bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum estimation of rotational speed in optomechanics
Authors: Li 李 Hao 浩 , Cheng 程 Jiong 泂
Published: July 2023

We study the quantum Fisher information (QFI) of the angular velocity of rotation in an optomechanical system. Based on the Gaussian measurements method, we derive the explicit form of a single-mode Gaussian QFI, which is valid for arbitrary angular velocity of rotation. The information about the angular velocity to be measured is contained in the optical covariance matrix, which can be experimentally determined via homodyne measurement. We find that QFI increases rapidly when driving the system close to the unstable boundary. This result can be attributed to the strong nonlinearity of the system at the unstable boundary. Our results indicate the possibility of using an optomechanical system for high precision detection of the angular velocity of rotation.
Toward a unified formulation of the acoustic transfer admittance of cylindrical cavities for reciprocity calibration of microphones
Authors: Rodrigues D , Vincent P
Published: July 2023

The pressure reciprocity technique for calibration of Laboratory Standard microphones provides the basis for primary measurement standards for sound pressure. This calibration method is described in the International Electrotechnical Commission (IEC) standard 61094-2:2009 where the key aspect relating to the calculation of the acoustic transfer admittance of couplers was recently completed and clarified in the amendment IEC 61094-2:2009/AMD1:2022. Three models are currently provided for calculating this quantity: the low-frequency solution suitable to low frequencies, the extended low-frequency solution suitable to low and medium frequencies, and the broadband solution suitable to medium and high frequencies. It is established that neither of these models is correct for all frequencies routinely considered in many National Metrology Institutes, namely from 2 Hz to 25 kHz, so that a transition must be made. Based on the fundamental equations of acoustics in thermoviscous fluid, this paper provides a unified formulation for the acoustic transfer admittance of cylindrical cavities. Under the common quasi-plane wave approximation, this paper provides a new form of solution for the Fourier equation, not restricted by any assumption on the pressure variation and leading to a new form of propagation equation in the coupler. Two techniques are used to solve the problem, the Laplace Adomian Decomposition Method and a stepped duct approximation technique. Numerical results are presented, providing substantial evidence to support the validity of these formulations. A high level of agreement is observed between the two models, approximately 10−6 dB for the amplitude and 10−4 degrees for the phase, excluding the resonance frequencies of couplers. Finally, this paper evaluates the compatibility of the extended low-frequency solution provided in the IEC amendment with the fundamental equations established in this study. A new simplified solution is provided, highlighting discrepancies in the application of the heat conduction corrective factor as compared to the guidelines outlined in the IEC amendment.
Research on Control Strategy of Constant Power Output in MCRWPT System
Authors: Li Zhongkui , Fu Yuan
Published: July 2023

During wireless charging, the change of battery resistance will cause the fluctuation of output power, which will shorten the battery life and affect the charging safety. According to the theoretical analysis of WPT, when the load resistance changes, the output power can be stabilized by adjusting the input voltage of the system. Aiming at the variable load MCRWPT system, that is, only the load resistance changes under the resonant state, this paper designs the MCRWPT constant power control system by using the principle of reflective impedance and using the phase-shifting control voltage regulation and builds a simulation model through Matlab/Simulink platform to verify that the output power is kept in a certain range, without additional communication loops, which reduces the volume of electrical equipment and saves costs.
A Concentration Prediction and Gas Classification Model Based on LSTM-Attention Multi-task Learning Framework Network
Authors: Zhao Linju , Li Wang , Wang Shun
Published: July 2023

The electronic nose (E-nose), a bionic olfactory system, has been widely used in gas identification and concentration prediction. However, these tasks are usually based on separate systems, leading to high detection costs. To address this issue, a multi-task learning network model based on LSTM-Attention (MTL-LSTMA) as a skeleton has been proposed to simultaneously train both species recognition and concentration prediction tasks. The introduction of an attention mechanism greatly reduces interference in gas feature information, improving the electronic nose pattern recognition algorithm’s efficiency. The MTL-LSTMA model was tested through five sets of comparison experiments, showing the best performance in both concentration prediction and species identification. The proposed model has broad application prospects and may revolutionize gas detection technology.
Image reconstruction method in grating interferometer with phase stepping using grating position and dose fluctuation correction
Authors: Oh Ohsung , Kim Daeseung , Kim Ho Kyung , Lee Seung Wook
Published: July 2023

In this paper, we propose a method for reducing artifacts in X-ray and neutron grating interferometer imaging by optimizing the grating position and dose fluctuation. Grating interferometer can obtain additional information about the object, such as phase-contrast image and dark-field image, compared to traditional X-ray imaging. However, several errors such as inaccurate grating positions and non-uniform X-ray intensity can cause artifacts in the image and degrade image quality. The proposed method can reduce the artifacts by minimizing the value in the sample-free region in the transmission and dark-field images. We conducted experiments on both simulated and X-ray and neutron experimental data and demonstrated the effectiveness of our method.
Sediment erosion and yield analysis on the coast of Kedah and Langkawi, Malaysia: A case study
Authors: Yusof Mohd Azlan Mohd , Razi Mohd Adib Mohammad , Daud Haji Zainalfikry Haji , Azhar Engku Ahmad Khalil , Rani Mohd Shahrulnizam Mat , Al-Gheethi Adel
Published: July 2023

