gebhart/patrepeval huggingface dataset:
Towards area‐based in vitro metabolic engineering: Assembly of Pfs enzyme onto patterned microfabricated chips (2008)

We report an approach for spatially selective assembly of an enzyme onto selected patterns of microfabricated chips. Our approach is based on electrodeposition of the aminopolysaccharide chitosan onto selected electrode patterns and covalent conjugation of a target enzyme to chitosan upon biochemical activation of a genetically fused "pro-tag." We report assembly of S-adenosylhomocysteine nucleosidase (Pfs) fused with a C-terminal pentatyrosine pro-tag. Pfs is a member of the bacterial autoinducer-2 biosynthesis pathway, catalyzing the irreversible cleavage of S-adenosylhomocysteine. The assembled Pfs retains its catalytic activity and structure, as demonstrated by retained antibody recognition. Assembly is controlled by the electrode area, resulting in reproducible rates of catalytic conversion for a given area, and thus allowing for area-based manipulation of catalysis and small molecule biosynthesis. Our approach enables optimization of small molecule biosynthesis in 1-step as well as multistep enzymatic reactions, including entire metabolic pathways, and we envision a wide variety of potential applications.
Detection of soluble E-selectin, ICAM-1, VCAM-1, and L-selectin in the cerebrospinal fluid of patients after subarachnoid hemorrhage (1998)

Adhesion molecules are known to be involved in white cell adherence to the endothelium and subsequent diapedesis and migration in which a role in initiation of tissue damage is postulated. The authors have demonstrated the elevation of three adhesion molecules, with severely elevated levels of E-selectin seen in patients who later develop vasospasm. A correlation with a role of vascular adhesion molecules in the pathogenesis of cerebral vasospasm is suggested.
B (1993)

Die →Freizügigkeit von Arbeitskräften innerhalb der EG bildet einen von vier Eckpunkten der Entwicklung des Binnenmarktes. Die grenzüberschreitende Arbeitskräftemobilität wird jedoch durch unterschiedliche Berufsausbildungssysteme und differierende Abschlüsse wesentlich erschwert. Trotz der vorherrschenden Vielfalt der nationalen Berufsausbildungen innerhalb der Gemeinschaft besteht Übereinstimmung darin, daß keine Harmonisierung der verschiedenen Ausbildungen angestrebt, sondern primär die Vergleichbarkeit der Abschlußqualifikationen erhöht werden soll. Vielmehr soll eine Öffnung der Berufsausbildungssysteme für wechselseitigen Informations- und Erfahrungsaustausch — statt einer Vereinheitlichung der Abschlüsse — das allmähliche Zusammenwachsen erleichtern.
Location of plasminogen-binding sites in human fibrin(ogen) (1983)

Affinity chromatography of various fibrinogen and fibrin fragments on Lys-plasminogen-Sepharose was used to localize the plasminogen-binding sites in human fibrin(ogen). The fragments studied in the present investigation were derived from the central (E) and the terminal (D) globular domains of fibrinogen and fibrin. Our results showed that these two different, sequentially nonidentical domains of fibrin(ogen) both carry plasminogen-binding sites. Competitive affinity chromatography of fragment D1 and fragments derived from it by proteolytic modification of its D gamma-chain revealed that this modification causes an 11-fold increase of the association constant of the interaction with Lys-plasminogen-Sepharose. This suggests that the carboxy-terminal region of the D gamma-chain is involved in controlling the plasminogen-binding site of the D domain. In contrast with its fragments, intact fibrinogen is not retained by Lys-plasminogen-Sepharose, indicating that the plasminogen-binding sites present in the constituent E and D domains are not fully functional in the parent molecule. It seems possible that the plasminogen-binding sites are present but hidden in fibrinogen and proteolytic dissection of the molecule uncovers these sites in E and D fragments by removing peptides masking the plasminogen-binding regions.
In Vivo Labeling and Analysis of Epidermal Stem Cells (2004)

