LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.

Single-cell sequencing has revolutionized our ability to dissect the heterogeneity within tumor populations. In this study, we present LoRA-TV (Low Rank Approximation with Total Variation), a novel method for clustering tumor cells based on the read depth profiles derived from single-cell sequencing data. Traditional analysis pipelines process read depth profiles of each cell individually. By aggregating shared genomic signatures distributed among individual cells using low-rank optimization and robust smoothing, the proposed method enhances clustering performance. Results from analyses of both simulated and real data demonstrate its effectiveness compared with state-of-the-art alternatives, as supported by improvements in the adjusted Rand index and computational efficiency.

Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis in Pseudomonas aeruginosa.

Pseudomonas aeruginosa is capable of causing acute and chronic infections in various host tissues, which depends on its abilities to effectively utilize host-derived nutrients and produce protein virulence factors and toxic compounds. However, the regulatory mechanisms that direct metabolic intermediates towards production of toxic compounds are poorly understood. We previously identified a regulatory protein PvrA that controls genes involved in fatty acid catabolism by binding to palmitoyl-coenzyme A (CoA). In this study, transcriptomic analyses revealed that PvrA activates the Pseudomonas quinolone signal (PQS) synthesis genes, while suppressing genes for production of polyhydroxyalkanoates (PHAs). When palmitic acid was the sole carbon source, mutation of pvrA reduced production of pyocyanin and rhamnolipids due to defective PQS synthesis, but increased PHA production. We further solved the co-crystal structure of PvrA with palmitoyl-CoA and identified palmitoyl-CoA-binding residues. By using pvrA mutants, we verified the roles of the key palmitoyl-CoA-binding residues in gene regulation in response to palmitic acid. Since the PQS signal molecules, rhamnolipids and PHA synthesis pathways are interconnected by common metabolic intermediates, our results revealed a regulatory mechanism that directs carbon flux from carbon/energy storage to virulence factor production, which might be crucial for the pathogenesis.

Repair Engineering of Crystal Structure in van der Waals Materials by Probe Electron Beam.

The advancement of electronic technology has led to increasing research on performance and stability. Continuous electrical pulse stimulation can cause crystal structure changes, affecting performance and accelerating aging. Controlled repair of these defects is crucial. In this study, we investigated crystal structure changes in van der Waals (vdW) InSe crystals under continuous electric pulses by using electron beam lithography (EBL) and spherical aberration corrected transmission electron microscopy (Cs-TEM). Results show that electrical pulses induce amorphous regions in the InSe lattice, increasing the device resistance. We used Cs-STEM probe scanning for precise repair, abbreviated SPRT, to optimize device performance. SPRT is related to electric fields induced by the electron beam and can be applied to other 2D materials like α-In2Se3 and CrSe2, offering a potential approach to extend device lifespan.

Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin.

Aeromonas hydrophila, a prevalent pathogen in the aquaculture industry, poses significant challenges due to its drug-resistant strains. Moreover, residues of antibiotics like streptomycin, extensively employed in aquaculture settings, drive selective bacterial evolution, leading to the progressive development of resistance to this agent. However, the underlying mechanism of its intrinsic adaptation to antibiotics remains elusive. Here, we employed a quantitative proteomics approach to investigate the differences in protein expression between A. hydrophila under streptomycin (SM) stress and nonstress conditions. Notably, bioinformatics analysis unveiled the potential involvement of metal pathways, including metal cluster binding, iron-sulfur cluster binding, and transition metal ion binding, in influencing A. hydrophila's resistance to SM. Furthermore, we evaluated the sensitivity of eight gene deletion strains related to streptomycin and observed the potential roles of petA and AHA_4705 in SM resistance. Collectively, our findings enhance the understanding of A. hydrophila's response behavior to streptomycin stress and shed light on its intrinsic adaptation mechanism.

Combining transcriptome and metabolome analysis to understand the response of sorghum to Melanaphis sacchari.

