gebhart/patrepeval huggingface dataset:
The Lungs as a Portal of Entry for Systemic Drug Delivery (2004)

The lung is naturally permeable to all small-molecule drugs studied and to many therapeutic peptides and proteins. Absorption can be estimated using a simple animal test, intratracheal instillation. Inhalation offers a noninvasive route for the delivery of peptides and proteins that otherwise must be injected. Peptides that have been chemically altered to inhibit peptidase enzymes exhibit very high bioavailabilities by the pulmonary route. Natural mammalian peptides, less than about 30 amino acids, are broken down in the lung by ubiquitous peptidases and have very poor bioavailabilities. In general, proteins with molecular weights between 6,000 and 50,000 D are relatively resistant to most peptidases and have good bioavailabilities following inhalation. For larger proteins the bioavailability picture is not clear. Although the lung is rich in antiproteases, aggregation of inhaled proteins will stimulate opsonization (coating) by special proteins in the lung lining fluids, which will then mark the aggregated proteins for phagocytosis and intracellular enzymatic destruction. Small peptides and proteins are absorbed more rapidly after inhalation than after subcutaneous injection. For other small molecules, inhalation is also a fast way to get into the body because drug efflux transporters and metabolizing enzymes are present in the lung at much lower levels than the gastrointestinal tract. Lipophilic small molecules are absorbed extremely fast, t(1/2) (abs) approximately 1 to 2 minutes. Water-soluble small molecules are absorbed rapidly t(1/2) (abs) approximately 65 minutes. Small molecules can exhibit prolonged absorption if they are highly insoluble or highly cationic. Encapsulation in slow release particles such as liposomes can also be used to control absorption.
The Insulin Receptor: A Multifunctional Protein (1990)

The insulin receptor is a multifunctional protein encoded by a modular gene. Certain discrete domains within the insulin-receptor structure subserve specific functional properties. In some instances, these discrete domains are encoded by individual exons. This organizational model of the insulin receptor predicts the existence of divergent signaling pathways facilitating specific bioeffects. Some of these signaling pathways are shared with the closely related insulinlike growth factor I receptor (convergent pathways), whereas others are different (divergent). The concept of discrete functional domains also provides several mechanisms whereby inactive insulin receptors (no kinase activity) can inhibit the function of normal receptors. The ability of kinase-inactive insulin receptors to inhibit the signaling function of normal insulin receptors may be an operative mechanism in certain insulin-resistant states.
Severe chronic graft-versus-host disease is characterized by a preponderance of CD4+ effector memory cells relative to central memory cells (2004)

Donor alloreactive CD4(+) T cells are important to the pathogenesis of chronic graft-versus-host disease (cGVHD), but specific subsets of CD4(+) T cells responsible for GVHD have not been defined. We hypothesized that cGVHD might be associated with a preponderance of CD4(+) effector memory cells (CCR7(-)/CD62L(low), CD4(EM)). We analyzed CCR7 and CD62L expression on CD4(+) T cells from stem cell transplantation patients, who did or did not develop cGVHD, and healthy donors. Patients with cGVHD had a higher percentage of CD4(EM) cells (35.5% +/- 2.9%) than healthy donors (13.8% +/- 0.7%; P <.0001) or patients without cGVHD that received a transplant (21.7% +/- 2.1%; P <.01). Using corticosteroid dose as a surrogate marker for cGVHD severity, severe cGVHD was associated with a higher percentage of CD4(EM) cells. The proportion of CD4(EM) cells in corticosteroid-dependent patients with systemic lupus erythematosis or Wegener granulomatosis did not differ from patients without cGVHD that received a transplant. This finding implies that overrepresentation of CD4(EM) cells is a unique feature of cGVHD.
Markers of Adenocarcinoma Characteristic of the Site of Origin: Development of a Diagnostic Algorithm (2005)

This classification scheme should enable better prediction on biopsy material of the primary site in patients with metastatic adenocarcinoma of unknown origin, leading to improved management and therapy.
Abstract B055: Enhanced detection of T-cells targeting unique neoantigens and shared mutated oncogenes for personalized cancer immunotherapy (2019)

