bluuebunny/crossref_metadata_2025 huggingface dataset:
Polarization evolution in Brillouin scattering with a partially polarized pump
Authors: Zhou Junhe , Liu Tengyuan , Wang Yunheng
Published: April 2024

Polarization sensitivity has been a major issue in Brillouin scattering-based optical fiber sensing systems. Randomization of the polarization state of the pump is one of the ways to circumvent the problem. However, there could exist a residual degree of polarization (DOP) for the pump after polarization randomization, and hence, a model to characterize the polarization evolution in Brillouin scattering with a partially polarized pump is essential for the performance evaluation. In this work, a comprehensive theoretical model to characterize the beam variation with the partially polarized pump wave and Stokes wave is proposed, which is based on a set of stochastic differential equations (SDEs). The polarized part of the pump wave and the Stokes wave, as well as the total powers of the waves, are incorporated in the coupled SDE simultaneously, which enables the comprehensive simulation of the polarization evolution in the fiber. It is revealed in the study that the DOPs of the pump wave and the Stokes wave affect the gain stability and should be reduced simultaneously by polarization scrambling to ensure a fixed Brillouin gain without fluctuations.
Rapid in-situ calibration of computational micro-spectrometer with few-shot meta-learning
Authors: Yang Meichen , Chen Xiuteng , Wu Xiaowei , Hu Qingfeng , Chen Yinpeng , Yang Zongyin , Sheng Yusong , Chen Yang , Han Likun , Zhu Jiaqi , Pan Mingzhong , Liu Shijie , Qi Hongxing , Zhu He , Dai Ning
Published: April 2024

Computational micro-spectrometers comprised of detector arrays and encoding structure arrays, such as on-chip Fabry-Perot (FP) cavity filters, have great potential in many in-situ applications owing to their compact size and snapshot imaging ability. Given manufacturing deviation and environmental influence are inevitable, easy and effective calibration for spectrometer is necessary, especially for in-situ applications. Currently calibration strategies based on iterative algorithms or neural networks require accurate measurements of pixel-level (spectral) encoding functions through monochromator or large amounts of standard samples. These procedures are time-consuming and expensive, thereby impeding in-situ applications. Meta-learning algorithms with few-shot learning ability can address this challenge by incorporating the prior knowledge in the simulated dataset. In this work, we propose a meta-learning algorithm free of measuring encoding function or large amounts of standard samples to calibrate a micro-spectrometer with manufacturing deviation effectively. Our micro-spectrometer comprises 16 types of FP filters covering a wavelength range of 550-720 nm. The center wavelength of each filter type deviates from the design up to 6 nm. After calibration with 15 different color data, the average reconstruction error on the test dataset decreased from 7.2 × 10
−
3 to 1.2 × 10
−
3, and further decreased to 9.4 × 10
−
4 when the calibration data increased to 24. The performance is comparable to algorithms trained with measured encoding function both in reconstruction error and generalization ability. We estimated that the cost of in-situ calibration through reflectance measurements of color chart decreased to one percent of the cost through monochromator measurements. By exploiting prior deviation information in simulation data with meta-learning, the efficiency and cost of calibration are significantly improved, thereby facilitating the large-scale production and in-situ application of micro-spectrometers.
Sidelobe suppression for accelerating beams
Authors: Zhang Cilong , Zhao Yanbo , Tan Qiaofeng
Published: April 2024

Although the control of trajectory, amplitude and beam-width in accelerating beams have been extensively investigated, sidelobes manipulation of such beams, which is required in many applications, has been surprisingly under-researched. This paper presents an approach for the generating of accelerating beams with significantly reduced sidelobes. The proposed method encompasses a two-step angular spectrum design, including employing a general model to establish the phase distribution and applying a stochastic parallel gradient descent (SPGD) algorithm to optimize the binary amplitude modulation. Experimental results confirm that the sidelobe intensity of accelerating beams can be reduced by over 50% with our method, thereby enhancing their applicability in many fields, such as micro-machining, particle manipulation, and optical communication.
Time sequence variation of incoherent and coherent random laser based on positive replica of abalone shell
Authors: Li Jiawei , Li Juntao , Hu Shu , Cai Xianglong , Gai Baodong , Tan Yannan , Guo Jingwei
Published: April 2024

Besides the scattering structures, the energy transfer (ET) process in the gain medium plays a significant role in the competition between coherent (comprising strongly coherent components) and incoherent (consisting of weakly coherent or “hidden” coherent components) modes of random lasers. In this study, bichromatic emission random lasers were successfully created using polydimethylsiloxane (PDMS) replicas with grooved structures that imitate the inner surface of abalone shells as scattering substrates. The influence mechanism of the ET process from the monomer to dimer in the Rhodamine 640 dye on the competition of random laser modes was thoroughly investigated from both spectral and temporal dimensions. It was confirmed that the ET process can reduce the gain of monomers while amplifying the gain of dimers. By considering the dominant high-efficiency ET processes, an energy transfer factor associated with the pump energy density was determined. Notably, for the first time, it was validated that the statistical distribution characteristics of the time sequence variations in the coherent random laser generated by dimers closely resemble a normal distribution. This finding demonstrates the feasibility of producing high-quality random number sequences.
Full C- and L-band covered second-order OAM mode generator based on a thinned helical long-period fiber grating
Authors: Huang Xinyue , Lu Huali , Chen Yu , Wang Yutao , Kong Zheng , Hao Hui , Zhao Hua , Wang Peng , Wang Xin , Li Hongpu
Published: April 2024