To identify slowly cycling (label-retaining) keratinocytes in the cutaneous epithelium of mice, newborn female pups were injected with [3H]-thymidine twice daily for 3 d beginning the third day after birth. At 8-10 wk of age, skin from the dorsal side of the mice was removed and fixed. The skin was processed for paraffin embedding, and serial sections were prepared. Dewaxed and ethanol-treated slides were dried and dipped into autoradiographic emulsion and allowed to dry in light tight box for 4 wk at 4 degrees C. After fixation with photographic fixer, the slides were washed, lightly stained, and viewed with a light microscope to observe and quantify cells that retained the labeling. Label-retaining cells were identified by the black silver grains over their nuclei.
5.625 Gbps bidirectional laser communications measurements between the NFIRE satellite and an Optical Ground Station (2011)

5.625 Gbps bidirectional laser communication at 1064 nm has been demonstrated on a repeatable basis between a Tesat coherent laser communication terminal with a 6.5 cm diameter ground aperture mounted inside the European Space Agency Optical Ground Station dome at Izana, Tenerife and a similar space based terminal (12.4 cm diameter aperture) on the Near Field Infrared Experiment low earth orbiting spacecraft. Both night and day bidirectional links were demonstrated with the longest being 177 seconds in duration. Correlation with atmospheric models and preliminary atmospheric r <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> and scintillation measurements have been made for the conditions tested, suggesting that such coherent systems can be deployed successfully at still lower altitudes without resorting to the use of adaptive optics for compensation.
PD-L1 Expression in Clear Cell Renal Cell Carcinoma: An Analysis of Nephrectomy and Sites of Metastases (2014)

The weak correlation between PD-L1 expression in primary and metastatic sites for a given patient suggests that expression in nephrectomy specimens cannot be used to select metastatic RCC patients for PD-L1 and PD-1 inhibitors. The intra-tumor heterogeneity seen in both primary and metastatic specimens indicates that a single core biopsy might not be sufficient to determine PD-L1 expression.
Evaluation of models that predict short-term outcome after traumatic brain injury (2007)

Most of the models included in this study have a good discriminatory power while lacking sufficient calibration. However, they all predict with relative accuracy at the level of individuals. Therefore, current models can be used to predict the survival rate of individual patients and may be useful to inform patients and relatives about the likelihood of a beneficial outcome.
Raster3D Version 2.0. A program for photorealistic molecular graphics (1994)

Raster3D Version 2.0 is a program suite for the production of photorealistic molecular graphics images. The code is hardware independent, and is particularly suited for use in producing large raster images of macromolecules for output to a film recorder or high-quality color printer. The Raster3D suite contains programs for composing illustrations of space-filling models, ball-and-stick models and ribbon-and-cylinder representations. It may also be used to render figures composed using other graphics tools, notably the widely used program Molscript [Kraulis (1991). J. Appl. Cryst. 24, 946-950].
Biological applications of gold nanoparticles (2008)

This critical review gives a short overview of the widespread use of gold nanoparticles in biology. We have identified four classes of applications in which gold nanoparticles have been used so far: labelling, delivering, heating, and sensing. For each of these applications the underlying mechanisms and concepts, the specific features of the gold nanoparticles needed for this application, as well as several examples are described (142 references).
An approach to color constancy using multiple images (2002)

A novel computational algorithm is proposed for color constancy suitable to robot vision. A robot, or a computer, can exactly memorize image information observed in the past. Then it is natural to use more than one image to achieve color constancy. In the algorithm, it is possible to recover the illumination color and the reflectance color only based on the RGB values of two objects identified on two images. It requires no specific assumption on the scene. Experiments show the validity of the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Proposed new electrolytic conductivity primary standards for KCl solutions (1991)

An absolute determination of aqueous electrolytic conductivity has been made for 0.01 molal (<i>m</i>) and 0.1 <i>m</i> potassium cliloride solutions, over the temperature range of 0 to 50 °C in 5 degree intervals. A cell with a removable center section of accurately known length and area was used for the measurements. Values were adjusted to be in conformity with the ITS-90 temperature scale. The overall uncertainty over the entire temperature range is estimated to be 0.03%. Values at 25 °C for 0.01 and 0.1 <i>m</i> are 0.00140823 and 0.0128246 S/cm, respectively. It is proposed that these values be adopted as primary standards for aqueous electrolytic conductivity, replacing the demal scale.
Proposal of Chlamydia Pecorum sp. nov. for Chlamydia Strains Derived from Ruminants (1992)

