Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional shape and topology analysis of tissue-cleared tumor samples

Purpose: We developed a semi-automated framework to obtain numerical descriptors of surface morphology and topology from volumetric microscopy of human cleared cancer tissues to enable quantitative studies of 3D tumor microarchitecture. Methods: Individual slices of immunolabeled confocal or light-sheet microscopic images of cleared cancer tissue samples are first segmented using the Chan-Vese morphological snake method. Then, the Marching Cubes algorithm is used to generate 3D models of the tumors. Surface area-volume ratio (SAV) of the 3D models is computed using the discrete divergence theorem. Geometries of model centerlines (obtained as shortest paths of maximal inscribed spheres) are quantified in terms of their curvature, torsion, and bifurcations angles. Topological analysis is performed on 3D point clouds generated by uniformly sampling the 3D models. Vietoris-Rips (VR) simplicial complexes of the point clouds are constructed, and their persistent diagrams are used to compute the lifetime of homological features such as connected components, loops, and voids. The framework is applied to cleared samples of extrahepatic cholangiocarcinoma labeled with CK19. Specifically, we investigate whether the proposed quantitative descriptors of tumor microarchitecture can differentiate cancers showing low-grade (LG) tumor budding (TB) from those presenting high-grade (HG) TB. Results: The proposed framework yielded 3D surface models of the tumors that retained the major morphological features (e.g., glands and protrusions) observable in the microscopic image stacks. Initial evidence from quantitative analysis of the 3D models (3 samples each of HG and LG tumors) indicates quantitative differences in the microarchitecture of HG and LG cancer tissues. The average SAV ratio of HG tumors was 0.153±0.0036 μm-1 compared to 0.235±0.0089 μm-1 for LG samples. Analysis of centerline geometries found less curvature in HG samples compared to LG (average curvature of 15.87±0.122 mm-1 vs. 20.87±0.122 mm-1), less torsion (51.54±1.077 mm-1 vs. 62.73±1.120 mm-1), and narrower bifurcation angles (0.543±0.0303 rads vs. 0.671±0.0281 rads). Persistent homology, via VR filtration, indicated that the connected components (homological dimension H0) have longer lifetime in LG tumors (mean lifetime 0.0349 ±0.00297) than in HG ones (mean lifetime 0.0284 ±0.00307). Conclusion: The proposed quantitative analysis framework yields potential geometrical and topological descriptors for statistical analysis of the rich 3D imaging data made available by the application of tissue clearing to human tumor samples.
A reconfigurable Si3N4 on-chip filter for programmable photonic processor

We propose and demonstrate an ultra-compact photonic integrated filter via dozens of tunable basic units (TBU) which allow one to obtain reconfigurable frequency selectivity from hundreds of MHz to several GHz. The chip has been fabricated in Si3N4 TriPleXTM technology and packaged for electrical programming, optical interfacing and testing in the lab. Each subunit can be independently configured both as an active processing subsystem as well as a pure interconnecting 2x2 device by proper programming of its internal coupling units. As a proof of concept, several signal processing configurations with increasing degrees of complexity are configured including broad and narrowband flat-top filtering, coherent channelization and I-Q mixing prior to an optical detection stage. This is an advanced demonstration of a programmable RF-Photonic processor built from the interconnection of independent processing subunits encompassing functions beyond optical filtering.
Localizing fish in highly turbid underwater images

Fisheries are one of the few disciplines in biology where data collection continues to rely on the removal and destruction of the objects being studied. This practice has come under increasing scrutiny in recent years as research projects have been terminated due to denied permits. In some instances, research budgets have had to absorb the cost of purchasing quota for the fish captured, with difficulty in publishing results due to animal welfare concerns. In this paper, we proposed a non-extractive sampling system to localize fishes from underwater images obtained at aquaculture farms, which suffered from several issues; being, 1) low luminance issues, which could be significantly in detecting fishes, 2) severe water‟s turbidity due to fish mass caged in an area, and 3) protection / enclosure designed for camera to ensure fishes shy away from it. These images acquired in highly turbid waters are difficult to be recovered; due to 1) the fish feeding process (fish feed) which add noises to the already turbid water, and 2) the existing healthy biodiversity at the aquaculture farms. In this work, we investigate the performance of Faster R-CNN to localize fishes in the highly turbid dataset, under different network architectures at the base network. Different base network such as MobileNet, MobileNetV2, DenseNet, and ResNet, are employed. Experimental results show that MobileNetV2, with learning rate 0.01, with 500 iteration and 15 epoch, and with 87.52 % classification accuracy, is the most feasible to be deployed in the resource constrained environment, with about 6.7M parameters requiring 27.2 MB storage. These findings will be useful when the equipment is embedded with the Faster R-CNN when placed underwater for monitoring purposes.
Moving target removal for lidar SLAM