A full C- and L-band covered second-order orbital-angular-momentum (OAM) mode generator has been proposed and experimentally demonstrated, which is realized by using a helical long-period fiber grating (HLPG) but inscribed in a thinned four-mode fiber. By optimizing the design of grating period and fiber diameter of the proposed HLPG, an ultra-broadband rejection filter with a depth of ∼23 dB, a bandwidth of ∼156 nm @-10 dB (ranging from 1522 nm to 1678 nm) and a bandwidth of ∼58 nm @-20 dB (ranging from 1574 nm to 1632 nm), has been successfully obtained as a typical sample. To the best of our knowledge, this is the first demonstration of such ultra-broadband second-order OAM mode generator by using only one fiber component, i.e., the thinned HLPG. In addition, the proposed generator is less polarization-dependent and less temperature-sensitive than those of the conventional HLPGs, which is believed to be considerably helpful to find potential applications of the device itself in wavelength division multiplexing (WDM) and OAM mode division multiplexing (MDM) optical fiber communication systems.
Spatial and mode selective switch for orbital angular momentum mode division multiplexing
Authors: Zhong Weihang , Lin Zhongzheng , Wu Lixun , Wu Zituo , Chen Hongjia , Chen Yujie , Yu Siyuan
Published: April 2024

In analogy to a wavelength selective switch in wavelength-division multiplexing (WDM) optical fiber communication systems, a spatial and optical mode selective switch (SMSS) would be an important component in future ultrahigh capacity optical fiber communication systems based on space and mode division multiplexing. In this work, a free-space SMSS for orbital angular momentum (OAM) mode-division multiplexing (MDM) is proposed and experimentally demonstrated. The SMSS consists of a separating part for transforming OAM modes to spatial modes and a recombining part for selecting and recombining the modes to any spatial channel. The SMSS is able to implement strictly non-blocking switching between a total of 36 SDM/MDM channels configured as four spatial channels each supporting nine OAM mode channels.
Demonstration of 4H-silicon carbide on an aluminum nitride integrated photonic platform
Authors: Wang Ruixuan , Li Jingwei , Cai Lutong , Li Qing
Published: April 2024

The existing silicon-carbide-on-insulator photonic platform utilizes a thin layer of silicon dioxide under silicon carbide (SiC) to provide optical confinement and mode isolation. Here, we replace the underneath silicon dioxide layer with 1-µm-thick aluminum nitride and demonstrate a 4H-silicon-carbide-on-aluminum-nitride integrated photonic platform for the first time to our knowledge. Efficient grating couplers, low-loss waveguides, and compact microring resonators with intrinsic quality factors up to 210,000 are fabricated. In addition, by undercutting the aluminum nitride layer, the intrinsic quality factor of the silicon carbide microring is improved by nearly one order of magnitude (1.8 million). Finally, an optical pump–probe method is developed to measure the thermal conductivity of the aluminum nitride layer, which is estimated to be over 30 times of that of silicon dioxide.
Snapshot spectral imaging based on aberration model-driven deep learning
Authors: Yue Qiuyu , Chen Bingliang , Liu Xinyu , Zheng Zhenrong
Published: April 2024

Coded aperture snapshot spectral imaging (CASSI) can capture hyperspectral images (HSIs) in one shot, but it suffers from optical aberrations that degrade the reconstruction quality. Existing deep learning methods for CASSI reconstruction lose some performance on real data due to aberrations. We propose a method to restore high-resolution HSIs from a low-resolution CASSI measurement. We first generate realistic training data that mimics the optical aberrations of CASSI using a spectral imaging simulation technique. A generative network is then trained on this data to recover HSIs from a blurred and distorted CASSI measurement. Our method adapts to the optical system degradation model and thus improves the reconstruction robustness. Experiments on both simulated and real data indicate that our method significantly enhances the image quality of reconstruction outcomes and can be applied to different CASSI systems.
Efficient operation of atomic frequency comb optical memory using an optical frequency comb in 167Er3+:Y2SiO5
Authors: Yasui Shoichiro , Inaba Tomohiro , Ishizawa Atsushi , Hitachi Kenichi , Omi Hiroo , Matsuura Kyuma , Kaji Reina , Tawara Takehiko , Adachi Satoru , Xu Xuejun , Sanada Haruki
Published: April 2024

