Evolutionary and developmental specialization of foveal cell types in the marmoset.

In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high-throughput single-cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all their foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia (MG), among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for MG in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.

Detecting the exponential relaxation spectrum in glasses by high-precision nanocalorimetry.

Nonexponential relaxations are universal characteristics for glassy materials. There is a well-known hypothesis that nonexponential relaxation peaks are composed of a series of exponential events, which have not been verified. In this Letter, we discover the exponential relaxation events during the recovery process using a high-precision nanocalorimetry, which are universal for metallic glasses and organic glasses. The relaxation peaks can be well fitted by the exponential Debye function with a single activation energy. The activation energy covers a broad range from α relaxation to ß relaxation and even the fast γ/ß' relaxation. We obtain the complete spectrum of the exponential relaxation peaks over a wide temperature range from 0.63Tg to 1.03Tg, which provides solid evidence that nonexponential relaxation peaks can be decomposed into exponential relaxation units. Furthermore, the contribution of different relaxation modes in the nonequilibrium enthalpy space is measured. These results open a door for developing the thermodynamics of nonequilibrium physics and for precisely modulating the properties of glasses by controlling the relaxation modes.

Size Dependent Phase Transformation of Liquid Gallium.

As the most popular liquid metal (LM), gallium (Ga) and its alloys are emerging as functional materials due to their unique combination of fluidic and metallic properties near room temperature. As an important branch of utilizing LMs, micro- and submicron-particles of Ga-based LM are widely employed in wearable electronics, catalysis, energy, and biomedicine. Meanwhile, the phase transition is crucial not only for the applications based on this reversible transformation process, but also for the solidification temperature at which fluid properties are lost. While Ga has several solid phases and exhibits unusual size-dependent phase behavior. This complex process makes the phase transition and undercooling of Ga uncontrollable, which considerably affects the application performance. In this work, extensive (nano-)calorimetry experiments are performed to investigate the polymorph selection mechanism during liquid Ga crystallization. It is surprisingly found that the crystallization temperature and crystallization pathway to either α -Ga or ß -Ga can be effectively engineered by thermal treatment and droplet size. The polymorph selection process is suggested to be highly relevant to the capability of forming covalent bonds in the equilibrium supercooled liquid. The observation of two different crystallization pathways depending on the annealing temperature may indicate that there exist two different liquid phases in Ga.

Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.

Trichomes are specialized glandular or non-glandular structures that provide physical or chemical protection against insect and pathogen attack. Trichomes in Arabidopsis have been extensively studied as typical non-glandular structures. By contrast, the molecular mechanism underlying glandular trichome formation and elongation remains largely unknown. We previously demonstrated that Hair is essential for the formation of type I and type VI trichomes. Here, we found that overexpression of Hair increased the density and length of tomato trichomes. Biochemical assays revealed that Hair physically interacts with its close homolog SlZFP8-like (SlZFP8L), and SlZFP8L also directly interacts with Woolly. SlZFP8L-overexpressing plants showed increased trichome density and length. We further found that the expression of SlZFP6, which encodes a C2H2 zinc finger protein, is positively regulated by Hair. Using chromatin immunoprecipitation, yeast one-hybrid, and dual-luciferase assays we identified that SlZFP6 is a direct target of Hair. Similar to Hair and SlZFP8L, the overexpression of SlZFP6 also increased the density and length of tomato trichomes. Taken together, our results suggest that Hair interacts with SlZFP8-like to regulate the initiation and elongation of trichomes by modulating SlZFP6 expression in tomato.

Bioremediation of lead-contaminated soil by inorganic phosphate-solubilizing bacteria immobilized on biochar.

