a robust gold standard as the class label for the train data to enhance prediction. Findings also show that a significant limitation of the machine learning approach is predicting conditionally essential genes. The essentiality status of a gene can change due to a specific condition of the organism. This review examines various methods applied to essential gene prediction task, their strengths, limitations and the factors responsible for effective computational prediction of essential genes. We discussed categories of features and how they contribute to the classification performance of essentiality prediction models. Five categories of features, namely, gene sequence, protein sequence, network topology, homology and gene ontology-based features, were generated for Caenorhabditis elegans to perform a comparative analysis of their essentiality prediction capacity. Gene ontology-based feature category outperformed other categories of features majorly due to its high correlation with the genes’ biological functions. However, the topology feature category provided the highest discriminatory power making it more suitable for essentiality prediction. The major limiting factor of machine learning to predict essential genes conditionality is the unavailability of labeled data for interest conditions that can train a classifier. Therefore, cooperative machine learning could further exploit models that can perform well in conditional essentiality predictions.

Short abstract

Identification of essential genes is imperative because it provides an understanding of the core structure and function, accelerating drug targets’ discovery, among other functions. Recent studies have applied machine learning to complement the experimental identification of essential genes. However, several factors are limiting the performance of machine learning approaches. This review aims to present the standard procedure and resources available for predicting essential genes in organisms, and also highlight the factors responsible for the current limitation in using machine learning for conditional gene essentiality prediction. The choice of features and ML technique was identified as an important factor to predict essential genes effectively.
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm
Authors: Liu Maidi , Ye Yanqing , Jiang Jiang , Yang Kewei
Published: April 2021

Motivation

Modeling microbiome systems as complex networks are known as the problem of network inference. Microbial association network inference is of great significance in applications on clinical diagnosis, disease treatment, pathological analysis, etc. However, most current network inference methods focus on mining strong pairwise associations between microorganisms, which is defective in reflecting the comprehensive interactive patterns participated by multiple microorganisms. It is also possible that the microorganisms involved in the generated network are not dominant in the microbiome due to the mere focus on the strength of pairwise associations. Some scholars tried to mine comprehensive microbial associations by association rule mining methods, but the adopted algorithms are relatively basic and have severe limitations such as low calculation efficiency, lacking the ability of mining negative correlations and high redundancy in results, making it difficult to mine high-quality microbial association rules and accurately infer microbial association networks.

Results

We proposed a microbial association network inference method ‘MANIEA’ based on the improved Eclat algorithm for mining positive and negative microbial association rules. We also proposed a new method for transforming association rules into microbial association networks, which can effectively demonstrate the co-occurrence and causal correlations in association rules. An experiment was conducted on three authentic microbial abundance datasets to compare the ‘MANIEA’ with currently popular network inference methods, which demonstrated that the proposed ‘MANIEA’ show advantages in aspects of correlation forms, computation efficiency, adjustability and network characteristics.

Availability and implementation

The algorithms and data are available at: https://github.com/MaidiL/MANIEA.
Dopaminergic restoration of prefrontal cortico-putaminal network in gene therapy for aromatic l-amino acid decarboxylase deficiency
Authors: Onuki Yoshiyuki , Ono Sayaka , Nakajima Takeshi , Kojima Karin , Taga Naoyuki , Ikeda Takahiro , Kuwajima Mari , Kurokawa Yoshie , Kato Mitsuhiro , Kawai Kensuke , Osaka Hitoshi , Sato Toshihiko , Muramatsu Shin-ichi , Yamagata Takanori
Published: April 2021