We demonstrated a highly efficient optical memory operation using an atomic frequency comb (AFC) created from a spectrally flattened optical frequency comb with an isotopically pure 167Er3+:Y2SiO5 crystal under zero magnetic field. Compared with standard AFC creation methods such as pulse train method, our method, called comb transfer method, can create a broadband and high-efficiency AFC at lower power and with less effort. This technique can make a significant improvement in the quality of AFCs in crystals doped with low concentrations of rare-earth ions.
A host-directed oxadiazole compound potentiates antituberculosis treatment via zinc poisoning in human macrophages and in a mouse model of infection
Authors: Maure Alexandra , Lawarée Emeline , Fiorentino Francesco , Pawlik Alexandre , Gona Saideep , Giraud-Gatineau Alexandre , Eldridge Matthew J. G. , Danckaert Anne , Hardy David , Frigui Wafa , Keck Camille , Gutierrez Claude , Neyrolles Olivier , Aulner Nathalie , Mai Antonello , Hamon Mélanie , Barreiro Luis B. , Brodin Priscille , Brosch Roland , Rotili Dante , Tailleux Ludovic
Published: April 2024

Antituberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multiresistant strains of Mycobacterium tuberculosis (MTB) are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high-content imaging, we identified novel 1,2,4-oxadiazole-based compounds, which allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, MTB became even more sensitive to antituberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.
Bruno 1/CELF regulates splicing and cytoskeleton dynamics to ensure correct sarcomere assembly in Drosophila flight muscles
Authors: Nikonova Elena , DeCata Jenna , Canela Marc , Barz Christiane , Esser Alexandra , Bouterwek Jessica , Roy Akanksha , Gensler Heidemarie , Heß Martin , Straub Tobias , Forne Ignasi , Spletter Maria L.
Published: April 2024

Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA-binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as Myotonic Dystrophy Type I (DM1). Here, we report a conserved function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog inDrosophila, during early muscle myogenesis. Loss of Bru1 in flight muscles results in disorganization of the actin cytoskeleton leading to aberrant myofiber compaction and defects in pre-myofibril formation. Temporally restricted rescue and RNAi knockdown demonstrate that early cytoskeletal defects interfere with subsequent steps in sarcomere growth and maturation. Early defects are distinct from a later requirement forbru1to regulate sarcomere assembly dynamics during myofiber maturation. We identify an imbalance in growth in sarcomere length and width during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion, and the formation of hollow myofibrils inbru1mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression in flight muscle development that is blocked inbru1mutants. We further demonstrate that temporally restricted Bru1 rescue can partially alleviate hypercontraction in late pupal and adult stages, but it cannot restore myofiber function or correct structural deficits. Our results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement.
Developmental fine-tuning of medial superior olive neurons mitigates their predisposition to contralateral sound sources
Authors: Sierksma Martijn C. , Borst J. Gerard G.
Published: April 2024

Having two ears enables us to localize sound sources by exploiting interaural time differences (ITDs) in sound arrival. Principal neurons of the medial superior olive (MSO) are sensitive to ITD, and each MSO neuron responds optimally to a best ITD (bITD). In many cells, especially those tuned to low sound frequencies, these bITDs correspond to ITDs for which the contralateral ear leads, and are often larger than the ecologically relevant range, defined by the ratio of the interaural distance and the speed of sound. Using in vivo recordings in gerbils, we found that shortly after hearing onset the bITDs were even more contralaterally leading than found in adult gerbils, and travel latencies for contralateral sound-evoked activity clearly exceeded those for ipsilateral sounds. During the following weeks, both these latencies and their interaural difference decreased. A computational model indicated that spike timing-dependent plasticity can underlie this fine-tuning. Our results suggest that MSO neurons start out with a strong predisposition toward contralateral sounds due to their longer neural travel latencies, but that, especially in high-frequency neurons, this predisposition is subsequently mitigated by differential developmental fine-tuning of the travel latencies.
Bacillus subtilis uses the SigM signaling pathway to prioritize the use of its lipid carrier for cell wall synthesis
Authors: Roney Ian J. , Rudner David Z.
Published: April 2024

Peptidoglycan (PG) and most surface glycopolymers and their modifications are built in the cytoplasm on the lipid carrier undecaprenyl phosphate (UndP). These lipid-linked precursors are then flipped across the membrane and polymerized or directly transferred to surface polymers, lipids, or proteins. Despite its essential role in envelope biogenesis, UndP is maintained at low levels in the cytoplasmic membrane. The mechanisms by which bacteria distribute this limited resource among competing pathways is currently unknown. Here, we report that the Bacillus subtilis transcription factor SigM and its membrane-anchored anti-sigma factor respond to UndP levels and prioritize its use for the synthesis of the only essential surface polymer, the cell wall. Antibiotics that target virtually every step in PG synthesis activate SigM-directed gene expression, confounding identification of the signal and the logic of this stress-response pathway. Through systematic analyses, we discovered 2 distinct responses to these antibiotics. Drugs that trap UndP, UndP-linked intermediates, or precursors trigger SigM release from the membrane in <2 min, rapidly activating transcription. By contrasts, antibiotics that inhibited cell wall synthesis without directly affecting UndP induce SigM more slowly. We show that activation in the latter case can be explained by the accumulation of UndP-linked wall teichoic acid precursors that cannot be transferred to the PG due to the block in its synthesis. Furthermore, we report that reduction in UndP synthesis rapidly induces SigM, while increasing UndP production can dampen the SigM response. Finally, we show that SigM becomes essential for viability when the availability of UndP is restricted. Altogether, our data support a model in which the SigM pathway functions to homeostatically control UndP usage. When UndP levels are sufficiently high, the anti-sigma factor complex holds SigM inactive. When levels of UndP are reduced, SigM activates genes that increase flux through the PG synthesis pathway, boost UndP recycling, and liberate the lipid carrier from nonessential surface polymer pathways. Analogous homeostatic pathways that prioritize UndP usage are likely to be common in bacteria.
Polarised cell intercalation during Drosophila axis extension is robust to an orthogonal pull by the invaginating mesoderm
Authors: Lye Claire M. , Blanchard Guy B. , Evans Jenny , Nestor-Bergmann Alexander , Sanson Bénédicte
Published: April 2024

