gebhart/patrepeval huggingface dataset:
Heat shock protein 70-associated peptides elicit specific cancer immunity. (1993)

Vaccination of mice with heat shock protein 70 (hsp70) preparations derived from the Meth A sarcoma, but not from normal tissues, renders the mice immune to a substantial challenge with Meth A sarcoma. The immunogenicity is dose dependent and tumor specific. Treatment of an antigenically active hsp70 preparation with ATP followed by removal of low-molecular weight material leaves hsp70 intact, as judged by SDS-PAGE but results in loss of antigenicity, as judged by tumor rejection assays. Separation of this low-molecular weight material on a C18 reverse-phase column shows a diverse array of peptides with molecular mass between 1,000 and 5,000 daltons. Our data indicate that antigenicity of hsp70 preparations derives, not from hsp70 per se, but from associated peptides. These observations may suggest a novel method of using the peptide-binding property of hsp70 for specific vaccination against cancer and infectious diseases.
Idiopathic hyperammonemia: a frequently lethal complication of bone marrow transplantation. (1996)

Idiopathic hyperammonemia (IHA) has been described as a rare complication of intensive chemotherapy, but there is little data regarding its occurrence after bone marrow transplantation (BMT). IHA is defined as elevated plasma ammonia concentrations (> 200 mumol/l) in the absence of significant liver function abnormality. From a 21 year BMT database of 2358 patients, we have identified 12 patients (0.5%) with IHA, ages 19 to 46 years. Diagnoses included ALL (n = 2), AML (n = 4), CLL (n = 1), CML (n = 3) and aplastic anemia (n = 2). Eight received marrow from a matched sibling donor, three from an unrelated donor and one autologous marrow. IHA occurred between 14 and 106 days after transplant (median, 25 days). Most frequently patients presented with symptoms of a metabolic encephalopathy, with lethargy and confusion evolving into unresponsiveness, metabolic coma and in eight cases, seizures. At diagnosis of IHA, liver functions were normal or only modestly abnormal. Ten of the 12 patients died 1 to 9 days (median 3.5 days) after diagnosis of IHA despite treatment with combinations of dialysis and ammonia-trapping therapy. While IHA is a rare complication of BMT, it is associated with a high mortality. Early recognition of the syndrome by measurement of plasma ammonia concentrations in patients with neurological symptoms may improve outcome.
Cell‐Free DNA in Urine (2001)

Intrigued by the rapid clearance of free fetal DNA from the maternal circulation, we have investigated whether this fetal genetic material could be cleared via the kidney. For this purpose, we examined for the presence of Y chromosome-specific DNA sequences in urine samples obtained from 8 women pregnant with male fetuses. No male-specific sequences could be detected, despite the use of a very sensitive nested PCR assay nor a highly reproducible real-time PCR assay. We did, however, detect maternal DNA sequences. To determine if this cell-free DNA was derived from the kidney or another source, we next examined urine from female kidney transplant patients who had received male kidneys. Y chromosome-specific sequences were indeed detectable by both nested and real-time PCR in these samples, thereby confirming a recent report describing urinary DNA microchimerism. Quantitative analysis of serially obtained samples furthermore suggests that transplant-derived sequences are elevated during periods of graft rejection. These results imply that the measurement of graft-derived urinary DNA may serve as a new marker for kidney graft tolerance.
‘Magic bullets’ for bone diseases: progress in rational design of bone-seeking medicinal agents (2006)

An ideal therapeutic agent for bone diseases should act solely on bone tissue with no pharmacological activity at other anatomical sites. Current therapeutic agents, however, do not usually display a preferential affinity to bones and non-specifically distribute throughout the body after administration. Attempts to design bone-specific agents have relied on engineering a desired therapeutic agent with bone-seeking molecules so that the latter delivers the therapeutic agents specifically to bones. In this critical review, we summarize the latest attempts to engineer bone-seeking therapeutic agents based on formulating therapeutic agents with bisphosphonates, a class of compounds with high affinity to biological apatite. We first provide a relevant summary of the structure of bone mineral and bisphosphonates, highlighting the mode of interaction between these two entities. The use of bisphosphonates in the diagnosis of bone diseases is then presented, since this application helps us to understand the bone-carrier properties of bisphosphonates under physiological conditions. A summary of recent attempts to formulate bisphosphonates with traditional therapeutic agents to restrict their activities to bone tissues is then provided, with special emphasis on the structure-function relationships of the engineered compounds. Finally, attempts to use bisphosphonates to deliver macromolecular therapeutics (i.e., proteins) are summarized, based on recent data from the authors' lab. The collective research into bone-seeking medicinal agents is progressively laying the foundation for next-generation 'magic bullets' that display desirable activities at the disease sites with no undesirable activity on other organ systems. (164 references.).
Isolation and Characterization of the Outer Membrane of Neisseria gonorrhoeae (1974)

