gebhart/patrepeval huggingface dataset:
Self-Assembled Masks for the Transfer of Nanometer-Scale Patterns into Surfaces:  Characterization by AFM and LFM (2001)

A new methodology has been used to create an extensive array of nanometer-sized features. The Ar+ milling of Si/SiOx and gold surfaces covered with a diblock copolymer mask with an intrinsic topological nanopattern yields transfer of the nanopattern. Mask removal was tracked using XPS, and the final arrays were characterized by AFM and LFM. Friction contrast observed throughout the transferred pattern is associated with a surface water layer.
Reversal of intractable septic shock with norepinephrine therapy (1988)

Ten patients with severe septic shock were studied. After plasma volume expansion to an optimal pulmonary artery wedge pressure, above which there were no further increases in cardiac index, all patients remained hypotensive and oliguric. The arterial hypotension was unresponsive to increasing doses of dopamine and dobutamine alone and to a fixed combination of both. In all patients studied, infusion of norepinephrine alone reversed the hypotension and increased significantly the mean arterial pressure, systemic vascular resistance and left ventricular stroke work index (p less than .005). There were only minor increases in heart rate. Oxygen transport indices measured in six patients demonstrated variable alterations in oxygen delivery and consumption.
A spreadsheet approach to information visualization (2002)

In information visualization, as the volume and complexity of the data increases, researchers require more powerful visualization tools that enable them to more effectively explore multidimensional datasets. We discuss the general utility of a novel visualization spreadsheet framework. Just as a numerical spreadsheet enables exploration of numbers, a visualization spreadsheet enables exploration of visual forms of information. We show that the spreadsheet approach facilitates certain information visualization tasks that are more difficult using other approaches. Unlike traditional spreadsheets, which store only simple data elements and formulas in each cell, a visualization spreadsheet cell can hold an entire complex data set, selection criteria, viewing specifications, and other information needed for a full-fledged information visualization. Similarly, inter-cell operations are far more complex, stretching beyond simple arithmetic and string operations to encompass a range of domain-specific operators. We have built two prototype systems that illustrate some of these research issues. The underlying approach in our work allows domain experts to define new data types and data operations, and enables visualization experts to incorporate new visualizations, viewing parameters, and view operations.
Inhibition of IL-1 Signaling by Antisense Oligonucleotide-mediated Exon Skipping of IL-1 Receptor Accessory Protein (IL-1RAcP) (2013)

The cytokine interleukin 1(IL-1) initiates a wide range of proinflammatory cascades and its inhibition has been shown to decrease inflammation in a variety of diseases. IL-1 receptor accessory protein (IL-1RAcP) is an indispensible part of the IL-1R complex that stabilizes IL-1/IL-1R interaction and plays an important role in the signal transduction of the receptor complex. The soluble form of IL-1RAcP (sIL-1RAcP) contains only the extracellular domain and serves as a natural inhibitor of IL-1 signaling. Therefore, increasing sIL-1RAcP levels might be an attractive therapeutic strategy to inhibit IL-1-driven inflammation. To achieve this we designed specific antisense oligonucleotides (AON), to redirect pre-mRNA IL-1RAcP splicing by skipping of the transmembrane domain encoding exon 9. This would give rise to a novel Δ9IL-1RAcP mRNA encoding a soluble, secreted form of IL-1RAcP, which might have similar activity as natural sIL-1RAcP. AON treatment resulted in exon 9 skipping both in vitro and in vivo. A single dose injection of 10 mg AON/kg body weight induced 90% skipping in mouse liver during at least 5 days. The truncated mRNA encoded for a secreted, soluble Δ9IL-1RAcP protein. IL-1RAcP skipping resulted in a substantial inhibition of IL-1 signaling in vitro. These results indicate that skipping of the transmembrane encoding exon 9 of IL-1RAcP using specific AONs might be a promising therapeutic strategy in a variety of chronic inflammatory diseases.Molecular Therapy - Nucleic Acids (2013) 2, e66; doi:10.1038/mtna.2012.58; published online 22 January 2013.
Shared Mechanisms of Neurodegeneration in Alzheimer’s Disease and Parkinson’s Disease (2014)