As tissues grow and change shape during animal development, they physically pull and push on each other, and these mechanical interactions can be important for morphogenesis. DuringDrosophilagastrulation, mesoderm invagination temporally overlaps with the convergence and extension of the ectodermal germband; the latter is caused primarily by Myosin II–driven polarised cell intercalation. Here, we investigate the impact of mesoderm invagination on ectoderm extension, examining possible mechanical and mechanotransductive effects on Myosin II recruitment and polarised cell intercalation. We find that the germband ectoderm is deformed by the mesoderm pulling in the orthogonal direction to germband extension (GBE), showing mechanical coupling between these tissues. However, we do not find a significant change in Myosin II planar polarisation in response to mesoderm invagination, nor in the rate of junction shrinkage leading to neighbour exchange events. We conclude that the main cellular mechanism of axis extension, polarised cell intercalation, is robust to the mesoderm invagination pull. We find, however, that mesoderm invagination slows down the rate of anterior-posterior cell elongation that contributes to axis extension, counteracting the tension from the endoderm invagination, which pulls along the direction of GBE.
Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models
Authors: Bouman Judith A. , Hauser Anthony , Grimm Simon L. , Wohlfender Martin , Bhatt Samir , Semenova Elizaveta , Gelman Andrew , Althaus Christian L. , Riou Julien
Published: April 2024

Compartmental models that describe infectious disease transmission across subpopulations are central for assessing the impact of non-pharmaceutical interventions, behavioral changes and seasonal effects on the spread of respiratory infections. We present a Bayesian workflow for such models, including four features: (1) an adjustment for incomplete case ascertainment, (2) an adequate sampling distribution of laboratory-confirmed cases, (3) a flexible, time-varying transmission rate, and (4) a stratification by age group. Within the workflow, we benchmarked the performance of various implementations of two of these features (2 and 3). For the second feature, we used SARS-CoV-2 data from the canton of Geneva (Switzerland) and found that a quasi-Poisson distribution is the most suitable sampling distribution for describing the overdispersion in the observed laboratory-confirmed cases. For the third feature, we implemented three methods: Brownian motion, B-splines, and approximate Gaussian processes (aGP). We compared their performance in terms of the number of effective samples per second, and the error and sharpness in estimating the time-varying transmission rate over a selection of ordinary differential equation solvers and tuning parameters, using simulated seroprevalence and laboratory-confirmed case data. Even though all methods could recover the time-varying dynamics in the transmission rate accurately, we found that B-splines perform up to four and ten times faster than Brownian motion and aGPs, respectively. We validated the B-spline model with simulated age-stratified data. We applied this model to 2020 laboratory-confirmed SARS-CoV-2 cases and two seroprevalence studies from the canton of Geneva. This resulted in detailed estimates of the transmission rate over time and the case ascertainment. Our results illustrate the potential of the presented workflow including stratified transmission to estimate age-specific epidemiological parameters. The workflow is freely available in the R package HETTMO, and can be easily adapted and applied to other infectious diseases.
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
Authors: Frost H. Robert
Published: April 2024

We have developed a new, and analytically novel, single sample gene set testing method called Reconstruction Set Test (RESET). RESET quantifies gene set importance based on the ability of set genes to reconstruct values for all measured genes. RESET is realized using a computationally efficient randomized reduced rank reconstruction algorithm (available via the RESET R package on CRAN) that can effectively detect patterns of differential abundance and differential correlation for self-contained and competitive scenarios. As demonstrated using real and simulated scRNA-seq data, RESET provides superior performance at a lower computational cost relative to other single sample approaches.
The impact of developmental stage, tissue type, and sex on DNA double-strand break repair in Drosophila melanogaster
Authors: Graham Elizabeth L. , Fernandez Joel , Gandhi Shagun , Choudhry Iqra , Kellam Natalia , LaRocque Jeannine R.
Published: April 2024

