bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites
Authors: Yip Alexander Y. G. , King Olivia G. , Omelchenko Oleksii , Kurkimat Sanjana , Horrocks Victoria , Mostyn Phoebe , Danckert Nathan , Ghani Rohma , Satta Giovanni , Jauneikaite Elita , Davies Frances J. , Clarke Thomas B. , Mullish Benjamin H. , Marchesi Julian R. , McDonald Julie A. K. 
Published: August 2023

AbstractThe intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Broad-spectrum antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. Here, we show that antibiotic-induced reduction of gut microbial populations leads to an enrichment of nutrients and depletion of inhibitory metabolites, which enhances CRE growth. Antibiotics decrease the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales) in ex vivo cultures of human faecal microbiota; this is accompanied by depletion of microbial metabolites and enrichment of nutrients. We measure the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several CRE strains. We find that CRE can use the nutrients (enriched after antibiotic treatment) as carbon and nitrogen sources for growth. These nutrients also increase in faeces from antibiotic-treated mice and decrease following intestinal colonisation with carbapenem-resistant Escherichia coli. Furthermore, certain microbial metabolites (depleted upon antibiotic treatment) inhibit CRE growth. Our results show that killing gut commensals with antibiotics facilitates CRE colonisation by enriching nutrients and depleting inhibitory microbial metabolites.
A planar defect spin sensor in a two-dimensional material susceptible to strain and electric fields
Authors: Udvarhelyi Péter , Clua-Provost Tristan , Durand Alrik , Li Jiahan , Edgar James H. , Gil Bernard , Cassabois Guillaume , Jacques Vincent , Gali Adam 
Published: August 2023

AbstractThe boron-vacancy spin defect ($${\,{{\mbox{V}}}}_{{{\mbox{B}}}\,}^{-}$$

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) in hexagonal boron nitride (hBN) has a great potential as a quantum sensor in a two-dimensional material that can directly probe various external perturbations in atomic-scale proximity to the quantum sensing layer. Here, we apply first-principles calculations to determine the coupling of the $${\,{{\mbox{V}}}}_{{{\mbox{B}}}\,}^{-}$$

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electronic spin to strain and electric fields. Our work unravels the interplay between local piezoelectric and elastic effects contributing to the final response to the electric fields. The theoretical predictions are then used to analyse optically detected magnetic resonance (ODMR) spectra recorded on hBN crystals containing different densities of $${\,{{\mbox{V}}}}_{{{\mbox{B}}}\,}^{-}$$

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centres. We prove that the orthorhombic zero-field splitting parameter results from local electric fields produced by surrounding charge defects. This work paves the way towards applications of $${\,{{\mbox{V}}}}_{{{\mbox{B}}}\,}^{-}$$

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centres for quantitative electric field imaging and quantum sensing under pressure.
A soft, high-density neuroelectronic array
Authors: Seo Kyung Jin , Hill Mackenna , Ryu Jaehyeon , Chiang Chia-Han , Rachinskiy Iakov , Qiang Yi , Jang Dongyeol , Trumpis Michael , Wang Charles , Viventi Jonathan , Fang Hui 
Published: August 2023

AbstractTechniques to study brain activities have evolved dramatically, yet tremendous challenges remain in acquiring high-throughput electrophysiological recordings minimally invasively. Here, we develop an integrated neuroelectronic array that is filamentary, high-density and flexible. Specifically, with a design of single-transistor multiplexing and current sensing, the total 256 neuroelectrodes achieve only a 2.3 × 0.3 mm2 area, unprecedentedly on a flexible substrate. A single-transistor multiplexing acquisition circuit further reduces noise from the electrodes, decreases the footprint of each pixel, and potentially increases the device’s lifetime. The filamentary neuroelectronic array also integrates with a rollable contact pad design, allowing the device to be injected through a syringe, enabling potential minimally invasive array delivery. Successful acute auditory experiments in rats validate the ability of the array to record neural signals with high tone decoding accuracy. Together, these results establish soft, high-density neuroelectronic arrays as promising devices for neuroscience research and clinical applications.
Early detection of lung cancer using artificial intelligence-enhanced optical nanosensing of chromatin alterations in field carcinogenesis
Authors: Daneshkhah Ali , Prabhala Sravya , Viswanathan Parvathi , Subramanian Hariharan , Lin Jianan , Chang Andrew S , Bharat Ankit , Roy Hemant Kumar , Backman Vadim 
Published: August 2023