Lidar SLAM is mainly suitable for static scenes without moving targets. The existence of motion in actual scenes will limit the application of the algorithm. If there are moving targets in the lidar field of view, the 3D point cloud map constructed by the lidar SLAM will include a series of fake point cloud from the moving target. This situation leads to insufficient accuracy of the constructed map and affects the applications such as navigation and route planning. In this paper, a moving target removal algorithm is proposed, which realizes the detection and removal of moving targets through multi-frame accumulation, change detection, and point cloud clustering of point clouds. The experiments base d on measured lidar point cloud show that the proposed algorithm can optimize the mapping results of the existing lidar SLAM, remove the continuous trajectory caused by the moving target, and construct a more accurate 3D map.
A contour drawing method for 3D animal models' fur

Drawing contour lines is one of the most important techniques for understanding the characteristics of 3D models in nonphotorealistic rendering. Conventional methods draw continuous contour lines with the same thickness. However, contour lines are depicted by set of short lines just like growing grasses in furred animal illustrations. To depict furred animal 3D models in non-photorealistic rendering, we propose a new method that expresses animals’ fur by drawing a set of short and skew lines crossing along the contours.
Testing the space optical telescope optical system with modified phase retrieval technology

With the continuous development of space optical technology, the aperture of optical system is becoming larger and larger, and the aperture of optical elements is required to be larger. When the traditional optical inspection means are used to detect optical elements such as large aperture optical plane, large aperture convex spherical surface and convex aspheric surface, optical reference mirror or optical auxiliary element with larger aperture than the detection element is usually needed, such as compensator and computer generated hologram (CGH) etc. However, these large-diameter optical reference mirrors and auxiliary components are not only difficult to process, but also have long processing cycle and high production cost. At the same time, some processing errors and assembly errors will be introduced. In order to solve these difficulties, this paper will introduce a modified phase retrieval (PR), which is phase-diversity phase retrieval (PDPR) algorithm can improve the PR accuracy of the unknown image, but also can provide a strong basis for the online testing of the future larger aperture astronomical telescope optical system and solve the difficulties in the detection of optical systems in space optical telescopes. Therefore, this study has important practical significance and application value in the online testing of the space optical telescope optical system.
Finite element simulation of the interaction between pulsed laser and mouse brain

The study of the interaction between laser and mouse brain tissue has important theoretical and practical significance for brain imaging. A two-dimensional simulation model that studies the propagation of light and heat transfer in brain tissue based on finite element has been developed by using the commercial finite element simulation software COMSOL Multiphysics. In this study, the model consists of three parts of 1) a layer of water on the surface of the brain, 2) brain tissue and 3) short pulsed laser source (the wavelength is 840nm). The laser point source is located in the middle of the layer of water above the brain tissue and irradiates the brain tissue. The propagation of light in brain tissue was simulated by solving the diffusion equation. And the temperature changes of gray matter and blood vessels were achieved by solving the biological heat transfer equation. The simulation results show that the light energy in the brain tissue decreases exponentially with the increase of penetration depth. Since the cerebral blood vessels have a stronger absorption on light compared with the surrounding tissues, the remaining light energy of the blood vessel in the cerebral cortex is ~ 74.86 % of the remaining light energy in the surrounding gray matter. In the process of biological heat transfer, due to more light deposition in blood vessels, the temperature of blood vessels is 0.65 K higher than that of gray matter, and the temperature of gray matter hardly changes. This research is helpful to understand the propagation of light in the brain and the interaction between them, and has certain theoretical guiding for the optical imaging of the brain.
An infrared data cycle extraction method based on CEEMDAN

Aiming at the problem of noise and the difficulty of periodic extraction in infrared data acquisition. In this paper, a line method of infrared data period extraction based on CEEMDAN is proposed, which can eliminate the noise and interference of infrared data and accurately extract the period. The method preprocesses the original foreign teacher data by determining the signal mode, so as to improve the quality of infrared data; However, the data cycle was accurately extracted by using the method of correlation split mean cap. Finally, the validity and correctness of the extraction method are verified by simulation experiments.
Optical design of a snapshot hyperspectral imaging spectrometer for facial colour diagnosis in traditional Chinese medicine