Accurate repair of DNA double-strand breaks (DSBs) is essential for the maintenance of genome integrity, as failure to repair DSBs can result in cell death. The cell has evolved two main mechanisms for DSB repair: non-homologous end-joining (NHEJ) and homology-directed repair (HDR), which includes single-strand annealing (SSA) and homologous recombination (HR). While certain factors like age and state of the chromatin are known to influence DSB repair pathway choice, the roles of developmental stage, tissue type, and sex have yet to be elucidated in multicellular organisms. To examine the influence of these factors, DSB repair in various embryonic developmental stages, larva, and adult tissues in Drosophila melanogaster was analyzed through molecular analysis of the DR-white assay using Tracking across Indels by DEcomposition (TIDE). The proportion of HR repair was highest in tissues that maintain the canonical (G1/S/G2/M) cell cycle and suppressed in both terminally differentiated and polyploid tissues. To determine the impact of sex on repair pathway choice, repair in different tissues in both males and females was analyzed. When molecularly examining tissues containing mostly somatic cells, males and females demonstrated similar proportions of HR and NHEJ. However, when DSB repair was analyzed in male and female premeiotic germline cells utilizing phenotypic analysis of the DR-white assay, there was a significant decrease in HR in females compared to males. This study describes the impact of development, tissue-specific cycling profile, and, in some cases, sex on DSB repair outcomes, underscoring the complexity of repair in multicellular organisms.
Who is missed in a community-based survey: Assessment and implications of biases due to incomplete sampling frame in a community-based serosurvey, Choma and Ndola Districts, Zambia, 2022
Authors: Kostandova Natalya , Mutembo Simon , Prosperi Christine , Mwansa Francis Dien , Nakazwe Chola , Namukoko Harriet , Nachinga Bertha , Chongwe Gershom , Chilumba Innocent , Matakala Kalumbu H. , Musukwa Gloria , Hamahuwa Mutinta , Mufwambi Webster , Matoba Japhet , Situtu Kenny , Mutale Irene , Kong Alex C. , Simulundu Edgar , Ndubani Phillimon , Hasan Alvira Z. , Truelove Shaun A. , Winter Amy K. , Carcelen Andrea C. , Lau Bryan , Moss William J. , Wesolowski Amy
Published: April 2024

Community-based serological studies are increasingly relied upon to measure disease burden, identify population immunity gaps, and guide control and elimination strategies; however, there is little understanding of the potential for and impact of sampling biases on outcomes of interest. As part of efforts to quantify measles immunity gaps in Zambia, a community-based serological survey using stratified multi-stage cluster sampling approach was conducted in Ndola and Choma districts in May—June 2022, enrolling 1245 individuals. We carried out a follow-up study among individuals missed from the sampling frame of the serosurvey in July—August 2022, enrolling 672 individuals. We assessed the potential for and impact of biases in the community-based serosurvey by i) estimating differences in characteristics of households and individuals included and excluded (77% vs 23% of households) from the sampling frame of the serosurvey and ii) evaluating the magnitude these differences make on healthcare-seeking behavior, vaccination coverage, and measles seroprevalence. We found that missed households were 20% smaller and 25% less likely to have children. Missed individuals resided in less wealthy households, had different distributions of sex and occupation, and were more likely to seek care at health facilities. Despite these differences, simulating a survey in which missed households were included in the sampling frame resulted in less than a 5% estimated bias in these outcomes. Although community-based studies are upheld as the gold standard study design in assessing immunity gaps and underlying community health characteristics, these findings underscore the fact that sampling biases can impact the results of even well-conducted community-based surveys. Results from these studies should be interpreted in the context of the study methodology and challenges faced during implementation, which include shortcomings in establishing accurate and up-to-date sampling frames. Failure to account for these shortcomings may result in biased estimates and detrimental effects on decision-making.
Behaviour and distribution of Aedes aegypti mosquitoes and their relation to dengue incidence in two transmission hotspots in coastal Ecuador
Authors: Ortega-López Leonardo D. , Betancourth Mauro Pazmiño , León Renato , Kohl Alain , Ferguson Heather M.
Published: April 2024

Background

Dengue (DENV) transmission is endemic throughout coastal Ecuador, showing heterogeneous incidence patterns in association with fine-scale variation in Aedes aegypti vector populations and other factors. Here, we investigated the impact of micro-climate and neighbourhood-level variation in urbanization on Aedes abundance, resting behaviour and associations with dengue incidence in two endemic areas.

Methodology/Principal findings

Aedes aegypti were collected in Quinindé and Portoviejo, two urban cantons with hyperendemic dengue transmission in coastal Ecuador. Aedes vectors were sampled in and around houses within urban and peri-urban neighbourhoods at four time periods. We tested for variation in vector abundance and resting behaviour in relation to neighbourhood urbanization level and microclimatic factors. Aedes abundance increased towards the end of the rainy season, was significantly higher in Portoviejo than in Quinindé, and in urban than in peri-urban neighbourhoods. Aedes vectors were more likely to rest inside houses in Portoviejo but had similar abundance in indoor and outdoor resting collections in Quinindé. Over the study period, DENV incidence was lower in Quinindé than in Portoviejo. Relationships between weekly Ae. aegypti abundance and DENV incidence were highly variable between trapping methods; with positive associations being detected only between BG-sentinel and outdoor Prokopack collections.

