gebhart/patrepeval huggingface dataset:
Affinity-chromatographic purification of human α2-antiplasmin (1980)

A new simple and efficient purification method for alpha 2-antiplasmin is described that is based on the interaction between alpha 2-antiplasmin and a fragment from elastase-digested plasminogen constituting the three N-terminal triple-loop structures in the plasmin A-chain (LBSI). After a single-step adsorption of the alpha 2-antiplasmin from plasminogen-depleted plasma to LBSI-Sepharose and elution with 6-aminohexanoic acid, an 80-90% pure preparation with a yield of 50-60% is obtained. The major impurity is fibrinogen, which can easily be removed by gel filtration, and, as a result, a homogeneous fully active alpha 2-antiplasmin preparation is obtained that has the same properties as previously described for alpha 2-antiplasmin. Evidence is put forward that a form of alpha 2-antiplasmin with less affinity for the lysine-binding sites in plasminogen may exist, even in unfractionated plasma.
Controlling the shape, orientation, and linkage of carbon nanotube features with nano affinity templates (2006)

Directed assembly of nanoscale building blocks such as single-walled carbon nanotubes (SWNTs) into desired architectures is a major hurdle for a broad range of basic research and technological applications (e.g., electronic devices and sensors). Here we demonstrate a parallel assembly process that allows one to simultaneously position, shape, and link SWNTs with sub-100-nm resolution. Our method is based on the observation that SWNTs are strongly attracted to COOH-terminated self-assembled monolayers (COOH-SAMs) and that SWNTs with lengths greater than the dimensions of a COOH-SAM feature will align along the boundary between the COOH-SAM feature and a passivating CH3-terminated SAM. By using nanopatterned affinity templates of 16-mercaptohexadecanonic acid, passivated with 1-octadecanethiol, we have formed SWNT dot, ring, arc, letter, and even more sophisticated structured thin films and continuous ropes. Experiment and theory (Monte Carlo simulations) suggest that the COOH-SAMs localize the solvent carrying the nanotubes on the SAM features, and that van der Waals interactions between the tubes and the COOH-rich feature drive the assembly process. A mathematical relationship describing the geometrically weighted interactions between SWNTs and the two different SAMs required to overcome solvent-SWNT interactions and effect assembly is provided.
Domino Reactions in Organic Synthesis (2006)

Introduction Cationic domino reactions Anionic domino reactions Radical domino reactions Pericyclic domino reactions Photochemically induced domino processes Transition metal catalysis Domino reactions initiated by oxidation or reduction Enzymes in domino reactions Multicomponent reactions Special techniques in domino reactions
Critical role of endothelial P-selectin glycoprotein ligand 1 in chronic murine ileitis (2006)

L-selectin ligands might be relevant for inflammatory cell trafficking into the small intestine in a spontaneous model of chronic ileitis (i.e., SAMP1/YitFc mice). Immunoblockade of peripheral node addressin or mucosal addressin cell adhesion molecule 1 failed to ameliorate ileitis, whereas P-selectin glycoprotein ligand 1 (PSGL-1) neutralization attenuated both the adoptively transferred and spontaneous disease. PSGL-1 was detected in venules of mesenteric lymph node and small intestine by immunohistochemistry and confirmed by real-time reverse transcription polymerase chain reaction and flow cytometry. In addition, reconstitution of wild-type mice with PSGL-1(-/-) bone marrow demonstrated that PSGL-1 messenger RNA and PSGL-1 protein expression remained on endothelium, localized within mesenteric lymph node and small intestine. Endothelial PSGL-1 bound P-selectin-IgG and its blockade or genetic deletion altered the recruitment of lymphocytes to the small intestine, as revealed by intravital microscopy and homing studies. Endothelial expression of PSGL-1 adds a new dimension to the various cellular interactions involved in small intestinal recruitment. Thus, the multiple roles of PSGL-1 may explain why targeting this single adhesion molecule results in attenuation of chronic murine ileitis, a disease previously resistant to antiadhesion molecule strategies.
The binding site for ribosomal protein S8 in 16S rRNA andspcmRNA fromEscherichia coli: minimum structural requirements and the effects of single bulged bases on S8 — RNA interaction (1994)