Aromatic l-amino acid decarboxylase (AADC) is an essential dopamine-synthesizing enzyme. In children with AADC deficiency, the gene delivery of AADC into the putamen, which functionally interacts with cortical regions, was found to improve motor function and ameliorate dystonia. However, how the restoration of dopamine in the putamen in association with cortico-putaminal networks leads to therapeutic effects remains unclear. Here, we examined neuroimaging data of eight patients with AADC deficiency (five males and three females, age range 4–19 years) who received the AADC gene therapy of the bilateral putamen in an open-label phase 1/2 study. Using high-resolution positron emission tomography with a specific AADC tracer, 6-[18F]fluoro-l-m-tyrosine (FMT), we showed that FMT uptake increased in the broad area of the putamen over the years. Then, with the structural connectivity-based parcellation of the putaminal area, we found that motor improvement is associated with dopaminergic restoration of the putaminal area that belongs to the prefrontal cortico-putaminal network. The prefrontal area dominantly belongs to the frontoparietal control network, which contributes to cognitive-motor control function, including motor initiation and planning. The results suggest that putaminal dopamine promotes the development of an immature motor control system, particularly in the human prefrontal cortex that is primarily affected by AADC deficiency.
Harmonization of LC-MS/MS Measurements of Plasma Free Normetanephrine, Metanephrine, and 3-Methoxytyramine
Authors: Peitzsch Mirko , Novos Talia , Kaden Denise , Kurlbaum Max , van Herwaarden Antonius E , Müller Daniel , Adaway Jo , Grouzmann Eric , McWhinney Brett , Hoad Kirsten , Woollard Gerald , Kema Ido , Boot Christopher , Fassnacht Martin , Sweep Fred , Loh Tze P , Horvath Andrea R , Eisenhofer Graeme
Published: April 2021

Background

Plasma-free normetanephrine and metanephrine (metanephrines) are the recommended biomarkers for testing of pheochromocytoma and paraganglioma (PPGL). This study evaluated the status of harmonization of liquid chromatography-tandem mass spectrometry-based measurements of plasma metanephrines and methoxytyramine and clinical interpretation of test results.

Methods

125 plasma samples from patients tested for PPGLs were analyzed in 12 laboratories. Analytical performance was also assessed from results of a proficiency-testing program. Agreement of test results from different laboratories was assessed by Passing-Bablok regression and Bland-Altman analysis. Agreement in clinical test interpretation based on laboratory specific reference intervals was also examined.

Results

Comparisons of analytical test results by regression analysis revealed strong correlations for normetanephrine and metanephrine (R ≥ 0.95) with mean slopes of 1.013 (range 0.975–1.078), and 1.019 (range 0.963–1.081), and intercepts of −0.584 (−53.736 to 54.790) and −3.194 (−17.152 to 5.933), respectively. The mean bias between methods was 1.2% (−11.6% to 16.0%) for metanephrine and 0.1% (−18.0% to 9.5%) for normetanephrine. Measurements of 3-methoxytyramine revealed suboptimal agreement between laboratories with biases ranging from −32.2% to 64.0%. Interrater agreement in test interpretation was >94% for metanephrine and >84% for normetanephrine; improvements in interrater agreement were observed with use of harmonized reference intervals, including age-specific cut-offs for normetanephrine.

Conclusions

Analytical methods for metanephrines are well harmonized between laboratories. However, the 16% disagreement in test interpretation for normetanephrine suggests use of suboptimal method-dependent reference intervals for clinical decision-making for this metabolite. Improved analytical methods and reference interval harmonization are particularly required for 3-methoxytyramine.
Cost-effectiveness calculators for health, well-being and safety promotion: a systematic review
Authors: Hult Marja , Halminen Olli , Linna Miika , Suominen Sakari , Kangasniemi Mari
Published: April 2021

Background

The health, well-being and safety of the general population are important goals for society, but forecasting outcomes and weighing up the costs and benefits of effective promotional programmes is challenging. This study aimed to identify and describe the cost-effectiveness calculators that analyze interventions that promote health, well-being and safety.

Methods

Our systematic review used the CINAHL, PsycINFO, SocINDEX, EconLit, PubMed and Scopus databases to identify peer-reviewed studies published in English between January 2010 and April 2020. The data were analyzed with narrative synthesis.

Results

The searches identified 6880 papers and nine met our eligibility and quality criteria. All nine calculators focussed on interventions that promoted health and well-being, but no safety promotion tools were identified. Five calculators were targeted at group-level initiatives, two at regional levels and two at national levels. The calculators combined different data sources, in addition to data inputted by users. This included empirical research and previous literature. The calculators created baseline estimates and assessed the cost-effectiveness of the interventions before or after they were implemented. The calculators were heterogeneous in terms of outcomes, the interventions they evaluated and the data and methods used.

