Microbial source tracking and identification of fecal contamination patterns in saltwater estuaries between base- and storm-flow events using dual genome-based approaches.

Fecal contamination from natural and anthropogenic sources poses significant threats to saltwater estuaries, particularly after storms or heavy rainfall. Monitoring fecal contamination is essential for protecting these vulnerable ecosystems having important ecological and economic values. In this study, we investigated the abundance, sources, and potential causes of fecal contamination at three marine and seven freshwater stations across Vaughn Bay (WA, USA), a shellfish growing district, during base- and storm-flow events. Additionally, we evaluated the performance of fecal indicator bacteria (FIB) quantification, optical brightener assessment, and qPCR analysis for fecal contamination quantification. We compared the effectiveness of qPCR-based microbial source tracking (MST), which targeted a broad range of hosts including, such as humans, birds, cows, horses, ruminants, dogs, and pigs, with sequencing-based MST in identifying fecal contamination sources. Both MST analysis approaches identified birds and humans as the primary sources of fecal contamination. For marine water stations, freshwater creeks VBU001, VBU002, and VB047, along with drain VB007, were identified as the main sources of human-derived fecal contamination in Vaughn Bay, based on Kendall's tau analysis (τ: 0.58-0.97). This information indicates that the septic systems in the catchment areas of these creeks and drains require further investigation to achieve effective fecal contamination control. Optical brightener, FIB enumeration and qPCR quantification results were generally higher during storm-flow events, although they showed poor correlation with each other (Pearson r < 0.40), likely due to physiological and phylogenetic differences among the target organisms of these methods. However, the sequencing-based method faces challenges in precise quantitative identification of differences in fecal contamination between base- and storm-flow events. Due to its high-throughput and cost-effectiveness, we recommend using sequencing-based analysis for large-scale identification of the primary sources of fecal contamination in water environments, followed by targeted qPCR quantification of MST markers for more precise assessments.

Exogenous Amyloid Fibrils Can Cause Significant Upregulation of Neurodegenerative Disease Proteins.

Neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, are associated with the formation of amyloid fibrils. In familial cases, the mutant causative genes accentuate disease progression through overexpression or misfolding of amyloidogenic proteins. Besides, considerable amyloidosis cases arise from external factors, but their origin and mechanisms are not yet fully understood. Herein, we found that amyloid fibrils generated from egg and milk proteins, in addition to their nutritional effects to intestinal cells, can selectively reduce the viability of nervous cells as well as pancreatic islet cells. In contrast, soy protein amyloid fibrils lacked cytotoxicity to the aforementioned cells. This protein source and cell type-dependent cytotoxicity are demonstrated to be associated with the significant upregulation of amyloidogenic proteins. The finding was also confirmed by the vein injection of beta-lactoglobulin fibrils to mice, exhibiting the pronounced upregulations of amyloid beta1-42 (Aß1-42) and islet amyloid polypeptide in vivo. The study therefore provides insight into the health implications of exogenous amyloid fibrils.

A structural rationale for reversible vs irreversible amyloid fibril formation from a single protein.

Reversible and irreversible amyloids are two diverging cases of protein (mis)folding associated with the cross-ß motif in the protein folding and aggregation energy landscape. Yet, the molecular origins responsible for the formation of reversible vs irreversible amyloids have remained unknown. Here we provide evidence at the atomic level of distinct folding motifs for irreversible and reversible amyloids derived from a single protein sequence: human lysozyme. We compare the 2.8 Å structure of irreversible amyloid fibrils determined by cryo-electron microscopy helical reconstructions with molecular insights gained by solid-state NMR spectroscopy on reversible amyloids. We observe a canonical cross-ß-sheet structure in irreversible amyloids, whereas in reversible amyloids, there is a less-ordered coexistence of ß-sheet and helical secondary structures that originate from a partially unfolded lysozyme, thus carrying a "memory" of the original folded protein precursor. We also report the structure of hen egg-white lysozyme irreversible amyloids at 3.2 Å resolution, revealing another canonical amyloid fold, and reaffirming that irreversible amyloids undergo a complete conversion of the native protein into the cross-ß structure. By combining atomic force microscopy, cryo-electron microscopy and solid-state NMR, we show that a full unfolding of the native protein precursor is a requirement for establishing irreversible amyloid fibrils.

