bluuebunny/crossref_metadata_2025 huggingface dataset:
Partially coherent laser beam shaping in a zoom homogenizer
Authors: Zheng Xin , Dai Shenyu , Zhao Shuai
Published: May 2023

This paper proposes a synthesis method including wave optics and geometric optics to design the zoom homogenizer for partially coherent laser beams and discusses the effects of the spatial coherence and system parameters on the beam performance. Based on the principles of pseudo-mode representation and matrix optics, a numerical model for fast simulation has been built and the parameter constraints for avoiding beamlet crosstalk have been presented. The relation of the size and the divergence angle of the highly uniform beams formed in the defocused plane with system parameters has been developed. The variations in the intensity profile and the uniformity of the variable-size beams during zooming have been explored.
On-chip non-uniform geometric metasurface for multi-channel wavefront manipulations
Authors: Fang Bin , Shu Fangzhou , Wang Zhizhang , Ji Jitao , Jin Zhongwei , Hong Zhi , Shen Changyu , Cheng Qingqing , Li Tao
Published: May 2023

Metasurfaces integrated with waveguides have been recently explored as a means to control the conversion between guided modes and radiation modes for versatile functionalities. However, most efforts have been limited to constructing a single free-space wavefront using guided waves, which hinders the functional diversity and requires a complex configuration. Here, a new, to the best of our knowledge, type of non-uniformly arranged geometric metasurface enabling independent multi-channel wavefront engineering of guided wave radiation is ingeniously proposed. By endowing three structural degrees of freedom into a meta-atom, two mechanisms (the Pancharatnam–Berry phase and the detour phase) of the metasurface are perfectly joined together, giving rise to three phase degrees of freedom to manipulate. Therefore, an on-chip polarization demultiplexed metalens, a wavelength-multiplexed metalens, and RGB-colored holography with an improved information capacity are successively demonstrated. Our results enrich the functionalities of an on-chip metasurface and imply the prospect of advancements in multiplexing optical imaging, augmented reality (AR) holographic displays, and information encryption.
Angle-insensitive topological interface states in hybrid one-dimensional photonic crystal heterostructures containing all-dielectric metamaterials
Authors: Wu Feng , Li Hongju , Hu Shi , Chen Ying , Long Yang
Published: May 2023

Topological interface states (TISs) in conventional one-dimensional (1D) photonic crystal (PhC) heterostructures strongly shift toward higher frequencies as the incident angle increases. This strong blueshift property of TISs intensively limits the operating angle ranges of TISs. Herein, we design two angle-insensitive photonic bandgaps (PBGs) in two hybrid 1D PhCs containing all-dielectric metamaterials. By cascading these two hybrid 1D PhCs to construct a hybrid 1D PhC heterostructure, we achieve an angle-insensitive TIS under transverse magnetic polarization. Empowered by the angle-insensitive property of the PBGs, the angular tolerance of the TIS reaches 69.65°, which is much higher than those of the TISs in conventional 1D PhC heterostructures. In addition, the angle-insensitive property of the TIS is robust against the layer thickness. Our work provides a viable route to achieving TISs with high angular tolerances and would facilitate the applications of photonic topological states.
Picometer-scale optical vortex interferometer using azimuthal complex spectrum analysis
Authors: Dong Jingtao , Zhang Tengda , Zhang Yuzhong , Yang Lei , Lu Rongsheng
Published: May 2023

An interferogram demodulation method based on azimuthal complex spectrum analysis is proposed for achieving picometer-scale accuracy with an optical vortex interferometer (OVI). The OVI uses conjugated p-radial-order Laguerre–Gaussian beams to produce a high-order petal-like interferogram. A camera with a multi-ring pattern written on its sensor is used to convert the interferogram into multiple azimuthal intensity profiles. A phase shift subjected to either uniform surface displacement or axisymmetric non-uniform surface deformation can be retrieved from the complex spectra of the azimuthal intensity profiles at the main frequency components. The experiment verified that the measurement error is 84 pm for a displacement of 10 nm and 0.359 nm for a deformation magnitude of 100 nm. The effect of surface misalignment on the measurement result is also discussed. The proposed method provides an effective and highly accurate method of interferogram demodulation for the OVI and extends the applicability of OVI from uniform surface displacement measurement to axisymmetric non-uniform surface deformation measurement.
Accurate and efficient prediction of photonic crystal waveguide bandstructures using neural networks
Authors: Schwahn Caspar F. , Schulz Sebastian A.
Published: May 2023

We demonstrate the use of neural networks to predict the optical properties of photonic crystal waveguides (PhCWs) with high accuracy and significantly faster computation times compared to traditional simulation methods. Using 100,000 PhCW designs and their simulated bandstructures, we trained a neural network to achieve a test set relative error of 0.103% in predicting gap guided bands. We use pre-training to improve neural network performance, and numerical differentiation to accurately predict group index curves. Our approach allows for rapid, application-specific tailoring of PhCWs with a runtime of sub-milliseconds per design, a significant improvement over conventional simulation techniques.
A convolutional neural network provides a generalizable model of natural sound coding by neural populations in auditory cortex
Authors: Pennington Jacob R. , David Stephen V.
Published: May 2023

