Spectral origami: an angle-variable, wavelength-selective concept with a highly efficient filter-based sensing.

This study demonstrates the concept of an angle-variable compact spectral module. As a key feature, the filter-based module enables highly efficient wavelength-selective light detection by applying the reflective beam path according to the origami example. It was accomplished through inclined mirrors, which allow for different incident angles on the wavelength separating interference filters used in a robust assembly with no moving parts. To experimentally verify the concept, a wavelength range between 550 and 700 nm was detected by 11 spectral channels. These initial results showed the potential to develop easily scalable and application-tailored sensors, which can overcome conventional filter-based sensor approaches that use upright or fixed-angle illumination.

Catadioptric sensor concept with interlaced beam paths for imaging and pinpoint spectroscopy.

This paper presents the concept, optical design, and implementation of a catadioptric sensor for simultaneous imaging of a scene and pinpoint spectroscopy of a selected position, with object distances ranging from tens of centimeters to infinity and from narrow to wide adjustable viewing angles. The use of reflective imaging elements allows the implementation of folded and interlaced beam paths for spectroscopy and image acquisition, which enables a compact setup with a footprint of approximately 90m m×80m m. Although the wavelength range addressed extends far beyond the visible spectrum and reaches into the near infrared (∼400n m to 1000 nm), only three spherical surfaces are needed to project the intermediate image onto the image detector. The anamorphic imaging introduced by the folded beam path with different magnification factors in the horizontal and vertical directions as well as distortion can be compensated by software-based image processing. The area of the scene to be spectrally analyzed is imaged onto the input of an integrated miniature spectrometer. The imaging properties and spectroscopic characteristics are demonstrated in scenarios close to potential applications such as product sorting and fruit quality control.

Compact double-pass Echelle spectrometer employing a crossed diffraction grating.

This contribution presents the design and implementation of a compact and robust Echelle-inspired cross-grating spectrometer which is arranged as a double pass setup. This allows use of the employed refractive elements for collimation of the incoming light and, after diffraction at the reflective crossed diffraction grating, for imaging the diffracted light onto the detector. The crossed diffraction grating combines the two dispersive functionalities of a classical Echelle spectrometer in a single element and is therefore formed by a superposition of two blazed linear gratings which are oriented perpendicularly. The refractive elements and the plane grating are arranged in a rigid objective group which is beneficial in terms of stability and robustness. The experimental tests prove that the designed resolving power of more than 300 is achieved for the addressed spectrum ranging from 400 nm to 1100 nm by using an entrance pinhole diameter of 105 µm. The utilization of a single mode fiber increases the resolving power to more than 1000, but leads to longer acquisition times.

Folded beam path architecture for highly efficient filter-based spectral sensors.

This paper demonstrates a method to significantly enhance the detection efficiency of filter-based spectral sensors without the use of additional dichroic optics for spectral preselection. The fundamental principle is that light reflected from one interference filter or filter segment can be used consecutively, reducing the overall system losses. The proof-of-concept is presented using two compact optical modules. The first module uses 10 individual filters between 520 and 800 nm, and the second is capable of continuous spectrum acquisition between 450 and 825 nm using a linear variable filter (LVF) as a key element. An efficiency increase factor of up to approximately 100 compared to a common system, where the entire LVF is directly illuminated, was demonstrated.

Variable ring-shaped lithography for the fabrication of meso- and microscale binary optical elements.

This paper presents concept, optical design, and the implementation of a novel, to the best of our knowledge, lithographic exposure tool for the fabrication of rotationally symmetric meso- and microscale optical structures using a variable ring-shaped light distribution. Compared to the conventional lithographic technique of direct writing in Cartesian coordinates, which is intrinsically suboptimal for the fabrication of rotationally symmetric optical structures, this approach allows for fast exposure and avoids disturbing stitching effects. The diameter of the exposure ring varies between 1.6 and 6.5 mm, and the ring width measures ∼75µm full width at half-maximum for all diameters. The basic capabilities of the exposure tool are demonstrated by the fabrication of exemplary meso- and microscale structures such as diffractive axicon elements, phase rings, Fresnel zone plates and zone plate arrays.

