gebhart/patrepeval huggingface dataset:
Pd(OH)2/C (Pearlman's Catalyst):  A Highly Active Catalyst for Fukuyama, Sonogashira, and Suzuki Coupling Reactions (2003)

Treatment of thiol esters 1 with zinc reagent 2 in the presence of a small amount (<ca. 1 mol %) of nonpyrophoric Pd(OH)(2)/C (Pearlman's catalyst) provided functionalized asymmetrical ketones 3 in high yields. The use of Pd(OH)(2)/C was further applied to Sonogashira and Suzuki coupling reactions to afford the desired products in high yields.
A novel carboxypeptidase B that processes native β‐amyloid precursor protein is present in human hippocampus (2000)

The processing of beta-amyloid precursor protein (APP) and generation of beta-amyloid (Abeta) are associated with the pathophysiology of Alzheimer's disease (AD). As the proteases responsible for the process in the human brain have yet to be clarified, we have searched for activities capable of cleaving native brain APP in the human hippocampus. A 40-kDa protein with proteolytic activity that degrades native brain APP in vitro was purified and characterized; molecular analysis identified it as a novel protease belonging to the carboxypeptidase B (CPB) family. PC12 cells overexpressing the cDNA encoding this protease generate a major 12-kDa beta-amyloid-bearing peptide in cytosol, a peptide which has also been detected in a cell-free system using purified brain APP as substrate. Although the protease is homologous to plasma CPB synthesized in liver, it has specific domains such as C-terminal 14 amino acid residues. Western analysis, cDNA-cloning process and Northern analysis suggested a brain-specific expression of this protease. An immunohistochemical study showed that the protease is expressed in various neuronal perikarya, including those of pyramidal neurons of the hippocampus and ependymal-choroid plexus cells, and in a portion of the microglia of normal brains. In brains of patients with sporadic AD, there is decreased neuronal expression of the protease, and clusters of microglia with protease immunoreactivity associated with its extracellular deposition are detected. These findings suggest that brain CPB has a physiological function in APP processing and may have significance in AD pathophysiology.
Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability (2016)

Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic transmission, is a typical case of a human protein that necessitates mammalian systems to obtain functional expression. We developed a computational strategy and designed an AChE variant bearing 51 mutations that improved core packing, surface polarity, and backbone rigidity. This variant expressed at ∼2,000-fold higher levels in E. coli compared to wild-type hAChE and exhibited 20°C higher thermostability with no change in enzymatic properties or in the active-site configuration as determined by crystallography. To demonstrate broad utility, we similarly designed four other human and bacterial proteins. Testing at most three designs per protein, we obtained enhanced stability and/or higher yields of soluble and active protein in E. coli. Our algorithm requires only a 3D structure and several dozen sequences of naturally occurring homologs, and is available at http://pross.weizmann.ac.il.
Discovery of a novel class of potent HIV-1 protease inhibitors containing the (R)-(hydroxyethyl)urea isostere (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiscovery of a novel class of potent HIV-1 protease inhibitors containing the (R)-(hydroxyethyl)urea isostereDaniel P. Getman, Gary A. DeCrescenzo, Robert M. Heintz, Kathryn L. Reed, John J. Talley, Martin L. Bryant, Michael Clare, Kathryn A. Houseman, J. Joseph Marr, and Cite this: J. Med. Chem. 1993, 36, 2, 288–291Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jm00054a014https://doi.org/10.1021/jm00054a014research-articleACS PublicationsRequest reuse permissionsArticle Views679Altmetric-Citations157LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR (2002)

Real-time reverse transcription followed by polymerase chain reaction (RT-PCR) is the most suitable method for the detection and quantification of mRNA. It offers high sensitivity, good reproducibility and a wide quantification range. Today, relative expression is increasingly used, where the expression of a target gene is standardised by a non-regulated reference gene. Several mathematical algorithms have been developed to compute an expression ratio, based on real-time PCR efficiency and the crossing point deviation of an unknown sample versus a control. But all published equations and available models for the calculation of relative expression ratio allow only for the determination of a single transcription difference between one control and one sample. Therefore a new software tool was established, named REST (relative expression software tool), which compares two groups, with up to 16 data points in a sample and 16 in a control group, for reference and up to four target genes. The mathematical model used is based on the PCR efficiencies and the mean crossing point deviation between the sample and control group. Subsequently, the expression ratio results of the four investigated transcripts are tested for significance by a randomisation test. Herein, development and application of REST is explained and the usefulness of relative expression in real-time PCR using REST is discussed. The latest software version of REST and examples for the correct use can be downloaded at http://www.wzw.tum.de/gene-quantification/.
Demystifying DNA Demethylation (2011)

