Tpgen: a language model for stable protein design with a specific topology structure.

BACKGROUND: Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not be met when generating sequences blindly. Research indicates that small proteins have notable advantages, including high stability, accurate resolution prediction, and facile specificity modification. RESULTS: This study involves the construction of a neural network model named TopoProGenerator(TPGen) using a transformer decoder. The model is trained with sequences consisting of a maximum of 65 amino acids. The training process of TopoProGenerator incorporates reinforcement learning and adversarial learning, for fine-tuning. Additionally, it encompasses a stability predictive model trained with a dataset comprising over 200,000 sequences. The results demonstrate that TopoProGenerator is capable of designing stable small protein sequences with specified topology structures. CONCLUSION: TPGen has the ability to generate protein sequences that fold into the specified topology, and the pretraining and fine-tuning methods proposed in this study can serve as a framework for designing various types of proteins.

Diverse mode operation fiber laser mode-locked by nonlinear multimode interference.

We present an all-fiber passively mode-locked (ML) laser with a nonlinear multimode interference (NLMI)-based saturable absorber (SA) capable of generating five pulse modes. The SA consists of two centrally aligned graded index multimode fiber (GIMF) with different diameters (105-50 µm) and features a widely adjustable transmission with saturable/reverse-saturable absorption. Based on this, dissipative soliton (DS), Q-switched rectangular pulse (QRP), dissipative soliton resonance (DSR), noise-like pulse (NLP) and bright-dark pulse pairs (BDP) are observed at three dispersions without additional filter. The DS has a pulse energy, bandwidth and duration of up to 1.15 nJ, 17.98 nm and ∼2.78 ps. The achievable pulse duration and energy of DSR and NLP are 5.21, 48.06 ns and 4.53, 5.12 nJ, respectively. Furthermore, it is demonstrated that the BDP is superimposed by a chair-case pulse (CP) and a rectangular pulse (RP) belonging to orthogonal polarization states. The versatility, flexibility, simplicity and energy scalability of the large-core hybrid GIMF-SA, make it interesting and highly attractive in ultrafast photonics.

Ultra-sensitive pressure sensor with low-temperature crosstalk based on the Vernier effect and helical structure.

What we believe to be a novel high-sensitivity fiber-optic pressure sensor based on the vernier effect and helical structure is proposed and experimentally verified. The sensor utilizes the superposition of higher-order mode Mach-Zehnder interference and Sagnac fundamental mode polarization interference in a single fiber ring to achieve the vernier effect. In addition, a non-invasive encapsulation structure was fabricated to convert the rise and fall of the pressure value into the change in the twist angle of the optical fiber. This approach reduces the interference of the detecting medium on the sensor signal while simultaneously increasing the sensitivity of the pressure sensor. According to experimental data, the detection sensitivity of the sensor can reach -67277 nm/MPa, which is 65 times higher than the sensitivity of the conventional vernier effect pressure sensor. It also solves the issue of temperature interference with the Vernier-effect structured fiber optic sensor. The sensor has a measured temperature cross-sensitivity of 0.000065 kPa/°C, which is significantly lower than that of comparable sensors. This makes the sensor highly sensitive and ideal for low crosstalk pressure measurement.

Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions.

Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.

Genome-wide mapping of GlnR-binding sites reveals the global regulatory role of GlnR in controlling the metabolism of nitrogen and carbon in Paenibacillus polymyxa WLY78.

BACKGROUND: Paenibacillus polymyxa WLY78 is a Gram-positive, endospore-forming and N2-fixing bacterium. Our previous study has demonstrated that GlnR acts as both an activator and a repressor to regulate the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) according to nitrogen availability, which is achieved by binding to the two GlnR-binding sites located in the nif promoter region. However, further study on the GlnR-mediated global regulation in this bacterium is still needed. RESULTS: In this study, global identification of the genes directly under GlnR control is determined by using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and electrophoretic mobility shift assays (EMSA). Our results reveal that GlnR directly regulates the transcription of 17 genes/operons, including a nif operon, 14 nitrogen metabolism genes/operons (glnRA, amtBglnK, glnA1, glnK1, glnQHMP, nasA, nasD1, nasD2EF, gcvH, ansZ, pucR, oppABC, appABCDF and dppABC) and 2 carbon metabolism genes (ldh3 and maeA1). Except for the glnRA and nif operon, the other 15 genes/operons are newly identified targets of GlnR. Furthermore, genome-wide transcription analyses reveal that GlnR not only directly regulates the expression of these 17 genes/operons, but also indirectly controls the expression of some other genes/operons involved in nitrogen fixation and the metabolisms of nitrogen and carbon. CONCLUSION: This study provides a GlnR-mediated regulation network of nitrogen fixation and the metabolisms of nitrogen and carbon.