Through specific interactions with rRNA and mRNA, ribosomal protein S8 of Escherichia coli plays a central role in both assembly of the 30S ribosomal subunit and translational regulation of spc operon expression. To better understand S8-RNA association, we have measured the affinity of S8 for a number of variants of its rRNA and mRNA binding sites prepared by in vitro transcription or chemical synthesis. With the aid of site-directed deletions, we demonstrate that an imperfect, 33-nucleotide helical stem encompassing nucleotides 588-603 and 635-651 possesses all of the structural information necessary for specific binding of S8 to the 16S rRNA. This segment consists of two short duplexes that enclose a conserved, asymmetric internal loop which contains features crucial for protein recognition. The S8 binding site in spc operon mRNA is very similar in both primary and secondary structure to that in 16S rRNA except for the presence of two single bulged bases in one of the duplex segments. In addition, the apparent association constant for the S8-mRNA interaction is approximately fivefold less than that for the S8-rRNA interaction. We show that the difference in affinity can be attributed to the effects of the bulged bases. Deletion of the bulged bases from the mRNA site increases its affinity for S8 to a level similar to that of the rRNA, whereas insertion of single-base bulges at equivalent positions within the rRNA site reduces its affinity for S8 to a value typical of the mRNA. Single-base bulges in the proximity of essential recognition features are therefore capable of modulating the strength of protein-RNA interactions.
Changes in protein expression during honey bee larval development (2008)

These data have allowed us to integrate disparate findings in previous studies to build a model of metabolism and maturity of the immune system during larval development. This publicly accessible resource for protein expression trends will help generate new hypotheses in the increasingly important field of honey bee research.
MyLifeBits (2002)

MyLifeBits is a project to fulfill the Memex vision first posited by Vannevar Bush in 1945. It is a system for storing all of one's digital media, including documents, images, sounds, and videos. It is built on four principles: (1) collections and search must replace hierarchy for organization (2) many visualizations should be supported (3) annotations are critical to non-text media and must be made easy, and (4) authoring should be via transclusion.
Electron spectroscopy of ion beam and hydrocarbon plasma generated diamondlike carbon films (1981)

Mechanically hard, electrically insulating (diamondlike) carbon thin films have been produced by low energy carbon ion beam deposition and by decomposition of butane gas. Deposition parameters are presented for these two methods. The ion beam films can be produced with or without a secondary discharge in the ion source and the parameters are given for these two modes of operation. ESCA and electron energy loss (EELS) techniques have been used to examine the electronic character of these films. ESCA carbon (1s) spectra show that the films are composed mostly of C–C bonds and that a negative bias is important to eliminate C–H bonds from the butane generated films. EELS data show that the films are more diamondlike in that the strong graphitic feature at 6.5 eV is not evident in these films. Among the other measured properties of these films, the refractive index (2.3 at 5 μm) and hardness (1850 knoop) are in keeping with the diamondlike character of these films.
Whitman's "Word of the Modern" and the First Modern War (1989)

Examines how "the battle lines drawn by the Civil War intensified the split between the ideas of individualism and union," and describes alternate contexts for the war offered by Whitman in Drum-Taps, stressing the potentially negative effects of the North's victory as creating conditions for an overly-centralized political authority and a conformist production of human individuality.
Translational termination efficiency in mammals is influenced by the base following the stop codon. (1995)

The base following stop codons in mammalian genes is strongly biased, suggesting that it might be important for the termination event. This proposal has been tested experimentally both in vivo by using the human type I iodothyronine deiodinase mRNA and the recoding event at the internal UGA codon and in vitro by measuring the ability of each of the 12 possible 4-base stop signals to direct the eukaryotic polypeptide release factor to release a model peptide, formylmethionine, from the ribosome. The internal UGA in the deiodinase mRNA is used as a codon for incorporation of selenocysteine into the protein. Changing the base following this UGA codon affected the ratio of termination to selenocysteine incorporation in vivo at this codon: 1:3 (C or U) and 3:1 (A or G). These UGAN sequences have the same order of efficiency of termination as was found with the in vitro termination assay (4th base: A approximately G >> C approximately U). The efficiency of in vitro termination varied in the same manner over a 70-fold range for the UAAN series and over an 8-fold range for the UGAN and UAGN series. There is a correlation between the strength of the signals and how frequently they occur at natural termination sites. Together these data suggest that the base following the stop codon influences translational termination efficiency as part of a larger termination signal in the expression of mammalian genes.
Physical layer design for packet data over IS-136 (2002)