Soil erosion and sedimentation are among the most crucial environmental hazards that arise from urban development. The Geographical Information System (GIS) based method is proposed to demonstrate for the identification of sediment source areas and the prediction of storm sediment yield from catchments. The gross soil erosion was calculated by using the revised Universal Soil Loss Equation (RUSLE). In general, soil loss of the river basins at Kedah mainland mostly falls under “low” and “moderate” erosion risk category according to Department of Agriculture guidelines. The highest recorded value is Sg. Ruat with soil loss rate of 93.77 tonnes / ha / year. For Pulau Langkawi, most of the river basins have higher soil loss and fall under “moderate” and “moderately high” erosion risk. It is worth mentioning that there is a river basin that recorded soil loss greater than 100 tonne/ha/year, which is classified as “high” risk. The said river basin is Sg. Datai, which is located in the northern part of Pulau Langkawi.
Spheroid on-demand printing and drug screening of endothelialized hepatocellular carcinoma model at different stages
Authors: Liu Tiankun , Zhou Chang , Ji Jingyuan , Xu Xiaolei , Xing Zhengyu , Shinohara Marie , Sakai Yasuyuki , Sun Taoping , Feng Xiaobin , Yu Zhuo , Pang Yuan , Sun Wei
Published: July 2023

Hepatocellular carcinoma (HCC) poses a significant threat to human health and medical care. Its dynamic microenvironment and stages of development will influence the treatment strategies in clinics. Reconstructing tumor–microvascular interactions in different stages of the microenvironment is an urgent need for in vitro tumor pathology research and drug screening. However, the absence of tumor aggregates with paracancerous microvascular and staged tumor–endothelium interactions leads to bias in the antitumor drug responses. Herein, a spheroid-on-demand manipulation strategy was developed to construct staged endothelialized HCC models for drug screening. Pre-assembled HepG2 spheroids were directly printed by alternating viscous and inertial force jetting with high cell viability and integrity. A semi-open microfluidic chip was also designed to form a microvascular connections with high density, narrow diameter, and curved morphologies. According to the single or multiple lesions in stages Ⅰ or Ⅰ HCC, endothelialized HCC models from micrometer to millimeter scale with dense tumor cell aggregation and paracancerous endothelial distribution were successively constructed. A migrating stage Ⅰ HCC model was further constructed under TGF-β treatment, where the spheroids exhibited a more mesenchymal phenotype with a loose cell connection and spheroid dispersion. Finally, the stage ⅠHCC model showed stronger drug resistance compared to the stage Ⅰ model, while the stage III showed a more rapid response. The corresponding work provides a widely applicable method for the reproduction of tumor–microvascular interactions at different stages and holds great promise for the study of tumor migration, tumor–stromal cell interactions, and the development of anti-tumor therapeutic strategies.
The linear and non-linear study of effect of rotation and internal heat source/sink on Bénard convection
Authors: Sanjalee  , Sharma Y D , Yadav O P
Published: July 2023

The primary objective of this study is to investigate non-linear Bénard convection in a single-walled carbon nanotube suspension saturated in a rotating porous medium with an internal heat sink/source. The modified Buongiorno model is utilized to formulate the governing equations for the flow. Both linear and weak non-linear stability analyses are conducted in this investigation. The linear stability analysis employs the truncated Fourier series transformation, while the weakly non-linear stability analysis utilizes the Lorenz model, assuming weak thermophoresis, porous friction, and small-scale convective motion. The cubic Ginzburg–Landau equation is formulated and subsequently solved to derive the expression for the amplitude. The influence of various parameters, such as the Taylor number, heat sink/source parameter, and viscosity parameter, is discussed in relation to the threshold criteria of convection, as well as heat and mass transport rates. Based on the linear stability analysis, it is determined that the introduction of a rotating frame of reference delays the initiation of convection, whereas the energy supplied to the system accelerates the onset of convection. The heat transfer rate increases by

22
%

when the nanofluidic system is placed in the rotating frame of reference under the presence of an internal heat source.
Quantum control via chirped coherent anti-Stokes Raman spectroscopy
Authors: Chathanathil Jabir , Budker Dmitry , Malinovskaya Svetlana A
Published: July 2023

A chirped-pulse quantum control scheme applicable to coherent anti-Stokes Raman scattering spectroscopy, named as C-CARS, is presented aimed at maximizing the vibrational coherence in molecules. It implies chirping of three incoming pulses in the four-wave mixing process of CARS, the pump, the Stokes and the probe, to fulfill the conditions of adiabatic passage. The scheme is derived in the framework of rotating wave approximation and adiabatic elimination of excited state manifold simplifying the four-level model system into a ‘super-effective’ two level system. We demonstrate that the selectivity of excitation of vibrational degrees of freedom can be controlled by carefully choosing the spectral chirp rate of the pulses. The robustness, spectral selectivity and adiabatic nature of this method are advantageous for improving the existing methods of CARS spectroscopy for sensing, imaging and detection.
Development of a 3-DOF flexible micro-motion platform based on a symmetrical two-stage magnifying mechanism
Authors: Zhang Shijun , Zhang Teng , Meng Fanxun
Published: July 2023