Black and white fused silica: modified sol-gel process combined with moth-eye structuring for highly absorbing and diffuse reflecting SiO2 glass.

Diffuse reflecting (white) and highly absorbing (black) fused silica based materials are presented, which combine volume modified substrates and surfaces equipped with anti-reflective moth-eye-structures. For diffuse reflection, micrometer sized cavities are created in bulk fused silica during a sol-gel process. In contrast, carbon black particles are added to get the highly absorbing material. The moth-eye-structures are prepared by block copolymer micelle nanolithography (BCML), followed by a reactive-ion-etching (RIE) step. The moth-eye-structures drastically reduce the specular reflectance on both diffuse reflecting and highly absorbing samples across a wide spectral range from 250 nm to 2500 nm and for varying incidence angles. The adjustment of the height of the moth-eye-structures allows us to select the spectral position of the specular reflectance minimum, which measures less than 0.1%. Diffuse Lambertian-like scattering and absorbance appear nearly uniform across the selected spectral range, showing a slight decrease with increasing wavelength.

Structured metal double-blazed dispersion grating for broadband spectral efficiency achromatization.

The majority of spectrometers use reflective dispersion gratings with a metal-coated blazed grating profile for spectral decomposition. They achieve high diffraction efficiency at the design wavelength, which decays considerably in the adjacent longer and shorter wavelength ranges. We introduce a structured metal double-blazed grating with a high diffraction efficiency for a broadband spectral range, consisting of a sawtooth-like structured metal surface filled with a first dielectric transparent material. The planarized upper surface is covered with a second blazed profile of a different transparent material. We present a systematical theoretical analysis of the diffraction efficiency in reflection geometry, based on a scalar approach involving fundamental dispersion parameters such as Abbe numbers and relative partial dispersions of the materials. We find material combinations reducing the profile heights down to 1-2 µm.

Realization of a compact cross-grating spectrometer and validating experimental tests.

Echelle inspired cross-grating spectrometers offer the potential to bridge the gap between classical high-end echelle spectrometers and curved-grating single-element instruments. In particular, the cross-grating approach offers the possibility to simultaneously achieve a high spectral resolution and a wide accessible spectral range in compact dimensions and without moving parts. We report on the complete realization and implementation details of an all-reflective cross-grating spectrometer based on a modified Czerny-Turner configuration including a folded beam path and a toric-convex mirror for aberration compensation. The applicability of the cross-grating spectrometer is demonstrated by test measurements including the recording of the spectra of different plant leaves. For the cross-grating spectrometer, with an accessible wavelength range between 330 and 1100 nm, a spectral resolution of 0.6 nm at 589 nm was achieved.

Toward Mass Video Data Analysis: Interactive and Immersive 4D Scene Reconstruction.

The technical progress in the last decades makes photo and video recording devices omnipresent. This change has a significant impact, among others, on police work. It is no longer unusual that a myriad of digital data accumulates after a criminal act, which must be reviewed by criminal investigators to collect evidence or solve the crime. This paper presents the VICTORIA Interactive 4D Scene Reconstruction and Analysis Framework ("ISRA-4D" 1.0), an approach for the visual consolidation of heterogeneous video and image data in a 3D reconstruction of the corresponding environment. First, by reconstructing the environment in which the materials were created, a shared spatial context of all available materials is established. Second, all footage is spatially and temporally registered within this 3D reconstruction. Third, a visualization of the hereby created 4D reconstruction (3D scene + time) is provided, which can be analyzed interactively. Additional information on video and image content is also extracted and displayed and can be analyzed with supporting visualizations. The presented approach facilitates the process of filtering, annotating, analyzing, and getting an overview of large amounts of multimedia material. The framework is evaluated using four case studies which demonstrate its broad applicability. Furthermore, the framework allows the user to immerse themselves in the analysis by entering the scenario in virtual reality. This feature is qualitatively evaluated by means of interviews of criminal investigators and outlines potential benefits such as improved spatial understanding and the initiation of new fields of application.

Combined 'moth-eye' structured and graded index-layer anti-reflecting coating for high index glasses.

