The recent progress in photon-counting detector technology using high-Z semiconductor sensors provides new possibilities for spectral x-ray imaging. The benefits of the approach to extract spectral information directly from measurements in the projection domain are very advantageous for material science studies with x-rays as polychromatic artifacts like beam-hardening are handled properly. Since related methods require accurate knowledge of all energy-dependent system parameters, we utilize an adapted semi-empirical model, which relies on a simple calibration procedure. The method enables a projection-based decomposition of photon-counting raw-data into basis material projections. The objective of this paper is to investigate the method’s performance applied to x-ray micro-CT with special focus on applications in material science and non-destructive testing. Projection-based dual-energy micro-CT is shown to be of good quantitative accuracy regarding material properties such as electron densities and effective atomic numbers. Furthermore, we show that the proposed approach strongly reduces beam-hardening artifacts and improves image contrast at constant measurement time. The concept of hybrid-pixel photon-counting detectors (PCDs) has been demonstrated for the first time at CERN in 1991  for the The significant progress of PCD technology achieved over the last years –5 createK of materials at N ≥ K energy levels E1⋯EN. The obtained set of energy-dependent CT images μ(Ei) can be expressed by the vectorN × K spectral basis function matrix B. The process of retrieving the basis material images a1 … aK from the measured spectral attenuation data is called material decomposition. Significant benefits of these spectral imaging methods using x-rays have already been demonstrated for many clinical applications [The concept of spectral x-ray imaging has first been developed for clinical CT in the late 1970’s by Alvarez and Macovski . For theications . HoweverImage-based approaches rely on reconstructed polychromatic CT images obtained with different effective x-ray spectra and therefore perform the material decomposition in the image domain, i.e. such methods perform the decomposition after the CT reconstruction. The most basic implementation uses a 2D scatter-plot of the voxel attenuation values at low and high energies, respectively. Using vector decomposition, some information about the sample composition can be obtained. Furthermore, previously known values of the energy-dependent spectral basis functions obtained in dedicated calibration scans can be used to directly invert the system of The second concept consists of raw data-based methods that performs the decomposition directly in the projection domain prior to CT image reconstruction, yielding basis component line-integrals. Methods that rely on a basis material decomposition in the projection domain are by their design capable of correctly modeling the hardening of polychromatic x-ray spectra penetrating an object. Hence, this concept is a very promising tool for quantitative x-ray imaging of material-science related samples since metal artifacts are often a major issue. In first attempts, the projection data obtained in dual-energy acquisitions was modeled by polynomials considering the energy dependence of Compton scattering and photoelectric absorption as the two predominant physical causes of attenuation . More reTherefore, a new concept based on a semi-empirical polychromatic Beer-Lambert forward model has been developed by the authors featuring a strongly simplified and fast calibration routine. In prior simulations , this meρel) and effective atomic number (Zeff) values within unkown objects. Although, there is a lot of literature on the determination of those quantities from dual-energy measurements [ρel and Zeff is challenging especially when using image-based approaches. Beam-hardening is a prominent effect occurring in conventional CT, especially when strongly absorbing structures like metals are present in the studied object. Thereby, cupping and streaks in the reconstructed images often decrease the quality and complicate the analysis and interpretation of CT images investigated for NDT [The previously published work only used simulated data and therefore neglected some effects that are incorporated when using PCDs in an experimental environment. Among those effects the most influential in an experimental measurement are sensor polarization , threshourements –21, most for NDT .The paper is structured in the following order. After recapitulation of the proposed model and giving a brief illustration of the algorithm used for the decomposition in the methods section, a detailed description of the calibration procedure and the used experimental set-up will be given. In the results section the quantitative accuracy and quality of the acquired spectral images will be illustrated based on phantom measurements. Furthermore, the method was used for imaging of a concrete drill core and a ethernet connector to study its practicalness in NDT applications. Subsequently, we will discuss the obtained results.In this study we make use of maximum-likelihood estimation (MLE)  of the bμ1,2 are the attenuation coefficients of the basis materials and a1,2 scalar factors describing their respective contribution to the total attenuation. The vector The linear attenuation coefficient of any material without K-edge discontinuities in the respective energy range (20 keV − 150 keV), can be approximated by a linear combination of two linearly independent contributions, the so-called basis materials , 25:μ, μ2(E)) in The parameters in A1 and A2 for the calibration. The number of exponential terms in Due to its reliability and unbiasedness , a MLE mAs common for spectral imaging techniques, the Poisson noise present in the registered count data propagates into the estimates of the basis materials. Whereas there is no correlation between the data in the different energy bins, the estimation introduces an anti-correlation to the basis material line-integrals, which also affects the image noise , 32. TheThe experimental measurements were performed on a tomographic setup consisting of a micro-focus x-ray tube, a photon-counting detector system and several positioning devices mounted on an optical table.μm(hor./vert.), which broadens with increasing target power to its maximum of approximately 150/320 m at a power of 120 W [2) with a native pixel size of 100 m, arranged in a horizontal pattern of 12 chip modules with a chip gap of one pixel. The system has two energy thresholds per pixel and comes with an integrated charge sharing correction. The maximum acquisition rate is up to 200 ⋅ 106The statically mounted x-ray tube  is a micro-focus tube with a tungsten reflection target and a 2mm thick beryllium window. It can be operated at tube voltages of up to 160 kVp and has a maximum target power output of 300 W. Furthermore, the tube has a minimal focal spot size of 2.0/3.0 of 120 W . The beax-, y- and z-direction, due to an arrangement of three linear stages. The rotation of the sample is realized by an additional rotation stage. The detector system can further be moved in the z-, and y-direction. Thus the set-up allows a flexible and accurate geometric alignment, including arbitrary selection of the geometric magnification as well as the correct alignment of the sample and the detector to the center of the cone beam. The set-up is equipped with a sample holder completely movable in The calibration phantoms are mounted onto two additional linear-stages between the x-ray tube and the sample holder. The phantoms consist of an aluminum frame that is equipped with cuboid blocks of Polyoxymethylen  and titanium foils (purity > 99.7%).4 counts per pixel).In order to assess the performance of the calibration routine a test grid of various thickness combinations of titanium and POM was consulted. The parameters in After the calibration routine the test-grid data was acquired and decomposed into line-integrals of titanium and POM. The test grid was different from the calibration grid and is indicated by the orange dots in j, and k and l label the titanium and POM thicknesses of the evaluated ‘test-grid’ in J = 40 × 1032, corresponding to the collimated detector area during the measurement. The total number of evaluated pixels was Based on a cylindrical phantom featuring various materials with exactly known material properties the quantitative accuracy of the proposed method was investigated. The phantom is made of four cylindrical rods consisting of titanium (Ti), polyacetal , aluminum (Al) and teflon , respectively. The acquisition parameters used for the phantom are summarized in σ is the standard deviation of the N voxels values within the evaluated region). The determined values show systematic deviations from the respective reference values. Thereby, the relative errors are within the range of 5 %. Given the high purity of the used materials (> 99.7%) the uncertainty of the reference values is negligible.The reconstructed basis material image volumes c. f.  were useIn order to study the method’s capability of handling beam-hardening properly a strongly attenuating copper wire (0.75 mm in diameter) was added to the evaluated phantom. In order to demonstrate the benefits of spectral micro-CT over conventional micro-CT, we performed CT scans of two material science related samples. The tomography parameters of the scans are listed in The first object was a concrete drill core with a diameter of approximately 1.5 cm and primarily should serve for the illustration of the contrast enhancement achieved by the basis component decomposition. Prior to a dual-energy CT scan, we performed the calibration procedure as described in the materials and methods section of the paper.As shown previously, the introduced method is able to model beam-hardening properly c.f.  and consWe evaluated the feasibility of spectral imaging for micro-CT applications in experimental measurements. The proposed method provides basis material images unaffected of beam-hardening and featuring quantitative image data. Different from other spectral imaging methods  the knowThe reliability of the proposed calibration routine and the accuracy of the resultant decomposed basis material line-integrals was evaluated by the measurement of a test grid which consisted of pre-defined thickness combinations of titanium and POM. The relative bias between the decomposition results and the respective ground truth values are in the range of single digit percentage values c. f.  and therIn phantom studies we evaluated the proposed method’s quantitative accuracy in computed tomography. Thereby, we exploited the basis material volume fractions obtained in the material decomposition to interplolate the chemical quantities of unkown materials from a set of basis materials used in the presented calibration routine. Our findings show a high accuracy for the determination of the effective atomic number and electron density values of unkown samples, even for high-Z materials c. f. . The obsThe obtained virtual monoenergetic images exhibit a good agreement with the reference values of the evaluated materials over a large energy range c. f. . As demoThe enhancement in contrast provided by the basis material images of the concrete drill core c. f.  providesThe reduction of beam-hardening artifacts in the spectral images of an ethernet connector is very promising for NDT of electronic components using x-rays. The safety demands of electronic connectors are becoming more and more important due to the trend of an increasing automatization in manufacturing processes and autonomous vehicles, where application-specific switches and sensors are critical devices. At the same time, the manufacturing of electronic connectors has become more complex as miniaturization has driven the need for components to become smaller with tighter tolerances, which requires a more accurate and detailed inspection. Therefore, micro-CT plays an increasingly important role in the quality assurance process, since it allows the inspection of both, the outer and the inner connector parts, with a very high precision and in an non-destructive manner. However, since electronic connectors contain high-absorbing materials such as copper wires and metal screws, the CT reconstruction suffers from strong beam-hardening, which makes a reliable inspection difficult or even impossible. Using a harder x-ray spectrum is typically associated with a decreased image contrast and the x-ray spectra emitted by tube sources need to be pre-filtered to eliminate low energies. This however will decrease the photon flux and thus leads to increased measurement times. As demonstrated in Apart from that, scattered radiation can influence the decomposed line-integral values. Similar to conventional attenuation based-imaging, scattering will add a low frequency bias to the acquired projection data. However, the bias introduced to spectral bin data is in general magnified by material decomposition algorithms , becauseIn this paper we have shown that photon-counting spectral micro-CT is a feasible and viable alternative to conventional micro-CT. Spectral data acquisition is performed by state-of-the-art photon-counting detectors without increase of required measurement time. Instead, enhanced image quality and the availabilty of quantitative material properties provide new possibilities for material science and NDT applications.