Convolutional neural networks (CNNs) can provide powerful and flexible models of neural sensory processing. However, the utility of CNNs in studying the auditory system has been limited by their requirement for large datasets and the complex response properties of single auditory neurons. To address these limitations, we developed a population encoding model: a CNN that simultaneously predicts activity of several hundred neurons recorded during presentation of a large set of natural sounds. This approach defines a shared spectro-temporal space and pools statistical power across neurons. Population models of varying architecture performed consistently and substantially better than traditional linear-nonlinear models on data from primary and non-primary auditory cortex. Moreover, population models were highly generalizable. The output layer of a model pre-trained on one population of neurons could be fit to data from novel single units, achieving performance equivalent to that of neurons in the original fit data. This ability to generalize suggests that population encoding models capture a complete representational space across neurons in an auditory cortical field.
Using social capital to address youth sexual and reproductive health and rights in disaster preparedness and response: A qualitative study highlighting the strengths of Pacific community organisations and networks
Authors: Murphy Nabreesa , Azzopardi Peter , Bowen Kathryn , Quinn Phoebe , Rarama Tamani , Dawainavesi Akanisi , Bohren Meghan A.
Published: May 2023

In the Pacific region, youth sexual and reproductive health and rights (SRHR) are strongly influenced by sociocultural and structural factors, which limit access to SRHR information and services for youth. As climate-related disasters intensify in the Pacific, existing challenges to youth SRHR may increase the risk of worse SRHR experiences and outcomes for youth before, during and after disasters. Community-based models of SRHR service provision models increase accessibility for youth in non-disaster times, but there is limited evidence of how community organisations address youth SRHR in disaster contexts. We conducted qualitative interviews with 16 participants from community organisations and networks in Fiji, Vanuatu, and Tonga following the 2020 Tropical Cyclone (TC) Harold. Guided by the Recovery Capitals Framework (natural, built, political, cultural, human, social, and financial capitals), we explored how community organisations addressed challenges to facilitate access to youth SRHR information and services. Social capital in the form of peer networks and virtual safe spaces was used to navigate challenges in political, financial, and natural capitals. Existing relationships and trusted collaborations were crucial to address cultural taboos related to youth SRHR. Previous experiences of disasters and knowledge of contexts enabled participants to provide sustainable solutions to identified SRHR needs. The work conducted by community organisations and networks pre-disaster made it easier to identify and address youth SRHR risks following disasters. Our research offers a unique perspective into how social capitals were used to mitigate challenges to youth SRHR across natural, human, financial, cultural, built, and political capitals. Findings offer important opportunities to invest in existing community strengths, for transformative action to advance the SRHR of Pacific youth.
In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses
Authors: Olmedo-Velarde Alejandro , Ochoa-Corona Francisco M. , Larrea-Sarmiento Adriana E. , Elbeaino Toufic , Flores Francisco
Published: May 2023

Twenty-four species of RNA viruses contain members infecting economically important crops that are classified within the genus Emaravirus, family Fimoviridae. There are at least two other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. This research aimed to explore the ability to predict HRM outputs coupled to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). To approach this goal a pair of degenerate genus-specific primers were designed for endpoint RT-PCR and RT-qPCR-HRM and the species in the genus Emaravirus were selected to framework the development of the assays. Both nucleic acid amplification methods were able to detect in-vitro several members of seven Emaravirus species with sensitivity up to one fg of cDNA. Specific parameters for in-silico prediction of the melting temperatures of each expected emaravirus amplicon are compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The high-resolution DNA melting curves of the RT-PCR products predicted in-silico using uMeltSM allowed saving time while designing and developing the RT-qPCR-HRM assay since the approach avoided extensive searching for optimal HRM assay regions and rounds of HRM tests in-vitro for optimization. The resultant assay provides sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
Geldanamycin treatment does not result in anti-cancer activity in a preclinical model of orthotopic mesothelioma
Authors: Orozco Morales M. Lizeth , Rinaldi Catherine A. , de Jong Emma , Lansley Sally M. , Lee Y. C. Gary , Zemek Rachael M. , Bosco Anthony , Lake Richard A. , Lesterhuis W. Joost
Published: May 2023