BACKGROUND: The sorghum aphid Melanaphis sacchari (Zehntner) (Homoptera: Aphididae) is an important insect in the late growth phase of sorghum (Sorghum bicolor L.). However, the mechanisms of sorghum response to aphid infestation are unclear. RESULTS: In this paper, the mechanisms of aphid resistance in different types of sorghum varieties were revealed by studying the epidermal cell structure and performing a transcriptome and metabolome association analysis of aphid-resistant and aphid-susceptible varieties. The epidermal cell results showed that the resistance of sorghum to aphids was positively correlated with epidermal cell regularity and negatively correlated with the intercellular space and leaf thickness. Transcriptome and metabolomic analyses showed that differentially expressed genes in the resistant variety HN16 and susceptible variety BTX623 were mainly enriched in the flavonoid biosynthesis pathway and differentially expressed metabolites were mainly related to isoflavonoid biosynthesis and flavonoid biosynthesis. The q-PCR results of key genes were consistent with the transcriptome expression results. Meanwhile, the metabolome test results showed that after aphidinfestation, naringenin and genistein were significantly upregulated in the aphid-resistant variety HN16 and aphid-susceptible variety BTX623 while luteolin was only significantly upregulated in BTX623. These results show that naringenin, genistein, and luteolin play important roles in plant resistance to aphid infestation. The results of exogenous spraying tests showed that a 1‰ concentration of naringenin and genistein is optimal for improving sorghum resistance to aphid feeding. CONCLUSIONS: In summary, the physical properties of the sorghum leaf structure related to aphid resistance were studied to provide a reference for the breeding of aphid-resistant varieties. The flavonoid biosynthesis pathway plays an important role in the response of sorghum aphids and represents an important basis for the biological control of these pests. The results of the spraying experiment provide insights for developing anti-aphid substances in the future.

Developing a novel heme biosensor to produce high-active hemoproteins in Pichia pastoris through comparative transcriptomics.

The development of a heme-responsive biosensor for dynamic pathway regulation in eukaryotes has never been reported, posing a challenge for achieving the efficient synthesis of multifunctional hemoproteins and maintaining intracellular heme homeostasis. Herein, a biosensor containing a newly identified heme-responsive promoter, CRISPR/dCas9, and a degradation tag N-degron was designed and optimized to fine-tune heme biosynthesis in the efficient heme-supplying Pichia pastoris P1H9 chassis. After identifying literature-reported promoters insensitive to heme, the endogenous heme-responsive promoters were mined by transcriptomics, and an optimal biosensor was screened from different combinations of regulatory elements. The dynamic regulation pattern of the biosensor was validated by the transcriptional fluctuations of the HEM2 gene involved in heme biosynthesis and the subsequent responsive changes in intracellular heme titers. We demonstrate the efficiency of this regulatory system by improving the production of high-active porcine myoglobin and soy hemoglobin, which can be used to develop artificial meat and artificial metalloenzymes. Moreover, these findings can offer valuable strategies for the synthesis of other hemoproteins.

Biosynthesis, acquisition, regulation, and upcycling of heme: recent advances.

Heme, an iron-containing tetrapyrrole in hemoproteins, including: hemoglobin, myoglobin, catalase, cytochrome c, and cytochrome P450, plays critical physiological roles in different organisms. Heme-derived chemicals, such as biliverdin, bilirubin, and phycocyanobilin, are known for their antioxidant and anti-inflammatory properties and have shown great potential in fighting viruses and diseases. Therefore, more and more attention has been paid to the biosynthesis of hemoproteins and heme derivatives, which depends on the adequate heme supply in various microbial cell factories. The enhancement of endogenous biosynthesis and exogenous uptake can improve the intracellular heme supply, but the excess free heme is toxic to the cells. Therefore, based on the heme-responsive regulators, several sensitive biosensors were developed to fine-tune the intracellular levels of heme. In this review, recent advances in the: biosynthesis, acquisition, regulation, and upcycling of heme were summarized to provide a solid foundation for the efficient production and application of high-value-added hemoproteins and heme derivatives.

The modification of heme special importer to improve the production of active hemoglobins in Escherichia coli.

To enhance the import of heme for the production of active hemoproteins in Escherichia coli C41 (DE3) lacking the special heme import system, heme receptor ChuA from E. coli Nissle 1917 was modified through molecular docking and the other components (ChuTUV) for heme import was overexpressed, while heme import was tested through growth assay and heme sensor HS1 detection. A ChuA mutant G360K was selected, which could import 3.91 nM heme, compared with 2.92 nM of the wild-type ChuA. In addition, it presented that the expression of heme transporters ChuTUV was not necessary for heme import. Based on the modification of ChuA (G360K), the titer of human hemoglobin and the peroxidase activity of leghemoglobin reached 1.19 µg g-1 DCW and 24.16 103 U g-1 DCW, compared with 1.09 µg g-1 DCW and 21.56 103 U g-1 DCW of the wild-type ChuA, respectively. Heme import can be improved through the modification of heme receptor and the engineered strain with improved heme import has a potential to efficiently produce high-active hemoproteins.

