gebhart/patrepeval huggingface dataset:
Plasmid-controlled colonization factor associated with virulence in Esherichia coli enterotoxigenic for humans (1975)

An enterotoxin-producing strain of Escherichia coli isolated from a case of cholera-like diarrhea (E. coli strain H-10407) was found to possess a surface-associated colonization factor. Colonization was manifested as the ability of small inocula (10(5) bacteria) to attain large (10(9)) populations in the infant rabbit intestine with a concomitant diarrheal response. A laboratory-passed derivative of E. coli H-10407, designated H-10407-P, failed to exhibit an increase in population in the infant rabbit and also failed to induce diarrhea. Cell-free culture supernatant fluids of E. coli H-10407 and H-10407-P produced equivalent enterotoxic responses in infant and in adult rabbits. Specific anti-colonization factor antiserum was produced by adsorbing hyperimmune anti-H-10407 serum with both heat-killed and living cells E. coli H-10407-P. This specific adsorbed serum protected infant rabbits from challenge with living E. coli H-10407 although the serum did not possess bactericidal activity. The anti-colonization factor serum did not agglutinate a strain of E. coli K-12 possessing the K88 colonization factor peculiar to E. coli enterotoxigenic for swine. By electron microscopy it was demonstrated that E. coli H-10407, but not H10407-, possessed pilus-like surface structures which agglutinated with the specific adsorbed (anti-colonization factor) antiserum. E. coli H-10407 possessed three species of plasmid deoxyribonucleic acid, measuring 60 X 10(6), 42 X 10(6), and 3.7 X 10(6) daltons, respectively. E. coli H-10407-P possessed only the 42 X 10(6)- and the 3.7 X 10(6)-dalton plasmid species. Spontaneous loss of the specific H-10407 surface-associated antigen was accompanied by loss of the 60 X 10(6)-dalton species of plasmid deoxyribonucleic acid and loss of colonizing ability. Thus, it is concluded that the E. coli colonization factor described here is a virulence factor which may play an important and possibly essential role in naturally occurring E. coli enterotoxic diarrhea in man.
The usefulness of monitoring WT1 gene transcripts for the prediction and management of relapse following allogeneic stem cell transplantation in acute type leukemia (2003)

In acute-type leukemia, no method for the prediction of relapse following allogeneic stem cell transplantation based on minimal residual disease (MRD) levels is established yet. In the present study, MRD in 72 cases of allogeneic transplantation for acute myeloid leukemia, acute lymphoid leukemia, and chronic myeloid leukemia (accelerated phase or blast crisis) was monitored frequently by quantitating the transcript of WT1 gene, a "panleukemic MRD marker," using reverse transcriptase-polymerase chain reaction. Based on the negativity of expression of chimeric genes, the background level of WT1 transcripts in bone marrow following allogeneic transplantation was significantly decreased compared with the level in healthy volunteers. The probability of relapse occurring within 40 days significantly increased step-by-step according to the increase in WT1 expression level (100% for 1.0 x 10(-2)-5.0 x 10(-2), 44.4% for 4.0 x 10(-3)-1.0 x 10(-2), 10.2% for 4.0 x 10(-4)-4.0 x 10(-3), and 0.8% for < 4.0 x 10(-4)) when WT1 level in K562 was defined as 1.0). WT1 levels in patients having relapse increased exponentially with a constant doubling time. The doubling time of the WT1 level in patients for whom the discontinuation of immunosuppressive agents or donor leukocyte infusion was effective was significantly longer than that for patients in whom it was not (P <.05). No patients with a short doubling time of WT1 transcripts (< 13 days) responded to these immunomodulation therapies. These findings strongly suggest that the WT1 assay is very useful for the prediction and management of relapse following allogeneic stem cell transplantation regardless of the presence of chimeric gene markers.
CC CKR5: A RANTES, MIP-1α, MIP-1β Receptor as a Fusion Cofactor for Macrophage-Tropic HIV-1 (1996)

