gebhart/patrepeval huggingface dataset:
Disulfide-mediated Oligomerization of Peripherin/Rds and Rom-1 in Photoreceptor Disk Membranes (2000)

Peripherin/Rds is a tetraspanning membrane protein that has been implicated in photoreceptor outer segment morphogenesis and inherited retinal degenerative diseases. Together with the structurally related protein, Rom-1, it forms a complex along the rims of rod and cone disc membranes. We have compared the oligomeric structure of these proteins from nonreduced and dithiothreitol reduced membranes by velocity sedimentation, SDS-gel electrophoresis, immunoaffinity chromatography, and chemical cross-linking. Under reducing conditions peripherin/Rds and Rom-1 existed as homomeric and heteromeric core complexes devoid of intermolecular disulfide bonds. Under nonreducing conditions core complexes associated through intermolecular disulfide bonds to form oligomers. One intermediate-size oligomer contained monomers and disulfide-linked dimers of peripherin/Rds and Rom-1, while larger oligomers consisted only of disulfide-linked peripherin/Rds dimers when analyzed on nonreducing SDS gels. Consistent with this result, disc membranes contained twice as much peripherin/Rds as Rom-1. Peripherin/Rds individually expressed in COS-1 cells also formed disulfide-linked oligomers bridged through Cys-150 residues, whereas Rom-1 showed little tendency to form oligomers. These results indicate that peripherin/Rds and Rom-1 associate noncovalently to form multisubunit core complexes. Peripherin/Rds containing core complexes interact through specific intermolecular disulfide bonds to form oligomers which may play a crucial role in photoreceptor disc morphogenesis and retinal degenerative diseases.
Adhesion force imaging in air and liquid by adhesion mode atomic force microscopy (1994)

A new imaging mode for the atomic force microscope (AFM), yielding images mapping the adhesion force between tip and sample, is introduced. The adhesion mode AFM takes a force curve at each pixel by ramping a piezoactuator, moving the silicon-nitride tip up and down towards the sample. During the retrace the tip leaves the sample with an adhesion dip showing up in the force curve. Adhesion force images mapping parameters describing this adhesion dip, such as peak value, width, and area, are acquired on-line together with the sample topography. Imaging in air gives information on the differences in hydrophobicity of sample features. While imaging a mercaptopentadecane-gold layer on glass in demineralized water, the adhesion force could be modulated by adding phosphate buffered saline.
Copolymerization of butadiene and styrene with a gadolinium tricarboxylate catalyst (1995)

Abstract Homo‐ and copolymerizations of butadiene (BD) and styrene (St) were carried out by gadolinium catalysts having various tricarboxylate ligands [Gd(OCOR) 3 : R = CH 3 , CH 2 Cl, CHCl 2 , CCl 3 , and CF 3 ], to investigate the effects of ligands and discuss the cis polymerization mechanism. Polymerization of BD with Gd(OCOR) 3 —( i —Bu) 3 Al—Et 2 AlCl catalysts was carried out in hexane at 50°C. By each catalyst, poly(BD) having a high cis content ( cis = 97–99%) in 22–85% yields for 2–24 h were obtained. The ligands with low pKa values increased the polymerization activity as follows: R of Gd(OCOR) 3 : CF 3 &gt; CCl 3 &gt; CHCl 2 &gt; CH 2 Cl ∼ CH 3 . On the other hand, in the polymerization of St or copolymerization of BD and St under similar conditions, the highest activity was attained by a Gd(OCOCCI 3 ) 3 ‐ based catalyst. The difference in the optimum ligand among the homo‐ and copolymerization of BD and St was discussed on the basis of energy levels of the catalysts. In the copolymers of BD and St, the cis ‐1,4 content of the BD unit decreased with increasing St content. Furthermore, according to the diad analysis of copolymers (St content ∼ 14.5 mol %) by 13 C NMR spectroscopy, the low cis value of the BD unit was observed in the St‐BD diad ( cis/trans/vinyl = 24/53/23), while the high cis value of the BD unit remained in the BD‐BD diad ( cis/trans/vinyl = 89/10/1). These results suggest that the terminal BD unit is controlled by the cis configuration by the coordination between the penultimate cis vinylene unit and the gadolinium metal catalyst, whereas the presence of the penultimate St unit interferes with cis polymerization of the terminal BD unit. The difference in the coordination mechanism in the course of polymerization between rare earth metal and transition metal catalysts such as the Ni(acac) 2 and Co(acac) 3 ‐based catalyst was also discussed. © 1995 John Wiley &amp; Sons, Inc.
CHARACTERIZATION OF LIVER X RECEPTORS IN PROSTATE CANCER CHOLESTEROL METABOLISM AND PULMONARY IMMUNE RESPONSE (2011)