The investigation of post-translational modifications (PTMs) plays an important role for the study of type 2 diabetes. The importance of PTMs has been realized with the advancement of analytical techniques. The challenging detection and analysis of post-translational modifications is eased by different enrichment methods and by high throughput mass spectrometry based proteomics studies. This technology along with different quantitation methods provide accurate knowledge about the changes happening in disease conditions as well as in normal conditions. In this review, we have discussed PTMs such as phosphorylation, N-glycosylation, O-GlcNAcylation, acetylation and advanced glycation end products in type 2 diabetes which have been characterized by high throughput mass spectrometry based proteomics analysis. Type 2 diabetes has become a global health problem as the diabetic population is estimated to increase to 552 million by the year of 2030 . This meHyperinsulinemia is able to increase IRS-1 tyrosine phosphorylation and PI3-kinase function in normal human skeletal muscle compared to skeletal muscle of non-insulin-dependent diabetic subjects .The activity of most of the proteins in type 2 diabetes is modulated by the presence of post-translational modifications (PTMs). There is great deal of challenge associated with detection and characterization of these post-translational modification and studies on the PTMs throws great deal of light into the biological activities of the proteins. The PTMs are required for cell signaling process.The non-enzymatic PTMs that are uncontrolled have harmful effect on proteins such as glycation which causes changes in conformation of proteins, form aggregates and Maillard cross-links . The oxiThe misfolding of proteins due to the contribution from PTMs is attracting attention also in the field of proteopathies , 16. TheThis review discusses different post-translational modifications that have been found in type 2 diabetes characterized by high throughput mass spectrometry based proteomics.The proteomic technologies are for identification and quantification of proteins and different post-translational modifications in proteins present in cells, tissues or an organism. The proteins are digested into peptides that are amenable to high resolution mass spectrometry based analysis. Before their identification and characterization by mass spectrometry, they are subjected to different enrichment methods for specific post-translational modifications that are described under different post-translational modifications.The choosing of the technology depends upon the aim of study and its availability. The most commonly used mass spectrometry for proteomics among other mass spectrometry  are thosThe most common way to fragment peptide ion is collision-induced dissociation (CID) that involves the collision of peptide or precursor ion with inert gas at low pressure , 25. The13C isotope and/or 15N isotope is used. Both light  and heavy (labelled) Lysine and Arginine is used in cell culture for the growth of two sets of cell populations. Here the cells incorporate these heavy isotopes as part of normal biosynthesis. The carboxylic end of the peptide contains a labeled amino acid after digestion with trypsin. The know molecular weight difference between the light and heavy isotope of Lysine and Arginine helps in identifying and quantifying the proteins. Triple SILAC labelling uses addition label of 13C6 Arginine and D-labelled Lysine thereby helping in comparison between three states proteomes and measurements involving time points. This technology is extended also to human tissue sample [15N has been used in C. elegans and D. melanogaster by feeding the respective organism by 15N labeled E. coli and yeast [One of the potential of mass spectrometry over traditional methods is the ability to quantitate accurately large number of proteins and its post-translational modifications. For highly accurate quantitative results, the two proteomes have to be compared one labelled and other non-labeled. One of the metabolic labelling methods is labeling with Stable isotope labelling by amino acids in cell culture (SIlAC) –34, where sample  and alsoe sample –38. Thise sample . Apart fnd yeast . Super-Snd yeast .There are many chemical labeling techniques that are used to quantify the proteome. One of the disadvantages of chemical labeling is side products that formed during chemical derivatization leading to the suppression in the identification rate of the proteins and presence of artifacts . The cheSometimes label-free quantitation offers the benefit where there is no experimental manipulation at the protein and at peptide levels  and offeThere have also been cases where absolute quantitation of proteins is required to determine their expression levels. The absolute quantification (AQUA) is one such method involving the use of known concentration of synthetic internal standard peptide with stable isotopes that mimics a peptide produced during the digestion of the target protein followed by analysis by selected reaction monitoring (SRM) in LC–MS/MS . AnotherAnalysis of proteomic data with the help of mass spectrometry involves extraction of signals from the peptides, identification of peptides with help of search engines to enable the identification of proteins and then protein quantification with false positive rate usually set to 1% . The quaThe importance of PTMs in the biological activity has been realized with the advancement of analytical techniques. Most of the therapeutic proteins approved or those in clinical trials have PTMs that affect the properties of the proteins, their stability that are important for therapeutic purposes. The post-translation modified peptides can be detected with mass spectrometry as it is very sensitive in the change of mass of the modified peptides along with the localization of the modification in particular amino acid. One of the challenges in mass spectrometry based proteomics is the detection and identifications of PTMs that are present at low stoichiometry’s thus necessitating the role of enrichments methods. There are many enrichment methods each specific for different PTMs as there are variety of protein modifications. Table 3+, Fe3+, Zr4+ and Ti4+ [In mass spectrometry, the identification of phosphorylation in proteins becomes tricky due to low ionization, fragmentation and stoichiometry of phosphopeptides. To overcome these problem many techniques were applied for analysis of phosphopeptides. The enrichment techniques for phospho-peptides which helps them to separate from non-phosphopeptides involves the immobilized metal affinity chromatography (IMAC) based on the coordination of phosphates to certain metal ions such as Gaand Ti4+ –62, compand Ti4+ , hydrophand Ti4+ , strong and Ti4+ , immunopand Ti4+ –69.The high throughput mass spectrometry studies have identified majority of protein phosphorylation occurring on serine and threonine residues compared to tyrosine residue. Interestingly, serine: threonine: tyrosine phosphorylation ratios were found to be 90:10:0.05 based on autoradiography measurements . The proProtein phosphorylation is important for the proper functioning of pancreatic β-cell. The pancreatic β-cells are the production house for insulin and are one of the factors for the healthy survival. When the β-cells of pancreas are stressed, they undergo dedifferentiation and dysfunction where they produce very less amount or no insulin , 72. Los+ T cell compartments signaling have been found in non-obese diabetes (NOD) mice compared to that of diabetic-resistant B6g7 mice suggesting dysregulation of T cell receptor signaling in NOD mice. These phosphopeptides were detected using immunoprecipitation by anti-phosphotyrosine antibody, and IMAC enrichment [The different cell types have varying insulin signaling pathways . On stimrichment .The disturbance in phosphorylation of ATP synthase beta subunit (ATPsyn-β) results in dysregulation of ATP synthesis along with decreased level of OxPhos proteins. This may lead to development of insulin resistance and type 2 diabetes. In obesity and type 2 diabetes there is increased phosphorylation at threonine 213 and tyrosine 361 sites of ATPsyn-β. Incidentally the activity of ATP synthase is decreased due to phosphorylation at serine residue of ATPsyn-β . IncreasIn skeletal muscle, the serine/threonine protein kinase 25 (STK25) is known to aggravate insulin resistance. Moreover, in skeletal muscle, the overexpression of STK25 increases the storage of fat and deregulates the mitochondrial function in mice. Notably, phosphoproteomics studies suggest alterations of phosphorylated proteins mainly in mitochondria and sarcomeric contractile muscle thereby identifying mediators of the action of STK25 .The O-GlcNAc and N-glycosylation modifications is a sensor linking cellular metabolism with various signaling pathways and is associated in the pathogenesis of diabetes  as theseN-glycosylation is the covalent bonding of glycans to the N-linked Asn residue. The enrichment techniques for N-glycosylated proteins or peptides involves various methods such as affinity with lectin , hydraziInsulin resistance is also linked with TNF-alpha. A quantitative study in SILAC labelled mouse 3T3-L1 adipocytes cells incubated with TNF-alpha revealed the presence of 1580 unique N-glycopeptides  group to the hydroxyl group of serine and threonine residues. The O-GlcNAcylated peptides or proteins can be enriched before mass spectrometry studies. This enrichment involves various methods including CTD110.6 anti-O-GlcNAc mouse monoclonal antibody , O-GlcNAThe O-GlcNAcylation is stimulated by high level of glucose through hexosamine biosynthetic pathway (HBP) . With th2+/calmodulin-dependent protein kinase II (CaMKII) thereby activating it and creating a feeling of the presence of Ca2+ even though its concentration is less leading to cardiac dysfunction and arrhythmias [2+ sensitivity [Elevated O-GlcNAc not only effects kidney cells, it also effects cardiac , liver ahythmias . The O-Gsitivity . Moreovesitivity .Upon insulin resistance, Insulin receptor substrate-1 (IRS-1) an important protein in insulin signaling pathway, was found to be O-GlcNAc modified by using β-elimination followed by Michael addition with DTT (BEMAD) prior to LC–MS/MS thereby suggesting important role of this modification site in insulin signaling by inhibiting phosphorylation at these sites . This moThe O-(2-acetamido-2-deoxy-d-glucopyranosylidene) amino-N-phenylcarbamate (PUGNAc) is an inhibitor of O-GlcNAcase leading to insulin resistance  as seen Interestingly, transcription factors and co-activators including FoxO1, PGC-1α, CRTC2 that play an important role in gluconeogenesis are O-GlcNAcylated under high glucose conditions resulting in activation of proteins such as phospho enol pyruvate carboxykinase and glucose 6-phosphate involved in gluconeogenesis –117. In The O-GlcNAc modified human erythrocyte proteins were found to be up-regulated and potential biomarker for diabetes and pre-diabetes, based on chemo enzymatic tagging with quantitative mass spectrometry. This led to identification and quantification of O-GlcNAc sites suggesting the development of targeted site specific antibodies will help in identifying pre-diabetes patients .Acetylation in proteins occurs typically in lysine residues as it has two active hydrogens in NH group at its side chain. Due to presence of two active hydrogens in NH group it can be mono-acetylated and di-acetylated. Most commonly, mono-acetylation occurs in the lysine residues of proteins. It is a reversible post-translational modification and is dependent on acetylases and deacetylases enzymes for its acetylation and de-acetylation.Acetylome