bluuebunny/crossref_metadata_2025_split huggingface dataset:
On-chip silicon electro-optical modulator with ultra-high extinction ratio for fiber-optic distributed acoustic sensing
Authors: Cheng Zhuo , Shu Xiaoqian , Ma Lingmei , Chen Bigeng , Li Caiyun , Sun Chunlei , Wei Maoliang , Yu Shaoliang , Li Lan , Lin Hongtao , Rao Yunjiang 
Published: November 2023

AbstractUltra-high extinction ratio (ER) optical modulation is crucial for achieving high-performance fiber-optic distributed acoustic sensing (DAS) for various applications. Bulky acousto-optical modulators (AOM) as one of the key devices in DAS have been used for many years, but their relatively large volume and high power consumption are becoming the bottlenecks to hinder the development of ultra-compact and energy-efficient DAS systems that are highly demanded in practice. Here, an on-chip silicon electro-optical modulator (EOM) based on multiple coupled microrings is demonstrated with ultra-high ER of up to 68 dB while the device size and power consumption are only 260 × 185 μm2and 3.6 mW, respectively, which are at least two orders of magnitude lower than those of a typical AOM. Such an on-chip EOM is successfully applied to DAS with an ultra-high sensitivity of −71.2 dB rad2/Hz (4 pε/√Hz) and a low spatial crosstalk noise of −68.1 dB rad2/Hz, which are very similar to those using an AOM. This work may pave the way for realization of next-generation ultra-compact DAS systems by integration of on-chip opto-electronic devices and modules with the capability of mass-production.
Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species
Authors: Lou Yue Clare , Rubin Benjamin E. , Schoelmerich Marie C. , DiMarco Kaden S. , Borges Adair L. , Rovinsky Rachel , Song Leo , Doudna Jennifer A. , Banfield Jillian F. 
Published: November 2023

AbstractThe early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2’-fucosyllactose (2’FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2’FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2’FL breakdown, thus critical for B. breve’s growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2’FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual’s microbiome.
An oocyte meiotic midbody cap is required for developmental competence in mice
Authors: Jung Gyu Ik , Londoño-Vásquez Daniela , Park Sungjin , Skop Ahna R. , Balboula Ahmed Z. , Schindler Karen 
Published: November 2023

AbstractEmbryo development depends upon maternally derived materials. Mammalian oocytes undergo extreme asymmetric cytokinesis events, producing one large egg and two small polar bodies. During cytokinesis in somatic cells, the midbody and subsequent assembly of the midbody remnant, a signaling organelle containing RNAs, transcription factors and translation machinery, is thought to influence cellular function or fate. The role of the midbody and midbody remnant in gametes, in particular, oocytes, remains unclear. Here, we examined the formation and function of meiotic midbodies (mMB) and mMB remnants using mouse oocytes and demonstrate that mMBs have a specialized cap structure that is orientated toward polar bodies. We show that that mMBs are translationally active, and that mMB caps are required to retain nascent proteins in eggs. We propose that this specialized mMB cap maintains genetic factors in eggs allowing for full developmental competency.
Masked alkynes for synthesis of threaded carbon chains
Authors: Patrick Connor W. , Gao Yueze , Gupta Prakhar , Thompson Amber L. , Parker Anthony W. , Anderson Harry L. 
Published: November 2023

AbstractPolyynes are chains of sp1 carbon atoms with alternating single and triple bonds. As they become longer, they evolve towards carbyne, the 1D allotrope of carbon, and they become increasingly unstable. It has been anticipated that long polyynes could be stabilized by supramolecular encapsulation, by threading them through macrocycles to form polyrotaxanes—but, until now, polyyne polyrotaxanes with many threaded macrocycles have been synthetically inaccessible. Here we show that masked alkynes, in which the C≡C triple bond is temporarily coordinated to cobalt, can be used to synthesize polyrotaxanes, up to the C68 [5]rotaxane with 34 contiguous triple bonds and four threaded macrocycles. This is the length regime at which the electronic properties of polyynes converge to those of carbyne. Cyclocarbons constitute a related family of molecular carbon allotropes, and cobalt-masked alkynes also provide a route to [3]catenanes and [5]catenanes built around cobalt complexes of cyclo[40]carbon and cyclo[80]carbon, respectively.
Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease
Authors: Spencer Chapman Michael , Cull Alyssa H. , Ciuculescu Marioara F. , Esrick Erica B. , Mitchell Emily , Jung Hyunchul , O’Neill Laura , Roberts Kirsty , Fabre Margarete A. , Williams Nicholas , Nangalia Jyoti , Quinton Joanne , Fox James M. , Pellin Danilo , Makani Julie , Armant Myriam , Williams David A. , Campbell Peter J. , Kent David G. 
Published: November 2023