Human immunodeficiency virus-type 1 (HIV-1) entry requires fusion cofactors on the CD4+ target cell. Fusin, a heterotrimeric GTP-binding protein (G protein)-coupled receptor, serves as a cofactor for T cell line-tropic isolates. The chemokines RANTES, MIP-1alpha, and MIP-1beta, which suppress infection by macrophage-tropic isolates, selectively inhibited cell fusion mediated by the corresponding envelope glycoproteins (Envs). Recombinant CC CKR5, a G protein-coupled receptor for these chemokines, rendered CD4-expressing nonhuman cells fusion-competent preferentially with macrophage-tropic Envs. CC CKR5 messenger RNA was detected selectively in cell types susceptible to macrophage-tropic isolates. CC CKR5 is thus a fusion cofactor for macrophage-tropic HIV-1 strains.
A Peripheral Neurovascular Pathology Associated with Fibromyalgia Patients (S17.006) (2013)

OBJECTIVE: To utilize multi-molecular immunolabeling to evaluate the innervation in 3mm punch biopsies from glabrous palmar skin and upper thoracic back skin in 24 female fibromyalgia patients and 23 age-matched female control subjects.
Entrapment of plasmid DNA by liposomes and their interactions with plant protoplasts (1979)

Lecithin and lecithin/cholesterol liposomes formed in aqueous solutions of DNA entrap covalently closed circular, open circular and linear DNA molecules of size up to at least 13 kilobases. The sequestered DNA molecules are efficiently protected against exogenous deoxyribonuclease action although nicking and linearization of circular DNA can be observed. The size of these liposomes ranges from approximately 0.5 to 7.5 mu with an average of 2.5--4 mu. DNA filled liposomes strongly interact with plant protoplasts under conditions inducing protoplast fusion. Results suggest that sequestered plasmid DNA can be transferred to protoplast nuclei.
Skin pH: From Basic SciencE to Basic Skin Care (2013)

The "acid mantle" is a topic not only of historical interest, but also of clinical significance and has recently been linked to vital stratum corneum function. Despite compelling basic science evidence placing skin pH as a key factor in barrier homeostasis, stratum corneum integrity, and antimicrobial defense, application of the acid mantle concept in clinical care is lacking. We review recent basic science investigations into skin pH, discuss skin disorders characterized by aberrant pH, and finally discuss practical application for preservation of the acid mantle. Recognizing factors that alter skin pH and selecting products that preserve the acid mantle is of prime importance in treating dermatologic patients.
Discovery of 7-(4-(3-Ethynylphenylamino)-7-methoxyquinazolin-6-yloxy)-N-hydroxyheptanamide (CUDC-101) as a Potent Multi-Acting HDAC, EGFR, and HER2 Inhibitor for the Treatment of Cancer (2010)

By incorporating histone deacetylase (HDAC) inhibitory functionality into the pharmacophore of the epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) inhibitors, we synthesized a novel series of compounds with potent, multiacting HDAC, EGFR, and HER2 inhibition and identified 7-(4-(3-ethynylphenylamino)-7-methoxyquinazolin-6-yloxy)-N-hydroxyheptanamide 8 (CUDC-101) as a drug candidate, which is now in clinical development. 8 displays potent in vitro inhibitory activity against HDAC, EGFR, and HER2 with an IC(50) of 4.4, 2.4, and 15.7 nM, respectively. In most tumor cell lines tested, 8 exhibits efficient antiproliferative activity with greater potency than vorinostat (SAHA), erlotinib, lapatinib, and combinations of vorinostat/erlotinib and vorinostat/lapatinib. In vivo, 8 promotes tumor regression or inhibition in various cancer xenograft models including nonsmall cell lung cancer (NSCLC), liver, breast, head and neck, colon, and pancreatic cancers. These results suggest that a single compound that simultaneously inhibits HDAC, EGFR, and HER2 may offer greater therapeutic benefits in cancer over single-acting agents through the interference with multiple pathways and potential synergy among HDAC and EGFR/HER2 inhibitors.
A model system for edible vaccination using recombinant avidin produced in corn seed (2000)

Due to the character of the original source materials and the nature of batch digitization, quality control issues may be present in this document. Please report any quality issues you encounter to digital@library.tamu.edu, referencing the URI of the item.
Combining ATR Suppression with Oncogenic Ras Synergistically Increases Genomic Instability, Causing Synthetic Lethality or Tumorigenesis in a Dosage-Dependent Manner (2010)

