Sensing prior constraints in deep neural networks for solving exploration geophysical problems.

One of the key objectives in geophysics is to characterize the subsurface through the process of analyzing and interpreting geophysical field data that are typically acquired at the surface. Data-driven deep learning methods have enormous potential for accelerating and simplifying the process but also face many challenges, including poor generalizability, weak interpretability, and physical inconsistency. We present three strategies for imposing domain knowledge constraints on deep neural networks (DNNs) to help address these challenges. The first strategy is to integrate constraints into data by generating synthetic training datasets through geological and geophysical forward modeling and properly encoding prior knowledge as part of the input fed into the DNNs. The second strategy is to design nontrainable custom layers of physical operators and preconditioners in the DNN architecture to modify or shape feature maps calculated within the network to make them consistent with the prior knowledge. The final strategy is to implement prior geological information and geophysical laws as regularization terms in loss functions for training the DNNs. We discuss the implementation of these strategies in detail and demonstrate their effectiveness by applying them to geophysical data processing, imaging, interpretation, and subsurface model building.

V-Doping Strategy Induces the Construction of the CoFe-LDHs/NF Electrodes with Higher Conductivity to Achieve Higher Energy Density for Advanced Energy Storage Devices.

Doping of metal ions shows promising potential in optimizing and modulating the electrical conductivity of layered double hydroxides (LDHs). However, there is still much room for improvement in common metal ions and conventional doping methods. In contrast to previous methodologies, a hollow triangular nanoflower structure of CoFeV-LDHs is devised, which is enriched with a greater number of oxygen vacancies. This resulted in a significant enhancement in the conductivity of the LDHs, leading to an increase in energy density following the appropriate doping of V. To investigate the impact of V-doping on the energy density of the LDHs, in situ XPS and in situ X-ray spectroscopy is employed. Regarding electrochemical performance, the CoFeV-LDHs/NF electrode with optimal doping ratio exhibited a specific capacitance of 881 F g-1 at a current density of 1 A g-1. The capacitance remained at 90.53% after 3000 cycles. In addition, the constructed battery-type supercapacitor CoFeV-LDHs/NF-2//AC exhibited an impressive energy density of 124.7 Wh kg-1 at a power density of 850 W kg-1 and capacitance remained almost unchanged at 95.2% after 3000 cycles. All the above demonstrates the great potential of V-doped LDHs and brings a new way for the subsequent research of LDHs.

Robust Second-Order Topological Insulators with Giant Valley Polarization in Two-Dimensional Honeycomb Ferromagnets.

Magnetic topological states have attracted great attention that provide exciting platforms for exploring prominent physical phenomena and applications of topological spintronics. Here, using a tight-binding model and first-principles calculations, we put forward that, in contrast to previously reported magnetic second-order topological insulators (SOTIs), robust SOTIs can emerge in two-dimensional ferromagnets regardless of magnetization directions. Remarkably, we identify intrinsic ferromagnetic 2H-RuCl2 and Janus VSSe monolayers as experimentally feasible candidates of predicted robust SOTIs with the emergence of nontrivial corner states along different magnetization directions. Moreover, under out-of-plane magnetization, we unexpectedly point out that the valley polarization of SOTIs can be huge and much larger than that of the known ferrovalley materials, opening up a technological avenue to bridge the valleytronics and higher-order topology with high possibility of innovative applications in topological spintronics and valleytronics.

N-acyl homoserine lactone mediating initial adhesion of microalgal biofilm formation.

While pioneering methods have demonstrated that bacterial N-acyl homoserine lactone (AHL) signaling molecules can influence the growth and self-aggregation of suspended microalgae, whether AHLs can affect the initial adhesion to a carrier has remained an open question. Here we revealed that the microalgae exhibited different adhesion potential under AHL mediation, where the performance was affiliated to both AHL types and concentrations. The result can be well explained by the interaction energy theory, where the energy barrier between the carriers and the cells varied due to AHL mediation. Depth analyses revealed that AHL acted through modifying the properties of the surface electron donor of the cells, which were dependent upon three major components, i.e., extracellular protein (PN) secretion, the PN secondary structure, and the PN amino acid composition. These findings expand the known diversity of AHLs mediation on microalgal initial adhesion and metabolisms, which may interface with other major cycles and become helpful to theoretically guide the application of AHLs in microalgal culture and harvesting.