Mesothelioma is characterised by its aggressive invasive behaviour, affecting the surrounding tissues of the pleura or peritoneum. We compared an invasive pleural model with a non-invasive subcutaneous model of mesothelioma and performed transcriptomic analyses on the tumour samples. Invasive pleural tumours were characterised by a transcriptomic signature enriched for genes associated with MEF2C and MYOCD signaling, muscle differentiation and myogenesis. Further analysis using the CMap and LINCS databases identified geldanamycin as a potential antagonist of this signature, so we evaluated its potential in vitro and in vivo. Nanomolar concentrations of geldanamycin significantly reduced cell growth, invasion, and migration in vitro. However, administration of geldanamycin in vivo did not result in significant anti-cancer activity. Our findings show that myogenesis and muscle differentiation pathways are upregulated in pleural mesothelioma which may be related to the invasive behaviour. However, geldanamycin as a single agent does not appear to be a viable treatment for mesothelioma.
Developing a computational toolbased on an artificial neural network for predicting and optimizing propolis oil, an important natural product for drug discovery
Authors: Nayak Gayatree , Sahu Akankshya , Bhuyan Sanat Kumar , Akbar Abdul , Bhuyan Ruchi , Kar Dattatreya , Nayak Guru Charan , Satapathy Swapnashree , Pattnaik Bibhudutta , Kuanar Ananya
Published: May 2023

Propolis is a promising natural product that has been extensively researched and studied for its potential health and medical benefits. The lack of requisite high oil-containing propolis and existing variation in the quality and quantity of essential oil within agro-climatic regions pose a problem in the commercialization of essential oil. As a result, the current study was carried out to optimize and estimate the essential oil yield of propolis. The essential oil data of 62 propolis samples from ten agro-climatic areas of Odisha, as well as an investigation of their soil and environmental parameters, were used to construct an artificial neural network (ANN) based prediction model. The influential predictors were determined using Garson’s algorithm. To understand how the variables interact and to determine the optimum value of each variable for the greatest response, the response surface curves were plotted. The results revealed that the most suited model was multilayer-feed-forward neural networks with an R2value of 0.93. According to the model, altitude was found to have a very strong influence on response, followed by phosphorous & maximum average temperature. This research shows that using an ANN-based prediction model with a response surface methodology technique to estimate oil yield at a new site and maximize propolis oil yield at a specific site by adjusting variable parameters is a viable commercial option. To our knowledge, this is the first report on the development of a model to optimize and estimate the essential oil yield of propolis.
Deleterious impact of COVID-19 pandemic: Male fertility was not out of the bag
Authors: Garrouch Siwar , Sallem Amira , Ben Fredj Manel , Kooli Rim , Bousabbeh Manel , Boughzala Ines , Sriha Asma , Hajjaji Awatef , Mehdi Meriem
Published: May 2023

Background

The emergence and the spread of coronavirus disease (COVID-19) induced by the SARS-CoV-2 virus has multiple consequences in all countries around the world. Male germ cells of infertile patients which are shown to be vulnerable to many environmental conditions, could be particularly vulnerable to such an exceptional pandemic situation. We aimed through the current study to investigate the potential variations in sperm quality of infertile patients during the COVID-19 pandemic in Tunisia.

Methods

This was a cohort study including 90 infertile patients addressed to Laboratory of Cytogenetics and Reproductive Biology of Monastir Department of Maternity and Neonatology in Monastir, during the two first COVID-19 waves in Tunisia and who already have a spermogram before the pandemic period.

Results

We have pointed out a significant decrease in both total and progressive sperm motility during COVID-19 pandemic (p<0.0001 and p = 0.001 respectively). The percentage of morphologically abnormal spermatozoa increased from 90.99±7.38 to 93.67±4.55% during the pandemic (p< 0.001). The remaining sperm parameters were similar between the two compared timepoints. Interestingly, the univariate analysis didn’t show any other associated factor to the observed impairment in sperm mobility and morphology.

Conclusion

These data highlight the severe impact of the pandemic of the male reproductive health of hypofertile patients. Delaying infertility investigations and management after pandemic waves is recommended to hope a better gamete quality and hence to improve conception potential.
Healthcare professionals’ experiences of providing care for patients with enterocutaneous fistula in hospital and in homecare: A qualitative study
Authors: Härle Karolina , Börjeson Sussanne , Hallböök Olof , Myrelid Pär , Thylén Ingela
Published: May 2023

Background

Enterocutaneous fistula is a rare but complex and serious condition that is both physically and psychologically demanding for the person affected. Infection, fistula dressing problems, electrolyte and fluid imbalance and malnutrition render the individual in need of long periods of in-hospital care and homecare. This place great demands on patients, families, and healthcare professionals. More research is needed to bridge the gap between hospital and home-based healthcare services.

Aim

To explore healthcare professionals’ experiences of providing care for patients with enterocutaneous fistula in hospital and in homecare.

Material and methods

A qualitative descriptive study design based on five focus group interviews involving 20 healthcare professionals. Data was analysed using content analysis.

Results

Three categories with seven corresponding subcategories were developed; 1) Providing care for patients with enterocutaneous fistula in the hospital and at home was complex and time and resource consuming. Participants were struggling with practical issues and lacked disease-specific knowledge and skills; 2) Caring requires an integrated approach but it was challenging to work interprofessionally and cope with barriers in collaboration between providers; 3) Building long lasting relationships with patients and their families was fundamental to the caring process. Participants needed to hide their own feelings related to smell and appearance of the fistula as well as frustration when the fistula dressing did not hold without leaking. The healthcare professionals expressed that the involvement of the patient and their close family was important when proving care, likewise, to have a great understanding of the patients’ suffering.

