bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the challenges and opportunities of public engagement with fundamental biology
Authors: Clements-Brod Naomi , Holmes Leah , Rawlins Emma L.
Published: September 2022

The Human Developmental Biology Initiative (HDBI) is a Wellcome-funded research consortium involving scientists based in institutions across the UK and Europe. It aims to pioneer new technologies and techniques to answer fundamental questions about human development and could, therefore, eventually improve treatments for fertility, birth defects and developmental diseases, as well as aiding regenerative medicine. HDBI research relies on human fetal and embryonic tissues donated following pregnancy terminations or fertility treatment. The situations in which these tissues are donated, their use in research and the potential healthcare impacts of this work all present complex ethical and moral questions that are of interest not only to scientists but also to the public. As such, HDBI's public engagement programme ‘What makes us human?’ aspires to test new ways of engaging the public with fundamental biology. In this brief Perspective, we provide an overview of this public engagement approach, exploring its challenges and opportunities, and outline our longer-term plans. We hope that by sharing our experiences we will encourage and enable others to organise similarly experimental public engagement, even if their research is very fundamental or potentially controversial.
Collagen (I) homotrimer potentiates the osteogenesis imperfecta (oim) mutant allele and reduces survival in male mice
Authors: Lee Katie J. , Rambault Lisa , Bou-Gharios George , Clegg Peter D. , Akhtar Riaz , Czanner Gabriela , van ‘t Hof Rob , Canty-Laird Elizabeth G.
Published: September 2022

The osteogenesis imperfecta murine (oim) model with solely homotrimeric (α1)3 type I collagen, owing to a dysfunctional α2(I) collagen chain, has a brittle bone phenotype, implying that the (α1)2(α2)1 heterotrimer is required for physiological bone function. Here, we comprehensively show, for the first time, that mice lacking the α2(I) chain do not have impaired bone biomechanical or structural properties, unlike oim homozygous mice. However, Mendelian inheritance was affected in male mice of both lines, and male mice null for the α2(I) chain exhibited age-related loss of condition. Compound heterozygotes were generated to test whether gene dosage was responsible for the less-severe phenotype of oim heterozygotes, after allelic discrimination showed that the oim mutant allele was not downregulated in heterozygotes. Compound heterozygotes had impaired bone structural properties compared to those of oim heterozygotes, albeit to a lesser extent than those of oim homozygotes. Hence, the presence of heterotrimeric type I collagen in oim heterozygotes alleviates the effect of the oim mutant allele, but a genetic interaction between homotrimeric type I collagen and the oim mutant allele leads to bone fragility.
Acute frataxin knockdown in induced pluripotent stem cell-derived cardiomyocytes activates a type I interferon response
Authors: Cotticelli M. Grazia , Xia Shujuan , Truitt Rachel , Doliba Nicolai M. , Rozo Andrea V. , Tobias John W. , Lee Taehee , Chen Justin , Napierala Jill S. , Napierala Marek , Yang Wenli , Wilson Robert B.
Published: September 2022

Friedreich ataxia, the most common hereditary ataxia, is a neuro- and cardio-degenerative disorder caused, in most cases, by decreased expression of the mitochondrial protein frataxin. Cardiomyopathy is the leading cause of premature death. Frataxin functions in the biogenesis of iron-sulfur clusters, which are prosthetic groups that are found in proteins involved in many biological processes. To study the changes associated with decreased frataxin in human cardiomyocytes, we developed a novel isogenic model by acutely knocking down frataxin, post-differentiation, in cardiomyocytes derived from induced pluripotent stem cells (iPSCs). Transcriptome analysis of four biological replicates identified severe mitochondrial dysfunction and a type I interferon response as the pathways most affected by frataxin knockdown. We confirmed that, in iPSC-derived cardiomyocytes, loss of frataxin leads to mitochondrial dysfunction. The type I interferon response was activated in multiple cell types following acute frataxin knockdown and was caused, at least in part, by release of mitochondrial DNA into the cytosol, activating the cGAS-STING sensor pathway.
Association of Accelerometer-Measured Physical Activity and Sedentary Time with Epigenetic Markers of Aging
Authors: Spartano Nicole L. , Wang Ruiqi , Yang Qiong , Chernofsky Ariel , Murabito Joanne M. , Vasan Ramachandran S. , Levy Daniel , Beiser Alexa S. , Seshadri Sudha
Published: September 2022

Introduction/Purpose

Physical activity may influence chronic disease risk, in part, through epigenetic mechanisms. Previous studies have demonstrated that an acute bout of physical activity can influence DNA methylation status. Few studies have explored the relationship between habitual, accelerometer-measured physical activity or sedentary time with epigenetic markers of aging.