Liver x receptors (LXRs) are central regulators cholesterol homeostasis and the innate immune response. As modulators of inflammation and cholesterol metabolism LXRs might diminish dyslipidemia and inflammation related pathologies caused by high fat (HF) diets or obesity. There is also data demonstrating that LXRs can protect against progression of prostate cancer (PCa), but little is known about the cholesterol modulating effects of LXRs in transformed cells. The goal of this project is to characterize the cholesterol modulating properties of LXRs in two models of PCa and the anti-inflammatory properties of LXRs in swine bronchial alveolar macrophages (AMs). This project will also examine whether the anti-inflammatory and lipid lowering properties of the dietary probiotic bacteria Lactobacillus casei (L. casei), can interact with the LXR axis in AMs. Studies in two PCa cell lines, LNCaP and PC-3, revealed that LXR ligands regulate the LXR responsive genes, ABCA1 and ABCG1 through the LXR&beta isoform and not LXR&alpha in PC-3 cells, but only ABCG1 in LNCaP. LXR- ABCA1 mediated reverse cholesterol transport (RCT) resulted in a decrease in plasma membrane lipid raft cholesterol domains in PC-3 cells, suggesting a potential anti-cancer axis for LXR activation. Studies in LNCaP and PC-3 cells also demonstrated that soy isoflavones can activate transcriptional activation of ABCA1 and ABCG1 in LNCaP and PC-3 cells through the LXR&beta isoform, but did not lead to an increase in RCT. Metabolic and anti-inflammatory studies of LXR in AM from Ossabaw pigs fed either a control (C) diet, HF, HF plus L casei (HFPB) or L. casei alone (CPB) diet revealed that AM from HF fed pigs had significantly higher concentrations of cholesteryl-esters (CE) compared with AM from control (C) diet fed pigs. Ex-vivo activation of LXR with the LXR ligand T0901317 opposed LPS mediated upregulation of IL-1&beta , IL-6, IL-8 and IL-10 mRNA levels in AM from HF, HFPB and CPB fed pigs. Finally, it was observed that LPS stimulation lead to significant inhibition of LXR transcription of LXR&alpha, ABCA1, ABCG1, cholesterol 25 hydroxylase (CH25H) and PPAR&gamma in AM. This effect was abrogated by L. casei for ABCA1, CH25H and PPAR&gamma mRNA expression
Faculty Opinions recommendation of Local delivery of minocycline from metal ion-assisted self-assembled complexes promotes neuroprotection and functional recovery after spinal cord injury. (2017)

Read the full review for this Faculty Opinions recommended article: Local delivery of minocycline from metal ion-assisted self-assembled complexes promotes neuroprotection and functional recovery after spinal cord injury.
A simple algorithm that discovers efficient perceptual codes (1997)

We describe the &amp;quot;wake-sleep&amp;quot; algorithm that allows a multilayer, unsupervised, neural network to build a hierarchy of representations of sensory input. The network has bottom-up &amp;quot;recognition&amp;quot; connections that are used to convert sensory input into underlying representations. Unlike most artificial neural networks, it also has top-down &amp;quot;generative&amp;quot; connections that can be used to reconstruct the sensory input from the representations. In the &amp;quot;wake&amp;quot; phase of the learning algorithm, the network is driven by the bottom-up recognition connections and the top-down generative connections are trained to be better at reconstructing the sensory input from the representation chosen by the recognition process. In the &amp;quot;sleep&amp;quot; phase, the network is driven top-down by the generative connections to produce a fantasized representation and a fantasized sensory input. The recognition connections are then trained to be better at recovering the fantasized representation from the fantasized sensory input. In both phases, the synaptic learning rule is simple and local. The combined effect of the two phases is to create representations of the sensory input that are efficient inthe following sense: On average, it takes more bits to describe each sensory input vector directly than to rst describe the representation of the sensory input chosen by the recognition process and then describe the difference between the sensory input and its reconstruction from the chosen representation.
Microbial and dietary factors associated with the 8-prenylnaringenin producer phenotype: a dietary intervention trial with fifty healthy post-menopausal Caucasian women (2007)

