gebhart/patrepeval huggingface dataset:
Role of proteomics in translational research in cervical cancer (2006)

Cervical cancer is one of the leading causes of cancer morbidity and mortality in women worldwide. More than 98% of cases are related to a human papillomavirus (HPV) infection. Infection with specific subtypes of HPV has been strongly implicated in cervical carcinogenesis. The identification and functional verification of host proteins associated with HPV E6 and E7 oncoproteins may provide useful information for understanding cervical carcinogenesis and the development of cervical cancer-specific markers. In addition, proteomic profiling of altered proteins by anticancer drugs on cervical cancer cells may contribute to providing the fundamental resources for investigation of disease-specific target proteins, elucidation of the novel mechanisms of action and development of new drugs. The advent of proteomics has provided the hope of discovering novel biological markers for use in the screening, early diagnosis and prediction of response to therapy. This review describes the studies where profiles of protein expression in cervical cancer have been generated.
Phosphonium salts exhibiting selective anti-carcinoma activity in vitro. (1989)

Tetraphenylphosphonium cation (TPP) and other phosphonium cations selectively inhibited the growth in vitro of human pancreatic carcinoma-derived cells (PaCa-2) and Ehrlich Lettre Ascites cells (ELA) when compared with untransformed monkey kidney epithelial cells (CV-1). In contrast, neither cisplatin nor cytosine arabinoside showed significant selectivity using these lines. Evidence is presented to support the conclusion that the carcinoma-selective antiproliferative activity of phosphonium salts is due to selective accumulation caused by the abnormally high membrane potentials in carcinoma cells. Inhibition of TPP uptake into PaCa-2 and ELA cells by potassium and (for PaCa-2) valinomycin demonstrates that higher membrane potentials account for the carcinoma-selective uptake and cytostatic selectivity of the cation. For TPP chloride and 16 other phosphonium chlorides with a variety of structures, selective inhibition of PaCa-2 growth relative to CV-1 was optimal for the eight falling in a narrow range of octanol/water partition coefficients (between 0.013 and 0.24). A similar optimal selectivity range was observed for ELA cells relative to CV-1. The relationship between partition coefficients and cytostatic selectivity suggests that the rates of diffusion across cytoplasmic and mitochondrial membranes are key factors in the structure/anticarcinoma selectivity relationship for delocalized phosphonium salts in vitro. The relationship could prove useful for the design of other carcinoma-selective delocalized cations.
Prediction of Potato Processing Quality by near Infrared Reflectance Spectroscopy of Ground Raw Tubers (2011)

The technique of near infrared reflectance spectroscopy was tested to predict the processing quality of potatoes by scanning (850–2500 nm) ground raw potatoes ( n = 2517) from nine growing seasons and four to five locations. Calibration equations were developed for dry matter, starch, reducing sugars, sucrose and total sugar as well as lightness of dehydrated potatoes and potato crisps, and quality score of finished French fries. Two strategies in modelling were compared, an annually repeated (incremental) and a retrospective calculation at the end of the project with inclusion or removal of spectral outliers. The best coefficients of determination ( r 2 ) within independent validation sets were about 0.99 for dry matter, 0.96 for starch, 0.43 for reducing sugars, 0.71 for sucrose and 0.66 for total sugar. The RPD statistic (ratio of standard error of prediction to sample standard deviation) was up to 8.5 and 5.4 (dry matter and starch content, respectively), but was unacceptably low in the case of reducing sugars (1.7) and low for sucrose (2.4) and total sugar (2.3). Direct prediction of processing quality resulted in r 2 values of 0.52 for dehydrated potatoes, 0.69 for potato crisps and 0.56 for French fries, but the RPD of these models were too low even for screening purposes ( RPD &lt; 2.0).
A phenylalanine‐55 to serine amino‐acid substitution in the human glycoprotein IX leucine‐rich repeat is associated with Bernard‐Soulier syndrome (1997)