Discussion

The care of patients with enterocutaneous fistula is complex and means engagement for long periods, both in hospital and in home-based healthcare. Regular team meetings of the multidisciplinary team, careful planning before discharge and providing person-centred care can facilitate the care process.
Wave-controlled aliasing in parallel imaging (Wave-CAIPI): Accelerating speed for the MRI-based diagnosis of enhancing intracranial lesions compared to magnetization-prepared gradient echo
Authors: Oh Hyunji , Yim Younghee , Chung Mi Sun , Byun Jun Soo
Published: May 2023

Purpose

We aimed to validate the diagnostic performance of accelerated post-contrast magnetization-prepared rapid gradient-echo (MPRAGE) using wave–controlled aliasing in parallel imaging (Wave-CAIPI) for enhancing intracranial lesions, compared with conventional MPRAGE.

Methods

A total of 233 consecutive patients who underwent post-contrast Wave-CAIPI and conventional MPRAGE (scan time: 2 min 39 s vs. 4 min 30 s) were retrospectively evaluated. Two radiologists independently assessed whole images for the presence and diagnosis of enhancing lesions. The diagnostic performance for non-enhancing lesions, quantitative parameters (diameter of enhancing lesions, signal-to-noise ratio [SNR], contrast-to-noise ratio [CNR], and contrast rate), qualitative parameters (grey-white matter differentiation and conspicuity of enhancing lesions), and image qualities (overall image quality and motion artifacts) were also surveyed. The weighted kappa and percent agreement were used to evaluate the diagnostic agreement between the two sequences.

Results

Wave-CAIPI MPRAGE achieved significantly high agreement for the detection (98.7%[460/466], κ = 0.965) and diagnosis (97.8%[455/466], κ = 0.955) of enhancing intracranial lesions with conventional MPRAGE in pooled analysis. Detection and diagnosis of non-enhancing lesions (97.6% and 96.9% agreement), and diameter of enhancing lesions (P>0.05) also demonstrated high agreements between two sequences. Although Wave-CAIPI MPRAGE show lower SNR (P<0.01) than conventional MRAGE, it fulfilled comparable CNR (P = 0.486) and higher contrast rate (P<0.01). The qualitative parameters show similar value (P>0.05). The overall image quality was slightly poor, however, motion artifacts were better in Wave-CAIPI MPRAGE (both P = 0.005).

Conclusion

Wave-CAIPI MPRAGE provides reliable diagnostic performance for enhancing intracranial lesions within half of the scan time compared with conventional MPRAGE.
Physical characteristics of soil-biodegradable and nonbiodegradable plastic mulches impact conidial splash dispersal of Botrytis cinerea
Authors: Wang Xuechun , Mattupalli Chakradhar , Chastagner Gary , Tymon Lydia , Wu Zixuan , Jung Sunghwan , Liu Hang , DeVetter Lisa Wasko
Published: May 2023

Botrytis cinerea causes gray mold disease of strawberry (Fragaria ×ananassa) and is a globally important pathogen that causes fruit rot both in the field and after harvest. Commercial strawberry production involves the use of plastic mulches made from non-degradable polyethylene (PE), with weedmat made from woven PE and soil-biodegradable plastic mulch (BDM) as emerging mulch technologies that may enhance sustainable production. Little is known regarding how these plastic mulches impact splash dispersal of B. cinerea conidia. The objective of this study was to investigate splash dispersal dynamics of B. cinerea when exposed to various plastic mulch surfaces. Mulch surface physical characteristics and conidial splash dispersal patterns were evaluated for the three mulches. Micrographs revealed different surface characteristics that have the potential to influence splash dispersal: PE had a flat, smooth surface, whereas weedmat had large ridges and BDM had an embossed surface. Both PE mulch and BDM were impermeable to water whereas weedmat was semi-permeable. Results generated using an enclosed rain simulator system showed that as the horizontal distance from the inoculum source increased, the number of splash dispersed B. cinerea conidia captured per plate decreased for all mulch treatments. More than 50% and approximately 80% of the total number of dispersed conidia were found on plates 10 and 16 cm away from the inoculum source across all treatments, respectively. A significant correlation between the total and germinated conidia on plates across all mulch treatments was detected (P<0.01). Irrespective of distance from the inoculum source, embossed BDM facilitated higher total and germinated splashed conidia (P<0.001) compared to PE mulch and weedmat (P = 0.43 and P = 0.23, respectively), indicating BDM’s or embossed film’s potential for enhancing B. cinerea inoculum availability in strawberry production under plasticulture. However, differences in conidial concentrations observed among treatments were low and may not be pathologically relevant.
The economic burden of antibiotic resistance: A systematic review and meta-analysis
Authors: Poudel Ak Narayan , Zhu Shihua , Cooper Nicola , Little Paul , Tarrant Carolyn , Hickman Matthew , Yao Guiqing
Published: May 2023

Introduction

Antibiotic resistance (ABR) has substantial global public health concerns. This systematic review aimed to synthesise recent evidence estimating the economic burden of ABR, characterised by study perspectives, healthcare settings, study design, and income of the countries.

