gebhart/patrepeval huggingface dataset:
IPI-504: A Novel hsp90 Inhibitor with In Vitro and In Vivo Anti-Tumor Activity. (2004)

Abstract We have previously shown that inhibitors of the hsp90 molecular chaperone (including geldanamycin, 17-allylamino-17-demethoxy-geldanamycin (17-AAG) and other members of the ansamycin family) potently induce growth arrest and apoptosis of a large panel of drug-sensitive and -resistant MM cell lines, as well as tumor cells freshly isolated from patients with relapsed refractory MM; and sensitize these cells to other pro-apoptotic anti-tumor agents. While multiple phase I clinical trials have shown that biologically active doses of 17-AAG can be administered without significant hsp90-related toxicities, the insolubility of this compound in most conventional clinical solvents, as well as the practical limitations of DMSO-based formulations that were used in the original clinical trials have generated the need to develop more effective and practical approaches to administer 17-AAG to patients. Herein we describe the in vitro and in vivo pre-clinical profile of IPI-504, a novel analog of 17-AAG, which is soluble in aqueous formulations and can bypass key limitations of the DMSO-based formulations for administration of 17-AAG. Our in vitro studies show that IPI-504 has anti-tumor activity against a broad panel of primary MM tumor cells as well as MM cell lines (including cells resistant to cytotoxic chemotherapeutics, proteasome inhibitor bortezomib, thalidomide or its immunomodulatory thalidomide derivatives, and/or Apo2L/TRAIL). Based on hierarchical clustering analyses, logistic and linear regression models, we observed that the profiles of drug sensitivity of MM cells to IPI-504 were consistent with the profiles of sensitivity to 17-AAG. Similarly, IPI-504 triggered a constellation of molecular sequelae that were consistent with hsp90 inhibition by 17-AAG, including suppression of cell surface expression and down-stream signaling (via PI-3K/Akt and Ras/Raf/MAPK) of receptors for IGF-1 and IL-6; decreased intracellular levels of several key kinases, including Akt, Raf, IKK-α; suppressed expression of several intracellular anti-apoptotic proteins (e.g. FLIP, XIAP, cIAP2); leading to tumor cell sensitization to other pro-apoptotic agents (e.g. cytotoxic chemotherapy or PS-341). Importantly, in our mouse model of diffuse MM bone lesions in SCID/NOD mice, IPI-504 (50 mg/kg, i.v. twice weekly) was able to prolong the survival of mice vs. vehicle-treated mice (p&lt;0.01, log-rank test), without significant treatment-related toxicities. These results indicate that hsp90 inhibitors have significant anti-MM activity in vivo, which, coupled with our ex vivo mechanistic and molecular profiling studies, have provided the framework for upcoming clinical trials of this novel class of agents in patients with MM.
The effect of recombinant α-interferon treatment on serum levels of hepatitis B virus-encoded proteins in man (1987)

The effect of alpha-interferon treatment on serum levels of hepatitis B virus-encoded proteins was analyzed in eight patients with chronic type B hepatitis who participated in a pilot study of interferon therapy. Three individuals became HBsAg-negative, 4 lost HBeAg but remained HBsAg-positive and 1 remained positive for both HBsAg and HBeAg. Initiation of interferon treatment was rapidly followed by reduction or loss of hepatitis B virus DNA in the serum but by little immediate change in hepatitis B virus antigen levels. Changes in hepatitis B virus antigens were usually delayed. Loss of HBsAg from the serum was preceded by the sequential disappearance of pre-S-encoded proteins (pre-S1 and polymerized human serum albumin) and HBeAg. In patients who lost HBeAg but remained HBsAg-positive, serum levels of pre-S1 and polymerized human serum albumin usually, but did not always, decrease. The individual who remained HBsAg- and HBeAg-positive had unchanged serum levels of pre-S1, polymerized human serum albumin and HBsAg. These results suggest that alpha-interferon inhibits hepatitis B virus DNA replication but has little direct effect on synthesis of hepatitis B virus gene products.
Effects of Atropine on Learning and Memory Functions in Dementia (1990)