The platelet membrane glycoprotein (GP) Ib-IX-V complex, the major von Willebrand factor receptor on platelets, is absent or dysfunctional in patients with the Bernard-Soulier syndrome (BSS). The four single subunits of the GPIb-IX-V complex (GPIb alpha, Ib beta, IX and V) are molecular products of different genes. Several point mutations and deletions affecting the GPIb alpha gene have been identified as the cause of BSS, whilst in four BSS families a GPIX gene defect has been reported. Moreover, a single case of BSS has been associated with a genetic defect of GPIb beta. We investigated the molecular basis of another case of BSS with a deficient expression of GPIX, as detected by immunofluorescence studies. After amplification of the entire GPIX coding region, nucleotide sequence analysis showed a homozygous single point mutation predicting a phenylalanine to serine substitution at position 55 of the mature GPIX within its unique leucine-rich repeat. By allele-specific oligonucleotide hybridization we confirmed the homozygosity of the patient as well as the carrier state of two out of three of his children studied. Although the parents of the patient, who were first cousins, were no longer alive and thus not available for study, we speculate that the molecular defect observed in the proband was inherited from both parents, who probably were heterozygous for this GPIX gene defect. This study confirms that BSS may be caused by many different subtle molecular defects that often prevent the assembly and expression of a functional GPIb-IX-V complex.
Lipoprotein(a) Catabolism Is Regulated by Proprotein Convertase Subtilisin/Kexin Type 9 through the Low Density Lipoprotein Receptor (2015)

Elevated levels of lipoprotein(a) (Lp(a)) have been identified as an independent risk factor for coronary heart disease. Plasma Lp(a) levels are reduced by monoclonal antibodies targeting proprotein convertase subtilisin/kexin type 9 (PCSK9). However, the mechanism of Lp(a) catabolism in vivo and the role of PCSK9 in this process are unknown. We report that Lp(a) internalization by hepatic HepG2 cells and primary human fibroblasts was effectively reduced by PCSK9. Overexpression of the low density lipoprotein (LDL) receptor (LDLR) in HepG2 cells dramatically increased the internalization of Lp(a). Internalization of Lp(a) was markedly reduced following treatment of HepG2 cells with a function-blocking monoclonal antibody against the LDLR or the use of primary human fibroblasts from an individual with familial hypercholesterolemia; in both cases, Lp(a) internalization was not affected by PCSK9. Optimal Lp(a) internalization in both hepatic and primary human fibroblasts was dependent on the LDL rather than the apolipoprotein(a) component of Lp(a). Lp(a) internalization was also dependent on clathrin-coated pits, and Lp(a) was targeted for lysosomal and not proteasomal degradation. Our data provide strong evidence that the LDLR plays a role in Lp(a) catabolism and that this process can be modulated by PCSK9. These results provide a direct mechanism underlying the therapeutic potential of PCSK9 in effectively lowering Lp(a) levels.
Determination of Disulfide Bond Assignment of Human Vitamin K-dependent γ-Glutamyl Carboxylase by Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (2003)

Vitamin K-dependent gamma-glutamyl carboxylase is a 758 amino acid integral membrane glycoprotein that catalyzes the post-translational conversion of certain protein glutamate residues to gamma-carboxyglutamate. Carboxylase has ten cysteine residues, but their form (sulfhydryl or disulfide) is largely unknown. Pudota et al. in Pudota, B. N., Miyagi, M., Hallgren, K. W., West, K. A., Crabb, J. W., Misono, K. S., and Berkner, K. L. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 13033-13038 reported that Cys-99 and Cys-450 are the carboxylase active site residues. We determined the form of all cysteines in carboxylase using in-gel protease digestion and matrix-assisted laser desorption/ionization mass spectrometry. The spectrum of non-reduced, trypsin-digested carboxylase revealed a peak at m/z 1991.9. Only this peak disappeared in the spectrum of the reduced sample. This peak's m/z is consistent with the mass of peptide 92-100 (Cys-99) disulfide-linked with peptide 446-453 (Cys-450). To confirm its identity, the m/z 1991.9 peak was isolated by a timed ion selector as the precursor ion for further MS analysis. The fragmentation pattern exhibited two groups of triplet ions characteristic of the symmetric and asymmetric cleavage of disulfide-linked tryptic peptides containing Cys-99 and Cys-450. Mutation of either Cys-99 or Cys-450 caused loss of enzymatic activity. We created a carboxylase variant with both C598A and C700A, leaving Cys-450 as the only remaining cysteine residue in the 60-kDa fragment created by limited trypsin digestion. Analysis of this fully active mutant enzyme showed a 30- and the 60-kDa fragment were joined under non-reducing conditions, thus confirming Cys-450 participates in a disulfide bond. Our results indicate that Cys-99 and Cys-450 form the only disulfide bond in carboxylase.
Human CD4+ T Cells Mediate Rejection of Porcine Xenografts (1999)

