gebhart/patrepeval huggingface dataset:
Combined fluorescent in situ hybridization for detection of microRNAs and immunofluorescent labeling for cell-type markers (2013)

Identification of the cell type of origin for normal or aberrant gene expression is critical for many studies, and poses a significant problem for some regulatory RNAs such as microRNAs. MicroRNAs are small non-coding RNAs that regulate cellular function by targeting specific mRNAs and reducing the level of their protein product. Aberrant expression of miRNAs in cell-types where they are not normally expressed occurs in several disease conditions. Therefore, it is important to determine not only the expression level of microRNAs, but also where they are expressed. Here we describe a detailed method for fluorescent in situ hybridization (FISH) combined with immunofluorescent labeling for cell-type markers in formalin fixed paraffin embedded (FFPE) sections along with modifications required to adapt the protocol for primary neurons grown in culture. We have combined the specificity and stability of locked nucleic acid (LNA) probes with tyramide signal amplification. To prevent loss of small RNA species, we performed post-fixation with ethylcarbodiimide (EDC). Additionally by omitting protease digestion and using only high temperature with sodium citrate buffer for FFPE sections, we were able to perform immunolabeling for proteins concurrently with in situ hybridization without compromising efficacy of either procedure.
Localization of T cell clonotypes using the Visium spatial transcriptomics platform (2022)

We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections. T cell receptor sequences identified by this protocol are readily recapitulated by single-cell sequencing. This technique enables detailed studies of the spatial organization of the human T cell repertoire, such as the localization of infiltrating T cell clones within the tumor microenvironment. For complete details on the use and execution of this protocol, please refer to Sudmeier et al. (2022).
Small-Molecule Electron Acceptors for Efficient Non-fullerene Organic Solar Cells (2018)

The development of organic electron acceptor materials is one of the key factors for realizing high performance organic solar cells. Compared to traditional fullerene acceptor materials, non-fullerene electron acceptors have attracted much attention due to their better optoelectronic tunabilities and lower cost as well as higher stability. Non-fullerene organic solar cells have recently experienced a rapid increase with power conversion efficiency of single-junction devices over 14% and a bit higher than 15% for tandem solar cells. In this review, two types of promising small-molecule electron acceptors are discussed: perylene diimide based acceptors and acceptor(A)-donor(D)-acceptor(A) fused-ring electron acceptors, focusing on the effects of structural modification on absorption, energy levels, aggregation and performances. We strongly believe that further development of non-fullerene electron acceptors will hold bright future for organic solar cells.
Antibodies to viral antigens, xenoantigens, and autoantigens in alzheimer's disease (1990)

Sera from 19 patients with Alzheimer's disease (AD) and 21 control subjects were studied by immunofluorescence and enzyme immunoassay for antibody activity against various viruses and 12 self- and non-self-antigens. Total IgG mean level was significantly higher in the AD group; the IgG level was above 15 g/L in 52.8% of AD patients versus 14.3% of control subjects. Antiviral antibody titers showed no significant differences except for antibodies to herpes simplex virus-1, which were increased in control group. In contrast, autoantibodies were more frequently found in AD patients, and the prevalence of antibodies to spectrin, peroxidase, and thyroglobulin was significantly increased. Thus, in our series, autoimmune but not antiviral responses were heightened in at least 42% of AD patients (versus 9% of the control group) suggesting the existence of two subpopulations in the AD group.
Fluorinated analogues of chrysanthemic acid (1980)

Abstract Novel halogenated chrysanthemic acid analogues have been prepared and the interesting properties of their esters are described. Among this group are the most active insecticides yet reported.
Anchoring of Suboccipital Lead: Case Report and Technical Note (2004)

Suboccipital stimulation is a relatively new method of neuromodulation for treatment of intractable occipital headache and occipital neuralgia. The most common complication besides an infection is a lead displacement. Anchoring of a lead at the entry place partially solves the problem. Migration of electrode's tip is a major problem so far. A case report of electrode migration and a technique of retrograde lead insertion and subcutaneous anchoring of the tip by means of contralateral incision and suturing of lead is described.
Retinopathy of prematurity: understanding ischemic retinal vasculopathies at an extreme of life (2010)

Retinopathy of prematurity (ROP) is a major complication of preterm birth. It encompasses a spectrum of pathologies that affect vision, from mild disease that resolves spontaneously to severe disease that causes retinal detachment and subsequent blindness. The pathologies are characterized by an arrest in normal retinal vascular development associated with microvascular degeneration. The resulting ischemia and retinal hypoxia lead to excessive abnormal compensatory blood vessel growth. However, this neovascularization can lead to fibrous scar formation and culminate in retinal detachment. Present therapeutic modalities to limit the adverse consequences of aberrant neovascularization are invasive and/or tissue-destructive. In this Review, we discuss current concepts on retinal microvascular degeneration, neovascularization, and available treatments, as well as present future perspectives toward more profound elucidation of the pathogenesis of ROP.
Synthesis of 5‐methyl‐4‐oxo‐2‐(coumarin‐3‐yl)‐<i>N</i>‐aryl‐3,4‐dihydrothieno[2,3‐d]‐pyrimidine‐6‐carboxamides (2007)