The relationship between the baseline geriatric nutritional risk index (GNRI) and neurological function at the convalescence stage in patients with stroke: a cross-sectional study.

BACKGROUND: Malnutrition is a common complication after stroke and may worsen neurological outcomes for patients. There are still no uniform tools for screening nutritional status for the patients with stroke. We aimed to explore the relationship between the baseline geriatric nutritional risk index (GNRI) and neurological function at the convalescence stage for patients with stroke and assessed the predictive value of the GNRI for adverse neurological outcomes. METHODS: A total of 311 patients with stroke were enrolled retrospectively. Basic information and laboratory results on admission since onset of stroke were collected. The GNRI on admission was calculated and neurological outcomes evaluated by the Barthel index at 1 month after the onset of stroke. Statistical analyses, including correlation coefficient tests, multivariate regression analyses, and receiver operating characteristic (ROC) analyses, were applied in this study. RESULTS: Compared with the good outcome group, the poor outcome group showed a significantly lower GNRI on admission (P < 0.05). GNRI was associated with Barthel index (r = 0.702, P < 0.01). The GNRI was independently correlated with the Barthel index (Standardization ß = 0.721, P < 0.01) and poor outcome 0.885 (95% CIs, 0.855-0.917, P < 0.01) after adjusting for covariates. Compared with no nutritional risk grades (Q4), the OR of GNRI to poor neurological outcome increased across increasing nutritional risk grades of GNRI (OR = 2.803, 95% CIs = 1.330-5.909 in Q3, 7.992, 95% CIs = 3.294-19.387 in Q2 and 14.011, 95% CIs = 3.972-49.426 in Q1, respectively, P for trend < 0.001). The area under ROC curves (AUC) of the GNRI was 0.804, which was larger than that of the NIHSS, BMI, or Albumin (P < 0.01), with an optimal cut-off value of 97.69, sensitivity of 69.51% and specificity of 77.27%. Combined GNRI with NIHSS gained the largest AUC among all the variables (all P < 0.05), with an AUC of 0.855, sensitivity of 84.75 and specificity of 72.73%. CONCLUSIONS: For patients with stroke, higher nutritional risk grades at baseline indicated worse neurological function at the convalescence stage. Compared with NIHSS, BMI, and Albumin, GNRI was a competitive indicator for the risk of poor neurological outcome. The predictive property of GNRI for adverse neurological outcomes might be more powerful when combined with NIHSS.

Botulinum toxin A injection using ultrasound combined with balloon guidance for the treatment of cricopharyngeal dysphagia: analysis of 21 cases.

BACKGROUND: As an upper oesophageal sphincter (UES) dysfunction disorder, cricopharyngeal achalasia (CPA) is a common cause of dysphagia and is associated with an increased risk of pulmonary complications. The aim of this study was to investigate the effectiveness and safety of BTX-A injection using ultrasound combined with balloon guidance for the treatment of CPA caused by stroke. METHODS: A total of 21 patients diagnosed with CPA were treated with BTX-A injection into the cricopharyngeal muscle using ultrasound combined with balloon guidance. Primary outcome measures, including the functional oral intake scale (FOIS), videofluoroscopic dysphagia scale (VDS) and penetration aspiration scale (PAS), which are quantitative measures for a video fluoroscopic swallowing study (VFSS), and scores of the self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were assessed from baseline to 12 weeks after treatment. Repeated measures analysis of variance was used to compare the scores between time points. RESULTS: BTX-A injection led to improved dysphagia symptoms and scores in 19 patients (90.48%). Among them, 5 cases were cured (23.81%), 11 cases showed significant improvement (52.38%), and 3 cases showed improvement (14.29%). Two cases were absolutely ineffective (9.52%). Compared with the scores prior to treatment, the scores on the FOIS, VDS, PAS, SAS and SDS significantly improved beginning at 3 days (p < .05) and lasting for at least 12 weeks after injection. CONCLUSIONS: Ultrasound with balloon-guided BTX-A injection is probably a relatively safe, easy, and effective technique for the treatment of CPA caused by stroke, with better visualization of the injection procedure. A well-designed controlled trial with a larger sample size is needed for more convincing conclusions.