Abstract Adoptive cell transfer (ACT) of selected tumor-infiltrating lymphocytes (TILs) targeting neoantigens can mediate tumor regression in selected patients with metastatic epithelial cancer. However, effectively identifying and harnessing neoantigen-reactive T-cells for patient treatment remains a challenge and it is unknown whether current methods to detect neoantigen-reactive T-cells are missing potentially clinically relevant neoantigen reactivities. We thus investigated whether the detection of tumor-neoantigen reactive TILs in epithelial cancers could be enhanced by enriching T-cells that express PD-1 and/or T-cell activation markers (CD134, CD137) followed by microwell culturing at limiting dilution cell concentrations to avoid overgrowth of non-reactive T-cells. Using this approach, in six patients with metastatic epithelial cancer including stomach, colon pancreatic and ovarian cancers, this method led to the detection of CD4 and CD8 T-cells targeting 19 neoantigens compared to only eight neoantigens recognized using our standard TIL fragment screening approach. In two patients, no recognition of mutated peptides was observed using our conventional screen, while our high-throughput approach led to the identification of five neoantigen reactive-TCRs against five different mutations from one patient and a highly potent MHC-II-restricted KRASG12V reactive TCR from a second patient. In addition, in a metastatic tumor sample from a patient with serous ovarian cancer, we isolated three MHC class-II-restricted TCRs targeting the TP53G245S “hot-spot” mutation. In conclusion, this approach provides a highly sensitive and specific platform to isolate clinically relevant neoantigen-reactive T-cells or their TCRs for cancer treatment. Citation Format: Rami Yossef, Eric Tran, Alena Gros, Drew Deniger, Gal Cafri, Steven A. Rosenberg. Enhanced detection of T-cells targeting unique neoantigens and shared mutated oncogenes for personalized cancer immunotherapy [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B055.
The green tea polyphenol (−)‐epigallocatechin gallate prevents the aggregation of tau protein into toxic oligomers at substoichiometric ratios (2014)

The accumulation of amyloid-beta (Aβ) and tau aggregates is a pathological hallmark of Alzheimer's disease. Both polypeptides form fibrillar deposits, but several lines of evidence indicate that Aβ and tau form toxic oligomeric aggregation intermediates. Depleting such structures could thus be a powerful therapeutic strategy. We generated a fragment of tau (His-K18ΔK280) that forms stable, toxic, oligomeric tau aggregates in vitro. We show that (-)-epigallocatechin gallate (EGCG), a green tea polyphenol that was previously found to reduce Aβ aggregation, inhibits the aggregation of tau K18ΔK280 into toxic oligomers at ten- to hundred-fold substoichiometric concentrations, thereby rescuing toxicity in neuronal model cells.
Filamentation byEscherichia colisubverts innate defenses during urinary tract infection (2006)

To establish disease, an infecting organism must overcome a vast array of host defenses. During cystitis, uropathogenic Escherichia coli (UPEC) subvert innate defenses by invading superficial umbrella cells and rapidly increasing in numbers to form intracellular bacterial communities (IBCs). In the late stages of the IBC pathway, filamentous and bacillary UPEC detach from the biofilm-like IBC, fluxing out of this safe haven to colonize the surrounding epithelium and initiate subsequent generations of IBCs, and eventually they establish a quiescent intracellular reservoir. Filamentous UPEC are not observed during acute infection in mice lacking functional Toll-like receptor 4 (TLR4), suggesting that the filamentous phenotype arises in response to host innate immunity. We investigated SulA, a cell division inhibitor associated with the SOS response, to gain insight into the role of filamentous UPEC in pathogenesis. A transcriptional reporter from P(sulA) revealed spatial and temporal differences in expression within IBCs, and it was active in the majority of filamentous UPEC. Although UTI89 and UTI89 DeltasulA both formed first-generation IBCs equally well, UTI89 DeltasulA was sharply attenuated in formation of second-generation IBCs and establishment of the quiescent intracellular reservoir. The virulence of UTI89 DeltasulA was restored in TLR4-deficient mice, suggesting that filamentation facilitates the transition to additional rounds of IBC formation by subverting innate immune responses. These findings demonstrate that transient SulA-mediated inhibition of cell division is essential for UPEC virulence in the murine model of cystitis.
Primary Pediatric Hyperhidrosis: A Review of Current Treatment Options (2008)