We present a hybrid antireflective coating (ARC) providing a complete continuous graded refractive index (GRIN) transition from a high-index substrate down to ambient air. The ARC comprises a first GRIN layer of dense silicon-oxy-nitride with a varying, height adjusted material composition. Secondly, a layer of quasi-periodic nanopillars imitating AR-"moth-eye structure" is added to the dense GRIN layer. Demonstrated on a high index glass with a refractive index of ne=1.73 the hybrid GRIN-ARC is applicable to a broad material selection and allows to eliminate any step-like transition up to a refractive index of the substrate of ∼2.0. The ARC offers antireflective properties for large incidence angles and over an extremely broad spectrum ranging from 400 nm up to 2.5 µm. Compared to the sole substrate, the hybrid GRIN-ARC results in an increase of transmittance of more than 10% in the maximum, and more than 6% in the peripheral regions of the spectrum.

Concept and optical design of a compact cross-grating spectrometer.

The concept of a new compact echelle-inspired cross-grating spectrometer is introduced, and a specific optical design is presented. The new concept aims to achieve simultaneously a high spectral resolution, a wide accessible spectral range, and compact dimensions. The essential system novelty concerns the combination of different aspects: the implementation of a crossed grating comprising both the main dispersion and order separation, a folded reflective beam path, which enables a reduction of the system volume, and the introduction of a form-adjustable mirror for aberration compensation. The exemplary optical design offers a spectral bandwidth ranging from 330-1100 nm with spectral resolution better than 1.4 nm in the fourth and 0.4 nm in the 11th order. The optical setup covers a volume of 110 mm×110 mm×30 mm.

Compact echelle spectrometer employing a cross-grating.

The concept and the implementation of a compact and simplified echelle spectrometer are presented, and the working principle is demonstrated by first experimental measurements. The crucial element of the setup is a cross-grating, combining an echelle grating utilizing several higher diffraction orders (5th up to 11th) and a superposed perpendicular-oriented cross-dispersing grating. Two alternative manufacturing approaches for the cross-grating are presented and discussed. The first approach combines Talbot lithography for the deep echelle grating and interference lithography for the cross-dispersing structure. As a second approach, direct laser-beam writing was applied. The compact echelle spectrometer covers a spectral range from 380 to 700 nm and offers a spectral resolution of ∼2 nm.

Variable diameter CO2 laser ring-cutting system adapted to a zoom microscope for applications on polymer tapes.

This paper presents the conception and implementation of a variable diameter ring-cutting system for a CO2 laser with a working wavelength of 10.6 µm. The laser-cutting system is adapted to an observation zoom microscope for combined use and is applicable for the extraction of small circular areas from polymer films, such as forensic adhesive tapes in a single shot. As an important characteristic for our application, the variable diameter ring-cutting system provides telecentricity in the target area. Ring diameters are continuously tunable between 500 µm and 2 mm. A minimum width of less than 20 µm was found for the ring profile edge. The basic characteristics of the system, including telecentricity, were experimentally evaluated and demonstrated by cutting experiments on different polymer tapes and further exemplary samples.

An Analysis of the Interplay and Mutual Benefits of Grounded Theory and Visualization.

Grounded theory (GT) is a research methodology that entails a systematic workflow for theory generation grounded on emergent data. In this paper, we juxtapose GT workflows with typical workflows in visualization and visual analytics (VIS), unveiling the characteristics shared by these workflows. We explore the research landscape of VIS to study where GT is applied to generate VIS theories, explicitly as well as implicitly. We discuss "why" GT can potentially play a significant role in VIS. We outline a "how" methodology for conducting GT research in VIS, which addresses the need for theoretical advancement in VIS while benefiting from other methods and techniques in VIS. We illustrate this "how" methodology with a use case of adopting GT approaches in studying visualization guidelines.

Genetic identity and biological phenotype of a transmitted/founder virus representative of nonpathogenic simian immunodeficiency virus infection in African green monkeys.