Conclusions/Significance

Aedes aegypti abundance was significantly higher in urban than peri-urban neighbourhoods, and their resting behaviour varied between study sites. This fine-scale spatial heterogeneity in Ae. aegypti abundance and behaviour could generate site-specific variation in human exposure and the effectiveness of indoor-based interventions. The trap-dependent nature of associations between Aedes abundance and local DENV incidence indicates further work is needed to identify robust entomological indicators of infection risk.
Inhibition of SRC-3 as a potential therapeutic strategy for aggressive mantle cell lymphoma
Authors: Bijou Imani , Liu Yang , Lu Dong , Chen Jianwei , Sloan Shelby , Alinari Lapo , Lonard David M. , O’Malley Bert W. , Wang Michael , Wang Jin
Published: April 2024

Mantle cell lymphoma (MCL) has a poor prognosis and high relapse rates despite current therapies, necessitating novel treatment regimens. Inhibition of SRC-3 show effectiveness in vivo and in vitro in other B cell lymphomas. Additionally, previous studies have shown that SRC-3 is highly expressed in the lymph nodes of B cell non-Hodgkin’s lymphoma patients, suggesting SRC-3 may play a role in the progression of B cell lymphoma. This study aimed to investigate novel SRC-3 inhibitors, SI-10 and SI-12, in mantle cell lymphoma. The cytotoxic effects of SI-10 and SI-12 were evaluated in vitro and demonstrated dose-dependent cytotoxicity in a panel of MCL cell lines. The in vivo efficacy of SI-10 was confirmed in two ibrutinib-resistant models: an immunocompetent disseminated A20 mouse model of B-cell lymphoma and a human PDX model of MCL. Notably, SI-10 treatment also resulted in a significant extension of survival in vivo with low toxicity in both ibrutinib-resistant murine models. We have investigated SI-10 as a novel anti-lymphoma compound via the inhibition of SRC-3 activity. These findings indicate that targeting SRC-3 should be investigated in combination with current clinical therapeutics as a novel strategy to expand the therapeutic index and to improve lymphoma outcomes.
Identification of bone mineral density associated genes with shared genetic architectures across multiple tissues: Functional insights for EPDR1, PKDCC, and SPTBN1
Authors: Jung Jongyun , Wu Qing
Published: April 2024

Recent studies suggest a shared genetic architecture between muscle and bone, yet the underlying molecular mechanisms remain elusive. This study aims to identify the functionally annotated genes with shared genetic architecture between muscle and bone using the most up-to-date genome-wide association study (GWAS) summary statistics from bone mineral density (BMD) and fracture-related genetic variants. We employed an advanced statistical functional mapping method to investigate shared genetic architecture between muscle and bone, focusing on genes highly expressed in muscle tissue. Our analysis identified three genes, EPDR1, PKDCC, and SPTBN1, which are highly expressed in muscle tissue and previously unlinked to bone metabolism. About 90% and 85% of filtered Single-Nucleotide Polymorphisms were in the intronic and intergenic regions for the threshold at P≤5×10−8 and P≤5×10−100, respectively. EPDR1 was highly expressed in multiple tissues, including muscles, adrenal glands, blood vessels, and the thyroid. SPTBN1 was highly expressed in all 30 tissue types except blood, while PKDCC was highly expressed in all 30 tissue types except the brain, pancreas, and skin. Our study provides a framework for using GWAS findings to highlight functional evidence of crosstalk between multiple tissues based on shared genetic architecture between muscle and bone. Further research should focus on functional validation, multi-omics data integration, gene-environment interactions, and clinical relevance in musculoskeletal disorders.
Neurotherapeutic effects of quercetin-loaded nanoparticles and Biochanin-A extracted from Trifolium alexandrinum on PI3K/Akt/GSK-3β signaling in the cerebral cortex of male diabetic rats
Authors: Newairy Al-Sayeda Al-Sayed , Hamaad Fatma Ahmad , Wahby Mayssaa Moharm , Ghoneum Mamdooh , Abdou Heba Mohamed
Published: April 2024