Abstract Possible approaches to synthesis of 5‐methyl‐4‐oxo‐2‐(coumarin‐3‐yl)‐ N ‐aryl‐3,4‐dihydrothieno[2,3‐ d ]pyrimidine‐6‐carboxamides 4 have been discussed. It is shown that the preferable approach is cyclization of 2‐iminocoumarin‐3‐carboxamides 1 , utilizing 5‐amino‐3‐methyl‐ N 2 ‐arylthiophene‐2,4‐dicarboxamides 2 as binucleophilic reagents. The proposed procedure allowed us to easily obtain 4 in two stages, using common reagents. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:341–346, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20303
Automated analysis of bounded response time for two NASA expert systems (1991)

article Automated analysis of bounded response time for two NASA expert systems Share on Authors: Chih-Kan Wang Department of Computer Science, University of Texas at Austin, Austin, Texas Department of Computer Science, University of Texas at Austin, Austin, TexasView Profile , Duu-Chung Tsou View Profile , Rwo-Hsi Wang View Profile , James C. Browne Department of Computer Science, University of Texas at Austin, Austin, Texas Department of Computer Science, University of Texas at Austin, Austin, TexasView Profile , Aloysius K. Mok Department of Computer Science, University of Texas at Austin, Austin, Texas Department of Computer Science, University of Texas at Austin, Austin, TexasView Profile Authors Info & Claims ACM SIGSOFT Software Engineering NotesVolume 16Issue 5Dec. 1991 pp 147–161https://doi.org/10.1145/123041.123067Online:01 September 1991Publication History 1citation100DownloadsMetricsTotal Citations1Total Downloads100Last 12 Months5Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Spontaneous periodic ordering on the surface and in the bulk of dielectrics irradiated by ultrafast laser: a shared electromagnetic origin (2017)

Periodic self-organization of matter beyond the diffraction limit is a puzzling phenomenon, typical both for surface and bulk ultrashort laser processing. Here we compare the mechanisms of periodic nanostructure formation on the surface and in the bulk of fused silica. We show that volume nanogratings and surface nanoripples having subwavelength periodicity and oriented perpendicular to the laser polarization share the same electromagnetic origin. The nanostructure orientation is defined by the near-field local enhancement in the vicinity of the inhomogeneous scattering centers. The periodicity is attributed to the coherent superposition of the waves scattered at inhomogeneities. Numerical calculations also support the multipulse accumulation nature of nanogratings formation on the surface and inside fused silica. Laser surface processing by multiple laser pulses promotes the transition from the high spatial frequency perpendicularly oriented nanoripples to the low spatial frequency ripples, parallel or perpendicular to the laser polarization. The latter structures also share the electromagnetic origin, but are related to the incident field interference with the scattered far-field of rough non-metallic or transiently metallic surfaces. The characteristic ripple appearances are predicted by combined electromagnetic and thermo-mechanical approaches and supported by SEM images of the final surface morphology and by time-resolved pump-probe diffraction measurements.
Purification and Characterization of Carbonic Anhydrase from Bovine Erythrocyte Plasma Membrane (2000)

Carbonic anhydrase (CA) was purified from bovine erythrocyte plasma membrane and characterized in this study. For this purpose, the blood taken from young animals was hemolysed, the membrane fraction was separated, and this fraction was repeatedly washed. The enzyme (CA) was removed from the membrane with buffered TritonX-100 (1%); it could be purified at a factor of 22.8 by affinity chromatography. The CA obtained from erythrocyte membrane has an esterase activity as well as hydratase activity. The Vmax and Km of the enzyme for the substrate (p-nitrophenyl acetate) are 1.948x10(-3) mM/L x dak, and 3.596 mM, respectively. The purification degree of the enzyme was controlled by SDS-PAGE (3-10), which showed two distinct bands. It was determined that the enzyme had activity within the pH range of 4.5-9.5 and that the optimal pH was 7.5. The temperature at which it showed activity was 20-60 degrees C and optimal temperature was 37 degrees C. Molecular weight of CA was found to be 29844 and 61706 Dalton by gel filtration. On the other hand, sulfanilamide and acetazolamide affected the enzyme.
Down‐regulation of the transcriptional mediator subunit Med1 contributes to the loss of expression of metastasis‐associated <i>dapk1</i> in human cancers and cancer cells (2009)