Alzheimer's disease (AD) and Parkinson's disease (PD) have markedly different clinical and pathological features, but these two diseases are the most common neurodegenerative disorders. Previous studies have showed that there are common mechanisms in AD and PD. Several genetic studies have revealed mutations in genes associated with the risk of AD and PD. Circumstantial evidences have shown that dysregulation of brain iron homeostasis leads to abnormal iron accumulation and results in AD as well as PD. α -Synuclein and tau take part in the mechanisms of these diseases by oxidative stress and mitochondrial dysfunction. Some studies indicated that the loss of LC noradrenergic neurons may occur early in the progression of AD and PD. Nicotinic acetylcholine receptors (nAChRs) are members of the Cys-loop superfamily of pentameric ligand-gated ion channels; some evidence showed that nicotinic receptors may be associated with AD and PD. These experimental and clinical studies may provide a scientific foundation for common shared mechanisms in AD and PD.
Binding of murine monoclonal antibodies to the active and inactive configurations of aequorin (1989)

Murine monoclonal IgG1 antibodies (MAb), designated Aq-11 and Aq-12, were prepared against the photoprotein aequorin from jelly fish. Aequorin is a calcium-sensitive photoprotein which consists of a single polypeptide chain, apoaequorin, and a functional chromophore, coelenterazine. Native aequorin consists of two species with molecular masses of 25 and 23.5 kDa. MAb Aq-12 was found by immunoblot analysis to bind specifically to the 25 kDa species, while MAb Aq-11 reacted with the 23.5 kDa protein. Activation of apoaequorin with coelenterazine was associated with a shift of the 23.5 kDa molecule to the 25 kDa species. In contrast, treatment with calcium ions induced a shift back to the 23.5 kDa form. These changes between the active and inactive forms were identified by reactivity with MAbs Aq-11 and Aq-12. The results thus indicate that these MAbs should be useful in monitoring activation of this photoprotein.
CD40 and its ligand, an essential ligand-receptor pair for thymus-dependent B-cell activation (1992)

The discovery of CD40 and its ligand, gp39, have created new perspectives on the activation of resting B cells by TH cells. Here, Randolph Noelle, Jeffrey Ledbetter and Alejandro Aruffo describe how these molecules were characterized and, from recent findings, examine their relevance to immune activation.
Polycrystalline and Monocrystalline Pore Arrays with Large Interpore Distance in Anodic Alumina (1999)

We have prepared hexagonally arranged pore arrays with large interpore distance by using two kinds of techniques: a self‐organization process and a prepattern guided anodization on aluminum. The self‐organized pore arrays were produced by anodizing aluminum in an aqueous phosphoric acid solution , and show a polycrystalline, i.e., poly‐domain, feature. Within each domain of several micrometers, the arrays are hexagonally arranged with an interpore distance of , while the domains are oriented randomly in plane. A monocrystalline pore array structure with variable interpore distance was prepared based on electron‐beam lithography and a subsequent anodization in oxalic acid solution. With a well‐designed set of anodization parameters, the prepattern can act as the initiation points and guide the pore growth in the anodic film. Very high aspect ratios (∼500) can be achieved. ©2000 The Electrochemical Society
Ursodeoxycholic Acid Therapy in Primary Biliary Cirrhosis (1994)

In a total of 1004 patients in 11 controlled trials, treatment with ursodeoxycholic acid (UDCA) 8-15 mg/kg bodyweight per day led to a decrease of pruritus in 30-60% of cases, a decrease in aminotransferases and cholestasis-indicating enzymes in serum by 20-80%, and a decrease of serum bilirubin by 3-40%. A statistically significant improvement in liver histology was found in only two of these studies; in three others there was a positive trend. In three more trials histology was not examined, and in three studies there was no improvement. In the four studies investigating the time elapsed before liver transplantation and the number of deaths, only one definitely found that this was prolonged by UDCA, although in two of the other three there was a positive trend. During treatment, UDCA constitutes 30-50% of the total bile acids in bile and serum; however, its influence on the toxic bile acids is debatable. Cholic acid decreases, but deoxycholic acid and chenodeoxycholic acid are reduced to a lesser degree. UDCA therapy has now been practiced for 12 years and all authors consider the treatment to be safe, but the mode of action of UDCA is still unknown.
Comparative incorporation of tritium from tritiated water versus tritiated thymidine, uridine or leucine. (1978)