Glutamine synthetase and GlnR regulate nitrogen metabolism in Paenibacillus polymyxa WLY78.

Paenibacillus polymyxa WLY78, a N2-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the transcription of the nif (nitrogen fixation) operon (nifBHDKENXhesAnifV) in P. polymyxa WLY78 by binding to two loci of the nif promoter according to nitrogen availability. However, the regulatory mechanisms of nitrogen metabolism mediated by GlnR in the Paenibacillus genus remain unclear. In this study, we have revealed that glutamine synthetase (GS) and GlnR in P. polymyxa WLY78 play a key role in the regulation of nitrogen metabolism. P. polymyxa GS (encoded by glnA within glnRA) and GS1 (encoded by glnA1) belong to distinct groups: GSI-α and GSI-ß. Both GS and GS1 have the enzyme activity to convert NH4+ and glutamate into glutamine, but only GS is involved in the repression by GlnR. GlnR represses transcription of glnRA under excess nitrogen, while it activates the expression of glnA1 under nitrogen limitation. GlnR simultaneously activates and represses the expression of amtBglnK and gcvH in response to nitrogen availability. Also, GlnR regulates the expression of nasA, nasD1D2, nasT, glnQHMP, and glnS. IMPORTANCE In this study, we have revealed that Paenibacillus polymyxa GlnR uses multiple mechanisms to regulate nitrogen metabolism. GlnR activates or represses or simultaneously activates and inhibits the transcription of nitrogen metabolism genes in response to nitrogen availability. The multiple regulation mechanisms employed by P. polymyxa GlnR are very different from Bacillus subtilis GlnR which represses nitrogen metabolism under excess nitrogen. Both GS encoded by glnA within the glnRA operon and GS1 encoded by glnA1 in P. polymyxa WLY78 are involved in ammonium assimilation, but only GS is required for regulating GlnR activity. The work not only provides significant insight into understanding the interplay of GlnR and GS in nitrogen metabolism but also provides guidance for improving nitrogen fixation efficiency by modulating nitrogen metabolism.

4*10 Gbps WDM communication system based on a tunable V-cavity semiconductor laser.

This paper is about the V-cavity tunable semiconductor laser with a 1550 nm band used as a transmitter to build a wavelength division multiplexing (WDM) optical fiber communication link. In the experiment, a 20 km optical fiber communication link with a reasonable eye diagram and low bit error rate (BER) transmitted by 40 Gbps can be established. The experimental results show that a single laser can achieve a wavelength tuning range of 25 nm, reach 32 channels at a 100 GHz frequency interval, and the average side mode suppression ratio (SMSR) is above 39 dB. The advantages and application potential of V-cavity tunable semiconductor laser (VCL) for wavelength routing in optical communication networking are verified by experiments.

High-Q cascaded single-passband microwave photonic filter based on an optical-electrical feedback loop.

A cascaded microwave photonic filter refers to a microwave photonic filter (MPF) with higher performance obtained by cascading a MPF with two different structures. A high-Q cascaded single-passband MPF is proposed experimentally based on stimulated Brillouin scattering (SBS) and an optical-electrical feedback loop (OEFL). In this experiment, the pump light of SBS is provided by a tunable laser. The Brillouin gain spectrum generated by the pump light is used to amplify the phase modulation sideband, and the narrow linewidth OEFL is subsequently used to compress the passband width of the MPF. By carefully adjusting the pump wavelength and tuning the tunable optical delay line, stable tuning can be achieved for a cascaded single-passband MPF with a high-Q value. The results have demonstrated that the MPF has characteristics of high-frequency selectivity and a wide frequency tuning range. Meanwhile, the filtering bandwidth is up to 300 kHz, the out-of-band suppression is more than 20 dB, the maximum Q-value is 5.333×104, and the center frequency tuning range is 1-17 GHz. The cascaded MPF proposed not only achieves a higher Q-value, but also has the advantages of tunability, a high out-of-band rejection ratio, and strong cascaded ability.

Observation of bound solitons generated by a figure-9 fiber laser in the 1 µm band.

The paper describes the observation of diverse bound-state patterns, including tightly bound states, loosely bound states, and composite bound states, in a figure-9 fiber laser. By performing dispersion management and using polarization-maintaining fibers with high gain coefficient, stable dispersion-managed solitons and bound solitons can be simultaneously generated. This work advances our understanding of complex soliton dynamics and presents a novel, to the best of our knowledge, approach for future applications of bound states. Additionally, the research involves integrated packaging, effectively enhancing overall work stability.