Oreonectes yuedongensis (Cypriniformes, Nemacheilidae), a new freshwater fish species from the Lianhua Mountains in eastern Guangdong, China.

In this work, we describe a new species of the genus Oreonectes, Oreonectes yuedongensis sp. nov., collected from the Lianhua Mountains in eastern Guangdong, China. Phylogenetic trees constructed based on the mitochondrial cytochrome b (Cyt b) gene showed that this new species represents an independent evolutionary lineage, with uncorrected genetic distances (Kimura 2-parameter model) from congeners ranging from 5.1% to 8.3%. In addition, nuclear DNA analysis indicated O. yuedongensis as an independent lineage separate from its closely related species. Morphologically, the new species can be distinguished from other six species in the genus Oreonectes by a combination of serial characters. The description of this new species suggests that it is necessary to reassess the biodiversity of Oreonectes platycephalus as a complex, especially in the middle reaches of the Pearl River near the border between Guangdong and Guangxi. Morphological and genetic evidence supports O. yenlingi as a synonym of O. platycephalus.

A meta-analysis of the consequences of cognitive training on the cognitive function of aged mild cognitive impairment patients.

Cognitive training has gained popularity as a means to aid older adults with mild cognitive impairment (MCI), a transitional phase between normal ageing and Alzheimer's disease (AD). MCI represents a critical and potentially reversible state that can either improve or progress to full-blown dementia. This study aims to evaluate the impact of cognitive training on cognitive function in aged patients with MCI. PubMed, Embase, Medline, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang databases were systematically retrieved from inception until May 2024. We rigorously applied the risk-of-bias methodology recommended by the Cochrane Handbook to assess the quality of the included studies. After two rounds of screening and removing duplicates, a total of 2685 articles were initially identified, from which 28 met the inclusion criteria. The meta-analysis included 28 randomised controlled trials with 1960 participants. In this meta-analysis, Review Manager 5.4 was used for statistical analysis. Findings revealed that cognitive training significantly improved the global cognitive function in aged MCI patients, as evidenced by the results of the Montreal Cognitive Assessment (standard mean difference (SMD) = 3.26; 95% CI, 2.69-3.82; P < 0.00001) and Mini-Mental State Examination (SMD = 2.27; 95% CI, 1.52-3.01; P < 0.00001). The beneficial effects of cognitive training interventions were consistent regardless of duration, including periods of 2 months or less (SMD = 1.94; 95% CI, 1.25-2.63; P < 0.00001), 2 to 6 months (SMD = 2.53; 95% CI, 1.52-3.53; P < 0.00001), and over 6 months (SMD = 4.12; 95% CI, 0.97-7.27; P = 0.01). The analysis indicates that cognitive training significantly benefits overall cognitive function, delayed memory, orientation, attention, and language skills in aged patients with MCI. Furthermore, cognitive training interventions are effective in enhancing cognitive function, irrespective of their duration.

P21 facilitates macrophage chemotaxis by promoting CCL7 in the lung epithelial cell lines treated with radiation and bleomycin.