Dynamic phase-differencing profilometry with number-theoretical phase unwrapping and interleaved projection.

High-speed 3D measurement is receiving increasing attention. However, simultaneously achieving high computational efficiency, algorithmic robustness, and reconstructing ratio is challenging. Therefore, a dynamic phase-differencing profilometry (DPDP) is proposed. By capturing the minimum three phase-shifting sinusoidal deformed patterns and establishing a brand-new model, the phase difference between the object on the reference plane and the reference plane is directly resolved to effectively improve computational efficiency. Although it is wrapped, by using only two auxiliary complementary gratings with a purposely designed lower frequency, a DPDP-based number-theoretical temporal phase unwrapping (NT-TPU) algorithm is also proposed to unwrap the wrapped phase difference rather than the phase itself with high robustness. Furthermore, compared to existing PSP-based NT-TPU, the proposed NT-TPU can normally work under more relaxed restrictions. In order to accomplish a high reconstructing ratio, a pentabasic interleaved projection (PIP) strategy based on time division multiplexing is proposed. It can improve the reconstructing ratio from one reconstruction per every five patterns to an equivalent of one reconstruction per every 1.67 patterns. Experimental results demonstrate that the proposed method achieves high computational efficiency, high algorithmic robustness, and high reconstructing ratio simultaneously and has prospective application in high-speed 3D measurement.

An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.

Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.

A multihole nozzle controls recrystallization of high-moisture extruded maize starches: Effect of cooling die temperature.

Hot extrusion is utilized for starch modification due to its high mechanical input and product output. Amylose recrystallization commences and primarily depends on intermolecular interactions after conventional extrusion. Hence, the design of a new component based on the existed extrusion system was aimed at facilitating molecular aggregation, potentially accelerating starch recrystallization. In this study, a nozzle sheet comprising 89 holes was integrated into the cooling die. The impact of the multihole nozzle on the structure and in vitro digestibility of extruded maize starches after retrogradation was examined at varying cooling die temperatures. The results showed that the nozzle-assembled extrusion system operated effectively without additional mechanical or yield losses. At 50 °C, the crystallinity of nozzle-produced starch was approximately 70 % higher than that of conventionally extruded starch, predominantly owing to the B-type allomorph of the amylose double helix. Recrystallized amylopectin was also found in these nozzle-produced starches, indicating that multihole nozzle-induced uniaxial elongational flow resulted in the rapid starch crystallization. The increased formation of recrystallized amylose led to improved molecular order in starch structures while reducing their digestibility. These findings revealed a new approach to improve starch crystallinity by incorporating a nozzle sheet in the extrusion process.

Orthogonal Spatial Binary Coding Method for High-Speed 3D Measurement.

Temporal phase unwrapping based on single auxiliary binary coded pattern has been proven to be effective for high-speed 3D measurement. However, in traditional spatial binary coding, it often leads to an imbalance between the number of periodic divisions and codewords. To meet this challenge, a large codewords orthogonal spatial binary coding method is proposed in this paper. By expanding spatial multiplexing from 1D to 2D orthogonal direction, it goes beyond the traditional 8 codewords to 27 codewords at three-level periodic division. In addition, a novel full-period connected domain segmentation technique based on local localization is proposed to avoid the time-consuming global iterative erosion and complex anomaly detection in traditional methods. For the decoding process, a purely spatial codewords recognition and a spatial-temporal hybrid codewords recognition methods are established to better suppress the percentage offset caused by static defocusing and dynamic motion, respectively. Obviating the need for intricate symbol recognition, the decoding process in our proposed method encompasses a straightforward analysis of statistical distribution. Building upon the development of special spatial binary coding, we have achieved a well-balance between low periodic division and large codewords for the first time. The experimental results verify the feasibility and validity of our proposed whole image processing method in both static and dynamic measurements.

Advances in the Interaction between Food-Derived Nanoparticles and the Intestinal Barrier.

The maintenance of the intestinal barrier is crucial for the overall balance of the gut and the organism. Dysfunction of the intestinal barrier is closely associated with intestinal diseases. In recent years, due to the increased presence of nanoparticles (NPs) in the human diet, there has been a growing concern regarding the safety and potential impact of these NPs on gastrointestinal health. The interactions between food-derived NPs and the intestinal barrier are numerous. This review provides an introduction to the structure and function of the intestinal barrier along with a comprehensive summary of the interactions between food NPs and the intestinal barrier. Additionally, we highlight the potential connection between the food NPs-induced dysfunction of the intestinal barrier and inflammatory bowel disease. Finally, we discuss the enhancement of food NPs on the repair of the intestinal barrier damage and the nutrients absorption. This review holds significant importance in furthering our understanding of the regulatory mechanisms of food-derived NPs on the intestinal barrier.