Whereas the radiotoxicity of tritium has been extensively studied, comparatively little information exists on its long-term effects as a potential environmental pollutant, particularly at small dosage. This investigation was primarily aimed at assessing comparatively a possible carcinogenic potency of tritiated water versus radioactive precursors of DNA, RNA and proteins, namely tritiated thymidine, uridine and leucine in C57 Black mice. Tritium is largely released in the environment in the form of tritiated water. There are many uncertainties, however, as to how tritium is incorporated from tritiated water into cell constituents quantitively and qualitatively. In 1965, we reported on the carcinogenic effect of tritium in the form of tritiated thymidine on newborn C57 BL mice in the dose range of 0.3--1.5 muCi/g [Mewissen. 1965]. Hence the selection of tritiated water, and of tritiated precursors, in an attempt to evaluate their respective role in the tritium transfer process and to correlate their possible late effects with their specific patterns or sites of incorporation. This study deals with tritium incorporation from tritiated water and various precursors at the 1 or 10 muCi level. RSA values, i.e., the ratio of organically bound tritium per hydrogen content of dry tissue over aqueous tritium per hydrogen content of water, were estimated for newborn, juvenile and adult mice, at various time intervals (1, 8, 15, 22 and 29 days) following single administration of tritiated water, tritiated thymidine, uridine or leucine. The data available at this time show that administration of tritiated water (or precursors) result in a complex time dependent and age dependent residual activity dynamics both in the organic component and in the aqueous fraction of tissue. A few preliminary conclusions can be made. Following a single acute or brief exposure to tritiated water, values of activity become exceedingly small after a relatively short time period. In a steady state equilibrium, resulting from chronic exposure to tritiated drinking water, RSA values tend to stabilize. However, wide variations between various organs are to be expected, as suggested by their respective RSA values following a single exposure. In view of these observations, it would seem that a realistic estimate of the internal dose to the radiosensitive nucleus must take into consideration the age dependent incorporation of tritium from tritiated water, as well as the variation between organs. The carcinogenic risk has often been estimated from a uniform dose dependency model. The influence of time and space microdistribution of dose within tissues and more particularly at specific sites (such as DNA, RNA or protein) has received, as yet, little attention, as well as the relative contributions of the time sequence of dose absorption during the usually long latency period. Such factors, among others, may be critical in carcinogenesis from internal irradiation...
Suppressed crystallization of Hf-based gate dielectrics by controlled addition of Al2O3 using atomic layer deposition (2002)

We demonstrate significantly improved thermal stability of the amorphous phase for hafnium-based gate dielectrics through the controlled addition of Al2O3. The (HfO2)x(Al2O3)1−x films, deposited using atomic layer deposition, exhibit excellent control over a wide range of composition by a suitable choice of the ratio between the Al and Hf precursor pulses. By this method, extremely predictable hafnium aluminate compositions are obtained, with Hf cation fractions ranging from 20% up to 100%, as measured by medium energy ion scattering. Using x-ray diffraction, we show that (HfO2)x(Al2O3)1−x films with Hf:Al∼3:1 (25% Al) remain amorphous up to 900 °C, while films with Hf:Al∼1:3 (75% Al) remain amorphous after a 1050 °C spike anneal.
The Effect of Precursor Structures on the Action of Glucosaminyl 3-O-Sulfotransferase-1 and the Biosynthesis of Anticoagulant Heparan Sulfate (2001)