AbstractGene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms.
Study of the strongest dust storm occurred in Uzbekistan in November 2021
Authors: Nishonov Bakhriddin E. , Kholmatjanov Bakhtiyar M. , Labzovskii Lev D. , Rakhmatova Natella , Shardakova Lyudmila , Abdulakhatov Erkin I. , Yarashev Darkhon U. , Toderich Kristina N. , Khujanazarov Temur , Belikov Dmitry A. 
Published: November 2023

AbstractWe studied and reconstructed a severe Central Asian dust storm of November 4, 2021, through high-resolution TROPOMI UVAI spaceborne observations, ground-based aerosol measurements, and Lagrangian particle modeling. The dust storm was caused by the front part of a cold polar anticyclone front from the Ural-Volga regions, which struck the central and eastern parts of Uzbekistan under favorable atmospheric conditions. Two plumes spread out, causing a thick haze to blanket the region. The most severe dust storm effects hit the capital of Uzbekistan (Tashkent) and the Fergana Valley, where the thick atmospheric dust layer dropped the visibility to 200 m. PM10 concentrations reached 18,000 µg/m3 (260-fold exceedance of the local long-term average). The PM2.5 concentrations remained above 300 µg/m3 for nearly ten days, indicating an extremely long-lasting event. The dust storm was caused by an extremely strong summer heatwave of 2021 in Kazakhstan with unprecedentedly high temperatures reaching 46.5 °C. The long-lasting drought dried up the soil down to 50 cm depth, triggering the soil cover denudation due to drying out vegetation and losing its moisture. This event was the worst since 1871 and considering the increasing aridity of Central Asia, the onset of potentially recurring severe dust storms is alarming.
Simulation examining the factors influencing capillary wick transport in a refrigerant direct cooling system for power battery packs
Authors: Hu Yun , Shan Fengwu , Zeng Jianbang , Liu Shaohuan , Xing Zhengyuan , Fu Wenxiang , Luo Yufeng 
Published: November 2023

AbstractThe effectiveness of power battery refrigerant direct cooling systems of electric vehicles incorporating capillary wicks is directly determined by these wicks’ transport performance. The Fries–Dreyer equation describes wicking behavior, but there is a significant gap between its predictions and the experimental results as reported in the literature. This work examines the factors influencing transport performance in an unconsolidated capillary wick with spherical particles. A mathematical and physical model is developed, the latter using the COMSOL software platform. Both the developed mathematical form and the numerically simulated results of this model are closer to the experimental results than those obtained using the Fries–Dreyer equation. The simulation results enable optimizing the equilibrium height and capillary time numbers providing a fitted Fries–Dreyer equation that is then used to analyze the influence of saturation, inclination angle, wick particle diameter, and tortuosity on the liquid rise mass and velocity and the equilibrium height, and the effects are in close but not perfect accord with experimental data. To narrow the gap, the Fries–Dreyer equation is further optimized using the numerically simulated results, substantially improving the accord with the experimental results.
Investigation of EDF evolution and charged particle transport in E × B plasma based negative ion sources using kinetic simulations
Authors: Shah Miral , Chaudhury Bhaskar , Bandyopadhyay Mainak 
Published: November 2023

AbstractA spatially varying transverse magnetic filter field (TMF) is present in an E $$\times$$
×
B plasma-based negative ion source to improve negative ion yield. The TMF strength ranges from 1 to 10 mT, causing the plasma electrons to become magnetized while leaving the ions either unmagnetized or partially magnetized. As a consequence, plasma drift, particle trapping, double layer (DL), and instabilities are observed in a negative ion source. The transport of plasma through the TMF is influenced by these phenomena, subsequently affecting the energy distribution functions (EDFs) of both electrons and ions in the plasma. Measurement of EDFs in such systems is a challenging task due to the presence of a strong magnetic field. To address this, a 2D-3V Particle-in-Cell Monte Carlo Collision (PIC MCC) model is employed to study the spatio-temporal evolution of the EDFs separately for electrons and ions. The electron EDF (EEDF) remains Maxwellian, while ion EDF (IEDF) gradually transitions to non-Maxwellian as measurements are taken closer to the TMF region. The present study reveals that the IEDF is more sensitive to the operational conditions compared to the EEDF, as evidenced by the changes observed in both EDFs under different plasma operational conditions.
MANet: a multi-attention network for automatic liver tumor segmentation in computed tomography (CT) imaging
Authors: Hettihewa Kasun , Kobchaisawat Thananop , Tanpowpong Natthaporn , Chalidabhongse Thanarat H. 
Published: November 2023

