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Disentangling the relationship of enhancers and genes is an ongoing challenge in epigenomics. We present STARE, our software to quantify the strength of enhancer-gene interactions based on enhancer activity and chromatin contact data. It implements the generalized Activity-by-Contact (gABC) score, which allows predicting putative target genes of candidate enhancers over any desired genomic distance. The only requirement for its application is a measurement of enhancer activity. In addition to regulatory interactions, STARE calculates transcription factor (TF) affinities on gene level. We illustrate its usage on a public single-cell data set of the human heart by predicting regulatory interactions on cell type level, by giving examples on how to integrate them with other data modalities, and by constructing TF affinity matrices.

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To reveal gene regulation mechanisms, it is essential to understand the role of regulatory elements, which are possibly distant from gene promoters. Integrative analysis of epigenetic and transcriptomic data can be used to gain insights into gene-expression regulation in specific phenotypes. Here, we discuss STITCHIT, an approach to dissect epigenetic variation in a gene-specific manner across many samples for the identification of regulatory elements without relying on peak calling algorithms. The obtained genomic regions are then further refined using a regularized linear model approach, which can also be used to predict gene expression. We illustrate the use of STITCHIT using H3k27ac ChIP-seq and RNA-seq data from the International Human Epigenome Consortium (IHEC).

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Thoracic aortic aneurysms (TAA) represent a critical health issue for which computational models can significantly contribute to better understand the physiopathology. Among different computational frameworks, the Homogenized Constrained Mixture Theory has shown to be a computationally efficient option, allowing the inclusion of several mechanically significant constituents into a layer-specific mixture. Different patient-specific Growth and Remodeling (G&R) models correctly predicted TAA progression, although simplifications such as the inclusion of a limited number of collagen fibers and imposed boundary conditions might limit extensive analyses. The current study aims to enhance existing models by incorporating several discrete collagen fibers and to remove restrictive boundary conditions of the previous models. The implementation of discretized fiber dispersion presents a more realistic description of the vessel, while the removal of boundary conditions was addressed by including cross-links in the model to provide a supplemental stiffness against through-thickness shearing, a feature that was previously absent, and by the development of a non-local framework that ensures the stable deposition and degradation of collagen fibers. With these improvements, the current model represents a step forward towards more robust and comprehensive simulations of TAA growth.

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Objective: This study aimed to explore the potential causal relationship between the gut microbiota and/or its metabolites and the progression of chronic hepatitis B (CHB). Method: The gut microbiota was used as the exposure factor. The training set exposure data were obtained from the China Nucleotide Sequence Archive (CNSA). Genome-wide association study (GWAS) data from Asia were used as the outcome variables. Outcome data for both the training and validation sets were sourced from the GWAS Catalog database. A dual-sample Mendelian randomization approach was used to analyze the causal relationships, with the inverse variance-weighted method serving as the main analytical strategy. Sensitivity analysis was conducted to assess the robustness of Mendelian randomization analysis results. Result: In the training set database, analysis using the inverse variance-weighted method revealed a positive correlation between Fusobacterium varium and chronic hepatitis B [OR = 1.122, 95% CI (1.016, 1.240), p = 0.022]. Conversely, Veillonella parvula exhibited a negative correlation with chronic hepatitis B [OR = 0.917, 95% CI (0.852, 0.987), p = 0.021]. Sensitivity analysis revealed no evidence of pleiotropy and heterogeneity. No gut microbiota metabolites with a causal effect on chronic hepatitis B were identified. Additionally, no associations between the gut microbiota and the progression of chronic hepatitis B were found in the validation data from the European cohort. Conclusion: This study suggests that F. varium may facilitate the progression of chronic hepatitis B, whereas V. parvula may impede it. No causal relationships between gut microbiota metabolites and chronic hepatitis B were established.

