bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription
Authors: Bressin Annkatrin , Jasnovidova Olga , Arnold Mirjam , Altendorfer Elisabeth , Trajkovski Filip , Kratz Thomas A. , Handzlik Joanna E. , Hnisz Denes , Mayer Andreas 
Published: August 2023

AbstractGene transcription by RNA polymerase II (Pol II) is under control of promoters and distal regulatory elements known as enhancers. Enhancers are themselves transcribed by Pol II correlating with their activity. How enhancer transcription is regulated and coordinated with transcription at target genes has remained unclear. Here, we developed a high-sensitive native elongating transcript sequencing approach, called HiS-NET-seq, to provide an extended high-resolution view on transcription, especially at lowly transcribed regions such as enhancers. HiS-NET-seq uncovers new transcribed enhancers in human cells. A multi-omics analysis shows that genome-wide enhancer transcription depends on the BET family protein BRD4. Specifically, BRD4 co-localizes to enhancer and promoter-proximal gene regions, and is required for elongation activation at enhancers and their genes. BRD4 keeps a set of enhancers and genes in proximity through long-range contacts. From these studies BRD4 emerges as a general regulator of enhancer transcription that may link transcription at enhancers and genes.
Rapid self-heating synthesis of Fe-based nanomaterial catalyst for advanced oxidation
Authors: Yu Fengbo , Jia Chao , Wu Xuan , Sun Liming , Shi Zhijian , Teng Tao , Lin Litao , He Zhelin , Gao Jie , Zhang Shicheng , Wang Liang , Wang Shaobin , Zhu Xiangdong 
Published: August 2023

AbstractIron-based catalysts are promising candidates for advanced oxidation process-based wastewater remediation. However, the preparation of these materials often involves complex and energy intensive syntheses. Further, due to the inherent limitations of the preparation conditions, it is challenging to realise the full potential of the catalyst. Herein, we develop an iron-based nanomaterial catalyst via soft carbon assisted flash joule heating (FJH). FJH involves rapid temperature increase, electric shock, and cooling, the process simultaneously transforms a low-grade iron mineral (FeS) and soft carbon into an electron rich nano Fe0/FeS heterostructure embedded in thin-bedded graphene. The process is energy efficient and consumes 34 times less energy than conventional pyrolysis. Density functional theory calculations indicate that the electron delocalization of the FJH-derived heterostructure improves its binding ability with peroxydisulfate via bidentate binuclear model, thereby enhancing ·OH yield for organics mineralization. The Fe-based nanomaterial catalyst exhibits strong catalytic performance over a wide pH range. Similar catalysts can be prepared using other commonly available iron precursors. Finally, we also present a strategy for continuous and automated production of the iron-based nanomaterial catalysts.
Microdiversity of the vaginal microbiome is associated with preterm birth
Authors: Liao Jingqiu , Shenhav Liat , Urban Julia A. , Serrano Myrna , Zhu Bin , Buck Gregory A. , Korem Tal 
Published: August 2023

AbstractPreterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find thatGardnerellaspecies drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence thatGardnerellaspp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.
In-plane reorientation induced single laser pulse magnetization reversal
Authors: Peng Y. , Salomoni D. , Malinowski G. , Zhang W. , Hohlfeld J. , Buda-Prejbeanu L. D. , Gorchon J. , Vergès M. , Lin J. X. , Lacour D. , Sousa R. C. , Prejbeanu I. L. , Mangin S. , Hehn M. 
Published: August 2023

AbstractSingle Pulse All Optical Switching represents the ability to reverse the magnetization of a nanostructure using a femtosecond single laser pulse without any applied field. Since the first switching experiments carried out on GdFeCo ferrimagnets, this phenomena has been only recently extended to a few other materials, MnRuGa alloys and Tb/Co multilayers with a very specific range of thickness and composition. Here, we demonstrate that single pulse switching can be obtained for a large range of rare earth–transition metal multilayers, making this phenomenon much more general. Surprisingly, the threshold fluence for switching is observed to be independent of the laser pulse duration. Moreover, at high laser intensities, concentric ring domain structures are induced. These striking features contrast to those observed in Gd based materials pointing towards a different reversal mechanism. Concomitant with the demonstration of an in-plane magnetization reorientation, a precessional reversal mechanism explains all the observed features.
Thin, soft, wearable system for continuous wireless monitoring of artery blood pressure
Authors: Li Jian , Jia Huiling , Zhou Jingkun , Huang Xingcan , Xu Long , Jia Shengxin , Gao Zhan , Yao Kuanming , Li Dengfeng , Zhang Binbin , Liu Yiming , Huang Ya , Hu Yue , Zhao Guangyao , Xu Zitong , Li Jiyu , Yiu Chun Ki , Gao Yuyu , Wu Mengge , Jiao Yanli , Zhang Qiang , Tai Xuecheng , Chan Raymond H. , Zhang Yuanting , Ma Xiaohui , Yu Xinge 
Published: August 2023