It has previously been demonstrated that xenograft rejection in rodents is dependent on CD4+ T cells. However, because of the lack of an appropriate in vivo model, little is known about the cellular basis of human T cell-mediated rejection of xenografts. In this study, we have evaluated the ability of human T cells to mediate rejection of porcine skin grafts in a novel in vivo experimental system using immunodeficient mice as recipients. Recombinase-activating gene-1-deficient mice (R-) lacking mature B and T cells were grafted with porcine skin and received human lymphocytes stimulated in vitro with irradiated porcine PBMC. Skin grafts on mice given either unseparated, activated human lymphocytes, or NK cell-depleted lymphocyte populations were rejected within 18 days after adoptive cell transfer. In contrast, skin grafts on mice given T cell-depleted human lymphocytes or saline showed no gross or histologic evidence of rejection up to 100 days after adoptive transfer. Purified CD4+ T cells were also able to mediate rejection of porcine skin grafts. These data suggest that human CD4+ T cells are sufficient to induce rejection of porcine xenografts. Thus, strategies directed toward CD4+ T cells may effectively prevent cellular rejection of porcine xenografts in humans.
JUN, FOS, KROX, and CREB transcription factor proteins in the rat cortex: Basal expression and induction by spreading depression and epileptic seizures (1993)

The expression of the nuclear c-JUN, JUN B, JUN D, c-FOS, FOS B, KROX-24, and CREB transcription factors was investigated in the cortex of adult rats by immunocytochemistry. The expression patterns were studied in untreated rats and up to 24 hours following topical application of 1 M KCl to the cortical surface (KCl) or i.v. injection of bicuculline (BIC). Topical KCl induced cortical spreading depression and systemic injection of bicuculline evoked generalized tonic-clonic seizures. In untreated rats, JUN B, c-FOS, and FOS B were expressed in a small number of neurons in the piriform, perirhinal, entorhinal, and insular cortex and in layers II, III, and VI of all neocortical areas. In contrast, c-JUN, JUN D, and KROX-24 were expressed in all cortical layers but with different intensities of immunoreactivity (IR): c-JUN-IR was generally weak and predominantly present in layers II, III, and VI. JUN D-IR was equally strong in all layers. KROX-24 showed a prominent expression in layers II, IV, and VI. The CREB protein exhibited a slight preponderance in layer II and piriform cortex. Following KCl or BIC, a strong induction was seen for c-FOS, JUN B, and KROX-24, whereas c-JUN, JUN D, and FOS B showed only a moderate increase compared to basal levels. Changes of CREB-IR could not be detected. The localization of induced JUN, FOS, and KROX proteins reflected the pattern of labelling in untreated animals but demonstrated a higher intensity of labelling and an increased number of immunoreactive nuclei. The intensity and persistence of IR as well as the number of labelled cells following BIC exceeded those following KCl. Following BIC, increased levels of FOS B and JUN D were still present after 24 hours. Counterstaining with cresyl-violet and GFAP, a marker for astrocytes, revealed that JUN, FOS, and KROX proteins were expressed in neurons but not in glial cell populations. The present data demonstrate that CREB, JUN, FOS, and KROX transcription factors exhibit a layer-specific expression in the cerebral cortex with only slight area-specific differences both in untreated rats and following stimulation with KCl and BIC. The expression of transcription factor proteins indicate complex molecular genetic changes in cortical neurons due to pathophysiological events such as seizure activity and spreading depression.
Regulatory T Cells: New Keys for Further Unlocking the Enigma of Fetal Tolerance and Pregnancy Complications (2014)