Enhanced four-wave mixing in borophene-microfiber waveguides at telecom C-band.

All-optical wavelength conversion technology based on two-dimensional (2D) materials has lately received keen interest. As a new 2D material, borophene displays acceptable photoelectric properties. We demonstrate the all-optical wavelength conversion through four-wave mixing (FWM) in borophene-microfiber hybrid waveguides. Borophene is deposited at the thinnest part of the tapered fiber and enhanced FWM occurs in this photonic device. By optimizing the effect of nonlinear polarization, wavelength tuning, and power variation, the conversion efficiency increases to -19.1dB, corresponding to 3 dB conversion bandwidth in a range of 7.1 nm. In addition, this photonic device is employed to achieve all-optical wavelength conversion of 10 Gb/s non-return-to-zero digital sequence. The signal quality of converted light such as optical signal-to-noise ratio, bit-error-rate, and eye diagram are investigated, which indicates that the proposed wavelength converter has high conversion efficiency and remarkable stability. This study shows that the borophene-microfiber waveguide has potential application prospects in all-optical signal processing.

Combined influence of the gain and dispersion of a mode-locked fiber laser on a time-stretching analog-to-digital conversion link.

Using theory and experiments, we demonstrated the combined influence of the spectral gain and dispersion of a dissipative soliton mode-locked fiber laser on a time-stretching analog-to-digital conversion link without an optical amplifier. The theoretical and experimental results indicate the following: first, the amplitude and envelope shape of the stretched signal are mainly affected by the spectral gain of the dissipative soliton at different central wavelengths under a radio frequency signal of 10 GHz. Second, at the higher frequency of 25 GHz, the influence of the phase shift induced by the dispersion of different spectral ranges on the amplitude of the stretched signal becomes clearer. The amplitude of the stretched signal across all spectral ranges decrease, and the envelope shape differs from that at 10 GHz. Moreover, the wavelength at the maximum amplitude of the stretched signal changes, for which the influence of the spectral dispersion is greater than that of the spectral gain. Finally, the ratio of the amplitude at 25 GHz to that at 10 GHz at different spectral ranges are different, which indicates that the amplitude of the stretched signal at different spectral ranges is affected by the phase shift by different degrees.

Transmission performance of a 1.96 µm active mode-locked laser in smoke channel.

We demonstrate the data transmission characteristics of a 1.96 µm laser in an indoor simulated smoke channel. An active mode-locked thulium-doped fiber laser at 1961.63 nm can be generated, and the repetition rate is 2.11 GHz corresponding pulse duration of 12.47 ps. Therefore, the pulse can be modulated by a 2.11 Gb/s digital sequence to act as a carrier light source. The transmission characteristics of signal light under different visibility conditions of 0.5, 0.05, and 0.005 km are studied. Compared with the back-to-back conditions, the signal-to-noise ratios of the carrier can decrease after passing through the smoke channels, which are 3.93, 7.1, and 9.08 dB, respectively. At the same time, the received power jitter can increase from ±0.16 to ±1.14dB. The sensitivity can be -19.52dBm at the visibility of 0.005 km. The experimental results show that thulium-doped mode-locked laser has an excellent performance in a smoke channel.

Low threshold soliton and a noise-like pulse conversion in an all-polarization-maintaining figure-eight cavity.

We experimentally report a low threshold soliton and a noise-like mode-locked fiber laser using an all-polarization-maintaining figure-eight cavity. We built a bidirectional pump structure without a phase shifter at the beginning of the experiment. The resonator has a high mode-locking threshold of 620 mW. Afterwards, we used a phase shifter in the resonator, and the laser can self-start in a conventional soliton (CS) mode-locked state when pump1 reaches the threshold of only 70 mW. The CS pulse with a duration of 863.8 fs can be observed at 1560 nm. When the two pump powers increase to 350 mW and 50 mW, the conventional soliton can convert to noise-like pulses. The central wavelength and pulse duration of noise-like mode-locked pulse are 1560.4 nm and 417.9 fs, respectively. The laser can realize conversion between ultrafast pulses and high-energy pulses, and have a low threshold that can be used for nonlinear frequency conversion, supercontinuum generation, sensing, etc.

Tunable peak power square-wave pulse based on an all-PM thulium-doped mode-locked fiber laser.

