gebhart/patrepeval huggingface dataset:
Spectral Reflectance Recovery from the Quadcolor Camera Signals Using the Interpolation and Weighted Principal Component Analysis Methods (2022)

The recovery of surface spectral reflectance using the quadcolor camera was numerically studied. Assume that the RGB channels of the quadcolor camera are the same as the Nikon D5100 tricolor camera. The spectral sensitivity of the fourth signal channel was tailored using a color filter. Munsell color chips were used as reflective surfaces. When the interpolation method or the weighted principal component analysis (wPCA) method is used to reconstruct spectra, using the quadcolor camera can effectively reduce the mean spectral error of the test samples compared to using the tricolor camera. Except for computation time, the interpolation method outperforms the wPCA method in spectrum reconstruction. A long-pass optical filter can be applied to the fourth channel for reducing the mean spectral error. A short-pass optical filter can be applied to the fourth channel for reducing the mean color difference, but the mean spectral error will be larger. Due to the small color difference, the quadcolor camera using an optimized short-pass filter may be suitable as an imaging colorimeter. It was found that an empirical design rule to keep the color difference small is to reduce the error in fitting the color-matching functions using the camera spectral sensitivity functions.
Non-Proteolytic Aeroallergens from Mites, Cat and Dog Exert Adjuvant-Like Activation of Bronchial Epithelial Cells (2010)

These results show that both mite and structurally unrelated cat and dog allergens can activate respiratory epithelial cells by adjuvant-like protease-independent mechanisms.
Quality Assessment of the Preanalytical Workflow in Liquid Biobanking: Taurine as a Serum-Specific Quality Indicator for Preanalytical Process Variations (2019)

The scientific impact of translational biomedical research largely depends on the availability of high-quality biomaterials. However, evidence-based and robust quality indicators (QIs) covering the most relevant preanalytical variations are still lacking. The aim of this study was to identify and validate a QI suitable for assessing time-to-centrifugation (TTC) delays in human liquid biospecimens originating from both healthy and diseased individuals. Serum and plasma samples with varying TTCs were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) in a pilot cohort of healthy individuals to identify a suitable QI candidate. Taurine (TAU), as a TTC QI candidate, was validated in healthy individuals and patients with rheumatologic and cardiologic diseases, considering the (1) preanalytical handling temperature, (2) platelet count, and (3) postcentrifugation delay. For discrimination of high TTC (TTC >60 minutes) from low TTC serum specimens, a probability calculation tool was developed (Triple-T-cutoff-model). TTC-dependent changes in healthy individuals were observed for amino acids, particularly TAU. Validation of the TAU levels in an independent cohort of healthy individuals revealed a time-dependent increase in serum, but not in plasma, for a TTC delay of 30-240 minutes. TAU increases were dependent on the handling temperature and platelet count and volume. By contrast, no changes in TAU concentrations were observed for additional postcentrifugation delays. Validation of TAU and the Triple-T-cutoff-model, in rheumatologic/cardiologic patient collectives, allowed the discrimination of samples with TTC ≤60 min/>60 min with estimated AUROC (area under the receiver operating characteristic curve) values of 89% [78%-100%]/86% [71%-100%] and 91% [79%-100%]/84% [68%-100%], respectively. Considering the preanalytical handling temperature and platelet count and volume, TAU and the Triple-T-cutoff-model represent reliable QIs for TTC >60 minutes in serum samples from healthy individuals and selected rheumatologic/cardiologic patients. However, further studies in larger patient collectives with various diseases are needed to assess the robustness and potential of the QIs presented in this article as biobanking quality assurance/quality control tools to support high-quality biomedical research.
A White Matter Connection of Schizophrenia and Alzheimer’s Disease (2020)