Methods

We used linear regression to examine cross-sectional associations of accelerometer-measured physical activity and sedentary time with extrinsic and intrinsic epigenetic age acceleration (EEAA and IEAA) models and GrimAge measured from blood samples from Framingham Heart Study participants with accelerometry and DNA methylation data (n = 2435; mean age, 54.9 ± 14.3; 46.0% men). Residuals of Hannum-, Horvath-, and GrimAge-predicted epigenetic age were calculated by regressing epigenetic age on chronological age. We took into account blood cell composition for EEAA, IEAA, and AdjGrimAge. Moderate to vigorous physical activity was log-transformed to normalize its distribution. Adjustment models accounted for family structure, age, sex, smoking status, cohort–laboratory indicator, and accelerometer wear time. We additionally explored adjustment for body mass index (BMI).

Results

Walking 1500 more steps per day or spending 3 fewer hours sedentary was associated with >10 months lower GrimAge biological age (or ~1 month lower AdjGrimAge, after adjusting for blood cells, P < 0.05). Every 5 min·d−1 more moderate to vigorous physical activity was associated with 19–79 d of lower GrimAge (4–23 d lower using EEAA or AdjGrimAge, P < 0.01). Adjusting for BMI attenuated these results, but all statistically significant associations with AdjGrimAge remained.

Conclusions

Greater habitual physical activity and lower sedentary time were associated with lower epigenetic age, which was partially explained by BMI. Further research should explore whether changes in physical activity influence methylation status and whether those modifications influence chronic disease risk.
Factor Analysis of Air Pollutants over Hyderabad - A Case Study
Authors: Vasudha Nannaparaju , Rao Polisetty Venkateswara
Published: September 2022

Pollution levels in Metros of India are raising to alarm levels in last decades. This issue needs to be addressed immediately because it is hazardous to people's health. The present work is focused to highlight the major air pollutants in various areas of Hyderabad using publicly available data at Kaggle.com. By consolidating more air pollutants into fewer factors, this study's key objective is to reduce the complexity of air pollution. This helps to understand the interdependency of air pollutants. Ten air pollution-causing components of five different locations including residential and industrial areas in Hyderabad were identified and analyzed using Factor Analysis. There was an attempt made to find out the contribution of various air pollutant components to air pollution using standard Karl Pearson's coefficient of correlation and factor analysis using the Varimax method. The results of the analysis showed similar air pollutant components resulting in factors depending on the nature of the location. Residential cum industrial areas, ICRISAT and ZOO park had PM2.5, PM10, NOx, CO grouped into Factor 1 as major contribution to AQI, VOCs were the second major contributors followed by NH3, SO2, O3. However, in the residential area HCU ten air pollutants resulted into only two factors; first factor being CO, SO2, O3 and VOCs as contributors generated due to residential communities and PM2.5, PM10, NOx, NH3 as factor two. Bollaram has PM2.5, PM10, CO, O3 as factor one as major pollution is contributed due to traffic and industries and Pashamylaram has NOx, SO2 and VOCs as factor one due to the presence of pharmaceutical industries in the vicinity.
Adapting Bruner’s 3-Tier Theory to Improve Teacher Trainees’ Conceptual Knowledge for Teaching Integers at the Basic School
Authors: Aduko Edmund Anamboi , Armah Robert Benjamin
Published: September 2022

The focus of this action research was to adapt Bruner’s 3-tier theory to enhance conceptual knowledge of teacher trainees on integer operations. It looks into how learners' conceptual knowledge of integer operations changes over time, as well as their attitudes toward using the 3-tier model. Eighty-two (82) teacher trainees, who were in their first year semester one of the 2020/2021 academic year were purposely selected for the study. Data was collected using test and semi-structured interviews. The study found that using Bruner’s 3-tier theory contributed to substantial gains in conceptual knowledge on integers operations among learners.  It was also found that learners proffered positive compliments about the Concrete-Iconic-Symbolic (C-I-S) construct of lesson presentation and how it built their understanding to apply knowledge on integers operations. Learners also largely proffered positive image about C-I-S construct as it aroused interest and activated unmotivated learners. On these bases, the study concludes that lessons presentations should mirror C-I-S construct in order to alleviate learning difficulties encountered on integer operations. To do this, the study suggests that workshops on lesson presentation using C-I-S construct be organized for both subject tutors, mentors and lead mentors to re-equip their knowledge and to buy-in the idea among others.
Implementing large-scale data quality validation in a national arthroplasty registry to improve compliance
Authors: Boulton Christopher , Harrison Carol , Wilton Timothy , Armstrong Richard , Young Elaine , Pegg Derek , Wilkinson J. Mark
Published: September 2022

Data of high quality are critical for the meaningful interpretation of registry information. The National Joint Registry (NJR) was established in 2002 as the result of an unexpectedly high failure rate of a cemented total hip arthroplasty. The NJR began data collection in 2003. In this study we report on the outcomes following the establishment of a formal data quality (DQ) audit process within the NJR, within which each patient episode entry is validated against the hospital unit’s Patient Administration System and vice-versa. This process enables bidirectional validation of every NJR entry and retrospective correction of any errors in the dataset. In 2014/15 baseline average compliance was 92.6% and this increased year-on-year with repeated audit cycles to 96.0% in 2018/19, with 76.4% of units achieving > 95% compliance. Following the closure of the audit cycle, an overall compliance rate of 97.9% was achieved for the 2018/19 period. An automated system was initiated in 2018 to reduce administrative burden and to integrate the DQ process into standard workflows. Our processes and quality improvement results demonstrate that DQ may be implemented successfully at national level, while minimizing the burden on hospitals.