Nanosecond dissipative soliton resonance pulse is a demonstration of an all polarization-maintaining (PM) thulium-doped fiber laser in a nonlinear amplifying loop mirror (NALM)-based figure-eight configuration. Each loop of the apparatus includes a controllable power amplifier. With increased amplifier power, pulse width broadens linearly from 3.6 to 13.5 ns, and maximum single pulse energy can reach 27.5 nJ. Interestingly, the output peak power presents two completely opposite proportional effects in terms of the variation of settings for two amplifiers, respectively. The experimental results show that the NALM loop plays an important role for tunable pulse duration, and the unidirectional ring part makes a significant contribution for power scaling.

Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa.

Ammonia is a major signal that regulates nitrogen fixation in most diazotrophs. Regulation of nitrogen fixation by ammonia in the Gram-negative diazotrophs is well-characterized. In these bacteria, this regulation occurs mainly at the level of nif (nitrogen fixation) gene transcription, which requires a nif-specific activator, NifA. Although Gram-positive and diazotrophic Paenibacilli have been extensively used as a bacterial fertilizer in agriculture, how nitrogen fixation is regulated in response to nitrogen availability in these bacteria remains unclear. An indigenous GlnR and GlnR/TnrA-binding sites in the promoter region of the nif cluster are conserved in these strains, indicating the role of GlnR as a regulator of nitrogen fixation. In this study, we for the first time reveal that GlnR of Paenibacillus polymyxa WLY78 is essentially required for nif gene transcription under nitrogen limitation, whereas both GlnR and glutamine synthetase (GS) encoded by glnA within glnRA operon are required for repressing nif expression under excess nitrogen. Dimerization of GlnR is necessary for binding of GlnR to DNA. GlnR in P. polymyxa WLY78 exists in a mixture of dimers and monomers. The C-terminal region of GlnR monomer is an autoinhibitory domain that prevents GlnR from binding DNA. Two GlnR-biding sites flank the -35/-10 regions of the nif promoter of the nif operon (nifBHDKENXhesAnifV). The GlnR-binding site Ⅰ (located upstream of -35/-10 regions of the nif promoter) is specially required for activating nif transcription, while GlnR-binding siteⅡ (located downstream of -35/-10 regions of the nif promoter) is for repressing nif expression. Under nitrogen limitation, GlnR dimer binds to GlnR-binding siteⅠ in a weak and transient association way and then activates nif transcription. During excess nitrogen, glutamine binds to and feedback inhibits GS by forming the complex FBI-GS. The FBI-GS interacts with the C-terminal domain of GlnR and stabilizes the binding affinity of GlnR to GlnR-binding site Ⅱ and thus represses nif transcription.

[Recognition of producing areas of Angelicae Sinensis Radix based on structure-texture image decomposition].

The pharmacological effects of Angelicae Sinensis Radix from different producing areas are uneven. Accurate identification of its producing areas by computer vision and machine learning(CVML) is conducive to evaluating the quality of Angelicae Sinensis Radix. This paper collected the high-definition images of Angelicae Sinensis Radix from different producing areas using a digital camera to construct an image database, followed by the extraction of texture features based on the grayscale relationship of adjacent pixels in the image. Then a support vector machine(SVM)-based prediction model for predicting the producing areas of Angelicae Sinensis Radix was built. The experimental results showed that the prediction accuracy reached up to 98.49% under the conditions of the model training set occupying 80%, the test set occupying 20%, and the sampling radius(r) of adjacent pixels being 2. When the training set was set to 10%, the prediction accuracy was still over 93%. Among the three producing areas of Angelicae Sinensis Radix, Huzhu county, Qinghai province exhibited the highest error rate, while Heqing county, Yunnan province the lowest error rate. Angelicae Sinensis Radix from Minxian county, Gansu province and Huzhu county, Qinghai province were both wrongly attributed to Heqing county, Yunnan province, while most of those from Huzhu county, Qinghai province were misjudged as the samples produced in Minxian county, Gansu province. The method designed in this paper enabled the rapid and non-destructive prediction of the producing areas of Angelicae Sinensis Radix, boasting high accuracy and strong stability. There were definite morphological differences between Angelicae Sinensis Radix samples from Minxian county, Gansu province and those from Huzhu county, Qinghai province. The wrongly predicted samples from Minxian county, Gansu province and Huzhu city, Qinghai province shared similar morphological characteristics with those from Heqing county, Yunnan province. Most wrongly predicted samples from Heqing county, Yunnan province were similar to the ones from Minxian county, Gansu province in morphological characteristics.

Transmission characteristics of 1.55 and 2.04 µm laser carriers in a simulated smoke channel based on an actively mode-locked fiber laser.