Previous studies indicate that oncogenic stress activates the ATR-Chk1 pathway. Here, we show that ATR-Chk1 pathway engagement is essential for limiting genomic instability following oncogenic Ras transformation. ATR pathway inhibition in combination with oncogenic Ras expression synergistically increased genomic instability, as quantified by chromatid breaks, sister chromatid exchanges, and H2AX phosphorylation. This level of instability was significantly greater than that observed following ATR suppression in untransformed control cells. In addition, consistent with a deficiency in long-term genome maintenance, hypomorphic ATR pathway reduction to 16% of normal levels was synthetic lethal with oncogenic Ras expression in cultured cells. Notably, elevated genomic instability and synthetic lethality following suppression of ATR were not due to accelerated cycling rates in Ras-transformed cells, indicating that these synergistic effects were generated on a per-cell-cycle basis. In contrast to the synthetic lethal effects of hypomorphic ATR suppression, subtle reduction of ATR expression (haploinsufficiency) in combination with endogenous levels of K-ras(G12D) expression elevated the incidence of lung adenocarcinoma, spindle cell sarcoma, and thymic lymphoma in p53 heterozygous mice. K-ras(G12D)-induced tumorigenesis in ATR(+/-)p53(+/-) mice was associated with intrachromosomal deletions and loss of wild-type p53. These findings indicate that synergistic increases in genomic instability following ATR reduction in oncogenic Ras-transformed cells can produce 2 distinct biological outcomes: synthetic lethality upon significant suppression of ATR expression and tumor promotion in the context of ATR haploinsufficiency. These results highlight the importance of the ATR pathway both as a barrier to malignant progression and as a potential target for cancer treatment.
Raman spectroscopy on amorphous carbon films (1996)

The origin and interpretation of the Raman features of amorphous (hydrogenated) carbon films deposited at room temperature in the region of 1000–1700 cm−1 is discussed in this paper. Possible interpretations of the linewidths, positions of the ‘‘G’’ graphite peak and ‘‘D’’ disordered peak, and their intensity ratios are examined using results obtained from magnetron sputtered and magnetic field enhanced plasma deposited films. It is shown that even small ‘‘clusters’’ of condensed benzene rings (cluster size below 20 Å) in carbon films can explain the observed Raman scattering. Besides the care that should be taken in the correct interpretation of Raman results, the utility of Raman scattering in obtaining an estimate of cluster sizes in amorphous (hydrogenated) carbon films is discussed. Carbon films prepared by magnetron sputtering show two additional Raman features at 1180 and 1490 cm−1 in addition to the G and D peaks. It is shown that a correlation exists between the 1180 cm−1 peak and the sp3 content in the films.
Production of Graphene Sheets by Direct Dispersion with Aromatic Healing Agents (2010)

A simple and scalable exfoliation approach is developed to produce high-quality single-layer graphene sheets without the use of toxic reduction agents of expensive solvents. Graphite powders are exfoliated in a water solution of pyrene derivatives, which act as dispersion agents, healing agents, and electric “glue” during the thermal annealing process.
A critical study on RO-4-1284 antagonism in mice. (1975)

Ro-4-1284 is found to produce ptosis, hypothermia, sedation and miosis in mice, and the antagonsim to these symptoms is investigated. The study reports the differential effects of various pharmacologically distinct classes of compounds. The relevance of this type of experiments to possible antidepressant drug activity is discussed.
Intralayer hydrogen-bond-directed self-assembly of nano-fibers from dicarboxylic valylvaline bolaamphiphiles (1998)

Dicarboxylic L-valyl-L-valine bolaamphiphiles produced nanoscale fibers with widths of 10–30 nm, via proton-triggered self-assembly in water, which are dominated by both intralayer, lateral hydrogen-bond networks between end carboxylic acid groups and parallel β-sheet networks between amide groups.
Rexinoids Isolated from Sophora tonkinensis with a Gene Expression Profile Distinct from the Synthetic Rexinoid Bexarotene (2014)

The retinoid X receptor (RXR) plays a critical role in transcriptional regulation via formation of an RXR homodimer or heterodimers with partner nuclear receptors. Despite the numerous beneficial effects, only a limited number of naturally occurring RXR agonists are known. In this report, two prenylated flavanones (1 and 2) isolated from Sophora tonkinensis were identified as new rexinoids that preferentially activated RXRs, relative to the retinoic acid receptor. The activities of 1 and 2 were the most potent among naturally occurring rexinoids, yet 2 orders of magnitude lower than the synthetic rexinoid bexarotene. Compounds 1 and 2 activated particular RXR heterodimers in a manner similar to bexarotene. A microarray assay followed by quantitative real-time polymerase chain reaction analyses on RNAs isolated from C2C12 myotubes treated with 1 or 2 demonstrated that they significantly increased mRNA levels of lipoprotein lipase, angiopoietin-like protein 4, and heme oxygenase-1. In contrast, bexarotene preferentially potentiated transcription of genes involved in lipogenesis and lipid metabolism such as sterol regulatory element-binding protein-1, fatty acid synthase, and apolipoprotein D by a liver X receptor agonist. In this study, we have demonstrated that two newly identified naturally occurring rexinoids, 1 and 2, possess properties different from bexarotene.
Trifluoromethoxylation of Arenes: Synthesis of ortho‐Trifluoromethoxylated Aniline Derivatives by OCF3 Migration (2014)