AbstractContinuous monitoring of arterial blood pressure (BP) outside of a clinical setting is crucial for preventing and diagnosing hypertension related diseases. However, current continuous BP monitoring instruments suffer from either bulky systems or poor user-device interfacial performance, hampering their applications in continuous BP monitoring. Here, we report a thin, soft, miniaturized system (TSMS) that combines a conformal piezoelectric sensor array, an active pressure adaptation unit, a signal processing module, and an advanced machine learning method, to allow real wearable, continuous wireless monitoring of ambulatory artery BP. By optimizing the materials selection, control/sampling strategy, and system integration, the TSMS exhibits improved interfacial performance while maintaining Grade A level measurement accuracy. Initial trials on 87 volunteers and clinical tracking of two hypertension individuals prove the capability of the TSMS as a reliable BP measurement product, and its feasibility and practical usability in precise BP control and personalized diagnosis schemes development.
Global analysis of ocean phytoplankton nutrient limitation reveals high prevalence of co-limitation
Authors: Browning Thomas J. , Moore C. Mark 
Published: August 2023

AbstractNutrient availability limits phytoplankton growth throughout much of the global ocean. Here we synthesize available experimental data to identify three dominant nutrient limitation regimes: nitrogen is limiting in the stratified subtropical gyres and in the summertime Arctic Ocean, iron is most commonly limiting in upwelling regions, and both nutrients are frequently co-limiting in regions in between the nitrogen and iron limited systems. Manganese can be co-limiting with iron in parts of the Southern Ocean, whilst phosphate and cobalt can be co-/serially limiting in some settings. Overall, an analysis of experimental responses showed that phytoplankton net growth can be significantly enhanced through increasing the number of different nutrients supplied, regardless of latitude, temperature, or trophic status, implying surface seawaters are often approaching nutrient co-limitation. Assessments of nutrient deficiency based on seawater nutrient concentrations and nutrient stress diagnosed via molecular biomarkers showed good agreement with experimentally-assessed nutrient limitation, validating conceptual and theoretical links between nutrient stoichiometry and microbial ecophysiology.
A nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore
Authors: Ji Meiyuan , Vandenhole Marilou , De Beer Berdien , De Rouck Sander , Villacis-Perez Ernesto , Feyereisen René , Clark Richard M. , Van Leeuwen Thomas 
Published: August 2023

AbstractThe role, magnitude, and molecular nature of trans-driven expression variation underlying the upregulation of detoxification genes in pesticide resistant arthropod populations has remained enigmatic. In this study, we performed expression quantitative trait locus (eQTL) mapping (n = 458) between a pesticide resistant and a susceptible strain of the generalist herbivore and crop pest Tetranychus urticae. We found that a single trans eQTL hotspot controlled large differences in the expression of a subset of genes in different detoxification gene families, as well as other genes associated with host plant use. As established by additional genetic approaches including RNAi gene knockdown, a duplicated gene with a nuclear hormone receptor HR96-related ligand-binding domain was identified as causal for the expression differences between strains. The presence of a large family of HR96-related genes in T. urticae may enable modular control of detoxification and host plant use genes, facilitating this species’ known and rapid evolution to diverse pesticides and host plants.
Skin-like cryogel electronics from suppressed-freezing tuned polymer amorphization
Authors: Zhang Xiansheng , Yan Hongwei , Xu Chongzhi , Dong Xia , Wang Yu , Fu Aiping , Li Hao , Lee Jin Yong , Zhang Sheng , Ni Jiahua , Gao Min , Wang Jing , Yu Jinpeng , Ge Shuzhi Sam , Jin Ming Liang , Wang Lili , Xia Yanzhi 
Published: August 2023

AbstractThe sole situation of semi-crystalline structure induced single performance remarkably limits the green cryogels in the application of soft devices due to uncontrolled freezing field. Here, a facile strategy for achieving multifunctionality of cryogels is proposed using total amorphization of polymer. Through precisely lowering the freezing point of precursor solutions with an antifreezing salt, the suppressed growth of ice is achieved, creating an unusually weak and homogenous aggregation of polymer chains upon freezing, thereby realizing the tunable amorphization of polymer and the coexistence of free and hydrogen bonding hydroxyl groups. Such multi-scale microstructures trigger the integrated properties of tissue-like ultrasoftness (Young’s modulus <10 kPa) yet stretchability, high transparency (~92%), self-adhesion, and instantaneous self-healing (<0.3 s) for cryogels, along with superior ionic-conductivity, antifreezing (−58 °C) and water-retention abilities, pushing the development of skin-like cryogel electronics. These concepts open an attractive branch for cryogels that adopt regulated crystallization behavior for on-demand functionalities.
Inactivation kinetics of horseradish peroxidase (HRP) by hydrogen peroxide
Authors: Morales-Urrea Diego , López-Córdoba Alex , Contreras Edgardo M. 
Published: August 2023