Colour diagnosis of traditional Chinese medicine (TCM) is the main content of “looking” inspection in the four-diagnosis methods of "looking, listening, asking and feeling the pulse". The action of light on the face is a very complex process, it is difficult to distinguish reflected light from internally reflected light by human eyes alone. In this paper, we discuss the relationship between TCM facial colour diagnosis and optics, integrate imaging spectroscopy to improve the objectified development of facial colour diagnosis in TCM. A visible band snapshot hyperspectral imaging spectrometer is designed based on a grating dispersion module. This imaging spectrometer is a snapshot system with 34° field of view and a measured spectrum from 400 nm to 680 nm. The spectral resolution reaches 3nm. The total length of the optical system is only 165mm, which can realize the miniaturization of products.
Hydroxyapatite/polyacrylic acid nanocrystals

Hydroxyapatite nanocrystals have been synthesized in the presence of polyacrylic acid in solution. The method leads to apatite crystals with a polyelectrolyte relative content which increases as a function of its concentration in solution and reaches a limit value of about 15% wt. Polyacrylic acid affects the degree of crystallinity, the coherent length of the perfect crystalline domains, as well as the dimensions and the morphology of the crystals. TEM images indicate that on increasing polyelectrolyte content, the dimensions of the crystals are reduced, while their morphology changes from plate-like to acicular, and, at high polyacrylic acid content, the crystals tend to aggregate in clusters. In agreement, the broadening of the X-ray diffraction reflections indicate a reduction of the coherent length along the long dimension (002) and the cross section (310) of the apatite crystals. The reduction is greater along the direction orthogonal to the c-axis, which can be rationalized by a preferential interaction of the carboxylate groups of the polyelectrolyte with the phosphate sites on the crystalline faces parallel to the c-axis.
A theoretical study towards water window attosecond light sources driven by a parametric waveform synthesizer

A source of isolated attosecond pulses with photon energies lying in the water window soft x-ray range is currently under development at Deutsches Elektronen-Synchrotron. Such a source will be driven by the newly developed sub-cycle millijoule-level parametric waveform synthesizer. In this proceeding on theoretical study, in order to optimize the x-ray pulse energy while maintaining good pulse isolation in the soft x-ray range, a multi-objective genetic algorithm is exploited to tailor the laser electric field waveform. The resulting synthesized waveform are then employed in a macroscopic propagation study to predict x-ray pulse characteristics from a real experiment.
Abrupt and gradual change analyses of moving objects in stereoscopic viewing

Human observers are able to allocate visual attention to multiple locations in a dynamic environment simultaneously. However, this ability depends on an individuals’ capacity to monitor the tracked objects' number, size, speed, and distance between objects. Moving objects in the real-world require that we independently allocate attentional resources to them. Recent studies have demonstrated that observers can focus attention on one location and ignore other locations; tracking performance improves when moving objects are rendered on a range of depth planes, and observers cannot track a moving object that abruptly changes depth in a 3D environment. We investigated whether an object’s abrupt or gradual changes improved attentive tracking under stereoscopic viewing in two experiments. These experiments indicated a similar pattern regardless of the depth-changing characteristics of the objects. Results demonstrated that abrupt- or gradual-changes of moving objects under stereoscopic viewing do not increase a tracking task's difficulty.
A Comparative Study on Acid Leaching of Low Grade Manganese Ore Using Some Industrial Wastes as Reductants

Local pyrolusite ore from Om-Bogma, Sinai, has been treated by sulfuric acid leaching process using either sawdust (C6H10O5)n or lactose (C12H22O11) as reducing agent to produce manganese sulfate. The manganese recoveries were 92.5 and 90.5% at sawdust and lactose respectively. Un minerai de pyrolusite local d'Om-Bogma, au Sinai, a ete traite par un procede de lessivage a l'acide sulfurique en utilisant de la sciure de bois (C6H10O5)n ou du lactose (C12H22O11) comme agent de reduction pour produire du sulfate de manganese. Les recuperations de manganese sont de 92,5% et 90,5% pour la sciure de bois et le lactose, respectivement.
The Impact of lncRNAs in Diabetes Mellitus: A Systematic Review and In Silico Analyses