The cell envelope of Neisseria gonorrhoeae strain 2686, colonial type 4, was isolated from spheroplasts formed by the action of ethylenediaminetetraacetic acid and lysozyme. Isopycnic centrifugation of osmotically ruptured spheroplasts resolved the cell envelope into two main membrane fractions. Chemical and enzymatic analyses were used to characterize these isolated membranes. Succinic dehydrogenase, reduced nicotinamide adenine dinucleotide oxidase, and d-lactate dehydrogenase were localized in the membrane fraction of buoyant density, rho degrees = 1.141 g/cm(3). Lipopolysaccharide and over half of the cell envelope protein were associated with the membrane that banded in sucrose at rho degrees = 1.219 g/cm(3). These fractions were consequently designated cytoplasmic and outer or L-membrane, respectively. Sodium dodecyl sulfate-polyacrylamide electrophoresis of isolated membranes demonstrated the relative simplicity of the protein spectrum of the outer membrane. The majority of the protein in this membrane could be accounted for by proteins of molecular weights 34,500, 22,000, and 11,500. The protein of molecular weight 34,500 accounted for 66% of the total protein of the L-membrane. Isoelectric precipitation at pH 4.6 with 10% acetic acid selectively removed this protein from a 150 mM NaCl in 10 mM tris(hydroxymethyl)aminomethane-hydrochloride, pH 7.4, extract of purified outer membrane. At pH 4.0, the other proteins of the L-membrane were precipitated. It was concluded that the membrane components of the cell envelope of N. gonorrhoeae were similar to those of other gram-negative bacteria. The cell envelope fractions described here, in particular the outer membrane, are sufficiently well defined to provide a valuable tool for future biochemical and immunological studies on N. gonorrhoeae.
Functional magnetic resonance imaging in real time (FIRE): Sliding-window correlation analysis and reference-vector optimization (2000)

New algorithms for correlation analysis are presented that allow the mapping of brain activity from functional MRI (fMRI) data in real time during the ongoing scan. They combine the computation of the correlation coefficients between measured fMRI time-series data and a reference vector with “detrending,” a technique for the suppression of non-stimulus-related signal components, and the “sliding-window technique.” Using this technique, which limits the correlation computation to the last N measurement time points, the sensitivity to changes in brain activity is maintained throughout the whole experiment. For increased sensitivity in activation detection a fast and robust optimization of the reference vector is proposed, which takes into account a realistic model of the hemodynamic response function to adapt the parameterized reference vector to the measured data. Based on the described correlation method, real-time fMRI experiments using visual stimulation paradigms have been performed successfully on a clinical MR scanner, which was linked to an external workstation for image analysis. Magn Reson Med 43:259–268, 2000. © 2000 Wiley-Liss, Inc.
Osteitic bone: a surrogate marker of eosinophilia in chronic rhinosinusitis (2012)

Osteitic bone: a surrogate marker of eosinophilia in chronic rhinosinusitis
Effect of Pioglitazone on Circulating Adipocytokine Levels and Insulin Sensitivity in Type 2 Diabetic Patients (2004)