[Analysis of an ABO subtype with a novel variation].

OBJECTIVE: To analyze the molecular characteristics of a ABO subgroup. METHODS: The ABO phenotype was determined with the tube method. Exons of the ABO gene were analyzed by Sanger sequencing, and haplotypes of exons 6 and 7 were analyzed by cloning sequencing. RESULTS: By forward typing, the red blood cells showed 3+ agglutination reaction with anti-A and 4+ agglutination with anti-B. A weak reaction with A1 cells and no agglutination reaction with B, O cells by the reverse typing. Sequencing results showed heterozygosity including c.297A>G, c.467C>T, c.526C>G, c.608A>G, c.657C>T, c.703G>A, c.796C>A, c.803G>C, c.930G>A. Cloning sequencing revealed a c.608A>G variant in the A allele compared with the ABO*A1.02. CONCLUSION: A new variant site of subtype A of c.608G variation has been identified.

Design of MOF-derived hierarchical Co@C@RGO composite with controllable heterogeneous interfaces as a high-efficiency microwave absorbent.

Carbon-based composites have triggered tremendous attention in the development of high-efficiency microwave absorbers, due to their compatibility, light weight, and high microwave absorption. However, fabricating carbon-based absorbers with a strong absorption ability in a broad frequency range is challenging. Hence, a facile strategy was used to produce Co@C derived from a zeolitic imidazolate framework (ZIF)@ graphene. The Co@C@RGO composite was obtained by annealing the ZIF67/GO nanocomposite precursor at 650 °C in a nitrogen atmosphere. Due to the magnetic loss induced by the Co particles, the dielectric loss generated by the carbon skeletons and graphene, and the interfacial polarization between the components, the hierarchical composite exhibits superior electromagnetic (EM) wave absorption properties. The optimal reflection loss (RL) of the Co@C@ RGO composite can be up to -67.5 dB at 2.6 mm, and the effective bandwidth (≥-10 dB) is 5.4 GHz (10-15.4 GHz) with a thickness of 2 mm at 20 wt% loading. The dipolar polarization caused by graphene, as well as enhanced impedance matching, synergistic effect and interfacial effect among the components, increase the microwave absorption performance of the composite. This work may open a new path to use the Co@C@RGO composite with its high-efficiency EM wave properties as an absorber.

Site-Specific Expression Pattern of PIWI-Interacting RNA in Skin and Oral Mucosal Wound Healing.

The oral mucosa exhibits exceptional healing capability when compared to skin. Recent studies suggest that intrinsic differences in coding genes and regulatory small non-coding RNA (sncRNA) genes (e.g., microRNAs) may underlie the exceptional healing that occurs in the oral mucosa. Here, we investigate the role of a novel class of sncRNA-Piwi-interacting RNA (piRNA)-in the tissue-specific differential response to injury. An abundance of piRNAs was detected in both skin and oral mucosal epithelium during wound healing. The expression of PIWI genes (the obligate binding partners of piRNAs) was also detected in skin and oral wound healing. This data suggested that PIWI-piRNA machinery may serve an unknown function in the highly orchestrated wound healing process. Furthermore, unique tissue-specific piRNA profiles were obtained in the skin and oral mucosal epithelium, and substantially more changes in piRNA expression were observed during skin wound healing than oral mucosal wound healing. Thus, we present the first clue suggesting a role of piRNA in wound healing, and provide the first site-specific piRNA profile of skin and oral mucosal wound healing. These results serve as a foundation for the future investigation of the functional contribution(s) of piRNA in wound repair and tissue regeneration.

Overexpression of the Oral Mucosa-Specific microRNA-31 Promotes Skin Wound Closure.

