CONCEPT PAPER | doi:10.20944/preprints202106.0505.v1
Subject: Physical Sciences, Acoustics Keywords: ATR, THz, synchrotron radiation, diagnostics, polariscopy, four polarisation method
Online: 21 June 2021 (11:28:36 CEST)
Capabilities of the Attenuated Total Reflection (ATR) at THz wavelengths for increased sub-surface depth characterisation of (bio-)materials is presented. The penetration depth of a THz evanescent wave in biological samples is dependent on the wavelength and temperature and can reach 0.1-0.5 mm depth due to strong refractive index change ∼0.4 of the ice-water transition; this is quite significant and important when studying biological samples. Technical challenges are discussed when using ATR for uneven, heterogeneous, high refractive index samples with possibility of frustrated total internal reflection (a breakdown of the ATR reflection-mode into transmission-mode). Local field enhancements at the interface are discussed with numerical/analytical examples. Maxwell’s scaling was used to model behaviour of absorber-scatterer inside materials at the interface with ATR prism for realistic complex refractive indices of bio-materials. Modality of ATR with polarisation analysis is proposed and its principle illustrated, opening an invitation for its experimental validation. The sensitivity of the polarised ATR mode to the refractive index between the sample and ATR prism is revealed. Design principles of polarisation active optical elements and spectral filters are outlined. The results and concepts are based on experiments carried out at the THz beamline of the Australian Synchrotron.
ARTICLE | doi:10.20944/preprints202301.0407.v1
Subject: Materials Science, Polymers & Plastics Keywords: weathering; photoageing; microplastics; polymer oxidation: ATR-FTIR spectroscopy
Online: 23 January 2023 (09:40:23 CET)
The main purpose of this work is to contribute to understanding the mechanism of oxidation of the polymeric components of common disposable masks used during the COVID-19 pandemic to offer the chemical basis to predict their long-term behaviour under typical environmental conditions. Artificial ageing of representative mask layers under isothermal conditions (110℃) or accelerated photoageing showed that all the PP-made components underwent a fast oxidation process, following the typical hydrocarbon oxidation mechanism. In particular, yellowing and the melting temperature drop are early indicators of their diffusion-limited oxidation. Morphology changes also induced a loss of mechanical properties, observable as embrittlement of the fabric fibres. Results were validated through preliminary outdoor ageing of masks, which allows us to predict they will suffer fast and extensive oxidation only in the case of contemporary exposure to sunlight and relatively high environmental temperature, leading to their extensive breakdown in the form of microfiber fragments, i.e., microplastics.
ARTICLE | doi:10.20944/preprints202102.0271.v1
Subject: Medicine & Pharmacology, Allergology Keywords: ATR; THz; synchrotron radiation; biological tissues; temperature variation
Online: 11 February 2021 (09:29:43 CET)
A novel method of investigating the temperature dependent variation of aspects of the complex refractive index n* in samples in the THz range using continuous, non-polarised, synchrotron radiation is presented. The method relies on the use of ATR apparatus, and retains the advantage of minimal sample preparation, which is a feature of ATR techniques. The method demonstrates the viability of rapidly monitoring temperature reflectance whilst continuously heating or cooling samples by using a temperature variable Thermal Sample Stage. The method remains useful when the refractive index of the sample precludes attenuated total reflection study. This is demonstrated with the water reflectance experiments. The temperature dependent ATR reflectance of tissue-representative fats (lard and Lurpak® butter) was investigated with the novel approach. Both are within the ATR range of the diamond crystal in a “true” ATR mode. Lard showed no clear temperature variation between -15 0C and 24 0C at 0.7 to 1.15 THz or 1.70 to 2.25 THz. Lard can be regarded as having invariable, constant, dielectric properties within mixtures when biological substances are being assessed for temperature dependent dielectric variation within the stated THz ranges. Lurpak® butter (water content 14.7%) displayed temperature dependent reflectance features with a steady decline in reflectivity with increasing temperature. This is in line with the temperature-dependent behaviour of liquid water. There is no rapid change in reflectance, even at -20 0C, suggesting that emulsified water retains liquid-water-like THz properties at freezing temperatures.