Chlamydia pecorum sp. nov. is proposed as the fourth species of the genus Chlamydia on the basis of the results of a genetic analysis of Chlamydia strains that were isolated from cattle and sheep which had various diseases, including sporadic encephalitis, infectious polyarthritis, pneumonia, and diarrhea. The levels of DNA-DNA homology between C. pecorum and strains of C. psittaci, Chlamydia pneumoniae, and Chlamydia trachomatis were less than 10%. Several DNA probes were used to identify C. pecorum. The C. pecorum strains were distinguished from C. psittaci strains by the results of immunological assays, including an immunofluorescence antibody assay performed with monoclonal antibodies and an immunoblot analysis of the immunological specificity of the major outer membrane protein. Species identification was based on results obtained from DNA analyses and serology. The type strain of C. pecorum is strain ATCC VR628.
Photobiomodulation for the treatment of retinal diseases: a review (2015)

Photobiomodulation (PBM), also known as low level laser therapy, has recently risen to the attention of the ophthalmology community as a promising new approach to treat a variety of retinal conditions including age-related macular degeneration, retinopathy of prematurity, diabetic retinopathy, Leber's hereditary optic neuropathy, amblyopia, methanol-induced retinal damage, and possibly others. This review evaluates the existing research pertaining to PBM applications in the retina, with a focus on the mechanisms of action and clinical outcomes. All available literature until April 2015 was reviewed using PubMed and the following keywords: "photobiomodulation AND retina", "low level light therapy AND retina", "low level laser therapy AND retina", and "FR/NIR therapy AND retina". In addition, the relevant references listed within the papers identified through PubMed were incorporated. The literature supports the conclusion that the low-cost and non-invasive nature of PBM, coupled with the first promising clinical reports and the numerous preclinical-studies in animal models, make PBM well-poised to become an important player in the treatment of a wide range of retinal disorders. Nevertheless, large-scale clinical trials will be necessary to establish the PBM therapeutic ranges for the various retinal diseases, as well as to gain a deeper understanding of its mechanisms of action.
N-acetyltransferase (NAT2) genotype and susceptibility to sporadic Alzheimer??s disease (1999)

The importance of environmental aggression and individual susceptibility to develop Alzheimer's Disease (AD) has been suggested by epidemiological studies on both typical familial and sporadic AD cases. In order to elucidate functions that can influence the susceptibility to AD pathogenesis, we genotyped a group of 53 sporadic late-onset AD patients, matched control individuals and a larger randomly selected non-demented population for the N-acetyltransferase (NAT2). We determined the relative frequencies of individual allele combinations that define a broad range of acetylator phenotypes. Inter-individual variability in the cytotoxic and genotoxic responses to a wide diversity of environmental chemicals is known to result from the polymorphism of NAT2 as well as other drug-metabolizing-enzyme genes. The results presented are the first to demonstrate a significant difference in the NAT2 genotype profiles of sporadic AD patients compared with the healthy population. A lower frequency of the recessive alleles NAT2*6 (chi-squared 1 d.f. = 12.56, P < 0.0004) and NAT2*5B (chi-squared 1 d.f. = 6.72, P < 0.01) was found among the AD population compared with control individuals, which was concomitant with a significantly higher number of NAT2*4 fully active allele homozygotes and heterozygotes (chi-squared 1 d.f. = 5.69, P = 0.017). The most notable observation was the absence of NAT2*5B/NAT2*6 heterozygotes among cases while being present in 22.5% of control individuals (chi-squared 1 d.f. = 13.08, P = 0.0003). These observations indicate that NAT2 is a potential low-penetrance gene in AD pathogenesis, determining an individual susceptibility trait predisposing to this degenerative disease.
Robust Disambiguation of Named Entities in Text (2011)