Conclusion

This review identified nine calculators that assessed the cost-effectiveness of health and well-being interventions and supported decision-making and resource allocations at local, regional and national levels, but none focussed on safety. Producing calculators that work accurately in different contexts might be challenging. Further research should identify how to assess sustainable evaluation of health, well-being and safety strategies.
Quantifying the precision of forest stand height and canopy cover estimates derived from air photo interpretation
Authors: Tompalski Piotr , White Joanne C , Coops Nicholas C , Wulder Michael A , Leboeuf Antoine , Sinclair Ian , Butson Christopher R , Lemonde Marc-Olivier
Published: April 2021

Quality information on forest resources is fundamental for sustainable forest management. Manual aerial photointerpretation is used as a cost-effective source of data for forest inventories; however, the process of photointerpretation is inherently subjective and is often undertaken by multiple photointerpreters for a given forest management area. In contrast, airborne laser scanning (ALS) data enable characterization of forest structure in a systematic fashion with quantifiable levels of accuracy and precision that often exceed required targets and standards. However, the gains associated with the use of new technologies for forest inventory are difficult to measure because the quality of existing photointepreted inventories have rarely been quantified. Using ALS data as reference, the objective of this study was to quantify the precision of photointerpreted estimates of forest stand height and canopy cover (CC). We examined forest inventories from three study sites in three different forest regions of Canada. Each of the study sites was located within a different provincial jurisdiction with unique photointerpretation standards and forest ecosystems. Stand-level estimates of forest height and cover were compared to reference estimates generated from the ALS data. Overall, our results indicated that precision was greater for photointerpreted estimates of height, with a relative standard deviation ranging from 22 per cent to 29 per cent among our three sites, compared to estimates for CC, with precision ranging from 28 per cent to 59 per cent. While the relationship between photointerpreted estimates of height and ALS estimates of height were generally linear and consistent for all study sites, relationships for CC were non-linear. We found that precision for both stand height and cover varied by dominant species, inventory stand structure, age, and ALS canopy complexity, and that in the majority of cases, the differences between the photointerpreted estimate and the ALS estimate were statistically significant. It is also noted that the variability in photointerpretation precision as a function of the aforementioned factors was not consistent among our three study sites, indicating that site-specific forest conditions and photointerpretation procedures influence the precision of photointerpreted estimates. The influence of local forest conditions and interpretation procedures are therefore important considerations when seeking to quantify the potential relative gains in precision, which may be afforded by technologies such as ALS for forest inventory programs. Moreover, approaches to improve consistency in photointerpreted estimates of cover would be useful for operational inventory programs.
Tree-level Growth of Four Oak Species in a Bottomland Hardwood Plantation: Implications for Silvicultural Treatments
Authors: Hossain Shaik M , Olson Matthew G , Bataineh Mohammad
Published: April 2021

A 41-year-old bottomland hardwood plantation experiment located in southeastern Arkansas was revisited in 2017 to evaluate basal area increment (BAI) of four oak species [cherrybark oak (Quercus pagoda Raf.), swamp chestnut oak (Q. michauxii Nutt.), Nuttall oak (Q. texana Buckl.), and water oak (Q. nigra L.)] planted in monoculture in relation with species, spacing, thinning, and neighborhood competition. Species had a significant effect on BAI (P = 0.04), with cherrybark oak and Nuttall oak demonstrating the greatest (21.5 ± 2.5 cm2 year−1) and lowest (12.7 ± 2.9 cm2 year−1) growth rates, respectively, whereas BAI declined significantly with increasing competition (P = 0.03). However, rates of growth decline with competition did not differ between species (P > 0.05 for competition × species term), and thinning and spacing treatments had no effect on BAI (P > 0.05). We recommend that repetitive thinning, rather than a single thinning, would be appropriate to maintain a positive impact on oak growth. Managing stand density would not only provide opportunities for improving timber production, but also would enhance ecological benefits (e.g., wildlife habitat) through diversification of structure within monoculture plantations.
Evaluating Long-Term Seedling Growth Across Densities Using Nelder Plots and the Forest Vegetation Simulator (FVS) in the Black Hills, South Dakota, USA
Authors: Tinkham Wade T , Battaglia Mike A , Hoffman Chad M
Published: April 2021