Methods

This systematic review included peer-reviewed articles from PubMed, Medline, and Scopus databases, and grey literature on the topic of the economic burden of ABR, published between January 2016 and December 2021. The study was reported in line with ‘Preferred Reporting Items for Systematic Review and Meta-Analysis’ (PRISMA). Two reviewers independently screened papers for inclusion first by title, then abstract, and then the full text. Study quality was assessed using appropriate quality assessment tools. Narrative synthesis and meta-analyses of the included studies were conducted.

Results

A total of 29 studies were included in this review. Out of these studies, 69% (20/29) were conducted in high-income economies and the remainder were conducted in upper-and-middle income economies. Most of the studies were conducted from a healthcare or hospital perspective (89.6%, 26/29) and 44.8% (13/29) studies were conducted in tertiary care settings. The available evidence indicates that the attributable cost of resistant infection ranges from -US$2,371.4 to +US$29,289.1 (adjusted for 2020 price) per patient episode; the mean excess length of stay (LoS) is 7.4 days (95% CI: 3.4–11.4), the odds ratios of mortality for resistant infection is 1.844 (95% CI: 1.187–2.865) and readmission is 1.492 (95% CI: 1.231–1.807).

Conclusion

Recent publications show that the burden of ABR is substantial. There is still a lack of studies on the economic burden of ABR from low-income economies, and lower-middle-income economies, from a societal perspective, and in relation to primary care. The findings of this review may be of value to researchers, policymakers, clinicians, and those who are working in the field of ABR and health promotion.

Systematic review registration

CRD42020193886
An improved golden jackal optimization for multilevel thresholding image segmentation
Authors: Wang Zihao , Mo Yuanbin , Cui Mingyue , Hu Jufeng , Lyu Yucheng
Published: May 2023

Aerial photography is a long-range, non-contact method of target detection technology that enables qualitative or quantitative analysis of the target. However, aerial photography images generally have certain chromatic aberration and color distortion. Therefore, effective segmentation of aerial images can further enhance the feature information and reduce the computational difficulty for subsequent image processing. In this paper, we propose an improved version of Golden Jackal Optimization, which is dubbed Helper Mechanism Based Golden Jackal Optimization (HGJO), to apply multilevel threshold segmentation to aerial images. The proposed method uses opposition-based learning to boost population diversity. And a new approach to calculate the prey escape energy is proposed to improve the convergence speed of the algorithm. In addition, the Cauchy distribution is introduced to adjust the original update scheme to enhance the exploration capability of the algorithm. Finally, a novel “helper mechanism” is designed to improve the performance for escape the local optima. To demonstrate the effectiveness of the proposed algorithm, we use the CEC2022 benchmark function test suite to perform comparison experiments. the HGJO is compared with the original GJO and five classical meta-heuristics. The experimental results show that HGJO is able to achieve competitive results in the benchmark test set. Finally, all of the algorithms are applied to the experiments of variable threshold segmentation of aerial images, and the results show that the aerial photography images segmented by HGJO beat the others. Noteworthy, the source code of HGJO is publicly available at https://github.com/Vang-z/HGJO.
Does adding MRI and CSF-based biomarkers improve cognitive status classification based on cognitive performance questionnaires?
Authors: Farina Mateo P. , Saenz Joseph , Crimmins Eileen M.
Published: May 2023

Background

Cognitive status classification (e.g. dementia, cognitive impairment without dementia, and normal) based on cognitive performance questionnaires has been widely used in population-based studies, providing insight into the population dynamics of dementia. However, researchers have raised concerns about the accuracy of cognitive assessments. MRI and CSF biomarkers may provide improved classification, but the potential improvement in classification in population-based studies is relatively unknown.

Methods

Data come from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We examined whether the addition of MRI and CSF biomarkers improved cognitive status classification based on cognitive status questionnaires (MMSE). We estimated several multinomial logistic regression models with different combinations of MMSE and CSF/MRI biomarkers. Based on these models, we also predicted prevalence of each cognitive status category using a model with MMSE only and a model with MMSE + MRI + CSF measures and compared them to diagnosed prevalence.

Results

Our analysis showed a slight improvement in variance explained (pseudo-R2) between the model with MMSE only and the model including MMSE and MRI/CSF biomarkers; the pseudo-R2 increased from .401 to .445. Additionally, in evaluating differences in predicted prevalence for each cognitive status, we found a small improvement in the predicted prevalence of cognitively normal individuals between the MMSE only model and the model with MMSE and CSF/MRI biomarkers (3.1% improvement). We found no improvement in the correct prediction of dementia prevalence.