Cite this article: Bone Jt Open 2022;3(9):716–725.
Changes in orbital angular momentum distribution of a twisted partially coherent array beam in anisotropic turbulence
Authors: Wang Jing , Zhang Yakai , Guo Yinlong , Qian Xianmei , Zhu Wenyue , Li Jinhong
Published: September 2022

Based on the generalized Huygens Fresnel integral, we derive the analytical formula of the cross-spectral density of a twisted partially coherent array beam propagating in non-Kolmogorov anisotropic turbulence, and investigate the changes in orbital angular momentum (OAM). The results show that the anisotropy of the turbulence causes different effects in horizontal and vertical directions. The spectral density distribution of twisted partially coherent array beam in turbulence presents self-splitting and rotation, which combines the interesting effects of the twist phase and coherent structure. Although OAM is conserved, the spatial distribution of OAM flux density can be changed by changing the propagation distance, power and anisotropy of turbulence, and the modulation of the twist phase affects not only the magnitude of OAM but also its distribution. Our work is helpful for exploring new forms of OAM sources, and promote the application of free-space optical communications and optical field modulation.
Improving the data reliability of phase modulated holographic storage using a reliable bit aware low-density parity-check code
Authors: Zhao Yahui , Wu Fei , Lin Xiao , Zhou Jian , Zhang Meng , Yu Qin , Tan Xiaodi , Xie Changsheng
Published: September 2022

Phase modulated holographic storage offers superior storage capacity and a longer life span compared with other storage technologies. However, its application is limited by its high raw bit error rate. We aimed to introduce low-density parity-check (LDPC) codes for data protection in phase modulated holographic storage systems. However, traditional LDPC codes can not fully exploit data error characteristics, causing inaccurate initial log-likelihood ratio (LLR) information, which degrades decoding performance, thus limiting the improvement degree of data reliability in phase modulated holographic storage. Therefore, we propose a reliable bit aware LDPC optimization method (RaLDPC) that analyzes and employs phase demodulation characteristics to obtain reliable bits. More accurate initial LLR weights are assigned to these reliable bits. Hence, the optimized initial LLR can reflect the reliability of the demodulated data more accurately. Experimental results show that RaLDPC can reduce the bit error rate by an average of 38.89% compared with the traditional LDPC code, improving the data reliability of phase modulated holographic storage.
Bendable long graded index lens microendoscopy
Authors: Liu Guigen , Kang Jeon Woong , Bhagavatula Sharath , Ahn Sebastian W. , So Peter T. C. , Tearney Guillermo J. , Jonas Oliver
Published: September 2022

Graded index (GRIN) lens endoscopy has broadly benefited biomedical microscopic imaging by enabling accessibility to sites not reachable by traditional benchtop microscopes. It is a long-held notion that GRIN lenses can only be used as rigid probes, which may limit their potential for certain applications. Here, we describe bendable and long-range GRIN microimaging probes for a variety of potential micro-endoscopic biomedical applications. Using a two-photon fluorescence imaging system, we have experimentally demonstrated the feasibility of three-dimensional imaging through a 500-µm-diameter and ∼11 cm long GRIN lens subject to a cantilever beam-like deflection with a minimum bend radius of ∼25 cm. Bend-induced perturbation to the field of view and resolution has also been investigated quantitatively. Our development alters the conventional notion of GRIN lenses and enables a range of innovative applications. For example, the demonstrated flexibility is highly desirable for implementation into current and emerging minimally invasive clinical procedures, including a pioneering microdevice for high-throughput cancer drug selection.
Self-powered, ultraviolet-to-near infrared broadband photodetector based on Ag-doped CsPbI3/PEDOT:PSS heterojunction
Authors: Weng Jiexin , Xu Meng , Wang Xinyue , Wang Fuhe , Shen Jingling , Zhang Bo
Published: September 2022

Metal halide perovskites are studied for photodetection applications because of their outstanding optical and electrical properties. A self-powered ultraviolet-to-near infrared broadband photodetector based on a Ag-doped CsPbI3/PEDOT:PSS heterojunction was investigated. The photodetector using a CsPbI3:Ag/PEDOT:PSS heterostructure with a planar photoconductive structure operated over a broad 355–1560 nm wavelength range in self-powered mode. A terahertz signal was modulated with the CsPbI3:Ag/PEDOT:PSS structure at low optical excitation intensity to investigate its photodetection mechanism. The experimentally designed detector can present images of the letters “C”, “N” and “U” in the visible and near-infrared wavelengths, indicating a potential broadband imaging application.
High-performance quantum cascade lasers at λ ∼ 9 µm grown by MOCVD
Authors: Sun Yongqiang , Yin Ran , Zhang Jinchuan , Liu Junqi , Fei Teng , Li Kun , Guo Kai , Jia Zhiwei , Liu Shuman , Lu Quanyong , Zhuo Ning , Wang Lijun , Liu Fengqi , Zhai Shenqiang
Published: September 2022