Small-tree development affects future stand dynamics and dictates many ecological processes within a site. Accurately representing this critical component of stand development is important for evaluating treatment alternatives from fuel hazard reduction to harvest scheduling. As with all forest growth, competition with other vegetation is known to regulate small-tree growth dynamics. This study uses three Nelder plots with 45 years of ponderosa pine growth to understand competition effects on seedling growth and evaluate the Forest Vegetation Simulator (FVS) Central Rockies (CR) variant’s ability to represent these dynamics. Removal of herbaceous competition before planting increased tree diameters by 50–135% and height by 35–75% across a planting density gradient at age 12. However, by age 45, the effect of herbaceous competition on tree size was no longer evident. Instead, trees at the lowest planting density had diameters 2.5–3 times larger than the most densely grown trees. Forest Vegetation Simulator (FVS) simulations underpredicted diameter at breast height (dbh) by 35–50% and 0–35% for 12 and 45-year-old trees, respectively. There was an underprediction bias of 15–20% for heights at age 12 and overpredictions of 5–10% at age 45. Continuous underprediction of dbh will affect the reliability of modeled fuel treatment longevity and sustainable harvest scheduling.
The Complete Nucleotide Sequence of the Mitochondrial Genome of the Lungfish (Protopterus dolloi) Supports Its Phylogenetic Position as a Close Relative of Land Vertebrates
Authors: Zardoya Rafael , Meyer Axel
Published: April 2021

The complete DNA sequence (16,646 bp) of the mitochondrial genome of the African lungfish, Protopterus dolloi, was determined. The evolutionary position of lungfish as possibly the closest living relative among fish of land vertebrates made its mitochondrial DNA sequence particularly interesting. Its mitochondrial gene order conforms to the consensus vertebrate gene order. Several sequence motifs and secondary structures likely involved in the regulation of the initiation of replication and transcription of the mitochondrial genome are conserved in the lungfish and are more similar to those of land vertebrates than those of ray-finned fish. A novel feature discovered is that the putative origin of L-strand replication partially overlaps the adjacent tRNAcys. The phylogenetic analyses of genes coding for tRNAs and proteins confirm the intermediate phylogenetic position of lungfish between ray-finned fishes and tetrapods. The complete nucleotide sequence of the African lungfish mitochondrial genome was used to estimate which mitochondrial genes are most appropriate to elucidate deep branch phylogenies. Only a combined set of either protein or tRNA mitochondrial genes (but not each gene alone) is able to confidently recover the expected phylogeny among vertebrates that have diverged up to but not over ~400 mya.
Mitochondrial DNA Analysis of Mongolian Populations and Implications for the Origin of New World Founders
Authors: Kolman Connie J , Sambuughin Nyamkhishig , Bermingham Eldredge
Published: April 2021

High levels of mitochondrial DNA (mtDNA) diversity were determined for Mongolian populations, represented by the Mongol-speaking Khalkha and Dariganga. Although 103 samples were collected across Mongolia, low levels of genetic substructuring were detected, reflecting the nomadic lifestyle and relatively recent ethnic differentiation of Mongolian populations. mtDNA control region I sequence and seven additional mtDNA polymorphisms were assayed to allow extensive comparison with previous human population studies. Based on a comparative analysis, we propose that indigenous populations in east Central Asia represent the closest genetic link between Old and New World populations. Utilizing restriction/deletion polymorphisms, Mongolian populations were found to carry all four New World founding haplogroups as defined by Wallace and coworkers. The ubiquitous presence of the four New World haplogroups in the Americas but narrow distribution across Asia weakens support for Greenberg and coworkers' theory of New World colonization via three independent migrations. The statistical and geographic scarcity of New World haplogroups in Asia makes it improbable that the same four haplotypes would be drawn from one geographic region three independent times. Instead, it is likely that founder effects manifest throughout Asia and the Americas are responsible for differences in mtDNA haplotype frequencies observed in these regions.