Wounds within the oral mucosa are known to heal more rapidly than skin wounds. Recent studies suggest that differences in the microRNAome profiles may underlie the exceptional healing that occurs in oral mucosa. Here, we test whether skin wound-healing can be accelerating by increasing the levels of oral mucosa-specific microRNAs. A panel of 57 differentially expressed high expresser microRNAs were identified based on our previously published miR-seq dataset of paired skin and oral mucosal wound-healing [Sci. Rep. (2019) 9:7160]. These microRNAs were further grouped into 5 clusters based on their expression patterns, and their differential expression was confirmed by TaqMan-based quantification of LCM-captured epithelial cells from the wound edges. Of these 5 clusters, Cluster IV (consisting of 8 microRNAs, including miR-31) is most intriguing due to its tissue-specific expression pattern and temporal changes during wound-healing. The in vitro functional assays show that ectopic transfection of miR-31 consistently enhanced keratinocyte proliferation and migration. In vivo, miR-31 mimic treatment led to a statistically significant acceleration of wound closure. Our results demonstrate that wound-healing can be enhanced in skin through the overexpression of microRNAs that are highly expressed in the privileged healing response of the oral mucosa.

Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping.

BACKGROUND: Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers. RESULTS: All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P < 0.005) were identified. Among these, five associations with Ca were repeatedly observed and six co-localized associations were identified. CONCLUSIONS: The identified marker alleles significantly associated with the traits provided important information for understanding genetic controls of alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

Nrdp1 is Associated with Neuronal Apoptosis in Lipopolysaccharide-Induced Neuroinflammation.

Neuregulin receptor degradation protein-1 (Nrdp1), a kind of ring finger E3 ubiquitin ligase, is expressed in several adult tissues, including the heart, testis, prostate and brain. Studies of this molecule have demonstrated its great importance in regulating cell growth, apoptosis and oxidative stress in various cell types. However, information regarding its expression and possible function in the central nervous system is still limited. In this study, we performed a neuroinflammation model by lipopolysaccharide (LPS) lateral ventral injection in adult rats. It was found that the expression of Nrdp1 was significantly increased in cerebral cortex after LPS injection. Immunofluorescence indicated that Nrdp1 was located in the neurons, but not astrocytes or microglia. Furthermore, there was a concomitant up-regulation of active caspase-3 and decreased expression of BRUCE (an inhibitor of apoptosis protein). In addition, decreasing Nrdp1 levels by RNA interference in cortical primary neurons reduced active caspase-3 expression but induced up-regulation of BRUCE. Collectively, all these results suggested that Nrdp1 might play a role in neuronal apoptosis by reducing the expression of BRUCE in neuroinflammation after LPS injection.

Up-regulation of podoplanin involves in neuronal apoptosis in LPS-induced neuroinflammation.

Podoplanin (PDPN) is a mucin-type transmembrane sialoglycoprotein expressed in multiple tissues in adult animals, including the brain, lungs, kidney, and lymphoid organs. Studies of this molecule have demonstrated its great importance in tumor metastasis, platelet aggregation, and lymphatic vessel formation. However, information regarding its regulation and possible function in the central nervous system is still limited. In this study, we performed a neuroinflammatory model by lipopolysaccharide (LPS) lateral ventral injection in adult rats and detected increased expression of PDPN in the brain cortex. Immunofluorescence indicated that PDPN was located in the neurons, but not astrocytes. Moreover, there was a concomitant up-regulation of active caspase-3, cyclin D1, and CDK4 in vivo and vitro studies. In addition, the expression of these three proteins in cortical primary neurons was decreased after knocking down PDPN by siRNA. Collectively, all these results suggested that the up-regulation of PDPN might be involved in neuronal apoptosis in neuroinflammation after LPS injection.

LIN28 expression in rat spinal cord after injury.

