Miracle-dz/UniFAR-FTUs huggingface dataset:
Image-based acquisition and modeling of polarimetric reflectance

Realistic modeling of the bidirectional reflectance distribution function (BRDF) of scene objects is a vital prerequisite for any type of physically based rendering. In the last decades, the availability of databases containing real-world material measurements has fueled considerable innovation in the development of such models. However, previous work in this area was mainly focused on increasing the visual realism of images, and hence ignored the effect of scattering on the polarization state of light, which is normally imperceptible to the human eye. Existing databases thus only capture scattered flux, or polarimetric BRDF datasets are too directionally sparse (e.g., in-plane) to be usable for simulation. While subtle to human observers, polarization is easily perceived by any optical sensor (e.g., using polarizing filters), providing a wealth of additional information about shape and material properties of the object under observation. Given the increasing application of rendering in the solution of inverse problems via analysis-by-synthesis and differentiation, the ability to realistically model polarized radiative transport is thus highly desirable. Polarization depends on the wavelength of the spectrum, and thus we provide the first polarimetric BRDF (pBRDF) dataset that captures the polarimetric properties of real-world materials over the full angular domain, and at multiple wavelengths. Acquisition of such reflectance data is challenging due to the extremely large space of angular, spectral, and polarimetric configurations that must be observed, and we propose a scheme combining image-based acquisition with spectroscopic ellipsometry to perform measurements in a realistic amount of time. This process yields raw Mueller matrices, which we subsequently transform into Rusinkiewicz-parameterized pBRDFs that can be used for rendering. Our dataset provides 25 isotropic pBRDFs spanning a wide range of appearances: diffuse/specular, metallic/dielectric, rough/smooth, and different color albedos, captured in five wavelength ranges covering the visible spectrum. We demonstrate usage of our data-driven pBRDF model in a physically based renderer that accounts for polarized interreflection, and we investigate the relationship of polarization and material appearance, providing insights into the behavior of characteristic real-world pBRDFs.
Quad-mesh based isometric mappings and developable surfaces

We discretize isometric mappings between surfaces as correspondences between checkerboard patterns derived from quad meshes. This method captures the degrees of freedom inherent in smooth isometries and enables a natural definition of discrete developable surfaces. This definition, which is remarkably simple, leads to a class of discrete developables which is much more flexible in applications than previous concepts of discrete developables. In this paper, we employ optimization to efficiently compute isometric mappings, conformal mappings and isometric bending of surfaces. We perform geometric modeling of developables, including cutting, gluing and folding. The discrete mappings presented here have applications in both theory and practice: We propose a theory of curvatures derived from a discrete Gauss map as well as a construction of watertight CAD models consisting of developable spline surfaces.
Continuous multiple importance sampling

Multiple importance sampling (MIS) is a provably good way to combine a finite set of sampling techniques to reduce variance in Monte Carlo integral estimation. However, there exist integration problems for which a continuum of sampling techniques is available. To handle such cases we establish a continuous MIS (CMIS) formulation as a generalization of MIS to uncountably infinite sets of techniques. Our formulation is equipped with a base estimator that is coupled with a provably optimal balance heuristic and a practical stochastic MIS (SMIS) estimator that makes CMIS accessible to a broad range of problems. To illustrate the effectiveness and utility of our framework, we apply it to three different light transport applications, showing improved performance over the prior state-of-the-art techniques.
Multiple-Band Terahertz Metamaterial Absorber Using Multiple Separated Sections of Metallic Rectangular Patch

Multiple-band metamaterial absorbers have been widely reported using the co-planar or layered design methods. However, these obtained absorption devices are of complex structure, large unit size, heavy weight, and time-consuming construction steps. Herein, an alternative design strategy is suggested to realize the multiple-band absorption at terahertz frequency. By introducing air gaps into the rectangular metallic patch, the original rectangular resonator can be divided into multiple sub-structures (or separated sections), and the combined effect of the localized resonance response of these sub-structures (or separated sections) gives rise to the multiple-band absorption. More importantly, the size, position and number of air gaps play the important roles in controlling the resonance performance of the absorption peaks and even in regulating the amount of the absorption peaks. Compared with the existing multiple-band absorption design strategies, the proposed approach does not increase the unit size, nor need to stack multiple layers, which provides important guidance for the design of multiple-band terahertz metamaterial absorbers with simple, compact, and easy to fabricate for full details.
Beyond Reef Restoration: Next-Generation Techniques for Coral Gardening, Landscaping, and Outreach