The immunological alterations required for successful pregnancy in eutherian placental mammals have remained a scientific enigma since the discovery of MHC haplotype diversity and unique immune signatures among individuals. Within the past 10 years, accumulating data suggest that immune-suppressive regulatory T cells (Tregs) confer essential protective benefits in sustaining tolerance to the semiallogeneic fetus during pregnancy, along with their more established roles in maintaining tolerance to self and "extended self" commensal Ags that averts autoimmunity. Reciprocally, many human pregnancy complications stemming from inadequacies in fetal tolerance have been associated with defects in maternal Tregs. Thus, further elucidating the immunological shifts during pregnancy not only have direct translational implications for improving perinatal health, they have enormous potential for unveiling new clues about how Tregs work in other biological contexts. In this article, epidemiological data in human pregnancy and complementary animal studies implicating a pivotal protective role for maternal Tregs are summarized.
Expression of mouse IgA by transgenic mice, pigs and sheep (1991)

The development of transgenic animal technology allows the introduction of desired traits into the germ line of mice and other animals. Since the production of antibody to various polysaccharide antigens can be protective against pathogenic bacteria, we generated transgenic mice, sheep and pigs carrying genes encoding the mouse alpha and kappa chains for antibodies against phosphorylcholine (PC) to determine whether transgene antibody might be used to influence susceptibility to disease. High serum levels of mouse IgA were detected in transgenic mice and pigs but not in transgenic sheep. It has been noted that transgene immunoglobulin expression can suppress endogenous immunoglobulin gene rearrangement and expression, and indeed, in one mouse line, expression of the transgene resulted in less than 10% of spleen B cells expressing endogenous IgM. Despite this suppression, significant levels of endogenous IgM were still secreted into the serum. Suppression of endogenous IgM expression was not seen in other mouse lines, nor was it seen in transgenic pigs. In the transgenic pigs, the mouse IgA was detected in the serum despite the absence of an intact mouse kappa transgene, so the secreted antibody presumably included pig light chains. Little if any of the mouse IgA in these sera showed binding specificity for PC. In one of the founder sheep, mouse IgA was detectable in peripheral lymphocytes but not in serum. Mouse kappa expression was not detected in the transgenic sheep harboring an intact kappa transgene. These results illustrate the potential of introducing beneficial traits such as germ-line-encoded immunity into large mammalian species.
Suppression of Adenovirus Replication by Cardiotonic Steroids (2016)

Despite human adenoviruses being a common and, in some instances, life-threating pathogen in humans, there are few well-tolerated therapies. In this report, we demonstrate that two cardiotonic steroids already in use in humans, digoxin and digitoxin, are potent inhibitors of multiple adenovirus species. A synthetic derivative of the cardiotonic steroid convallotoxin was even more potent than digoxin and digitoxin when tested with HAdV-C5. These drugs alter the cascade of adenovirus gene expression, acting after initiation of early gene expression to block viral DNA replication and synthesis of viral structural proteins. These findings validate a novel approach to treating adenovirus infections through the modulation of host cell processes.
Factor XI Binding to the Platelet Glycoprotein Ib-IX-V Complex Promotes Factor XI Activation by Thrombin (2002)

Factor XI binds to high affinity sites on the surface of stimulated platelets where it is efficiently activated by thrombin. Here, we provide evidence that the factor XI binding site on platelets is in the glycoprotein (GP) Ibalpha subunit of the GP Ib-IX-V complex as follows. 1) Bernard-Soulier platelets, lacking the complex, are deficient in factor XI binding; 2) two GP Ibalpha ligands, SZ-2 (a monoclonal antibody) and bovine von Willebrand factor, inhibit factor XI binding to platelets; 3) by surface plasmon resonance, factor XI bound specifically to glycocalicin (the extracellular domain of GP Ibalpha) in Zn(2+)-dependent fashion (K(d)( app) approximately 52 nm). We then investigated whether glycocalicin could promote factor XI activation by thrombin, another GP Ibalpha ligand. In the presence of high molecular weight kininogen (45 nm), Zn(2+) and Ca(2+) ions, thrombin activated factor XI in the presence of glycocalicin at rates comparable with those seen in the presence of dextran sulfate (1 microg/ml). With higher high molecular weight kininogen concentrations (360 nm), the rate of thrombin-catalyzed factor XI activation in the presence of glycocalicin was comparable with that on activated platelets. Thus, factor XI binds to the GP Ib-IX-V complex, promoting its activation by thrombin.
Analysis of Acrylamide, a Carcinogen Formed in Heated Foodstuffs (2002)