The effect of intravenous atropine (1 mg) or saline on mnemonic function was tested in patients with various forms of dementia and age-matched controls. Examinees consisted of 12 subjects having Alzheimer's disease (AD), multi-infarct dementia (MID), Parkinson's disease without dementia or with dementia, and normal aged controls. Wechsler's adult memory scale was used. Orientation, visual reproduction, and associative learning were not affected by this small dose of atropine in any of the subgroups. On the other hand, digit span and logical memory were selectively impaired by atropine in AD. The more sensitive parameters were the improvement on retesting (reflecting learning abilities). This study suggests that cholinergic dysfunction is responsible for abnormalities in logical memory and digit span in AD or the dementia of Parkinson's disease but not in MID.
Free radicals and redox signalling in cardiovascular disease (2004)

The generation of reactive oxygen species (ROS) is an inevitable consequence of life in an aerobic environment. ROS are characterised by their high chemical reactivity and include both free radicals (that is, species with one or more unpaired electrons, such as superoxide (O2 . −) and hydroxyl radicals (OH . )), and non-radical species such as hydrogen peroxide (H2O2). In health, there is a balance between ROS generation and the activity of enzymatic and non-enzymatic antioxidant systems that scavenge or reduce ROS concentrations.1 Redox imbalance caused by increased ROS production and/or reduced antioxidant reserve causes oxidative stress—that is, an enhanced susceptibility of biological molecules and membranes to reaction with ROS.

Traditionally, oxidative stress has been considered deleterious due to free radical induced oxidation and damage of macromolecules, membranes and DNA. ROS generation by phagocytic cells such as neutrophils is a pivotal component of their antimicrobial actions and as such deleterious for ingested organisms, but is, however, clearly beneficial for the host. On the other hand, the restoration of oxygen supply during myocardial reperfusion after prolonged ischaemia is accompanied by a burst of free radical production that is damaging for the heart.2 Oxidative stress induced damage includes acceleration of cell death through apoptosis and necrosis, mechanisms that may also be of relevance in advanced heart failure.

Recently, however, it has been recognised that oxidative stress may exert more subtle modulatory effects. Firstly, the tightly regulated production of ROS can modulate the activity of diverse intracellular molecules and signalling pathways (a mechanism commonly termed “redox signalling”), with the potential to induce highly specific acute and chronic changes in cell phenotype.3 This use of oxygen species to transmit biological information provides at least a teleological explanation for the widespread occurrence of ROS even in health. Secondly, inactivation …
INTRAVITREAL BEVACIZUMAB TREATMENT OF CHOROIDAL NEOVASCULARIZATION SECONDARY TO AGE-RELATED MACULAR DEGENERATION (2006)

There were no apparent short-term safety concerns for intravitreal bevacizumab injection for CNV. Treated eyes had a significant decrease in macular thickness and improvement in visual acuity. The follow-up was too short to make any specific treatment recommendations, but the favorable short-term results suggest further study is needed.
Defining principles of combination drug mechanisms of action (2012)

Combination chemotherapies have been a mainstay in the treatment of disseminated malignancies for almost 60 y, yet even successful regimens fail to cure many patients. Although their single-drug components are well studied, the mechanisms by which drugs work together in clinical combination regimens are poorly understood. Here, we combine RNAi-based functional signatures with complementary informatics tools to examine drug combinations. This approach seeks to bring to combination therapy what the knowledge of biochemical targets has brought to single-drug therapy and creates a statistical and experimental definition of "combination drug mechanisms of action." We show that certain synergistic drug combinations may act as a more potent version of a single drug. Conversely, unlike these highly synergistic combinations, most drugs average extant single-drug variations in therapeutic response. When combined to form multidrug regimens, averaging combinations form averaging regimens that homogenize genetic variation in mouse models of cancer and in clinical genomics datasets. We suggest surprisingly simple and predictable combination mechanisms of action that are independent of biochemical mechanism and have implications for biomarker discovery as well as for the development of regimens with defined genetic dependencies.
Preparations of 2,4-Disubstituted Oestradiols (1989)

2,4-Dibromoestra-1,3,S(10)-triene-3,17 ß- diol 3-(2'-hydroxyethyl) ether (8) undergoes reaction with copper(11) chloride/sodium methoxide to afford a 4-bromo [2,3]- dioxan derivative (9) as the major product together with a minor amount of a 2-bromo [3,4]- dioxan derivative (10). These compounds were used to prepare a number of 2,4-disubstituted oestradiol derivatives. &amp;nbsp; Alternative routes to other 2,4-disubstituted oestradiols are described.
Enzyme immunoassays in diagnostic medicine. Theory and practice. (1976)