We demonstrate a high power InP-based quantum cascade laser (QCL) (λ ∼ 9 µm) with high characteristic temperature grown by metalorganic chemical vapor deposition (MOCVD) in this article. A 4-mm-long cavity length, 10.5-µm-wide ridge QCL with high-reflection (HR) coating demonstrates a maximum pulsed peak power of 1.55 W and continuous-wave (CW) output power of 1.02W at 293 K. The pulsed threshold current density of the device is as low as 1.52 kA/cm2. The active region adopted a dual-upper-state (DAU) and multiple-lower-state (MS) design and it shows a wide electroluminescence (EL) spectrum with 466 cm−1 wide full-width at half maximum (FWHM). In addition, the device performance is insensitive to the temperature change since the threshold-current characteristic temperature coefficient, T0, is as high as 228 K, and slope-efficiency characteristic temperature coefficient, T1, is as high as 680 K, over the heatsink-temperature range of 293 K to 353 K.
Reducing phase noise coupled by wavefront errors in optical telescopes for the space measurement of gravitational waves
Authors: Chen Shengnan , Wang Chunyan , Jiang Huilin , Sun Hao , Tao ZongHui
Published: September 2022

Space-based gravitational-wave observatories (SGOs) promise to measure pico-meter variations in gigameter separations of a triangular constellation. Telescopes play an essential role in transmitting and receiving laser beams measuring the constellation arms with the heterodyne laser interferometry. The wavefront aberrations of the telescopes are coupled with the unavoidable misalignments caused by jitters and pointing tilts and induce additional phase changes into the heterodyne signal. As a critical aspect of achieving the measuring stability of

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, we analytically investigate the above process and determine that by properly controlling the relevant key aberrations in the design of the telescopes, the phase noise can be reduced exponentially, which makes the heterodyne signal insensitive to jitter and reduces the demand for wavefront quality. This method is validated whether the LISA Pathfinder (LPF) signal definition or the Average Phase (AP) signal definition is adopted, underpinning the guidance for the design and manufacturing of the optical telescope in SGOs.
Extrapolating distortion correction with local measurements for space-based multi-module splicing large-format infrared cameras
Authors: Jiang Linyi , Li Liyuan , Li Xiaoyan , Jiao Jingjie , Chen Fansheng
Published: September 2022

Conventional distortion correction methods with the classical models, including radial, decentering, and thin prism distortions and with the interpolation template, depend heavily on the evenly distributed measurement data on the entire focal plane. However, owing to the restricted cubage of the vacuum tank and the large size of the assembled camera, there is no more extra space for the amounted large-format camera to adjust with the 2D turntable during laboratory vacuum experiment, which, accordingly, makes the collected measurement points gathered in just one module of the focal plane and eventually results in poor correction accuracy of the mentioned approaches. Here, in terms of the problems above, an extrapolating distortion correction method with local measurements for space-based multi-module splicing large-format infrared cameras was proposed in this paper. Benefiting from the polynomial model not being affected by the distribution of data, a third-order polynomial model adopted for distortion correction is solved by using local measurements and extrapolated reasonably, which guarantees the global camera calibration. Experimental results show that the mean distortion error can be corrected within 0.5 pixels. This method overcoming the deficiency of local test points can effectively improve the correction accuracy of the large-format camera and provide a new idea for global high-precision calibration of on-orbit payloads based on local measurements.
Tilt-angle stimulated Raman projection tomography
Authors: Lin Peng , Li Chuan , Flores-Valle Andres , Wang Zian , Zhang Meng , Cheng Ran , Cheng Ji-Xin
Published: September 2022

Stimulated Raman projection tomography is a label-free volumetric chemical imaging technology allowing three-dimensional (3D) reconstruction of chemical distribution in a biological sample from the angle-dependent stimulated Raman scattering projection images. However, the projection image acquisition process requires rotating the sample contained in a capillary glass held by a complicated sample rotation stage, limiting the volumetric imaging speed, and inhibiting the study of living samples. Here, we report a tilt-angle stimulated Raman projection tomography (TSPRT) system which acquires angle-dependent projection images by utilizing tilt-angle beams to image the sample from different azimuth angles sequentially. The TSRPT system, which is free of sample rotation, enables rapid scanning of different views by a tailor-designed four-galvo-mirror scanning system. We present the design of the optical system, the theory, and calibration procedure for chemical tomographic reconstruction. 3D vibrational images of polystyrene beads and C. elegans are demonstrated in the C-H vibrational region.
Robust contrast enhancement method using a retinex model with adaptive brightness for detection applications
Authors: Khan Rizwan , Mehmood Atif , Zheng Zhonglong
Published: September 2022