AbstractSupranucleosomal chromatin structure, including chromatin domain conformation, is involved in the regulation of gene expression and its dysregulation has been associated with carcinogenesis. Prior studies have shown that cells in the buccal mucosa carry a molecular signature of lung cancer among the cigarette-smoking population, the phenomenon known as field carcinogenesis or field of injury. Thus, we hypothesized that chromatin structural changes in buccal mucosa can be predictive of lung cancer. However, the small size of the chromatin chain (approximately 20 nm) folded into chromatin packing domains, themselves typically below 300 nm in diameter, preclude the detection of alterations in intradomain chromatin conformation using diffraction-limited optical microscopy. In this study, we developed an optical spectroscopic statistical nanosensing technique to detect chromatin packing domain changes in buccal mucosa as a lung cancer biomarker: chromatin-sensitive partial wave spectroscopic microscopy (csPWS). Artificial intelligence (AI) was applied to csPWS measurements of chromatin alterations to enhance diagnostic performance. Our AI-enhanced buccal csPWS nanocytology of 179 patients at two clinical sites distinguished Stage-I lung cancer versus cancer-free controls with an area under the ROC curve (AUC) of 0.92 ± 0.06 for Site 1 (in-state location) and 0.82 ± 0.11 for Site 2 (out-of-state location).
Gut bacterial population and community dynamics following adult emergence in pest tephritid fruit flies
Authors: Mason Charles J. , Auth Jean , Geib Scott M. 
Published: August 2023

AbstractGut microbiota are important contributors to insect success. Host-microbe interactions are dynamic and can change as hosts age and/or encounter different environments. A turning point in these relationships the transition from immature to adult life stages, particularly for holometabolous insects where there is radical restructuring of the gut. Improved knowledge of population and community dynamics of gut microbiomes upon adult emergence inform drivers of community assembly and physiological aspects of host-microbe interactions. Here, we evaluated the bacterial communities of the pest tephritid species melon fly (Zeugodacus cucurbitae) and Medditeranean fruit fly (medfly, Ceratitis capitata) associated with the pupae life stage and timepoints immediately following adult eclosion. We used a combination of culturing to determine cultivatable bacterial titers, qPCR to determine 16S-rRNA SSU copy numbers, and 16S V4 sequencing to determine changes in communities. Both culturing and qPCR revealed that fly bacterial populations declined upon adult emergence by 10 to 100-fold followed by recovery within 24 h following eclosion. Titers reached ~ 107 CFUs (~ 108 16S rRNA copies) within a week post-emergence. We also observed concurrent changes in amplicon sequence variance (ASVs), where the ASV composition differed overtime for both melon fly and medfly adults at different timepoints. Medfly, in particular, had different microbiome compositions at each timepoint, indicating greater levels of variation before stabilization. These results demonstrate that tephritid microbiomes experience a period of flux following adult emergence, where both biomass and the makeup of the community undergoes dramatic shifts. The host-microbe dynamics we document suggest plasticity in the community and that there may be specific periods where the tephritid gut microbiome may be pliable to introduce and establish new microbial strains in the host.
Improved processing speed and decreased functional connectivity in individuals with chronic stroke after paired exercise and motor training
Authors: Andrushko Justin W. , Rinat Shie , Greeley Brian , Larssen Beverley C. , Jones Christina B. , Rubino Cristina , Denyer Ronan , Ferris Jennifer K. , Campbell Kristin L. , Neva Jason L. , Boyd Lara A. 
Published: August 2023

AbstractAfter stroke, impaired motor performance is linked to an increased demand for cognitive resources. Aerobic exercise improves cognitive function in neurologically intact populations and may be effective in altering cognitive function post-stroke. We sought to determine if high-intensity aerobic exercise paired with motor training in individuals with chronic stroke alters cognitive-motor function and functional connectivity between the dorsolateral prefrontal cortex (DLPFC), a key region for cognitive-motor processes, and the sensorimotor network. Twenty-five participants with chronic stroke were randomly assigned to exercise (n = 14; 66 ± 11 years; 4 females), or control (n = 11; 68 ± 8 years; 2 females) groups. Both groups performed 5-days of paretic upper limb motor training after either high-intensity aerobic exercise (3 intervals of 3 min each, total exercise duration of 23-min) or watching a documentary (control). Resting-state fMRI, and trail making test part A (TMT-A) and B were recorded pre- and post-intervention. Both groups showed implicit motor sequence learning (p < 0.001); there was no added benefit of exercise for implicit motor sequence learning (p = 0.738). The exercise group experienced greater overall cognitive-motor improvements measured with the TMT-A. Regardless of group, the changes in task score, and dwell time during TMT-A were correlated with a decrease in DLPFC-sensorimotor network functional connectivity (task score: p = 0.025; dwell time: p = 0.043), which is thought to reflect a reduction in the cognitive demand and increased automaticity. Aerobic exercise may improve cognitive-motor processing speed post-stroke.
The oncogene Musashi1 encodes novel miRNAs in breast cancer
Authors: Lachinani Liana , Forouzanfar Mahboobeh , Dormiani Kianoush , Soltani Bahram Mohammad , Dolatshahi Kamran , Hakimian Sayyed Mohammadreza , Dokanehiifard Sadat , Nasr-Esfahani Mohammad Hossein 
Published: August 2023