NSD family proteins: Rising stars as therapeutic targets.

Epigenetic modifications, including DNA methylation and histone post-translational modifications, intricately regulate gene expression patterns by influencing DNA accessibility and chromatin structure in higher organisms. These modifications are heritable, are independent of primary DNA sequences, undergo dynamic changes during development and differentiation, and are frequently disrupted in human diseases. The reversibility of epigenetic modifications makes them promising targets for therapeutic intervention and drugs targeting epigenetic regulators (e.g., tazemetostat, targeting the H3K27 methyltransferase EZH2) have been applied in clinical therapy for multiple cancers. The NSD family of H3K36 methyltransferase enzymes-including NSD1 (KMT3B), NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1)-are now receiving drug development attention, with the exciting advent of an NSD2 inhibitor (KTX-1001) advancing to Phase I clinical trials for relapsed or refractory multiple myeloma. NSD proteins recognize and catalyze methylation of histone lysine marks, thereby regulating chromatin integrity and gene expression. Multiple studies have implicated NSD proteins in human disease, noting impacts from translocations, aberrant expression, and various dysfunctional somatic mutations. Here, we review the biological functions of NSD proteins, epigenetic cooperation related to NSD proteins, and the accumulating evidence linking these proteins to developmental disorders and tumorigenesis, while additionally considering prospects for the development of innovative epigenetic therapies.

Carboxyl graphene modified PEDOT:PSS organic electrochemical transistor for in situ detection of cancer cell morphology.

Circulating tumor cells in human peripheral blood play an important role in cancer metastasis. In addition to the size-based and antibody-based capture and separation of cancer cells, their electrical characterization is important for rare cell detection, which can prove fatal in point-of-care testing. Herein, an organic electrochemical transistor (OECT) biosensor made of solution-gated carboxyl graphene mixed with PEDOT:PSS for the detection of cancer cells in situ is reported. Carboxyl graphene was used in this work to modulate cancer cell morphology, which differs significantly from normal blood cells, to achieve rare cancer cell detection. When the concentration of carboxyl graphene mixed in PEDOT:PSS was increased from 0 to 5 mg mL-1, the cancer cell surface area increased from 218 µm2 to 530 µm2, respectively. A change in cell morphology was also detected by the OECT. Negative charges in the cancer cells induced a positive shift in gate voltage, which was approximately 40 mV for spherical-shaped cells. When the cell surface area increased, transfer curves of transistor revealed a negative shift in gate voltage. Therefore, the sensor can be used for in situ detection of cancer cell morphology during the cell capture process, which can be used to identify whether the captured cells are deformable.

High-moisture extrusion of curdlan: Texture and structure.

High-moisture extrusion is a promising thermomechanical technology extensively employed in manufacturing fibrous meat analogues from plant-based proteins, garnering considerable research attention. However, polysaccharide-based extrusion has been rarely explored. The present study investigates the effects of varying extruder barrel temperatures (130 °C-200 °C) on the texture and structure of curdlan extrudates, and highlights the formation mechanism. Results showed that the single chain of curdlan aggregates to form triple-helix chains upon extrusion, consequently enhancing the crystallinity, particularly at 170 °C. The hardness, chewiness, and mechanical properties improved with increasing barrel temperature. Moreover, barrel temperatures affected the macrostructure, the extrudates maintained intact morphologies except at 160 °C due to the melting of curdlan gel as confirmed by the differential scanning calorimetry thermogram. Microstructural analysis revealed that curdlan extrudates transited through three phases: original gel (130 °C, 140 °C, and 150 °C), transition state (160 °C), and regenerated gel (170 °C, 180 °C, 190 °C, and 200 °C). The steady state of regenerated gel (170 °C) exhibited higher crystallinity and smaller fractal dimension, resulting in a more compact and crosslinked gel network. This study elucidates the structure transition of curdlan gel at extremely high temperatures, offering valuable technical insights for developing theories and methods with respect to polysaccharide-based extrusion that may find applications in food-related fields.