Understanding the lack of disease progression in nonpathogenic simian immunodeficiency virus (SIV) infections is essential for deciphering the immunopathogenesis of human AIDS. Yet, in vivo studies have been hampered by a paucity of infectious molecular clones (IMCs) of SIV suitable to dissect the viral and host factors responsible for the nonpathogenic phenotype. Here, we describe the identification, cloning, and biological analysis of the first transmitted/founder (T/F) virus representing a nonpathogenic SIV infection. Blood was collected at peak viremia from an acutely infected sabaeus monkey (Chlorocebus sabaeus) inoculated intravenously with an African green monkey SIV (SIVagm) strain (Sab92018) that had never been propagated in vitro. To generate IMCs, we first used conventional (bulk) PCR to amplify full-length viral genomes from peripheral blood mononuclear cell (PBMC) DNA. Although this yielded two intact SIVagmSab genomes, biological characterization revealed that both were replication defective. We then performed single-genome amplification (SGA) to generate partially overlapping 5' (n = 10) and 3' (n = 13) half genomes from plasma viral RNA. Analysis of these amplicons revealed clusters of nearly identical viral sequences representing the progeny of T/F viruses. Synthesis of the consensus sequence of one of these generated an IMC (Sab92018ivTF) that produced infectious CCR5-tropic virions and replicated to high titers in Molt-4 clone 8 cells and African green monkey PBMCs. Sab92018ivTF also initiated productive infection in sabaeus monkeys and faithfully recapitulated the replication kinetics and nonpathogenic phenotype of the parental Sab92018 strain. These results thus extend the T/F virus concept to nonpathogenic SIV infections and provide an important new tool to define viral determinants of disease nonprogression.

The Value of Immersive Visualization.

In recent years, research on immersive environments has experienced a new wave of interest, and immersive analytics has been established as a new research field. Every year, a vast amount of different techniques, applications, and user studies are published that focus on employing immersive environments for visualizing and analyzing data. Nevertheless, immersive analytics is still a relatively unexplored field that needs more basic research in many aspects and is still viewed with skepticism. Rightly so, because in our opinion, many researchers do not fully exploit the possibilities offered by immersive environments and, on the contrary, sometimes even overestimate the power of immersive visualizations. Although a growing body of papers has demonstrated individual advantages of immersive analytics for specific tasks and problems, the general benefit of using immersive environments for effective analytic tasks remains controversial. In this article, we reflect on when and how immersion may be appropriate for the analysis and present four guiding scenarios. We report on our experiences, discuss the landscape of assessment strategies, and point out the directions where we believe immersive visualizations have the greatest potential.

Origin and biology of simian immunodeficiency virus in wild-living western gorillas.

Western lowland gorillas (Gorilla gorilla gorilla) are infected with a simian immunodeficiency virus (SIVgor) that is closely related to chimpanzee and human immunodeficiency viruses (SIVcpz and HIV-1, respectively) in west central Africa. Although existing data suggest a chimpanzee origin for SIVgor, a paucity of available sequences has precluded definitive conclusions. Here, we report the molecular characterization of one partial (BQ664) and three full-length (CP684, CP2135, and CP2139) SIVgor genomes amplified from fecal RNAs of wild-living gorillas at two field sites in Cameroon. Phylogenetic analyses showed that all SIVgor strains clustered together, forming a monophyletic lineage throughout their genomes. Interestingly, the closest relatives of SIVgor were not SIVcpzPtt strains from west central African chimpanzees (Pan troglodytes troglodytes) but human viruses belonging to HIV-1 group O. In trees derived from most genomic regions, SIVgor and HIV-1 group O formed a sister clade to the SIVcpzPtt lineage. However, in a tree derived from 5' pol sequences ( approximately 900 bp), SIVgor and HIV-1 group O fell within the SIVcpzPtt radiation. The latter was due to two SIVcpzPtt strains that contained mosaic pol sequences, pointing to the existence of a divergent SIVcpzPtt lineage that gave rise to SIVgor and HIV-1 group O. Gorillas appear to have acquired this lineage at least 100 to 200 years ago. To examine the biological properties of SIVgor, we synthesized a full-length provirus from fecal consensus sequences. Transfection of the resulting clone (CP2139.287) into 293T cells yielded infectious virus that replicated efficiently in both human and chimpanzee CD4(+) T cells and used CCR5 as the coreceptor for viral entry. Together, these results provide strong evidence that P. t. troglodytes apes were the source of SIVgor. These same apes may also have spawned the group O epidemic; however, the possibility that gorillas served as an intermediary host cannot be excluded.