Conclusion

MRI and CSF biomarkers, while important for understanding dementia pathology in clinical research, were not found to substantially improve cognitive status classification based on cognitive status performance, which may limit adoption in population-based surveys due to costs, training, and invasiveness associated with their collection.
Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
Authors: Nord Alexander J. , Wheeler Travis J.
Published: May 2023

The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need for MSA software that can appropriately account for isoforms and the exon-length insertions or deletions that isoforms may have relative to each other. We previously developed Mirage, a software package for generating MSAs for isoforms spanning multiple species. Here, we present Mirage2, which retains the fundamental algorithms of the original Mirage implementation while providing substantially improved translated mapping and improving several aspects of usability. We demonstrate that Mirage2 is highly effective at mapping proteins to their encoding exons, and that these protein-genome mappings lead to extremely accurate intron-aware alignments. Additionally, Mirage2 implements a number of engineering improvements that simplify installation and use.
The ecological consequences and evolution of retron-mediated suicide as a way to protect Escherichia coli from being killed by phage
Authors: Berryhill Brandon A. , Manuel Joshua A. , Garcia Rodrigo , Levin Bruce R.
Published: May 2023

Retrons were described in 1984 as DNA sequences that code for a reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). It would not be until 2020 that a function was shown for retrons, when compelling evidence was presented that retrons activate an abortive infection pathway in response to bacteriophage (phage) infection. When infected with the virulent mutant of the phage lambda, λVIR, and to a lesser extent, other phages, a retron designated Ec48 is activated, the Escherichia coli bearing this retron element dies, and the infecting phage is lost. With the aid of a mathematical model, we explore the a priori conditions under which retrons will protect bacterial populations from predation by phage and the conditions under which retron-bearing bacteria will evolve in populations without this element. Using isogenic E. coli with and without Ec48 and λVIR, we estimated the parameters of our model and tested the hypotheses generated from our analysis of its properties. Our models and experiments demonstrate that cells expressing a retron-mediated abortive infection system can protect bacterial populations. Our results demonstrate that retron bearing bacteria only have a competitive advantage under a limited set of conditions.
Employees’ support strategies for mental wellbeing during and beyond the COVID-19 pandemic: Recommendations for employers in the UK workforce
Authors: Bailey Kerri , Scheutzow Johanna , Cooke Emily , Taylor Katie , Silvestrin Francesco , Naumenko Anna , Hadley Rebecca , Huxley Adam , Ponzo Sonia
Published: May 2023

Throughout the COVID-19 pandemic, and beyond for many businesses, employees have had to adapt to new ways of working due to disruptions in traditional practices. It is therefore crucial to understand the new challenges that employees are facing when it comes to taking care of their mental wellbeing at work. To that end, we distributed a survey to full-time UK employees (N = 451) to explore how supported they felt throughout the pandemic, and to identify whether there are any additional types of support they would like to receive. We also compared employees’ intentions to seek help before versus during the COVID-19 pandemic, and assessed their current attitudes toward mental health. Based on direct employee feedback, our results show remote workers felt more supported throughout the pandemic compared to hybrid workers. We also found that employees who had previously experienced an episode of anxiety or depression were significantly more likely to want extra support at work compared to those who had not. Furthermore, employees were significantly more likely to seek help for their mental health during the pandemic compared to before. Interestingly, the largest increase in intentions to seek help during the pandemic compared to before was with digital health solutions. Finally, we found that the strategies managers have adopted to better support their employees, an employee’s mental health history, and their attitude to mental health all contributed to significantly increasing the likelihood that an employee would disclose a mental health concern to their line manager. We provide recommendations that encourage organisations to make changes to better support their employees, and we highlight the importance of mental health awareness training for both managers and employees. This work is of particular interest to organisations who are looking to tailor their current employee wellbeing offer to a post-pandemic world.
Racial differences in quantitative optical coherence tomography angiography findings between older non-diabetics with co-morbidities
Authors: Moir John , Rodriguez Sarah H. , Chun Lindsay Y. , Massamba Nathalie , Skondra Dimitra
Published: May 2023

This cross-sectional study compared optical coherence tomography angiography (OCTA) parameters between older Black and White adults with systemic comorbidities in an effort to further understand racial differences in the retinal microvasculature. We analyzed vessel density at the superficial (SCP), intermediate (ICP), and deep capillary plexuses (DCP), foveal avascular zone (FAZ) parameters, and blood flow area (BFA) at the choriocapillaris. We used a mixed-effects linear regression model, controlling for hypertension and two eyes from the same subject, to compare OCTA parameters. Black subjects had lower foveal vessel density at the SCP and ICP, while no differences were observed at the parafovea or 3x3 mm macular area of any capillary layer. Black subjects had greater FAZ area, perimeter, and FD-300, a measurement of vessel density in a 300 μm wide ring around the FAZ. Black subjects also had lower BFA at the choriocapillaris. Within a cohort of subjects without hypertension, these differences remained statistically significant, with the exception of foveal vessel density at the SCP and foveal BFA of the choriocapillaris. These findings suggest that normative databases of OCTA parameters must strive to be diverse in nature to adequately capture differences across patient populations. Further study is required to understand if baseline differences in OCTA parameters contribute to epidemiological disparities in ocular diseases.
Adolescent screen time and unhealthy food consumption in the context of the digital development in New Caledonia
Authors: Nedjar-Guerre Akila , Wattelez Guillaume , Serra-Mallol Christophe , Frayon Stéphane , Galy Olivier
Published: May 2023