DAPK1, a ca(+2)/calmodulin regulated serine/threonine kinase, is a major tumor suppressor, whose expression is lost in multiple tumor types. However, the mechanisms contributing to it are unclear. We have recently shown that CCAAT/Enhancer binding protein-beta (C/EBP-beta) is required for the basal and interferon gamma (IFN-gamma)-induced expression of dapk1 in many cell types. C/EBP-beta interacts with the transcriptional Mediator, a multisubunit complex that couples enhancer bound transcription factors to the basal transcriptional machinery in an IFN-gamma dependent manner for regulating dapk1 expression. Specifically, the Med1 (TRAP220/PBP/DRIP220/CRSP220) subunit associates with the enhancer bound C/EBP-beta at the CRE/ATF site of dapk1 in an IFN-gamma dependent manner for stimulating gene expression. Therefore, we investigated if the mechanism responsible for the loss of dapk1 expression in human cancers involves a failure to recruit C/EBP-beta and/or Med1 to the dapk1 promoter. We compared the relative occupancy of these factors at the dapk1 promoter at CRE/ATF sites in normal and cancer cell lines. A significantly lower binding of these factors to the CRE/ATF site of dapk1 promoter occurred in human cancer cell lines than in normal cells. We show that loss of Med1 expression correlates with a corresponding loss of dapk1 expression in a number of primary human lung carcinomas. Med1 levels were significantly lower in cancer cell lines than in normal controls. Importantly, we show that restoration of Med1 induces the expression of dapk1 in these cancer cells and also attenuates their metastatic potential in vivo. Our studies reveal a critical parameter limiting dapk1 expression in cancer cell lines.
Development of a sensor-based learning approach to prognostics in intelligent vehicle health monitoring (2008)

This paper reports the development and testing of an intelligent sensing network for monitoring corrosion of aircraft structures. The agent-based system uses sensed microclimate and corrosion data with an innovative analysis approach to diagnose corrosion and to infer the presence of corrosion in locations such as crevices and fasteners where it cannot be sensed directly. An important feature of the system is its ability to provide prognostic information to enable timely corrective maintenance scheduling.
Graph Neural Networks for Channel Decoding (2022)

In this work, we propose a fully differentiable graph neural network (GNN)-based architecture for channel decoding and showcase a competitive decoding performance for various coding schemes, such as low-density parity-check (LDPC) and BCH codes. The idea is to let a neural network (NN) learn a generalized message passing algorithm over a given graph that represents the forward error correction (FEC) code structure by replacing node and edge message updates with trainable functions. Contrary to many other deep learning-based decoding approaches, the proposed solution enjoys scalability to arbitrary block lengths and the training is not limited by the curse of dimensionality. We benchmark our proposed decoder against state-of-the-art in conventional channel decoding as well as against recent deep learning-based results. For the (63,45) BCH code, our solution outperforms weighted belief propagation (BP) decoding by approximately 0.4 dB with significantly less decoding iterations and even for 5G NR LDPC codes, we observe a competitive performance when compared to conventional BP decoding. For the BCH codes, the resulting GNN decoder can be fully parametrized with only 9640 weights.
Activation of OX40 down-regulates IL-17 production (91.10) (2007)

Abstract IL-17 is an important cytokine involved in multiple inflammatory diseases partially through the up-regulation of various pro-inflammatory cytokines and chemokines. The regulation of IL-17 production has been well studied, but the role of OX40 on IL-17 regulation has not been fully illustrated. In this study, we investigated the effect of activation of OX40 on IL-17 production. As expected, stimulation of PHA activated human peripheral blood mononuclear cells (PBMCs) with soluble OX40L increased both Th1 (IFNγ) and Th2 (IL-4 and IL-13) cytokine production. However, addition of soluble OX40L significantly inhibited IL-17 production, and this inhibition was abrogated by IFNγ mAb. IL-23 is a major stimulator for IL-17 and IL-23 enhanced IL-17 production was also inhibited by soluble OX40L in purified human CD4 and CD8 T cells. The downregulation of IL-17 by activation of OX40 was also demonstrated in murine splenocytes from OVA TCR transgenic mice. Blockage of OX40/OX40L interaction with either OX40L antibody or mouse OX40/Fc protein enhanced IL-17 production. In addition, agonistic OX40 antibody inhibited antigen induced IL-17 production and antagonistic OX40 antibody enhanced IL-17 production in splenocytes from OVA transgenic mice. Taken together, our results show that activation of OX40 exerts a negative regulation on IL-17 production. The inhibition is probably mediated through the up regulation of IFNγ production.
Di‐myo‐inositol‐1, 1′‐phosphate: A new inositol phosphate isolated from <i>Pyrococcus woesei</i> (1992)

