bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biophysical Drivers of Coastal Treeline Elevation
Authors: Molino G. D. , Carr J. A. , Ganju N. K. , Kirwan M. L. 
Published: December 2023

AbstractSea level rise is leading to the rapid migration of marshes into coastal forests and other terrestrial ecosystems. Although complex biophysical interactions likely govern these ecosystem transitions, projections of sea level driven land conversion commonly rely on a simplified “threshold elevation” that represents the elevation of the marsh‐upland boundary based on tidal datums alone. To determine the influence of biophysical drivers on threshold elevations, and their implication for land conversion, we examined almost 100,000 high‐resolution marsh‐forest boundary elevation points, determined independently from tidal datums, alongside hydrologic, ecologic, and geomorphic data in the Chesapeake Bay, the largest estuary in the U.S. located along the mid‐Atlantic coast. We find five‐fold variations in threshold elevation across the entire estuary, driven not only by tidal range, but also salinity and slope. However, more than half of the variability is unexplained by these variables, which we attribute largely to uncaptured local factors including groundwater discharge, microtopography, and anthropogenic impacts. In the Chesapeake Bay, observed threshold elevations deviate from predicted elevations used to determine sea level driven land conversion by as much as the amount of projected regional sea level rise by 2050. These results suggest that local drivers strongly mediate coastal ecosystem transitions, and that predictions based on elevation and tidal datums alone may misrepresent future land conversion.
Role of Mantle Drag on the Tectonics of Subduction Zones: Insights From Laboratory Models
Authors: Geffroy T. , Guillaume B. , Simoes M. , Replumaz A. , Lacassin R. , Husson L. , Kermarrec J. J. 
Published: December 2023

AbstractAlong convergent boundaries, the role played by mantle drag remains poorly understood despite its potential impact on subduction dynamics and in turn on the deformation regime of the overriding plate. In this study, we present 11 three‐dimensional analog models of subduction including an overriding plate, in which mantle drag at the base of the lower or upper plate results from an imposed unidirectional horizontal mantle flow perpendicular to the trench, and in which the plate opposite to the flow is fixed. We varied the direction and the velocity of the imposed horizontal mantle flow between 0 and 10 cm/yr to quantify its impact on horizontal and vertical upper plate deformation, velocities of plates and subduction, and slab geometry. In our experiments, we show that a mantle flow lower than 5 cm/yr tends to laterally translate the slab rather than to generate internal deformation, resulting in limited differences in slab geometries between models. We also show that plate velocity correlates linearly with the imposed mantle flow velocity and associated mantle drag. The upper plate most often deforms by trench‐orthogonal shortening, with shortening rates increasing linearly with mantle flow. Shortening rates are higher when mantle flow is directed toward the fixed upper plate and when the slab has not yet reached the upper‐lower mantle discontinuity. Minimum trench‐orthogonal shortening rates of 2.5 × 10−15 s−1 are required to thicken upper plates. This study suggests that mantle drag can exert first‐order controls on the dynamics of subduction zones and associated tectonics.
Adjustable Robust Optimization for Water Distribution System Operation Under Uncertainty
Authors: Perelman Gal , Ostfeld Avi 
Published: December 2023

AbstractThe optimal operation of water distribution systems (WDS) is a paramount objective for water utilities due to the substantial energy consumption associated with pumping. A major challenge in optimizing WDS operation is addressing uncertainties such as those related to consumer demands. Real‐time operation under uncertainty necessitates a dynamic approach that can utilize the newly observed information and adjust the operational policy accordingly. This study presents an adjustable robust optimization (ARO) approach to tackle this challenge. Unlike static optimization methods, ARO generates a decision rule policy that is dynamically adjusted as new data becomes available and the operational horizon evolves, thereby ensuring adaptability to changing conditions. Furthermore, the study includes a quantitative analysis of typical demand uncertainty that supports the formulation of the ARO model. The proposed method is evaluated through two case studies and compared with traditional folding horizon approaches. The results indicate that the ARO method is competitive with traditional methods in terms of objective value and surpasses them in terms of robustness. An additional advantage of the method is its offline operation capability which enables it to produce decision rules independent of real‐time programs. This feature facilitates various practical applications such as what‐if analyses, maintenance work planning, and preparation for other special events.
Super-enhancers and the super-enhancer reader BRD4: tumorigenic factors and therapeutic targets
Authors: Qian Haihong , Zhu Min , Tan Xinyu , Zhang Yixing , Liu Xiangning , Yang Li 
Published: December 2023