We examined the effect of pioglitazone (PIO) on circulating adipocytokine levels to elucidate the mechanisms by which thiazolidinediones improve insulin resistance in type 2 diabetes mellitus (T2DM). Twenty-three subjects with T2DM (age 54 +/- 2 yr, body mass index 29 +/- 1 kg/m(2)) were randomly assigned to receive placebo (n = 11) or PIO, 45 mg/d (n = 12), for 4 months. Before and after treatment, subjects received a 75-g oral glucose tolerance test (OGTT); euglycemic insulin clamp (40 mU/m(2).min) with 3-(3)H-glucose; determination of fat mass ((3)H(2)O); and measurement of fasting glucose, free fatty acids (FFAs), leptin, adiponectin, and TNFalpha concentrations. After 4 months of PIO, fasting plasma glucose concentration (Delta = -2.7 mol/liter), mean plasma glucose during OGTT (Delta = -3.8 mol/liter), and hemoglobin A(1c) (Delta = 1.7%) decreased (P < 0.05 vs. placebo) without change in fasting or post-OGTT plasma insulin levels. Fasting FFAs (Delta = 168 micromol/liter) and TNFalpha (Delta = 0.7 pg/ml) concentrations decreased (P < 0.05 vs. placebo), whereas adiponectin (Delta = 8.7 microg/ml) increased (P < 0.01 vs. placebo). Despite the increase in body fat mass (Delta = 3.4 kg) after PIO, plasma leptin concentration did not change significantly. No changes in plasma glucose, FFAs, or adipocytokine levels were observed in placebo-treated subjects. During the insulin clamp, endogenous (hepatic) glucose production decreased (Delta = -2.67 micromol/fat-free mass.min, P < 0.05 vs. placebo), whereas metabolic clearance rate of glucose (MCR) increased (Delta = 0.58 ml/fat-free mass.min, P < 0.05 vs. placebo) after PIO. In all subjects, before and after PIO, the decrease in plasma FFA concentration was correlated with the changes in both endogenous (hepatic) glucose production (r = 0.47, P < 0.05) and MCR (r = -0.41, P < 0.05), whereas the increase in plasma adiponectin concentration was correlated with the change in endogenous (hepatic) glucose production (r = -0.70, P < 0.01) and MCR (r = 0.49, P < 0.05). These results suggest that the direct effects of PIO on adipose tissue to decrease plasma FFA levels and increase plasma adiponectin contribute to the improvements in hepatic and peripheral insulin sensitivity and glucose tolerance in patients with T2DM.
Microporosity in Carbonate Rocks: GEOLOGICAL NOTES (1971)

Large pores in carbonate rocks hold and transmit fluids, whereas associated micropores may hold irreducible water; i.e., water not available for flow. Analysis of borehole logs of microporous carbonate rocks can result in misleadingly high calculated water saturations and possibly bypassing of a potential oil or gas reservoir. Microporosity occurs in carbonate rocks that range from friable to well indurated. Intercrystalline micropores may be present in micrite and within ooids, pisolites, micrite intraclasts, pellets, and cryptocrystalline grains. Micropores in ancient rocks appear to result from (1) formation of micrite envelopes, (2) void space present after transition of aragonite to calcite, or (3) incipient weathering and dissolution. Aggrading neomorphism of micrite to microspar tends to destroy microporosity.
Determination of the activation energy for the heterogeneous nucleation of misfit dislocations in Si1−xGex/Si deposited by selective epitaxy (1997)

Si 0.84 Ge 0.16 /Si heterostructures with variable finite lateral dimensions (10–300 μm) and different layer thicknesses grown by selective low pressure chemical vapor deposition epitaxy at a temperature of 700 °C were investigated with regard to relaxation by formation of misfit dislocations. While in small structures only nucleation and propagation occur, the dislocation–dislocation interaction (mainly multiplication) becomes more and more important in larger structures. Therefore it was possible to separate the three different mechanisms which play a role in relaxation, i.e., nucleation, propagation, and multiplication, and to study them independently. From the analysis of the misfit dislocations at the initial stage of relaxation it was possible to determine the nucleation site density and an activation energy of 2.8 eV for the heterogeneous nucleation of misfit dislocations.
Reconstruction and Future Trends of the AIDS Epidemic in the United States (1991)