Low light image enhancement with adaptive brightness, color and contrast preservation in degraded visual conditions (e.g., extreme dark background, lowlight, back-light, mist. etc.) is becoming more challenging for machine cognition applications than anticipated. A realistic image enhancement framework should preserve brightness and contrast in robust scenarios. The extant direct enhancement methods amplify objectionable structure and texture artifacts, whereas network-based enhancement approaches are based on paired or large-scale training datasets, raising fundamental concerns about their real-world applicability. This paper presents a new framework to get deep into darkness in degraded visual conditions following the fundamental of retinex-based image decomposition. We separate the reflection and illumination components to perform independent weighted enhancement operations on each component to preserve the visual details with a balance of brightness and contrast. A comprehensive weighting strategy is proposed to constrain image decomposition while disrupting the irregularities of high frequency reflection and illumination to improve the contrast. At the same time, we propose to guide the illumination component with a high-frequency component for structure and texture preservation in degraded visual conditions. Unlike existing approaches, the proposed method works regardless of the training data type (i.e., low light, normal light, or normal and low light pairs). A deep into darkness network (D2D-Net) is proposed to maintain the visual balance of smoothness without compromising the image quality. We conduct extensive experiments to demonstrate the superiority of the proposed enhancement. We test the performance of our method for object detection tasks in extremely dark scenarios. Experimental results demonstrate that our method maintains the balance of visual smoothness, making it more viable for future interactive visual applications.
Data augmentation using a generative adversarial network for a high-precision instantaneous microwave frequency measurement system
Authors: Jabin Md Asaduzzaman , Fok Mable P.
Published: September 2022

In this Letter, an unsupervised-learning platform—generative adversarial network (GAN)—is proposed for experimental data augmentation in a deep-learning assisted photonic-based instantaneous microwave frequency measurement (IFM) system. Only 75 sets of experimental data are required and the GAN can augment the small amount of data into 5000 sets of data for training the deep learning model. Furthermore, frequency measurement error of the estimated frequency has improved by an order of magnitude from 50 MHz to 5 MHz. The proposed use of GAN effectively reduces the amount of experimental data needed by 98.75% and reduces measurement error by 10 times.
Femtosecond filamentation of optical vortices for the generation of optical air waveguides
Authors: Fu Silin , Mahieu Benoit , Mysyrowicz André , Houard Aurelien
Published: September 2022

We study the filamentation in air of multi-millijoule optical vortices and compare them with the classical filamentation regime. The femtosecond vortex beam generates multiple plasma filaments organized in a cylindrical geometry. This plasma configuration evolves into a meter-scale tubular neutral gas column that can be used as a waveguide for nanosecond laser pulses at 532 nm. It appears that optical vortices produce a more uniform heating along the propagation axis, when compared with Gaussian or super-Gaussian beams, and that the resulting low-density channel is poorly sensitive to the laser input power thanks to the combination of filamentation intensity clamping and phase vorticity.
Higher-order nodal ring photonic semimetal
Authors: Zhang Yuexin , Tang Jie , Dai Xiaoyu , Zhang Sheng , Xiang Yuanjiang
Published: September 2022

The intriguing discovery of higher-order topology has tremendously promoted the development of topological physics. Three-dimensional topological semimetals have emerged as an ideal platform for investigating novel topological phases. Consequently, new proposals have been theoretically revealed and experimentally realized. However, most existing schemes are implemented on the acoustic system, while similar concepts are rarely launched in photonic crystals due to the complicated optical manipulation and geometrical design. In this Letter, we propose a higher-order nodal ring semimetal protected by C2 symmetry originating from C6 symmetry. The higher-order nodal ring is predicted in three-dimensional momentum space with desired hinge arcs connected by two nodal rings. Fermi arcs and topological hinge modes generate significant marks in higher-order topological semimetals. Our work successfully proves the presence of a novel higher-order topological phase in photonic systems that we will strive to apply practically in high-performance photonic devices.
Inverse design paradigm for fast and accurate prediction of a functional metasurface via deep convolutional neural networks
Authors: Du Xudong , Zhou Chengan , Bai Hongbai , Liu Xingxing
Published: September 2022

Data-driven deep learning frameworks have significantly advanced the development of modern machine learning, and after achieving great success in the field of image, speech, and video recognition and processing, they have also begun to permeate other disciplines such as physics, chemistry, and the discovery of new drugs and new materials. Our work proposes a deep learning-based model consisting of two parts: a forward simulation network that contains a transposed convolutional network, up and down sampling blocks and dense layers can rapidly predict optical responses from metasurface structures, and an inverse design network that contains convolutional neural networks and dense layers can automatically construct metasurface based on the input optical responses. Our model assists in discovering the complex and non-intuitive relationship between the moth-eye metasurface and optical responses, and designs a metasurface with excellent optical properties (ultra-broadband anti-reflection or nonlinear function of reflectivity), while avoiding traditional time-consuming case-by-case numerical simulations in the metasurface design. This work provides a fast, practical, and robust method to study complex light-matter interactions and to accelerate the demand-based design of nanophotonic devices, opening a new avenue for the development of real nanophotonic applications.
Edge coupling for hybrid mono-crystalline silicon and lithium niobate thin films
Authors: Li Qingyun , Zhang Honghu , Zhu Houbin , Chen Zhihua , Hu Hui
Published: September 2022