Aryl trifluoromethoxylation by a two-step sequence of O-trifluoromethylation of N-aryl-N-hydroxylamine derivatives and intramolecular OCF3 migration is presented. This protocol allows easy access to a wide range of synthetically useful ortho-OCF3 aniline derivatives. In addition, it utilizes bench-stable reagents, is operationally simple, shows high functional-group tolerance, and is amenable to gram-scale as well as one-pot synthesis. A reaction mechanism of a heterolytic cleavage of the NOCF3 bond followed by recombination of the resulting nitrenium ion and trifluoromethoxide is proposed for the OCF3 -migration reaction.
Turnover of Ia-peptide complexes is facilitated in viable antigen-presenting cells: biosynthetic turnover of Ia vs. peptide exchange. (1989)

Macrophages and B cells process antigens to produce antigenic peptides that associate with class II major histocompatibility complex molecules (e.g., Ia molecules); these Ia-peptide complexes are recognized by CD4+ T lymphocytes. Processing of the antigen hen egg white lysozyme was inhibited by cycloheximide in peritoneal exudate cells (PECs, largely macrophages), but not in TA3 B-lymphoma cells. The uptake and metabolism of hen egg white lysozyme was largely intact in cycloheximide-treated PECs, implicating a blockade in other steps in the formation of Ia-peptide complexes. Turnover of Ia-peptide complexes was markedly enhanced in viable antigen-presenting cells (TA3 and PEC) as compared to such complexes studied on fixed cells or in isolated preparations of Ia and peptide. In B cells the half-life of Ia-peptide complexes was much shorter than the half-life of the Ia molecules, implying turnover of Ia-peptide complexes by dissociatin and peptide exchange. In PECs, the dissociation of Ia-peptide complexes was more limited; the enhanced Ia-peptide turnover in viable PECs reflected in part biosynthetic turnover of Ia molecules. Specific mechanisms may exist in TA3 cells to facilitate exchange of peptides bound to Ia, allowing recycling of Ia to present another antigenic peptide; such Ia recycling would explain the ability of these cells to process and present antigen in the absence of Ia synthesis.
Photodarkening measurements in large mode area fibers (2007)

Yb-doped fibers are widely used in applications requiring high average output powers and high power pulse amplification. Photodarkening is one limiting factor in these fibers. In this paper, characterization of photodarkening in large-mode-area (LMA) fibers is presented building upon our previous work, which indicated that meaningful comparison of photodarkening properties from different fibers can be made as long as care is taken to equalize the excited state Yb concentration between samples. We have developed a methodology that allows rapid and reproducible photodarkening measurements to be performed and that enables quantitative comparison of the photodarkening propensity among fibers with different compositions and under different operating conditions. We have shown that this measurement technique can be used effectively for LMA fibers by employing cladding pumping rather than the more standard core pumping. Finally, we observe a seventh-order dependence of the initial photodarkening rate on the excited-state Yb population for two different Yb-doped fibers; this result implies that photodarkening of a Yb-doped fiber source fabricated using a particular fiber will be strongly dependent on the device configuration.
Two complementary methods for predicting peptides binding major histocompatibility complex molecules (1997)