BACKGROUND: Interstitial lung diseases (ILDs) can be induced and even exacerbated by radiotherapy in thoracic cancer patients. The roles of immune responses underlying the development of these severe lung injuries are still obscure and need to be investigated. METHODS: A severe lung damage murine model was established by delivering 16 Gy X-rays to the chest of mice that had been pre-treated with bleomycin (BLM) and thus hold ILDs. Bioinformatic analyses were performed on the GEO datasets of radiation-induced lung injury (RILI) and BLM-induced pulmonary fibrosis (BIPF), and RNA-sequencing data of the severely damaged lung tissues. The screened differentially expressed genes (DEGs) were verified in lung epithelial cell lines by qRT-PCR assay. The injured lung tissue pathology was analyzed with H&E and Masson's staining, and immunohistochemistry staining. The macrophage chemotaxis and activity promoted by the stressed epithelial cells were determined by using a cell co-culture system. The expressions of p21 in MLE-12 and Beas-2B cells were detected by qRT-PCR, western blot, and immunofluorescence. The concentration of CCL7 in cell supernatant was measured by ELISA assay. In some experiments, Beas-2B cells were transfected with p21-siRNA or CCL7-siRNA before irradiation and/or BLM treatment. RESULTS: After the treatment of irradiation and/or BLM, the inflammatory and immune responses, chemokine-mediated signaling pathways were steadily activated in the severely injured lung, and p21 was screened out by the bioinformatic analysis and further verified to be upregulated in both mouse and human lung epithelial cell lines. The expression of P21 was positively correlated with macrophage infiltration in the injured lung tissues. Co-culturing with stressed Beas-2B cells or its conditioned medium containing CCL7 protein, U937 macrophages were actively polarized to M1-phase and their migration ability was obviously increased along with the damage degree of Beas-2B cells. Furthermore, knockdown p21 reduced CCL7 expression in Beas-2B cells and then decreased the chemotaxis of co-cultured macrophages. CONCLUSIONS: P21 promoted CCL7 release from the severely injured lung epithelial cell lines and contributed to the macrophage chemotaxis in vitro, which provides new insights for better understanding the inflammatory responses in lung injury.

PitA Controls the H2- and H3-T6SSs through PhoB in Pseudomonas aeruginosa.

Pseudomonas aeruginosa possesses three type VI secretion systems (T6SSs) that are involved in interspecies competition, internalization into epithelial cells, and virulence. Host-derived mucin glycans regulate the T6SSs through RetS, and attacks from other species activate the H1-T6SS. However, other environmental signals that control the T6SSs remain to be explored. Previously, we determined PitA to be a constitutive phosphate transporter, whose mutation reduces the intracellular phosphate concentration. Here, we demonstrate that mutation in the pitA gene increases the expression of the H2- and H3-T6SS genes and enhances bacterial uptake by A549 cells. We further found that mutation of pitA results in activation of the quorum sensing (QS) systems, which contributes to the upregulation of the H2- and H3-T6SS genes. Overexpression of the phosphate transporter complex genes pstSCAB or knockdown of the phosphate starvation response regulator gene phoB in the ΔpitA mutant reduces the expression of the QS genes and subsequently the H2- and H3-T6SS genes and bacterial internalization. Furthermore, growth of wild-type PA14 in a low-phosphate medium results in upregulation of the QS and H2- and H3-T6SS genes and bacterial internalization compared to those in cells grown in a high-phosphate medium. Deletion of the phoB gene abolished the differences in the expression of the QS and T6SS genes as well as bacterial internalization in the low- and high- phosphate media. Overall, our results elucidate the mechanism of PitA-mediated regulation on the QS system and H2- and H3-T6SSs and reveal a novel pathway that regulates the T6SSs in response to phosphate starvation. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogenic bacterium that causes acute and chronic infections in humans. The type VI secretion systems (T6SSs) have been shown to associate with chronic infections. Understanding the mechanism used by the bacteria to sense environmental signals and regulate virulence factors will provide clues for developing novel effective treatment strategies. Here, we demonstrate a relationship between a phosphate transporter and the T6SSs and reveal a novel regulatory pathway that senses phosphate limitation and controls bacterial virulence factors in P. aeruginosa.

Photonic parallel channel estimation of MIMO-OFDM wireless communication systems.

Channel estimation is a key technology in MIMO-OFDM wireless communication systems. Increasingly extensive application scenarios and exponentially growing data volumes of MIMO-OFDM systems have imposed greater challenges on the speed, latency, and parallelism of channel estimation based on electronic processors. Here, we propose a photonic parallel channel estimation (PPCE) architecture which features radio-frequency direct processing. Proof-of-concept experiment is carried out to demonstrate the general feasibility of the proposed architecture at different frequency bands (100 MHz, 4 GHz, and 10 GHz). The mean square errors (MSEs) between the experimental channel estimation results and the theoretically simulated ones lie on the order of 10-3. The bit error rates (BERs) are below the pre-forward error correction (pre-FEC) threshold. Besides, we analyze the performance of PPCE under different signal-to-noise ratios (SNRs), baseband symbol forms, and weight tuning precisions. The proposed PPCE architecture has the potential to achieve high-speed, highly parallel channel estimation in large-scale MIMO-OFDM systems after the photonic-electronic chip integration.