plays an important role in understanding the physiological difference between Goto-Kakizaki (GK) rats and normoglycemic Brown Norway (BN) rats. The difference was the down-regulation of Sirtuin-3 by promotor SNP in GK rat .Increase of acetylation on lysine residue in retinal histones histone H3 and H4 in diabetes leads to regulation of pro-inflammatory proteins activities in diabetic retinas suggesting their contribution towards the pathogenesis of the disease . SimilarAnother quantitative global analysis of the liver of diabetes mice led to the mapping of 1604 acetylation sites (Table An AGEs is the non-enzymatic covalent bonding of sugars such as glucose or fructose to the free amino or guanidinium group of proteins, lipids and nucleic acids. The initial product is Schiff base which rearranges itself to Amadori product. The Amadori product degrades giving rise to AGEs. The compounds that are widely studied as examples of AGEs are N-carboxymethyl-lysine, N-carboxyethyl-lysine, pentosidine, or methylglyoxal derivatives, pyrraline, imidazolone, lysine–lysine cross-links. By boronate affinity chromatography enrichment studies, 7749 highest unique glycated peptides were identified in diabetes plasma and erythrocytes Table  by mass The AGEs is an oxidative PTM resulting from oxidative stress disrupting biological activities thereby associating it with several diseases example, diabetes. There are several cell surface receptors for AGEs  that medMass spectrometry based proteomics technology has provided an opportunity to study proteins, their PTMs like phosphorylation, acetylation, N-glycosylation, O-GlcNAcylation and Advanced glycation end products in type 2 diabetes. In future, the proteomic technologies will have to be sensitive to detect the concentration of the proteins that are playing an important role in the disease condition or detect the fast turnover of newly synthesized proteins. With the advancement in high resolution mass spectrometry and with the combination of good quality sample preparation, enrichment techniques along with improvement of computational tools one can study large number of PTMs that modify the signaling pathways in type 2 diabetes. Development of mass spectrometry especially quantitative and targeted proteomics will be of great alternate to antibody validation. Furthermore, the advancement in proteomics technology will help in detection and studying the cross-talk between multiple low abundant PTMs thereby enabling to get further insight into type 2 diabetes.Most of the proteins involved in type 2 diabetes have PTMs that affect the properties of the proteins, their stability and may serve as targets for therapeutic purposes. A good understanding of structure–function relationship of the PTMs is required for the generation of products of therapeutic importance  and also


The cornea is an extraordinary component of vision that functions as the principal barrier to pathogens in the eye while allowing light transmission into the retina. Understanding the cellular and molecular mechanisms that maintain homeostasis in this tissue is the subject of intense scientific study given the high prevalence of corneal disease. Over the past decade, the interactions between lectins and glycans on plasma membranes have emerged as important regulatory factors in corneal biology. In particular, members of the galectin family have been shown to bind multiple β-galactoside-containing receptors to regulate immunopathological processes associated with viral and bacterial infection, transplantation, wound healing, dry eye, angiogenesis, and lymphangiogenesis. In this review, we describe the current understanding of how these surface interactions intersect with different pathways to activate unique cellular responses in cornea as well as their potential therapeutic implications. Lectins are proteins widely distributed among the animal kingdom that specifically recognize carbohydrates. Traditionally, they have been classified based on their ability to recognize specific carbohydrate sequences but, with the advent of new molecular biology methods, novel classes have been defined based on the presence of unique structural domains within their amino acid sequences. This novel classification stems from the presence of highly conserved carbohydrate-recognition domains (CRDs) that appear to have evolved from shared ancestral genes . ExampleGalectins are expressed by different cell types, including epithelial, stromal, endothelial, and immune cells and typically bind β-galactose-containing glycoconjugates. They are grouped into three categories based on structure: (1) prototypical, with a single CRD that may associate to form homodimers, 2) chimeric, with a single CRD and a large amino-terminal domain that contributes to self-aggregation and, 3) tandem-repeat, with at least two CRDs occurring within a single polypeptide  . DectinsThe cornea is a clear, curved surface covering the anterior segment of the eye. It is responsible for refracting light onto the lens and retina in addition to resisting infection and damage. The lack of lymphatic and blood vessels is essential to maintaining the transparency of the cornea. Injury resulting from infection, transplantation, autoimmune conditions, and other pathologies can lead to the abnormal growth of vessels and loss of vision .Structurally, the cornea consists primarily of the epithelial, stromal and endothelial compartments Figure . The epiThe apical surface of the corneal epithelium constitutes an exceptional barrier against foreign particles and microorganisms that attempt to penetrate the eye. Highly glycosylated transmembrane mucins emanating from ridge-like folds of the plasma membrane are an essential component of this protective layer. They have single membrane-spanning regions with large extracellular domains that form rod-like structures, which extend over 100 nm from the cell surface, far above other glycoconjugates in the glycocalyx  infection result in viral replication and destruction of the infected cells. This process triggers non-specific innate host defenses that contribute to infection control but also adaptive responses when dendritic cells leave the site and carry viral antigens to draining lymph nodes . A largenfection . Other ge cornea .Pseudomonas aeruginosa to corneal epithelial cells could be blocked by an antibody targeting galectin-3, a binding receptor for bacterial lipopolysaccharides (P. aeruginosa resulted in overall downregulation of galectin-3 and upregulation of galectins-8 and−9 (P. aeruginosa-mediated inflammation by impairing the infiltration of neutrophils and CD4+ T cells, particularly proinflammatory Th17 cells (It was the Hazlett laboratory that first reported in 1997 the presence of a member of the galectin family in cornea and its potential pathogenic contribution to bacterial infection. Using binding inhibition assays, this group found that adhesion of charides . Further17 cells .Aspergillus fumigatus to promote recruitment of neutrophils into the corneal stroma and trigger fungal killing (A. fumigatus spores express RodA hydrophobin, a surface protein that confers hydrophobicity and covers cell wall components that would otherwise activate dectin-1 and dectin-2 (Candida albicans (Fusarium solani (Fungal infection is a major cause of corneal ulceration in developing countries and tropical regions commonly associated with severe inflammation. Evidence suggests that the C-type lectin receptors dectin-1 and dectin-2 play important roles in regulating disease severity and survival. Dectin-1 on corneal macrophages can be activated by β-glucans on  killing . Interesdectin-2 . Dectin-albicans  and Fusam solani  infectioCorneas are among the most common and successful transplanted tissue worldwide. They express factors that contribute to immune privilege by inhibiting the induction and function of alloimmune T cells among others . Recent E-selectin is a carbohydrate-binding protein commonly expressed during corneal inflammatory disease . It locaAlmost 40 years ago Gipson and Anderson reported the requirement of carbohydrate moieties on cell surface glycoproteins and basement membrane to promote epithelial cell migration during the healing of corneal abrasions . This inIt is now clear that not all kinds of injury lead to a similar expression pattern of galectins in cornea. The expression of galectin-3 is downregulated in mouse corneas following bacterial infection and chemical burn . Yet, gaDisruption of barrier function at the ocular surface is associated with a wide range of inflammatory disorders that includes dry eye, an age-related disease affecting millions of people worldwide, and whose pharmacological treatment remains unresolved. Both N- and O-glycosylation are altered in the ocular surface epithelia of dry eye patients , which hCorneal angiogenesis represents a major public health problem affecting 1.4 million individuals each year in the United States alone . The groIn addition to galectin-3, other lectins have been implicated in corneal angiogenesis. Galectin-1 and−9 have been shown to possess anti-angiogenic activity in a mouse model of herpetic keratitis, where they decrease the production of proinflammatory cytokines and molecules involved in the formation of new vessels , 21. C-tThe lymphatic vasculature plays an important role in coordinating antigen transport and immune-cell trafficking from peripheral tissues to secondary lymphoid organs. At the ocular surface and under inflammatory conditions, lymphatics in the limbal region can give rise to new vessels that extend pathologically into the cornea . There iProgress has been made in providing mechanistic insights into the role of lectin-glycan interactions in cornea Figure . ManipulDA and PA reviewed the literature and wrote the article.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Wide bandgap AlGaN is one of the most promising materials for the fabrication of radiation hard, double-response particle detectors for future collider facilities. However, the formation of defects during growth and fabrication of AlGaN-based devices is unavoidable. Furthermore, radiation defects are formed in detector structures during operation at extreme conditions. In this work, study of evolution of the proton-induced luminescence spectra and short-circuit current has been simultaneously performed during 1.6 MeV proton irradiation. GaN and AlGaN (with various Al concentrations) epi-layers grown by metalorganic chemical vapour deposition technique and Schottky diode structures have been examined. Variations of spectral and electrical parameters could be applied for the remote dosimetry of large hadron fluences. The wide bandgap AlGaN with varied Al content is one of the most promising materials for fabrication of radiation hard ,2, doublStudy of the evolution of the proton-induced luminescence spectra and diode short-circuit current during 1.6 MeV proton irradiation has been simultaneously performed in this work. GaN and AlGaN (with various Al content) epi-layers grown by metalorganic chemical vapour deposition technique have been examined. Thin epi-layers ensured the penetrative conditions for 1.6 MeV protons. To evaluate a correlation of the parameters of emission and cross-sections of the photon–electron coupling, ascribed to technological and radiation defects in the GaN/AlGaN crystals, the complementary ex situ measurements were performed by pulsed photo-ionization spectroscopy on several GaN/AlGaN samples and by UV pulsed laser-induced photo-luminescence in pristine and the largest proton fluence irradiated samples.15 cm−2. Variations of spectral and electrical parameters could be applied for the remote dosimetry of large hadron fluences.It has been shown in this