AbstractTranscriptional super-enhancers and the BET bromodomain protein BRD4 are emerging as critical drivers of tumorigenesis and therapeutic targets. Characterized by substantial accumulation of histone H3 lysine 27 acetylation (H3K27ac) signals at the loci of cell identity genes and critical oncogenes, super-enhancers are recognized, bound and activated by BRD4, resulting in considerable oncogene over-expression, malignant transformation, cancer cell proliferation, survival, tumor initiation and progression. Small molecule compound BRD4 BD1 and BD2 bromodomain inhibitors block BRD4 binding to super-enhancers, suppress oncogene transcription and expression, reduce cancer cell proliferation and survival, and repress tumor progression in a variety of cancer types. Like other targeted therapy agents, BRD4 inhibitors show moderate anticancer effects on their own, and exert synergistic anticancer effects in vitro and in preclinical models, when combined with other anticancer agents including CDK7 inhibitors, CBP/p300 inhibitors and histone deacetylase inhibitors. More recently, BRD4 BD2 bromodomain selective inhibitors, proteolysis-targeting chimera (PROTAC) BRD4 protein degraders, and dual BRD4 and CBP/p300 bromodomain co-inhibitors have been developed and shown better anticancer efficacy and/or safety profile. Importantly, more than a dozen BRD4 inhibitors have entered clinical trials in patients with cancer of various organ origins. In summary, super-enhancers and their reader BRD4 are critical tumorigenic drivers, and BRD4 BD1 and BD2 bromodomain inhibitors, BRD4 BD2 bromodomain selective inhibitors, PROTAC BRD4 protein degraders, and dual BRD4 and CBP/p300 bromodomain co-inhibitors are promising novel anticancer agents for clinical translation.
Transition to the Haldane phase driven by electron-electron correlations
Authors: Jażdżewska A. , Mierzejewski M. , Środa M. , Nocera A. , Alvarez G. , Dagotto E. , Herbrych J. 
Published: December 2023

AbstractOne of the most famous quantum systems with topological properties, the spin $${{{{{{{\mathcal{S}}}}}}}}=1$$
S
=
1
antiferromagnetic Heisenberg chain, is well-known to display exotic $${{{{{{{\mathcal{S}}}}}}}}=1/2$$
S
=
1
/
2
edge states. However, this spin model has not been analyzed from the more general perspective of strongly correlated systems varying the electron-electron interaction strength. Here, we report the investigation of the emergence of the Haldane edge in a system of interacting electrons – the two-orbital Hubbard model—with increasing repulsion strength U and Hund interaction JH. We show that interactions not only form the magnetic moments but also form a topologically nontrivial fermionic many-body ground-state with zero-energy edge states. Specifically, upon increasing the strength of the Hubbard repulsion and Hund exchange, we identify a sharp transition point separating topologically trivial and nontrivial ground-states. Surprisingly, such a behaviour appears already at rather small values of the interaction, in a regime where the magnetic moments are barely developed.
Epithelial SIRT6 governs IL-17A pathogenicity and drives allergic airway inflammation and remodeling
Authors: Quan Jingyun , Wen Xiaoxia , Su Guomei , Zhong Yu , Huang Tong , Xiong Zhilin , Huang Jiewen , Lv Yingying , Li Shihai , Luo Shuhua , Luo Chaole , Cai Xin , Lai Xianwen , Xiang Yuanyuan , Zheng Song Guo , Shao Yiming , Lin Haitao , Gao Xiao , Tang Jing , Lai Tianwen 
Published: December 2023

AbstractDysregulation of IL-17A is closely associated with airway inflammation and remodeling in severe asthma. However, the molecular mechanisms by which IL-17A is regulated remain unclear. Here we identify epithelial sirtuin 6 (SIRT6) as an epigenetic regulator that governs IL-17A pathogenicity in severe asthma. Mice with airway epithelial cell-specific deletion of Sirt6 are protected against allergen-induced airway inflammation and remodeling via inhibiting IL-17A-mediated inflammatory chemokines and mesenchymal reprogramming. Mechanistically, SIRT6 directly interacts with RORγt and mediates RORγt deacetylation at lysine 192 via its PPXY motifs. SIRT6 promotes RORγt recruitment to the IL-17A gene promoter and enhances its transcription. In severe asthma patients, high expression of SIRT6 positively correlates with airway remodeling and disease severity. SIRT6 inhibitor (OSS_128167) treatment significantly attenuates airway inflammation and remodeling in mice. Collectively, these results uncover a function for SIRT6 in regulating IL-17A pathogenicity in severe asthma, implicating SIRT6 as a potential therapeutic target for severe asthma.
mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents
Authors: Roier Sandro , Mangala Prasad Vidya , McNeal Monica M. , Lee Kelly K. , Petsch Benjamin , Rauch Susanne 
Published: December 2023