Serological methods are playing an increasingly important role in the diagnosis and epidemiological assessment of diseases. Simple, inexpensive methods for large-scale application are urgently needed. The enzyme immunoassay methods developed recently and reviewed here hold great promise for application in a wide variety of conditions. Under laboratory conditions they can be as sensitive as radio-immunoassay, but they can also be adapted as simple field screening procedures. These methods are based on the use of antibodies or antigens that are linked to an insoluble carrier surface. This is then used to "capture" the relevant antigen or antibody in the test solution and the complex is detected by means of an enzyme-labelled antibody or antigen. The degradation of the enzyme substrate, measured photometrically, is proportional to the concentration of the unknown "antibody" or "antigen" in the test solution. The application of these techniques to endocrinology, immunopathology, haematology, microbiology, and parasitology is reviewed.
Proliferation, differentiation, and tube formation by endothelial progenitor cells in response to shear stress (2003)

Endothelial progenitor cells (EPCs), circulating in peripheral blood, migrate toward target tissue, differentiate, and contribute to the formation of new vessels. In this study, we report that shear stress generated by blood flow or tissue fluid flow can accelerate the proliferation, differentiation, and capillary-like tube formation of EPCs. When EPCs cultured from human peripheral blood were subjected to laminar shear stress, the cells elongated and oriented their long axes in the direction of flow. The cell density of the EPCs exposed to shear stress was higher, and a larger percentage of these cells were in the G2-M phase of the cell cycle, compared with EPCs cultured under static conditions. Shear stress markedly increased the EPC expression of two vascular endothelial growth factor receptors, kinase insert domain-containing receptor and fms-like tyrosine kinase-1, and an intercellular adhesion molecule, vascular endothelial-cadherin, at both the protein and mRNA levels. Assays for tube formation in the collagen gels showed that the shear-stressed EPCs formed tubelike structures and developed an extensive tubular network significantly faster than the static controls. These findings suggest that EPCs are sensitive to shear stress and that their vasculogenic activities may be modulated by shear stress.
Internalization of transforming growth factor‐β and its receptor in BALB/c 3T3 fibroblasts (1986)

The fate of 125I-labeled transforming growth factor-beta (125I-TGF beta) after binding to its cells surface receptor has been investigated in BALB/c 3T3 mouse fibroblasts. Binding of 125I-TGF beta to cellular receptors at 4 degrees C is pH-sensitive, being markedly decreased at pH less than 6. Most (approximately 90%) of the 125I-TGF beta bound to cells at 4 degrees C can be removed by a brief treatment with acidic medium but is converted into an acid-resistant state rapidly after shifting the cells to 37 degrees C. Cell-bound 125I-TGF beta is degraded at 37 degrees C and the degradation products are released into the medium. The lysosomotropic bases chloroquine, methylamine, and ammonium and the carboxylic ionophore monensin inhibit the degradation and release of 125I-TGF beta from the cells. Cells allowed to accumulate 125I-TGF beta intracellularly by the action of chloroquine or monensin were treated with the bifunctional agent disuccinimidyl suberate in the presence of detergent Triton X-100; this treatment caused the cross-linking of internalized 125I-TGF beta with the 280-kilodalton TGF beta receptor component. Under conditions in which sustained binding and degradation of saturating 125I-TGF beta concentrations occurs, there is no marked decrease in the binding capacity of the cells even when protein synthesis is blocked with cycloheximide. These results indicate that after TGF beta binding the TGF beta:receptor complex becomes rapidly internalized and that TGF beta is directed towards lysosomes where it is degraded and released. However, the cell surface is replenished with TGF beta receptors recycled after internalization or supplied by a large intracellular pool.
Human T-Cell Lymphotropic Virus Type 1 Gag Indeterminate Western Blot Patterns in Central Africa: Relationship toPlasmodium falciparumInfection (2000)

