bluuebunny/crossref_metadata_2025_split huggingface dataset:
16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling
Authors: Deissová Tereza , Zapletalová Martina , Kunovský Lumír , Kroupa Radek , Grolich Tomáš , Kala Zdeněk , Bořilová Linhartová Petra , Lochman Jan 
Published: August 2023

Abstract16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1–V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1–V2M primers. Moreover, the V1–V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1–V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research.
Social media analysis reveals environmental injustices in Philadelphia urban parks
Authors: Walter Matthew , Bagozzi Benjamin E. , Ajibade Idowu , Mondal Pinki 
Published: August 2023

AbstractThe United Nations Sustainable Development Goal (SDG) target 11.7 calls for access to safe and inclusive green spaces for all communities. Yet, historical residential segregation in the USA has resulted in poor quality urban parks near neighborhoods with primarily disadvantaged socioeconomic status groups, and an extensive park system that addresses the needs of primarily White middle-class residents. Here we center the voices of historically marginalized urban residents by using Natural Language Processing and Geographic Information Science to analyze a large dataset (n = 143,913) of Google Map reviews from 2011 to 2022 across 285 parks in the City of Philadelphia, USA. We find that parks in neighborhoods with a high number of residents from historically disadvantaged demographic groups are likely to receive lower scores on Google Maps. Physical characteristics of these parks based on aerial and satellite images and ancillary data corroborate the public perception of park quality. Topic modeling of park reviews reveal that the diverse environmental justice needs of historically marginalized communities must be met to reduce the uneven park quality—a goal in line with achieving SDG 11 by 2030.
Photonic synaptic transistors with new electron trapping layer for high performance and ultra-low power consumption
Authors: Kim Taewoo , Yun Kwang-Seok 
Published: August 2023

AbstractPhotonic synaptic transistors are being investigated for their potential applications in neuromorphic computing and artificial vision systems. Recently, a method for establishing a synaptic effect by preventing the recombination of electron–hole pairs by forming an energy barrier with a double-layer consisting of a channel and a light absorption layer has shown effective results. We report a triple-layer device created by coating a novel electron-trapping layer between the light-absorption layer and the gate-insulating layer. Compared to the conventional double-layer photonic synaptic structure, our triple-layer device significantly reduces the recombination rate, resulting in improved performance in terms of the output photocurrent and memory characteristics. Furthermore, our photonic synaptic transistor possesses excellent synaptic properties, such as paired-pulse facilitation (PPF), short-term potentiation (STP), and long-term potentiation (LTP), and demonstrates a good response to a low operating voltage of − 0.1 mV. The low power consumption experiment shows a very low energy consumption of 0.01375 fJ per spike. These findings suggest a way to improve the performance of future neuromorphic devices and artificial vision systems.
Numerical analysis of pore-scale CO2-EOR at near-miscible flow condition to perceive the displacement mechanism
Authors: Behnoud Parisa , Khorsand Movaghar Mohammad Reza , Sabooniha Ehsan 
Published: August 2023

AbstractGas flooding through the injection of $$\text{CO}_{2}$$

CO
2

is generally performed to achieve optimum oil recovery from underground hydrocarbon reservoirs. However, miscible flooding, which is the most efficient way to achieve maximum oil recovery, is not suitable for all reservoirs due to challenge in maintaining pressure conditions. In this circumstances, a near-miscible process may be more practical. This study focuses on pore-scale near-miscible $$\text{CO}_{2}$$

CO
2

–Oil displacement, using available literature criteria to determine the effective near-miscible region. For the first time, two separate numerical approaches are coupled to examine the behavior of $$\text{CO}_{2}$$

CO
2

–oil at the lower-pressure boundary of the specified region. The first one, the Phase-field module, was implemented to trace the movement of fluids in the displacement $$\text{CO}_{2}$$

CO
2

–Oil process by applying the Navier–Stokes equation. Next is the TDS module which incorporates the effect of $$\text{CO}_{2}$$

CO
2

mass transfer into the oil phase by coupling classical Fick’s law to the fluids interface to track the variation of $$\text{CO}_{2}$$