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As the derivative of konjac glucomannan (KGM), carboxymethyl konjac glucomannan (CMK) has attracted increasing attention in the polysaccharide hydrogel fields with the aim of improving the performance related to drug delivery and release. In this study, we prepared a CMK-based hydrogel with dual characteristic crosslinks, and unlocked new applications of this type of hydrogel in soft sensor fields. CMK and poly (vinyl alcohol) were used as substrates, and physical crosslinks were constructed via the freeze-thawing treatments and covalent crosslinks were built via the boronic ester bonding. As-prepared hydrogel possessed significantly improved mechanical performance because the boronic ester bonding, on the one hand, well associated the two kinds of polymer chains, and on the other hand, played the role of 'sacrificial crosslinks'. Furthermore, the occurrence of dynamic boronic ester bonding gave the hydrogel strain- and temperature-sensitive ionic conductivity, and therefore, the hydrogels could be used to identify human motions and as-resulted environmental temperature alterations, and worked well in various scenarios. This work activates new application of CMK in the multimodal sensing field, and also proposes an intriguing way of building multiple crosslinks in the KGM derivative-based hydrogels.

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In this work, the exponential synchronization issue of stochastic complex networks with time delays and time-varying multi-links (SCNTM) is discussed via a novel aperiodic intermittent dynamic event-triggered control (AIDE-TC). The AIDE-TC is designed by combining intermittent control with an exponential function and dynamic event-triggered control, aiming to minimize the number of the required triggers. Then, based on the proposed control strategy, the sufficient conditions for exponential synchronization in mean square of SCNTM are obtained by adopting graph theoretic approach and Lyapunov function method. In the meanwhile, it is proven that the Zeno behavior can be excluded under the AIDE-TC, which ensures the feasibility of the control mechanism to realize the synchronization of SCNTM. Finally, we provide a numerical simulation on islanded microgrid systems to validate the effectiveness of main results and the simulation comparison results show that the AIDE-TC can reduce the number of event triggers.

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The highly blistering sulfur mustard analogue agent T (bis(2-chloroethylthioethyl) ether), also known as O-mustard or oxy-mustard, is a common impurity in military grade sulfur mustard (SM) and a component of mixtures such as "HT" that are still found in old munitions. Together with sesquimustard (Q), it is the most important SM analogue and tightly regulated as a Schedule 1 chemical under the Chemical Weapons Convention. We report the adducts of T with nucleophilic Cys34 and other residues in human serum albumin (HSA) formed in vitro. A micro liquid chromatography electrospray ionization high-resolution tandem-mass spectrometry method (µLC-ESI MS/HR MS) was developed for the detection and identification of biomarker peptides alkylated by a T-derived hydroxyethylthioethyloxyethylthioethyl (HETEOETE)-moiety (as indicated by an asterisk below). Following proteolysis of T-exposed human plasma with pronase, the dipeptide Cys34*Pro and the single amino acid residue His* were produced. The use of proteinase K yielded Cys34*ProPhe and the use of pepsin generated ValThrGlu48*Phe, AlaGlu230*ValSerLysLeu, and LeuGlyMet329*Phe. Corresponding peptide-adducts of SM and Q were detected in a common workflow that in principle allowed the estimation of the mustard or mustard composition encountered during exposure. Novel adducts of Q at the Glu230 and Met239 residues were detected and are reported accordingly. Based on molecular dynamics simulations, we identified regular interactions of the Cys34(-HETEOETE)-moiety with several glutamic acid residues in HSA including Glu86, which is not an obvious interaction partner by visual inspection of the HSA crystal structure. The existence of this and other intramolecular cross-links was experimentally proven for the first time.