Hop-derived food supplements and beers contain the prenylflavonoids xanthohumol (X), isoxanthohumol (IX) and the very potent phyto-oestrogen (plant-derived oestrogen mimic) 8-prenylnaringenin (8-PN). The weakly oestrogenic IX can be bioactivated via O-demethylation to 8-PN. Since IX usually predominates over 8-PN, human subjects may be exposed to increased doses of 8-PN. A dietary intervention trial with fifty healthy post-menopausal Caucasian women was undertaken. After a 4 d washout period, participants delivered faeces, blank urine and breath samples. Next, they started a 5 d treatment with hop-based supplements that were administered three times per d and on the last day, a 24 h urine sample was collected. A semi-quantitative FFQ was used to estimate fat, fibre, alcohol, caffeine and theobromine intakes. The recoveries of IX, 8-PN and X in the urine were low and considerable inter-individual variations were observed. A five-fold increase in the dosage of IX without change in 8-PN concentration resulted in a significant lower IX recovery and a higher 8-PN recovery. Classification of the subjects into poor (60%), moderate (25%) and strong (15%) 8-PN producers based on either urinary excretion or microbial bioactivation capacity gave comparable results. Recent antibiotic therapy seemed to affect the 8-PN production negatively. A positive trend between methane excretion and 8-PN production was observed. Strong 8-PN producers consumed less alcohol and had a higher theobromine intake. From this study we conclude that in vivo O-demethylation of IX increases the oestrogenic potency of hop-derived products.
Detection of pollen grains in multifocal optical microscopy images of air samples (2009)

Pollen is a major cause of allergy and monitoring pollen in the air is relevant for diagnostic purposes, development of pollen forecasts, and for biomedical and biological researches. Since counting airborne pollen is a time-consuming task and requires specialized personnel, an automated pollen counting system is desirable. In this article, we present a method for detecting pollen in multifocal optical microscopy images of air samples collected by a Burkard pollen sampler, as a first step in an automated pollen counting procedure. Both color and shape information was used to discriminate pollen grains from other airborne material in the images, such as fungal spores and dirt. A training set of 44 images from successive focal planes (stacks) was used to train the system in recognizing pollen color and for optimization. The performance of the system has been evaluated using a separate set of 17 image stacks containing 65 pollen grains, of which 86% was detected. The obtained precision of 61% can still be increased in the next step of classifying the different pollen in such a counting system. These results show that the detection of pollen is feasible in images from a pollen sampler collecting ambient air. This first step in automated pollen detection may form a reliable basis for an automated pollen counting system.
A flexible processor for object based HDTV motion estimation (2002)

Object based motion estimation with a compensation of rotation and zoom as well as a variable shape of the matched region gains more and more importance (MPEG4). In this paper we describe a new concept for object based motion estimation consisting of a preprocessing unit and a standard block matching processor. In the preprocessing unit the motion components zoom and rotation and the shape of objects are estimated. Then the blocks are manipulated according to the estimated parameters and a standard block matching is performed. For the standard block matching a flexible block matching motion estimation processor with a computational power of 200 GOPS is described. The chip performs block matching on a search area of /spl plusmn/15 vertically and horizontally for a variable block size of up to 32/spl times/32 pixels. For larger search areas devices can be cascaded. Full search can be processed as well as fast search strategies. Sub-pel precision motion vectors can be derived using a smaller search area or cascading devices. The chip has a die size of 170 mm/sup 2/ in a 0.5-/spl mu/m CMOS technology.
Singular value decomposition metrics show limitations of detector design in diffuse fluorescence tomography (2010)