Schizophrenia (SZ) is a severe psychiatric illness associated with an elevated risk for developing Alzheimer's disease (AD). Both SZ and AD have white matter abnormalities and cognitive deficits as core disease features. We hypothesized that aging in SZ patients may be associated with the development of cerebral white matter deficit patterns similar to those observed in AD. We identified and replicated aging-related increases in the similarity between white matter deficit patterns in patients with SZ and AD. The white matter "regional vulnerability index" (RVI) for AD was significantly higher in SZ patients compared with healthy controls in both the independent discovery (Cohen's d = 0.44, P = 1·10-5, N = 173 patients/230 control) and replication (Cohen's d = 0.78, P = 9·10-7, N = 122 patients/64 controls) samples. The degree of overlap with the AD deficit pattern was significantly correlated with age in patients (r = .21 and .29, P < .01 in discovery and replication cohorts, respectively) but not in controls. Elevated RVI-AD was significantly associated with cognitive measures in both SZ and AD. Disease and cognitive specificities were also tested in patients with mild cognitive impairment and showed intermediate overlap. SZ and AD have diverse etiologies and clinical courses; our findings suggest that white matter deficits may represent a key intersecting point for these 2 otherwise distinct diseases. Identifying mechanisms underlying this white matter deficit pattern may yield preventative and treatment targets for cognitive deficits in both SZ and AD patients.
A Customized Gene Expression Microarray Reveals That the Brittle Stem Phenotypefs2of Barley Is Attributable to a Retroelement in theHvCesA4Cellulose Synthase Gene (2010)

Abstract The barley (Hordeum vulgare) brittle stem mutants, fs2, designated X054 and M245, have reduced levels of crystalline cellulose compared with their parental lines Ohichi and Shiroseto. A custom-designed microarray, based on long oligonucleotide technology and including genes involved in cell wall metabolism, revealed that transcript levels of very few genes were altered in the elongation zone of stem internodes, but these included a marked decrease in mRNA for the HvCesA4 cellulose synthase gene of both mutants. In contrast, the abundance of several hundred transcripts changed in the upper, maturation zones of stem internodes, which presumably reflected pleiotropic responses to a weakened cell wall that resulted from the primary genetic lesion. Sequencing of the HvCesA4 genes revealed the presence of a 964-bp solo long terminal repeat of a Copia-like retroelement in the first intron of the HvCesA4 genes of both mutant lines. The retroelement appears to interfere with transcription of the HvCesA4 gene or with processing of the mRNA, and this is likely to account for the lower crystalline cellulose content and lower stem strength of the mutants. The HvCesA4 gene maps to a position on chromosome 1H of barley that coincides with the previously reported position of fs2.
Polymorphism in Benzene-1,3,5-tricarboxamide Supramolecular Assemblies in Water: A Subtle Trade-off between Structure and Dynamics (2018)

In biology, polymorphism is a well-known phenomenon by which a discrete biomacromolecule can adopt multiple specific conformations in response to its environment. The controlled incorporation of polymorphism into noncovalent aqueous assemblies of synthetic small molecules is an important step toward the development of bioinspired responsive materials. Herein, we report on a family of carboxylic acid functionalized water-soluble benzene-1,3,5-tricarboxamides (BTAs) that self-assemble in water to form one-dimensional fibers, membranes, and hollow nanotubes. Interestingly, one of the BTAs with the optimized position of the carboxylic group in the hydrophobic domain yields nanotubes that undergo reversible temperature-dependent dynamic reorganizations. SAXS and Cryo-TEM data show the formation of elongated, well-ordered nanotubes at elevated temperatures. At these temperatures, increased dynamics, as measured by hydrogen-deuterium exchange, provide enough flexibility to the system to form well-defined nanotube structures with apparently defect-free tube walls. Without this flexibility, the assemblies are frozen into a variety of structures that are very similar at the supramolecular level, but less defined at the mesoscopic level.
Damping Flexure Mechanisms Using Low-Density, Low-Wave-Speed Media (2005)

Lightly damped poles and zeros in the response of flexure-based servomechanisms often limit their dynamic performance. In this paper, we measure the frequency response of a single-and a double-parallelogram flexure stage coupled to low-density, low-wave-speed foams in various configurations, and find that addition of the foam yields relatively high damping of in-plane, out-of-plane, and higher-order resonances. At frequencies high enough for waves to propagate into the foam, strong interactions between the foam and flexure structure occur, giving rise to a great deal of damping. This is a promising method for improvement of the dynamic performance of positioning and constraint systems that employ flexures.
A new concept for isotope ratio monitoring liquid chromatography/mass spectrometry (2004)