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In this work, a noncoplanar terphenyl served as a building block to synthesize a novel 3,3'-substituted bipyridyl ligand (L1) which further reacted with binuclear half-sandwich units A/B, giving rise to two aesthetic 41 metalla-knots in high yields via a coordination-driven self-assembly strategy. Furthermore, given the inherent compactness of the 41 metalla-knots, it creates favorable conditions for the emergence of steric repulsion. We focused on progressively introducing nitrogen atoms featuring a lone pair of electrons (LPEs) into ligand L1 to manipulate the balance of H⋅⋅⋅H/LPEs⋅⋅⋅LPEs steric repulsion during the assembly process, ultimately achieving controlled assembly from 41 metalla-knots to the pseudo-Solomon link and then to molecular tweezer-like assembly facilitated by stacking interactions. All the assemblies were well characterized by solution-state NMR techniques, ESI-TOF/MS, and single-crystal X-ray diffraction. The evolutionary process of the topological architectures is equivalent to visualizing the synergistic effect of steric hindrance and stacking interactions on structural assembly, providing a new avenue for achieving the controlled synthesis of different topologies.

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Vitrimers are a new class of heterogeneous polymers that combine the best features of thermosets with those of thermoplastics. The introduction of cross-links strongly changes the viscoelastic behavior of vitrimer materials. However, the characterization and understanding of the nanostructures and interfaces in vitrimers resulting from dynamic cross-linking formation remain a major challenge. Here, using dynamic modes of atomic force microscopy (AFM), namely intermodulation AFM (ImAFM) and AFM-based dynamic mechanical analysis (AFM-nDMA), local viscoelastic properties and interfaces at the nanoscale length of high-density polyethylene (HDPE) vitrimer materials are reported. ImAFM imaging in combination with the k-means clustering algorithm clearly reveals two distinct phases in the vitrimer system with highly different viscoelastic properties. AFM-nDMA further provides quantitative nanoviscoelastic properties at the nanoscale to confirm that there is a cross-linking-rich aggregation area forming a nanosize network structure in the cross-linking-poor matrix phase. The cross-linking-rich region shows a similar elastic modulus but much higher adhesion force measured by AFM compared to the cross-linking-poor HDPE matrix. Furthermore, the frequency influence on the local viscoelastic properties of HDPE vitrimer at the nanoscale was initially screened. The observed HDPE vitrimer nanostructures and viscoelastic properties at the nanoscale also provide explanations on the observed bulk HDPE vitrimer crystallinity decrease and dimensional stability increase compared to HDPE. Therefore, probing the viscoelastic properties and interfaces of HDPE vitrimer provides important insights into understanding of the correlations between the vitrimer nanostructure and the bulk mechanical and rheological behaviors.

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Phenotypic links are the potential for "carryover" of effects of experience during one life history stage into performance and selection at subsequent stages. They reflect plastic responses to the environment experienced during an early phase on the phenotype of subsequent phases. We are studying these effects by following individuals of the shrimp Palaemon serratus from the embryonic (eggs carried by females) through the larval phase (pelagic) to the juvenile phase (benthic). In experiment 1, we investigated the effects of larval prey concentration (10, 4 and 2 Artemia/mL) and larval incubation temperature (16 and 22 °C) on larval performance (metamorphosis rate, developmental duration and growth) and then on juvenile performance (survival and Specific Growth Rate, SGR, at 18 and 24 °C in 14 days). In experiment 2, we investigated the effects of embryonic incubation temperature (larval biomass and lipid content of newly hatched larvae from embryos incubated at 12 and 18 °C) and larval prey concentration on larval performance and then on juvenile performance. In both experiments, the larvae plastically increased their development time in response to the reduction in temperature and prey concentration, whereas their survival decreased with temperature and prey concentration. The quantity of lipids available at hatching decreased with decreasing embryonic incubation temperature, which reduced the larval performance, particularly with a low concentration of prey. Survival at 14 days post-metamorphosis was significantly reduced when the embryos were incubated at 12 °C compared with those incubated at 18 °C, regardless of the subsequent larval incubation conditions, revealing phenotypic links between overconsumption of embryonic yolk reserves and post-metamorphic fitness. Overall, juveniles had a better SGR at 24 than at 18 °C, and even better when incubated under stressful embryo-larval conditions (temperature and prey concentration). This study highlighted phenotypic links between developmental stages and over developmental periods of several months.