AbstractIn recent years, the peroxidase enzymes have generated wide interest in several industrial processes, such as wastewater treatments, food processing, pharmaceuticals, and the production of fine chemicals. However, the low stability of the peroxidases in the presence of hydrogen peroxide (H2O2) has limited its commercial use. In the present work, the effect of H2O2 on the inactivation of horseradish peroxidase (HRP) was evaluated. Three states of HRP (E0, E2, and E3) were identified. While in the absence of H2O2, the resting state E0 was observed, in the presence of low and high concentrations of H2O2, E2, and E3 were found, respectively. The results showed that HRP catalyzed the H2O2 decomposition, forming the species Ex, which was catalytically inactive. Results suggest that this loss of enzymatic activity is an intrinsic characteristic of the studied HRP. A model from a modified version of the Dunford mechanism of peroxidases was developed, which was validated against experimental data and findings reported by the literature.
Genetic variation among elite inbred lines suggests potential to breed for BNI-capacity in maize
Authors: Petroli César D. , Subbarao Guntur V. , Burgueño Juan A. , Yoshihashi Tadashi , Li Huihui , Franco Duran Jorge , Pixley Kevin V. 
Published: August 2023

AbstractBiological nitrification inhibition (BNI) is a plant function where root systems release antibiotic compounds (BNIs) specifically aimed at suppressing nitrifiers to limit soil-nitrate formation in the root zone. Little is known about BNI-activity in maize (Zea mays L.), the most important food, feed, and energy crop. Two categories of BNIs are released from maize roots; hydrophobic and hydrophilic BNIs, that determine BNI-capacity in root systems. Zeanone is a recently discovered hydrophobic compound with BNI-activity, released from maize roots. The objectives of this study were to understand/quantify the relationship between zeanone activity and hydrophobic BNI-capacity. We assessed genetic variability among 250 CIMMYT maize lines (CMLs) characterized for hydrophobic BNI-capacity and zeanone activity, towards developing genetic markers linked to this trait in maize. CMLs with high BNI-capacity and ability to release zeanone from roots were identified. GWAS was performed using 27,085 SNPs (with unique positions on the B73v.4 reference genome, and false discovery rate = 10), and phenotypic information for BNI-capacity and zeanone production from root systems. Eighteen significant markers were identified; three associated with specific BNI-activity (SBNI), four with BNI-activity per plant (BNIPP), another ten were common between SBNI and BNIPP, and one with zeanone release. Further, 30 annotated genes were associated with the significant SNPs; most of these genes are involved in pathways of “biological process”, and one (AMT5) in ammonium regulation in maize roots. Although the inbred lines in this study were not developed for BNI-traits, the identification of markers associated with BNI-capacity suggests the possibility of using these genomic tools in marker-assisted selection to improve hydrophobic BNI-capacity in maize.
Application of artificial intelligence in endoscopic image analysis for the diagnosis of a gastric cancer pathogen-Helicobacter pylori infection
Authors: Lin Chih-Hsueh , Hsu Ping-I , Tseng Chin-Dar , Chao Pei-Ju , Wu I-Ting , Ghose Supratip , Shih Chih-An , Lee Shen-Hao , Ren Jia-Hong , Shie Chang-Bih , Lee Tsair-Fwu 
Published: August 2023

AbstractHelicobacter pylori(H. pylori) infection is the principal cause of chronic gastritis, gastric ulcers, duodenal ulcers, and gastric cancer. In clinical practice, diagnosis ofH. pyloriinfection by a gastroenterologists’ impression of endoscopic images is inaccurate and cannot be used for the management of gastrointestinal diseases. The aim of this study was to develop an artificial intelligence classification system for the diagnosis ofH. pyloriinfection by pre-processing endoscopic images and machine learning methods. Endoscopic images of the gastric body and antrum from 302 patients receiving endoscopy with confirmation ofH. pyloristatus by a rapid urease test at An Nan Hospital were obtained for the derivation and validation of an artificial intelligence classification system. TheH. pyloristatus was interpreted as positive or negative by Convolutional Neural Network (CNN) and Concurrent Spatial and Channel Squeeze and Excitation (scSE) network, combined with different classification models for deep learning of gastric images. The comprehensive assessment forH. pyloristatus by scSE-CatBoost classification models for both body and antrum images from same patients achieved an accuracy of 0.90, sensitivity of 1.00, specificity of 0.81, positive predictive value of 0.82, negative predicted value of 1.00, and area under the curve of 0.88. The data suggest that an artificial intelligence classification model using scSE-CatBoost deep learning for gastric endoscopic images can distinguishH. pyloristatus with good performance and is useful for the survey or diagnosis ofH. pyloriinfection in clinical practice.
Room temperature multiferroicity in a transition metal dichalcogenide
Authors: Cardenas-Chirivi G. , Vega-Bustos K. , Rojas-Páez H. , Silvera-Vega D. , Pazos J. , Herrera O. , Macías M. A. , Espejo C. , López-Pérez W. , Galvis J. A. , Giraldo-Gallo P. 
Published: August 2023