LIN28, an RNA-binding protein, is known to be involved in the regulation of many cellular processes, such as embryonic stem cell proliferation, cell fate succession, developmental timing, and oncogenesis. However, its expression and function in central nervous system still unclear. In this study, we performed an acute spinal cord contusion injury (SCI) model in adult rats and investigated the dynamic changes of LIN28 expression in spinal cord. Western blot and immunohistochemistry analysis revealed that LIN28 was present in normal spinal cord. It gradually increased, reached a peak at 3 day, and then nearly declined to the basal level at 14 days after SCI. Double immunofluorescence staining showed that LIN28 immunoreactivity was found in neurons, astrocytes and a handful of microglia. Interestingly, LIN28 expression was increased predominantly in astrocytes but not in neurons. Moreover, the colocalization of LIN28 and proliferating cell nuclear antigen was detected after injury. Western blot showed that LIN28 participated in lipopolysaccharide (LPS) induced astrocytes inflammatory responses by NF-κB signaling pathway. These results suggested that LIN28 may be involved in the pathologic process of SCI, and further research is needed to have a good understanding of its function and mechanism.

Improving the thermal stability and catalytic activity of ulvan lyase by the combination of FoldX and KnowVolution campaign.

Thermal stability is one of the most important properties of ulvan lyases for their application in algae biomass degradation. The Knowledge gaining directed eVolution (KnowVolution) protein engineering strategy could be employed to improve thermostability of ulvan lyase with less screening effort. Herein, the unfolding free energies (ΔΔG) of the loop region were calculated using FoldX and four sites (D103, G104, T113, Q229) were selected for saturation mutagenesis, resulting in the identification of a favorable single-site mutant Q229M. Subsequently, iteration mutation was carried out with the mutant N57P (previously obtained by our group) to further enhance the performance of ulvan lyase. The results showed that the most beneficial variant N57P/Q229M exhibited a 1.67-fold and 2-fold increase in residual activity compared to the wild type after incubation at 40 °C and 50 °C for 1 h, respectively. In addition, the variant produced 1.06 mg/mL of reducing sugar in 2 h, which was almost four times as much as the wild type. Molecular dynamics simulations revealed that N57P/Q229M mutant enhanced the structural rigidity by augmenting intramolecular hydrogen bonds. Meanwhile, the shorter proton transmission distance between the general base of the enzyme and the substrate contributed to the glycosidic bond breakage. Our research showed that in silico saturation mutagenesis using position scan module in FoldX allowed for faster screening of mutants with improved thermal stability, and combining it with KnowVolution enabled a balanced effect of thermal stability and enzyme activity in protein engineering.

Natural flavonoid hesperetin blocks amyloid ß-protein fibrillogenesis, depolymerizes preformed fibrils and alleviates cytotoxicity caused by amyloids.

The aggregation of ß-amyloid (Aß) peptides to form amyloid plaques is one of the primary hallmarks for Alzheimer's disease (AD). Dietary flavonoid supplements containing hesperetin have an ability to decline the risk of developing AD, but the molecular mechanism is still unclear. In this work, hesperetin, a flavanone abundant in citrus fruits, has been proven to prevent the formation of Aß aggregates and depolymerized preformed fibrils in a concentration-dependent fashion. Hesperetin inhibited the conformational conversion from the natural structure to a ß-sheet-rich conformation. It was found that hesperetin significantly reduced the cytotoxicity and relieved oxidative stress eventuated by Aß aggregates in a concentration-dependent manner. Additionally, the beneficial effects of hesperetin were confirmed in Caenorhabditis elegans, including the inhibition of the formation and deposition of Aß aggregates and extension of their lifespan. Finally, the results of molecular dynamics simulations showed that hesperetin directly interacted with an Aß42 pentamer mainly through strong non-polar and electrostatic interactions, which destroyed the structural stability of the preformed pentamer. To summarize, hesperetin exhibits great potential as a prospective dietary supplement for preventing and improving AD.

Study on the effect of different high-voltage electric field polarization process parameters on the vitality of dried chili pepper seeds.