To understand how 2-O-sulfation of uronic acid residues influences the biosynthesis of anticoagulant heparan sulfate, the cDNA encoding glucosaminyl 3-O-sulfotransferase-1 (3-OST-1) was introduced into wild-type Chinese hamster ovary cells and mutant pgsF-17 cells, which are defective in 2-O-sulfation. 3-OST-1-transduced cells gained the ability to bind to antithrombin. Structural analysis of the heparan sulfate chains showed that 3-OST-1 generates sequences containing GlcUA-GlcN(SO(3))3(SO(3)) and GlcUA-GlcN(SO(3))3(SO(3))6(SO(3)) in both wild-type and mutant cells. In addition, IdoUA-GlcN(SO(3))3(SO(3)) and IdoUA-GlcN(SO(3))3(SO(3))6(SO(3)) accumulate in the mutant chain. These disaccharides were also observed by tagging [6-(3)H]GlcN-labeled pgsF-17 heparan sulfate in vitro with [(35)S]PAPs and purified 3-OST-1. Heparan sulfate derived from the transduced mutant also had approximately 2-fold higher affinity for antithrombin than heparan sulfate derived from the transduced wild-type cells, and it inactivated factor Xa more efficiently. This study demonstrates for the first time that (i) 3-O-sulfation by 3-OST-1 can occur independently of the 2-O-sulfation of uronic acids, (ii) 2-O-sulfation usually occurs before 3-O-sulfation, (iii) 2-O-sulfation blocks the action of 3-OST-1 at glucosamine residues located to the reducing side of IdoUA units, and (iv) that alternative antithrombin-binding structures can be made in the absence of 2-O-sulfation.
Understanding the neural mechanisms of lisdexamfetamine dimesylate (LDX) pharmacotherapy in Binge Eating Disorder (BED): a study protocol (2019)

ACTRN12618000623291, Australian and New Zealand Clinical Trials Registry URL: https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=374913&isReview=true. Date of Registration: 20 April 2018.
Anatomy of Escherichia coli σ 70 promoters (2006)

Information theory was used to build a promoter model that accounts for the -10, the -35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base -7, rather than -11, of the -10 may be flipping to initiate transcription. We found that the sequence conservation of sigma70 binding sites is 6.5 +/- 0.1 bits. Some promoters lack a -35 region, but have a 6.7 +/- 0.2 bit extended -10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended -10 binding and the -35 suggest that the flexible bipartite sigma factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5' mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the -35, so bending allows distal activators to reach the polymerase.
Novel Monoclonal Antibodies with Specificity for Chelated Uranium(VI):  Isolation and Binding Properties (2004)

A derivative of 1,10-phenanthroline that binds to UO(2)(2+) with nanomolar affinity was found to be a very effective immunogen for the generation of antibodies directed toward chelated complexes of hexavalent uranium. This study describes the synthesis of 5-isothiocyanato-1,10-phenanthroline-2,9-dicarboxylic acid and its use in the generation and functional characterization of a group of monoclonal antibodies that recognize the most soluble and toxic form of uranium, the hexavalent uranyl ion (UO(2)(2+)). Three different monoclonal antibodies (8A11, 10A3, and 12F6) that recognize the 1:1 complex between UO(2)(2+) and 2,9-dicarboxy-1,10-phenanthroline (DCP) were produced by the injection of BALB/c mice with DCP-UO(2)(2+) covalently coupled to a carrier protein. Equilibrium dissociation constants for the binding of DCP-UO(2)(2+) to antibodies 8A11, 10A3, and 12F6 were 5.5, 2.4, and 0.9 nM, respectively. All three antibodies bound the metal-free DCP with roughly 1000-fold lower affinity. The second-order rate constants for the bimolecular association of each antibody with soluble DCP-UO(2)(2+) were in the range of 1 to 2 x 10(7) M(-1) s(-1). Binding studies conducted with structurally related chelators and 21 metal ions demonstrated that each of these three antibodies was highly specific for the soluble DCP-UO(2)(2+) complex. Detailed equilibrium binding studies conducted with three other derivatives of DCP, either complexed with UO(2)(2+) or metal-free, suggested that the antigen binding sites on the three antibodies have significant functional and structural similarities. Biomolecules that bind specifically to uranium will be at the heart of any new biotechnology developed to monitor and control uranium contamination. The three antibodies described herein possess sufficient affinity and specificity to support the development of immunoassays for hexavalent uranium in environmental and clinical samples.
Bone Marrow Plasminogen Activator Inhibitor-1 Influences the Development of Obesity (2006)