There has been considerable uncertainty in estimates of past and current human immunodeficiency virus (HIV) infection rates in the United States. Statistical estimates of historical infection rates can be obtained from acquired immunodeficiency syndrome (AIDS) incidence data and the incubation period. However, this approach is subject to a number of sources of uncertainty and two other approaches, epidemic models of HIV transmission and surveys of HIV prevalence, are used to corroborate and refine the statistical estimates. Analyses suggest the HIV infection rate in the United States grew rapidly in the early 1980s, peaked in the mid-1980s, and subsequently declined markedly. Due both to the decline in the underlying infection rate and to the development of effective therapies that may delay AIDS diagnosis, overall AIDS incidence may plateau during the next 5 years. However, the number of individuals with advanced HIV disease without a diagnosis of AIDS who could potentially benefit from therapy is expected to increase 40% by 1995 as infected individuals progress to more advanced stages of HIV disease. Thus, although the overall HIV infection rate has declined, the demands on the U.S. health care system for treatment and care of HIV-infected individuals remain enormous.
EGF-Induced Cell Migration Is Mediated by ERK and PI3K/AKT Pathways in Cultured Human Lens Epithelial Cells (2006)

Cataract is considered as the most common cause of blindness, which is curable only by surgery. Postsurgery, however, many patients gradually develop the complication of posterior capsule opacification (PCO) or secondary cataract, arising from stimulated cell proliferation and cell migration within the lens capsule. The migration of human lens epithelial cells (HLECs) plays crucial roles in the remodeling of lens capsule and cataract formation, but less is known about the cell-signaling mechanism of migration. We observed that epithelial growth factor (EGF) induced cell migration in cultured human lens epithelial cells through the ERK and PI3K/AKT pathways. EGF induced cell migration in a dose-dependent manner; EGF-induced EGFR phosphorylation and downstream activation of c-Jun N-terminal protein kinase (JNK), p38 MAP kinase (p38), extracellular signal-regulated kinase (ERK1/2) and AKT, were inhibited by PD153035 (EGFR inhibitor), JNKi (JNK inhibitor), SB203580 (p38 inhibitor), U0126 (MEK/ERK inhibitor), and LY294002 (PI3K/AKT inhibitor), respectively. Furthermore, we found that EGF induced activity of matrix metalloproteinase-2 (MMP-2) in cultured HLECs. EGF-induced MMP-2 activity was significantly inhibited by treatment of PD153035, U0126, and LY294002, but not SB203580 and JNK inhibitor, suggesting that ERK and the phosphatidylinositol-3-kinase (PI3K)/AKT pathways selectively mediate EGF-stimulated MMP-2 activity and cell migration in cultured HLECs in vitro. Taken together, our results suggest that the cell-signaling pathways involved in EGF-stimulated cell migration may constitute potential therapeutic targets in the treatment of PCO.
Adverse outcome in pregnancy following amniotic fluid isolation of Ureaplasma urealyticum (1992)

Infections in pregnancy with Ureaplasma urealyticum have been associated with a wide range of adverse outcomes, such as early abortion, stillbirth, prematurity, and neonatal morbidity and mortality. Causality has been difficult to demonstrate secondary to the high prevalence of asymptomatic lower genital tract (LGT) colonization and culture data from inaccessible or potentially contaminated sites. Between 1985 and 1989, 2461 second-trimester genetic amniocenteses were evaluated at the cytogenetics section of the Children's Hospital Medical Center of Akron. All were cultured for the genital mycoplasmas: Mycoplasma hominis and Ureaplasma urealyticum. A total of nine patients were positive, all for Ureaplasma urealyticum, with one patient excluded because of subsequent therapeutic abortion. In addition, complete follow-up data, such as indication for amniocentesis, serum alpha-fetoprotein levels, gestational age at parturition, and outcome of pregnancy, were available on 86 Ureaplasma-negative (U-) patients during an approximate 2-year span within the time-frame of the study. This was in part due to physician response to a questionnaire sent after amniocentesis. Of the eight positive cultures, 100 per cent were associated with an adverse outcome, defined as fetal loss or premature delivery. This was significant compared with the U- group (p less than 0.001) with a more than eight times greater risk of adverse outcome. Six (75 per cent) resulted in spontaneous miscarriage within 4 weeks of amniocentesis and at less than 21 weeks' gestation. Two (25 per cent) delivered prematurely, with one (12.5 per cent) neonatal death at 24+ weeks. Histological examination of all eight placentae and the seven fetuses revealed a 100 per cent incidence of chorioamnionitis and pneumonia, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Unimolecular Dual Incretins Maximize Metabolic Benefits in Rodents, Monkeys, and Humans (2013)