Objective

For several years, the Pacific Island Countries and Territories (PICTs) have been undergoing digital developments that have had an impact on the time adolescents spend in front of screens. The association between screen time and the overconsumption of unhealthy foods has been observed but little studied in New Caledonia. The twofold aim of this research was to analyze adolescent screen time based on the number of screens at home, gender, place of living, ethnic community and family socio-professional category and determine the link with the consumption of unhealthy food and drinks.

Methods

Self-report questionnaires on time spent in front of tablets, computers and mobile phones, as well as the consumption of unhealthy food and drinks, were administered between July 2018 and April 2019 to 867 adolescents from 11 to 15 years old during school hours in eight schools across the three provinces of New Caledonia.

Results

Adolescents in rural areas had fewer screens than their urban counterparts, and the number of screens determined the amount of screen time, which was significantly higher among the adolescents living in urban areas (3.05 h/day weekdays vs rural 2.33 h/day). Screen time was not related to gender, socio-professional category or ethnic community, but correlations were found between screen time and consumption of unhealthy food and drinks. Those who consumed less than 1 u/day of unhealthy drinks watched screens for 3.30 h/day, whereas those who consumed more than 1 u/day watched screens for 4.13 h/day. Also, those who consumed less than 1 u/day of unhealthy food watched screens for 2.82 h/day and those consuming more than 1 u/day did so for 3.62 h/day. Melanesians and Polynesians consumed greater quantities of unhealthy food and drinks than Europeans. As the consumption of unhealthy products is linked to screen time in the context of digital development, there is an urgent need to address the excessive consumption of unhealthy foods in Oceanian populations, particularly among young people.
Etiology and outcome of penetrating keratoplasty in bullous keratopathy post-cataract surgery vs post-glaucoma surgery
Authors: Jung Young-ho , Choi Hyuk Jin , Kim Mee Kum , Oh Joo Youn
Published: May 2023

Purpose

To investigate the causes of bullous keratopathy (BK) in the Korean population and analyze the results of penetrating keratoplasty (PK) in BK eyes associated with the top two causes: pseudophakic bullous keratopathy (PBK) and glaucoma surgery-associated BK (GBK).

Methods

Medical records were reviewed of patients diagnosed with BK at a tertiary referral center between 2010 and 2020. The predisposing conditions, clinical characteristics and therapeutic outcomes after PK were analyzed and compared.

Results

Of total 340 BK eyes, 70% (238 eyes) were associated with ocular surgery; most commonly, cataract surgery (48%, 162 eyes) and glaucoma surgery/laser (21%, 70 eyes). The BK onset was faster following glaucoma surgery/laser (91.7 ± 94.4 months) than following cataract surgery (160.7 ± 138.0 months, p < 0.001). The median survival time of allografts was shorter in GBK than in PBK (24.0 vs 51.0 months, p = 0.020). Best-corrected logMAR visual acuities were lower in GBK than in PBK after PK (1.4 ± 0.7 vs 0.9 ± 0.6, p = 0.017 at one year; 1.8 ± 0.7 vs 1.1 ± 0.8, p = 0.043 at three years).

Conclusions

Intraocular surgery is the major predisposing condition of BK in Korea. GBK developed earlier and its therapeutic outcome was poorer, compared to PBK.
Blurring the boundary between models and reality: Visual perception of scale assessed by performance
Authors: Meese Tim S. , Baker Daniel H. , Summers Robert J.
Published: May 2023

One of the primary jobs of visual perception is to build a three-dimensional representation of the world around us from our flat retinal images. These are a rich source of depth cues but no single one of them can tell us about scale (i.e., absolute depth and size). For example, the pictorial depth cues in a (perfect) scale model are identical to those in the real scene that is being modelled. Here we investigate image blur gradients, which derive naturally from the limited depth of field available for any optical device and can be used to help estimate visual scale. By manipulating image blur artificially to produce what is sometimes called fake tilt shift miniaturization, we provide the first performance-based evidence that human vision uses this cue when making forced-choice judgements about scale (identifying which of an image pair was a photograph of a full-scale railway scene, and which was a 1:76 scale model). The orientation of the blur gradient (relative to the ground plane) proves to be crucial, though its rate of change is less important for our task, suggesting a fairly coarse visual analysis of this image parameter.
Bioprospection of the trichomonacidal activity of lipid extracts derived from marine macroalgae Gigartina skottsbergii
Authors: Barbosa Tallyson Nogueira , Silva Mara Thais de Oliveira , Sena-Lopes Ângela , Kremer Frederico Schmitt , Sousa Fernanda Severo Sabedra , Seixas Fabiana Kommling , Collares Tiago Veiras , de Pereira Cláudio Martin Pereira , Borsuk Sibele
Published: May 2023