Several forward error correction (FEC), interleaving and automatic repeat request (ARQ) schemes are evaluated for transmitting packet data over IS-136 TDMA. The objective is to identify the combination of FEC, interleaving and ARQ that provides maximum data throughput at reasonable computational complexity. The FEC schemes considered are rate-n/n+1 punctured convolutional codes, long constraint length convolutional codes and punctured turbo codes. The ARQ schemes considered are ARQ with majority voting, ARQ with metric combining and ARQ with code combining (or Type III ARQ). The performance of these techniques when used with one-slot and two-slot interleaving is studied. Results show that highest throughput is achieved when a rate-5/6 convolutional code is used with one-slot interleaving and Type III ARQ scheme.
Transcriptional and genetic analyses of the herpes simplex virus type 1 genome: coordinates 0.29 to 0.45 (1984)

We have constructed a map of the genes encoded by a 23,000-nucleotide-pair region of herpes simplex virus type 1. This region, defined by the three adjacent EcoRI fragments N (map coordinates 0.298 to 0.315), F (0.315 to 0.421), and M (0.421 to 0.448), has previously been shown by genetic analysis to contain the genes for thymidine kinase, nucleocapsid protein p40, glycoprotein B, DNA-binding protein, and DNA polymerase. We report the identification and mapping of RNAs defining 13 viral genes encoded by the region 0.298 to 0.448. The transcriptional pattern shows families of overlapping messages, similar to those observed in other regions of the viral genome. We also isolated mutants representing four distinct complementation groups and physically mapped several of the mutations to regions within EcoRI fragment F by marker rescue. Mutations representing complementation groups 1-9 (glycoprotein B), 1-1 (DNA-binding protein), and 1-3 (DNA polymerase) were mapped to coordinates 0.361 to 0.368 to 0.411, and 0.411 to 0.421, respectively. A fourth previously undefined complementation group was mapped to the region between glycoprotein B and DNA-binding protein. Comparing the transcription mapping with marker rescue data suggests that the genes for glycoprotein B, DNA-binding protein, DNA polymerase, and nucleocapsid protein p40 are expressed as 3.3-, 4.2-, 4.3- or 4.2- or both, and 2.4-kilobase mRNAs, respectively.
TGF-beta2-induced matrix modification and cell transdifferentiation in the human lens capsular bag. (2002)

Addition of TGF-beta2 accelerates transdifferentiation and contraction of the capsular bag, resulting in light scatter. CAT-152 inhibited all the effects of TGF-beta2 that were examined and therefore has the potential to suppress development of PCO and provide potential therapeutic benefit to cataract patients.
Crossregulation Between Th1 and Th2 Cells (1998)

Th1 and Th2 subsets have been characterized on the basis of the cytokines they secrete and the immune functions they mediate. Th1 cells secrete IL-2, IFN-gamma, and lymphotoxin and are important in the cell-mediated response; Th2 cells secrete IL-4, IL-5, IL-10, and IL-13 and are important in the control of macrophage function and in the stimulation of particular immunoglobulin isotypes. Cytokines secreted by Th1 and Th2 cells regulate the growth and differentiation of Th1 and Th2 cells in both positive and negative ways; this has been termed crossregulation. Much work has concentrated on the factors important in the differentiation of these Th subsets, and it has been established that Th cells become committed to a Th1 or Th2 phenotype within 48 hrs of antigenic stimulation. During the differentiation process irreversible changes in the expression and function of cytokine receptors occur that provide an explanation for the observed crossregulatory features of Th1 and Th2 cells. In this review we summarize the crossregulation between Th1 and Th2 cells in terms of the changes in cytokine receptor expression and function that occur during differentiation.
A Continuous Cell-Free Translation System Capable of Producing Polypeptides in High Yield (1988)