Disambiguating named entities in natural-language text maps mentions\nof ambiguous names onto canonical entities like people or places,\nregistered in a knowledge base such as DBpedia or YAGO. This paper\npresents a robust method for collective disambiguation, by\nharnessing context from knowledge bases and using a new form of\ncoherence graph. It unifies prior approaches into a comprehensive\nframework that combines three measures: the prior probability of an\nentity being mentioned, the similarity between the contexts of a\nmention and a candidate entity, as well as the coherence among\ncandidate entities for all mentions together. The method builds a\nweighted graph of mentions and candidate entities, and computes a\ndense subgraph that approximates the best joint mention-entity\nmapping. Experiments show that the new method significantly\noutperforms prior methods in terms of accuracy, with robust behavior\nacross a variety of inputs.
A role for surface lymphotoxin in experimental autoimmune encephalomyelitis independent of LIGHT (2003)

In studies using genetically deficient mice, a role for the lymphotoxin (LT) system in the pathogenesis of experimental autoimmune encephalomyelitis (EAE) has remained controversial. Here, we have reassessed this conclusion by using a fusion protein decoy that blocks the LT pathway in vivo without evoking the developmental defects inherent in LT-deficient mice. We have found that inhibition of the LT pathway prevented disease in two models of EAE that do not rely on the administration of pertussis toxin. Surprisingly, disease attenuation was due to specific blockade of LTalphabeta binding rather than the binding of LIGHT to its receptors. In a third system that requires pertussis toxin, LT inhibition did not affect disease, as was observed when the same model was used with LT-deficient mice. Disease prevention in pertussis toxin-free models was associated with defects in T cell responses and migration. When the DO11.10 T cell transgenic system was used, inhibition of the LT pathway was shown to uncouple T cell priming from T cell recall responses. Therefore, it is hypothesized that the LT pathway and its ability to maintain lymphoid microenvironments is critical for sustaining late-phase T cell responses in multiple sclerosis.
Review: Gene- and Stem Cell–Based Therapeutics for Bone Regeneration and Repair (2007)

Many clinical conditions require regeneration or implantation of bone. This is one focus shared by neurosurgery and orthopedics. Current therapeutic options (bone grafting and protein-based therapy) do not provide satisfying solutions to the problem of massive bone defects. In the past few years, gene- and stem cell-based therapy has been extensively studied to achieve a viable alternative to current solutions offered by modern medicine for bone-loss repair. The use of adult stem cells for bone regeneration has gained much focus. This unique population of multipotential cells has been isolated from various sources, including bone marrow, adipose, and muscle tissues. Genetic engineering of adult stem cells with potent osteogenic genes has led to fracture repair and rapid bone formation in vivo. It is hypothesized that these genetically modified cells exert both an autocrine and a paracrine effects on host stem cells, leading to an enhanced osteogenic effect. The use of direct gene delivery has also shown much promise for in vivo bone repair. Several viral and nonviral methods have been used to achieve substantial bone tissue formation in various sites in animal models. To advance these platforms to the clinical setting, it will be mandatory to overcome specific hurdles, such as control over transgene expression, viral vector toxicity, and prolonged culture periods of therapeutic stem cells. This review covers a prospect of cell and gene therapy for bone repair as well as some very recent advancements in stem cell isolation, genetic engineering, and exogenous control of transgene expression.
A Novel N-(Pyrrolidinyl-2-methyl)glycine-Based PNA with a Strong Preference for RNA over DNA (2002)

A novel, N-(pyrrolidinyl-2-methyl)glycine-based (Pmg-based) PNA is introduced. The synthesis of the backbone was accomplished in good yield, starting from prolinol. Thymine (S)- and (R)-Pmg and adenine- and cytosine-derived (R)-Pmg monomers were prepared. Five different fragments − two with either the (R) or the (S) isomer of the thymine Pmg monomer, two oligomers with two consecutive (R)- or (S)-thymine Pmg units, and fully modified (R)-Pmg decamer − were assembled on a solid support. UV thermal melting experiments with complementary DNA and RNA were performed in order to determine the effects of conformational restriction, steric hindrance, and chirality on the duplex stability. It was found that the (R)-Pmg-containing PNAs bound better to DNA and RNA than those containing the (S)-Pmg isomer and that both (S)- and (R)-Pmg-containing PNAs preferentially bound to complementary RNA with a selectivity higher than that of 2-(aminoethyl)glycine (Aeg) PNA. However, even (R)-Pmg-containing oligomers showed poorer duplex stability than nonmodified Aeg-PNA, while no detectable binding either to the DNA or to the RNA was observed with the fully modified (R)-Pmg decamer. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Peptide Synthesis Protocols (1994)