AbstractThe coexistence of multiple ferroic orders, i.e., multiferroicity, is a scarce property to be found in materials. Historically, this state has been found mainly in 3-dimensional complex oxides, but so far, this state has still been elusive for the most widely studied and characterized family of 2-dimensional compounds, the transition metal dichalcogenides. In this study, we report the experimental realization of multiferroic states in this family of materials, at room temperature, in bulk single crystals of Te-doped WSe2. We observe the coexistence of ferromagnetism and ferroelectricity, evidenced in the presence of magnetization and piezoresponse force microscopy hysteresis loops. These findings open the possibility of widening the use and study of van der Waals-based multifunctional devices for nanoelectronics and spintronics applications.
Fossil brains provide evidence of underwater feeding in early seals
Authors: Lyras George A. , Werdelin Lars , van der Geer Bartholomeus G. M. , van der Geer Alexandra A. E. 
Published: August 2023

AbstractPinnipeds (seals and related species) use their whiskers to explore their environment and locate their prey. Today they live mostly in marine habitats and are adapted for a highly specialised amphibious lifestyle with their flippers for locomotion and a hydrodynamically streamlined body. The earliest pinnipeds, however, lived on land and in freshwater habitats, much like mustelids today. Here we reconstruct the underwater foraging behaviour of one of these earliest pinnipeds (Potamotherium), focusing in particular on how it used its whiskers (vibrissae). For this purpose, we analyse the coronal gyrus of the brain of 7 fossil and 31 extant carnivorans. This region receives somatosensory input from the head. Our results show that the reliance on whiskers in modern pinnipeds is an ancestral feature that favoured survival of stem pinnipeds in marine habitats. This study provides insights into an impressive ecological transition in carnivoran evolution: from terrestrial to amphibious marine species. Adaptations for underwater foraging were crucial for this transition.
Transcriptional profiling of canine osteosarcoma identifies prognostic gene expression signatures with translational value for humans
Authors: Mannheimer Joshua D. , Tawa Gregory , Gerhold David , Braisted John , Sayers Carly M. , McEachron Troy A. , Meltzer Paul , Mazcko Christina , Beck Jessica A. , LeBlanc Amy K. 
Published: August 2023

AbstractCanine osteosarcoma is increasingly recognized as an informative model for human osteosarcoma. Here we show in one of the largest clinically annotated canine osteosarcoma transcriptional datasets that two previously reported, as well as de novo gene signatures devised through single sample Gene Set Enrichment Analysis (ssGSEA), have prognostic utility in both human and canine patients. Shared molecular pathway alterations are seen in immune cell signaling and activation including TH1 and TH2 signaling, interferon signaling, and inflammatory responses. Virtual cell sorting to estimate immune cell populations within canine and human tumors showed similar trends, predominantly for macrophages and CD8+ T cells. Immunohistochemical staining verified the increased presence of immune cells in tumors exhibiting immune gene enrichment. Collectively these findings further validate naturally occurring osteosarcoma of the pet dog as a translationally relevant patient model for humans and improve our understanding of the immunologic and genomic landscape of the disease in both species.
Exploring the phase diagram of 3D artificial spin-ice
Authors: Saccone Michael , Van den Berg Arjen , Harding Edward , Singh Shobhna , Giblin Sean R. , Flicker Felix , Ladak Sam 
Published: August 2023

AbstractArtificial spin-ices consist of lithographic arrays of single-domain magnetic nanowires organised into frustrated lattices. These geometries are usually two-dimensional, allowing a direct exploration of physics associated with frustration, topology and emergence. Recently, three-dimensional geometries have been realised, in which transport of emergent monopoles can be directly visualised upon the surface. Here we carry out an exploration of the three-dimensional artificial spin-ice phase diagram, whereby dipoles are placed within a diamond-bond lattice geometry. We find a rich phase diagram, consisting of a double-charged monopole crystal, a single-charged monopole crystal and conventional spin-ice with pinch points associated with a Coulomb phase. In experimental demagnetised systems, broken symmetry forces formation of ferromagnetic stripes upon the surface, forbidding the lower energy double-charged monopole crystal. Instead, we observe crystallites of single magnetic charge, superimposed upon an ice background. The crystallites are found to form due to the distribution of magnetic charge around the 3D vertex, which locally favours monopole formation.