A symmetrical 3-PRR flexible motion platform kinematic dynamic model is built. The natural frequency analysis of the platform is studied in this paper. Firstly, a flexible lever displacement two-stage amplification mechanism is proposed. A pseudo-rigid body model is established. A kinematics model is established by using the vector closed-loop method. The relationship between the input and output of the flexible lever displacement two-stage amplification mechanism is obtained. Secondly, based on the two-stage amplification mechanism of flexible lever displacement, a 3-PRR flexible motion platform is designed. The Jacobian matrix of input displacement of piezoelectric ceramics and output displacement of flexible motion platform is obtained by using the coordinate transformation method and vector equation closed-loop method. Considering the elastic potential energy of the flexible hinge and biaxial hinge, the Lagrange equation is established, and the expression of the natural frequency of the 3-PRR flexible motion platform is obtained. Finally, the correctness of the theoretical dynamic model is verified by theoretical calculation and finite element software simulation.
Design and analysis of multiple beams phased array microstrip antenna for 5G applications
Authors: Nigam Harshal , Mathur Monika
Published: July 2023

The paper presents a novel and compact antenna array design fed through a 3 dB BLC for producing phase shift in the array. Beam steering is an attractive design feature for avoiding obstacles in the path of the beam. It is achieved by switching the beam to another path by simply varying the phase shift between elements. The proposed structure exhibits resonance in the frequency having range of 27.6 GHz −29.6 GHz with a minimal return loss value of −45 dB for frequency applications of 28 GHz, which can be further employed for 5G frequency applications, there are two multiple beams observed, with main beam at theta equal to −35 degrees, the main beam shifts to +28 degrees by changing the feed port of the coupler. A stable gain of around 11.5 dB is obtained for the entire frequency range. The input phase has been varied for different elements in the array, and best results were obtained for a 90 degree phase difference, which required the use of a 3 dB BLC. Rogers RT Duroid 5880, having a dielectric of 2.2 and a 0.51 mm dielectric height, was used as a substrate for antenna fabrication. The simulations were performed on the CST Microwave studio and the measurements were done on VNA (Agilent N5247A).
Efficient generation of stable linear machine-learning force fields with uncertainty-aware active learning
Authors: Briganti Valerio , Lunghi Alessandro
Published: July 2023

Machine-learning (ML) force fields (FFs) enable an accurate and universal description of the potential energy surface of molecules and materials on the basis of a training set ofab initiodata. However, large-scale applications of these methods rest on the possibility to train accurate ML models with a small number ofab initiodata. In this respect, active-learning (AL) strategies, where the training set is self-generated by the model itself, combined with linear ML models are particularly promising. In this work, we explore an AL strategy based on linear regression and able to predict the model’s uncertainty on predictions for molecular configurations not sampled by the training set, thus providing a straightforward recipe for the extension of the latter. We apply this strategy to the spectral neighbor analysis potential and show that only tens ofab initiosimulations of atomic forces are required to generate FFs for room-temperature molecular dynamics at or close to chemical accuracy and which stability can be systematically improved by the user at modest computational expenses. Moreover, the method does not necessitate any conformational pre-sampling, thus requiring minimal user intervention and parametrization.
Alloteropsis semialata as a study system for C4 evolution in grasses
Authors: Pereira Lara , Bianconi Matheus E , Osborne Colin P , Christin Pascal-Antoine , Dunning Luke T
Published: July 2023

Background

Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economic importance of C4 photosynthesis has motivated intense research, often relying on comparisons between distantly related C4 and non-C4 plants. The photosynthetic type is fixed in most species, with the notable exception of the grass Alloteropsis semialata. This species includes populations exhibiting the ancestral C3 state in southern Africa, intermediate populations in the Zambezian region and C4 populations spread around the palaeotropics.

Scope

We compile here the knowledge on the distribution and evolutionary history of the Alloteropsis genus as a whole and discuss how this has furthered our understanding of C4 evolution. We then present a chromosome-level reference genome for a C3 individual and compare the genomic architecture with that of a C4 accession of A. semialata.