Absolute phase retrieval based on fringe amplitude encoding without any additional auxiliary pattern.

An absolute phase retrieval method based on fringe amplitude encoding is proposed. Different from the conventional intensity coding methods which are based on time division multiplexing with multiple additional auxiliary patterns, the proposed fringe order encoding strategy is codeword overlapping interaction based on space division multiplexing. It just directly encodes different fringe amplitudes for different periods in corresponding sinusoidal phase-shifting patterns to generate space division multiplexing composite sinusoidal phase-shifting patterns and quantifies the fringe amplitudes into four levels as encoding strategy, so it can retrieve absolute phase without any additional auxiliary patterns. To improve the anti-interference capability of the proposed method, a codeword extraction method based on image morphological processing is proposed to segment the grayscale. Consequently, both the phase-shifting sinusoidal deformed patterns and the single frame space division multiplexing four gray-level codewords for fringe order recognition can be extracted respectively from the captured composite deformed patterns. Then, a half-period single-connected domain correction method is also proposed to correct the codewords. Moreover, in order to suppress the effect of jump errors, the phase zero points are constructed to segment the positive and negative ranges of the phase, making the phase unwrapping process segmented. The experimental results demonstrate the feasibility and effectivity of the proposed method.

Fabrication of PEDOT:PSS-based solution gated organic electrochemical transistor array for cancer cells detection.

Organic electrochemical transistor (OECT) was applied in chemical and biological sensing. In this work, we developed a simple and repeatable method to fabricate OECT array, which had been successfully used to detect cancer cells. PEDPT:PSS conductive film between source and drain electrodes were patterned through photolithography, which can achieve uniform devices with same electrical characterization. When MCF-7 cancer cells are captured on the PEDOT:PSS surface via specifical antibody, the transfer characteristic of OECT shifts to higher gate electrode voltage due to the electrostatic interaction between cancer cells and device. The effective gate voltage shift can reach about 63 mV when the concentration of cancer cells increased to 5000. The shift of effective gate voltage is related to the cancer cell morphology, which is increased in the first 1 h and decreased when the capture time was larger than 1 h. The device of OECT array can increase the sample flux and make the detection result more accurate. It is expected that OECT array will have promising practical applications in single cancer cell detection in the future.

Enhanced Fourier-Hilbert-transform suppression for saturation-induced phase error in phase-shifting profilometry.

Intensity saturation tends to induce severe errors in high dynamic range three-dimensional measurements using structured-light techniques. This paper presents an enhanced Fourier-Hilbert-transform (EFHT) method to suppress the saturation-induced phase error in phase-shifting profilometry, by considering three types of residual errors: nonuniform-reflectivity error, phase-shift error, and fringe-edge error. Background normalization is first applied to the saturated fringe patterns to suppress the effect of the nonuniform reflectivity. A self-correction method is proposed to correct the large phase-shift error in the compensated phase. The self-corrected phase error is detected to assist in locating the fringe-edge area, within which the true phase is computed based on the sub-period phase error model. Experimental results demonstrated the effectiveness of the proposed method in suppressing the saturation-induced phase error and other three types of residual errors with fewer images.

Saturation-Induced Phase Error Compensation Method Using Complementary Phase.

Intensity saturation can induce phase error and, thus, measurement error in fringe projection profilometry. To reduce saturation-induced phase errors, a compensation method is developed. The mathematical model of saturation-induced phase errors is analyzed for N-step phase-shifting profilometry, and the phase error is approximately N-folder of the frequency of the projected fringe. Additional N-step phase-shifting fringe patterns with initial phase-shift π/N are projected for generating a complementary phase map. The final phase map is obtained by averaging the original phase map extracted from the original fringe patterns and the complementary phase map, and then the phase error can be canceled out. Both simulations and experiments demonstrated that the proposed method can substantially reduce the saturation-induced phase error and realize accurate measurements for a highly dynamic range of scenarios.

The establishment of city commercial banks and China's green economy development.