The hybridization of mono-crystalline silicon and lithium niobate thin films (Si-LNOI) combines the excellent electrical properties and mature micro-nano processing technology of Si, as well as the remarkable optical properties of LN. The Si-LNOI platform will drive new and promising integrated photonics devices. High-efficiency fiber-waveguide optical coupling is necessary to realize the full potential of devices and practical applications. In this study, a spot-size converter (SSC) was designed and demonstrated for efficient edge coupling between a Si-LNOI waveguide and lens fiber. The SSC was fabricated by standard semiconductor process, which consisted of an inverted-tapered Si and a silicon-rich nitride (SRN) waveguide overlying the inverted-tapered Si. At a wavelength of 1550 nm, the TE and TM light achieved coupling losses of 1.9 and 2.1 dB/facet, respectively. The coupling efficiency was stable in the wavelength range of 1500–1600 nm. The tolerance of alignment was also evaluated.
A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research
Authors: Figueiredo Ludmilla , Scherer Cédric , Cabral Juliano Sarmento
Published: September 2022

The ubiquitous use of computational work for data generation, processing, and modeling increased the importance of digital documentation in improving research quality and impact. Computational notebooks are files that contain descriptive text, as well as code and its outputs, in a single, dynamic, and visually appealing file that is easier to understand by nonspecialists. Traditionally used by data scientists when producing reports and informing decision-making, the use of this tool in research publication is not common, despite its potential to increase research impact and quality. For a single study, the content of such documentation partially overlaps with that of classical lab notebooks and that of the scientific manuscript reporting the study. Therefore, to minimize the amount of work required to manage all the files related to these contents and optimize their production, we present a starter kit to facilitate the implementation of computational notebooks in the research process, including publication. The kit contains the template of a computational notebook integrated into a research project that employs R, Python, or Julia. Using examples of ecological studies, we show how computational notebooks also foster the implementation of principles of Open Science, such as reproducibility and traceability. The kit is designed for beginners, but at the end we present practices that can be gradually implemented to develop a fully digital research workflow. Our hope is that such minimalist yet effective starter kit will encourage researchers to adopt this practice in their workflow, regardless of their computational background.
Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization
Authors: Kelley Michael A. , Leiderman Karin
Published: September 2022

Thrombin is an enzyme produced during blood coagulation that is crucial to the formation of a stable clot. Thrombin cleaves soluble fibrinogen into fibrin, which polymerizes and forms an insoluble, stabilizing gel around the growing clot. A small fraction of circulating fibrinogen is the variant γA/γ′, which has been associated with high-affinity thrombin binding and implicated as a risk factor for myocardial infarctions, deep vein thrombosis, and coronary artery disease. Thrombin is also known to be strongly sequestered by polymerized fibrin for extended periods of time in a way that is partially regulated by γA/γ′. However, the role of γA/γ′-thrombin interactions during fibrin polymerization is not fully understood. Here, we present a mathematical model of fibrin polymerization that considered the interactions between thrombin, fibrinogen, and fibrin, including those with γA/γ′. In our model, bivalent thrombin-fibrin binding greatly increased thrombin residency times and allowed for thrombin-trapping during fibrin polymerization. Results from the model showed that early in fibrin polymerization, γ′ binding to thrombin served to localize the thrombin to the fibrin(ogen), which effectively enhanced the enzymatic conversion of fibrinogen to fibrin. When all the fibrin was fully generated, however, the fibrin-thrombin binding persisted but the effect of fibrin on thrombin switched quickly to serve as a sink, essentially removing all free thrombin from the system. This dual role for γ′-thrombin binding during polymerization led to a paradoxical decrease in trapped thrombin as the amount of γ′ was increased. The model highlighted biochemical and biophysical roles for fibrin-thrombin interactions during polymerization and agreed well with experimental observations.
Information and communication technology-based health interventions for transgender people: A scoping review
Authors: Wong Horas T. H. , Prankumar Sujith Kumar , Cui Jialiang , Tumwine Christopher , Addo Isaac Yeboah , Kan Wansang , Noor Muhammad Naveed
Published: September 2022