Virtual Reality Potentiates Emotion and Task Effects of Alpha/Beta Brain Oscillations.

The progress of technology has increased research on neuropsychological emotion and attention with virtual reality (VR). However, direct comparisons between conventional two-dimensional (2D) and VR stimulations are lacking. Thus, the present study compared electroencephalography (EEG) correlates of explicit task and implicit emotional attention between 2D and VR stimulation. Participants (n = 16) viewed angry and neutral faces with equal size and distance in both 2D and VR, while they were asked to count one of the two facial expressions. For the main effects of emotion (angry vs. neutral) and task (target vs. nontarget), established event related potentials (ERP), namely the late positive potential (LPP) and the target P300, were replicated. VR stimulation compared to 2D led to overall bigger ERPs but did not interact with emotion or task effects. In the frequency domain, alpha/beta-activity was larger in VR compared to 2D stimulation already in the baseline period. Of note, while alpha/beta event related desynchronization (ERD) for emotion and task conditions were seen in both VR and 2D stimulation, these effects were significantly stronger in VR than in 2D. These results suggest that enhanced immersion with the stimulus materials enabled by VR technology can potentiate induced brain oscillation effects to implicit emotion and explicit task effects.

MiR-130a in the adipogenesis of human SGBS preadipocytes and its susceptibility to androgen regulation.

Objectives: Adipogenesis is the differentiation process generating mature adipocytes from undifferentiated mesenchymal stem cells. The differentiation can be inhibited by androgens, although knowledge about intracellular effectors of this inhibition is scarce. Recently, androgen-regulated microRNAs were detected as interesting candidates in this context. In this study, we analyse the role of miR-130a and miR-301 in the adipogenesis of human SGBS preadipocytes and whether they are prone to androgen regulation. Materials and Methods: microRNA expression during adipogenic differentiation with or without androgen stimulation was measured by qPCR. Putative target genes of miR-130a and miR-301 were identified by target database search and validated in luciferase reporter assays. Results: miR-130a and miR-301 are both significantly downregulated on day 3 and day 5 of adipogenic differentiation in comparison to day 0. Under androgen stimulation, a significant upregulation of miR-130a was detected after 7 days of adipogenesis lasting to day 14, while miR-301 did not change significantly until day 14. Luciferase reporter assays revealed the androgen receptor (AR), adiponectin (ADIPOQ) and tumour necrosis factor alpha (TNFα) as miR-130a target genes. Conclusions: miR-130a is an androgen-regulated microRNA that is downregulated during the early phase of adipogenesis and exerts its functions by regulating AR and ADIPOQ translation. These data may help to identify new signalling pathways associated with the androgen-mediated inhibition of adipogenesis.

VIS4ML: An Ontology for Visual Analytics Assisted Machine Learning.

While many VA workflows make use of machine-learned models to support analytical tasks, VA workflows have become increasingly important in understanding and improving Machine Learning (ML) processes. In this paper, we propose an ontology (VIS4ML) for a subarea of VA, namely "VA-assisted ML". The purpose of VIS4ML is to describe and understand existing VA workflows used in ML as well as to detect gaps in ML processes and the potential of introducing advanced VA techniques to such processes. Ontologies have been widely used to map out the scope of a topic in biology, medicine, and many other disciplines. We adopt the scholarly methodologies for constructing VIS4ML, including the specification, conceptualization, formalization, implementation, and validation of ontologies. In particular, we reinterpret the traditional VA pipeline to encompass model-development workflows. We introduce necessary definitions, rules, syntaxes, and visual notations for formulating VIS4ML and make use of semantic web technologies for implementing it in the Web Ontology Language (OWL). VIS4ML captures the high-level knowledge about previous workflows where VA is used to assist in ML. It is consistent with the established VA concepts and will continue to evolve along with the future developments in VA and ML. While this ontology is an effort for building the theoretical foundation of VA, it can be used by practitioners in real-world applications to optimize model-development workflows by systematically examining the potential benefits that can be brought about by either machine or human capabilities. Meanwhile, VIS4ML is intended to be extensible and will continue to be updated to reflect future advancements in using VA for building high-quality data-analytical models or for building such models rapidly.