Anthropogenic disturbances have led to the degradation of coral reef systems globally, calling for proactive and progressive local strategies to manage individual ecosystems. Although restoration strategies such as assisted evolution have recently been proposed to enhance the performance of coral reef populations in response to current and future stressors, scalability of these concepts and implementation in habitat or ecosystem-wide management remains a major limitation for logistical and financial reasons. We propose to implement these restoration efforts into an ecotourism approach that embeds land-based coral gardening efforts as architectural landscape elements to enhance and beautify coastal development sites, providing additional value and rationale for ecotourism stakeholders to invest. Our approach extends and complements existing concepts integrating coral reef restoration in ecotourism projects by creating a participatory platform that can be experienced by the public, while effectively integrating numerous restoration techniques, and providing opportunities for long-term restoration and monitoring studies. In this context, we discuss options for pre-selection of corals and systematic, large-scale monitoring of coral genotype performance targeting higher resilience to future stressors. To reduce operating costs during out-planting, we suggest to create coral seeding hubs, clusters of closely transplanted conspecifics, to quickly and efficiently restore/enhance active reproduction. We discuss our land-based coral gardening approach in the context of positive impacts beyond reef restoration. By restoring and strengthening resilience of local populations, we believe this strategy will contribute to a net positive conservation impact, create a culture on restoration and enhance and secure blue economical investments that rely on healthy marine systems.
Spore dispersal of ectomycorrhizal fungi on a glacier forefront by mammal mycophagy

Fecal pellets of small mammals (chipmunks, marmots and pikas), mountain goats and deer col? lected from the forefront of the rapidly receding Ly- man Glacier in the North Cascade Mountains of Wash? ington contained spores of both hypogeous and epigeous, ectomycorrhizal fungi. The forefront has been colonized by ectomycorrhizal hosts in the Pina- ceae and Salix spp. Animal mycophagy thus provides inoculum for diversifying the populations of mycor? rhizal fungi for early successional plants in the newly developing soils in this climatically stressful habitat.
NAD+ Metabolism as an Emerging Therapeutic Target for Cardiovascular Diseases Associated With Sudden Cardiac Death

In addition to its central role in mediating oxidation reduction in fuel metabolism and bioenergetics, nicotinamide adenine dinucleotide (NAD+) has emerged as a vital co-substrate for a number of proteins involved in diverse cellular processes, including sirtuins, poly(ADP-ribose) polymerases and cyclic ADP-ribose synthetases. The connection with aging and age-associated diseases has led to a new wave of research in the cardiovascular field. Here, we review the basics of NAD+ homeostasis, the molecular physiology and new advances in ischemic-reperfusion injury, heart failure, and arrhythmias, all of which are associated with increased risks for sudden cardiac death. Finally, we summarize the progress of NAD+-boosting therapy in human cardiovascular diseases and the challenges for future studies.
The Challenges in the Development of Diabetes Prevention and Care Models in Low-Income Settings

In low- and middle-income countries (LMICs), the burden of non-communicable diseases such as diabetes is rapidly rising, overpassing the existing burden of communicable diseases. Patients with diabetes living in low-income communities face unique challenges related to lack of awareness, difficulty in accessing health care systems and medications, and consequently failure in achieving optimal diabetes management and preventing complications. Effective diabetes prevention and care models could help reduce the rising burden by standardizing guidelines for prevention and management, improving access to care, engaging community and peers, improving the training of professionals and patients and using the newest technology in the management of the disease. In this article, we review the latest research and evidence on effective models of diabetes prevention and diabetes care delivery in low- income settings. We also provide existing evidence relating to the effectiveness of these models in low-resource contexts, with the aim to highlight characteristics and strengths that make their implementation successful and long-lasting.
Efficient bijective parameterizations

We propose a novel method to efficiently compute bijective parameterizations with low distortion on disk topology meshes. Our method relies on a second-order solver. To design an efficient solver, we develop two key techniques. First, we propose a coarse shell to substantially reduce the number of collision constraints that are used to guarantee overlap-free boundaries. During the optimization process, the shell ensures the Hessian matrix with a fixed nonzero structure and a low density, thereby significantly accelerating the optimization. The second is a triangle inequality-based barrier function that effectively ensures non-intersecting boundaries. Our barrier function is C∞ inside the locally supported region and its convex second-order approximation is able to be analytically obtained. Compared to state-of-the-art methods for optimizing bijective parameterizations, our method exhibits better scalability and is about six times faster. The performance of our bijective parameterization algorithm is comparable to state-of-the-art methods of locally flip-free parameterizations. A large number of experimental results have shown the capability and feasibility of our method.
11 Findings and hurdles on the path leading from formamide to the spontaneous generation of RNA