Long non-coding RNAs (lncRNAs) are non-coding transcripts that have emerged as one of the largest and diverse RNA families that regulate gene expression. Accumulating evidence has suggested a number of lncRNAs are involved in diabetes mellitus (DM) pathogenesis. However, results about lncRNA expressions in DM patients are still inconclusive. Thus, we performed a systematic review of the literature on the subject followed by bioinformatics analyses to better understand which lncRNAs are dysregulated in DM and in which pathways they act. Pubmed, Embase, and Gene Expression Omnibus (GEO) repositories were searched to identify studies that investigated lncRNA expression in cases with DM and non-diabetic controls. LncRNAs consistently dysregulated in DM patients were submitted to bioinformatics analysis to retrieve their target genes and identify potentially affected signaling pathways under their regulation. Fifty-three eligible articles were included in this review after the application of the inclusion and exclusion criteria. Six hundred and thirty-eight lncRNAs were differentially expressed between cases and controls in at least one study. Among them, six lncRNAs were consistently dysregulated in patients with DM (Anril, Hotair, Malat1, Miat, Kcnq1ot1, and Meg3) compared to controls. Moreover, these six lncRNAs participate in several metabolism-related pathways, evidencing their importance in DM. This systematic review suggests six lncRNAs are dysregulated in DM, constituting potential biomarkers of this disease.
A Deep-Sea Sponge Loop? Sponges Transfer Dissolved and Particulate Organic Carbon and Nitrogen to Associated Fauna

Cold-water coral reefs and sponge grounds are deep-sea biological hotspots, equivalent to shallow-water tropical coral reefs. In tropical ecosystems, biodiversity and productivity are maintained through efficient recycling pathways, such as the sponge loop. In this pathway, encrusting sponges recycle dissolved organic matter (DOM) into particulate detritus. Subsequently, the sponge-produced detritus serves as a food source for other organisms on the reef. Alternatively, the DOM stored in massive sponges was recently hypothesized to be transferred to higher trophic levels through predation of these sponges, instead of detritus production. However, for deep-sea sponges, the existence of all prerequisite, consecutive steps of the sponge loop have not yet been established. Here, we tested whether cold-water deep-sea sponges, similar to their tropical shallow-water counterparts, take up DOM and transfer assimilated DOM to associated fauna via either detritus production or predation. We traced the fate of 13carbon (C)- and 15nitrogen (N)-enriched DOM and particulate organic matter (POM) in time using a pulse-chase approach. During the 24-h pulse, the uptake of 13C/15N-enriched DOM and POM by two deep-sea sponge species, the massive species Geodia barretti and the encrusting species Hymedesmia sp. , was assessed. During the subsequent 9-day chase in label-free seawater, we investigated the transfer of the consumed food by sponges into brittle stars via two possible scenarios: (1) the production and subsequent consumption of detrital waste or (2) direct feeding on sponge tissue. We found that particulate detritus released by both sponge species contained C from the previously consumed tracer DOM and POM, and, after 9-day exposure to the labeled sponges and detritus, enrichment of 13C and 15N was also detected in the tissue of the brittle stars. These results therefore provide the first evidence of all consecutive steps of a sponge loop pathway via deep-sea sponges. We cannot distinguish at present whether the deep-sea sponge loop is acting through a detrital or predatory pathway, but conclude that both scenarios are feasible. We conclude that sponges could play an important role in the recycling of DOM in the many deep-sea ecosystems where they are abundant, although in situ measurements are needed to confirm this hypothesis.
Yeast Culture Improves Egg Quality and Reproductive Performance of Aged Breeder Layers by Regulating Gut Microbes

This study aimed to investigate the effects of dietary yeast culture (YC) supplementation on egg production, egg quality, reproductive performance, immune functions, antioxidant capacity, and intestinal microbial structure of aged hens. A total of 224 Hy-Line Brown layers (54 weeks old) were randomly assigned to two dietary treatments. The control group was fed a basal diet and the YC group was supplemented with YC at 2.0 g/kg of their diet. Each group had seven replicates with 16 hens each. The study was conducted over a period of 8 weeks. Results indicated that YC addition had no significant effect on laying performance. However, it significantly improved egg quality and hatching rate, enhanced ileum crude fat digestibility, increased the serum parameters of lysozyme (LZM) and total antioxidation capacity (T-AOC) (P < 0.05), and reduced serum aspartate aminotransferase (AST) levels (P < 0.05). Using 16S rRNA analysis, we found that addition of YC significantly altered ileum microbial composition. Linear discriminant analysis of effect size (LEfSe) showed significant enrichment of Bacilli and Lactobacilli in the YC group. PICRUSt analysis of the ileal microbiota found that glutathione metabolism, ubiquinone, and other terpenoid-quinone biosynthesis and lipopolysaccharide biosynthesis protein pathways were highly enriched in the YC group compared with the basal diet group. In summary, the addition of YC can improve egg quality, immune functions, antioxidant capacity, reproduction efficiency, and digestive absorption by increasing the abundance of Lactobacilli and Bacilli. Furthermore, it also improves the biosynthesis of lipopolysaccharide proteins, glutathione metabolism, and the synthesis of ubiquinone and other terpenoid-quinone metabolic pathways.