DNA modifying and repair enzymes make a new connection in the mechanism of DNA demethylation.
Synthesis of Thermally Stable Carboxymethyl Cellulose/Metal Biodegradable Nanocomposites for Potential Biological Applications (2007)

A green approach is described that generates bulk quantities of nanocomposites containing transition metals such as Cu, Ag, In, and Fe at room temperature using a biodegradable polymer, carboxymethyl cellulose (CMC), by reacting respective metal salts with the sodium salt of CMC in aqueous media. These nanocomposites exhibit broader decomposition temperatures when compared with control CMC, and Ag-based CMC nanocomposites exhibit a luminescent property at longer wavelengths. The noble metals such as Au, Pt, and Pd do not react at room temperature with aqueous solutions of CMC, but do so rapidly under microwave irradiation (MW) conditions at 100 degrees C. This environmentally benign approach, which provides facile entry to the production of multiple shaped noble nanostructures without using any toxic reducing agent such as sodium borohydride (NaBH4), hydroxylamine hydrochloride, and so forth, and/or a capping/surfactant agent, and which uses a benign biodegradable polymer CMC, could find widespread technological and medicinal applications. The ensuing nanocomposites derived at room temperature and MW conditions were characterized using scanning electron microscopy, transmission electron microscopy, infrared spectroscopy, UV-visible spectroscopy, X-ray mapping, energy-dispersive analysis, and thermogravimetric analysis.
Tumor Biologic Factors and Breast Cancer Prognosis Among White, Hispanic, and Black Women in the United States (1994)

A number of biologic factors associated with poor prognosis are found with a significantly increased frequency in breast tumors from Hispanic and, particularly, from black women. Tumors with a more aggressive biology could lead to a higher stage at diagnosis and a poorer survival for the group as a whole.
Growth factors in the treatment of diabetic foot ulcers (2003)

Abstract Background Chronic foot ulceration is a major source of morbidity in diabetic patients. Despite traditional comprehensive wound management, including vascular reconstruction, there remains a cohort of patients with non-responding wounds, often resulting in amputation. These wounds may benefit from molecular manipulation of growth factors to enhance the microcirculation. Methods A review of the current literature was performed using Pubmed, with secondary references obtained from key articles. Results and conclusion There has been a generally disappointing clinical outcome from growth factor trials, although topical platelet-derived growth factor has shown significant benefit and should be considered in non-healing, well perfused ulcers after failure of conventional wound care. The modulatory role of the extracellular matrix in the cellular response to growth factors and data from regenerative-type fetal wound healing are further areas of interest. The chemical induction of microvessel formation may become a future therapeutic option.
Non‐coding RNAs: regulators of disease (2009)

For 50 years the term 'gene' has been synonymous with regions of the genome encoding mRNAs that are translated into protein. However, recent genome-wide studies have shown that the human genome is pervasively transcribed and produces many thousands of regulatory non-protein-coding RNAs (ncRNAs), including microRNAs, small interfering RNAs, PIWI-interacting RNAs and various classes of long ncRNAs. It is now clear that these RNAs fulfil critical roles as transcriptional and post-transcriptional regulators and as guides of chromatin-modifying complexes. Here we review the biology of ncRNAs, focusing on the fundamental mechanisms by which ncRNAs facilitate normal development and physiology and, when dysfunctional, underpin disease. We also discuss evidence that intergenic regions associated with complex diseases express ncRNAs, as well as the potential use of ncRNAs as diagnostic markers and therapeutic targets. Taken together, these observations emphasize the need to move beyond the confines of protein-coding genes and highlight the fact that continued investigation of ncRNA biogenesis and function will be necessary for a comprehensive understanding of human disease.
Wetting on Fractal Superhydrophobic Surfaces from “Core−Shell” Particles: A Comparison of Theory and Experiment (2009)