Conclusions

Alloteropsis semialata is one of the best systems in which to investigate the evolution of C4 photosynthesis because the genetic and phenotypic variation provides a fertile ground for comparative and population-level studies. Preliminary comparative genomic investigations show that the C3 and C4 genomes are highly syntenic and have undergone a modest amount of gene duplication and translocation since the different photosynthetic groups diverged. The background knowledge and publicly available genomic resources make A. semialata a great model for further comparative analyses of photosynthetic diversification.
Large-scale predicting protein functions through heterogeneous feature fusion
Authors: Zheng Rongtao , Huang Zhijian , Deng Lei
Published: July 2023

As the volume of protein sequence and structure data grows rapidly, the functions of the overwhelming majority of proteins cannot be experimentally determined. Automated annotation of protein function at a large scale is becoming increasingly important. Existing computational prediction methods are typically based on expanding the relatively small number of experimentally determined functions to large collections of proteins with various clues, including sequence homology, protein–protein interaction, gene co-expression, etc. Although there has been some progress in protein function prediction in recent years, the development of accurate and reliable solutions still has a long way to go. Here we exploit AlphaFold predicted three-dimensional structural information, together with other non-structural clues, to develop a large-scale approach termed PredGO to annotate Gene Ontology (GO) functions for proteins. We use a pre-trained language model, geometric vector perceptrons and attention mechanisms to extract heterogeneous features of proteins and fuse these features for function prediction. The computational results demonstrate that the proposed method outperforms other state-of-the-art approaches for predicting GO functions of proteins in terms of both coverage and accuracy. The improvement of coverage is because the number of structures predicted by AlphaFold is greatly increased, and on the other hand, PredGO can extensively use non-structural information for functional prediction. Moreover, we show that over 205 000 ($\sim $100%) entries in UniProt for human are annotated by PredGO, over 186 000 ($\sim $90%) of which are based on predicted structure. The webserver and database are available at http://predgo.denglab.org/.
An interpretable block-attention network for identifying regulatory feature interactions
Authors: Prakash Anil , Banerjee Moinak
Published: July 2023

The importance of regulatory features in health and disease is increasing, making it crucial to identify the hallmarks of these features. Self-attention networks (SAN) have given rise to numerous models for the prediction of complex phenomena. But the potential of SANs in biological models was limited because of high memory requirement proportional to input token length and lack of interpretability of self-attention scores. To overcome these constraints, we propose a deep learning model named Interpretable Self-Attention Network for REGulatory interactions (ISANREG) that combines both block self-attention and attention-attribution mechanisms. This model predicts transcription factor-bound motif instances and DNA-mediated TF–TF interactions using self-attention attribution scores derived from the network, overcoming the limitations of previous deep learning models. ISANREG will serve as a framework for other biological models in interpreting the contribution of the input with single-nucleotide resolution.
1LocusSim a mobile-friendly simulator for teaching population genetics
Authors: Carvajal-Rodríguez Antonio
Published: July 2023

Motivation

Biology students often struggle with the fundamental concepts of evolutionary genetics, including genetic drift, mutation and selection. To address this problem, 1LocusSim was developed to simulate the interaction of different factors, such as population size, mutation, selection and dominance, to study their effect on allelic frequency during evolution. With 1LocusSim, students can compare theoretical results with simulation outputs and solve and analyze different problems of population genetics. The 1LocusSim web has a responsive design which means that it has been specifically designed to be used on smartphones.

Results

To demonstrate its use, I review the classical overdominance model of population genetics and highlight a characteristic that is often not explicitly stated. Specifically, it is emphasized that the equilibrium of the model does not depend on the homozygous selection coefficients but rather on the ratio of the selection coefficients. This is already clear from the classical formula but maybe not so much for students. Also it implies that the equilibrium can be expressed solely in terms of the dominance coefficient h. To verify this theoretical prediction, I utilize the simulator and calculate the equilibrium for the well-known case of sickle cell anemia. By utilizing this tool, students can learn at their own pace and convenience, anywhere and anytime.

Availability and implementation

1LocusSim if freely available at https://1LocusSim-biosdev.pythonanywhere.com/. Website implemented under the Bottle micro web-framework for Python, with all major browsers supported.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
‘There’s No Hope for Any Kind of Decent Life’: A Qualitative Study to Explore the Perspectives of People Experiencing Homelessness with a Recent Non-Fatal Overdose in Scotland
Authors: Farmer Natalia , McPherson Andrew , Thomson Jim , Reilly Frank , Williamson Andrea , Lowrie Richard
Published: July 2023

The past ten years has seen a marked increase in the numbers of people experiencing homelessness globally and an associated public health epidemic of drug-related deaths. Drawing from qualitative interviews as part of a wider pilot randomised controlled trial (RCT) conducted in Glasgow, Scotland with National Health Service pharmacists and third sector homeless outreach caseworkers, insights from those with living experience of both homelessness and a recent non-fatal drug overdose will be presented. Twenty people experiencing homelessness with at least one drug overdose in the past six months were interviewed in person, in a homelessness drop in centre or in emergency accommodation between November 2021 and January 2022. Findings from our study indicate that participants’ drug use and overdose risk were exacerbated during the Covid-19 pandemic due to the pervasive availability of illicit drugs for those placed in emergency accommodation, alongside reduced support and access to health and social care services. Additionally, multi-agency stressors such as a lack of autonomy and dehumanising experiences were reported, leading to a significant sense of powerlessness. Furthermore, the necessity of advocacy-based services as critical aspects of support was identified, with importance placed upon dedicated, homelessness staff and access to safe environments.
Wnt4 increases the thickness of the epidermis in burn wounds by activating canonical Wnt signalling and decreasing the cell junctions between epidermal cells
Authors: Xiang Fei , Wang Pei , Gong Hao , Luo Jia , Zhou Xin , Zhan Chenglin , Hu Tianxing , Wang Mengru , Xing Yizhan , Guo Haiying , Luo Gaoxing , Li Yuhong
Published: July 2023

Background

Burn wound healing is a complex process and the role of Wnt ligands varies in this process. Whether and how Wnt4 functions in burn wound healing is not well understood. In this study, we aim to reveal the effects and potential mechanisms of Wnt4 in burn wound healing.