AbstractRNA-binding protein Musashi1 (MSI1) shows an increased expression level in several cancers and has been introduced as a prognostic marker in some malignancies. It is expected that if any miRNA is encoded by this gene, it might have a role in cancer development or could be considered as a prognostic biomarker. Accordingly, in this study, we aimed to find novel miRNA(s) inside the intronic regions of the MSI1 gene. Here, we report two novel miRNAs within intron 4 of MSI1 gene, named MSM2 and MSM3, which were selected among several miRNA precursors predicted by bioinformatic studies. For experimental analysis, corresponding precursor miRNAs were transfected into HEK293T cells and exogenous expression of the mature miRNAs were detected. Two mature miRNAs, MSM3-3p and MSM3-5p were generated by MSM3 precursor and one, MSM2-5p was derived from MSM2. Besides, endogenous expression of MSM2-5p and MSM3-3p was detected in MCF-7 and SH-SY5Y cell lines. Expression of both mature miRNAs was also detected in clinical samples of breast cancer. Additionally, the interaction between the MSM3-3p and 3′UTR region of PDE11A was confirmed by dual luciferase assay. Overall, our data demonstrated that MSI1 gene encodes two novel miRNAs in breast cancer cells.
Modelling the effects of topographic heterogeneity on distribution of Nitraria tangutorum Bobr. species in deserts using LiDAR-data
Authors: Zhou Huoyan , Feng Linyan , Fu Liyong , Sharma Ram P. , Zhou Xiao , Zhao Xiaodi 
Published: August 2023

AbstractMicroclimate ecology is attracting renewed attention because of its fundamental importance in understanding how organisms respond to climate change. Many hot issues can be investigated in desert ecosystems, including the relationship between species distribution and environmental gradients (e.g., elevation, slope, topographic convergence index, and solar insolation). Species Distribution Models (SDMs) can be used to understand these relationships. We used data acquired from the important desert plant Nitraria tangutorum Bobr. communities and desert topographic factors extracted from LiDAR (Light Detection and Ranging) data of one square kilometer in the inner Mongolia region of China to develop SDMs. We evaluated the performance of SDMs developed with a variety of both the parametric and nonparametric algorithms (Bioclimatic Modelling (BIOCLIM), Domain, Mahalanobi, Generalized Linear Model, Generalized Additive Model, Random Forest (RF), and Support Vector Machine). The area under the receiver operating characteristic curve was used to evaluate these algorithms. The SDMs developed with RF showed the best performance based on the area under curve (0.7733). We also produced the Nitraria tangutorum Bobr. distribution maps with the best SDM and suitable habitat area of the Domain model. Based on the suitability map, we conclude that Nitraria tangutorum Bobr. is more suited to southern part with 0–20 degree slopes at an elevation of approximately 1010 m. This is the first attempt of modelling the effects of topographic heterogeneity on the desert species distribution on a small scale. The presented SDMs can have important applications for predicting species distribution and will be useful for preparing conservation and management strategies for desert ecosystems on a small scale.
Water resources allocation considering water supply and demand uncertainties using newsvendor model-based framework
Authors: He Yanhu , Zheng Yanhui , Chen Xiaohong , Liu Binfen , Tan Qian 
Published: August 2023

AbstractA novel newsvendor model-based framework for regional industrial water resources allocation that considers uncertainties in water supply and demand was proposed in this study. This framework generates optimal water allocation schemes while minimizing total costs. The total cost of water allocation consists of the allocated water cost, the opportunity loss for not meeting water demand, and the loss of the penalty for exceeding water demand. The uncertainties in water demand and supply are expressed by cumulative distribution functions. The optimal water allocation for each water use sector is determined by the water price, the unit loss of the penalty and opportunity loss, and the cumulative distribution functions. The model was then applied to monthly water allocation for domestic, industrial, and agricultural water use in two counties of Huizhou City, China, whose water supply mainly depends on Baipenzhu Reservoir. The water demand for each water use sector and the monthly reservoir inflow showed good fits with the uniform and P-III distributions, respectively. The water demand satisfied ratio for each water use sector was stable and increased for the optimal water allocation scheme from the newsvendor model-based framework, and the costs were lower compared with the actual water allocation scheme. The novel framework is characterized by less severe water shortages, lower costs, and greater similarity to actual water use compared with the traditional deterministic multi-objective analysis model, and demonstrates strong robustness in the advantages of lower released surplus water and higher water demand satisfied ratio. This novel framework yields the optimal water allocation for each water use sector by integrating the properties of the market (i.e., determining the opportunity loss for not meeting water demand) with the government (i.e., determining the water price and the loss of the penalty for exceeding water demand) under the strictest water resources management systems.
Serum components influence antibody reactivity to glycan and DNA antigens
Authors: Okuda Tetsuya , Kato Katsuya 
Published: August 2023