Variation analysis of photonic lantern mode control ability under mode oscillation: a new approach.

In this Letter, we present a novel, to the best of our knowledge, image-based approach to analyze the mode control ability of a photonic lantern employed in diode laser beam combining, aiming to achieve a stable beam output. The proposed method is founded on theories of power flow and mode coupling and is validated through experiments. The findings demonstrate that the analysis of the beam combining process is highly reliable when the main mode component of the output light is the fundamental mode. Moreover, it is experimentally demonstrated that the mode control performance of the photonic lantern significantly influences the beam combining loss and the fundamental mode purity. In the essence of the variation-based analysis, a key advantage of the proposed method is its applicability even in the situation of a poor combined beam stability. The experiment only requires the collection of the far-field light images of the photonic lantern to characterize the model control ability, achieving an accuracy greater than 98%.

Efficient heterologous expression of cytochrome P450 enzymes in microorganisms for the biosynthesis of natural products.

Natural products, a chemically and structurally diverse class of molecules, possess a wide spectrum of biological activities, have been used therapeutically for millennia, and have provided many lead compounds for the development of synthetic drugs. Cytochrome P450 enzymes (P450s, CYP) are widespread in nature and are involved in the biosynthesis of many natural products. P450s are heme-containing enzymes that use molecular oxygen and the hydride donor NAD(P)H (coupled via enzymic redox partners) to catalyze the insertion of oxygen into C-H bonds in a regio- and stereo-selective manner, effecting hydroxylation and several other reactions. With the rapid development of systems biology, numerous novel P450s have been identified for the biosynthesis of natural products, but there are still several challenges to the efficient heterologous expression of active P450s. This review covers recent developments in P450 research and development, including the properties and functions of P450s, discovery and mining of novel P450s, modification and screening of P450 mutants, improved heterologous expression of P450s in microbial hosts, efficient whole-cell transformation with P450s, and current applications of P450s for the biosynthesis of natural products. This resource provides a solid foundation for the application of highly active and stable P450s in microbial cell factories to biosynthesize natural products.

Fungi-enabled pore channel regulation and defect engineering of a novel micro-reactor for treating complex effluents.

Defect engineering has become a significant research area in recent years; however, little has been reported on the biological method for modulating the intrinsic carbon defects of the biochar framework. Herein, a fungi-enabled method for the fabrication of porous carbon/Fe3O4/Ag (PC/Fe3O4/Ag) composites was developed, and the mechanism underlying the hierarchical structure is elucidated for the first time. By regulating the cultivation process of fungi on water hyacinth biomass, a well-developed interconnected structure and carbon defects acting as potential catalytic active sites were formed. This new material with antibacterial, adsorption and photodegradation properties could be an excellent choice for treating the mixed dyestuff effluents with oils and bacteria, also guiding pore channel regulation and defect engineering in materials science. Numerical simulations were carried out to demonstrate the remarkable catalytic activity.

Exosomal protein angiopoietin-like 4 mediated radioresistance of lung cancer by inhibiting ferroptosis under hypoxic microenvironment.

BACKGROUND: Hypoxia-mediated radioresistance is a major reason for the adverse radiotherapy outcome of non-small cell lung cancer (NSCLC) in clinical, but the underlying molecular mechanisms are still obscure. METHODS: Cellular and exosomal ANGPTL4 proteins under different oxygen status were examined. Colony survival, lipid peroxidation and hallmark proteins were employed to determine the correlation between ferroptosis and radioresistance. Gene regulations, western blot and xenograft models were used to explore the underlying mechanisms of the role of ANGPTL4 in radioresistance. RESULTS: ANGPTL4 had a much higher level in hypoxic NSCLC cells compared to normoxic cells. Up- or down- regulation of ANGPTL4 positively interrelated to the radioresistance of NSCLC cells and xenograft tumours. GPX4-elicited ferroptosis suppression and lipid peroxidation decrease were authenticated to be involved in the hypoxia-induced radioresistance. ANGPTL4 encapsulated in the exosomes from hypoxic cells was absorbed by neighbouring normoxic cells, resulting in radioresistance of these bystander cells in a GPX4-dependent manner, which was diminished when ANGPTL4 was downregulated in the donor exosomes. CONCLUSION: Hypoxia-induced ANGPTL4 rendered radioresistance of NSCLC through at least two parallel pathways of intracellular ANGPTL4 and exosomal ANGPTL4, suggesting that ANGPTL4 might applicable as a therapeutic target to improve the therapeutic efficacy of NSCLC.