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Increased fracture risk in type 1 diabetes (T1D) patients is not fully captured by bone mineral density (BMD) by DXA. Advanced glycation end-products (AGEs) have been implicated in the increased fracture risk in T1D, yet recent publications question this. To test the hypothesis that enzymatic collagen cross-links rather than AGEs correlate with fracture incidence in T1D, we analyzed iliac crest biopsies from sex-matched, fracturing T1D patients (N = 5; T1DFx), 6 non-fracturing T1D patients (T1DNoFx), and 6 healthy subjects, by Raman microspectroscopy as a function of tissue age (based on double fluorescent labels), in intracortical and trabecular bone, to determine pyridinoline (Pyd), ε-N-Carboxymethyl-L-lysine, and pentosidine (PEN)). There were no differences in the clinical characteristics between the T1DFx and T1DNoFx groups. At trabecular forming surfaces, T1DFx patients had higher PEN and Pyd content compared to T1DNoFx ones. Previous studies have shown that elevated PEN does not necessarily correlate with fracture incidence in postmenopausal, long-term T1D patients. On the other hand, the elevated Pyd content in the T1DFx patients would be consistent with published studies showing a significant correlation between elevated trivalent enzymatic collagen cross-links and fracture occurrence independent of BMD. Collagen fibers with high Pyd content are more brittle. Thus, a plausible suggestion is that it is the enzymatic collagen cross-links that either by themselves or in combination with the adverse effects of increased AGE accumulation that result in fragility fracture in T1D.

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Although mechanically interlocked molecules (MIMs) display unique properties and functions associated with their intricate connectivity, limited assembly strategies are available for their synthesis. Herein, we presented a synergistic assembly strategy based on coordination and noncovalent interactions (π-π stacking and CH⋯π interactions) to selectively synthesize molecular closed three-link chains ([Formula: see text] links), highly entangled figure-eight knots ([Formula: see text] knots), trefoil knot ([Formula: see text] knot), and Borromean ring ([Formula: see text] link). [Formula: see text] links can be created by the strategic assembly of nonlinear multicurved ligands incorporating a furan or phenyl group with the long binuclear half-sandwich organometallic Cp*RhIII (Cp* = η5-pentamethylcyclopentadienyl) clip. However, utilizing much shorter binuclear Cp*RhIII units for union with the 2,6-naphthyl-containing ligand led to a [Formula: see text] knot because of the increased π-π stacking interactions between four consecutive stacked layers and CH⋯π interactions. Weakening such π-π stacking interactions resulted in a [Formula: see text] knot. The universality of this synergistic assembly strategy for building [Formula: see text] knots was verified by utilizing a 1,5-naphthyl-containing ligand. Quantitative conversion between the [Formula: see text] knot and the simple macrocycle species was accomplished by adjusting the concentrations monitored by NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS). Furthermore, increasing the stiff π-conjugated area of the binuclear unit afforded molecular Borromean ring, and this topology is a topological isomer of the [Formula: see text] link. These artificial metalla-links and metalla-knots were confirmed by single-crystal X-ray diffraction, NMR and ESI-MS. The results offer a potent strategy for building higher-order MIMs and emphasize the critical role that noncovalent interactions play in creating sophisticated topologies.

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One of the main tasks in expertise of living persons is to determine the harm caused to human health. According to the regulations, only harm to human health caused by an injury and causally related with it is taken into account in the forensic examination of a living person. The establishment of a causal link allows to assess correctly the harm severity caused to human health. In this respect, the study of the effect of biological damaging factor on human body (cause) and the result of this interaction (effect) is a new step in modern science. The article presents the analysis of data from the reports of the Russian Reference Center on monitoring of enteric infection agents for 2016-2021; the results of examinations of subjects who suffered from acute enteric infections for 2018-2019 to study causal links in forensic medicine in cases of acute intestinal infections.