To gain insight on the significance of human T-cell lymphotropic virus type 1 (HTLV-1) indeterminate serological reactivities, we studied villagers of South Cameroon, focusing on a frequent and specific HTLV-1 Gag indeterminate profile (HGIP) pattern (gag p19, p26, p28, and p30 without p24 or Env gp21 and gp46). Among the 102 sera studied, 29 from all age groups had a stable HGIP pattern over a period of 4 years. There was no epidemiological evidence for sexual or vertical transmission of HGIP. Seventy-five percent of HGIP sera reacted positively on MT2 HTLV-1-infected cells by immunofluorescence assay. However, we could not isolate any HTLV-1 virus or detect the presence of p19 Gag protein in cultures of peripheral blood mononuclear cells obtained from individuals with strong HGIP reactivity. PCR experiments conducted with primers for HTLV-1 and HTLV-2 (HTLV-1/2 primers) encompassing different regions of the virus did not yield HTLV-1/2 proviral sequences from individuals with HGIP. Using 11 peptides corresponding to HTLV-1 or HTLV-2 immunodominant B epitopes in an enzyme-linked immunosorbent assay, one epitope corresponding to the Gag p19 carboxyl terminus was identified in 75% of HGIP sera, while it was recognized by only 41% of confirmed HTLV-1-positive sera. A positive correlation between HTLV-1 optical density values and titers of antibody to Plasmodium falciparum was also demonstrated. Finally, passage of sera through a P. falciparum-infected erythrocyte-coupled column was shown to specifically abrogate HGIP reactivity but not the HTLV-1 pattern, suggesting the existence of cross-reactivity between HTLV-1 Gag proteins and malaria-derived antigens. These data suggest that in Central Africa, this frequent and specific Western blot is not caused by HTLV-1 infection but could instead be associated with P. falciparum infection.
Point source for ions and electrons (1988)

Field-ion techniques have been used to create physical point sources for ions and electrons with emission areas and angles orders of magnitude smaller than in any other available source. The monatomic pyramidal tips emit electrons or ionize noble-gas atoms originating from the single front atom. The angular divergence from the normal direction above the single W atom is less than 0.5° for ion beams produced by field ionization. The angular spread for emission from small clusters is somewhat larger for field ionization and electron emission. By employing tips as sources for free electrons in an STM-like setup, we were able to obtain high-resolution images of surfaces with an electron beam of only 15 eV primary energy. The image information is contained in the yield of the secondary electrons created at the sample surface.
Application of reproductive technologies to improve dairy cattle genomic selection (2016)

Genomic selection implies assessing the breeding value of an animal based on the DNA markers uniformly covering the whole genome. This review summarizes the information on the modern trends in dairy cattle genomic selection and the use of reproductive technologies allowing for the increase of breeding efficiency. The main trends in the advance of genomic selection are the improvement of the accuracy of breeding value estimations by pooling the reference populations; use of female genotyping in breeding programs; imputation of genotypes based on lower marker density SNP arrays; and prediction of animal genotypes from the genotyped relatives. Genomic selection can be even more profitable in combination with the state-of-the-art reproductive biotechnologies, such as semen sexing, multiple ovulation and embryo transfer, ovum pick-up followed by in vitro fertilization, embryo genotyping, and cloning of the best breeders. In dairy cattle genomic selection programs, biotechnological manipulations with gametes and embryos allow for the improvement of many factors determining breeding efficiency, namely, selection intensity, accurate breeding value assessment, and the generation interval. Successful embryo genotyping methods for numerous markers after biopsy at the morula or blastocyst stage are based on the whole-genome amplification of the embryo’s DNA. Eventually, these achievements will provide the grounds for new approaches to reducing the generation interval, selecting elite cows, reducing the inbreeding rate, etc.
Controlled aggregation of primary human pancreatic islet cells leads to glucose‐responsive pseudoislets comparable to native islets (2015)