Promoting sustainable economic development has been pursued by all countries, and achieving green economic development is crucial to sustainable economic development. This study uses the non-radial direction distance function (NDDF) method to calculate the level of development of the green economy in Chinese cities during 2003-2014. Next, it uses the establishment of China's city commercial banks as an exogenous policy shock to build a staggered difference-in-differences model to empirically test the impact of the establishment of city commercial banks on green economy development. This study found that, first, the establishment of city commercial banks significantly promoted green economy development. Second, in areas with a high proportion of small and medium-sized enterprises (SMEs), the establishment of city commercial banks is imperative to promoting green economy development. SMEs are crucial carriers to city commercial banks to promote green economy development. Third, financing constraints mitigation, green innovation, and pollution emission reduction are important channels for city commercial banks affecting green economy development. This study enriches the relevant research on the impact of financial market reform on green economy development.

Ultra-fast 3D imaging by a big codewords space division multiplexing binary coding.

Patternless binary coding strategies have been a challenge for ultra-fast 3D imaging with structured light. This Letter proposes a big codewords space division multiplexing binary coding method. From the third to the multiple order, a special spatial binary coding instead of the Gray code is created for the first time, to the best of our knowledge, to achieve an ultra-wide unambiguous range with only one auxiliary pattern. Advantageously, a connection domain segmentation technique with anomaly detection is proposed to achieve decoding of the fringe order, which cleverly avoids the misalignment problem. Additionally, a center of gravity method is applied to compensate for the codewords of the residual connected domain. The robustness and effectiveness of the proposed method for complex, isolated, and non-uniform reflectivity objects, as well as the ultra-fast 3D imaging of dynamic measurements, are experimentally verified.

Three-Dimensional PLGA Nanofiber-Based Microchip for High-Efficiency Cancer Cell Capture.

A 3D network capture substrate based on poly(lactic-co-glycolic acid) (PLGA) nanofibers was studied and successfully used for high-efficiency cancer cell capture. The arc-shaped glass micropillars were prepared by chemical wet etching and soft lithography. PLGA nanofibers were coupled with micropillars by electrospinning. Given the size effect of the microcolumn and PLGA nanofibers, a three-dimensional of micro-nanometer spatial network was prepared to form a network cell trapping substrate. After the modification of a specific anti-EpCAM antibody, MCF-7 cancer cells were captured successfully with a capture efficiency of 91%. Compared with the substrate composed of 2D nanofibers or nanoparticles, the developed 3D structure based on microcolumns and nanofibers had a greater contact probability between cells and the capture substrate, leading to a high capture efficiency. Cell capture based on this method can provide technical support for rare cells in peripheral blood detection, such as circulating tumor cells and circulating fetal nucleated red cells.

Temporal phase unwrapping based on unequal phase-shifting code.

In fringe projection profilometry (FPP) based on temporal phase unwrapping (TPU), reducing the number of projecting patterns has become one of the most important works in recent years. To remove the 2π ambiguity independently, this paper proposes a TPU method based on unequal phase-shifting code. Wrapped phase is still calculated from N-step conventional phase-shifting patterns with equal phase-shifting amount to guarantee the measuring accuracy. Particularly, a series of different phase-shifting amounts relative to the first phase-shifting pattern are set as codewords, and encoded to different periods to generate one coded pattern. When decoding, Fringe order with a large number can be determined from the conventional and coded wrapped phases. In addition, we develop a self-correction method to eliminate the deviation between the edge of fringe order and the 2π discontinuity. Thus, the proposed method can achieve TPU but need to only project one additional coded pattern (e. g. 3+1), which can significantly benefit dynamic 3D shape reconstruction. The theoretical and experimental analysis verify that the proposed method performs high robustness on the reflectivity of the isolated object while ensuring the measuring speed.

Dynamic computer-generated moiré profilometry based on high-density binary coding.

A dynamic computer-generated moiré profilometry based on high-density binary coding is proposed. For making full use of the maximum refresh rate and the maximum resolution of the digital light projector (DLP), the binary coded fringe is used to replace the conventional 256-gray-scale sinusoidal fringe, which can increase the refresh rate from the traditional 120 Hz to more than 1 kHz and meet the needs of dynamic measurement from the source. To realize the minimum equivalent wavelength and obtain the purest calculated moiré fringe, a minimum four-pixel period high-density binary fringe that satisfies the sampling theorem is designed for the DLP. The measuring accuracy of computer-generated moiré profilometry is effectively improved due to its minimum equivalent wavelength. The experimental results show the feasibility and practicability of the proposed method. It not only possesses higher measuring accuracy, but also possesses a proper potential application in dynamic three-dimensional measurement.