Hyperhidrosis is a disorder of excessive sweating beyond what is physiologically necessary for thermoregulation. Primary hyperhidrosis is localized; it can affect the axillae, palms, soles, face, and other areas and is idiopathic. The prevalence of hyperhidrosis in the United States is estimated to be 2.8% of the population, with about one-half (1.4%) of these individuals having the axillary form. Hyperhidrosis occurs in both children and adults, with the average age of onset of primary hyperhidrosis being 14-25 years. This disorder can be detrimental to a patient's social, professional, psychological, and physical well-being. Early detection and management can significantly improve a patient's quality of life, yet hyperhidrosis remains widely under diagnosed and under treated, particularly among pediatric patients. The purpose of this article is to review the treatment of pediatric hyperhidrosis, and to increase awareness and inspire further research on this important and often overlooked medical problem.
Chemical Composition of the Essential Oil from Croton Oblongifolius and its Antibacterial Activity Against Propionibacterium Acnes (2015)

The essential oil of C. oblongifolius Roxb. stem bark was obtained by hydrodistillation. Chemical analysis by GC-MS identified 29 compounds. Terpinen-4-ol (17.8%) was a major component, together with α-guaiene (7.9%), E-caryophyllene (7.0%), myrcene (6.7%), (+)-cyclosativene (5.1%), sabinene (4.8%), aciphyllene (4.7%), pogostol (4.6%), gamma-terpinene (3.4%), α-muurolol (3.2%) and germecrene D (3.2%). The essential oil exhibited antibacterial activity against Propionibacterium acnes ATCC 6919 with an MIC of 0.125%, v/v.
Inclusion of Vitamin D2 in β-Cyclodextrin. Evaluation of Different Complexation Methods (1993)

Evaluation of inclusion complexation of vitamin D2 with β-cyclodextrin in aqueous solution and solid state was performed by Phase Solubility Diagramm, HPLC, DSC, X-RAY Diffractometry, NMR. Solid inclusion complexes were prepared by spray-drying, kneading and solid dispersion. The dissolution profiles of the complex either in powder or in tablets were studied in order to select the best inclusion process.
Preparation of Heteroarenecarbonitriles by Reaction of Haloheteroarenes with Potassium Cyanide Catalyzed by Sodium p-Toluenesulfinate (1994)

Several heteroarenecarbonimles were prepared by reaction of haloheteroarenes with potassium cyanide catalyzed by sodium p-toluenesulfinate (1) or sodium methanesulfinate (2).In the reaction pathway, the cyanation proceeds through the fonnation of the sulfonylheteroarenes.
Natriuretic Peptide Receptors, NPR-A and NPR-B, in Cultured Rabbit Retinal Pigment Epithelium Cells (1999)

We tried to detect natriuretic peptide (NP) receptor (NPR-A and NPR-B) mRNAs in cultured rabbit retinal pigment epithelium (RPE) cells and examined the regulation of their expression in relation to subretinal fluid absorption or RPE cell proliferation. RPE cells from 2-4 passages were grown to confluence on microporous membranes and analyzed for levels of expression of receptor mRNAs by quantitative RT-PCR and Northern blotting. The expression of NPR-B mRNA was approximately tenfold higher than that of NPR-A mRNA. The expression of NPR-A mRNA was not affected by treatments that may change subretinal fluid transport, while that of NPR-B mRNA was inhibited by transmitters involved in light- and dark-adaptation such as dopamine and melatonin. Expression of NPR-B mRNA was also suppressed by platelet-derived growth factor and transforming growth factor-beta. Furthermore, atrial natriuretic peptide (ANP) and C-type natriuretic peptide (CNP), ligands for NPR-A and B, respectively, inhibited the proliferation of RPE cells, as analyzed by incorporation of [3H]thymidine. These findings suggest that ANP may be involved in constitutive absorption of subretinal fluid and that NPs form an important regulatory system of proliferation in RPE cells.
ZEOLITE CATALYZED RING OPENING OF EPOXIDES TO ACETYLATED DIOLS WITH ACETIC ANHYDRIDE* (2001)

HY Zeolite is found to be a versatile catalyst for opening of epoxides to the corresponding acetylated 1,2-Diols with acetic anhydride in good yields.
Experimental validation of time reversal ultra wide-band communication system for high data rates (2010)

An experimental validation of high data rate communication for a time reversal (TR) ultra wide-band (UWB) communication system is performed using binary pulse amplitude modulation (BPAM) in two different dense multipath propagation channels for different data rates (15.62 Mbps≤Rb≤1 Gbps). From the measured received signals, signal, interference and noise contributions are separated. At very high data rates, interference has the most dominant contribution of all. Furthermore, without any processing and equalisation at the receiver, bit error rate (BER) performance is compared for different Rb. It is shown that for Rb≤125 Mbps, TR system gives a good BER performance. Finally, the authors introduce a modified TR scheme in which total bandwidth of the TR system is divided into N sub-bands contributing equal power in the power spectral density (PSD). This technique enables a flat PSD of the TR transmitted signal, reduces inter symbol interference (ISI) and therefore improves the BER performance of the system.
Homologous recombination in hybridoma cells: dependence on time and fragment length. (1990)