CO
2

diffusion coefficient. To better recognize the oil recovery mechanism in pore-scale, qualitative analysis indicates that interface is moved into the by-passed oil due to low interfacial tension in the near-miscible region. Moreover, behind the front ahead of the main flow stream, the $$\text{CO}_{2}$$

CO
2

phase can significantly displace almost all the bypassed oil in normal pores and effectively decrease the large amounts in small pores. The results show that by incorporating mass transfer and capillary cross-flow mechanisms in the simulations, the displacement of by-passed oil in pores can be significantly improved, leading to an increase in oil recovery from 92 to over 98%, which is comparable to the result of miscible gas injection. The outcome of this research emphasizes the significance of applying the $$\text{CO}_{2}$$

CO
2

-EOR process under near-miscible operating conditions.
Functional toner for office laser printer and its application for printing of paper-based superwettable patterns and devices
Authors: Liu Yanhua , Liu Xingfei , Chen Juanning , Zhang Zhuanli , Feng Libang 
Published: August 2023

AbstractLaserjet printing is a kind of facile and digital do-it-yourself strategies, which is of importance to fabricate inexpensive paper-based microfluidic devices. However, the printed hydrophobic barrier is not hydrophobic enough due to the weak hydrophobicity and requires subsequent heating, which can lead to the pyrolysis of cellulose in the paper and influence the detection results. Here, for the first time, we report a kind of functional toner including toner and polydopamine (PDA) nanocapsules which contains oleic acid modified ferric tetroxide (OA-Fe3O4) and octadecylamine (ODA), which is suitable for printing with desired shapes and sizes to lead to formation of superhydrophobic barriers. Moreover, patterns printed with functional toner have good stability, including resistance to moisture, ultraviolet (UV) and bending. Finally, a proof-of-concept of metal and nitrite ions testing is demonstrated using colorimetric analysis, and the results show that the printed devices successfully perform instant detection of ions. The developed functional toner offers easy fabrication, cost-effectiveness and mass production of paper-based devices. In general, this strategy provides a new idea and technical support for the rapid prototyping of microfluidic paper-based analytical devices (μPADs) using laserjet printing.
Multiquanta flux jumps in superconducting fractal
Authors: Vlasko-Vlasov Vitalii K. , Divan Ralu , Rosenmann Daniel , Welp Ulrich , Glatz Andreas , Kwok Wai-Kwong 
Published: August 2023

AbstractWe study the magnetic field response of millimeter scale fractal Sierpinski gaskets (SG) assembled of superconducting equilateral triangular patches. Directly imaged quantitative induction maps reveal hierarchical periodic filling of enclosed void areas with multiquanta magnetic flux, which jumps inside the voids in repeating bundles of individual flux quanta Φ0. The number Ns of entering flux quanta in different triangular voids of the SG is proportional to the linear size s of the void, while the field periodicity of flux jumps varies as 1/s. We explain this behavior by modeling the triangular voids in the SG with effective superconducting rings and by calculating their response following the London analysis of persistent currents, Js, induced by the applied field Ha and by the entering flux. With changing Ha, Js reaches a critical value in the vertex joints that connect the triangular superconducting patches and allows the giant flux jumps into the SG voids through phase slips or multiple Abrikosov vortex transfer across the vertices. The unique flux behavior in superconducting SG patterns, may be used to design tunable low-loss resonators with multi-line high-frequency spectrum for microwave technologies.
The high-throughput atomization of polymer solutions for fiber synthesis in a single step aided with corona ionizers
Authors: Modesto-López Luis B. , Gañán-Calvo Alfonso M. 
Published: August 2023

