Miracle-dz/UniFAR-FTUs huggingface dataset:
VASCO: Volume and Surface Co-Decomposition for Hybrid Manufacturing

Additive and subtractive hybrid manufacturing (ASHM) involves the alternating use of additive and subtractive manufacturing techniques, which provides unique advantages for fabricating complex geometries with otherwise inaccessible surfaces. However, a significant challenge lies in ensuring tool accessibility during both fabrication procedures, as the object shape may change dramatically, and different parts of the shape are interdependent. In this study, we propose a computational framework to optimize the planning of additive and subtractive sequences while ensuring tool accessibility. Our goal is to minimize the switching between additive and subtractive processes to achieve efficient fabrication while maintaining product quality. We approach the problem by formulating it as a Volume-And-Surface-CO-decomposition (VASCO) problem. First, we slice volumes into slabs and build a dynamic-directed graph to encode manufacturing constraints, with each node representing a slab and direction reflecting operation order. We introduce a novel geometry property called hybrid-fabricability for a pair of additive and subtractive procedures. Then, we propose a beam-guided top-down block decomposition algorithm to solve the VASCO problem. We apply our solution to a 5-axis hybrid manufacturing platform and evaluate various 3D shapes. Finally, we assess the performance of our approach through both physical and simulated manufacturing evaluations.
DR-Occluder: Generating Occluders Using Differentiable Rendering

The target of the occluder is to use very few faces to maintain similar occlusion properties of the original 3D model. In this paper, we present DR-Occluder, a novel coarse-to-fine framework for occluder generation that leverages differentiable rendering to optimize a triangle set to an occluder. Unlike prior work, which has not utilized differentiable rendering for this task, our approach provides the ability to optimize a 3D shape to defined targets. Given a 3D model as input, our method first projects it to silhouette images, which are then processed by a convolution network to output a group of vertex offsets. These offsets are used to transform a group of distributed triangles into a preliminary occluder, which is further optimized by differentiable rendering. Finally, triangles whose area is smaller than a threshold are removed to obtain the final occluder. Our extensive experiments demonstrate that DR-Occluder significantly outperforms state-of-the-art methods in terms of occlusion quality. Furthermore, we compare the performance of our method with other approaches in a commercial engine, providing compelling evidence of its effectiveness.
Computational Design of Flexible Planar Microstructures

Mechanical metamaterials enable customizing the elastic properties of physical objects by altering their fine-scale structure. A broad gamut of effective material properties can be produced even from a single fabrication material by optimizing the geometry of a periodic microstructure tiling. Past work has extensively studied the capabilities of microstructures in the small-displacement regime, where periodic homogenization of linear elasticity yields computationally efficient optimal design algorithms. However, many applications involve flexible structures undergoing large deformations for which the accuracy of linear elasticity rapidly deteriorates due to geometric nonlinearities. Design of microstructures at finite strains involves a massive increase in computation and is much less explored; no computational tool yet exists to design metamaterials emulating target hyperelastic laws over finite regions of strain space. We make an initial step in this direction, developing algorithms to accelerate homogenization and metamaterial design for nonlinear elasticity and building a complete framework for the optimal design of planar metamaterials. Our nonlinear homogenization method works by efficiently constructing an accurate interpolant of a microstructure's deformation over a finite space of macroscopic strains likely to be endured by the metamaterial. From this interpolant, the homogenized energy density, stress, and tangent elasticity tensor describing the microstructure's effective properties can be inexpensively computed at any strain. Our design tool then fits the effective material properties to a target constitutive law over a region of strain space using a parametric shape optimization approach, producing a directly manufacturable geometry. We systematically test our framework by designing a catalog of materials fitting isotropic Hooke's laws as closely as possible. We demonstrate significantly improved accuracy over traditional linear metamaterial design techniques by fabricating and testing physical prototypes.
Capturing Animation-Ready Isotropic Materials Using Systematic Poking