Mutant hybridoma-myeloma cell lines that are defective in immunoglobulin production are expected to be useful for defining the molecular requirements of immunoglobulin gene expression. The analysis of such mutants would be greatly facilitated if they could be mapped by marker rescue, i.e., by identifying the segments of wild-type DNA that can restore the normal phenotype by homologous recombination with the mutant chromosomal immunoglobulin gene. To assess the feasibility of this type of mapping, we have measured the efficiency with which fragments of wild-type DNA recombine with a mutant hybridoma immunoglobulin gene and restore normal immunoglobulin production. We found that most if not all recombinants were detectable 2 days after DNA transfer and that the frequency of gene restoration increased with increasing length of the transferred mu gene fragments, between 1.2 and 9.5 kilobases. These results indicate that the available technology should be adequate to map mutations in the mu gene to within approximately 1 kilobase.
Sealed Inside-Out and Right-Side-Out Plasma Membrane Vesicles (1990)

Plasma membrane preparations of high purity (about 95%) are easily obtained by partitioning in aqueous polymer two-phase systems. These preparations, however, mainly contain sealed right-side-out (apoplastic side out) vesicles. Part of these vesicles have been turned inside-out by freezing and thawing, and sealed inside-out and right-side-out vesicles subsequently separated by repeating the phase partition step. Increasing the KCI concentration in the freeze/thaw medium as well as increasing the number of freeze/thaw cycles significantly increased the yield of inside-out vesicles. At optimal conditions, 15 to 25% of total plasma membrane protein was recovered as inside-out vesicles, corresponding to 5 to 10 milligrams of protein from 500 grams of sugar beet (Beta vulgaris L.) leaves. Based on enzyme latency, trypsin inhibition of NADH-cytochrome c reductase, and H(+) pumping capacity, a cross-contamination of about 20% between the two fractions of oppositely oriented vesicles was estimated. Thus, preparations containing about 80% inside-out and 80% right-side-out vesicles, respectively, were obtained. ATPase activity and H(+) pumping were both completely inhibited by vanadate (K(i) approximately 10 micromolar), indicating that the fractions were completely free from nonplasma membrane ATPases. Furthermore, the polypeptide patterns of the two fractions were close to identical, which shows that the vesicles differed in sidedness only. Thus, preparations of both inside-out and right-side-out plasma membrane vesicles are now available. This permits studies on transport, signal transduction mechanisms, enzyme topology, etc., using plasma membrane vesicles of either orientation.
Long Term Exendin-4 Treatment Reduces Food Intake and Body Weight and Alters Expression of Brain Homeostatic and Reward Markers (2014)

Repeated administration of the long-acting glucagon-like peptide 1 receptor agonist exendin-4 (EX-4) has been shown to reduce food intake and body weight and do so without a rebound increase in food intake after treatment termination. The current study examines the neural mechanisms underlying these actions. After 6 weeks of maintenance on a standard chow or a high-fat (HF) diet, male Sprague Dawley rats were treated with EX-4 (3.2 μg/kg, i.p., twice a day) or vehicle for 9 consecutive days. Food intake and body weight (BW) were monitored daily. Expression of the genes for the hypothalamic arcuate nucleus (ARC) peptides proopiomelanocortin (POMC), neuropeptide Y (NPY), and agouti gene-related protein was determined. Expression of the dopamine precursor tyrosine hydroxylase (TH) gene in the ventral tegmental area and genes for dopamine receptors 1 (D1R) and dopamine receptor 2 in the nucleus accumbens were also determined. Pair-fed groups were included to control for the effects of reduced food intake and BW. Treatment with EX-4 significantly decreased food intake and BW over the 9-day period in both the standard chow and HF groups. HF feeding decreased POMC without changing NPY/agouti gene-related protein gene expression in the ARC. Treatment with EX-4 increased POMC and decreased NPY expression independent of the reduction of food intake and BW. Mesolimbic TH and D1R gene expression were decreased significantly in chronic HF diet-fed rats, and these changes were reversed in both EX-4 and pair-fed conditions. These results suggest a role for increased POMC and decreased NPY expression in the ARC in the effects of EX-4 on food intake and BW. Our findings also suggest that EX-4 induced the recovery of mesolimbic TH and D1R expression in HF diet-fed rats may be secondary to HF intake reduction and/or weight loss.
Selection of Optimal Prostate Specific Antigen Cutoffs for Early Detection of Prostate Cancer: Receiver Operating Characteristic Curves (1994)