A new interface for the on-line coupling of a liquid chromatograph to a stable isotope ratio mass spectrometer has been developed and tested. The interface is usable for (13)C/(12)C determination of organic compounds, allowing measurement of small changes in (13)C abundance in individual analyte species. All of the carbon in each analyte is quantitatively converted into CO(2) while the analyte is still dissolved in the aqueous liquid phase. This is accomplished by an oxidizing agent such as ammonium peroxodisulfate. The CO(2) is separated from the liquid phase and transferred to the mass spectrometer. It is shown that the whole integrated process does not introduce isotope fractionation. The measured carbon isotope ratios are accurate and reproducible. The sensitivity of the complete system allows isotope ratio determination down to 400 ng of compound on-column. By-passing the high-performance liquid chromatography (HPLC) separation allows bulk isotopic analysis with substantially lower sample amounts than those required by conventional elemental analyzers. The results of the first applications to amino acids, carbohydrates, and drugs, eluted from various types of HPLC columns, are presented. The wide range of chromatographic methods enables the analysis of compounds never before amenable to isotope ratio mass spectrometry techniques and may lead to the development of many new assays.
Selective randomized load balancing and mesh networks with changing demands (2006)

We consider the problem of building cost-effective networks that are robust to dynamic changes in demand patterns. We compare several architectures using demand-oblivious routing strategies. Traditional approaches include single-hop architectures based on a (static or dynamic) circuit-switched core infrastructure and multihop (packet-switched) architectures based on point-to-point circuits in the core. To address demand uncertainty, we seek minimum cost networks that can carry the class of hose demand matrices. Apart from shortest-path routing, Valiant's randomized load balancing (RLB), and virtual private network (VPN) tree routing, we propose a third, highly attractive approach: selective randomized load balancing (SRLB). This is a blend of dual-hop hub routing and randomized load balancing that combines the advantages of both architectures in terms of network cost, delay, and delay jitter. In particular, we give empirical analyses for the cost (in terms of transport and switching equipment) for the discussed architectures, based on three representative carrier networks. Of these three networks, SRLB maintains the resilience properties of RLB while achieving significant cost reduction over all other architectures, including RLB and multihop Internet protocol/multiprotocol label switching (IP/MPLS) networks using VPN-tree routing.
Subjective Assessment of High Dynamic Range Videos Under Different Ambient Conditions (2022)

High Dynamic Range (HDR) videos can represent a much greater range of brightness and color than Standard Dynamic Range (SDR) videos and are rapidly becoming an industry standard. HDR videos have more challenging capture, transmission, and display requirements than legacy SDR videos. With their greater bit depth, advanced electro-optical transfer functions, and wider color gamuts, comes the need for video quality algorithms that are specifically designed to predict the quality of HDR videos. Towards this end, we present the first publicly released large-scale subjective study of HDR videos. We study the effect of distortions such as compression and aliasing on the quality of HDR videos. We also study the effect of ambient illumination on perceptual quality of HDR videos by conducting the study in both a dark lab environment and a brighter living-room environment. A total of 66 subjects participated in the study and more than 20,000 opinion scores were collected, which makes this the largest in-lab study of HDR video quality ever. We anticipate that the dataset will be a valuable resource for researchers to develop better models of perceptual quality for HDR videos.
Towards hairstyle reconstruction using thermal imaging (2011)

The reconstruction of hairstyles is one of the most challenging tasks in the field of hair modeling.
Fluorescent properties of an unnatural nucleobase, 2-amino-6-(2-thienyl)purine, in DNA and RNA fragments (2005)