Capturing material properties of real-world elastic solids is both challenging and highly relevant to many applications in computer graphics, robotics and related fields. We give a non-intrusive, in-situ and inexpensive approach to measure the nonlinear elastic energy density function of man-made materials and biological tissues. We poke the elastic object with 3d-printed rigid cylinders of known radii, and use a precision force meter to record the contact force as a function of the indentation depth, which we measure using a force meter stand, or a novel unconstrained laser setup. We model the 3D elastic solid using the Finite Element Method (FEM), and elastic energy using a compressible Valanis-Landel material that generalizes Neo-Hookean materials by permitting arbitrary tensile behavior under large deformations. We then use optimization to fit the nonlinear isotropic elastic energy so that the FEM contact forces and indentations match their measured real-world counterparts. Because we use carefully designed cubic splines, our materials are accurate in a large range of stretches and robust to inversions, and are therefore "animation-ready" for computer graphics applications. We demonstrate how to exploit radial symmetry to convert the 3D elastostatic contact problem to the mathematically equivalent 2D problem, which vastly accelerates optimization. We also greatly improve the theory and robustness of stretch-based elastic materials, by giving a simple and elegant formula to compute the tangent stiffness matrix, with rigorous proofs and singularity handling. We also contribute the observation that volume compressibility can be estimated by poking with rigid cylinders of different radii, which avoids optical cameras and greatly simplifies experiments. We validate our method by performing full 3D simulations using the optimized materials and confirming that they match real-world forces, indentations and real deformed 3D shapes. We also validate it using a "Shore 00" durometer, a standard device for measuring material hardness.
Assessing Risky Behaviors Based on the Indicator Analysis of Statistics on Accidents at Work

Abstract The aim of the paper was to analyze risky behaviors in the mining industry on the example of the indicator analysis of the statistics on accidents at work. Selected criteria of generic analysis (structure index – causes of accidents) and indicator analysis (intensity index – frequency indicator of accidents) were used in the research. The source of data for the analysis of accident rate were the publications of the Statistics Poland entitled “Accidents at work” in Poland for 2010-2021. The study aimed at human causes, which included the following five groups: lack or improper handling of a material factor by the employee, failure to use protective equipment by the employee, improper willful behavior of the employee, improper mental and physical state of the employee, improper behavior of the employee. For the analysis of risky behaviors, the proposition of the frequency indicator of accidents at work was used in the form of the probability indicator of accidents caused by risky behaviors per 1,000 working people. Based on the indicator analysis of risky behaviors, a comparative analysis of statistics on accidents at work in the period 2010-2021 according to the criterion of human causes was developed for Poland and mining. The research is based on the data of the Statistics Poland (GUS), but can be extended with other data, e.g. industry data according to the State Mining Authority (WUG). The results of the research can be used for a comparative analysis of the statistics on accidents at work in relation to other sectors and sections of economic activity of the NACE (PKD). The publication contains the original results of the indicator analysis of the statistics on accidents at work according to the criterion of human causes in the mining industry, and they can be addressed to persons managing of mining plants and managers of mining supervision authorities.
Testing SIPA1L2 as a modifier of CMT1A using mouse models

Charcot-Marie-Tooth 1A is a demyelinating peripheral neuropathy caused by the duplication of peripheral myelin protein 22 (PMP22), which produces muscle weakness and loss of sensation in the hands and feet. A recent case-only genome wide association study by the Inherited Neuropathy Consortium identified a strong association between variants in signal induced proliferation associated 1 like 2 (SIPA1L2) and strength of foot dorsiflexion. To validate SIPA1L2 as a candidate modifier, and to assess its potential as a therapeutic target, we engineered mice with a deletion in SIPA1L2 and crossed them to the C3-PMP22 mouse model of CMT1A. We performed neuromuscular phenotyping and identified an interaction between Sipa1l2 deletion and muscular endurance decrements assayed by wire-hang duration in C3-PMP22 mice, as well as several interactions in femoral nerve axon morphometrics such as myelin thickness. Gene expression changes suggested an involvement of Sipa1l2 in cholesterol biosynthesis, which was also implicated in C3-PMP22 mice. Though several interactions between Sipa1l2 deletion and CMT1A-associated phenotypes were identified, validating a genetic interaction, the overall effect on neuropathy was small.
MechanoProDB: A Web Based Database for Exploring the Mechanical Properties of Proteins