In the recent past, there has been a strong interest in the use of information and communication technology (ICT) to deliver healthcare to ‘hard-to-reach’ populations. This scoping review aims to explore the types of ICT-based health interventions for transgender people, and the concerns on using these interventions and ways to address these concerns. Guided by the scoping review frameworks offered by Arksey & O’Malley and the PRISMA-ScR checklist, literature search was conducted in May 2021 and January 2022 in three databases (PubMed, CINAHL and Scopus). The two searches yielded a total of 889 non-duplicated articles, with 47 of them meeting the inclusion criteria. The 47 articles described 39 unique health projects/programs, covering 8 types of ICT-based interventions: videoconferencing, smartphone applications, messaging, e-coaching, self-learning platforms, telephone, social media, and e-consultation platforms. Over 80% of the health projects identified were conducted in North America, and 62% focused on HIV/sexual health. The findings of this review suggest that transgender people had often been regarded as a small subsample in ICT-based health projects that target other population groups (such as ‘men who have sex with men’ or ‘sexual minority’). Many projects did not indicate whether transgender people were included in the development or evaluation of the project. Relatively little is known about the implementation of ICT-based trans health interventions outside the context of HIV/sexual health, in resource limiting settings, and among transgender people of Asian, Indigenous or other non-White/Black/Hispanic backgrounds. While the range of interventions identified demonstrate the huge potentials of ICT to improve healthcare access for transgender people, the current body of literature is still far from adequate for making comprehensive recommendations on the best practice of ICT-based interventions for transgender people. Future ICT-based interventions need to be more inclusive and specified, in order to ensure the interventions are safe, accessible and effective for transgender people.
Two snakebite antivenoms have potential to reduce Eswatini’s dependency upon a single, increasingly unavailable product: Results of preclinical efficacy testing
Authors: Menzies Stefanie K. , Litschka-Koen Thea , Edge Rebecca J. , Alsolaiss Jaffer , Crittenden Edouard , Hall Steven R. , Westhorpe Adam , Thomas Brent , Murray James , Shongwe Nondusimo , Padidar Sara , Lalloo David G. , Casewell Nicholas R. , Pons Jonathan , Harrison Robert A.
Published: September 2022

Background

Snakebite is a major public health concern in Eswatini, where treatment relies upon one antivenom—SAIMR Polyvalent. Although effective in treating snakebite, SAIMR Polyvalent is difficult to source outside its manufacturing country (South Africa) and is dauntingly expensive. We compared the preclinical venom-neutralising efficacy of two alternative antivenoms with that of SAIMR Polyvalent against the lethal and tissue-destructive effects of venoms from five species of medically important snakes using in vivo murine assays. The test antivenoms were ‘Panafrican’ manufactured by Instituto Clodomiro Picado and ‘PANAF’ manufactured by Premium Serums & Vaccines.

Principal findings

In vivo murine preclinical studies identified both test antivenoms were equally or more effective than SAIMR Polyvalent at neutralising lethal and tissue-destructive effects of Naja mossambica venom. Both test antivenoms were less effective than SAIMR Polyvalent at neutralising the lethal effects of Bitis arietans, Dendroaspis polylepis, Hemachatus haemachatus and Naja annulifera venoms, but similarly effective at neutralising tissue damage induced by B. arietans and H. haemachatus venoms.

In vitro immunological assays identified that the titres and toxin-specificities of immunoglobulins (iGs) in the test antivenoms were comparable to that of SAIMR Polyvalent. Plasma clotting disturbances by H. haemachatus and N. mossambica were neutralised by the test antivenoms, whereas SAIMR Polyvalent failed to neutralise this bioactivity of N. mossambica venom. B. arietans SVMP activity was equally reduced by all three antivenoms, and H. haemachatus and N. mossambica PLA2 activities were neutralised by all three antivenoms.

Conclusions

While both Panafrican and PANAF antivenoms exhibited promising preclinical efficacies, both were less poly-specifically effective than SAIMR Polyvalent in these murine assays. The efficacy of these antivenoms against the lethal and tissue-destructive effects of N. mossambica venom, the most common biting species in Eswatini, identify that Panafrican and PANAF antivenoms offer effective alternatives to SAIMR Polyvalent for the treatment of snakebite in Eswatini, and potentially for neighbouring countries.
T-cell receptor variable region usage in Chagas disease: A systematic review of experimental and human studies
Authors: de Souza-Silva Thaiany Goulart , Gollob Kenneth J. , Dutra Walderez O.
Published: September 2022

T cells recognize their ligand, the peptide major histocompatibility complex (MHC), via the T-cell receptor (TCR), which is composed of covalently linked α and β or γ and δ chains. This recognition is critical for T-cell ontogeny and controls the selection, activation, and function of T lymphocytes. Specific TCR αβ variable regions have been associated with immunopathogenesis of Chagas disease. Here, we present a systematic review that compiles experimental in vivo and human data regarding the preferential expression of variable alpha (Vα) and variable beta (Vβ) chain regions inTrypanosoma cruziinfection. The original studies indexed in PubMed/Medline, Scopus, and Web of Science databases were screened according to the PRISMA strategy. The analysis showed that expression of TCR Vα subfamilies were evaluated in one human study, and, unlike TCR Vβ, TCR Vα presented a more restricted usage. Despite the great variability in the usage of TCR Vβ regions in human Chagas disease, a down-regulation of TCR Vβ5 expression by T cells from patients in the acute phase of the disease was shown. Opposingly, this TCR region was found overly expressed in CD4+ T cells from chronic Chagas patients. It was also demonstrated that murine Vβ9+ T cells derived from nonlymphoid organs ofT.cruzi-infected animals had a modulatory profile, while splenic Vβ9+ T cells produced inflammatory cytokines, indicating that although they display the same TCR Vβ region usage, these cells are functionally distinct. Despite the limitations of few papers and year of publication of the studies, compiling the data derived from them reveals that further investigation of TCR usage will point to their potential role in protective or pathogenic responses, as biomarkers of disease progression, and in the search for dominant peptides potentially useful for the development of vaccines or therapies.
A community-developed extension to Darwin Core for reporting the chronometric age of specimens
Authors: Brenskelle Laura , Wieczorek John , Davis Edward , Wallis Neill J. , Emery Kitty , LeFebvre Michelle J. , Guralnick Rob
Published: September 2022