We experimentally demonstrate a free-space data transmission system in an indoor simulated smoke chamber with a laser carrier of an erbium-doped actively mode-locked fiber laser and a holmium-doped actively mode-locked fiber laser. Two additional semiconductor lasers operating at 0.85 and 1.06 µm are used to calibrate the visibility of a smoke channel using the Ijaz model and compare smoke attenuation with 1.55 and 2.04 µm lasers. The eye patterns and bit error rates of 1.55 and 2.04 µm laser carriers with a data rate of 4.04 Gbps are investigated experimentally at 0.5, 0.05, and 0.005 km visibilities. The experimental results show that the smoke attenuation is wavelength dependent for V < 0.5 km. As the visibility decreases, the long wavelength laser is less affected by the attenuation and power fluctuation caused by Mie scattering. The measured optical signal-to-noise ratios of the 1.55 and 2.04 µm laser carriers for V = 0.005 km are 4.83 and 8.62 dB, respectively. The corresponding link sensitivities are -14.59 and -17.74 dBm, respectively, indicating that the 2.04 µm data transmission system is more reliable under an extremely dense smoke condition.

Switchable generation of a sub-200 fs dissipative soliton and a noise-like pulse in a normal-dispersion Tm-doped mode-locked fiber laser.

We report on the switchable generation of a dissipative soliton (DS) pulse and a noise-like pulse (NLP) in an all-fiberized Tm-doped fiber laser in the normal-dispersion region. Mode-locking operation is achieved through a nonlinear polarization rotation component, and the cavity dispersion is compensated using ultra-high numerical aperture (UHNA4) fiber that is easy to integrate and low in cost. At a pump threshold of 510 mW, DS operation can first be achieved without additional filter. The 3 dB spectrum bandwidth of the DS pulse is greater than 50 nm, and the duration of the de-chirped pulse is 193 fs. By increasing the pump power to 880 mW, the mode-locking state can evolve into NLP operation with proper cavity polarization state. The 3 dB spectrum bandwidth and duration of de-chirped coherence spike are 105.6 nm and 121 fs, respectively. Meanwhile, ultra-broadband NLP (over 150 nm considering 3 dB spectrum width) can also be observed with the appropriate cavity parameters. All the proposed pulse patterns present good capacity for achieving narrow pulse width and withstanding high pulse energy.

Low SNR difference Nyquist-WDM channels with optical sinc-shaped pulses based on flat electro-optic frequency combs.

We experimentally demonstrate Nyquist wavelength-division-multiplexed (WDM) channels with a low signal-to-noise ratio (SNR) difference based on flat electro-optic combs (EOCs), which reduce the interchannel crosstalk penalty in Nyquist-WDM transmission with no guard band. The five Nyquist-WDM channels are generated through the insertion of uniform and coherent lines around each line of the EOCs from a dual-parallel Mach-Zehnder modulator. For the five channels, the normalized root-mean-square error of optical sinc-shaped pulses at a repetition rate of 9 GHz is between 1.23% and 2.04%. The SNRs of the Nyquist signal can be better than 30 dB by using flat EOCs with a narrow linewidth as WDM sources, and the difference in SNR is less than 0.6 dB for the WDM channels. The transmission performance of five Nyquist-WDM channels with no guard band is compared in a 56 km fiber link. The results show that our scheme provides a minimum interchannel sensitivity penalty of 0.7 dB at the forward-error-correction limit. The Nyquist-WDM channels with low SNR difference can effectively improve the communication performance of the Nyquist-WDM system.

Receiving sensitivity improvement by wide-spectrum OAM with OTDM and polarization multiplexing in weak atmospheric turbulence.

In this paper, a wide-spectrum orbital angular momentum (OAM) system with a polarization and optical time division multiplexing (OTDM) free-space transmission system is experimentally demonstrated. To enhance the system transmission performance in atmospheric turbulent channel, a wide-spectrum laser and an OAM beam are used. The wide-spectrum laser can be generated by utilizing pumped laser to pump nonlinear fiber, and OAM can be generated with a special light modulator. Furthermore, OTDM and polarization multiplexing methods are used to enhance the communication rate from 4 Gbit/s to 32 Gbit/s. With the use of the wide-spectrum laser and the OAM beam, the receiving scintillation index (SI) can be reduced, and detection sensitivity can be improved. It is the first time a wide-spectrum OAM communication system performance has been studied. It is shown that under weak atmospheric turbulence condition, the SI can be reduced by 38% and the receiving sensitivity can be improved by 3.18 dB via wide-spectrum OAM beams.