A new inositol derivative could be isolated from the Archaeum Pyrococcus woesei and identified as di-myo-inositol-1,1'-phosphate by 1H, 31P NMR spectroscopy, mass spectrometry and thin layer chromatography. In P. woesei, this inositol phosphate represents the dominant counterion of K+ which ranges from 500 to 600 mM. The role of the potassium salt of di-myo-inositol-1,1'-phosphate as thermostabilizer is discussed.
Image relaxation matching based on feature points for DSM generation (2004)

In photogrammetry and remote sensing, image matching is a basic and crucial process for automatic DEM generation. In this paper we presented a image relaxation matching method based on feature points. This method can be considered as an extention of regular grid point based matching. It avoids the shortcome of grid point based matching. For example, with this method, we can avoid low or even no texture area where errors frequently appear in cross correlation matching. In the mean while, it makes full use of some mature techniques such as probability relaxation, image pyramid and the like which have already been successfully used in grid point matching process. Application of the technique to DEM generaton in different regions proved that it is more reasonable and reliable.
Testing for the Robustness of Okun’s Law with Breakpoint Analysis : Evidence from Korea (2018)

This study re-evaluated Okun’s law by applying breakpoint analysis; concerning this, the study analyzed six models including the first differenced, modified, and gap models. Empirical evidence reveals that models without breakpoints support the proposition of the conventional Okun’s law, even though the estimated Okun’s coefficients do not match up to the expected values. A few models with breakpoints also support Okun’s law at all the breakpoints. Apparently, the robustness of Okun’s law has been demonstrated in the Korean economy. However, the signs of Okun’s coefficients have been mixed in the gap model since the 2000s. Such changes provide robust evidence that Okun’s law has been weak since the 2000s. Therefore, Okun’s law may not hold if it discusses the potential real GDP and full employment. Taken together, it can be said that the effectiveness of an employment policy based on the manipulation of the national income level may be questionable in the Korean economy. Particularly, when the policy, potential real GDP, and full employment are interrelated, it has to be elaborately established to maximize the effectiveness of the policy.
An analog neural network processor and its application to high-speed character recognition (2002)

A high-speed programmable neural network chip and its application to character recognition are described. A network with over 130000 connections has been implemented on a single chip and operates at a rate of over 1000 classifications per second. The chip performs up to 2000 multiplications and additions simultaneously. Its datapath is suitable for the convolutional architectures that are typical in pattern classification networks, but can also be configured for fully connected or feedback topologies. Computations were performed with 6 bits accuracy for the weights and 3 bits for the states. The chip uses analog processing internally for higher density and reduced power dissipation, but all input/output is digital to simplify system integration.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Pair of resonant fiducial markers for localization of endovascular catheters at all catheter orientations (2003)

A pair of two individually tuned and decoupled RCs is well suited for MR guidance of endovascular catheters.
Learning opportunities in three years of hazmat headlines (2013)

The development of Internet-based electronic information tools has enabled new opportunities to understand the chemical safety needs of a variety of workplaces. The work reported here used Google's Reader service over a period of 3 years to catalog over 5300 public hazmat responses and 533 laboratory-related incidents. These incidents are organized according to various parameters to help assess the number, type and magnitude of hazmat events which reach the popular press. Events of particular interest for development of lab safety training programs are events in laboratory settings. The challenges and opportunities for using this information are discussed, from both a practical and a systems perspective.
Structured Liquids in Liquid State Machines (2011)

In this thesis we look at improving the performance of Liquid State Machines on a speech recognition and a music recognition task, by making structural changes to the liquid. The changes are designed, rather than evolved or learnt, to have more insight into what the effect of particular changes on performance are. We conclude that the effect of any designed structural changes is far outweighed by the random generation of liquids and that the evaluation of LSMs should focus on using sufficiently complex and preferably realistic tasks.
Architecture of the native major royal jelly protein 1 oligomer (2018)

Honeybee caste development is nutritionally regulated by royal jelly (RJ). Major royal jelly protein 1 (MRJP1), the most abundant glycoprotein among soluble royal jelly proteins, plays pivotal roles in honeybee nutrition and larvae development, and exhibits broad pharmacological activities in humans. However, its structure has long remained unknown. Herein, we identify and report a 16-molecule architecture of native MRJP1 oligomer containing four MRJP1, four apisimin, and eight unanticipated 24-methylenecholesterol molecules at 2.65 Å resolution. MRJP1 has a unique six-bladed β-propeller fold with three disulfide bonds, and it interacts with apisimin mainly by hydrophobic interaction. Every four 24-methylenecholesterol molecules are packaged by two MRJP1 and two apisimin molecules. This assembly dimerizes to form an H-shaped MRJP1<sub>4</sub>-apisimin<sub>4</sub>-24-methylenecholesterol<sub>8</sub> complex via apisimin in a conserved and pH-dependent fashion. Our findings offer a structural basis for understanding the pharmacological effects of MRJPs and 24-methylenecholesterol, and provide insights into their unique physiological roles in bees.