The mechanical stability of proteins is crucial for biological processes. To understand the mechanical functions of proteins, it is important to know the protein structure and mechanical properties. Protein mechanics is usually investigated through force spectroscopy experiments and simulations that probe the forces required to unfold the protein of interest. While there is a wealth of data in the literature on force spectroscopy experiments and steered molecular dynamics simulations of forced protein unfolding, this information is spread and difficult to access by non-experts. Here we introduce MechanoProDB, a novel web-based database resource for collecting and mining data obtained from experimental and computational works. MechanoProDB provides a curated repository for a wide range of proteins, including muscle proteins, adhesion molecules and membrane proteins. The database incorporates relevant parameters that provide insights into the mechanical stability of proteins and their conformational stability such as the unfolding forces, energy landscape parameters and contour lengths of unfolding steps. Additionally, it provides intuitive annotations of the unfolding pathways of each protein, allowing users to explore the individual steps during mechanical unfolding. The user-friendly interface of MechanoProBD allows researchers to efficiently navigate, search and download data pertaining to specific protein folds or experimental conditions. Users can visualize protein structures using interactive tools integrated within the database, such as Mol*, and plot available data through integrated plotting tools. To ensure data quality and reliability, we have carefully manually verified and curated the data currently available on MechanoProDB. Furthermore, the database also features an interface that enables users to contribute new data and annotations, promoting community-driven comprehensiveness. The freely available MechanoProDB aims to streamline and accelerate research in the field of mechanobiology and biophysics by offering a unique platform for data sharing and analysis. MechanoProDB is freely available at https://mechanoprodb.ibdm. univ-amu.fr.
Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling

The sequence of nucleotides that make up an RNA determines its structure, which determines its function. The RNA hairpin, also known as a stem-loop, is a ubiquitous and fundamental feature of RNA secondary structure. A common method of randomizing an RNA sequence is dinucleotide shuffling with the Altschul-Erickson algorithm, which preserves the dinucleotide content of the sequence. This algorithm generates randomized sequences by sampling Eulerian paths through the de Bruijn graph representation of the original sequence. We identified a subset of RNA hairpins in the bpRNA-1m meta-database that always form hairpins after repeated application of dinucleotide shuffling. We investigated these “unbreakable hairpins” and found several common properties. First, we found that unbreakable hairpins had on average similar folding energies compared to other hairpins of similar lengths, although they frequently contained ultra-stable hairpin loops. We found that they tend to be split by purines and pyrimidines on opposite strands of the stem. Furthermore, we found that this specific sequence feature restricts the number of distinct Eulerian paths through their de Bruijn graph representation, resulting in a small number of distinguishable dinucleotide-shuffled sequences. Beyond this algorithmic means of identification, these distinct sequences may have biological significance because we found that a significant percentage occur in a specific location of 16S ribosomal RNAs. Finally, we present a formula to calculate the number of possible unique dinucleotide shuffled sequences for an input RNA sequence, which has utility for the general application of the Altschul-Erickson algorithm.
The ALS-associated TDP-43M337V mutation dysregulates microglia-derived extracellular microRNAs in a sex-specific manner

Evidence suggests the presence of microglial activation and microRNA (miRNA) dysregulation in amyotrophic lateral sclerosis (ALS), the most common form of adult motor neuron disease. However, few studies have investigated whether the miRNA dysregulation may originate from microglia. Furthermore, TDP-43, involved in miRNA biogenesis, aggregates in tissues of ∼98% of ALS cases. Thus, this study aimed to determine whether expression of the ALS-linked TDP-43M337V mutation in a transgenic mouse model dysregulates microglia-derived miRNAs. RNA sequencing identified several dysregulated miRNAs released by transgenic microglia, and a differential miRNA release by lipopolysaccharide-stimulated microglia, which was more pronounced in cells from female mice. We validated the downregulation of two candidate miRNAs, miR-16-5p and miR-99a-5p by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), and identified their predicted targets, which include primarily genes involved in neuronal development and function. These results suggest that altered TDP-43 function leads to changes in the miRNA population released by microglia in a sex dependent manner, which may in turn influence disease progression in ALS. This has important implications for the role of neuroinflammation in ALS pathology and could provide potential therapeutic targets.
Herbaceous plant community structure in south-east Cameroon : ecological drivers and use by western lowland gorillas