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Underwater optical wireless communication (UOWC) has gained interest in recent years with the introduction of autonomous and remotely operated mobile systems in blue economic ventures such as offshore food production and energy generation. Here, we devised a model for estimating the received power distribution of diffused line-of-sight mobile optical links, accommodating irregular intensity distributions beyond the beam-spread angle of the emitter. We then used this model to conduct a spatial analysis investigating the parametric influence of the placement, orientation, and angular spread of photodiodes in array-based receivers on the mobile UOWC links in different Jerlov seawater types. It revealed that flat arrays were best for links where strict alignment could be maintained, whereas curved arrays performed better spatially but were not always optimal. Furthermore, utilizing two or more spectrally distinct wavelengths and more bandwidth-efficient modulation may be preferred for received-signal intensity-based localization and improving link range in clearer oceans, respectively. Considering the geometric implications of the array of receiver photodiodes for mobile UOWCs, we recommend the use of dynamically shape-shifting array geometries.

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Hydrogels are soft materials engineered to suit a multitude of applications that exploit their tunable mechanochemical properties. Dynamic hydrogels employing noncovalent, physically cross-linked networks dominated by either enthalpic or entropic interactions enable unique rheological and stimuli-responsive characteristics. In contrast to enthalpy-driven interactions that soften with increasing temperature, entropic interactions result in largely temperature-independent mechanical properties. By engineering interfacial polymer-particle interactions, we can induce a dynamic-to-covalent transition in entropic hydrogels that leads to biomimetic non-ergodic aging in the microstructure without altering the network mesh size. This transition is tuned by varying temperature and formulation conditions such as pH, which allows for multivalent tunability in properties. These hydrogels can thus be designed to exhibit either temperature-independent metastable dynamic cross-linking or time-dependent stiffening based on formulation and storage conditions, all while maintaining structural features critical for controlling mass transport, akin to many biological tissues. Such robust materials with versatile and adaptable properties can be utilized in applications such as wildfire suppression, surgical adhesives, and depot-forming injectable drug delivery systems.

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Geopolymers exhibit broad application prospects, including construction and radiation shielding, which require excellent mechanical performances. However, investigations on the nature of geopolymerization reactions and their consequential impact on mechanical performance are still vague. In this study, the effect of the major factors of Si/Al ratio and curing time on the geopolymerization reaction and flexural strength were studied based on the microstructure evolution and chemical bonding formation analyzed using the SEM, FTIR, peak deconvolution, and XRD methods. The microstructure of geopolymers was transferred from initially layered smooth particles of kaolinite to a 3D network porous structure, corresponding to sodalite. A spectrum exclusive to the geopolymer structure occurred at 973 cm-1, corresponding to the sodium aluminum silicate hydrate (N-A-S-H) links, the integral area of which represents the degree of geopolymerization reaction. Furthermore, a controllable reaction degree was achieved by adjusting the Si/Al ratio and curing time, where the maximum reaction degree of 55% was achieved at a Si/Al ratio of 1.94 when cured for 7 d. The correlation between the flexural strength and reaction degree was found to follow a proportional relationship, achieving a flexural strength of 21.11 MPa with a degree of 45%. This study provides insight into the development of mechanical strength through controlling the reaction process.