The spatial resolution and recovered contrast of images reconstructed from diffuse fluorescence tomography data are limited by the high scattering properties of light propagation in biological tissue. As a result, the image reconstruction process can be exceedingly vulnerable to inaccurate prior knowledge of tissue optical properties and stochastic noise. In light of these limitations, the optimal source-detector geometry for a fluorescence tomography system is non-trivial, requiring analytical methods to guide design. Analysis of the singular value decomposition of the matrix to be inverted for image reconstruction is one potential approach, providing key quantitative metrics, such as singular image mode spatial resolution and singular data mode frequency as a function of singular mode. In the present study, these metrics are used to analyze the effects of different sources of noise and model errors as related to image quality in the form of spatial resolution and contrast recovery. The image quality is demonstrated to be inherently noise-limited even when detection geometries were increased in complexity to allow maximal tissue sampling, suggesting that detection noise characteristics outweigh detection geometry for achieving optimal reconstructions.
CHARACTERIZATION OF T CELL RECEPTOR ?? CHAINS OF ACCUMULATING T CELLS IN SKIN ALLOGRAFTS IN MICE1 (1996)

The study of T cells involved in the immune reaction that occurs in engrafted organs should provide information that would be helpful in the regulation of allograft rejection in organ transplantation. Toward this end, we focused on detection and characterization of accumulating T cells in mouse skin allografts from B10.A(4R) to C57BL/6 mice in vivo. T cell receptor beta genes were amplified by reverse transcriptase-PCR from mRNA of the skin grafts, and accumulating T cell receptor beta gene clonotypes were identified by their single strand conformation polymorphism. Their joining region usage and the amino acid sequences of the complementarity-determining region-3 were then determined. The results were as follows: (1) Distinct oligoclonal accumulation of T cells was more prevalent in the skin allografts than in the syngenic skin grafts. (2) Although the accumulating T cell clonotypes appeared to use many different variable-region gene families, preferential combinations of variable region-joining region were found. (3) Several homologous amino acid sequences were found in these accumulating TCR beta genes in allografts, suggesting that these T cells are driven by the same or similar antigens. (4) In addition, little T cell accumulation was found in spleens from the mice with allografts or syngenic skin grafts. Taken together, accumulating T cells in the skin allografts were detected in vivo, and some appeared to have characteristics in common. This may lead to T cell clonotype-specific therapy in organ transplantation.
Development and quality assessment of honey nut drink (2020)

Abstract The objective of this study was to standardize the formulation of honey nut drink, to assess the quality parameters like pH, brix, acidity, brix acid ratio and sensory characteristics of formulated honey nut drink under 12 days of storage at ambient temperature (32±2°C). The pH values varied from 3.5 to 3.9 during storage. The brix found in three different products ranged from 7 to 13%. The acidity possesses during the entire storage period between 0.16 to 0.32%. The brix acid ratio higher found in product 2 (59.99) and lower in product 3 (35.0) under storage. The sensory profile of three different formulation was evaluated in terms of color, flavor, taste and overall acceptability. Among the three-products formulation product 1 retained better quality followed by product 3 and product 2 considering pH, brix and acidity percentage although after increasing time of storage their value also increased. The sensory profile of product 3 found in much better score followed by the product 1 and product 2 which are significantly different (p≤0.05). In conclusion, both formulation of product 1 and product 3 could be produced in commercial purpose.
A Discrete STFT Processor for Real-time Spectrum Analysis (2006)

A discrete STFT processor for real-time spectrum analysis is proposed. To overcome the drawbacks of previous discrete STFT algorithms and architectures, a new architecture based on FFT array is presented. By exploiting the symmetry of window function, multipliers for window multiplication can reduce to N/2. And the utilization rate of the multiplier in FFT processing unit can be improved by introducing switch arrays. The design has been synthesized using SMIC 0.18mum standard cell library using a Verilog model. After placed and routed, static timing analysis and dynamic simulation with timing back annotated show that under worst-case conditions, 180MHz clock rate can be achieved, which means that the real time spectrum analysis demand can be fulfilled under the same sample rate
ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein (2012)