Pseudomonas aeruginosa Phosphate Transporter PitA (PA4292) Controls Susceptibility to Aminoglycoside Antibiotics by Regulating the Proton Motive Force.

Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium that causes nosocomial infections in immunocompromised patients. ß-lactam and aminoglycoside antibiotics are commonly used in the treatment of P. aeruginosa infections. Previously, we found that mutation in a PA4292 gene increases bacterial resistance to ß-lactam antibiotics. In this study, we demonstrated that mutation in PA4292 increases bacterial susceptibility to aminoglycoside antibiotics. We further found enhanced uptake of tobramycin by the ΔPA4292 mutant, which might be due to an increase of proton motive force (PMF). Sequence analysis revealed PA4292 is homologous to the Escherichia coli phosphate transporter PitA. Mutation of PA4292 indeed reduces intracellular phosphate concentration. We thus named PA4292 as pitA. Although the PMF is enhanced in the ΔpitA mutant, the intracellular ATP concentration is lower than that in the isogenic wild-type strain PA14, which might be due to lack of the ATP synthesis substrate phosphate. Overexpression of the phosphate transporter complex genes pstSCAB in the ΔpitA mutant restores the intracellular phosphate concentration, PMF, ATP synthesis, and aminoglycosides resistance. In addition, growth of wild-type PA14 in a low-phosphate medium resulted in higher PMF and aminoglycoside susceptibility compared to cells grown in a high-phosphate medium. Overall, our results demonstrate the roles of PitA in phosphate transportation and reveal the relationship between intracellular phosphate and aminoglycoside susceptibility.

Mutation of PA4292 in Pseudomonas aeruginosa Increases ß-Lactam Resistance through Upregulating Pyocyanin Production.

Metallo-ß-lactamase (MBL)-producing Pseudomonas aeruginosa is increasingly reported worldwide and usually causes infections with high mortality rates. Aztreonam/avibactam is a ß-lactam/ß-lactamase inhibitor (BLBLI) combination that is under clinical trials. The advantage of aztreonam/avibactam over the currently used BLBLIs lies in its effectiveness against MBL-producing pathogens, making it one of the few drugs that can be used to treat infections caused by MBL-producing P. aeruginosa. However, the molecular mechanisms underlying aztreonam/avibactam resistance development remain unexplored. Here, in this study, we performed an in vitro evolution assay by using a previously identified MBL-producing P. aeruginosa clinical isolate, NKPa-71, and found mutations in a novel gene, PA4292, in the aztreonam/avibactam-resistant mutants. By mutation of PA4292 in the reference strain PA14, we verified the role of PA4292 in the resistance to aztreonam/avibactam and ß-lactams. Transcriptomic analyses revealed upregulation of pyocyanin biosynthesis genes among the most overexpressed in the PA4292 mutant. We further demonstrated that pyocyanin overproduction in the PA4292 mutant increased the bacterial resistance to ß-lactams by reducing drug influx. These data revealed a novel mechanism that might lead to the development of resistance to aztreonam/avibactam and ß-lactams.

Parallel optical coherent dot-product architecture for large-scale matrix multiplication with compatibility for diverse phase shifters.

Photonics physically promises high-speed and low-consumption computing of matrix multiplication. Nevertheless, conventional approaches are challenging to achieve large throughput, high precision, low power consumption, and high density simultaneously in a single architecture, because the integration scale of conventional approaches is strongly limited by the insertion loss of cascaded optical phase shifters. Here, we present a parallel optical coherent dot-product (P-OCD) architecture, which deploys phase shifters in a fully parallel way. The insertion loss of phase shifters does not accumulate at large integration scale. The architecture decouples the integration scale and phase shifter insertion loss, making it possible to achieve superior throughput, precision, energy-efficiency, and compactness simultaneously in a single architecture. As the architecture is compatible with diverse integration technologies, high-performance computing can be realized with various off-the-shelf photonic phase shifters. Simulations show that compared with conventional architectures, the parallel architecture can achieve near 100× higher throughput and near 10× higher energy efficiency especially with lossy phase shifters. The parallel architecture is expected to perform its unique advantage in computing-intense applications including AI, communications, and autonomous driving.