AbstractDespite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we developed mRNA-based vaccine candidates targeting the viral spike protein VP8*. Our monomeric P2 (universal T cell epitope)-VP8* mRNA design is equivalent to a protein vaccine currently in clinical development, while LS (lumazine synthase)-P2-VP8* was designed to form nanoparticles. Cyro-electron microscopy and western blotting-based data presented here suggest that proteins derived from LS-P2-VP8* mRNA are secreted in vitro and self-assemble into 60-mer nanoparticles displaying VP8*. mRNA encoded VP8* was immunogenic in rodents and introduced both humoral and cellular responses. LS-P2-VP8* induced superior humoral responses to P2-VP8* in guinea pigs, both as monovalent and trivalent vaccines, with encouraging responses detected against the most prevalent P genotypes. Overall, our data provide evidence that trivalent LS-P2-VP8* represents a promising mRNA-based next-generation rotavirus vaccine candidate.
The dual activity of CaONPs as a cancer treatment substance and at the same time resistance to harmful microbes
Authors: Awaad Amr , Olama Zakia A. , El-Subruiti Gehan M. , Ali Safaa M. 
Published: December 2023

AbstractNanotechnology holds significant promise for the development of novel and necessary products that enhance human health. Pharmacology and nanotechnology have contributed to developing advanced and highly effective drugs for cancer treatment and combating microbial infections. The microbiological effectiveness against the variety of examined microorganisms was assessed using the time killer curve, scanning electron microscopy (SEM), MIC techniques, and the agar well diffusion method. SEM was utilized to enhance the analysis of the mechanisms underlying the bio-interface interaction and intracellular localization of calcium oxide nanoparticles (CaONPs). The MTT test was used to examine the cytotoxicity of CaONP anticancer activity in various cancer cells, including colon, breast, and hepatic cells. The efficacy of CaONPs as an anticancer medication was elucidated by analyzing the gene expression of both treated and untreated cancer cells. MIC and MBC of CaONPs againstEscherichia coliandStaphylococcus epidermidiswere 150, 150, 150, and 200 µg/ml, respectively. The MIC and MFC of CaONPs againstCandida albicanswere 200 µg/ml and 250 µg/ml, respectively. The IC50 values of various CaONPs vary depending on the type of cancer cells. The gene expression analysis of breast cancer cells undergoing treatment revealed the identification of several cancer-controlling genes, namely BAX, BCL2, P53, TERT, KRAS1, KRAS2, and RB1. The study demonstrated the notable antibacterial efficacy of CaONPs, highlighting their potential as cancer therapies.
The investigation on shale mechanical characteristics and brittleness evaluation
Authors: Lei Wei , Liu Xiangjun , Ding Yi , Xiong Jian , Liang Lixi 
Published: December 2023

AbstractRock mechanical property is significant for shale gas development and exploitation. Shale compressive strength, tensile strength, elastic deformation and so on, are necessary parameters for drilling, completion and fracturing work in shale formation. Among all these shale mechanical parameters, brittleness is a tricky and significant rock property, which has been widely used to hydraulic fracturing design. Currently, although so many works have been conducted to investigate shale brittleness, there is no precise definition of brittleness. In particular, there is no consensus on which method is the most reliable for shale brittleness evaluation. It is vital to figure out how to evaluate shale brittleness in a reliable method. Thus, this paper presents an experimental study on shale mechanical properties, analyzing mechanical features in stress strain curve, relation between mineral content and strength, mechanical parameters at varying confined stress. Based on shale mechanical characteristics and its brittle exhibition, stress strain curve from triaxial compression test is divided into 3 stages, namely, elastic stage, plastic stage and post peak stage. In combined with brittle characteristics in 3 stages of axial and radial stress–strain curves, a new brittleness index has been established for assessing shale brittleness. In order to prove the applicability of new brittleness index, its result is compared with shale failure sample after triaxial test and existing brittleness indexes based on mineral content, elastic deformation, energy, stress and strain, showing a good consistency and proving its practicability. Based on this brittleness index, influence factors of shale brittleness have been discussed. It is shown that elastic module is the most important factor of shale brittleness. Bedding plane makes shale brittleness have strong anisotropy. Brittleness is not only relied on its structure and mineral (like bedding plane, silicate and clay mineral content), but is also highly affected by external stress. Large confined pressure is able to impair shale brittleness. Outcome in this study can offer theoretical guidance for shale exploitation.
Home range overlap between small Indian mongooses and free roaming domestic dogs in Puerto Rico: implications for rabies management
Authors: Sauvé Caroline C. , Berentsen Are R. , Llanos Steven F. , Gilbert Amy T. , Leighton Patrick A. 
Published: December 2023