AbstractPolymer microfibers are ubiquitous structures across virtually all technological fields. Their applications include, for instance, filter media, tissue regeneration, wound healing and dressing, and reinforcement materials. The most effective methods for fabrication of fibrous micro and nanomaterials rely on electric fields to spin a liquid jet into an ultrafine thread that rapidly dries up forming a fiber. Continuous spinning and collection leads to formation of fiber mats. Here we report a robust yet simple approach for the massive production of liquid threads, which upon acquiring electrical charges in-flight are collected downstream in the form of fibers. The entire process takes place on-line in a single step. The liquid threads are produced through the fragmentation of a polymer solution bulk due to a turbulent interaction of a gas–liquid interface in the interior of an engineered device, a so-called Flow Blurring atomizer. The particularity of this approach consists precisely in such vigorous interaction, at the micrometer scale, which triggers a bubbly motion in the interior of the device, that is a “micro-mixing”. Subsequently, the threads are passed through ionized air currents, at ambient conditions, and then stretched to sub-micrometer dimensions by electric fields. Polyvinylpyrrolidone (PVP) as well as carbon nanotubes (CNTs) or graphene oxide sheets (GOSs)-containing PVP fibers, with diameters in the range 100–900 nm, were synthesized via this approach. In the cases studied herein the method was operated at liquid flow rates (i.e. production rates) of 0.2 mL/min but it could be readily increased up to a few tens of mL/min. The method requires further improvement and optimization, nevertheless it is a promising alternative for mass production of polymer fibers.
A pilot radiometabolomics integration study for the characterization of renal oncocytic neoplasia
Authors: Klontzas Michail E. , Koltsakis Emmanouil , Kalarakis Georgios , Trpkov Kiril , Papathomas Thomas , Sun Na , Walch Axel , Karantanas Apostolos H. , Tzortzakakis Antonios 
Published: August 2023

AbstractDifferentiating benign renal oncocytic tumors and malignant renal cell carcinoma (RCC) on imaging and histopathology is a critical problem that presents an everyday clinical challenge. This manuscript aims to demonstrate a novel methodology integrating metabolomics with radiomics features (RF) to differentiate between benign oncocytic neoplasia and malignant renal tumors. For this purpose, thirty-three renal tumors (14 renal oncocytic tumors and 19 RCC) were prospectively collected and histopathologically characterised. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) was used to extract metabolomics data, while RF were extracted from CT scans of the same tumors. Statistical integration was used to generate multilevel network communities of -omics features. Metabolites and RF critical for the differentiation between the two groups (delta centrality > 0.1) were used for pathway enrichment analysis and machine learning classifier (XGboost) development. Receiver operating characteristics (ROC) curves and areas under the curve (AUC) were used to assess classifier performance. Radiometabolomics analysis demonstrated differential network node configuration between benign and malignant renal tumors. Fourteen nodes (6 RF and 8 metabolites) were crucial in distinguishing between the two groups. The combined radiometabolomics model achieved an AUC of 86.4%, whereas metabolomics-only and radiomics-only classifiers achieved AUC of 72.7% and 68.2%, respectively. Analysis of significant metabolite nodes identified three distinct tumour clusters (malignant, benign, and mixed) and differentially enriched metabolic pathways. In conclusion, radiometabolomics integration has been presented as an approach to evaluate disease entities. In our case study, the method identified RF and metabolites important in differentiating between benign oncocytic neoplasia and malignant renal tumors, highlighting pathways differentially expressed between the two groups. Key metabolites and RF identified by radiometabolomics can be used to improve the identification and differentiation between renal neoplasms.
Bovine milk-derived cells express transcriptome markers of pluripotency and secrete bioactive factors with regenerative and antimicrobial activity
Authors: Danev Nikola , Harman Rebecca M. , Oliveira Leane , Huntimer Lucas , Van de Walle Gerlinde R. 
Published: August 2023

AbstractThe bovine mammary stem/progenitor cell secretome stimulates regeneration in vitro and contains proteins associated with antimicrobial defense. This has led to the exploration of the secretome as a biologic treatment for mastitis, a costly inflammation of the udder commonly caused by bacteria. This study reports on a population of bovine mammary stem/progenitor cells isolated non-invasively from milk (MiDCs). MiDCs were characterized by immunophenotyping, mammosphere formation assays, and single cell RNA sequencing. They displayed epithelial morphology, exhibited markers of mammary stem/progenitor cells, and formed mammospheres, like mammary gland tissue-isolated stem/progenitor cells. Single cell RNA sequencing revealed two sub-populations of MiDCs: epithelial cells and macrophages. Functionally, the MiDC secretome increased fibroblast migration, promoted angiogenesis of endothelial cells, and inhibited the growth of mastitis-associated bacteria, including antibiotic-resistant strains, in vitro. These qualities of MiDCs render them a source of stem cells and stem cell products that may be used to treat diseases affecting the dairy industry, including mastitis.
The adenine-modified edible chitosan films containing choline chloride and citric acid mixture
Authors: Gierszewska Magdalena , Jakubowska Ewelina , Richert Agnieszka 
Published: August 2023