We report the discovery and translational therapeutic efficacy of a peptide with potent, balanced co-agonism at both of the receptors for the incretin hormones glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP). This unimolecular dual incretin is derived from an intermixed sequence of GLP-1 and GIP, and demonstrated enhanced antihyperglycemic and insulinotropic efficacy relative to selective GLP-1 agonists. Notably, this superior efficacy translated across rodent models of obesity and diabetes, including db/db mice and ZDF rats, to primates (cynomolgus monkeys and humans). Furthermore, this co-agonist exhibited synergism in reducing fat mass in obese rodents, whereas a selective GIP agonist demonstrated negligible weight-lowering efficacy. The unimolecular dual incretins corrected two causal mechanisms of diabesity, adiposity-induced insulin resistance and pancreatic insulin deficiency, more effectively than did selective mono-agonists. The duration of action of the unimolecular dual incretins was refined through site-specific lipidation or PEGylation to support less frequent administration. These peptides provide comparable pharmacology to the native peptides and enhanced efficacy relative to similarly modified selective GLP-1 agonists. The pharmacokinetic enhancement lessened peak drug exposure and, in combination with less dependence on GLP-1-mediated pharmacology, avoided the adverse gastrointestinal effects that typify selective GLP-1-based agonists. This discovery and validation of a balanced and high-potency dual incretin agonist enables a more physiological approach to management of diseases associated with impaired glucose tolerance.
The multipartite system that mediates entry of herpes simplex virus into the cell (2007)

The multipartite entry-fusion system of herpes simplex virus is made of a quartet of glycoproteins-gD, gB, gH.gL-and three alternative gD receptors, herpesvirus entry mediator (HVEM), nectin1 and modified sites on heparan sulphate. This multipartite system recapitulates the basic steps of virus-cell fusion, i.e. receptor recognition, triggering of fusion and fusion execution. Specifically, in addition to serving as the receptor-binding glycoprotein, gD triggers fusion through a specialised domain, named pro-fusion domain (PFD), located C-terminally in the ectodomain. In the unliganded gD the C-terminal region folds around the N-terminal region, such that gD adopts a closed autoinhibited conformation. In HVEM- and nectin1-bound gD the C-terminal region is displaced (opened conformation). gD is the tool for modification of HSV tropism, through insertion of ligands to heterologous tumour-specific receptors. It is discussed whether gD responds to the interaction with the natural and the heterologous receptors by adopting similar conformations, and whether the closed-to-open switch in conformation is a generalised mechanism of activation. A peculiar recombinant highlighted that the central Ig-folded core of gD may not encode executable functions for entry and that the 219-314 aa segment may be sufficient to trigger fusion. With respect to fusion execution, gB appears to be a prospective fusogen based on its coiled-coil trimeric structure, similar to that of another fusion glycoprotein. On the other hand, gH exhibits molecular elements typical of class 1 fusion glycoproteins, in particular heptad repeats and strong tendency to interact with lipids. Whether fusion execution is carried out by gB or gH.gL, or both glycoproteins in complex or sequentially remains to be determined.
Wellbore Heat Losses and Casing Temperatures during Steam Injection (1966)

Well-bore heat loss, steam condensation rate, and casing temperature during wet steam injection can be predicted with existing theory, but tedious calculations are necessary for accurate results. However, the calculations can be handled graphically and are here so presented, covering all practical injection pressures, injection periods, and tubing-casing combinations. Equations on which the graphs are based, together with conductivity and emissivity data, were taken from the literature. Modes of heat transfer from tubing to casing, i.e., radiation, conduction and convection, are briefly discussed. Radiation is by far the largest, and any scheme for reducing heat loss and casing-temperature rise should take this into account. Heat transfer from tubing to casing was checked experimentally and found to agree well with predictions. The worst case was only 15% higher than predicted; usually the difference was much less. (10 refs.)
Population differences in S‐warfarin metabolism between CYP2C9 genotype‐matched Caucasian and Japanese patients (2003)

These findings indicate that population differences in the frequencies of known variant CYP2C9 alleles account only in part for the variability observed in in vivo CYP2C9 activity in different populations. In addition, a gene-dose effect of defective CYP2C9 alleles on the in vivo CYP2C9 activity is evident in Japanese patients but not in Caucasian patients. Further studies are required to identify currently unknown factor(s) (eg, transcriptional regulation) responsible for the large intrapopulation and interpopulation variability in CYP2C9 activity.