The assembly of static supramolecular structures is a culminating event of developmental programs. One such structure, the proteinaceous shell (called the coat) that surrounds spores of the bacterium Bacillus subtilis, is composed of about 70 different proteins and represents one of the most durable biological structures known. The coat is built atop a basement layer that contains an ATPase (SpoIVA) that forms a platform required for coat assembly. Here, we show that SpoIVA belongs to the translation factors class of P-loop GTPases and has evolutionarily lost the ability to bind GTP; instead, it uses ATP hydrolysis to drive its self-assembly into static filaments. We demonstrate that ATP hydrolysis is required by every subunit for incorporation into the growing polymer by inducing a conformational change that drives polymerization of a nucleotide-free filament. SpoIVA therefore differs from other self-organizing polymers (dynamic cytoskeletal structures and static intermediate filaments) in that it uses ATP hydrolysis to self-assemble, not disassemble, into a static polymer. We further show that polymerization requires a critical concentration that we propose is only achieved once SpoIVA is recruited to the surface of the developing spore, thereby ensuring that SpoIVA polymerization only occurs at the correct subcellular location during spore morphogenesis.
The Effects of Dexamethasone on Plasma Homovanillic Acid and 3-Methoxy-4-hydroxyphenylglycol (1987)

We investigated the possible interactions between corticosteroids and catecholamines in depression by studying the effects of the synthetic glucocorticoid dexamethasone on plasma levels of homovanillic acid (HVA) and 3-methoxy-4-hydroxyphenylglycol (MHPG) in a group of depressed patients and normal controls. In comparison with metabolite levels on a control day, normal controls showed a significant dexamethasone-induced increase in the plasma HVA level and a trend toward a decrease in the plasma MHPG level at 4 PM following dexamethasone administration (1 mg orally at 11 PM). Conversely, depressed patients, particularly those with psychotic features, showed a significant dexamethasone-induced increase in the plasma MHPG level and a blunting of the plasma HVA response relative to the normal controls. Dexamethasone-induced increases in the plasma MHPG level were directly correlated with the severity of depressive symptoms and with postdexamethasone cortisol levels in the depressed patients. These data suggest abnormal corticosteroid-catecholamine interactions in depression and, specifically, in depressed patients with psychotic features.
The IRE1 Inhibitor Kira6 Curtails The Inflammatory Trait Of Immunogenic Anticancer Treatments By Targeting Hsp60 Independent Of IRE1 (2020)

ABSTRACT Cellular stress evoked by immunogenic anticancer treatments engaging the unfolded protein response (UPR) can elicit inflammation with conflicting therapeutic outcomes. To define cell-autonomous mechanisms coupling the UPR to molecular mediators of inflammation, we profiled the transcriptome of cancer cells responding to immunogenic or weakly immunogenic-treatments. Bioinformatics-driven pathway analysis indicated that immunogenic treatments instigated NF-κB/AP-1-inflammatory pathways, which were abolished by the IRE1α-kinase inhibitor KIRA6. Cell-free fractions of chemotherapy and KIRA6 co-treated cancer cells were deprived of pro-inflammatory/chemoattractant factors and failed to mobilize innate immune cells. Strikingly, these potent KIRA6 anti-inflammatory effects were found to be independent of IRE1α. Generation of a KIRA6-clickable photoaffinity probe, mass spectrometry and co-immunoprecipitation analysis identified cytosolic HSP60 as a KIRA6 off-target in the NF-κB pathway. In sum, our study unravels that inflammation evoked by immunogenic treatments is curtailed by KIRA6 independently of IRE1α and further suggests great caution in interpreting the anti-inflammatory action of IRE1α chemical inhibitors.
Large-scale speaker identification (2014)

Speaker identification is one of the main tasks in speech processing. In addition to identification accuracy, large-scale applications of speaker identification give rise to another challenge: fast search in the database of speakers. In this paper, we propose a system based on i-vectors, a current approach for speaker identification, and locality sensitive hashing, an algorithm for fast nearest neighbor search in high dimensions. The connection between the two techniques is the cosine distance: on the one hand, we use the cosine distance to compare i-vectors, on the other hand, locality sensitive hashing allows us to quickly approximate the cosine distance in our retrieval procedure. We evaluate our approach on a realistic data set from YouTube with about 1,000 speakers. The results show that our algorithm is approximately one to two orders of magnitude faster than a linear search while maintaining the identification accuracy of an i-vector-based system.