Nucleoside derivatives of 2-amino-6-(2-thienyl)purine (s) are fluorescent and can be site-specifically incorporated into RNA by transcription mediated by unnatural base pairs between s and its complementary bases. To utilize the fluorescent s base as a probe, we examined the fluorescent properties of s in DNA and RNA fragments. The nucleoside of s exhibited a fluorescence emission centered at 432 nm, characterized by two major excitation maxima (299 and 352 nm), and its quantum yield was 0.41 at pH 7.0. The fluorescence intensity of s in DNA fragments (12-mer) differed depending on circumstances such as the base components, stacking, and pairings. The s base was introduced into a tRNA at specific positions by specific transcription using the unnatural base pairs. The fluorescence intensity of s at each position reflected the local structural features of the tRNA molecules.
Gas phase hydration of halogenated benzene cations. Is it hydrogen or halogen bonding? (2017)

Halogen bonding (XB) non-covalent interactions can be observed in compounds containing chlorine, bromine, or iodine which can form directed close contacts of the type R1-XY-R2, where the halogen X acts as a Lewis acid and Y can be any electron donor moiety including electron lone pairs on hetero atoms such as O and N, or π electrons in olefin double bonds and aromatic conjugated systems. In this work, we present the first evidence for the formation of ionic halogen bonds (IXBs) in the hydration of bromobenzene and iodobenzene radical cations in the gas phase. We present a combined thermochemical investigation using the mass-selected ion mobility (MSIM) technique and density functional theory (DFT) calculations of the stepwise hydration of the fluoro, chloro, bromo, and iodobenzene radical cations. The binding energy associated with the formation of an IXB in the hydration of the iodobenzene cation (11.2 kcal mol<sup>-1</sup>) is about 20% higher than the typical unconventional ionic hydrogen bond (IHB) of the CH<sup>δ+</sup>OH<sub>2</sub> interaction. The formation of an IXB in the hydration of the iodobenzene cation involves a significant entropy loss (29 cal mol<sup>-1</sup> K<sup>-1</sup>) resulting from the formation of a more ordered structure and a highly directional interaction between the oxygen lone pair of electrons of water and the electropositive region around the iodine atom of the iodobenzene cation. In comparison, the hydration of the fluorobenzene and chlorobenzene cations where IHBs are formed, -ΔS° = 18-21 cal mol<sup>-1</sup> K<sup>-1</sup> consistent with the formation of less ordered structures and loose interactions. The electrostatic potentials on the lowest energy structures of the hydrated halogenated benzene radical cations show clearly that the formation of an IXB is driven by a positively charged σ-hole on the external side of the halogen atom X along the C-X bond axis. The size of the σ-hole increases significantly in bromobenzene and iodobenzene radical cations which results in strong interaction potentials with the electron lone pairs of the oxygen atom of the water molecules and thus IXBs provide the most stable hydrated structures of the bromobenzene and iodobenzene radical cations. The results clearly distinguish the hydration behaviors resulting from the ionic hydrogen and halogen bonding interactions of fluorobenzene and iodobenzene cations, respectively, and establish the different bonding and structural features of the two interactions.
Cancer Therapy With Tetrathiomolybdate: Antiangiogenesis by Lowering Body Copper—A Review (2002)

A new anticopper drug, tetrathiomolybdate (TM), developed for Wilson's disease, is a very promising antiangiogenic agent. Copper levels lowered into an antiangiogenic window by TM have shown efficacy against cancer in a variety of animal models as well as in patients. The only significant toxicity so far results from overtreatment and excessive bone marrow depletion of copper. The resulting anemia and/or leukopenia is easily treatable by dose reduction or drug holiday. The underlying concept for TM efficacy as an anticancer agent is that when the body's copper status is in the window, cellular copper needs are met and toxicity is avoided. Copper status is relatively easily monitored by following serum ceruloplasmin, a copper-containing protein secreted by the liver at a rate dependent upon the amount of copper in the liver available to incorporate into the protein. The authors speculate that the copper level is a primitive angiogenesis and growth-signaling regulator that has been retained throughout evolution.
Data from A Transient Increase in Eosinophils Is Associated with Prolonged Survival in Men with Metastatic Castration-Resistant Prostate Cancer Who Receive Sipuleucel-T (2023)