Methods

First, the expression of Wnt4 during burn wound healing was determined by immunofluorescence, Western blotting and qPCR. Then, Wnt4 was overexpressed in burn wounds. The healing rate and healing quality were analysed by gross photography and haematoxyline and eosin staining. Collagen secretion was observed by Masson staining. Vessel formation and fibroblast distribution were observed by immunostaining. Next, Wnt4 was knocked down in HaCaT cells. The migration of HaCaT cells was analysed by scratch healing and transwell assays. Next, the expression of β-catenin was detected by Western blotting and immunofluorescence. The binding of Frizzled2 and Wnt4 was detected by coimmunoprecipitation and immunofluorescence. Finally, the molecular changes induced by Wnt4 were analysed by RNA sequencing, immunofluorescence, Western blotting and qPCR in HaCaT cells and burn wound healing tissues.

Results

The expression of Wnt4 was enhanced in burn wound skin. Overexpression of Wnt4 in burn wound skin increased the thickness of epidermis. Collagen secretion, vessel formation and fibroblast distribution were not significantly impacted by Wnt4 overexpression. When Wnt4 was knocked down in HaCaT cells, the ratio of proliferating cells decreased, the ratio of apoptotic cells increased and the ratio of the healing area in the scratch healing assay to the number of migrated cells in the transwell assay decreased. The nuclear translocation of β-catenin decreased in shRNA of Wnt4 mediated by lentivirus-treated HaCaT cells and increased in Wnt4-overexpressing epidermal cells. RNA-sequencing analysis revealed that cell junction-related signalling pathways were significantly impacted by Wnt4 knockdown. The expression of the cell junction proteins was decreased by the overexpression of Wnt4.

Conclusions

Wnt4 promoted the migration of epidermal cells. Overexpression of Wnt4 increased the thickness of the burn wound. A potential mechanism for this effect is that Wnt4 binds with Frizzled2 and increases the nuclear translocation of β-catenin, thus activating the canonical Wnt signalling pathway and decreasing the cell junction between epidermal cells.
A novel pathogenic variant in the FZD6 gene causes recessive nail dysplasia in a Moroccan family
Authors: Lanvin Pierre-Louis , Lebreton Louis , Lasseaux Eulalie , Creveaux Isabelle , Léauté-Labrèze Christine , Boralevi Franck , Morice-Picard Fanny
Published: July 2023

This report describes a patient with a novel homozygous nonsense variant, nail dysplasia and diabetes. Only a few patients have been described with FZD6 mutations and nail dysplasia, and the spectrum of associated manifestations has not been identified. Indeed, it is questionable whether there is a link between pancreatic involvement and the genetic abnormality identified.
‘Poroma-like’ branched vessels with rounded endings in dermoscopy of basal cell carcinoma: a new unusual structure
Authors: Cavallo Francesco , Mazzoletti Vanessa , Zelin Enrico , Avallone Gianluca , Roccuzzo Gabriele , Bottomicca Flavia , Quaglino Pietro , Zalaudek Iris , Ribero Simone
Published: July 2023

We report the cases of three patients with basal cell carcinoma that showed branched vessels with rounded endings, a vascular pattern never described in basal cell carcinoma and previously associated with eccrine poroma. We also speculate about the meaning of this pattern and underline the importance of this atypical vascular presentation in the differential diagnosis of malignant melanoma.
The locus of recognition memory signals in human cortex depends on the complexity of the memory representations
Authors: Sanders D Merika W , Cowell Rosemary A
Published: July 2023

According to a “Swiss Army Knife” model of the brain, cognitive functions such as episodic memory and face perception map onto distinct neural substrates. In contrast, representational accounts propose that each brain region is best explained not by which specialized function it performs, but by the type of information it represents with its neural firing. In a functional magnetic resonance imaging study, we asked whether the neural signals supporting recognition memory fall mandatorily within the medial temporal lobes (MTL), traditionally thought the seat of declarative memory, or whether these signals shift within cortex according to the content of the memory. Participants studied objects and scenes that were unique conjunctions of pre-defined visual features. Next, we tested recognition memory in a task that required mnemonic discrimination of both simple features and complex conjunctions. Feature memory signals were strongest in posterior visual regions, declining with anterior progression toward the MTL, while conjunction memory signals followed the opposite pattern. Moreover, feature memory signals correlated with feature memory discrimination performance most strongly in posterior visual regions, whereas conjunction memory signals correlated with conjunction memory discrimination most strongly in anterior sites. Thus, recognition memory signals shifted with changes in memory content, in line with representational accounts.
Teaching Whiteness in Shakespeare’s ‘Sonnet 18’
Authors: Stacey Richard
Published: July 2023