AbstractAutomatic liver tumor segmentation is a paramount important application for liver tumor diagnosis and treatment planning. However, it has become a highly challenging task due to the heterogeneity of the tumor shape and intensity variation. Automatic liver tumor segmentation is capable to establish the diagnostic standard to provide relevant radiological information to all levels of expertise. Recently, deep convolutional neural networks have demonstrated superiority in feature extraction and learning in medical image segmentation. However, multi-layer dense feature stacks make the model quite inconsistent in imitating visual attention and awareness of radiological expertise for tumor recognition and segmentation task. To bridge that visual attention capability, attention mechanisms have developed for better feature selection. In this paper, we propose a novel network named Multi Attention Network (MANet) as a fusion of attention mechanisms to learn highlighting important features while suppressing irrelevant features for the tumor segmentation task. The proposed deep learning network has followed U-Net as the basic architecture. Moreover, residual mechanism is implemented in the encoder. Convolutional block attention module has split into channel attention and spatial attention modules to implement in encoder and decoder of the proposed architecture. The attention mechanism in Attention U-Net is integrated to extract low-level features to combine with high-level ones. The developed deep learning architecture is trained and evaluated on the publicly available MICCAI 2017 Liver Tumor Segmentation dataset and 3DIRCADb dataset under various evaluation metrics. MANet demonstrated promising results compared to state-of-the-art methods with comparatively small parameter overhead.
Anticancer activity, phytochemical investigation and molecular docking insights of Citrullus colocynthis (L.) fruits
Authors: Mandour Yasmine M. , Refaat Esraa , Hassanein Heba D. 
Published: November 2023

AbstractCancer disease is regarded as one of the most significant public health issues, regardless of economic standards. Medicinal plants are now regarded as a natural source of anticancer medicines due to their antioxidant and anti-mutagenic actions. Cucurbitaceae is considered to be one of the most economically significant families. One family species is Citrullus colocynthis (L.), which has a high concentration of many active secondary chemical metabolites. Various C. colocynthis plant extracts showed cytotoxicity against some cancer cells. This study aims to identify the C. colocynthis fruit components and determine whether they have anticancer action against MIA PaCa-2 and A431 cells. High-Performance Liquid Chromatography/Quadrupole Time of Flight/Mass Spectrometry (HPLC/QTOF/MS); the technique was accustomed to investigate the compounds of the ethyl acetate (EtOAc) fruit extract. Anticancer activity was investigated on both MIAPaCa-2 and A-431 cell lines. DPPH assay for antioxidant activity was carried out. Molecular modelling was employed to help understand the molecular basis for the observed anticancer activity. 24 compounds were tentatively identified by comparing the extract’s fragmentation pattern in positive mode against reference compounds spectra and literature. The EtOAc extract of C. colocynthis had effective positive results on cancer cells (MIAPaCa-2 and A-431) and was characterized by slight or no harmful effect on normal (healthy) cells. For the DPPH assay, EtOAc and BuOH extracts exhibited high antioxidant activity (86 and 76%, respectively) compared with the oxidative potential of the standard compound (Caffeic acid, 98%). One of the major cucurbitacin derivatives that LC/MS tentatively identified in the EtOAc extract was Cucurbita-5(10),6,23-triene-3β,25-diol. During this study, docking experiments and MD simulations were carried out, which suggested the anti-pancreatic cancer activity of C. colocynthis extract to be attributed to EGFR inhibition by Cucurbita-5(10),6,23-triene-3β,25-diol. Therefore, expansion of this type of research should be encouraged in the hope of obtaining natural therapeutics for cancerous tumors in the future, having the advantage of being cheaper, safer, and with fewer side effects.
Establishing the normal range of sperm DNA fragmentation index (% DFI) for rhesus macaques
Authors: Burch Fernanda C. , Leung Philberta Y. , McDonald Eric , Jensen Jared , Mishler Emily , Piekarski Nadine , Mendes Camilla M. , Sylwester Andrew , Hanna Carol B. 
Published: November 2023

AbstractThe Sperm Chromatin Structure Assay (SCSA) is a robust test with high repeatability and precision. It is a clinically accepted assay that defines risk for infertility in men by measuring the degree of DNA fragmentation (% DFI) in sperm. The objective of this study was to adapt and validate the SCSA for rhesus macaques (Macaca mulatta) and establish a range for % DFI in fertile males. Sperm samples from two different males were used to produce a % DFI validation curve before establishing a range using additional samples from n = 11 males. Sperm labeled with acridine orange were analyzed by flow cytometry to measure green fluorescence (native or intact DNA) and red fluorescence (fragmented DNA). Data were exported to FlowJo software to determine the % DFI for each sample. DNA fragmentation ranged from 0.1 to 2.4% DFI, with a mean ± SD = 1.1 ± 0.7% DFI (validation curve optimized to R2 > 0.95). In conclusion, we were able to successfully validate the SCSA in our institution and establish the first normal range for sperm DNA fragmentation in rhesus macaques. Our study provides a quantitative baseline for future evaluations to assess macaque fertility through the SCSA test.
Lactic acid enhances vaginal epithelial barrier integrity and ameliorates inflammatory effects of dysbiotic short chain fatty acids and HIV-1
Authors: Schwecht Ingrid , Nazli Aisha , Gill Biban , Kaushic Charu 
Published: November 2023