To study the effect of different high-voltage electric field polarisation treatment process parameters on the viability of seeds of dried chili peppers. In this study, a high-voltage electrostatic polarisation treatment system was constructed to carry out experiments on the effects of different high-voltage electric field polarisation treatment process parameters on the viability of dried chili seeds. Conduct one-way tests to determine the preferred polarisation method and the preferred interval for output voltage and polarisation time. Two-factor, five-level central combination test with output voltage and polarization time as test factors and seed conductivity as a response indicator. Determining the better combination of parameters for output voltage and polarization time; Conducting seed germination trials to validate the effectiveness of the polarisation process. The results of the one-way test showed that: Negative-voltage polarisation was more effective than positive-voltage polarisation and alternating positive-negative-voltage polarisation in promoting seed vigor, with a better output voltage in the range of 10-14 kV, and a better polarisation time in the range of 20-40 s; The results of orthogonal tests showed that: Under the condition of negative voltage polarisation treatment, the output voltage of 12.08 kV and polarisation time of 30.32 s was the better parameter combination, at which the seed conductivity was minimum 159.87 uS/(cm g). Analyzing the function of cell membrane selective semi-permeability by seed conductivity change and revealing the mechanism of seed viability enhancement by high voltage electric field polarisation treatment; In the seed germination test, compared with the control group, seed germination potential increased by 9.09%, germination rate increased by 20.45%, germination index increased by 3.49, and vigor index increased by 41.66 under high-voltage electrostatic polarisation treatment, and all vigor indexes were significantly improved. The results of this study can provide a basis for the selection of processes and parameters for subsequent high-voltage electric field polarisation treatment of crop seeds.

A Critical Review on Immobilized Sucrose Isomerase and Cells for Producing Isomaltulose.

Isomaltulose is a novel sweetener and is considered healthier than the common sugars, such as sucrose or glucose. It has been internationally recognized as a safe food product and holds vast potential in pharmaceutical and food industries. Sucrose isomerase is commonly used to produce isomaltulose from the substrate sucrose in vitro and in vivo. However, free cells/enzymes were often mixed with the product, making recycling difficult and leading to a significant increase in production costs. Immobilized cells/enzymes have the following advantages including easy separation from products, high stability, and reusability, which can significantly reduce production costs. They are more suitable than free ones for industrial production. Recently, immobilized cells/enzymes have been encapsulated using composite materials to enhance their mechanical strength and reusability and reduce leakage. This review summarizes the advancements made in immobilized cells/enzymes for isomaltulose production in terms of refining traditional approaches and innovating in materials and methods. Moreover, innovations in immobilized enzyme methods include cross-linked enzyme aggregates, nanoflowers, inclusion bodies, and directed affinity immobilization. Material innovations involve nanomaterials, graphene oxide, and so on. These innovations circumvent challenges like the utilization of toxic cross-linking agents and enzyme leakage encountered in traditional methods, thus contributing to enhanced enzyme stability.

IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer's disease.

Alzheimer's disease (AD) is a universal neurodegenerative disease with the feature of progressive dementia. Currently, there are only seven Food and Drug Administration-approved drugs for the treatment of AD, which merely offer temporary relief from symptom deterioration without reversing the underlying disease process. The identification of inhibitors capable of interacting with proteins associated with AD plays a pivotal role in the development of effective therapeutic interventions. However, a vast number of such inhibitors are dispersed throughout numerous published articles, rendering it inconvenient for researchers to explore potential drug candidates for AD. In light of this, we have manually compiled inhibitors targeting proteins associated with AD and constructed a comprehensive database known as IPAD-DB (Inhibitors of Proteins associated with Alzheimer's Disease Database). The curated inhibitors within this database encompass a diverse range of compounds, including natural compounds, synthetic compounds, drugs, natural extracts and nano-inhibitors. To date, the database has compiled >4800 entries, each representing a correspondent relationship between an inhibitor and its target protein. IPAD-DB offers a user-friendly interface that facilitates browsing, searching and downloading of its records. We firmly believe that IPAD-DB represents a valuable resource for screening potential AD drug candidates and investigating the underlying mechanisms of this debilitating disease. Access to IPAD-DB is freely available at http://www.lamee.cn/ipad-db/ and is compatible with all major web browsers. Database URL: http://www.lamee.cn/ipad-db/.