&lt;div&gt;Abstract&lt;p&gt;Sipuleucel-T is an autologous cellular immunotherapy used to treat asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC). Traditional short-term indicators of clinical response commonly used with chemotherapy have not correlated with survival in patients treated with sipuleucel-T. This retrospective study aimed to evaluate laboratory parameters as possible early biomarkers associated with clinical benefit following sipuleucel-T treatment. Patients treated with sipuleucel-T from three randomized, controlled, phase III clinical trials in mCRPC were considered: IMPACT (NCT00065442; &lt;i&gt;n&lt;/i&gt; = 512), D9901 (NCT00005947; &lt;i&gt;n&lt;/i&gt; = 127), and D9902A (NCT01133704; &lt;i&gt;n&lt;/i&gt; = 98). Patients from these trials were included in this study if their samples were analyzed by the central laboratory and if data were available from baseline and ≥1 posttreatment time point (&lt;i&gt;n&lt;/i&gt; = 377). We found that sipuleucel-T treatment was associated with a transient increase in serum eosinophil count at week 6 that resolved by week 14 in 28% of patients (105 of 377). This eosinophil increase correlated with induced immune response, longer prostate cancer–specific survival [HR, 0.713; 95% confidence interval (CI), 0.525–0.970; &lt;i&gt;P&lt;/i&gt; = 0.031], and a trend in overall survival (HR, 0.753; 95% CI, 0.563–1.008; &lt;i&gt;P&lt;/i&gt; = 0.057). Median serum globulin protein levels also increased transiently, which was associated with antigen-specific antibody responses; however, this finding did not correlate with longer survival. We conclude that transient increases in eosinophils at week 6 may be a useful, objective, short-term indicator of global immune activation and survival benefit with sipuleucel-T in patients with mCRPC. This observation warrants prospective evaluation in future clinical trials. &lt;i&gt;Cancer Immunol Res; 2(10); 988–99. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Increasing camera dynamic range through in-sensor multi-exposure white balancing (2011)

In typical image sensors the spectral sensitivity of color channels is fixed. The illumination spectrum in natural scenes can vary to a great extent. This leads to an unbalanced response in color channels and hence a reduction in dynamic range. We propose a new method to adjust the relative sensitivity of color channels based on multi-exposure frame combination. Instead of a single long exposure we capture a different number of gapless exposures in each color channel and combine them. This offers a digital option for reducing sensitivity for some color channels and aligns the color channels. The method preserves motion blur and can be used in any long exposure or moving picture photography. We can now get a higher dynamic range from a camera system under any unfavorable illumination conditions with very little effort.
The therapeutic potential of the mesenchymal stem cell secretome in a mouse model of chronic inflammatory lung disease (2019)

Mesenchymal stem cells (MSCs) are spindle-shaped multipotent cells with immunomodulatory and reparative properties, which can be found in the mesenchymal stroma or connective tissues of the body. An ongoing pre-clinical study within our lab has found MSC-based therapy to significantly reduce inflammation and tissue damage in the lungs of <i>Scnn1b</i>-transgenic mice. These mice exhibit a chronic inflammatory lung disease due to airway-specific overexpression of the β-subunit of the epithelial sodium channel. Subsequently, we investigated whether administration of the MSC secretome, in a complementary cell-free approach, would exert similar effects. <i>Scnn1b</i>-transgenic mice were subcutaneously injected with control media or MSC-conditioned media (MSC-CM) every second day from birth to postnatal day 12, after which they were sacrificed at postnatal day 14. Analysis of the bronchoalveolar lavage fluid revealed significant reductions in both polymorphonuclear neutrophils and eosinophils in mice treated with MSC-CM. Histological analyses revealed that MSC-CM administration significantly improved two parameters of lung damage – the mean linear intercept and the destructive index. Overall, these results highlight the potential of the MSC secretome to limit lung damage and/or promote pulmonary repair/regeneration in the <i>Scnn1b</i>-transgenic mouse model of chronic lung disease.