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Osteopontin (OPN) and Bone Sialoprotein (BSP), abundantly expressed by osteoblasts and osteoclasts, appear to have important, partly overlapping functions in bone. In gene-knockout (KO, -/-) models of either protein and their double (D)KO in the same CD1/129sv genetic background, we analyzed the morphology, matrix characteristics, and biomechanical properties of femur bone in 2 and 4 month old, male and female mice. OPN-/- mice display inconsistent, perhaps localized hypermineralization, while the BSP-/- are hypomineralized throughout ages and sexes, and the low mineralization of young DKO mice recovers with age. The higher contribution of primary bone remnants in OPN-/- shafts suggests a slow turnover, while their lower percentage in BSP-/- indicates rapid remodeling, despite FTIR-based evidence in this genotype of a high maturity of the mineralized matrix. In 3-point bending assays, OPN-/- bones consistently display higher Maximal Load, Work to Max. Load and in young mice Ultimate Stress, an intrinsic characteristic of the matrix. Young male and old female BSP-/- also display high Work to Max. Load along with low Ultimate Stress. Principal Component Analysis confirms the major role of morphological traits in mechanical competence, and evidences a grouping of the WT phenotype with the OPN-/- and of BSP-/- with DKO, driven by both structural and matrix parameters, suggesting that the presence or absence of BSP has the most profound effects on skeletal properties. Single or double gene KO of OPN and BSP thus have multiple distinct effects on skeletal phenotypes, confirming their importance in bone biology and their interplay in its regulation.

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When contributors' goals and legislative and political structures vary, as they often do in the case of worldwide fish populations, it becomes more challenging to implement ethical fishing tactics. Canada, the United States, and Mexico all fish from Pacific regions anchovies in the California Modern. Climate-driven numbers and geographic dynamics may pollute the waters of collaborative aquaculture and lead to overloading. This research expands upon prior works using a game theoretic model of Tran's boundary sardine fisheries in different climatic conditions to account for ecological links. More significant economic advantages accrue from cooperation fishing tactics that consider the mackerel's role as feed for other species in the natural system, as opposed to plans that merely take note of the worth of mackerel harvests to a particular fishing nation. The maximum environmental benefit is obtained at a fishery rate for sardines barely less than the sardine Fishery Management Safe Yield. Ecological-based control of fisheries can increase sustainability and profits, but only if investors and policy makers consider the ecology in business-applicable models. Understanding and adapting to the fast alterations in habitat distributions due to climate change and designing ways to achieve viable and lucrative fishery amidst altering environments will necessitate an increased emphasis on ecosystem-based governance.

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Acrylic adhesive sheets have been used for many applications, from popular seal materials to high-end electrical devices. One of the basic and critical design features of adhesives is effective covalent cross-linking for superior adhesive properties. On the other hand, covalent cross-linking prevents reuse or recycling of the adhesive. This makes the adhesive sheets insoluble and poorly workable. For development of sustainable adhesives, we investigated the adhesive sheets based on acrylic elastomers with "Movable Cross-links" (M-PEA-CD (0.5)) copolymerized with 0.5 mol % cyclodextrin monomers. The peel strength and creep resistance of M-PEA-CD (0.5) were greater than those of adhesives (N-PEA) without any cross-links. M-PEA-CD (0.5) was recyclable via dissolution in ethyl acetate. Furthermore, the recycled M-PEA-CD (0.5) from solution exhibited the same adhesion properties as virgin M-PEA-CD (0.5). Spectroscopic and mechanical measurements indicated that topological cross-linking with Cyclodextrin (CD) moieties generated novel recyclable adhesive sheets without restricting the polymer main chains, unlike covalent cross-linking (CC-PEA). The movable cross-links were maintained in both the solid state and in solution, which allowed recycling of the elastomer via simple methods.

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The quality of traditional Chinese medicine preparations is directly related to the safety of patients. Among the various factors, the process and corresponding critical equipment are critical factors influencing the quality of the preparations. To improve the quality of traditional Chinese medicine preparations, this article summarizes and analyzes the problems in the process links and corresponding critical equipment in the manufacturing process of traditional Chinese medicine preparations. Furthermore, a critical quality attribute evaluation system is established based on safety and effectiveness combined with the drug properties, preparation process, and preparation characteristics, providing a basis for the process and equipment improvements aimed at quality enhancement.

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