In this study, a bio-composite (IBWS700) was prepared using inorganic phosphate-solubilizing bacteria (iPSB), which were immobilized on biochar produced from wheat straw (WS700). Further, the bio-remediation effects of the composite for lead (Pb) in soil were also investigated. The presence of different Pb species, physicochemical properties, enzyme activities, and immobilization mechanisms of Pb in soil were also evaluated. Compared to free iPSB and biochar, IBWS700 significantly decreased the lead bio-availability whereas increased the residual fraction, also affected available phosphorus (AP), cation exchange capacity (CEC), organic matter (OM) and activity of urease, alkaline phosphatase, sucrase and catalase. Interestingly, the changes in the enzyme activity, AP and OM performed twice increases with increasing Pb concentration, which was rarely reported. The reason might be attributed to the reconstruction of bacteria communities with high Pb load. Further, the immobilization mechanisms mainly included bio-adsorption and bio-precipitation. SEM revealed that the surface of IBWS700 covered with a large number of heterogeneous colonization of iPSB and white stack after Pb2+ adsorption. FTIR spectra showed that O-H, C-O-P, CO, and C =C could play important roles in bio-adsorption. Moreover, XRD analysis indicated that bio-precipitates were mainly Pb5(PO4)3Cl. In general, the use of IBWS700 could effectively immobilize Pb2+ and improve soil quality.

Transcriptomic and functional analyses uncover the regulatory role of lncRNA000170 in tomato multicellular trichome formation.

Trichomes are universal specific structures originating from nearly all terrestrial plants. Although quantities of long non-coding RNAs (lncRNAs) have been identified in many plant species, the role of lncRNAs in trichome formation still remains unknown. Here, we identified a total of 1303 lncRNAs in the young stems of woolly mutant LA3560 (Wo) and its non-woolly segregants (WT). Out of these lncRNAs, 86 lncRNAs were obviously upregulated in Wo and 110 lncRNAs were downregulated. We determined that seven lncRNAs were highly expressed in stem trichomes compared to trichome-free stems and several other tissues of LA3560 by a quantitative reverse transcriptase-polymerase chain reaction, including lncRNA000746, lncRNA000170, lncRNA000277, lncRNA000774, lncRNA000756, lncRNA000100, and lncRNA000898. Transgenic experiments revealed that overexpression of lncRNA000170 inhibited type I trichome formation on the lower stems of the adult transgenic plants. We further determined that lncRNA000170 was transcribed from the complementary strand of Solyc10g006360, for which expression can be induced by lncRNA000170 in its overexpression lines and woolly mutants. Solyc10g006360 overexpression also caused type I trichome decrease. In addition, several trichome regulators, such as Wo, H, SlCycB2, and SlCycB3, were markedly downregulated in lncRNA000170 overexpression lines. These findings demonstrate that lncRNA000170 may be involved in the regulatory pathway mediated by these trichome regulators.

Activation Entropy as a Key Factor Controlling the Memory Effect in Glasses.

As opposed to the common monotonic relaxation process of glasses, the Kovacs memory effect describes an isothermal annealing experiment, in which the enthalpy and volume of a preannealed glass first increases before finally decreasing toward equilibrium. This interesting behavior has been observed for many materials and is generally explained in terms of heterogeneous dynamics. In this Letter, the memory effect in a model Au-based metallic glass is studied using a high-precision high-rate calorimeter. The activation entropy (S^{*}) during isothermal annealing is determined according to the absolute reaction rate theory. We observe that the memory effect appears only when the second-annealing process has a large S^{*}. These results indicate that a large value of S^{*} is a key requirement for observation of the memory effect and this may provide a useful perspective for understanding the memory effect in both thermal and athermal systems.

Temperature Characteristics of a Pressure Sensor Based on BN/Graphene/BN Heterostructure.