Reaction products (adducts) of acrylamide with N termini of hemoglobin (Hb) are regularly observed in persons without known exposure. The average Hb adduct level measured in Swedish adults is preliminarily estimated to correspond to a daily intake approaching 100 microg of acrylamide. Because this uptake rate could be associated with a considerable cancer risk, it was considered important to identify its origin. It was hypothesized that acrylamide was formed at elevated temperatures in cooking, which was indicated in earlier studies of rats fed fried animal feed. This paper reports the analysis of acrylamide formed during heating of different human foodstuffs. Acrylamide levels in foodstuffs were analyzed by an improved gas chromatographic-mass spectrometric (GC-MS) method after bromination of acrylamide and by a new method for measurement of the underivatized acrylamide by liquid chromatography-mass spectrometry (LC-MS), using the MS/MS mode. For both methods the reproducibility, given as coefficient of variation, was approximately 5%, and the recovery close to 100%. For the GC-MS method the achieved detection level of acrylamide was 5 microg/kg and for the LC-MS/MS method, 10 microg/kg. The analytic values obtained with the LC-MS/MS method were 0.99 (0.95-1.04; 95% confidence interval) of the GC-MS values. The LC-MS/MS method is simpler and preferable for most routine analyses. Taken together, the various analytic data should be considered as proof of the identity of acrylamide. Studies with laboratory-heated foods revealed a temperature dependence of acrylamide formation. Moderate levels of acrylamide (5-50 microg/kg) were measured in heated protein-rich foods and higher contents (150-4000 microg/kg) in carbohydrate-rich foods, such as potato, beetroot, and also certain heated commercial potato products and crispbread. Acrylamide could not be detected in unheated control or boiled foods (<5 microg/kg). Consumption habits indicate that the acrylamide levels in the studied heated foods could lead to a daily intake of a few tens of micrograms.
Passive Material Properties of Intact Ventricular Myocardium Determined From a Cylindrical Model (1991)

The equatorial region of the canine left ventricle was modeled as a thick-walled cylinder consisting of an incompressible hyperelastic material with homogeneous exponential properties. The anisotropic properties of the passive myocardium were assumed to be locally transversely isotropic with respect to a fiber axis whose orientation varied linearly across the wall. Simultaneous inflation, extension, and torsion were applied to the cylinder to produce epicardial strains that were measured previously in the potassium-arrested dog heart. Residual stress in the unloaded state was included by considering the stress-free configuration to be a warped cylindrical arc. In the special case of isotropic material properties, torsion and residual stress both significantly reduced the high circumferential stress peaks predicted at the endocardium by previous models. However, a resultant axial force and moment were necessary to cause the observed epicardial deformations. Therefore, the anisotropic material parameters were found that minimized these resultants and allowed the prescribed displacements to occur subject to the known ventricular pressure loads. The global minimum solution of this parameter optimization problem indicated that the stiffness of passive myocardium (defined for a 20 percent equibiaxial extension) would be 2.4 to 6.6 times greater in the fiber direction than in the transverse plane for a broad range of assumed fiber angle distributions and residual stresses. This agrees with the results of biaxial tissue testing. The predicted transmural distributions of fiber stress were relatively flat with slight peaks in the subepicardium, and the fiber strain profiles agreed closely with experimentally observed sarcomere length distributions. The results indicate that torsion, residual stress and material anisotropy associated with the fiber architecture all can act to reduce endocardial stress gradients in the passive left ventricle.