Our laboratories analyze the synthetic reactions leading from formamide, NH2COH to prebiotically relevant compounds in the presence of catalysts. We have described the formation of all the biological nucleic bases of carboxylic acids of two aminoacids, and of condensing agents in the presence of catalysts of terrestrial origin (Saladino et al., 2012) and of one meteorite. Heat-dependent synthetic reactions from NH2COH lead to the synthesis of acyclonucleosides, not (yet? ) to that of nucleosides [hurdle # 1]. Nucleosides are phosphorylated in the presence of NH2COH and a phosphate source yielding cyclic nucleotides as well. (Costanzo et al., 2007). 3′,5′-cyclic GMP nonenzymatically polymerizes up to at least 25mers, as shown by PAGE, MALDI ToF, 31P-NMR, specific RNAse and inhibitors analyses (Costanzo et al., 2012). The reaction is stimulated by 1,8-diazabicycloundec-7-ene and dimethylformamide. 3′,5′-cUMP does not polymerize spontaneously [hurdle # 2], 3′,5′-cAMP polymerizes very poorly [hurdle # 3]. We will discuss data on the polymerization of 3′,5′-cCMP and on a ribozyme activity exerted by oligomers neosynthesized from cyclic nucleotides. This approach finds its larger perspective in the evolutionary scenario depicted by Trifonov (2009).
Freqüência De Visitas De Abelhas Do Gênero Bombus Em Função Da Disponibilidade De Flores E Energia

Introducao Recursos florais variam espaco-temporalmente em funcao da distribuicao dos individuos, dos padroes fenologicos, da producao de nectar e da deplecao dos recursos por outros visitantes (Real & Rathcke 1988), sendo considerados um dos mais importantes fatores que determinam os padroes de movimento de visitantes florais. A percepcao da variacao de recursos florais pelos visitantes esta relacionada a habilidade desses animais em distinguir diferencas na distribuicao dos recursos, e esta pode ser realizada em escalas distintas devido aos atributos morfofisiologicos e comportamentais das especies animais. Alguns visitantes florais podem ser capazes de reconhecer a variacao na producao de nectar (volume e/ou concentracao de acucares) em flores de um mesmo individuo, ao passo que outros reconhecem a variacao na producao de recursos florais somente entre plantas ou manchas maiores de recurso (Kotliar & Wiens 1990). Abelhas do genero Bombus formam um grupo de importantes polinizadores para muitas especies vegetais e estudos tem mostrado sua habilidade em reconhecer diferencas na densidade de flores e na quantidade de nectar disponivel nas flores (Goulson et al. 1998, Vrieling et al. 1999).
Testing of Polymer Materials: What Methods Should be Used?

Tests, performed over a ten-year period, on 653 polymers intended for use in extracorporeal renal replacement therapy, were evaluated. The test battery used included animal tests, in vitro tests and chemical tests. Some tests were found to have a very low sensitivity. Thus, acute systemic toxicity testing in mice with sodium chloride, ethanol or paraffin oil as extractants was performed on a total of 806 occasions. Only two of these resulted in a “fail” decision. The final outcome of the tests for the majority of materials could be predicted by the results of the UV absorption, chloride, inhibition of cell growth, and tin tests. Of the materials that passed these four tests, less than 2% were not approved on the basis of the whole test battery. The experiments show that only a limited number of tests have to be performed when testing polymers intended for use in extracorporeal renal replacement therapy.
A guinea pig model of human respiratory syncytial virus lung infection