ARTICLE | doi:10.20944/preprints201909.0166.v3
Online: 4 August 2020 (08:21:22 CEST)
Acne vulgaris is a chronic skin disease, which occurs due to inflammation of the hair follicles and sebum producing (sebaceous) glands of the skin called pilosebaceous unit and the anaerobic propionic acne bacterium, P.acne. Human sebum is dominantly made up of 57.5% of triglycerides and fatty acids, 26%wax esters, 12% Squalene and 4.5% Cholesterol. The increased level Androgen hormone, sebum lipid composition, P.acne over growth which induces monocytes and pro inflammatory cytokines attracts neutrophils, basophils, and T cells to the pilosebaceous unit and drive epithelial hyper proliferation i.e., Acne vulgaris. The actual biomolecular changes due to acne vulgaris disease are present in the blood, in the sebum, and in the noninvasive sample of human scalp hair follicles. The main objectives of the present study are to analyze human scalp hair follicles samples using FTIR-ATR spectroscopy to compare and discriminate the spectral signatures of acne vulgaris and healthy scalp hair tissue samples through acne biomarkers Protein, Amide I, Amide II and Squalene (LDL), using the method of internal ratio parameters. This work represents a first step in the development of an analytical tool for future drug development.
ARTICLE | doi:10.20944/preprints201804.0251.v1
Subject: Mathematics & Computer Science, Information Technology & Data Management Keywords: ATR; ISAR/SAR images; saliency attention; SIFT; multitask-SRC
Online: 19 April 2018 (10:32:02 CEST)
In this paper, we propose a novel approach to recognize radar targets on inverse synthetic aperture radar (ISAR) and synthetic aperture radar (SAR) images. This approach is based on the multiple salient keypoint descriptors (MSKD) and multitask sparse representation based classification (MSRC). Thus, to characterize the targets in the radar images, we combine the scale-invariant feature transform (SIFT) and the saliency map. The goal of this combination is to reduce the SIFT keypoints and their time computing time by maintaining only those located in the target area (salient region). Then, we compute the feature vectors of the resulting salient SIFT keypoints (MSKD). This methodology is applied for both training and test images. The MSKD of the training images leads to construct the dictionary of a sparse convex optimization problem. To achieve the recognition, we adopt the MSRC taking into consideration each vector in the MSKD as a task. This classifier solves the sparse representation problem for each task over the dictionary and determines the class of the radar image according to all sparse reconstruction errors (residuals). The effectiveness of the proposed approach method has been demonstrated by a set of extensive empirical results on ISAR and SAR images databases. The results show the ability of our method to predict adequately the aircraft and the ground targets.
ARTICLE | doi:10.20944/preprints201710.0128.v1
Subject: Chemistry, Organic Chemistry Keywords: kraft lignin; photolysis; photocatalysis; actinometry; OH-number; SEC; UV-VIS; ATR-FTIR; XRD
Online: 18 October 2017 (08:55:29 CEST)
Today, more than 70 million tons of lignin are produced by the pulp and paper industry every year. However, the utilization of lignin as a source for chemical synthesis is still limited due to the complex and heterogeneous lignin structure. The purpose of this study was a selective photodegradation of industrially available kraft lignin in order to obtain appropriate fragments and building block chemicals for further utilization, e.g. polymerization. Thus, kraft lignin obtained from soft wood black liquor by acidification was dissolved in sodium hydroxide and irradiated at a wavelength of 254 nm with and without the presence of titanium dioxide in various concentrations. Analyses of the irradiated products via SEC showed decreasing molar masses and decreasing polydispersity indices over time. At the end of the irradiation period the lignin was depolymerised to form fragments as small as the lignin monomers. TOC analyses showed minimal mineralisation due to the depolymerisation process.
ARTICLE | doi:10.20944/preprints201909.0338.v1
Subject: Life Sciences, Virology Keywords: genus beta human papillomavirus; ATM; ATR; nucleotide excision repair; translesion synthesis; cell cycle; uv
Online: 30 September 2019 (04:17:08 CEST)
Given the high prevalence of cutaneous genus beta human papillomavirus (β-HPV) infections, it is important to understand how they are manipulating their host cells. This is particularly true for cellular responses to UV damage, since our skin is continually exposed to UV. The E6 protein from β-HPV (β-HPV E6) decreases the abundance of two essential UV-repair kinases (ATM and ATR). Since β-HPV E6 reduces their availability, the impact on downstream signaling events has been uncertain. We demonstrate that β-HPV E6 decreases ATM and ATR activation. This inhibition extended to XPA, an ATR target necessary for UV repair, lowering both its phosphorylation and accumulation. β-HPV E6 hinders POLη phosphorylation and foci formation, critical steps in translesion synthesis. ATM’s phosphorylation of BRCA1 is also attenuated by β-HPV E6. However, β-HPV E6’s hindrance of ATM/ATR signaling during UV-associated cell cycle arrest was incomplete. While there was less phosphorylation of immediate downstream targets (CHK1), events further down the cascade were not decreased. These observations are consistent with β-HPV infections making UV radiation more deleterious and support the proposed role of β-HPV in early stages of non-melanoma skin cancer development.