Temperature is a significant factor in the application of graphene-based pressure sensors. The influence of temperature on graphene pressure sensors is twofold: an increase in temperature causes the substrates of graphene pressure sensors to thermally expand, and thus, the graphene membrane is stretched, leading to an increase in the device resistance; an increase in temperature also causes a change in the graphene electrophonon coupling, resulting in a decrease in device resistance. To investigate which effect dominates the influence of temperature on the pressure sensor based on the graphene-boron nitride (BN) heterostructure proposed in our previous work, the temperature characteristics of two BN/graphene/BN heterostructures with and without a microcavity beneath them were analyzed in the temperature range 30-150 °C. Experimental results showed that the resistance of the BN/graphene/BN heterostructure with a microcavity increased with the increase in temperature, and the temperature coefficient was up to 0.25%°C-1, indicating the considerable influence of thermal expansion in such devices. In contrast, with an increase in temperature, the resistance of the BN/graphene/BN heterostructure without a microcavity decreased with a temperature coefficient of -0.16%°C-1. The linearity of the resistance change rate (ΔR/R)-temperature curve of the BN/graphene/BN heterostructure without a microcavity was better than that of the BN/graphene/BN heterostructure with a microcavity. These results indicate that the influence of temperature on the pressure sensors based on BN/graphene/BN heterostructures should be considered, especially for devices with pressure microcavities. BN/graphene/BN heterostructures without microcavities can be used as high-performance temperature sensors.

Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network.

BACKGROUND: Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predict protein-lncRNA interactions, but few studies make use of the topological information of heterogenous biological networks associated with the lncRNAs. RESULTS: In this work, we propose a novel approach, PLIPCOM, using two groups of network features to detect protein-lncRNA interactions. In particular, diffusion features and HeteSim features are extracted from protein-lncRNA heterogenous network, and then combined to build the prediction model using the Gradient Tree Boosting (GTB) algorithm. Our study highlights that the topological features of the heterogeneous network are crucial for predicting protein-lncRNA interactions. The cross-validation experiments on the benchmark dataset show that PLIPCOM method substantially outperformed previous state-of-the-art approaches in predicting protein-lncRNA interactions. We also prove the robustness of the proposed method on three unbalanced data sets. Moreover, our case studies demonstrate that our method is effective and reliable in predicting the interactions between lncRNAs and proteins. AVAILABILITY: The source code and supporting files are publicly available at: http://denglab.org/PLIPCOM/ .

Circ-SATB2 upregulates STIM1 expression and regulates vascular smooth muscle cell proliferation and differentiation through miR-939.

The prevention and treatment of coronary heart disease (CHD) is a difficult problem to be solved. More and more studies have found that circular RNAs (circRNAs) may play important roles in the development of CHD. Here detection of vascular smooth muscle cells (VSMCs) showed that circ-SATB2 and STIM1 were up-regulated in proliferative VSMCs, while miR-939 were down-regulated. Circ-SATB2 and miR-939 did not affect the expression of each other, but circ-SATB2 could promote while miR-939 inhibited the expression of STIM1 (a target gene of miR-939). Circ-SATB2 overexpression could inhibit the expression of SM22-alpha (SM22α, a marker of contractile VSMCs), while the expression of SM22α was promoted by miR-939. STIM1 could promote cell proliferation and migration, and circ-SATB2 had similar effects, but its linear sequence had no such functions. MiR-939 had the opposite effects, could promote cell apoptosis and inhibit cell proliferation and migration, and siRNAs targeting circ-SATB2 had similar effects. When co-transfected with circ-SATB2 over-expression vector and miR-939 mimics or STIM1 siRNAs, the changes of cell proliferation, apoptosis and migration were not significant. Therefore, circ-SATB2 can regulate VSMC phenotypic differentiation, proliferation, apoptosis and migration by promoting the expression of STIM1. This discovery will provide a theoretical reference for exploring the role of circRNA in VSMCs and the pathogenesis of CHD.

Insight into the surfactin production of Bacillus velezensis B006 through metabolomics analysis.