A cell-free translation system has been constructed that uses a continuous flow of the feeding buffer [including amino acids, adenosine triphosphate (ATP), and guanosine triphosphate (GTP)] through the reaction mixture and a continuous removal of a polypeptide product. Both prokaryotic (Escherichia coli) and eukaryotic (wheat embryos, Triticum sp.) versions of the system have been tested. In both cases the system has proven active for long times, synthesizing polypeptides at a high constant rate for tens of hours. With the use of MS2 phage RNA or brome mosaic virus RNA 4 as templates, 100 copies of viral coat proteins per RNA were synthesized for 20 hours in the prokaryotic or eukaryotic system, respectively. With synthetic calcitonin messenger RNA, 150 to 300 copies of calcitonin polypeptide were produced per messenger RNA in both types of continuous translation systems for 40 hours.
Optical sensor for hemoglobin content and oxygen saturation. Application to artificial heart research. (1989)

A hybrid optical sensor that can measure both hemoglobin content ([ Hb]) and oxygen saturation (OS) of whole blood has been developed. The measurement errors in [Hb] and OS are 0.5 g% and 1.2%, respectively, over an hematocrit range of 25 to 45%. The oxygen content derived from the optical sensor yielded a standard error of 0.1 to 0.2 vol%. The sensors were mounted in the outflow ports of left and right artificial hearts that maintained the entire circulation and were used to chronically monitor arterial and mixed venous [Hb] and OS. In combination with pump output and pressure measurements, oxygen delivery and oxygen consumption of the animal was derived on-line using a microprocessor. In the experiment that lasted 40 days, both sensors functioned well, with stable measurements, and no thrombus formation around the sensor at the time of autopsy. The optical sensors are useful for monitoring cardiopulmonary function and metabolic status of patients without requiring blood samples. In addition, the pump output may be controlled through the level of mixed venous OS or in combination with the arterial OS.
Inflammatory Bronchial Polyps Associated With Asthma (1983)

We report a case of inflammatory bronchial polyps associated with asthma in a 10-year-old boy. He expelled about 50 polyps varying in size from 0.4 to 1.8 cm without difficulty. Microscopically, the polyps were lined by columnar epithelium supported by stroma consisting of a loose connective tissue with many capillary vessels and a chronic inflammatory infiltration composed mainly of lymphocytes, plasma cells, and eosinophils. The blood and urine laboratory data were normal except for blood eosinophilia of 3% to 10%, and a chest roentgenogram that showed a left perihilar small nodular lesion and a small irregular area in the right upper lobe. Test results of pulmonary function and blood gases were normal. The association of bronchial inflammatory polyps with asthma and the clinical manifestation in this patient is very uncommon.
Quick regulation of mRNA functions by a few seconds of photoirradiation (2012)

3-Cyanovinylcarbazole nucleoside, which effectively photocrosslinks to the pyrimidine base in complementary RNA strands, was incorporated into antisense oligonucleotides, and we evaluated the photoreactivity and the sequence selectivity to mutated K-ras oligoRNAs, as well as the regulation of the function of K-ras mRNA. We demonstrated that the reverse transcription and the translation activity of K-ras mRNA were quickly suppressed by a few seconds of photoirradiation with the addition of the photoresponsive antisense ODN.
Multimodality treatment of stage IIIA non-small-cell lung carcinoma: a critical review of the literature and strategies for future research. (1992)

Without question, randomized phase III trials are required at this time to define what is to be considered optimal treatment. An attempt is made to define the most important questions that should be addressed in future phase III trials. Additionally, a number of study designs are suggested to best answer the therapeutic questions posed.
Retrospective clinical evaluation of gauze‐based negative pressure wound therapy* (2008)

Negative pressure wound therapy (NPWT) is an established modality in the treatment of challenging wounds. However, most existing clinical evidence is derived from the use of open-cell polyurethane foam at -125 mmHg. Alternative negative pressure systems are becoming available, which use gauze at a pressure of -80 mmHg. This study describes clinical results from a retrospective non comparative analysis of 30 patients treated with Chariker-Jeter gauze-based negative pressure systems (V1STA, Versatile-1 and EZ-Care; Smith & Nephew, Inc.) in a long-term care setting. The mean age of the patients was 72 years. The wounds consisted of chronic (n = 11), surgical dehiscence (n = 11) and surgical incision (n = 8). Wound volume and area were recorded at commencement and at the cessation of therapy. Discontinuation of therapy was instigated upon closure through secondary intention or when size and exudate were sufficiently reduced that the wounds could be managed by conventional wound dressing (median 41 days). An overall median reduction in wound volume of 88.0% (P < 0.001) and a 68.0% reduction in area (P < 0.001) compared with baseline were observed over the course of NPWT. The overall rate of volume reduction (15.1% per week) compares favourably with published data from foam-based systems.
Cotinine binding to nicotinic acetylcholine receptors in bovine chromaffin cell and rat brain membranes (2001)