This article will outline several strategies which can be used to teach Shakespeare’s poem ‘Sonnet 18’ in the pre-University classroom. Although one of the most famous texts in the canon, and regularly read in non-educational contexts, ‘Sonnet 18’ is rarely discussed in relation to its racial politics and its normalizing treatment of metaphorical whiteness. Being able to detect the operative invisibility of white imagery is a crucial critical skill, as it empowers students to assess the significance of the racialized effects of the poetic evidence placed before them. I touch on the five Assessment Objectives at Key Stage 5 at various stages to meld current critical methodologies with A-Level pedagogical structures. The focus on ‘Sonnet 18’ will also help to sharpen awareness of the coercive properties of canonical texts which are often presented to the reader as ideologically neutral, particularly those on bucolic or ‘English’ themes.
Structure and Function of RhoBTB1 Required for Substrate Specificity and Cullin-3 Ubiquitination
Authors: Kumar Gaurav , Fang Shi , Golosova Daria , Lu Ko-Ting , Brozoski Daniel T , Vazirabad Ibrahim , Sigmund Curt D
Published: July 2023

We identified Rho-related BTB domain containing 1 (RhoBTB1) as a key regulator of phosphodiesterase 5 (PDE5) activity, and through PDE5, a regulator of vascular tone. We identified the binding interface for PDE5 on RhoBTB1 by truncating full-length RhoBTB1 into its component domains. Co-immunoprecipitation analyses revealed that the C-terminal half of RhoBTB1 containing its two BTB domains and the C-terminal domain (B1B2C) is the minimal region required for PDE5 recruitment and subsequent proteasomal degradation via Cullin-3 (CUL3). The C-terminal domain was essential in recruiting PDE5 as constructs lacking this region could not participate in PDE5 binding or proteasomal degradation. We also identified Pro353 and Ser363 as key amino acid residues in the B1B2C region involved in CUL3 binding to RhoBTB1. Mutation of either of these residues exhibited impaired CUL3 binding and PDE5 degradation, although the binding to PDE5 was preserved. Finally, we employed ascorbate peroxidase 2 (APEX2) proximity labeling using a B1B2C–APEX2 fusion protein as bait to capture unknown RhoBTB1 binding partners. Among several B1B2C-binding proteins identified and validated, we focused on SET domain containing 2 (SETD2). SETD2 and RhoBTB1 directly interacted, and the level of SETD2 increased in response to pharmacological inhibition of the proteasome or Cullin complex, CUL3 deletion, and RhoBTB1-inhibition with siRNA. This suggests that SETD2 is regulated by the RhoBTB1–CUL3 axis. Future studies will determine whether SETD2 plays a role in cardiovascular function.
Clinical features of gastric adenoma detected within 3 years after negative screening endoscopy in Korea
Authors: Kim Hyun Young
Published: July 2023

Background

Early detection and management of gastric adenoma are important for preventing gastric cancer. The present study aimed to evaluate the predictors of missed gastric adenoma on screening endoscopy in Korea and identify the risk factors associated with interval precancerous gastric lesions.

Methods

All cases of gastric adenomas diagnosed via screening endoscopy between 2007 and 2019 were reviewed. Among them, those who had undergone endoscopy within 3 years were included in the present study. Missed gastric adenoma was defined as gastric adenoma diagnosed within 3 years after negative screening endoscopy.

Results

In total, 295 cases of gastric adenoma were identified. Of these, 95 (32.2%) were missed gastric adenoma cases (mean age, 60.6 years; average interval between final and index endoscopies, 12.6 months); the remaining 200 (67.8%) were newly detected adenoma cases. Univariate analysis revealed that male sex, endoscopist experience, observation time, and presence of gastric intestinal metaplasia (pathologically proven) were associated with missed gastric adenoma. Multivariate analysis revealed that gastric intestinal metaplasia (odds ratio [OR], 2.736; 95% confidence interval [CI], 1.320–5.667; P = 0.007) and shorter observation time of the index screening endoscopy (B, −0.011; OR, 0.990; 95% CI, 0.986–0.993; P < 0.001) were independent risk factors for missed gastric adenoma. The optimal cut-off for the observation time for detecting gastric adenoma was 3.53 minutes (area under curve, 0.738; 95% CI, 0.677–0.799; P < 0.001).