work that these combined methods of the in situ and ex situ measurements enable ones to trace evolution of the electrical and scintillation characteristics of AlGaN layers with proton fluence up to 4 × 10Several sets of samples were examined. The first set consists of the commercial photo-detectors GUVA-T216D-U, GUVB-T216D-U and GUVC-T206D-U , adapted for registration of different spectral range radiation. Therefore, these planar Schottky diodes were made of AlGaN materials with different Al content. For spectral measurements during irradiation, the mount of the detector was removed. The microscopy image of the commercial photo-detectors with indicated Schottky and ohmic contacts is shown in This bare diode structure was examined by X-ray diffraction (XRD) and scanning electron microscopy (SEM) together with energy dispersed X-ray spectroscopy (EDXS) techniques. A SEM instrument Hitachi SU8230  equipped with an EDX Bruker spectrometer  was then employed. Samples were XRD characterized using a high resolution (HRXRD) Rigaku SmartLab instrument equipped with Ge(400) double monochromator and scintillation detector SC-70 . The XRD 2-theta spectra obtained for these GUVA–GUVC samples are illustrated in The elemental content determined by EDXS for these GUVA–GUVC samples is listed in It can be deduced from The second set of samples was prepared as mesa structures made of top 1 μm thick GaN layer and several AlGaN layers underneath grown on Si substrates b. The AlSCI) induced by a proton beam.The latter mesa steps were covered by metal mask, impermeable for proton beam, during irradiation, successively leaving only single mesa-step uncovered to have a response only from the single layer. The 1.6 MeV irradiations were performed by a Tandetron 4110A accelerator with proton currents in the range of 20–40 nA. The GUVA–GUVC diode structures also were electrically connected to Keithley pico-ampermeter for simultaneous control of the short-circuit current (Φ)-dependent evolution of the proton-induced luminescence (PIL) spectra in different layers of the mesa structure samples with various content of aluminium is illustrated in The fluence 0 [N- [Ga [To identify the origin of different PIL components, the predominant spectral components have been correlated with pulsed photo-ionization spectra (PPIS), measured on satellite mesa structures of the same material. The PPIS technique and its application for defect spectroscopy in GaN materials is described in recent our articles ,6,7,8. TNON)0  (peaked ON)0 [N-   variations  diodes. Consequently, the dynamic range of SCI variations is the widest using these GUVA diodes. Thereby, sensitivity to fluence changes is also the highest for the GUVA diodes. An increase of bandgap with Al content leads to reduction of the SCI current. Therefore, a recordable change of SCI as a function of fluence is obtained in 32% Al containing material only for the moderate fluences of Φ > 3 × 1013 p/cm2. Even the less values and changes of SCI (for Φ > 1014 p/cm2) were obtained in diodes (GUVC) of 50% Al content  = A[f)− possible changes) are there denoted and ascribed to the specific defects in The spectral components have been tentatively associated with defects in ternary AlGaN materials identified in literature referenced. These components are listed in x ascribed to definite defects.Thereby, the Ga vacancies or DAP centres and V-O complexes prevail in both sets of AlGaN sample sets, keeping in mind the blue-shift of PIL peak position with enhancement of SCI values have been obtained. Also, the concentration of the proton generated secondary electron–hole pairs have been estimated by comparing the intensity of spectral PL components and SCI. These measurements are inevitable in calibration of the double-response dosimeters.The stability of the fluence-dependent modifications of the spectral and electrical characteristics has been verified by comparing the UV pulsed laser-excited photo-luminescence (PL) spectra and electrical signals measured ex situ before and after proton irradiations. The coincidence of spectrum structures and 0.08Ga0.92N structures. Concerning the aspect of linearity of the PIL dose-dependent characteristic, control of the PIL spectral component EPILD,4 peaked at 2.95 eV would be preferable . Control of regimes of the measurement devices and data display was implemented via LAN connection on the remote PC.The AlGaN structures can be applied for the remote sensing of particle beams and of accumulated their fluences. The solar-blind and small leakage current AlGaN detectors are insensitive to the visible (VIS)–near infrared (NIR) spectrum background emissions and thereby preferable in comparison with Si-based sensors. A tentative scheme (employed in this work) for remote dosimetry of particle beams is sketched in 0.08Ga0.92N structures. The linearity of the PIL dose-dependent characteristic can be achieved for the PIL spectral component peaked at 2.95 eV. The defects prevailing in modifications of PIL spectra have been tentatively identified. The point defects are predominant in formation and dose-dependent modification of PIL spectra regardless of the high density of dislocations inherent for the MOCVD-grown AlGaN materials. The Ga vacancy and oxygen-rich AlGaN materials with small content of Al and doped with carbon would be desirable in the fabrication of wide dynamic range dosimeters. The junction structures are preferable to record the different types of electrical signals. A possible scheme for remote dosimetry of particle beams has been approved in this work for measurements in a vacuum chamber and harsh environment of irradiations.The AlGaN structures of different Al content have been examined in order to fabricate the efficient double-response particle sensors and dosimeters. The double-response sensors are preferable when it is important to simultaneously control the instantaneous particle flux and the accumulated fluence at the fixed location of the sensor or to increase sensitivity and reliability of the dosimeter in the range of large fluences. It has been shown that the most acceptable structures in design of the double-response dosimeters are GaN/Al


In addition, case studies also confirm the effectiveness of our methods in identifying promising indications for existing drugs in practical applications.Identification of potential drug–associated indications is critical for either approved or novel drugs in drug repositioning. Current computational methods based on drug similarity and disease similarity have been developed to predict drug–disease associations. When more reliable drug- or disease-related information becomes available and is integrated, the prediction precision can be continuously improved. However, it is a challenging problem to effectively incorporate multiple types of prior information, representing different characteristics of drugs and diseases, to identify promising drug–disease associations. In this study, we propose an overlap matrix completion (OMC) for bilayer networks (OMC2) and tri-layer networks (OMC3) to predict potential drug-associated indications, respectively. OMC is able to efficiently exploit the underlying low-rank structures of the drug–disease association matrices. In OMC2, first of all, we construct one bilayer network from drug-side aspect and one from disease-side aspect, and then obtain their corresponding block adjacency matrices. We then propose the OMC2 algorithm to fill out the values of the missing entries in these two adjacency matrices, and predict the scores of unknown drug–disease pairs. Moreover, we further extend OMC2 to OMC3 to handle tri-layer networks. Computational experiments on various datasets indicate that our OMC methods can effectively predict the potential drug–disease associations. Compared with the other state-of-the-art approaches, our methods yield higher prediction accuracy in 10-fold cross-validation and  de novo experiments on three datasets. Our computational results demonstrate that both OMC2 and OMC3 generally outperform five state-of-the-art methods in terms of ROC curve, PR curve, and top-ranked predictions.This work introduces a computational approach, namely overlap matrix completion (OMC), to predict potential associations between drugs and diseases. The novelty of OMC lies in constructing an efficient framework of incorporating multiple types of prior information in bilayer and tri-layer networks. OMC for bilayer networks (OMC2) can approximate the low-rank structures of the drug–disease association matrices from both drug-side and disease-side. In addition, we further improve the prediction accuracy by extending OMC to handle tri-layer networks and develop its corresponding algorithm (OMC3). To evaluate the performance of OMC2 and OMC3, we conduct 10-fold cross-validation and  The development of new drugs is extremely time-consuming and expensive . It is ret al. constructed a heterogenous graph between drug and target and proposed the HGBI (Heterogeneous Graph Based Inference) algorithm to predict potential drug–target interactions Reviewer's Responses to QuestionsComments to the Authors:Please note here if the review is uploaded as an attachment.Reviewer #1: This paper formulates computational drug repositioning problem based on matrix completion. An overlap matrix completion method is proposed to predict the potential drug-associated indications by integrating reliable drug-related and disease-related information in bilayer and tri-layer networks. Experimental studies on three different datasets show that the proposed approach can outperform several baseline methods, especially in tri-layer networks.1. When I take a look at case studies, only three drugs are used as examples. In order to give more references for medical researchers, the predicted top-30 indications of each drug need to be listed in the supplementary file.2. Could MBiRW algorithm be used for comparison in tri-layer networks? Please clarify it.3. The first letter of 'hyperplastic' should be capitalized in Table 2.4. There are some writing and grammatical errors in the manuscript. The author should examine and revise the article carefully.5. The quality of pictures in the manuscript need to be improved.6．Drug combination can be regarded as a new way of drug repositioning. Could you give some discussions whether your method could be used for synergistic drug combination prediction in the future (PMID: 27415801 should be discussed)? In addition, could you consider the possibility of developing computational models for drug repositioning based on drug related miRNA, a new kind of drug target? Some important studies should be discussed (PMIDs: 30325405 and 29943160).7. Please analyze the novelty and limitations of the method in the section of Conclusions.Reviewer #2: This manuscript proposed a new method, namely the overlap matrix completion (OMP) method, to find potential drug-associated relationship. Numerical results show that the new algorithm can achieve accurate results with high efficiency. This is a well-written and well-organized work to address an important issue in computational biology.Major issue:The computation to find the optimal values of alpha, beta and K may not be optimal. First the samples are not evenly distributed, for example, alpha \\in . It may be possible the optimal value is actually around 2 or around 5. In addition, the work first fixed K=1 and found the optimal value of alpha=1, beta=10. Then based on alpha=1, beta=10, found the optimal value was K=10. The question is, if K=10, what is the optimal values of alpha and beta? Is there any possibility to develop an iterated scheme to search for the optimal values?Minor issueThere are many curves in each figure, and 11 figures in this work. It may be better to put some figures in supplementary information and show the remaining figures in larger size.**********Have all data underlying the figures and results presented in the manuscript been provided?PLOS Computational Biologydata availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.Large-scale datasets should be made available via a public repository as described in the Reviewer #1: YesReviewer #2: Yes**********what does this mean?). If published, this will include your full peer review and any attached files.PLOS authors have the option to publish the peer review history of their article .One of the goals of PLOS is to make science accessible to educators and the public. PLOS staff issue occasional press releases and make early versions of PLOS Computational Biology articles available to science writers and journalists. PLOS staff also collaborate with Communication and Public Information Offices and would be happy to work with the relevant people at your institution or funding agency. If your institution or funding agency is interested in promoting your findings, please ask them to coordinate their releases with PLOS . If published, this will include your full peer review and any attached files.PLOS authors have the option to publish the peer review history of their article  1223-442824 | ploscompbiol.org | @PLOSCompBiolPLOS Computational Biology | Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom


With more than 71 million people chronically infected, hepatitis C virus (HCV) is one of the leading causes of liver disease and hepatocellular carcinoma. While efficient antiviral therapies have entered clinical standard of care, the development of a protective vaccine is still elusive. Recent studies have shown that the HCV life cycle is closely linked to lipid metabolism. HCV virions associate with hepatocyte-derived lipoproteins to form infectious hybrid particles that have been termed lipo-viro-particles. The close association with lipoproteins is not only critical for virus entry and assembly but also plays an important role during viral pathogenesis and for viral evasion from neutralizing antibodies. In this review, we summarize recent findings on the functional role of apolipoproteins for HCV entry and assembly. Furthermore, we highlight the impact of HCV–apolipoprotein interactions for evasion from neutralizing antibodies and discuss the consequences for antiviral therapy and vaccine design. Understanding these interactions offers novel strategies for the development of an urgently needed protective vaccine. With more than 71 million people chronically infected , hepatitDespite the combined efforts of the HCV research community, HCV vaccine design has been hampered by the ability of HCV to rapidly mutate and escape from protective immune responses . This isFlaviviridae family. The viral particle consists of a nucleocapsid containing the viral RNA surrounded by an endoplasmic reticulum (ER)-derived envelope in which viral E1 and E2 glycoproteins are embedded as heterodimers  they stabilize the lipoprotein structure and solubilize the lipid fraction, (ii) they interact with lipoprotein receptors and participate in lipoprotein clearance, and (iii) they act as cofactors for specific enzymes involved in lipoprotein metabolism , 21 Tab. The rolThe initiation of HCV entry is triggered by LVP binding to cell surface heparan sulfate proteoglycans (HSPGs). Interestingly, it was demonstrated that ApoE plays a role in this process by interacting with syndecan 1 and syndecan 4 HSPGs –27. OtheLipo-viro-particle entry into hepatocytes is also influenced by changes in lipoprotein composition. One of the best examples is the action of the lipoprotein lipase (LPL) on lipoprotein-associated triglycerides. By hydrolyzing triglycerides, LPL decreases the size of the particles and induces a loss of LVP-associated ApoE. The loss of ApoE results in a strong decrease in LVP infectivity , 37. ConAPOB and APOE, the Matsuura group revealed that ApoB and ApoE redundantly participate in the formation of infectious HCV particles  are strictly ApoE dependent, regardless of ApoE isoforms. Indeed, the three main ApoE isoforms, ApoE3, ApoE2, and ApoE4, differing at only two amino acid positions (residues 112 and/or 158) seem to complement HCV production to a comparable degree.The molecular mechanism by which ApoE associates with HCV particles was recently highlighted. Indeed, ApoE was found to interact with the viral protein NS5A through its C-terminal α-helix domain , 54. FurClinical evidence indicates that chronic HCV infection is associated with dysregulated circulating lipoproteins and apolipoproteins within the HCV-infected hepatocytes. HCV infection induces the accumulation of lipoproteins and apolipoproteins by upregulation of genes involved in lipid synthesis , 62. DisHepatitis C virus infection appears to disturb serum apolipoprotein levels depending on the genotype of the virus. Seki et al. reported that infection with genotype 1b was associated with elevated serum levels of ApoA-II and ApoE and reduced levels of ApoC-II and ApoC-III. By contrast, genotype 2 infection only reduced ApoC-II and ApoC-III serum levels. In infected patients, a reduction in ApoC-II and ApoC-III serum levels may enhance HCV infection. In particular, low ApoC-II serum levels were found to be associated with advanced liver fibrosis, which indicate an important role in liver pathogenesis . A similFinally, it has been observed that single-nucleotide polymorphisms (SNPs) in apolipoproteins are associated with HCV infection and alteration of lipid metabolism. Two studies reported that SNP rs12979860 near the IL28B gene, which encodes for interferon-λ-3, is associated with the response to IFN treatment , 67. A fNeutralizing antibodies to HCV are mainly directed at the E2 glycoprotein with a wide range of specificity and degree of conservation. The majority of broadly neutralizing antibodies mediate neutralization by blocking virus binding to CD81, a tetraspanin HCV co-receptor . Fine epThe N-terminal region of E2 (amino acid 384–410) is hypervariable and some antibodies to this region, designated as HVR1, do mediate virus neutralization. These antibodies are directed at epitopes located at the C-terminal portion of HVR1 that includes key residues that are also found to be involved in the initial attachment step of virus entry to heparan sulfate and subsequent interaction with SR-BI –76. WhilWith about 75–80% of all HCV infections progressing to chronic disease, it is clear that evasion from the neutralizing antibody response is a key feature of HCV: although patients during the chronic phase often have high levels of serum neutralizing antibodies, in most cases, the immune system is not able to control the infection. A potential determinant for viral escape is the close association of HCV with lipid metabolism .Early indications that HCV-lipoprotein interactions are involved in viral escape from the neutralizing antibody response stem from reinfection experiments in chimpanzees, where infection could only be transmitted by low-density fractions of serum-derived HCV .A very similar effect was observed in virus derived from humanized mice: those particles displayed lower density and higher infectivity than cell culture-derived viruses. However, this effect was lost after a single passage in cell culture, indicating the responsibility of host-derived factors . Indeed,The development of cell culture-derived HCV (HCVcc) that displays a similar lipid composition as native serum-derived HCV particles allowed for a more detailed analysis of the involved mechanism. Immature intracellular HCVcc that are characterized by a lower lipoprotein content, when compared with released HCVcc were more sensitive to neutralization by anti-E2 antibodies and less sensitive to anti-ApoE antibodies than mature HCVcc , indicatA recent publication showed that ApoE levels in HCV-producing cells directly determined the ability of HCV to evade the neutralizing antibody response . VirusesIt has been shown that lipoproteins attenuated antibody binding to HCVpp and HCVcc by augmenting virus entry in an SR-BI-dependent fashion . HDL actIn addition, apolipoproteins might not only be involved in the escape from adaptive immune responses. Experimental evidence suggests that ApoE3 also mediates escape from the innate effector molecule Ficolin-2 that blocks HCV entry at an early time point during infection . ApoE3 iTaken together, apolipoproteins contribute to viral escape by two different mechanisms. Association of HCV particles with lipid components in LVPs directly inhibits neutralization by anti-envelope antibodies. In addition, interaction with apolipoproteins enhances viral entry, which limits the exposure of the virus to neutralizing antibodies. Understanding the mechanisms by which HCV usurps apolipoproteins for viral escape might offer new strategies for antiviral intervention and could pave the way toward the development of a protective vaccine.The close association of HCV with the host lipid metabolism has several important implications for HCV treatment and vaccine design. Modulation of the apolipoprotein–HCV interaction may open new opportunities for antiviral therapies and vaccines: targeting the interaction sites of apolipoproteins and viral envelope proteins could be an approach to block HCV infection and at the same time to restrict its capacity to evade from the neutralizing antibody response. In particular, viral variants isolated from patients undergoing liver transplantation are characterized by efficient viral escape , 90, whiAnother promising approach might be the development of monoclonal antibodies targeting E1 since the shielding function of apolipoproteins was primarily directed against epitopes located on the envelope protein E2. Finally, a detailed understanding of the HCV–lipoprotein–antibody interactions may help to design immunogens inducing broadly neutralizing antibodies for protection of infection and may guide the way toward the development of a protective HCV vaccine.All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Non-perforated ballistic impacts were conducted on the two types of panels under the same level of impact energy. Post-mortem examination on the non-perforated panels was conducted through the cross-sectional images, planar projected delamination and 3D damage volume extracted from the non-destructive tests. Three distinctive sections of damage were segmented from the non-perforated panels, each indicating different material failure modes upon impact. Under the same areal density, the coarser composite panel P10B with a larger ply areal density and fewer reinforcement plies would result in less damage. The damage volume of P10B is nearly one-third that of the P17C. The findings are instructive for the design of 3D woven fabric continuously reinforced composites with doubly-curved shapes.This paper studied the ballistic performance of 3D woven angle-interlock fabric reinforced composites with different types of panel construction. Two types of composites P10B and P17C were designed to have the same areal density of around 12 kg/m The high-performance fibre reinforced textile composites have applications in an increasingly wider range of areas, including impact protective equipment. Ballistic impacts on composites result in localised deformation at the impact location and the composite materials fracture to absorb this impact energy. As a result, damages in forms of fibre breakage, matrix cracks, delamination between plies and indentation are often found. Due to the limitations imposed by the thickness of the conventional 2D reinforcing fabrics and the unidirectionally-laid fibre tows, the multiply reinforcing construction must be adopted in the making of advanced composites. The resin bonded multiple fabric layers within a composite panel allow for the development of delamination damage. Boussu  proposed®/epoxy composites both improved when the matrix was toughened with the multi-walled carbon nanotube. Hosur et al. The ballistic performance of the composite panels was examined on a ballistic range, as illustrated in m is the mass of the projectile in grams, iv and rv are the impact and residual velocities of the projectile, respectively. For non-perforated tests, the energy absorption EA is regarded as being equal to the impact kinetic energy carried by the projectile initially as the projectile residual velocity is zero. The ballistic performance of the composite targets can be evaluated by the energy absorption (EA), which can be worked out based on Equation (1):After this, the ballistic impacted composites were subjected to non-destructive post-mortem examinations for their damage morphology. The planar damage areas, cross-sectional distribution and the 3D damage volumes were extracted by through transmission ultrasonic C-scan and X-ray computed tomography. 