Clinical islet transplantation is a promising treatment for patients with type 1 diabetes. However, pancreatic islets vary in size and shape affecting their survival and function after transplantation because of mass transport limitations. To reduce diffusion restrictions and improve islet cell survival, the generation of islets with optimal dimensions by dispersion followed by reassembly of islet cells, can help limit the length of diffusion pathways. This study describes a microwell platform that supports the controlled and reproducible production of three-dimensional pancreatic cell clusters of human donor islets. We observed that primary human islet cell aggregates with a diameter of 100-150 μm consisting of about 1000 cells best resembled intact pancreatic islets as they showed low apoptotic cell death (<2%), comparable glucose-responsiveness and increasing PDX1, MAFA and INSULIN gene expression with increasing aggregate size. The re-associated human islet cells showed an a-typical core shell configuration with beta cells predominantly on the outside unlike human islets, which became more randomized after implantation similar to native human islets. After transplantation of these islet cell aggregates under the kidney capsule of immunodeficient mice, human C-peptide was detected in the serum indicating that beta cells retained their endocrine function similar to human islets. The agarose microwell platform was shown to be an easy and very reproducible method to aggregate pancreatic islet cells with high accuracy providing a reliable tool to study cell-cell interactions between insuloma and/or primary islet cells.
Real World Experiences: Pirfenidone and Nintedanib are Effective and Well Tolerated Treatments for Idiopathic Pulmonary Fibrosis (2016)

Idiopathic Pulmonary Fibrosis (IPF) now has two licensed treatments available. Pirfenidone was the first drug to be licensed and approved for use, followed by nintedanib. We set out our real world experience with these agents in terms of their adverse events profile outside the restrictions of a clinical trial. We have demonstrated in the real world setting, that side effects are common and predominantly gastrointestinal with both therapies. Our study shows that the side effects can be effectively managed in the majority of patients with an acceptable discontinuation rate similar to that seen in the clinical trials. These findings are compelling despite the fact that the patients in our study are older, have severer disease as depicted by baseline lung function and more co-morbidities. Our data provides ongoing evidence of the safety and tolerability of both pirfenidone and nintedanib in patients who would not have met the rigorous criteria to be included in a clinical trial. Both these agents are effective in the management of IPF and slow the progression of this debilitating life limiting condition.
Volatile organic compound production by organisms in the genus Ascocoryne and a re-evaluation of myco-diesel production by NRRL 50072 (2010)

The Patagonian fungal endophyte NRRL 50072 is reported to produce a variety of medium-chain and highly branched volatile organic compounds (VOCs) that have been highlighted for their potential as fuel alternatives and are collectively termed myco-diesel. To assess the novelty of this observation, we determined the extent to which ten closely related Ascocoryne strains from commercial culture collections possess similar VOC production capability. DNA sequencing established a high genetic similarity between NRRL 50072 and each Ascocoryne isolate, consistent with its reassignment as Ascocoryne sarcoides. The Ascocoryne strains did not produce highly branched medium-chain-length alkanes, and efforts to reproduce the branched alkane production of NRRL 50072 were unsuccessful. However, we confirmed the production of 30 other products and expanded the list of VOCs for NRRL 50072 and members of the genus Ascocoryne. VOCs detected from the cultures consisted of short- and medium-chain alkenes, ketones, esters and alcohols and several sesquiterpenes. Ascocoryne strains NRRL 50072 and CBS 309.71 produced a more diverse range of volatiles than the other isolates tested. CBS 309.71 also showed enhanced production compared with other strains when grown on cellulose agar. Collectively, the members of the genus Ascocoryne demonstrated production of over 100 individual compounds, with a third of the short- and medium-chain compounds also produced when cultures were grown on a cellulose substrate. This comparative production analysis could facilitate future studies to identify and manipulate the biosynthetic machinery responsible for production of individual VOCs, including several that have a potential application as biofuels.
Radiation and apoptosis (2000)

Apoptosis is a major style of cell death induced by radiation.The mechanism of gene regulation for apoptosis is precise and complex.P53,bcl 2 family,Fas,system,c myc,P34cdc2,caspases all regulate apoptosis induced by radiation.Apoptosis in involved in a cascade that is triggerde by activation of apoptogenic proteases,and regulated by signals from death receptors.The lag period from radiation to apoptosis is different in different cells.Apoptosis rates are effected by LET and radiation dose.
Choice of Starting Dose for Molecularly Targeted Agents Evaluated in First-in-Human Phase I Cancer Clinical Trials (2010)

The derivation of starting dose for first-in-human phase I trials of molecularly targeted agents in patients with cancer is safe but is based on diverse practices using a variety of preclinical toxicologic parameters.