AbstractThe small Indian mongoose (Urva auropunctata) is the primary terrestrial wildlife rabies reservoir on at least four Caribbean islands, including Puerto Rico. In Puerto Rico, mongooses represent a risk to public health, based on direct human exposure and indirectly through the transmission of rabies virus to domestic animals. To date, the fundamental ecological relationships of space use among mongooses and between mongooses and domestic animals remain poorly understood. This study is the first to report mongoose home range estimates based on GPS telemetry, as well as concurrent space use among mongooses and free roaming domestic dogs (FRDD; Canis lupus familiaris). Mean (± SE) home range estimates from 19 mongooses in this study (145 ± 21 ha and 60 ± 14 ha for males and females, respectively) were greater than those reported in prior radiotelemetry studies in Puerto Rico. At the scale of their home range, mongooses preferentially used dry forest and shrubland areas, but tended to avoid brackish water vegetation, salt marshes, barren lands and developed areas. Home ranges from five FRDDs were highly variable in size (range 13–285 ha) and may be influenced by availability of reliable anthropogenic resources. Mongooses displayed high home range overlap (general overlap index, GOI = 82%). Home range overlap among mongooses and FRDDs was intermediate (GOI = 50%) and greater than home range overlap by FRDDs (GOI = 10%). Our results provide evidence that space use by both species presents opportunities for interspecific interaction and contact and suggests that human provisioning of dogs may play a role in limiting interactions between stray dogs and mongooses.
Rapid non-invasive prenatal screening test for trisomy 21 based on digital droplet PCR
Authors: Laššáková Soňa , Šenkyřík Pavel , Pazourková Eva , Hořínek Aleš , Calda Pavel , Břešťák Miroslav , Světnicová Kamila , Neužil Pavel , Korabečná Marie 
Published: December 2023

AbstractNon-invasive prenatal tests for the detection of fetal aneuploidies are predominantly based on the analysis of cell-free DNA (cfDNA) from the plasma of pregnant women by next-generation sequencing. The development of alternative tests for routine genetic laboratories is therefore desirable. Multiplex digital droplet PCR was used to detect 16 amplicons from chromosome 21 and 16 amplicons from chromosome 18 as the reference. Two fluorescently labeled lock nucleic acid probes were used for the detection of reaction products. The required accuracy was achieved by examining 12 chips from each patient using Stilla technology. The plasma cfDNA of 26 pregnant women with euploid pregnancies and 16 plasma samples from pregnancies with trisomy 21 were analyzed to determine the cutoff value for sample classification. The test was validated in a blind study on 30 plasma samples from pregnant patients with a risk for trisomy 21 ranging from 1:4 to 1:801. The results were in complete agreement with the results of the invasive diagnostic procedure (sensitivity, specificity, PPV, and NPV of 100%). Low cost, and speed of analysis make it a potential screening method for implementation into the clinical workflow to support the combined biochemical and ultrasound results indicating a high risk for trisomy 21.
The influence of season, hunting mode, and habitat specialization on riparian spiders as key predators in the aquatic-terrestrial linkage
Authors: Bollinger Eric , Zubrod Jochen P. , Englert Dominic , Graf Nadin , Weisner Oliver , Kolb Sebastian , Schäfer Ralf B. , Entling Martin H. , Schulz Ralf 
Published: December 2023

AbstractFreshwater ecosystems subsidize riparian zones with high-quality nutrients via the emergence of aquatic insects. Spiders are dominant consumers of these insect subsidies. However, little is known about the variation of aquatic insect consumption across spiders of different hunting modes, habitat specializations, seasons, and systems. To explore this, we assembled a large stable isotope dataset (n > 1000) of aquatic versus terrestrial sources and six spider species over four points in time adjacent to a lotic and a lentic system. The spiders represent three hunting modes each consisting of a wetland specialist and a habitat generalist. We expected that specialists would feed more on aquatic prey than their generalist counterparts. Mixing models showed that spiders’ diet consisted of 17–99% of aquatic sources, with no clear effect of habitat specialization. Averaged over the whole study period, web builders (WB) showed the highest proportions (78%) followed by ground hunters (GH, 42%) and vegetation hunters (VH, 31%). Consumption of aquatic prey was highest in June and August, which is most pronounced in GH and WBs, with the latter feeding almost entirely on aquatic sources during this period. Additionally, the elevated importance of high-quality lipids from aquatic origin during fall is indicated by elemental analyses pointing to an accumulation of lipids in October, which represent critical energy reserves during winter. Consequently, this study underlines the importance of aquatic prey irrespective of the habitat specialization of spiders. Furthermore, it suggests that energy flows vary substantially between spider hunting modes and seasons.
Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages
Authors: Fang Zheng , Xu Man , Shen Shan , Sun Weiwei , Yu Qing , Wu Qingshan , Xiang Lan , Weng Qingbei 
Published: December 2023

AbstractProphages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.