Bacillus velezensis B006 is a biocontrol agent which functions through effective colonization and surfactin production. To reveal the surfactin-producing mechanism, gas chromatography-mass spectrometry based untargeted metabolomics was performed to compare the metabolite profiles of strain B006 grown in industrial media M3 and M4. Based on the statistical and pathway topology analyses, a total of 31 metabolites with a fold change of less than - 1.0 were screened as the significantly altered metabolites, which distributed in 15 metabolic pathways. Fourteen amino acids involving in the metabolisms of alanine/aspartate/glutamate, glycine/serine/threonine, arginine/proline, glutathione/cysteine/methionine and valine/leucine/isoleucine as well as succinic acid in TCA cycle were identified to be the hub metabolites. Aminoacyl-tRNA biosynthesis, glycerolipid metabolism, and pantothenate/CoA biosynthesis also contributed to surfactin production. To the best of our knowledge, this study is the first to investigate the metabolic pathways of B. velezensis on surfactin production, and will benefit the optimization of commercial fermentation for higher surfactin yield.

Nucleation of shear bands in amorphous alloys.

The initiation and propagation of shear bands is an important mode of localized inhomogeneous deformation that occurs in a wide range of materials. In metallic glasses, shear band development is considered to center on a structural heterogeneity, a shear transformation zone that evolves into a rapidly propagating shear band under a shear stress above a threshold. Deformation by shear bands is a nucleation-controlled process, but the initiation process is unclear. Here we use nanoindentation to probe shear band nucleation during loading by measuring the first pop-in event in the load-depth curve which is demonstrated to be associated with shear band formation. We analyze a large number of independent measurements on four different bulk metallic glasses (BMGs) alloys and reveal the operation of a bimodal distribution of the first pop-in loads that are associated with different shear band nucleation sites that operate at different stress levels below the glass transition temperature, Tg. The nucleation kinetics, the nucleation barriers, and the density for each site type have been determined. The discovery of multiple shear band nucleation sites challenges the current view of nucleation at a single type of site and offers opportunities for controlling the ductility of BMG alloys.

Expression of vitamin D receptor as a potential prognostic factor and therapeutic target in pancreatic cancer.

AIMS: Vitamin D insufficiency and deficiency are common among patients with pancreatic carcinoma, but epidemiological studies have shown inconsistent results for vitamin D intake/circulation level and pancreatic cancer risk. The study aims were to investigate the effects of vitamin D on patient survival, and the proliferation or survival of pancreatic cancer cell lines. METHODS AND RESULTS: The present study examined the local expression of vitamin D receptor (VDR) in pancreatic normal and tumour tissues from a cohort of 61 patients, and analysed the potential correlation between VDR and pathological characteristics, including disease prognosis. Among 61 pairs of normal and tumour specimens, VDR was detected in all normal tissues, and was abundantly expressed in 62.5% (15/24) of tumour tissues with high differentiation, but had a significantly lower or undetectable expression level in 75.7% (28/37) of tissues with moderate or low differentiation (P = 0.004). Moreover, high VDR expression was detected in 63.6% (14/22) of small tumours (≤25 mm) and in only 25.6% (10/39) of large tumours (>25 mm) (P = 0.06). Kaplan-Meier analysis showed that a low level of VDR expression in tumour tissues was associated with a poor prognosis (P = 0.037). CONCLUSIONS: VDR expression could be a potential prognostic factor for patients with pancreatic adenocarcinoma, and its effects should be examined in a prospective study. Vitamin D analogues may provide a therapeutic choice for patients with high VDR expression in tumours but a low vitamin D level in the circulation.

Possible existence of two amorphous phases of D-mannitol related by a first-order transition.