Algal extracts are sources of bioactive substances with applications in the development of novel alternative drugs against several diseases, including trichomoniasis sexually transmitted infection caused by Trichomonas vaginalis. Factors such as clinical failures and resistant strains limit the success of the existing drugs available for treating this disease. Therefore, searching for viable alternatives to these drugs is essential for the treatment of this disease. The present study was conducted for, in vitro and in silico characterization of extracts obtained from marine macroalgae Gigartina skottsbergii at stages gametophidic, cystocarpic, and tetrasporophidic. In addition, antiparasitic activity of these extracts against the ATCC 30236 isolate of T. vaginalis, their cytotoxicity, and gene expression of trophozoites after treatment were evaluated. The minimum inhibitory concentration and 50% inhibition concentration were determined for each extract. Results: In vitro analysis of the extracts’ anti-T. vaginalis activity revealed an inhibitory effect of 100%, 89.61%, and 86.95% for Gigartina skottsbergii at stages gametophidic, cystocarpic, and tetrasporophidic, respectively, at 100 μg/mL. In silico analysis revealed the interactions between constituents of the extracts and enzymes from T. vaginalis, with significant free energy values obtained for the binding. None of the extract concentrations exhibited cytotoxic effects on VERO cell line compared to control, while cytotoxicity on HMVII vaginal epithelial cells line was observed at 100 μg/mL (30% inhibition). Gene expression analysis revealed differences in the expression profile of T. vaginalis enzymes between the extract-treated and control groups. According to these results, Gigartina skottsbergii extracts exhibited satisfactory antiparasitic activity.
Factors associated with underutilization of antenatal care in India: Results from 2019–2021 National Family Health Survey
Authors: Thakkar Nandan , Alam Prima , Saxena Deepak
Published: May 2023

Introduction

Despite progress in recent years, full antenatal care utilization in India continues to be relatively low and inequitable, particularly between states and districts. In 2015–2016, for example, only 51% of women aged 15–49 in India attended antenatal care at least four times during pregnancy. Using data from the fifth iteration of India’s National Family Health Survey, our study aims to explore factors related to the underutilization of antenatal care in India.

Materials and methods

Data from the most recent live birth in the past five years among women aged 15–49 years were included in our analysis (n = 172,702). Our outcome variable was “adequate antenatal care visits”, defined as four or more antenatal visits. Utilizing Andersen’s behavioral model, 14 factors were identified as possible explanatory variables. We used univariate and multivariate binary logistic regression models to analyze the association between explanatory variables and adequate visits. Associations were considered statistically significant if p<0.05.

Results

Of the 172,702 women in our sample, 40.75% (95% CI: 40.31–41.18%) had an inadequate number of antenatal care visits. In multivariate analysis, women with less formal education, from poorer households and more rural areas had higher odds of inadequate visits. Regionally, women from Northeastern and Central states had higher odds of inadequate antenatal care utilization compared to those from Southern states. Caste, birth order, and pregnancy intention were also among the variables associated with utilization of antenatal care.

Discussion

Despite improvements in antenatal care utilization, there is cause for concern. Notably, the percentage of Indian women receiving adequate antenatal care visits is still below the global average. Our analysis also reveals a continuity in the groups of women at highest risk for inadequate visits, which may be due to structural drivers of inequality in healthcare access. To improve maternal health and access to antenatal care services, interventions aimed at poverty alleviation, infrastructure development, and education should be pursued.
Neurocan expression associates with better survival and viral positivity in Merkel cell carcinoma
Authors: Salmikangas Marko , Laaksonen Maria , Edgren Henrik , Salgado Marco , Suoranta Anu , Mattila Pirkko , Koljonen Virve , Böhling Tom , Sihto Harri
Published: May 2023

Merkel cell carcinoma (MCC) is a rare cutaneous neuroendocrine carcinoma that is frequently divided into Merkel cell polyomavirus negative and positive tumors due their distinct genomic and transcriptomic profiles, and disease outcomes. Although some prognostic factors in MCC are known, tumorigenic pathways, which that explain outcome differences in MCC are not fully understood. We investigated transcriptomes of 110 tissue samples of a formalin-fixed, paraffin-embedded MCC series by RNA sequencing to identify genes showing a bimodal expression pattern and predicting outcome in cancer and that potentially could play a role in tumorigenesis. We discovered 19 genes among which IGHM, IGKC, NCAN, OTOF, and USH2A were associated also with overall survival (all p-values < 0.05). From these genes, NCAN (neurocan) expression was detected in all 144 MCC samples by immunohistochemistry. Increased NCAN expression was associated with presence of Merkel cell polyomavirus DNA (p = 0.001) and viral large T antigen expression in tumor tissue (p = 0.004) and with improved MCC-specific survival (p = 0.027) and overall survival (p = 0.034). We conclude that NCAN expression is common in MCC, and further studies are warranted to investigate its role in MCC tumorigenesis.