AbstractA series of biopolymeric chitosan-based (Ch) films were prepared with choline chloride and citric acid plasticizer (deep eutectic solvent, DES). An effect of adenine (A, vitamin B4) addition on the functional properties of these films was evaluated. Several physicochemical and mechanical properties were tested: Fourier-transformed infrared spectra proved DES's plasticizing and crosslinking effect, while scanning electron microscopy and atomic force microscopy techniques confirmed the possible phase separation after adenine addition. These changes affected the mechanical characteristics and the water vapor and oxygen permeability. The prepared materials are not water soluble because the CA acts as a crosslinker. The adenine addition on antioxidative and antimicrobial properties was also checked. It was found that Ch-DES materials with A exhibit improved antioxidative properties (55.8–66.1% of H2O2 scavenging activity) in contrast to the pristine chitosan-DES material (51.1% of H2O2 scavenging activity), while the material is still non-mutagenic (lack of growth of Salmonella typhimurium) and possesses antimicrobial features (no E. coli observed for all the tested films and inhibition zones noted for S. aureus). The mentioned properties, reduced oxygen transmission (1.6–2.1 g m−2 h−1), and mechanical characteristics within the range of typical food packaging plastics proved the potential of Ch-DES-A films in the packaging sector. Moreover, the antioxidative properties, usage of substrates being allowed as food additives, and the presence of adenine create the advantage of the Ch-DES-A materials as edible coatings, being also a source of Vitamin B4.
The importance of face-shape masculinity for perceptions of male dominance depends on study design
Authors: Dong Junzhi , Leger Kathlyne , Shiramizu Victor K. M. , Marcinkowska Urszula M. , Lee Anthony J. , Jones Benedict C. 
Published: August 2023

AbstractDominance perceptions play an important role in social interactions. Although many researchers have proposed that shape masculinity is an important facial cue for dominance perceptions, evidence for this claim has come almost exclusively from studies that assessed perceptions of experimentally manipulated faces using forced-choice paradigms. Consequently, we investigated the role of masculine shape characteristics in perceptions of men’s facial dominance (1) when shape-manipulated stimuli were presented in a forced-choice paradigm and (2) when unmanipulated face images were rated for dominance and shape masculinity was measured from face images. Although we observed large effects of masculinity on dominance perceptions when we used the forced-choice method (Cohen’s ds = 2.51 and 3.28), the effect of masculinity on dominance perceptions was considerably smaller when unmanipulated face images were rated and shape masculinity measured from face images (Cohen’s ds = 0.44 and 0.62). This pattern was observed when faces were rated separately for physical dominance, social dominance, and masculinity, and was seen for two different sets of stimuli. Collectively, these results suggest that shape masculinity may not be a particularly important cue for dominance perceptions when faces vary simultaneously on multiple dimensions, as is the case during everyday social interactions.
Resensitizing multidrug-resistant Gram-negative bacteria to carbapenems and colistin using disulfiram
Authors: Chen Chen , Cai Jinju , Shi Jingru , Wang Zhiqiang , Liu Yuan 
Published: August 2023