We report that the common polyalcohol D-mannitol may have two amorphous phases related by a first-order transition. Slightly above its glass transition temperature Tg (284 K), the supercooled liquid (SCL) of D-mannitol transforms to a low-energy, apparently amorphous phase with stronger hydrogen bonds. The enthalpy of this so-called Phase X is approximately halfway between those of the known amorphous and crystalline phases, a position low for glass aging and high for crystal polymorphs. Similar to the SCL, Phase X is transparent with broad X-ray diffraction and Raman scattering; upon temperature cycling, it exhibits a glass-transition-like change of heat capacity. On fast heating, Phase X transforms back to the SCL near Tg + 50 K, enabling a determination of their equilibrium temperature. The presence of D-sorbitol as a plasticizer enables observation of a first-order transition from the SCL to Phase X entirely in the liquid state (liquid-liquid transition). The transition from D-mannitol's SCL to Phase X has intriguing similarities with the formation of the glacial phase of triphenyl phosphite (TPP) and the conversion from high-density to low-density amorphous ice, both studied intensely in the context of polyamorphism. All three processes occur near Tg with substantial enthalpy decrease toward the crystalline phases; the processes in water and D-mannitol both strengthen the hydrogen bonds. In contrast to TPP, D-mannitol's Phase X forms more rapidly and can transform back to the SCL. These features make D-mannitol a valuable new model for understanding polyamorphism.

Multi-objective optimization using improved NSGA-II for integrated process planning and scheduling problems in a machining job shop for large-size valve.

This paper studied an integrated process planning and scheduling problem from a machining workshop for large-size valves in a valve manufacturing plant. Large-size valves usually contain several key parts and are generally produced in small-series production. Almost all the parts need to be manufactured in the same workshop at the same time in the plant. Facilities have to handle various items in one order, including different models, sizes, and types. It is a classical NP-hard problem on a large scale. An improved NSGA-II algorithm is suggested to obtain satisfactory solutions for makespan and manufacturing costs, which involve large optimization parameters and interactions. A two-section encoding method and an inserting greedy decoding method are chosen to enable the algorithm. The dynamic population update strategy based on dynamic population update and the adaptive mutation technique depending on the population entropy changing rate are selected for enhancing both the solution quality and population diversity. The methodology was successfully implemented in a real-life case at a major valve machining workshop operated by Yuanda Valve Company in China. By taking into account realistic factors and restrictions that have been identified from a real-world manufacturing setting, this technique aids in bridging the knowledge gap between present IPPS research and practical valve production implementations.

Enhancing the Consistency and Performance of Graphene-Based Devices via Al Intermediate-Layer-Assisted Transfer and Patterning.

Graphene has garnered widespread attention, and its use is being explored for various electronic devices due to its exceptional material properties. However, the use of polymers (PMMA, photoresists, etc.) during graphene transfer and patterning processes inevitably leaves residues on graphene surface, which can decrease the performance and yield of graphene-based devices. This paper proposes a new transfer and patterning process that utilizes an Al intermediate layer to separate graphene from polymers. Through DFT calculations, the binding energy of graphene-Al was found to be only -0.48 eV, much lower than that of PMMA and photoresist with graphene, making it easier to remove Al from graphene. Subsequently, this was confirmed through XPS analysis. A morphological characterization demonstrated that the graphene patterns prepared using the Al intermediate layer process exhibited higher surface quality, with significantly reduced roughness. It is noteworthy that the devices obtained with the proposed method exhibited a notable enhancement in both consistency and sensitivity during electrical testing (increase of 67.14% in temperature sensitivity). The low-cost and pollution-free graphene-processing method proposed in this study will facilitate the further commercialization of graphene-based devices.

Designing Advanced Amorphous/Nanocrystalline Alloys by Controlling the Energy State.