A prospective clinical trial of prostate cancer screening was conducted at 6 university centers including 6,630 men 50 years old or older who underwent a serum prostate specific antigen (PSA) determination and digital rectal examination. Biopsies were performed if the PSA level was greater than 4.0 ng./ml. (Hybritech Tandem assay) or digital rectal examination was suspicious for cancer. We evaluated the effect on biopsy rate and cancer detection if the cutoff value was shifted from 4.0 to age-specific reference ranges recommended in the literature. In men 50 to 59 years old with normal digital rectal examination findings a decrease from 4.0 to 3.5 ng./ml. would have resulted in a 45% increase in the number of biopsies (39 of 87) and a projected 15% increase in cancer detection. An increase from 4.0 to 4.5 ng./ml. in men 60 to 69 years old would result in 15% fewer biopsies (35 of 238) and would miss 8% of the organ confined tumors (2 of 25). Increasing the cutoff to 6.5 ng./ml. in men 70 years old or older would result in 44% fewer biopsies (70 of 159) and would miss 47% of the organ confined cancers (7 of 15). The number of biopsies performed for each cancer detected with a PSA level of greater than 4.0 ng./ml. remains constant across age groupings, which suggests that the cutoff of 4.0 ng./ml. does not need to be altered in the older men, since it is apparently unaffected by the simultaneously increasing prevalence of benign prostatic hyperplasia and cancer with age. We conclude that a serum PSA concentration of 4.0 ng./ml. should be used as a general guideline for biopsy in all age groups.
Tumor-derived expression of vascular endothelial growth factor is a critical factor in tumor expansion and vascular function. (1999)

There is considerable controversy concerning the importance of tumor-derived angiogenic factors to the neovascularization of solid tumors. Tumor, endothelial, and stromal expression of vascular endothelial growth factor (VEGF) have been hypothesized to be critical for tumor angiogenesis. To determine the relative contribution of tumor versus nontransformed tissue expression of VEGF to tumor growth, we used gene targeting and cre-loxP recombination to generate embryonic stem cell lines in which VEGF can be conditionally deleted. These lines were used to derive mouse embryonic fibroblast lines with null mutations in both alleles of VEGF. Upon immortalization and H-ras transformation, we used these VEGF null fibroblasts to make fibrosarcomas in immunocompromised mice. We report that tumorigenic VEGF expression is critical for ras-mediated tumorigenesis, and the loss of tumorigenic expression causes dramatic decreases in vascular density and vascular permeability and increases in tumor cell apoptosis.
Enzymatic reduction of oxidized alpha-1-proteinase inhibitor restores biological activity. (1981)

The major serum inhibitor of proteolytic activity, alpha-1-proteinase inhibitor (alpha-1-PI), (or alpha-1-antitrypsin) can be readily inactivated by oxidation [Carp, H. & Janoff, A. (1978) Am. Rev. Resp. Dis. 118, 617-621]. This inactivation appears to be due to the oxidation of a critical methionine(s) in alpha-1-PI that is required for the inhibition of elastase activity. An enzyme from Escherichia coli that reduces methionine sulfoxide residues in protein [Brot, N., Weissbach, L., Werth, J. & Weissbach, H. (1981) Proc. Natl. Acad. Sci. USA 78, 2155-2158] can restore the biological inhibitory activity of canine oxidized alpha-1-PI.
Tetrahydroquinoline Derivatives as Potent and Selective Factor XIa Inhibitors (2014)

Antithrombotic agents that are inhibitors of factor XIa (FXIa) have the potential to demonstrate robust efficacy with a low bleeding risk profile. Herein, we describe a series of tetrahydroquinoline (THQ) derivatives as FXIa inhibitors. Compound 1 was identified as a potent and selective tool compound for proof of concept studies. It exhibited excellent antithrombotic efficacy in rabbit thrombosis models and did not prolong bleeding times. This demonstrates proof of concept for the FXIa mechanism in animal models with a reversible, small molecule inhibitor.