AbstractThe vaginal microenvironment is key in mediating susceptibility to sexually transmitted infections. A polymicrobial environment with reduced Lactobacilllus spp. is characteristic of vaginal dysbiosis, associated with increased production of several short chain fatty acids (SCFAs), vaginal inflammation and an increased risk of HIV-1 acquisition. In contrast, a eubiotic vaginal microbiome (VMB), dominated by Lactobacillus spp. correlates with increased production of lactic acid (LA), an acidic milieu and protection against HIV-1. Vaginal metabolites, specifically LA and SCFAs including butyric, succinic and acetic acids are associated with modulation of HIV-1 risk. We assessed the impact of combined and individual SCFAs and LA on vaginal epithelial cells (VK2) grown in air–liquid interface cultures. Treatment of VK2 cells with eubiotic SCFA + LA mixture showed increased epithelial barrier integrity, reduced FITC dextran leakage and enhanced expression of cell–cell adhesion proteins. Treatment with dysbiotic SCFA + LA mixture diminished epithelial barrier integrity, increased NFκB activation and inflammatory mediators: TNF-α, IL-6, IL-8 and RANTES. LA was found to be the primary contributor of the beneficial effects. Eubiotic SCFA + LA mixture ameliorated HIV-1 mediated barrier disruption and HIV-1 leakage, whereas dysbiotic SCFA + LA treatment exacerbated HIV-1 effects. These findings indicate a key role for LA in future prophylactic strategies.
Distribution and co-occurrence patterns of charophytes and angiosperms in the northern Baltic Sea
Authors: Herkül Kristjan , Torn Kaire , Möller-Raid Tiia , Martin Georg 
Published: November 2023

AbstractThe distribution data of 11 soft substrate charophyte and angiosperm species were analyzed. Our study aimed to elucidate the co-occurrence patterns among these sympatric macrophyte species and quantify their distribution areas. The central hypothesis of this study proposed that the observed co-occurrence patterns among the studied species deviate from what would be expected by random chance. Macrophyte occurrence data was derived from an extensive field sampling database. Environmental variables available as georeferenced raster layers including topographical, hydrodynamic, geological, physical, chemical, and biological variables were used as predictor variables in the random forest models to predict the spatial distribution of the species. Permutation tests revealed statistically significant deviations from random co-occurrence patterns. The analysis demonstrated that species tended to co-occur more frequently within their taxonomic groups (i.e., within charophytes and within angiosperms) than between these groups. The most extensive distribution overlap was observed betweenChara asperaWilld. andChara canescensLoisel., whileZostera marinaL. exhibited the least overlap with the other species. The mean number of co-occurring species was the highest inChara baltica(Hartman) Bruzelius whileZ. marinahad the largest share of single-species occurrences. Based on the distribution models,Stuckenia pectinata(L.) Börner had the largest distribution area.
Simulated eye height impacts size perception differently depending on real-world posture
Authors: Ghasemi Fatemeh , Harris Laurence R. , Jörges Björn 
Published: November 2023

AbstractChanges in perceived eye height influence visually perceived object size in both the real world and in virtual reality. In virtual reality, conflicts can arise between the eye height in the real world and the eye height simulated in a VR application. We hypothesized that participants would be influenced more by variation in simulated eye height when they had a clear expectation about their eye height in the real world such as when sitting or standing, and less so when they did not have a clear estimate of the distance between their eyes and the real-life ground plane, e.g., when lying supine. Using virtual reality, 40 participants compared the height of a red square simulated at three different distances (6, 12, and 18 m) against the length of a physical stick (38.1 cm) held in their hands. They completed this task in all combinations of four real-life postures (supine, sitting, standing, standing on a table) and three simulated eye heights that corresponded to each participant’s real-world eye height (123cm sitting; 161cm standing; 201cm on table; on average). Confirming previous results, the square’s perceived size varied inversely with simulated eye height. Variations in simulated eye height affected participants’ perception of size significantly more when sitting than in the other postures (supine, standing, standing on a table). This shows that real-life posture can influence the perception of size in VR. However, since simulated eye height did not affect size estimates less in the lying supine than in the standing position, our hypothesis that humans would be more influenced by variations in eye height when they had a reliable estimate of the distance between their eyes and the ground plane in the real world was not fully confirmed.