Procedures to Improve Difficult Couplings, Michael W. Pennington and Michael E. Byrnes. Methods for Removing the Fmoc Group, Gregg B. Fields. Solvents for Solid-Phase Peptide Synthesis, Cynthia G. Fields and Gregg B. Fields. HF Cleavage and Deprotection Procedures for Peptides Synthesized Using a Boc/Bzl Strategy, Michael W. Pennington. Acid Cleavage/Deprotection in Fmoc/tBu-Solid Phase Peptide Synthesis, Fritz Dick. Bromoacetylated Synthetic Peptides: Starting Materials for Cyclic Peptides, Peptomer, and Peptide Conjugates. Frank A. Robey. Formation of Disulfide Bonds in Synthetic Peptides and Proteins, David Andreau, Fernando Albericio, Nuria A. Sole, Mark C. Munson, Marc Ferrer, and George Barany. Site-Specific Chemical Modification Procedures, Michael W. Pennington. Synthesis of Phosphopeptides Containing O-Phosphoserine and O-Phosphothreonine, Anatol Arendt and Paul A. Hargrave. Solid-Phase Synthesis of Phosphorylated Tyr-Peptides by 'Phosphite Triester' Phosphorylation, Michael W. Pennington. Design of Novel Synthetic Peptides Including Cyclic Conformationally and Topographically Constrained Analogs, Victor J. Hruby and G. Gregg Bonner. Solid-Phase Synthesis of Peptides Containing the CH2NH Reduced Bond Surrogate, Michael W. Pennington. Approaches to the Asymmetric Synthesis of Unusual Amino Acids, Victor J. Hruby and Xinhua Qian. Synthesis of Fully Protected Peptide Fragments, Monika Mergler. Peptide Synthesis via Fragment Condensation, Rolf Nyfeler. Index.
Protein kinase inhibitors flavopiridol and 7-hydroxy-staurosporine down-regulate antiapoptosis proteins in B-cell chronic lymphocytic leukemia (2000)

Abstract Compounds that inhibit protein kinases are currently undergoing clinical evaluation for the treatment of a variety of malignancies. The kinase inhibitors flavopiridol and 7 hydroxy-staurosporine (UCN-01) were examined for their effects on B-cell chronic lymphocytic leukemia (B-CLL) cells in vitro (n = 49). Flavopiridol and UCN-01 induced concentration-dependent apoptosis of most B-CLL samples tested, with greater than 50% cell killing occurring at concentrations of less than 1 μmol/L, and with flavopiridol displaying more potent activity than UCN-01. Flavopiridol (0.1 μmol/L) and UCN-01 (1 μmol/L) also induced striking decreases in the levels of the antiapoptosis proteins Mcl-1, X-linked inhibitor of apoptosis (XIAP), and BAG-1 in nearly all cases of B-CLL and of Bcl-2 in approximately half of B-CLL specimens evaluated. In contrast, expression of the proapoptotic proteins Bax and Bak was not significantly influenced by these kinase inhibitors. Flavopiridol-induced decreases in the levels of antiapoptosis proteins Mcl-1 and XIAP preceded apoptosis and were not substantially affected by the addition of caspase inhibitors to cultures. In contrast, UCN-01–stimulated decreases in antiapoptosis proteins were slower, occurred concurrently with apoptosis, and were partially prevented by caspase inhibitors. The findings suggest that flavopiridol and UCN-01 induce apoptosis of B-CLL cells through different mechanisms. The potent apoptotic activities of flavopiridol and UCN-01 against cultured B-CLL cells suggest that they may be effective as single agents in the treatment of B-CLL or for sensitizing B-CLL cells to conventional cytotoxic drugs.