ARTICLE | doi:10.20944/preprints201812.0149.v1
Subject: Chemistry, Organic Chemistry Keywords: Organic nanomaterials, bispidines; supramolecular gels; SEM, TEM, AFM study; X-ray diffraction; FT IR-spectroscopy; ATR-spectroscopy; SAXS
Online: 12 December 2018 (13:06:31 CET)
The acylation of unsymmetrical N-benzylbispidinols in aromatic solvents without external base led to formation of supramolecular gels, which possess different thickness and stability depending on the substituents in para-positions of benzylic group and nature of acylating agent as well as on the nature of the solvent used. Structural features of the native gels as well as of their dried forms were studied by complementary techniques including FT IR- and ATR-spectroscopy, AFM, TEM, SEM, SAXS. Structures of the key crystalline compounds were established by X-ray diffraction. Analysis of obtained data allowed speculating on the crucial structural and condition factors that governed the gel formation. The most important factors were: (i) absence of base, either external or internal; (ii) presence of HCl; (iii) presence of carbonyl and hydroxyl groups to allow hydrogen bonding; (iv) presence of two (hetero)aromatic rings at both sides of the molecule. The hydrogen bonding involving amide carbonyl, hydroxyl at 9th position and, very probably, ammonium N-H+ and Cl- anion appear to be responsible for the formation of infinite molecular chains required for the first step of gel formation. Subsequent lateral cooperation of molecular chains into fibers occured, presumably, due to the aromatic pi-pi-stacking interactions. sc-CO2 drying of the gels gave rise to aerogels morphology different from that of air dried samples.
ARTICLE | doi:10.20944/preprints202211.0243.v1
Subject: Engineering, Electrical & Electronic Engineering Keywords: deep neural network (DNN); synthetic aperture radar automatic target recognition (SAR-ATR); universal adversarial perturbation (UAP); U-Net; attention heatmap; layer-wise relevance propagation (LRP)
Online: 14 November 2022 (06:37:35 CET)
Recent studies have proven that synthetic aperture radar (SAR) automatic target recognition (ATR) models based on deep neural networks (DNN) are vulnerable to adversarial examples. However, existing attacks are easily failed in the case where adversarial perturbations cannot be fully fed to victim models. We call this situation perturbation offset. Moreover, since background clutter takes up most of the areas in SAR images and has low relevance to recognition results, fooling models with global perturbations is quite inefficient. This paper proposes a semi-whitebox attack network, called Universal Local Adversarial Network (ULAN), to generate universal adversarial perturbations (UAP) for the target regions of SAR images. In the proposed network, we calculate the model’s attention heatmaps through layer-wise relevance propagation (LRP), which is used to locate the target regions of SAR images that have high relevance to recognition results. In particular, we utilize a generator based on the U-Net to learn the mapping from noise to UAPs and craft adversarial examples by adding the generated local perturbations to target regions. Experiments indicate that the proposed method fundamentally prevents perturbation offset and achieves comparable attack performance to conventional global UAPs by perturbing only a quarter or less of SAR image areas.
REVIEW | doi:10.20944/preprints202001.0353.v1
Subject: Life Sciences, Genetics Keywords: chromothripsis; structural variants; DNA-repair; DNA-repair disorders; DNA-double strand breaks (DSBs); ataxia telangiectasia mutated (ATM); ataxia-telangiectasia and Rad3-related (ATR); TP53; micronuclei; chromosome pulverization.
Online: 29 January 2020 (11:58:58 CET)
Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underly chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei followed by incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA-repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in Sonic-Hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA-repair genes resulting in chromosome instability and chromothripsis-like rearrangements.