Cotinine is the major metabolite of nicotine. It has nicotine-like biological activity, but its potency is low. We studied cotinine binding to nicotinic receptors labelled with [3H]epibatidine. In membranes from cultured bovine chromaffin cells [3H]epibatidine bound to two apparent sites with K(d) values of 93 and 1400 pM. The low-affinity binding represented two-thirds of the binding sites. In rat frontal cortex and hippocampus homogenate membranes, only one apparent binding site was detected. The Kd values were 40 and 62 pM, in frontal cortex and hippocampus, respectively. Nicotine displaced [3H]epibatidine 10 times more potently from the brain than from the chromaffin cell membranes, and cotinine had over two orders of magnitude lower affinity than nicotine. In addition, the competitive nicotinic receptor antagonists methyllycaconitine and dihydro beta-erythroidine displaced [3H]epibatidine (100 pM and 1 nM) from the chromaffin cell membranes. Alpha-bungarotoxin did not affect the binding of 100 pM [3H]epibatidine. However, upon labelling with 1 nM [3H]epibatidine alpha-bungarotoxin (10 nM to 10 microM) displaced one-sixth of the bound radioligand. Our results demonstrate that 100 pM to 1 nM [3H]epibatidine labels mostly neuronal heteropentameric nicotinic receptors in bovine chromaffin cell membranes, and that cotinine is a low-affinity nicotinic ligand both in the adrenal chromaffin cell and in the brain receptors.
WebView: A Graphical Aid for Revisiting Web Pages (1999)

Current commercial web browsers such as Netscape Navigator and Microsoft Internet Explorer provide a wide and diverse range of utilities, such as history lists and bookmarks, that support revisiting previously seen pages on the web. Yet previous research indicates that these utilities are largely unused. In this paper, we present an alternative utility called WebView; a prototype designed to improve the efficiency and usability of page revisitation. It does this by paying particular attention to how previous pages are represented visually, and by integrating many revisitation capabilities into a single display space. Our preliminary evaluation of WebView indicates that users are enthusiastic about the functionality provided, and that it improves the efficiency of some navigational acts.
How a T Cell Receptor-like Antibody Recognizes Major Histocompatibility Complex-bound Peptide (2008)

We determined the crystal structures of the T cell receptor (TCR)-like antibody 25-D1.16 Fab fragment bound to a complex of SIINFEKL peptide from ovalbumin and the H-2K(b) molecule. Remarkably, this antibody directly "reads" the structure of the major histocompatibility complex (MHC)-bound peptide, employing the canonical diagonal binding mode utilized by most TCRs. This is in marked contrast with another TCR-like antibody, Hyb3, bound to melanoma peptide MAGE-A1 in association with HLA-A1 MHC class I. Hyb3 assumes a non-canonical orientation over its cognate peptide-MHC and appears to recognize a conformational epitope in which the MHC contribution is dominant. We conclude that TCR-like antibodies can recognize MHC-bound peptide via two different mechanisms: one is similar to that exploited by the preponderance of TCRs and the other requires a non-canonical antibody orientation over the peptide-MHC complex.
Anticardiolipin antibodies in acute myeloid leukemia: Prevalence and clinical significance (1998)

This prospective study was designed to explore the prevalence and the clinical and prognostic significance of anticardiolipin (ACL) antibodies in patients with acute myeloid leukemia (AML). The study includes 37 consecutive AML patients >15 years old without previous history of thromboembolism, recurrent fetal loss, or autoimmune disease and with no evidence of infection at the time of enrollment. ACL antibodies were found in 25 patients (68%). None of the patients had high positive titers; 8 had moderately positive while 17 had low positive ACL antibody titers. ACL antibody positivity did not predict response to chemotherapy and was not correlated with age, gender, FAB class, platelet and white blood cell counts at presentation, and the risk of thromboembolism. ACL antibody titers did correlate, however, with AML activity in the majority of patients (93%) during 4-19 months of follow up. These results demonstrate a high prevalence of ACL antibodies in AML patients and suggest that serum ACL antibodies may be a useful adjunct in predicting relapse and documenting disease activity and therapy response.