AbstractWe previously generated three types of anti-glycan monoclonal IgM antibodies that react with certain structures on the glycans of glycosphingolipids and glycoproteins. As the nucleotide sequences for the variable regions of these IgM antibodies showed homology with those of anti-DNA antibodies deposited in public databases, we analyzed the reactivity of the anti-glycan IgM antibodies to DNA by ELISA. We found that anti-α2,6-sialyl LacNAc IgM in the supernatant of a hybridoma culture cross-reacted with DNA, and after purification of the IgM by zirconia column chromatography, the highly purified IgM showed increased cross-reactivity to DNA. As most of the contaminating bovine serum proteins in the culture supernatant were removed by the purification process, it is likely that a part of the removed components influences antibody reactivity to DNA. Purified anti-DNA antibodies prepared from lupus model NZB/W F1 and MRL/lpr mouse sera and normal human serum were then analyzed, and similar results showing increased reactivity to DNA were obtained. Furthermore, ELISA using these purified antibodies and various carbohydrate antigens showed that the antigen-binding specificity of these antibodies was altered by the purification process from serum-containing antibody preparations. Our results indicate that mammalian serum contains components that strongly influence antibody reactivity to carbohydrate antigens, including DNA.
Tokenization of social media engagements increases the sharing of false (and other) news but penalization moderates it
Authors: Alizadeh Meysam , Hoes Emma , Gilardi Fabrizio 
Published: August 2023

AbstractSome major social media companies are announcing plans to tokenize user engagements, derived from blockchain-based decentralized social media. This would bring financial and reputational incentives for engagement, which might lead users to post more objectionable content. Previous research showed that financial or reputational incentives for accuracy decrease the willingness to share misinformation. However, it is unclear to what extent such outcome would change if engagements instead of accuracy were incentivized, which is a more realistic scenario. To address this question, we conducted a survey experiment to examine the effects of hypothetical token incentives. We find that a simple nudge about the possibility of earning token-based points for the achieved user engagements increases the willingness to share different kinds of news, including misinformation. The presence of penalties for objectionable posts diminishes the positive effect of tokenization rewards on misinformation sharing, but it does not eliminate it. These results have policy implications for content moderation practices if platforms embrace decentralization and engagement tokenization.
Changes in anisometropia by age in children with hyperopia, myopia, and antimetropia
Authors: Lin Han-Wen , Young Meng-Ling , Pu Christy , Huang Chung-Ying , Lin Ken-Kuo , Lee Jiahn-Shing , Hou Chiun-Ho 
Published: August 2023

AbstractAnisometropia is a unique condition of both eyes and it is associated with vision problems such as amblyopia and reduced stereoacuity. Previous studies have not reported its change pattern by age and its correlation with the refractive condition of both eyes. This study aims to compare the changes in anisometropia by age in children with hyperopia, myopia, and antimetropia. In total, 156 children were included. Children aged 3–11 years with anisometropia ≥ 1.00 D were followed up for ≥ 1 year with ≥ 2 visits at two medical centers in Taiwan. Refractive errors by cycloplegic autorefractometry, best-corrected visual acuity, eye position, and atropine use were recorded. The children were divided into hyperopic, myopic, and antimetropic groups. The results showed that anisometropia decreased in children aged < 6 years (3.34–2.96 D; P = 0.038) and increased in older children (2.16–2.55 D; P = 0.005). In children aged 3, 4, 5, and 6 years, the mean anisometropia was higher in children with myopia and antimetropia than in those with hyperopia (P = 0.005, 0.002, 0.001, and 0.011, respectively). The differences were not significant in children aged > 6 years (all P > 0.05). The factors associated with changes in anisometropia were age, refractive group, amblyopia, and strabismus. Anisometropia decreased with age in children younger than 6 years, and the changes in anisometropia was found in children with myopia and antimetropia.
Wolf genetic diversity compared across Europe using the yardstick method
Authors: Jan Maja , Stronen Astrid Vik , Boljte Barbara , Černe Rok , Huber Đuro , Iosif Ruben , Kljun Franc , Konec Marjeta , Kos Ivan , Krofel Miha , Kusak Josip , Luštrik Roman , Majić Skrbinšek Aleksandra , Promberger–Füerpass Barbara , Potočnik Hubert , Rigg Robin , Trontelj Peter , Skrbinšek Tomaž 
Published: August 2023

AbstractIntegrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the “yardstick” method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4–17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.