Peptides that bind to major histocompatibility complex products (MHC) are known to exhibit certain sequence motifs which, though common, are neither necessary nor sufficient for binding: MHCs bind certain peptides that do not have the characteristic motifs and only about 30% of the peptides having the required motif, bind. In order to develop and test more accurate methods we measured the binding affinity of 463 nonamer peptides to HLA-A2.1. We describe two methods for predicting whether a given peptide will bind to an MHC and apply them to these peptides. One method is based on simulating a neural network and another, called the polynomial method, is based on statistical parameter estimation assuming independent binding of the side-chains of residues. We compare these methods with each other and with standard motif-based methods. The two methods are complementary, and both are superior to sequence motifs. The neural net is superior to simple motif searches in eliminating false positives. Its behavior can be coarsely tuned to the strength of binding desired and it is extendable in a straightforward fashion to other alleles. The polynomial method, on the other hand, has high sensitivity and is a superior method for eliminating false negatives. We discuss the validity of the independent binding assumption in such predictions.
Monoclonal antibodies to αVβ3 (7E3 and LM609) inhibit sickle red blood cell–endothelium interactions induced by platelet-activating factor (2000)

Abnormal interaction of sickle red blood cells (SS RBC) with the vascular endothelium has been implicated as a factor in the initiation of vasoocclusion in sickle cell anemia. Both von Willebrand factor (vWf) and thrombospondin (TSP) play important roles in mediating SS RBC-endothelium interaction and can bind to the endothelium via alphaVbeta3 receptors. We have used monoclonal antibodies (MoAb) directed against alphaVbeta3 and alphaIIbbeta3 (GPIIb/IIIa) integrins to dissect the role of these integrins in SS RBC adhesion. The murine MoAb 7E3 inhibits both alphaVbeta3 and alphaIIbbeta3 (GPIIb/IIIa), whereas MoAb LM609 selectively inhibits alphaVbeta3, and MoAb 10E5 binds only to alphaIIbbeta3. In this study, we have tested the capacity of these MoAbs to block platelet-activating factor (PAF)-induced SS RBC adhesion in the ex vivo mesocecum vasculature of the rat. Infusion of washed SS RBC in preparations treated with PAF (200 pg/mL), with or without a control antibody, resulted in extensive adhesion of these cells in venules, accompanied by frequent postcapillary blockage and increased peripheral resistance units (PRU). PAF also caused increased endothelial surface and interendothelial expression of endothelial vWf. Importantly, pretreatment ofthe vasculature with either MoAb 7E3 F(ab')(2) or LM609, but not 10E5 F(ab')(2), after PAF almost completely inhibited SS RBC adhesion in postcapillary venules, the sites of maximal adhesion and frequent blockage. The inhibition of adhesion with 7E3 or LM609 was accompanied by smaller increases in PRU and shorter pressure-flow recovery times. Thus, blockade of alphaVbeta3 may constitute a potential therapeutic approach to prevent SS RBC-endothelium interactions under flow conditions. (Blood. 2000;95:368-374)
Consequences for exchange energy density functional of exponentially decaying nature of atomic electron densities (1999)

A simple model is studied for the atomic exchange energy density functional, which is based on the exponential decaying feature of the density and the Fermi–Amaldi model for exchange correlation. The model is exact for hydrogen-like atoms. It is shown to provide a reasonable approximation for many-electron atoms. The local exchange energy density and potential are expressed as universal functions of r, ρ(r), and |∇ρ(r)|, and go beyond the generalized gradient approximation (GGA) framework in which Ex[ρ]=∫ex(ρ, ∇ρ) dr. The conclusion reached previously by Gill and Pople (Phys. Rev. A 1993, 47, 2383), that the general atomic exchange functional cannot be of the GGA form, is supplemented by the more optimistic conclusion that it could well have the form Ex[ρ]=∫ex(r, ρ, ∇ρ) dr. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 2–11, 1999
Cardiotonic agents. 2. Synthesis and structure-activity relationships of 4,5-dihydro-6-[4-(H-imidazol-1-yl)phenyl]-3(2H)-pyridazinones: a new class of positive inotropic agents (1985)

A series of 4,5-dihydro-6-[4-(1H-imidazol-1-yl)phenyl]-3(2H)-pyridazinones and related compounds were synthesized and evaluated for positive inotropic activity. Most members of this series produced dose-related increases in myocardial contractility that were associated with relatively minor increases in heart rate and decreases in systemic arterial blood pressure. Introduction of a methyl substituent at the 5-position of 1 (CI-914) produced the most potent compound in this series (11, CI-930). Compound 1 is more potent than amrinone whereas compound 11 is more potent than milrinone. The inotropic effects of 1 and 11 are not mediated via stimulation of beta-adrenergic receptors. Selective inhibition of cardiac phosphodiesterase fraction III represents the principal component of the positive inotropic action of 1 and 11.