AbstractThe increasing incidence of bacterial infections caused by multidrug-resistant (MDR) Gram-negative bacteria has deepened the need for new effective treatments. Antibiotic adjuvant strategy is a more effective and economical approach to expand the lifespan of currently used antibiotics. Herein, we uncover that alcohol-abuse drug disulfiram (DSF) and derivatives thereof are potent antibiotic adjuvants, which dramatically potentiate the antibacterial activity of carbapenems and colistin against New Delhi metallo-β-lactamase (NDM)- and mobilized colistin resistance (MCR)-expressing Gram-negative pathogens, respectively. Mechanistic studies indicate that DSF improves meropenem efficacy by specifically inhibiting NDM activity. Moreover, the robust potentiation of DSF to colistin is due to its ability to exacerbate the membrane-damaging effects of colistin and disrupt bacterial metabolism. Notably, the passage and conjugation assays reveal that DSF minimizes the evolution and spread of meropenem and colistin resistance in clinical pathogens. Finally, their synergistic efficacy in animal models was evaluated and DSF-colistin/meropenem combination could effectively treat MDR bacterial infections in vivo. Taken together, our works demonstrate that DSF and its derivatives are versatile and potent colistin and carbapenems adjuvants, opening a new horizon for the treatment of difficult-to-treat infections.
Inference of long-range cell-cell force transmission from ECM remodeling fluctuations
Authors: Nahum Assaf , Koren Yoni , Ergaz Bar , Natan Sari , Miller Gad , Tamir Yuval , Goren Shahar , Kolel Avraham , Jagadeeshan Sankar , Elkabets Moshe , Lesman Ayelet , Zaritsky Assaf 
Published: August 2023

AbstractCells sense, manipulate and respond to their mechanical microenvironment in a plethora of physiological processes, yet the understanding of how cells transmit, receive and interpret environmental cues to communicate with distant cells is severely limited due to lack of tools to quantitatively infer the complex tangle of dynamic cell-cell interactions in complicated environments. We present a computational method to systematically infer and quantify long-range cell-cell force transmission through the extracellular matrix (cell-ECM-cell communication) by correlating ECM remodeling fluctuations in between communicating cells and demonstrating that these fluctuations contain sufficient information to define unique signatures that robustly distinguish between different pairs of communicating cells. We demonstrate our method with finite element simulations and live 3D imaging of fibroblasts and cancer cells embedded in fibrin gels. While previous studies relied on the formation of a visible fibrous ‘band’ extending between cells to inform on mechanical communication, our method detected mechanical propagation even in cases where visible bands never formed. We revealed that while contractility is required, band formation is not necessary, for cell-ECM-cell communication, and that mechanical signals propagate from one cell to another even upon massive reduction in their contractility. Our method sets the stage to measure the fundamental aspects of intercellular long-range mechanical communication in physiological contexts and may provide a new functional readout for high content 3D image-based screening. The ability to infer cell-ECM-cell communication using standard confocal microscopy holds the promise for wide use and democratizing the method.
Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota
Authors: Ji Ming , Xu Xiaojiang , Xu Qing , Hsiao Yun-Chung , Martin Cody , Ukraintseva Svetlana , Popov Vladimir , Arbeev Konstantin G. , Randall Tom A. , Wu Xiaoyue , Garcia-Peterson Liz M. , Liu Juan , Xu Xin , Andrea Azcarate-Peril M. , Wan Yisong , Yashin Anatoliy I. , Anantharaman Karthik , Lu Kun , Li Jian-Liang , Shats Igor , Li Xiaoling 
Published: August 2023

AbstractRestriction of methionine (MR), a sulfur-containing essential amino acid, has been reported to repress cancer growth and improve therapeutic responses in several preclinical settings. However, how MR impacts cancer progression in the context of the intact immune system is unknown. Here we report that while inhibiting cancer growth in immunocompromised mice, MR reduces T cell abundance, exacerbates tumour growth and impairs tumour response to immunotherapy in immunocompetent male and female mice. Mechanistically, MR reduces microbial production of hydrogen sulfide, which is critical for immune cell survival/activation. Dietary supplementation of a hydrogen sulfide donor or a precursor, or methionine, stimulates antitumour immunity and suppresses tumour progression. Our findings reveal an unexpected negative interaction between MR, sulfur deficiency and antitumour immunity and further uncover a vital role of gut microbiota in mediating this interaction. Our study suggests that any possible anticancer benefits of MR require careful consideration of both the microbiota and the immune system.