Conclusions

Gastric intestinal metaplasia is an indication of missed gastric adenoma. Therefore, careful inspection of gastric mucosa with gastric intestinal metaplasia and proper observation time can lower the possibility of missing the gastric adenoma during screening.
Neoproterozoic and Cretaceous crustal structures revealed by a 3-D magnetotelluric investigation of the onshore Espírito Santo Basin and the contiguous Araçuaí Orogen (SE Brazil)
Authors: Oliveira J R D , La Terra E F , Panetto L P , Tupinambá M , Fontes S L
Published: July 2023

The study region in southeastern Brazil is composed of two domains: the Cretaceous onshore Espírito Santo Basin and the Neoproterozoic Araçuaí Orogen. In this region, associations among geological evolution, observed structures and geophysical data are limited. Therefore, this study aimed to further investigate this region using magnetotelluric (MT) data obtained from 22 W-E spanning stations over the Espírito Santo State. Because the dimensionality analysis revealed a substantial 3-D characteristic of the data, a 3-D MT inversion using the ModEM code was performed to generate a regional geoelectric model, and potential and well data were used as qualitative support for the interpretation. The resistivity profile obtained from the model revealed a resistive pattern for the Precambrian terrain and a conductive pattern for the sedimentary rocks of the onshore Espírito Santo Basin. The basement of the basin was delimited in the resistivity model, revealing consistency with the basement depths from the well data. Furthermore, three crustal conductors inserted in a resistive Precambrian orogen were identified. These conductors may be related to the recent circulation of saline fluids associated with plume action during the Upper Cretaceous and Cenozoic. However, the structures in which these fluids circulate exhibit different genesis along the resistivity profile. The conductors to the west of the profile may be related to plutons and dykes associated with the NNW Colatina Lineaments generated by the gravitational collapse of the orogen (530–490 Ma). Conversely, the conductor to the east under the Espírito Santo Basin appears to be related to the primary detachment rift fault generated during the Cretaceous breakup of Gondwana.
Mission design aspects for the mass change and geoscience international constellation (MAGIC)
Authors: Heller-Kaikov Betty , Pail Roland , Daras Ilias
Published: July 2023

The Mass Change and Geoscience International Constellation (MAGIC) is planned as the first realization of a double-pair low-low satellite-to-satellite (ll-sst) tracking gravity mission consisting of a polar and an inclined satellite pair. Due to the much increased spatial and temporal resolution and multidirectionality of the data to be collected by this mission, new possibilities regarding the resolvability of mass transport processes in space and time are expected. In order to maximize the scientific and societal outcome of this mission, an optimization of both the mission design as well as the methods to process the expected data is fundamental. Using numerical closed-loop simulations, we investigate the impact of several key mission design aspects on the gravity retrieval from a double-pair constellation such as the planned MAGIC mission. Specifically, we show how the choice of the second pair’s inclination poses a trade-off between a reduction of retrieval errors at latitudes covered by data from both pairs and at higher latitudes, thereby requiring a compromise between the latitude-dependent accuracy requirements of different user groups. One of the key mission goals is to provide fast-track gravity products with short latency for operational service applications. Towards the estimation of such short-term gravity fields of a few days, we investigate if coordinating the polar and inclined pairs’ orbits to achieve a stable ground-track coverage is necessary for obtaining a homogeneous accuracy of subsequent gravity solutions. Indeed, combining two freely drifting, uncontrolled orbits significantly degrades short-term gravity fields in time periods in which both pairs show coinciding ground track gaps. Finally, we analyse the relative performance of the two satellite pairs. Double-pair scenarios that are strongly dominated by the inclined pair’s data reveal degraded gravity solutions when co-estimating daily gravity fields as de-aliasing strategy. This effect can be mitigated by choosing a more balanced double-pair configuration, for example by choosing similar orbit heights and instrument noise levels for both satellite pairs. The findings presented in our study will serve to optimize the system design of the upcoming MAGIC constellation.
Characterizing coastal cod vocalization using a towed hydrophone array
Authors: Seri Sai Geetha , Schinault Matthew Edward , Penna Seth Michael , Zhu Chenyang , Sivle Lise Doksæter , de Jong Karen , Handegard Nils Olav , Ratilal Purnima
Published: July 2023

To better understand spawning vocalizations of Norwegian coastal cod (Gadus morhua), a prototype eight-element coherent hydrophone array was deployed in stationary vertical and towed horizontal modes to monitor cod sounds during an experiment in spring 2019. Depth distribution of cod aggregations was monitored concurrently with an ultrasonic echosounder. Cod vocalizations recorded on the hydrophone array are analysed to provide time–frequency characteristics, and source level distribution after correcting for one-way transmission losses from cod locations to the hydrophone array. The recorded cod vocalization frequencies range from ∼20 to 600 Hz with a peak power frequency of ∼60 Hz, average duration of 300 ms, and mean source level of 163.5 ± 7.9 dB re 1 μPa at 1 m. Spatial dependence of received cod vocalization rates is estimated using hydrophone array measurements as the array is towed horizontally from deeper surrounding waters to shallow water inlet areas of the experimental site. The bathymetric-dependent probability of detection regions for cod vocalizations are quantified and are found to be significantly reduced in shallow-water areas of the inlet. We show that the towable hydrophone array deployed from a moving vessel is invaluable because it can survey cod vocalization activity at multiple locations, providing continuous spatial coverage that is complementary to fixed sensor systems that provide continuous temporal coverage at a given location.
Evidence-based appraisal of two guidelines for the diagnosis of suspected, uncomplicated urinary tract infections in primary care: a diagnostic accuracy validation study
Authors: Fanshawe Thomas R , Judge Rebecca K , Mort Sam , Butler Christopher C , Hayward Gail N
Published: July 2023