Plasma levels of plasminogen activator inhibitor-1 (PAI-1) are elevated in obesity and correlate with body mass index. The increase in PAI-1 associated with obesity likely contributes to increased cardiovascular risk and may predict the development of type 2 diabetes mellitus. Although adipocytes are capable of synthesizing PAI-1, the bulk of evidence indicates that cells residing in the stromal fraction of visceral fat are the primary source of PAI-1. We hypothesized that bone marrow-derived PAI-1, e.g. derived from macrophages located in visceral fat, contributes to the development of diet-induced obesity. To test this hypothesis, male C57BL/6 wild-type mice and C57BL/6 PAI-1 deficient mice were transplanted with either PAI-1(-/-), PAI-1(+/-), or PAI-1(+/+) bone marrow. The transplanted animals were subsequently fed a high fat diet for 24 weeks. Our findings show that only the complete absence of PAI-1 protects from the development of diet-induced obesity, whereas the absence of bone marrow-derived PAI-1 protects against expansion of the visceral fat mass. Remarkably, there is a link between the PAI-1 levels, the degree of inflammation in adipose tissue, and the development of obesity. Based on these findings we suggest that bone marrow-derived PAI-1 has an effect on the development of obesity through its effect on inflammation.
Enzyme-linked Immunoassay (1975)

Rabbit anti-human IgG antibody was mildly reduced in the presence of 10 mM 2-mercaptoethylamine and then coupled to beta-D-galactosidase [EC 3.2.1.23] from Escherichia coli using N,N'-o-phenylenedimaleimide. Human IgG and the anti-human IgG antibody-beta-D-galactosidase complex were successively adsorbed on Sepharose 4B binding rabbit anti-human IgG antibody. In this way amounts of human IgG as small as 5X10(-15) moles could be measured by determining the activity of beta-D-galactosidase bound to the Sepharose.
Comprehensive in vitro characterization of PD-L1 small molecule inhibitors (2019)

Blockade of the programmed cell death 1 (PD-1)/programmed cell death-ligand 1 (PD-L1) interaction has emerged as a powerful strategy in cancer immunotherapy. Recently, there have been enormous efforts to develop potent PD-1/PD-L1 inhibitors. In particular, Bristol-Myers Squibb (BMS) and Aurigene Discovery Technologies have individually disclosed several promising PD-1/PD-L1 inhibitors, whose detailed experimental data are not publicly disclosed. In this work, we report the rigorous and systematic in vitro characterization of a selected set of potent PD-1/PD-L1 macrocyclic peptide (BMSpep-57) and small-molecule inhibitors (BMS-103, BMS-142) from BMS and a peptidomimetic small-molecule inhibitor from Aurigene (Aurigene-1) using a series of biochemical and cell-based assays. Our results confirm that BMS-103 and BMS-142 are strongly active in biochemical assays; however, their acute cytotoxicity greatly compromised their immunological activity. On the other hand, Aurigene-1 did not show any activity in both biochemical and immunological assays. Furthermore, we also report the discovery of a small-molecule immune modulator, whose mode-of-action is not clear; however, it exhibits favorable drug-like properties and strong immunological activity. We hope that the results presented here will be useful in guiding the development of next-generation PD-1/PD-L1 small molecule inhibitors.
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing (2010)

The extreme genetic heterogeneity of nonsyndromic hearing loss (NSHL) makes genetic diagnosis expensive and time consuming using available methods. To assess the feasibility of target-enrichment and massively parallel sequencing technologies to interrogate all exons of all genes implicated in NSHL, we tested nine patients diagnosed with hearing loss. Solid-phase (NimbleGen) or solution-based (SureSelect) sequence capture, followed by 454 or Illumina sequencing, respectively, were compared. Sequencing reads were mapped using GSMAPPER, BFAST, and BOWTIE, and pathogenic variants were identified using a custom-variant calling and annotation pipeline (ASAP) that incorporates publicly available in silico pathogenicity prediction tools (SIFT, BLOSUM, Polyphen2, and Align-GVGD). Samples included one negative control, three positive controls (one biological replicate), and six unknowns (10 samples total), in which we genotyped 605 single nucleotide polymorphisms (SNPs) by Sanger sequencing to measure sensitivity and specificity for SureSelect-Illumina and NimbleGen-454 methods at saturating sequence coverage. Causative mutations were identified in the positive controls but not in the negative control. In five of six idiopathic hearing loss patients we identified the pathogenic mutation. Massively parallel sequencing technologies provide sensitivity, specificity, and reproducibility at levels sufficient to perform genetic diagnosis of hearing loss.