Data from forest herbaceous plants in a site of known species richness in Cameroon were used to test the performance of rarefaction and eight species richness estimators (ACE, ICE, Chao1, Chao2, Jack1, Jack2, Bootstrap and MM). Bias, accuracy, precision and sensitivity to patchiness and sample grain size were the evaluation criteria. An evaluation of the effects of sampling effort and patchiness on diversity estimation is also provided. Stems were identified and counted in linear series of 1-m2 contiguous square plots distributed in six habitat types. Initially, 500 plots were sampled in each habitat type. The sampling process was monitored using rarefaction and a set of richness estimator curves. Curves from the first dataset suggested adequate sampling in riparian forest only. Additional plots ranging from 523 to 2143 were subsequently added in the undersampled habitats until most of the curves stabilized. Jack1 and ICE, the nonparametric richness estimators, performed better, being more accurate and less sensitive to patchiness and sample grain size, and significantly reducing biases that could not be detected by rarefaction and other estimators. This study confirms the usefulness of non-parametric incidence-based estimators, and recommends Jack1 or ICE alongside rarefaction while describing taxon richness and comparing results across areas sampled using similar or different grain sizes. As patchiness varied across habitat types, accurate estimations of diversity did not require the same number of plots. We suggest that communities should first be sampled thoroughly using appropriate taxon sampling curves before explaining differences in diversity.
Germline transformation of the West Nile Virus and avian malaria vector Culex quinquefasciatus Say using the piggyBac transposon system

Culex quinquefasciatus Say is a mosquito which acts as a vector for numerous diseases including West Nile Virus, lymphatic filariasis and avian malaria, over a broad geographical range. As the effectiveness of insecticidal mosquito control methods declines, the need has grown to develop genetic control methods to curb the spread of disease. The piggyBac transposon system - the most widely used genetic transformation tool in insects, including mosquitoes - generates quasi-random insertions of donor DNA into the host genome. However, despite the broad reported species range of piggyBac, previous attempts to use this tool to transform Culex quinquefasciatus mosquitoes have failed. Here we report the first successful transformation of Culex quinquefasciatus with the piggyBac transposon system. Using commercially synthesised piggyBac mRNA as a transposase source, we were able to generate three independent insertions of a ZsGreen fluorescent marker gene, with transformation efficiencies of up to 5%. Through this work, we have expanded the genetic toolkit available for the genetic manipulation of Culex mosquitoes and thus removed a barrier to developing novel genetic control methods in this important disease vector.
Bidirectional Energy Flow in the Photosystem II Supercomplex

The water splitting capability of Photosystem II (PSII) of plants and green algae requires the system to balance efficient light harvesting along with effective photoprotection against excitation in excess of photosynthetic capacity 1,2, particularly under the naturally fluctuating sunlight intensity. The comparatively flat energy landscape of the multi-component structure, inferred from spectra of the individual pigment-protein complexes and the rather narrow and featureless absorption spectrum, is well known 3–7. However, how the combination of the required functions emerge from the interactions among the multiple components of the PSII supercomplex (PSII-SC) cannot be inferred from the individual pigment-protein complexes. In this work, we investigate the energy transfer dynamics of the C2S2-type PSII-SC with a combined spectroscopic and modeling approach. Specifically, two-dimensional electronic-vibrational (2DEV) spectroscopy 8,9 provides enhanced spectral resolution and the ability to map energy evolution in real space, while the quantum dynamical simulation allows complete kinetic modeling of the 210 chromophores. We demonstrate that additional pathways emerge within the supercomplex. In particular, we show that excitation energy can leave the vicinity of the charge separation components, the reaction center (RC), faster than transferring to it. This enables activatable quenching centers in the periphery of the PSII-SC to be effective in removing excessive energy in cases of over-excitation 2. Overall, we provide a quantitative description of how the seemingly contradictory functions of PSII-SC arise from the combination of its individual components. This provides a fundamental understanding that will allow further improvement of artificial solar energy devices and bioengineering processes for increasing crop yield 10.
Risk assessment of cyberattacks in conditions of hybrid war based on analysis of cybersecurity basic capacity in the civil security sector in Ukraine

The article focuses on hybrid threats’ study in the civil security sector in Ukraine. The main emphasis is on evaluative variations in the perception of the capacity or vulnerability of the law enforcement system. The analysis covers the whole range of activities of the Ministry of Internal Affairs of Ukraine, taking into account the activities of National Police, National Guard, State Border Service, State Emergency Service, State Migration Service and service centers. An empirical study of the relationship between cyberattacks and cyber-hygiene in the civil security sector is presented. Unique empirical materials are used - the results of a survey of specialists of the Ministry of Internal Affairs and these CEBs on the identification and assessment of hybrid threats in the civil security sector, as well as quantification of the ability of law enforcement agencies to combat these threats. The basic characteristics of cyber-hygiene are used to estimate the level and impact of internal and external factors of law enforcement. Based on the application of linear regression, the risk assessment of the spread of hybrid cyber threat "use of cyber operations" is assessed, priority risk reduction factors are identified and an appropriate forecast model is built.