Amorphous alloys, also known as metallic glasses, exhibit many advanced mechanical, physical, and chemical properties. Owing to the nonequilibrium nature, their energy states can vary over a wide range. However, the energy relaxation kinetics are very complex and composed of various types that are coupled with each other. This makes it challenging to control the energy state precisely and to study the energy-properties relationship. This brief review introduces the recent progresses on studying the enthalpy relaxation kinetics during isothermal annealing, for example, the observation of two-step relaxation phenomenon, the detection of relaxation unit (relaxun), the key role of large activation entropy in triggering memory effect, the influence of glass energy state on nanocrystallization. Based on the above knowledge, a new strategy is proposed to design a series of amorphous alloys and their composites consisting of nanocrystals and glass matrix with superior functional properties by precisely controlling the nonequilibrium energy states. As the typical examples, Fe-based amorphous alloys with both advanced soft magnetism and good plasticity, Gd-based amorphous/nanocrystalline composites with large magnetocaloric effect, and Fe-based amorphous alloys with high catalytic performance are specifically described.

Performance and microbial mechanism in sulfide-driven autotrophic denitrification by different inoculation sources in face of various sulfide and sulfate stress.

To develop a reliable sulfide (S2-) autotrophic denitrification (SAD) process under S2- and SO42- salinity stresses, the biofilm performance and microbial mechanisms were comparatively studied using different inocula of activated sludge (AS) and intertidal sediment (IS). Biofilm IS enriched more denitrification genes (0.34 %) and S2- oxidation genes (0.29 %) than those with AS. Higher denitrification performance was obtained under S2- (100 mg/L) and SO42- (5-15 g/L Na2SO4) stresses, but no significantly differences were observed under levels of 0-200 mg/L S2- and 30 g/L Na2SO4. Notably, biofilm samples in SAD systems with IS still had more S2- oxidation genes at high S2- levels of 100-200 mg/L and Na2SO4 level of 30 g/L. The key functional genus Thiobacillus accumulated well at 30 g/L Na2SO4, but was strongly inhibited at 200 mg/L S2-. The findings were advantage to SAD application under sulfide and salinity stresses.

[Orthopaedic robot assisted femoral neck dynamic cross fixation system for the treatment of femoral neck fractures].

OBJECTIVE: To explore and compare the clinical efficacy of orthopedic robot assisted femoral neck system （FNS） and traditional manual FNS in the treatment of femoral neck fractures in middle-aged and young people. METHODS: The clinical data of 62 consecutive patients with femoral neck fracture and age less than 65 years old admitted to the Intelligent Orthopaedic Department of Beijing Jishuitan Hospital from June 2021 to June 2022 were retrospectively analyzed. According to whether orthopedic robot-assisted surgery the patients were divided into two groups：30 patients aged 34 to 56 years old were treated with orthopedic robot assisted FNS internal fixation after closed or limited open reduction（experimental group）； 32 patients aged 33 to 54 years old underwent FNS internal fixation after closed or limited open reduction（control group）. The age, gender, time from injury to admission, average hospital stay, surgical duration, intraoperative bleeding volume, and intraoperative fluoroscopy frequency of two groups of patients were analyzed and compared. The hip joint function in both groups of patients was evaluated using the Harris hip joint scoring standard at 6 months after surgery. RESULTS: All 62 patients with femoral neck fractures successfully completed the surgery. There was no significant difference（P>0.05） between the experimental group and the control group in terms of baseline data such as age, gender, time from injury to admission, time from admission to surgery and the intraoperative bleeding. The surgical duration of the experimental group was significantly shorter than that of the control group [42.1（28.5, 50.7）min vs. 53.4（36.9, 62.5） min, Z=-2.338, P=0.019]. The intraoperative X-ray fluoroscopy frequency of the experimental group was significantly lower than that of the control group[8.0 （6.0, 11.0） times vs. 15.0（13.0, 17.0） times, Z=-5.960, P<0.001]. In terms of postoperative hip joint function, there was no significant difference in Harris score between the two groups of patients at 6-month follow-up（P>0.05）. CONCLUSION: Compared with manual operation of FNS, orthopedic robot assisted FNS in the treatment of femoral neck fractures can help shorten surgical time, reduce intraoperative fluoroscopy frequency, and have similar therapeutic effects on long-term hip joint function recovery.