Children who have an episode of acute respiratory syncytial virus (RSV) bronchiolitis are at increased risk for developing asthma, a disorder characterized by reversible airway obstruction, airway hyperresponsiveness and airway inflammation. Because latent or persistent pulmonary viral infections have been implicated in the pathogenesis of the airway inflammation underlying asthma, a guinea pig model of human RSV lung infection was developed to test the hypothesis that RSV persists within the lung following resolution of acute bronchiolitis. One month old, "juvenile" guinea pigs, intranasally inoculated with human RSV, were compared on day 6 post-inoculation to two month old, "adolescent" RSV-inoculated animals and uninfected controls by clinical examination, gross lung examination and lung histopathological examination using a semi-quantitative scoring system for bronchiolar inflammation. The natural history of intrapulmonary RSV was studied in juvenile animals on days 6, 14, 60 and 125 using viral culture to test for replicating virus, transmission electron microscopy (TEM) to test for assembled virus, immunohistochemistry to test for RSV antigens and the reverse transcriptase-polymerase chain reaction (RT-PCR) to test for RSV genomic RNA. The experiments showed that juvenile guinea pigs inoculated with human RSV developed statistically significant bronchiolar inflammation by day 6 that resolved by day 14, similar to human acute bronchiolitis. Intrapulmonary RSV was documented by culture, TEM, immunohistochemistry and RT-PCR during acute infection on day 6; in the longer term studies, replicating RSV was cultured up to 14 days post-inoculation, RSV antigens were identified within alveolar macrophages up to day 60 and RSV genomic RNA was identified on day 125. In conclusion, human RSV produced a self-limited acute bronchiolitis in juvenile guinea pigs, with evidence of subsequent persistent infection of alveolar macrophages. Persistent RSV infection of alveolar macrophages may represent a mechanism by which host pulmonary defense mechanisms are compromised against other, non-specific environmental agents implicated in the pathogenesis of asthma.
Natural Products Impacting DNA Methyltransferases and Histone Deacetylases

Epigenetics refers to heritable changes in gene expression and chromatin structure without change in a DNA sequence. Several epigenetic modifications and respective regulators have been reported. These include DNA methylation, chromatin remodeling, histone post-translational modifications, and non-coding RNAs. Emerging evidence has revealed that epigenetic dysregulations are involved in a wide range of diseases including cancers. Therefore, the reversible nature of epigenetic modifications concerning activation or inhibition of enzymes involved could be promising targets and useful tools for the elucidation of cellular and biological phenomena. In this review, emphasis is laid on natural products that inhibit DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) making them promising candidates for the development of lead structures for anticancer-drugs targeting epigenetic modifications. However, most of the natural products targeting HDAC and/or DNMT lack isoform selectivity, which is important for determining their potential use as therapeutic agents. Nevertheless, the structures presented in this review offer the well-founded basis that screening and chemical modifications of natural products will in future provide not only leads to the identification of more specific inhibitors with fewer side effects, but also important features for the elucidation of HDAC and DNMT function with respect to cancer treatment.
Management of Genetic Diversity in the Era of Genomics

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.
Genome-Wide Transcription Start Site Mapping and Promoter Assignments to a Sigma Factor in the Human Enteropathogen Clostridioides difficile

The emerging human enteropathogen Clostridioides difficile is the main cause of diarrhea associated with antibiotherapy. Regulatory pathways underlying the adaptive responses remain understudied and the global view of C. difficile promoter structure is still missing. In the genome of C. difficile 630, 22 genes encoding sigma factors are present suggesting a complex pattern of transcription in this bacterium. We present here the first transcriptional map of the C. difficile genome resulting from the identification of transcriptional start sites (TSS), promoter motifs and operon structures. By 5′-end RNA-seq approach, we mapped more than 1000 TSS upstream of genes. In addition to these primary TSS, this analysis revealed complex structure of transcriptional units such as alternative and internal promoters, potential RNA processing events and 5′ untranslated regions. By following an in silico iterative strategy that used as an input previously published consensus sequences and transcriptomic analysis, we identified candidate promoters upstream of most of protein-coding and non-coding RNAs genes. This strategy also led to refine consensus sequences of promoters recognized by major sigma factors of C. difficile. Detailed analysis focuses on the transcription in the pathogenicity locus and regulatory genes, as well as regulons of transition phase and sporulation sigma factors as important components of C. difficile regulatory network governing toxin gene expression and spore formation. Among the still uncharacterized regulons of the major sigma factors of C. difficile, we defined the SigL regulon by combining transcriptome and in silico analyses. We showed that the SigL regulon is largely involved in amino-acid degradation, a metabolism crucial for C. difficile gut colonization. Finally, we combined our TSS mapping, in silico identification of promoters and RNA-seq data to improve gene annotation and to suggest operon organization in C. difficile. These data will considerably improve our knowledge of global regulatory circuits controlling gene expression in C. difficile and will serve as a useful rich resource for scientific community both for the detailed analysis of specific genes and systems biology studies.