Objectives

Given the lack of accurate rapid diagnostics for urinary tract infection (UTI) in women, many countries have developed guidelines aiming to support appropriate antibiotic prescribing, but some guidelines have not been validated. We performed a diagnostic accuracy validation study of two guidelines: Public Health England (GW-1263) and Scottish Intercollegiate Guidelines Network (SIGN160).

Methods

We used data from women with symptoms suggestive of uncomplicated UTI from a randomized controlled trial comparing urine collection devices. Symptom information was recorded via baseline questionnaire and primary care assessment. Women provided urine samples for dipstick testing and culture. We calculated the number within each risk category of diagnostic flowcharts who had positive/mixed growth/no significant growth urine culture. Results were presented as positive/negative predictive values, with 95% CIs.

Results

Of women aged under 65 years, 311/509 (61.1%, 95% CI 56.7%–65.3%) classified to the highest risk category (recommended to consider immediate antibiotic prescribing) and 80/199 (40.2%, 95% CI 33.4%–47.4%) classified to the lowest risk category (recommended to reassure that UTI is less likely) by the GW-1263 guideline (n = 810) had positive culture. For the SIGN160 guideline (n = 814), the proportion with positive culture ranged from 60/82 (73.2%, 95% CI 62.1%–82.1%) in those for whom immediate treatment was indicated to 33/76 (43.4%, 95% CI 32.3%–55.3%) in those recommended a self-care/waiting strategy.

Conclusions

Clinicians should be aware of the potential for diagnostic error when using diagnostic guidelines for managing uncomplicated UTI and making antimicrobial prescribing decisions. Infection cannot be excluded on the basis of symptoms and dipstick testing alone.
Spatial regulation of plant hormone action
Authors: Wong Cynthia , Alabadí David , Blázquez Miguel A
Published: July 2023

Although many plant cell types are capable of producing hormones, and plant hormones can in most cases act in the same cells in which they are produced, they also act as signaling molecules that coordinate physiological responses between different parts of the plant, indicating that their action is subject to spatial regulation. Numerous publications have reported that all levels of plant hormonal pathways, namely metabolism, transport, and perception/signal transduction, can help determine the spatial ranges of hormone action. For example, polar auxin transport or localized auxin biosynthesis contribute to creating a differential hormone accumulation across tissues that is instrumental for specific growth and developmental responses. On the other hand, tissue specificity of cytokinin actions has been proposed to be regulated by mechanisms operating at the signaling stages. Here, we review and discuss current knowledge about the contribution of the three levels mentioned above in providing spatial specificity to plant hormone action. We also explore how new technological developments, such as plant hormone sensors based on FRET (fluorescence resonance energy transfer) or single-cell RNA-seq, can provide an unprecedented level of resolution in defining the spatial domains of plant hormone action and its dynamics.
Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops
Authors: Cui Yue , Cao Qiao , Li Yongpeng , He Mingqi , Liu Xigang
Published: July 2023

Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.
Control ofListeria monocytogenesin a fresh cheese using aromatic and medicinal plants and enterocin: a comparative study
Authors: Ananou Samir , Bouraqqadi Meryem , Zouhri Nada , El Kinany Said , Manni Laila
Published: July 2023

The aim of this study was to investigate the effectiveness of essential oils (EOs) or crude extracts (CEs) of eight aromatic and medicinal plants (AMPs) and its association with enterocin OS1 on Listeria monocytogenes and food spoilage bacteria in Moroccan fresh cheese. The cheese batches were treated with EO of Rosmarinus officinalis, Thymus vulgaris, Syzygium aromaticum, Laurus nobilis, Allium sativum, Eucalyptus globulus, or CE of Crocus sativus and Carthamus tinctorius, and/or enterocin OS1, and stored for 15 days at 8°C. The data were subjected to correlations analysis, variance analysis, and principal components analysis. Results clearly showed a positive correlation between L. monocytogenes reduction and storage time. Moreover, reduction on Listeria counts induced by Allium-EO and Eucalyptus-EO reached 2.68 and 1.93 Log CFU/g with respect to untreated samples after 15 days, respectively. Similarly, enterocin OS1 alone has significantly reduced the L. monocytogenes population with 1.46 Log CFU/g. The most promising result was the synergy observed between many AMPs and enterocin. Indeed, treatments with Eucalyptus-EO + OS1 and Crocus-CE + OS1 decreased the Listeria population to undetectable after only 2 days and throughout the storage period. These findings suggest a promising application/use of this natural combination, which preserves the safety and long-lasting conservation of fresh cheese.