2. The damage area can then be worked out by counting the number of pixels based on the grey scale differences. The C-scan was conducted on a Midas NDT C-scan system with Zeus software used for image processing. The projections of damage from each reinforcement ply were superimposed into a planar damage distribution. The scan resolution is 72 × 72 pixels per inch®/epoxy composite panels, the presence of steep edges in the projectile contour leads to dramatic changes in the number of X-rays transmitted and absorbed around the projectile. Hence, streaking and aliasing artefacts were noticed around the edges of the projectile This paper presents an experimental study examining the effects of panel construction on the ballistic performance of multiply 3D TTAI fabric reinforced composites. Two types of composites reinforced by TTAI with different ply areal densities and number of plies were compared for their ballistic damage morphology under the same panel areal density. Non-destructive testing methods of through transmission ultrasonic C-scan and X-ray CT were adopted for the damage evaluation. We found that the P10B reinforced by 10-ply heavier TTAI had better overall ballistic performance than that of the P17C. The penetration percentage, indentation, planar distribution and volume of delamination of P10B were all smaller than P17C. All these findings indicate that the use of reinforcements with a greater ply areal density and smaller number of reinforcement plies would result in less damage. Three distinctive damage sections through the thickness of the impacted panels were noticed. The differences in failure modes within different sections is important for the design of multiply fabric reinforced hybrid ballistic composites accordingly. With TTAI fabrics being highly mouldable over doubly-curved parts, the study presented would guide the design of multiply TTAI continuously reinforced composites for ballistic protection.


Aging and disease-related changes in the arteriovasculature have been linked to elevated levels of cardiac cycle-induced pulsatility in the cerebral microcirculation. Functional magnetic resonance imaging (fMRI), acquired fast enough to unalias the cardiac frequency contributions, can be used to study these physiological signals in the brain. Here, we propose an iterative dual regression analysis in the frequency domain to model single voxel power spectra of echo planar imaging (EPI) data using external recordings of the cardiac and respiratory cycles as input. We further show that a data-driven variant, without external physiological traces, produces comparable results. We use this framework to map and quantify cardiac and respiratory contributions in healthy aging. We found a significant increase in the spatial extent of cardiac modulated white matter voxels with age, whereas the overall strength of cardiac-related EPI power did not show an age effect. •We present a dual regression method to model power spectra of ultra-fast EPI data to map and quantify physiological contributions.•The method was used to study cardiac and respiratory contributions to the EPI data in healthy aging.•We found a significant increase in the spatial extent of cardiac modulated voxels in white matter with age.•The strength of cardiac-related EPI power did not show an age effect. Blood-oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI), in particular echo planar imaging (EPI), has traditionally been used to study neuronal activity in the resting state (rs-fMRI) or whilst performing a task. The fMRI time series is a composite of neurovascular and additional noise contributions, the latter of which are often regarded as unwanted and are removed from the data in post processing   data do not exactly resemble the cardiac cycle-induced power spectra in the brain. Even within the brain, in particular between different tissues, we expect differences in the physiologically-related EPI power contributions. To approach the “true” cardio-respiratory spectra in each tissue we ran an iterative dual regression, where the externally measured physiological spectra serve as the initial “guess”. Additionally, we explore a data-driven dual regression approach that solely recreates the cardio-respiratory spectra from the EPI time series data themselves.PET-CO2) , bulk moPET-CO2) . Above tPET-CO2)  as well We then use this framework to test if the cardiac contributions to the EPI power spectrum show an age effect in healthy adults. Specifically, we compare the strength and spatial extent of those contributions in normal ageing.P of this signal is calculated as the amplitude of its Fourier-transform (FT)N is the total number of sampled time points. Let We normalise each voxel's power spectrum between the lower cut-off frequency of 0.2 Hz and α value than a voxel with physiological signals. Similarly, two voxels with identical respiratory-related fluctuations but different levels of cardiac-related signal variations will not only differ in As such the PEs are inter-dependent. A voxel with no significant cardio-respiratory fluctuations will have a higher baseline 1.Run a GLM according to the model in Eq. 2.1. Written out explicitly this isSeparate the resulting 3.Iterate over steps 1 and 2 using the refined spectra from step 2 until a convergence criterion is met.4.The final outputs are the refined spectra and associated refined spatial mapsThe principle of dual regression has been introduced by Beckmann et al. and Filippini et al  in the cData-driven reconstruction of physiologically-induced fMRI signal components is a common approach in physiological noise cleaning methods  using a 1 channel Tx/32 channel Rx head coil  under institutional ethics approval. Subjects were recruited from an existing volunteer pool. When included into this pool, each volunteer received an initial brain MRI at 3T comprising at least a 3D T1-weighted scan and a FLAIR scan, which were screened for accidental findings by an experienced physician. Additional exclusion criteria were any form of known neurological condition and hypertension. Subjects had their blood pressure measured on the day of the scan to confirm their systolic pressure to be below 140 mmHg, which we used as the upper limit for normal blood pressure. Physiological traces were recorded at 1 kHz throughout the scans using a respiratory pad and a pulse-ox that was attached to the index finger . The traces were later sub-sampled to the TR of the rs-fMRI scan.21 subjects, between the ages of 19 and 77, were scanned on a 7T whole-body scanner  maps for tissue segmentation  to perform the subsequent analysis.We calculated the average PE-values in each subject and tissue. To ensure that we only calculate the average from voxels that indeed show significant modulation by the cardiac cycle and respiration we thresholded PE maps at a maximum p-value of 0.01. To account for age-related differences in partial volume effects we included a voxel-wise PVE weighting in the calculation of the PE averages. Putting this together, the tissue-specific average PE was calculated asWe further calculated the spatial extent, defined as the ratio of significantly modulated tissue mask volume to total tissue mask volumeapplywarp and maps were subsequently averaged.We ran partial correlations between age and For a comparison with the previous literature we calculated the cardiac pulsatility metric as proposed by One subject (65 years old) exhibited multiple absolute head displacements of about the voxel dimension (3 mm) during the scan and was therefore excluded from the results.We found a significant increase of the spatial extent of the cardiac cycle-induced fluctuations, Initial analysis suggested a decrease of the mean cardiac PE We did not find any age effect for the respiratory component. Any correlation between the The results of the cardiac pulsatility metric, when calculated from voxels in a tissue mask, showed an increase in cardiac pulsatility in white matter with age (2 fluctuations that alter blood flow velocities and modify the haemodynamic BOLD response, thoracic pressure changes that influence venous return flow velocities and further bulk motion. Another explanation for the variability observed is high-frequency resting-state network activity above 0.1 Hz (The GLM approach allows the identification of voxels with significant power contributions from physiological sources and the disentanglement of the high frequency spectrum into its thermal noise, cardiac and respiratory-related contributions. The iterative dual regression further refines this analysis and can be used to create tissue-specific cardiac and respiratory power spectra. Indeed, we found that these tissue-specific cardiac spectra differ substantially from the external pulse-ox spectrum. Specifically, we found that the dominant cardiac frequency carries more power than the pulse-ox spectrum. Cardiac cycle-induced fluctuations in the EPI time series are caused by multiple mechanisms, from inflow effects, partial volume fluctuations to non-rigid brain motion . As suche 0.1 Hz .The broadband spectra offered enough degrees of freedom to reach comparable results for a data-driven dual regression. The data-driven cardiac spectrum had smaller power at the dominant frequencies, whereas the respiratory spectra were negligibly different. Spatial PE maps were in good agreement. The data-driven approach thus offers an alternative for this power spectrum analysis where external recordings are not available.Here, we only found a significant age effect in the white matter mask, with an increase in the spatial extent of cardiac cycle-related EPI signal fluctuations with age. The most prominent source of these signal fluctuations is the inflow effect of arterial blood, but further intra-voxel partial volume exchanges contribute to the signal pulsatility . The latWe further calculated the recently proposed cardiac pulsatility metric by We introduced an iterative dual regression methodology that maps and quantifies physiological contributions to the EPI spectrum. Using this analysis framework we found a spatial increase of cardiac cycle-induced power in white matter with age. Changes in cardiac pulsatility in white matter with healthy aging, small vessel disease and Alzheimer's disease have been suggested in the literature. However, the number of reports is small, and here we only studied a small number of subjects. The data-driven dual regression approach might offer the ability to apply similar analysis on already existing fast rs-fMRI data sets, even when external physiological recordings are missing.


Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt and cheese. We report here the complete genome sequence of the industrial strain S. thermophilus N4L, which is used in dairy technology for its fast-acidifying phenotype. Streptococcus thermophilus is one of the most used dairy starters for the production of yogurt and cheese. We report here the complete genome sequence of the industrial strain S. thermophilus N4L, which is used in dairy technology for its fast-acidifying phenotype. Streptococcus thermophilus is a well-known lactic acid bacterium (LAB) widely used for the production of dairy products in association with other LAB species, such as Lactococcus lactis and Lactobacillus delbrueckii subsp. bulgaricus, for cheese and yogurt production, respectively. It belongs to the salivarius group and recently evolved from a commensal ancestor  was subjected to genomic DNA (gDNA) extraction using the GenElute bacterial gDNA kit  following the protocol indicated by the manufacturer. Its gDNA was then sequenced  on a PacBio RS II system  using single-molecule real-time (SMRT) sequencing technology .The complete genome sequence of


To explore the existing evidence of the real-world implementation of patient-reported outcomes (PROs) in oncology clinical practice and address two aims: (1) summarize available evidence of PRO use in clinical practice using a framework based on the International Society for Quality of Life Research (ISOQOL) PRO Implementation Guide; and (2) describe reports of real-world, standardized PRO administration in oncology conducted outside of scope of a research study.A Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol was developed to guide the systematic literature review (SLR) that was conducted in MEDLINE and Embase databases. A two step search strategy was implemented including two searches based on previously completed reviews. Studies published from 2006 to 2017 were synthesized using a framework based on the ISOQOL PRO Implementation Guide.n = 10, 28%); use of 38 other PRO measures was also reported. Only three studies (8%) reported real-world PRO implementation.After screening 4427 abstracts, 36 studies met the eligibility criteria. Most elements of the ISOQOL PRO Implementation Guide were followed. Two notable exceptions were found: 1) providing PRO score interpretation guidelines (39% of studies); and 2) providing patient-management guidance for addressing issues identified by PROs (25% of studies). Of the 22 studies with an intervention component, 19 (86%) reported intervention effects on study outcomes. The European Organisation for Research and Treatment of Cancer Quality-of-Life Questionnaire-Core 30 (EORTC QLQ-C30) was the most commonly used PRO (Reports of real-world PRO implementation are limited. Reports from studies conducted in clinical settings suggest gaps in information on PRO score interpretation and the use of PRO results to inform patient management. Before the promise of practice-based PRO assessment in oncology can be truly realized, investigators need to advance the state-of-the-art of real-time PRO score interpretation as well as developing guidance on how to use PRO insights to drive clinically-meaningful patient-management strategies. There has been growing interest in the assessment of patient-reported outcomes (PROs) over the last 40 years, and the use of PROs in clinical and health services research is common . PROs haMore recently, routine use of PROs in oncology practice has been identified as a priority area by the President’s Cancer Panel  as well The interest in implementation of PROs specifically in oncology care is exemplified by the number of recent reviews on PRO clinical applications and their impact on health outcomes –34. All The objective of this systematic literature review (SLR) was to explore and summarize the existing evidence of PRO use in oncology clinical practice. We address two key aims in the review: (1) summarize available evidence of PRO use in clinical practice using a framework based on the ISOQOL PRO Implementation Guide ; (2) desWe conducted a SLR in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines , 40. TheThe literature search was conducted in two databases: MEDLINE and Embase. Blocks of medical subject heading (MeSH) terms were used to identify the most relevant articles and conference papers that describe PRO implementation in oncology clinical practice.The SLR search strategy was developed in consultation with a professional librarian and used a two-step approach for identifying studies. The first step included a search strategy and approach based on a previously published systematic review of use of PROs in oncology care . As partArticles were included in the review if they met the following inclusion criteria: (1) cancer focus; (2) articles published in the past 10 years from 2006 to 2016 (inclusive) and abstracts from meetings held in 2015–2016 to ensure review of the current state of the field; (3) published in English; (4) title, abstract, or article contained information pertaining to the measurement of treatment satisfaction, process of care, treatment adherence, treatment decision-making, patient activation, PROs of health-related quality of life (HRQoL), symptoms, or function; and (5) the study design was a randomized controlled trial or an observational study in a clinical-practice setting or a report of PRO implementation in clinical practice.Exclusion criteria were: (1) articles focused on non-cancer populations; (2) measures did not pertain to clinical outcomes or PROs associated with cancer treatment; (3) basic science studies ; (4) study designs not relevant including study protocols, case studies, case reports, case series, editorials, reviews, commentary, news, or study protocols; and (5) non-English language.All abstracts were reviewed using DistillerSR® —a systemWe used the ISOQOL PRO Implementation Guide  as the bn = 16, 44%) followed by the United Kingdom (UK) , Germany , Canada , The Netherlands , other individual European Union (EU) countries , and Australia .As shown in the PRISMA diagram Fig. , a totaln = 19, 58%), feasibility research , combination intervention and feasibility , real-world implementation reports ; and an intervention for quality improvement  We initially summarized findings related to design considerations of PRO integration in clinical practice within the specified ISOQOL categories  followed by evidence in categories related to reporting and use of PRO results . Table Data from all 36 reports of PRO measures used in clinical settings were summarized according to the ISOQOL PRO Implementation Guide Framework . .Public n = 10, 8%, combin = 13, 36%), improving quality of care , enhancing patient-provider communication , and delivering patient-centered care  . Most studies were conducted with adult populations (94%) in outpatient settings (92%). PROs were administered most often at the clinic immediately before seeing the doctor (36%) or during a visit (33%). The type of cancer patient varied with a majority of studies including three or more cancer types (69%), and only seven studies (19%) with a single cancer type.n = 15, 42%) or cancer-specific HRQoL  outcomes. The most widely-used measure was the EORTC QLQ-C30  followed by the Hamilton Anxiety and Depression Scale (HADS) .A total of 46 PRO measures were used across the 36 studies; 33 of the PRO measures were rarely used and were included in only one or two studies suggesting wide variability in measures used. Studies predominantly reported measuring symptoms  followed by paper-and-pencil . Two studies used interactive voice response (IVR) .All but one of the studies reported the mode of PRO administration. Electronic administration was the most common mode  or a printed copy of PRO results  while e-mails/telephones  were used less often. Results were most often presented only to the clinical team ; only three studies (11%) presented the PRO results to both the clinician and the patient, and one study presented results to patients only.The summary of information on PRO results indicated that the preferred format of results presentation was an electronic summary report  failed to report information on how to interpret PRO scores. Eleven studies (31%) provided PRO scores alone with no interpretation guidance, and six articles (17%) did not report any information on PRO score interpretation. Fifteen studies (42%) provided scores in the form of a graphical display which may aid in score interpretation. About half of the papers reviewed  reported PRO scores along with some information on threshold values, cut-off scores, or severity levels. Only three studies (8%) provided reference groups or norms information for the selected PRO.A large proportion of studies  with single studies also suggesting specialist referrals, reporting adverse events (AEs), and/or providing educational materials to patients.The majority of studies did not provide any instructions on follow-up steps when PRO scores raised areas of concern. In 13 studies (36%), no instructions were given on next steps or patient-management action items based on PRO results; eight studies (22%) did not include sufficient information on whether PRO results were addressed. The plans for addressing issues identified by the PROs were often related to discussing the identified issues with the provider (n = 13) and patient-provider communication (n = 8) (Table Only 19 studies (53%) included results of PRO intervention on patient outcomes. The outcomes for which most studies reported evidence of PRO intervention effect included patient reported symptoms, functioining or quality of life scores (8) Table . Eleven 8) Table .Table 4IOur review identified only three reports of real-world implementation of PRO measures in clinical practice which we defined as the ongoing administration of a standardized PRO and related clinical actions to manage patient care in routine clinical practice beyond the scope of a specific research study.The first study  used retTrautmann and colleagues  describeThe authors acknowledged a number of obstacles in the study—even though there was an increased number of patients recruited, the usage of PROs in the patient-physician interaction was limited due to physician turnover and lack of completion time provided to patient prior to consultation. The authors concluded that PRO assessments should be more carefully selected to be more clearly of benefit to the health care provider and patient. Additionally, sustaining the implementation and interpretation of PROs should be constantly reinforced with clinicians .Wagner and colleagues  assessedIn order to be able to follow the ISOQOL PRO Implementation Guide, researchers need to have a body of evidence to guide choices on recommended categories.The first aim of our review was to examine existing information on recommended implementation based on published information from