We report an experimental and theoretical investigation of the wetting behavior of different model polar and nonpolar liquids and their mixtures on superhydrophobic fractal surfaces made of polymer- or silane-coated "core-shell" particles. We compared the experimental results with the theoretical predictions made according to the theories of Onda-Shibuichi (describes wetting on fractal surfaces) and Cassie-Baxter (describes wetting on generic rough composite surfaces). We found that the experimental findings deviate from the behavior predicted by the Onda-Shibuichi model. On the other hand, the wetting properties were found to be close to the predictions made by the Cassie-Baxter model in the hydrophobic region (the intrinsic contact angle on the flat surface is larger than 90 degrees). However, the wetting behavior in the hydrophilic region (the intrinsic contact angle is less than 90 degrees) could not be described by the Onda-Shibuichi or Cassie-Baxter model. The observed inconsistency between the experimental results and theoretical predictions was explained by the formation of metastable states of a liquid droplet on a fabricated fractal surface according to the theory developed by Johnson and Dettre for generic rough surfaces. The entrapments of the liquid droplets in metastable states resulted in superhydrophobic behavior on fractal surfaces as well, made from nonfluorinated material such as polystyrene with a surface free energy of about 30 mJ/m2. This finding is very promising for real industrial applications where fluorinated compounds are willing to be reduced. It can be concluded that employing a texture with fractal geometry is necessary for the design of superhydrophobic coatings. Thereby, extremely lowering the surface free energy of materials by fluorination is not an obligatory factor for the generation of liquid-repellent superhydrophobic materials. We believe that the results we presented in the paper give new insight into the understanding of wetting not only on general superhydrophobic rough surfaces but also on fractal surfaces.
CHEMICAL MODIFICATIONS OF PROTEINS: A REVIEW (1998)

The chemical modifications of proteins are reviewed. Subjects include: (1) modifications done to study protein function; (2) two naturally occurring modifications: carbonylamine reactions and reactions with nitric oxide; (3) applications for bioconjugation and mass spectral analysis; and (4) modifications of food proteins.
Physical and chemical properties of boronic acids: Formulation implications (2006)

References Acknowledgements Boronic acid compounds are the focus of increasing interest as therapeutic agents due to their ability to inhibit enzyme activity, among other characteristics. Many peptide boronic acid compounds have been investigated as enzyme inhibitors with implications in pathologies as varied as Alzheimer’s disease, cervical cancer, blood clotting disorders, hepatitis C, etc. (1). In 2003 the drug Velcade® (bortezomib), figure 1, was approved by the FDA as a second-line treatment for multiple myeloma, it acts via inhibition of the 26S proteasome in mammalian cells (2). As shown in scheme 1, the role of the boronic acid moiety in this inhibition is to interact with the hydroxyl of the N-terminal threonine of the β-subunit of the proteasome (3).
Structural basis for acyl-group discrimination by human Gcn5L2 (2016)

Gcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modifications in vivo, the acyl-chain specificity of the acetyltransferase human Gcn5 (Gcn5L2) was examined. Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 becomes progressively weaker with increasing acyl-chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA were determined. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor of Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl-chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group.
Recent advances in energy-efficient networks and their application in 5G systems (2015)

This article provides an overview on research in energy-efficient wireless networks during the past decade and discusses its potential applications toward the fifth generation cellular systems. After analyzing the trade-off between spectrum efficiency and energy efficiency, various research results are summarized within a framework of energy-efficient resource allocation with optimization as a common tool. Then potential energy efficiency improving approaches in both physical layer and deployment aspects are provided. Finally, energy efficiency related open problems in massive multiple-input multiple- output, device-to-device communications, ultra dense networks, and other emerging technologies are identified.
Liver Stiffness Measurement Using XL Probe in Patients With Nonalcoholic Fatty Liver Disease (2012)

LSM by XL probe can be performed successfully in most NAFLD patients, but obesity is associated with less accurate and reliable measurements.
Targeting of Polyelectrolyte RNA Complexes to Cell Surface Integrins as an Efficient Cytoplasmic Transfection Mechanism (2002)

This is the first demonstration of receptor-mediated delivery of mRNA and establishes a new approach to gene therapy. Messenger RNA (mRNA) provides a promising alternative to plasmid DNA as a genetic material for delivery in non-viral gene therapy strategies. Since it does not require access to the nucleus and is less dependent on the cell cycle for expression, mRNA delivered using cationic lipids or short cationic polymers can be effectively translated within target cells. In this study, mRNA formed discrete nanoparticles following self assembly with a range of cationic polymers. Based on transfection activities, the low molecular weight polycations were more efficient than high molecular weight, while protamine and polyethylenimine were far more efficient than poly(L-lysine). Receptor-mediated delivery of mRNA was demonstrated using the synthetic polyamino acid (K) 16 GACDCRGDCFCA designed to promote cell entry following interaction with cell surface α υ integrins. RGD-bearing mRNA complexes showed very high levels of expression, reaching over 60% transduction of B16F10 cells.
Chromosome aberrations and sister chromatid exchanges in chinese hamster ovary cells: Evaluations of 108 chemicals (1987)

Results from the testing of 108 coded chemicals in Chinese hamster ovary (CHO) cells for the induction of chromosome aberrations and sister chromatid exchanges (SCEs) are presented. All chemicals were tested with and without exogenous metabolic activation, using protocols designed to allow testing up to toxic doses. Cell harvest times could also be extended if chemical-induced cell cycle delay was seen. Chromosome aberrations were induced by 43 of the chemicals, and 66 induced SCEs; 37 of the chemicals were positive for both endpoints.
Structure of the human prealbumin gene. (1985)