Diabetes mellitus (DM) is a severe metabolic disease that can have significant consequences for cognitive health. Bioflavonoids such as Trifolium alexandrinum (TA), quercetin (Q), and Biochanin-A (BCA) are known to exert a wide range of pharmacological functions including antihyperglycemic activity. This study aimed to investigate the neurotherapeutic effects of quercetin-loaded nanoparticles (Q-LNP) and BCA extracted from TA against diabetes-induced cerebral cortical damage through modulation of PI3K/Akt/GSK-3β and AMPK signaling pathways. Adult male Wistar albino rats (N = 25) were randomly assigned to one of five groups: control, diabetics fed a high-fat diet (HFD) for 2 weeks and intraperitoneally (i.p.) injected with STZ (40 mg/kg), and diabetics treated with Q-LNP (50 mg/kg BW/day), BCA (10 mg/kg BW/day), or TA extract (200 mg/kg BW/day). Treatments were applied by oral gavage once daily for 35 days. Diabetic rats treated with Q-LNP, BCA, and TA extract showed improvement in cognitive performance, cortical oxidative metabolism, antioxidant parameters, and levels of glucose, insulin, triglyceride, and total cholesterol. In addition, these treatments improved neurochemical levels, including acetylcholine, dopamine, and serotonin levels as well acetylcholinesterase and monoamine oxidase activities. Furthermore, these treatments lowered proinflammatory cytokine production for TNF-α and NF-κB; downregulated the levels of IL-1β, iNOS, APP, and PPAR-γ; and attenuated the expressions of PSEN2, BACE, IR, PI3K, FOXO 1, AKT, AMPK, GSK-3β, and GFAP. The histopathological examinations of the cerebral cortical tissues confirmed the biochemical results. Overall, the present findings suggest the potential therapeutic effects of TA bioflavonoids in modulating diabetes-induced cerebral cortical damage.
Interlaboratory comparison of high-throughput protein biomarker assay quantifications for radiation exposure classification
Authors: Nemzow Leah , Boehringer Thomas , Mayenburg Jessica , Beaton-Green Lindsay A. , Wilkins Ruth C. , Turner Helen C.
Published: April 2024

In the event of a widespread radiological incident, thousands of individuals will require rapid assessment of exposure using validated biodosimetry assays to inform clinical triage. In this scenario, multiple biodosimetry laboratories may be necessary for large-volume sample processing. To meet this need, we have developed a high-throughput assay for the rapid measurement of intracellular protein biomarkers in human peripheral blood samples using an Imaging Flow Cytometry (IFC) platform. The objective of this work was to harmonize and validate the reproducibility of our blood biomarker assay for radiation exposure across three IFC instruments, two located at Columbia University (CU) and the third at Health Canada. The Center for Radiological Research (CRR) at CU served as the central laboratory and reference instrument, where samples were prepared in triplicate, labeled with two radiation responsive leukocyte biomarkers (BAX and phosphor-p53 (Ser37)), and distributed for simultaneous interrogation by each IFC. Initial tests showed that significantly different baseline biomarker measurements were generated on each instrument when using the same acquisition settings, suggesting that harmonization of signal intensities is necessary. Subsequent tests harmonized biomarker measurements after irradiation by modulating laser intensity using two reference materials: unstained samples and standardized rainbow beads. Both methods generated measurements on each instrument without significant differences between the new and references instruments, allowing for the use of one master template to quantify biomarker expression across multiple instruments. Deming regression analyses of 0–5 Gy dose-response curves showed overall good correlation of BAX and p53 values across new and reference instruments. While Bland-Altman analyses indicated low to moderate instrument biases, ROC Curve analyses ultimately show successful discrimination between exposed and unexposed samples on each instrument (AUC values > 0.85).
Geographical distribution of mobile genetic elements in microbial communities along the Yucatan coast
Authors: Guillén-Chable Francisco , Valdez Iuit Johnny Omar , Avila Castro Luis Alejandro , Rosas Carlos , Merino Enrique , Rodríguez-Escamilla Zuemy , Martínez-Núñez Mario Alberto
Published: April 2024

Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan’s microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It’s important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
Disparities in COVID-19 vaccine uptake among rural hard-to-reach population and urban high-risk groups of Bangladesh
Authors: Jannat Zerin , Das Hemel , Ali Md. Wazed , Wahed Tasnuva , Alam Md. Nurul , Uddin Md. Jasim
Published: April 2024

Background

Vaccination has been an indispensable step in controlling the coronavirus disease pandemic. In early 2021, Bangladesh launched a mass vaccination campaign to boost the COVID-19 vaccination rate when doses were available and immunized millions in the country. Although deemed a success, disparities became conspicuous in vaccination coverage across population of different socioeconomic background.

Methods

The purpose of this cross-sectional study was to assess the vaccination coverage for three doses and detect disparities in uptake of the COVID-19 vaccine among rural population of hard-to-reach areas and urban individuals belonging to the high-risk group -defined in our study as individuals from elusive population such as floating population/street dwellers, transgender, addicts and disabled population. We conducted household survey (n = 12,298) and survey with high risk group of people (2,520). The collected primary data were analysed using descriptive statistical analysis.

Results

Our findings show that coverage for the first dose of COVID-19 vaccination was high among respondents from both rural Hard-to-reach (HTR) (92.9%) and non-HTR (94.6%) areas. However, the coverage for subsequent doses was observed to reduce significantly, especially for third dose (52.2% and 56.4% for HTR and non-HTR, respectively).