Darwin Core, the data standard used for sharing modern biodiversity and paleodiversity occurrence records, has previously lacked proper mechanisms for reporting what is known about the estimated age range of specimens from deep time. This has led to data providers putting these data in fields where they cannot easily be found by users, which impedes the reuse and improvement of these data by other researchers. Here we describe the development of the Chronometric Age Extension to Darwin Core, a ratified, community-developed extension that enables the reporting of ages of specimens from deeper time and the evidence supporting these estimates. The extension standardizes reporting about the methods or assays used to determine an age and other critical information like uncertainty. It gives data providers flexibility about the level of detail reported, focusing on the minimum information needed for reuse while still allowing for significant detail if providers have it. Providing a standardized format for reporting these data will make them easier to find and search and enable researchers to pinpoint specimens of interest for data improvement or accumulate more data for broad temporal studies. The Chronometric Age Extension was also the first community-managed vocabulary to undergo the new Biodiversity Informatics Standards (TDWG) review and ratification process, thus providing a blueprint for future Darwin Core extension development.
Patient perceptions by race of educational animations about living kidney donation made for a diverse population
Authors: Keller Maria M. , Lucas Todd , Cadzow Renee , Feeley Thomas , Tumiel Berhalter Laurene , Kayler Liise
Published: September 2022

Introduction

This qualitative study sought to identify potential design and delivery alterations to inform cultural adaptation of educational animations about living donor kidney transplantation (LDKT)–previously developed for a diverse population–to better fit Black Americans’ needs.

Methods

We conducted a secondary analysis of 88 transcripts derived from interviews and focus groups conducted with diverse target users (62 kidney failure patients, 36 prior/potential donors, and 11 care partners) to develop 12 animations about LDKT, named KidneyTIME. Statements were abstracted and coded pertaining to cognitive and communication barriers to LDKT, and the perceived value of using the videos to learn and share the information with social network members using content analysis. Incidence counts of each content code were also calculated to assess differences between Black and non-Black patients.

Results

Cognitive barrier codes included lack of knowledge, ambivalence, and concern for donor. Communication barrier codes included reluctance and difficulty talking about LDKT. Cognitive facilitating codes included attention-getting, efficient learning, manageable content, emotional impact, and new knowledge. Communication facilitating codes included delivery through many dissemination channels and broadly shareable. Compared to non-black patients (n = 33) Black patients (n = 29) more often stated concern for donor and reluctance/difficulty talking about LDKT as barriers, and less often stated efficient learning and manageable content as facilitators.

Conclusion

Findings highlight the value of LDKT informational content that is visually appealing, digestible, non-threatening, and highly shareable. Heterogeneity may exist when considering access and intervention preferences in using KidneyTIME videos and highlight a potential for further cultural targeting or tailoring.
Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods
Authors: Xue Zhengyao , Marco Maria L.
Published: September 2022

Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine bulk milk, we assembled and tested a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. The following protocol variations were examined:: BCMC enumeration (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 104 cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. Cell lysis procedures conferred the greatest changes to milk microbiota composition and these effects were confirmed to provide similar results for commercial milk samples. Overall, our systematic approach with the BCMC is broadly applicable to other milk, food, and environmental samples therefore recommended for improving accuracy of culture-independent, DNA sequence-based analyses of microbial composition in different habitats.
The effectiveness of weighted least squares means and variance adjusted based fit indices in assessing local dependence of the rasch model: Comparison with principal component analysis of residuals
Authors: Han HyunSuk
Published: September 2022

Local independence is a principal assumption of applying latent variable models. Violations of this assumption might be stemmed from dimensionality (trait dependence) and statistical independence of item responses (response dependence). The purpose of this study is to evaluate the sensitivity of weighted least squares means and variance adjusted (WLSMV) based global fit indices to violations of local independence in Rasch models, and compare those indices to principal component analysis of residuals (PCAR) that is widely used for Rasch models. Dichotomous Rasch model is considered in this simulation study. The results show that WLSMV-based fit indices could detect trait dependence, but are to be limited with regard to response dependence. Additionally, WLSMV-based fit indices have advantages over the use of PCAR since WLSMV-based global fit indices are consistent regardless of sample size and test length. Though it is not recommended to apply exact benchmarks for those indices, they would provide practitioners with a method for evaluating the degree to which assumption violation is problematic for their data diagnostic purpose.