Using cloned human prealbumin cDNA as a probe, Southern blot hybridization of human genomic DNA revealed that the prealbumin gene consists of an unique, single-copy DNA. The nucleotide sequences of the entire human prealbumin gene, including both 581 base pairs of the 5'- and 95 base pairs of the 3'-flanking sequences, were determined. The gene spans about 7.0 kilobase pairs and consists of four exons and three introns. As in most eukaryotic genes, the consensus TATA and CAAT sequences are found 30 and 101 nucleotides, respectively, upstream from the putative cap site, and a polyadenylation signal sequence AA-TAAA is found in the 3'-untranslated region. Unexpectedly, two independent open reading frames provided with respective regulatory sequences were found within the gene: one in the first intron and the other in the third intron.
CXCR4 chemokine receptors, histone deacetylase inhibitors and acute lymphoblastic leukemia (2005)

Acute lymphoblastic leukemia (ALL) is a malignancy with the potential to infiltrate the liver, spleen, lymph nodes and brain. The mechanism for selective homing of ALL cells to preferential sites has long been unclear. Recent reports indicate that the chemokine receptor CXCR4 is found on ALL cells and its ligand is highly expressed at sites associated with ALL-induced organ infiltration. This results in chemotaxis, or directed migration of leukemic cells from the bone marrow via the circulation to preferential sites of extramedullary organ infiltration. Because overexpression of CXCR4 on ALL cells is associated with high extramedullary organ infiltration and shorter disease-free survival, numerous pharmacological agents affecting CXCR4 have currently been investigated. The most promising data are available for histone deacetylase inhibitors (HDAIs), which have been shown to be safe and well tolerated in phase I clinical trials. In vitro, HDAIs extensively down-regulate CXCR4 protein and mRNA levels. As a result, the ability of CXCR4 ligand to induce cellular migration is impaired. Wider recognition of the role of CXCR4 in ALL and manipulation of this important mechanism may lead to novel approaches in the treatment and outcome of this disease.
Isolation of Avian Pneumovirus from an Outbreak of Respiratory Illness in Minnesota Turkeys (2000)

Antibodies to avian pneumovirus (APV) were first detected in Minnesota turkeys in 1997. Virus isolation was attempted on 32 samples (28 tracheal swabs, 4 pools of trachea and turbinates) that were positive for APV by reverse transcriptase polymerase chain reaction (RT-PCR). The cell cultures used were chicken embryo fibroblast (CEF), Vero cells, and QT-35 cells. Five virus isolates were obtained from these samples, and the identity of the isolates was confirmed by RT-PCR. Four isolates were obtained by inoculation of CEF cells, and 1 isolate was obtained in QT-35 cells after 3-7 blind passages in cell cultures. Vero cells did not yield any isolate on primary isolation; however, all 5 isolates could be adapted to grow in Vero cells following primary isolation in CEF or QT-35 cells. This is the first report of isolation of APV in Minnesota and also the first report of primary isolation of APV in QT-35 cells.
New Donor−Acceptor Pair for Fluorescent Immunoassays by Energy Transfer (1999)

A novel Förster donor-acceptor dye pair for an immunoassay based on resonance energy transfer (RET) is characterized with respect to its photophysical properties. As donor and acceptor, we chose the long-wavelength excitable cyanine dyes Cy5 and Cy5.5, respectively. Due to the perfect spectral overlap, an exceptionally high R(0) value of 68.7 A is obtained in solution. For biochemical applications, antibodies (IgG) are labeled with Cy5, while a tracer for competitive binding is synthesized by labeling bovine serum albumin (BSA) with an analyte derivative and Cy5.5. Binding the dyes to proteins at a low dye/protein ratio increases the fluorescence lifetimes and quantum yields, leading to an enhanced R(0) value of 85.2 A. At higher dye/protein ratios, the formation of nonfluorescent dimeric species causes a decrease in the fluorescence lifetime and quantum yield due to RET from monomeric dyes to dimers within one protein molecule. The Förster distances could be calculated using the dimer absorption spectra to 83.9 and 83.6 A for Cy5 and Cy5.5, respectively. Upon binding of the Cy5-labeled IgG to the tracer, efficient quenching of Cy5 fluorescence is observed. Steady-state and time-resolved measurements reveal that approximately 50% of the quenching results in Förster-type RET, while the residual quenching effect is caused by static quenching processes. The applicability of this dye pair is demonstrated in a homogeneous competitive immunoassay for the pesticide simazine.