oncology clinical settings. While no studies in our review directly referenced the ISOQOL PRO Implementation Guide , publicaMost studies adequately described the planned goal for PRO data collection, study setting, and selection of PRO and mode of administration. Electronic administration, which allows for flexible integration of PROs in clinical care, was used by the majority of studies, but most were not formally integrated into the electronic health record. In addition, formal integration into the EHR may require intensive resources and stakeholder buy-in that have been lacking perhaps due to limited evidence of the improvement in patient outcomes or lack of financial alignment (or incentives).While the EORTC QLQ-C30 was the most commonly-used measure across studies, a wide variety of PRO measures was reported suggesting there is little consensus on core domains or the “best” PRO to use or consideration whether a measure is developed for clinical trial or clinical practice use. Such variability may be an implementation barrier for PROs in everyday oncology practice—the burden to individual organizations associated with selecting PRO measures, developing assessment guidelines for the selected PROs, and interpreting PRO results may discourage adoption in routine clinical care.The main gap in evidence identified by this review was the sparsity of interpretation guidelines for PRO results provided to care providers. While most of the reviewed studies provided PRO scores, fewer added interpretation guidelines to these scores or provided follow-up instructions or procedures in case a problem was identified by the PRO. This is an important gap. Without clarity on the meaning, significance, and interpretation of collected PRO data, how can clinical actions be effected to result in improved health care processes and outcomes?Based on the review of the published literature, the use of PRO measures in routine cancer clinical practice outside the context of feasibility or research intervention studies is seldom reported. Only three reports of routine implementation of PROs in clinical settings were identified by the current review and provided limited information for our first key aim The multi-stage process that is required for developing, introducing, testing, integrating, and monitoring PROs in EHR systems has been achieved in only a few US medical centers . NumerouWhile our review suggests that PRO implementation in real-world settings outside of research context is scarce, it is possible that PRO implementation in real-world oncology clinical practice may be underreported in the research literature. Implementation efforts may be viewed more as quality-improvement efforts that are building on existing evidence but not always viewed as generating evidence warranting dissemination . TherefoSome of our findings are consistent with the results from earlier literature reviews evaluating different aspects of PROs in the context of oncology care Table . We confThe strengths of this review include the compliance with PRISMA guidelines, development of a comprehensive two-step search strategy, and review of results in the context of a framework built on the ISOQOL PRO Implementation Guide . The resThe existing evidence of PRO implementation in real-world clinical care in the published literature is very limited. It is unclear whether implementation efforts are not being studied, not being reported in peer-reviewed journals, simply being published in the grey literature, or not taking place at all.While publication on PRO real-world implementation is uncommon, a good number of publications on PRO feasibility and/or PRO use in research in oncology clinical care exists as evidenced by our work and earlier literature reviews. This paper also aimed to organize findings of published studies in a framework informed by the ISOQOL PRO Implementation Guide . ResultsBased on the findings from our review, we offer two insights to help enable more widespread PRO implementation in routine clinical practice. First, adequate interpretation guidelines are needed for PRO results to be acted upon in clinical practice. Second, exploration should be conducted into how to best address issues raised by PRO results—particularly when the identified needs of patients extend beyond the expertise or training found in a routine oncology clinical practice such as depression or lack of social support. In the absence of available information on these key elements, implementation of PROs in clinical practice is unlikely to bridge the gap between perceived usefulness by researchers and routine uptake in oncology practice by clinicians.


The fact that structural RNA motifs can direct RNAs to fold and self-assemble into predictable pre-defined structures is an attractive quality and driving force for RNA’s use in nanotechnology. RNA’s recognized diversity concerning cellular and synthetically selected functionalities, however, help explain why it continues to draw attention for new nano-applications. Herein, we report the modification of a bifurcated reporter system based on the previously documented Spinach aptamer/DFHBI fluorophore pair that affords the ability to confirm the assembly of contiguous RNA strands within the context of the previously reported multi-stranded RNA nanoring. Exploration of the sequence space associated with the base pairs flanking the aptamer core demonstrate that fluorescent feedback can be optimized to minimize the fluorescence associated with partially-assembled RNA nanorings. Finally, we demonstrate that the aptamer-integrated nanoring is capable of assembling directly from transcribed DNA in one pot. RNA nanotechnology leverages the formation of programmable base pairs and regular three-dimensional folding patterns of structural RNA moieties to construct materials with precise, predefined shapes ,2,3,4,5.A promising strategy that has been developed to visualize RNA in recent years involves the use of light-up RNA aptamer/fluorophore pairs ,15,16,17Given its unique structure and demonstrated ability to be functionalized with a variety of RNA-based functional groups, we chose to integrate the split-Spinach aptamer into the previously reported RNA nanoring ,37. The taq DNA polymerase  via polymerase chain reaction (PCR), and isolated by a DNA purification kit . Transcription of amplified DNA was accomplished using T7 RNA polymerase  in vitro. The resulting transcripts were purified by polyacrylamide gel electrophoresis (PAGE) . Excised gel fragments containing RNA were placed in Crush and Soak buffer , shook overnight at 5 °C, and the RNA was isolated the next day via ethanol precipitation. The fluorophore, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), was synthesized as previously reported according the protocol of the Paige research group . Ge. Ge41]. After evaluating stem stabilities and linker contributions we identified several sequence combinations that provided at least a 10-fold increase in signal between the split-aptamer in the presence of all the ring components compared to split-aptamer strands incubated by themselves with the highest ratio reaching nearly a 20-fold fluorescence gain. Following these results we evaluated the ability for the split-aptamer system to distinguish between fully- and partially-assembled nanorings. Partially-assembled rings (composed of five out of the six nanoring struts) were expected to produce a higher fluorescent signal than the split-aptamer dimers alone because, like the fully-assembled nanorings, they provide a physical conduit for the split-aptamer strands to be brought together. Previous evaluation of the nanoring however showed that partially-assembled rings are not as thermodynamically stable as fully-assembled rings and so we postulated that the split-aptamer system should be able to show some level of discrimination between the two  In orderEvaluation of the partially-assembled rings revealed a number of interesting insights . In the A distinct advantage of RNA-based nanoparticles relates to their ability to self-assemble isothermally directly from their transcription via DNA templates ,18,43. T2) were used to compare the resulting RNA assemblies of the transcription mixture with an RNA ladder prepared via snap-cooled assembly of the corresponding nanoring. Native PAGE reveals that the fully-assembled nanorings constitute the primary assembly product  require careful testing. This suggests that full-scale automation of the design process remains elusive and that the design of new sytems will undoubtedly contain their own particular parameters which will also require their own experimental optimization. Simply put, the overall performance of variants is and remains context dependent and very difficult to predict. In this regard, even though in vitro studies provide a baseline for assessing the behavior of the a self-assembling nanoparticle/split-aptamer/fluorophore system, evaluation in increasingly complex environments remain necessary for validation and further refinenment. Modeling and design provide an essential starting point but due to myriad of parameters, experimental refinement remains absolutely necessity. Our work also shows that the destablization of stems surrounding the aptamer core generally provide increased sensitivity between fully- and partially assembled nanoparticles. The same is likely to be true for future developments with different nanoparticles—where the goal or purpose of nanoparticle assembly functions, at least in part, to restore and/or compensate the intentionally diminished stabilities of the altered stems.The split-aptamer/nanoparticle system demonstrates the ability, not only to monitor the assembly of multiple strands, but the ability to monitor the assembly of RNA strands not directly linked to the aptamer units. To our knowledge this is the first system developed that demonstrates the ability to detect the formation of tertiary interactions on contiguous strands of RNA. We demonstrate further that fluorescent signaling associated with fully-assembled nanorings can be maximized over the partially assembled split-aptamer system associated with two or five strand mixtures. Given its ability to assemble isothermally from DNA templates, we propose that the co-transcriptional assembly of the split-aptamer/nanoring system provides a robust platform for the further development of a variety of automated and/or high-throughput applications. The nanoring’s four other struts are readily functionalizable and because the nanoring’s helical struts can be increased a full helical turn to accommodate a larger interior space, it is possible that more complex aptamer systems may be able to be incorporated (such as the addition of secondary modular aptamer domain). Finally, fluorescent reporting of fully-formed nanorings provides instant feedback for the previously proposed automated assembly of therapeutic RNA nanoparticles .