Conclusion

Vaccination coverage among urbanites of high-risk group was found to be critically low. Vaccine hesitancy was also found to be high among individuals of this group. It is essential that the individuals of urban high-risk group be prioritized. Individuals from this group could be provided incentives (transport for disabled, monetary incentive to transgenders; food and medicine for drug user and floating people) and vaccination centers could be established with flexible schedule (morning/afternoon/evening sessions) so that they receive vaccine at their convenient time. Community engagement can be used for both high-risk group and rural population to enhance the COVID-19 vaccination coverage and lower disparities in uptake of the vaccine doses nationwide.
Characteristics of mesoscale eddies in the Mozambique Channel
Authors: Bai Linfei , Zhu Guohao , Huang Haojie , Zhang Liqiong , LÜ Haibin , Zhang Yinyi
Published: April 2024

The mesoscale eddy characteristics of the Mozambique Warm Current were investigated by detecting and tracking satellite altimetry data from 2010 to 2019. A total of 1,086 eddies were identified in the Mozambique Channel, comprising 509 cyclonic eddies and 577 anticyclonic eddies. The results revealed that the bay area on the northwest coast of Madagascar was the main hotspot of eddy generation, and the mean amplitude and radius of the anticyclonic eddies in the Mozambique Channel were 24.23 cm and 82.7 km, respectively, which are larger than those of the cyclonic eddies. Local wind forcing had a significant impact on the formation of mesoscale eddies in the Mozambique Channel. In winter, the wind stress in the northern and southern areas of the Mozambique Channel exhibited a strong correlation with the distribution of eddy kinetic energy (EKE), where both monsoonal winds in the north and trade winds in the south could facilitate mesoscale anticyclonic eddy formation. In addition, the variability in the number of anticyclonic and cyclonic eddies in the Mozambique Channel may have exerted a significant influence on the seasonal anomalous fluctuations in local sea surface temperatures (SSTs). This study presented a novel analysis of the mesoscale eddy characteristics in the Mozambique Channel.
Association between the severity of hard-to-treat psoriasis and the prevalence of metabolic syndrome: A hospital-based cross-sectional study in Jakarta, Indonesia
Authors: Evyana Dina , Novianto Endi , Budianti Windy K. , Krisanti Roro I. A. , Wisnu Wismandari , Wibawanti Retno , Nilasari Hanny , Legiawati Lili , Hapsari Saskia A. R. , Mutmainnah Euis
Published: April 2024

Psoriatic lesions on the scalp, face, intertriginous, genitals, palms/soles, and nails are often delay diagnosed, hard-to-treat, and cause disability. Metabolic syndrome (MetS) is one of the most frequent and significant comorbidities in psoriasis. Many studies have discovered a link between psoriasis and MetS, but none have specifically assessed the hard-to-treat psoriasis in Indonesian population. This is a multicenter study involving four dermatology referral hospitals to investigate the association between psoriasis severity that has hard-to-treat lesions with the prevalence of MetS in Jakarta, Indonesia. Data was collected from April to October 2022. The severity of 84 hard-to-treat psoriasis patients was measured by Psoriasis Area Severity Index (PASI) scores. The participants divided into PASI score >10 (severe) and ≤ 10 (mild-moderate) groups. MetS was identified based on the modified National Cholesterol Education Program Adult Treatment Panel III. MetS was found in 64.3% of patients. Patients with a PASI score>10 had a significantly higher risk of metabolic syndrome compared to those with a score ≤ 10 (78.6% vs 50%, OR 3.667; 95% CI 1.413–9.514; p = 0.006). The prevalence of hypertension (p = 0.028), low levels of high-density lipoprotein (HDL) cholesterol (p = 0.01), mean fasting blood sugar (p = 0.018), and triglyceride levels (p = 0.044) between the two groups differed significantly. This study found most frequent components of MetS were abdominal obesity, decreased levels of HDL cholesterol, hypertension, hyperglycemia, and hypertriglyceridemia respectively. Individuals with severe hard-to-treat psoriasis had a 3.67 times more likely to have MetS rather than the mild-moderate group.
Bioremediation of Pb contaminated water using a novel Bacillus sp. strain MHSD_36 isolated from Solanum nigrum
Authors: Maumela Pfariso , Magida Sinomncedi , Serepa-Dlamini Mahloro Hope
Published: April 2024

The Pb bioremediation mechanism of a multi-metal resistant endophytic bacteria Bacillus sp. strain MHSD_36, isolated from Solanum nigrum, was characterised. The strain tested positive for the presence of plant growth promoters such as indoleacetic acid, 1-aminocyclopropane-1-carboxylate deaminase, siderophores, and phosphate solubilization. The experimental data illustrated that exopolysaccharides and cell hydrophobicity played a role in Pb uptake. The data further showed that the cell wall biosorbed a significant amount (71%) of the total Pb (equivalent to 4 mg/L) removed from contaminated water, compared to the cell membrane (11%). As much as 11% of the Pb was recovered from the cytoplasmic fraction, demonstrating the ability of the strain to control the influx of toxic heavy metals into the cell and minimize their negative impacts. Pb biosorption was significantly influenced by the pH and the initial concentration of the toxic ions. Furthermore, the presence of siderophores and biosurfactants, when the strain was growing under Pb stress, was detected through liquid chromatography mass spectrometry. The strain demonstrated a multi-component based Pb biosorption mechanism and thus, has a great potential for application in heavy metal bioremediation.