gebhart/patrepeval huggingface dataset:
Antigens shared by Leishmania species and Trypanosoma cruzi: immunological comparison of the acidic ribosomal P0 proteins (1994)

Patients with visceral leishmaniasis produce high levels of immunoglobulin, but the specificities of antibodies produced are not well characterized. In an effort to identify leishmania antigens that are specific to Leishmania species or are cross-reactive with other parasitic protozoa, we have cloned and characterized full-length genomic and cDNA clones encoding a Leishmania chagasi acidic ribosomal antigen, LcP0, recognized during human infections. The protein is homologous to the Trypanosoma cruzi and human ribosomal proteins TcP0 and HuP0, respectively. Unlike most higher eukaryotes, but similar to TcP0, LcP0 has a C-terminal heptapeptide sequence resembling those of the archaebacterial acidic (P-like) proteins. The highly charged C-terminal acidic domain of LcP0 contains a serine residue typically found in most eukaryotes but lacking in all T. cruzi P proteins we have characterized thus far. L. chagasi-infected individuals as well as those with T. cruzi infections have antibodies cross-reactive with recombinant LcP0 and TcP0 as well as HuP0. However, the properties of anti-P0 antibodies in T. cruzi and L. chagasi infection sera are quite different. Through the use of synthetic peptides, we showed that while T. cruzi infection anti-TcP0 antibodies are exclusively directed against the C-terminal domain of TcP0, L. chagasi infection sera contain antibodies reactive with epitopes other than the C-terminal sequence of LcP0. Thus, anti-LcP0 antibodies in L. chagasi infection sera represent the first characterized deviation from the restricted immunodominant C-terminal epitope involved in the generation of anti-P0 antibodies following infection or autoimmune diseases.
A Multifunctional Acyl-Acyl Carrier Protein Desaturase from Hedera helix L. (English Ivy) Can Synthesize 16- and 18-Carbon Monoene and Diene Products (2005)

A desaturase with 83% sequence identity to the coriander delta(4)-16:0-ACP desaturase was isolated from developing seeds of Hedera helix (English ivy). Expression of the ivy desaturase in Arabidopsis resulted in the accumulation of 16:1delta(4) and its expected elongation product 18:1delta(6) (petroselinic acid). Expression in Escherichia coli resulted in the accumulation of soluble, active protein that was purified to apparent homogeneity. In vitro assays confirmed delta(4) desaturation with 16:0-ACP; however, with 18:0-acyl acyl carrier protein (ACP) desaturation occurred at the delta(9) position. The ivy desaturase also converted 16:1delta(9)-ACP and 18:1delta(9)-ACP to the corresponding delta(4,9) dienes. These data suggest at least two distinct substrate binding modes, one placing C4 at the diiron active site and the other placing C9 at the active site. In the latter case, 18:0 would likely bind in an extended conformation as described for the castor desaturase with 9-carbons accommodated in the cavity beyond the dirron site. However, delta(4) desaturation would require the accommodation of 12 carbons for C16 substrates or 14 carbons for C18 substrates. The amino acids lining the substrate binding cavity of ivy and castor desaturases are conserved except for T117R and P179I (castor/ivy). Paradoxically, both substitutions, when introduced into the castor desaturase, favored the binding of shorter acyl chains. Thus, it seems likely that delta(4) desaturation would require a non-extended, perhaps U-shaped, substrate conformation. A cis double bond may facilitate the initiation of such a non-extended conformation in the monounsaturated substrates. The multifunctional properties of the ivy desaturase make it well suited for further dissection of the determinants of regiospecificity.
Lactate turnover in rat glioma measured by in vivo nuclear magnetic resonance spectroscopy. (1998)

Elevated tissue lactate concentrations typically found in tumors can be measured by in vivo nuclear magnetic resonance (NMR) spectroscopy. In this study, lactate turnover in rat C6 glioma was determined from in vivo 1H NMR measurements of [3-13C]lactate buildup during steady-state hyperglycemia with [1-13C]glucose. With this tumor model, a narrow range of values was observed for the first-order rate constant that describes lactate efflux, k2 = 0.043 +/- 0.007 (n = 12) SD min-1. For individual animals, the standard error in k2 was small (< 18%), which indicated that the NMR data fit the kinetic model well. Lactate measurements before and after infusing [1-13C]glucose showed that the majority of the tumor lactate pool was metabolically active. Signals from 13C-labeled glutamate in tumors were at least 10-fold smaller than the [3-13C]lactate signal, whereas spectra of the contralateral hemispheres revealed the expected labeling of [4-13C]glutamate, as well as [2-13C] and [3-13C]glutamate, which indicates that label cycled through the tricarboxylic acid cycle in the brain tissue. Lack of significant 13C labeling of glutamate was consistent with low respiratory metabolism in this glioma. It is concluded that lactate in rat C6 glioma is actively turning over and that the kinetics of lactate efflux can be quantified noninvasively by 1H NMR detection of 13C label. This noninvasive NMR approach may offer a valuable tool to help evaluate tumor growth and metabolic responsiveness to therapies.
High density lipoprotein metabolism. (1984)

The intestine as a source of HDL and HDL 2.
Human melanoma cell invasion is inhibited in vitro by swainsonine and deoxymannojirimycin with a concomitant decrease in collagenase IV expression (1991)

A 48 h pretreatment of two malignant and invasive human melanoma cell lines with either swainsonine (an inhibitor of Golgi alpha-mannosidase II) or deoxymannojirimycin (a Golgi alpha-mannosidase I inhibitor) resulted in a dose-dependent decrease in the cells' ability to invade a reconstituted basement membrane in vitro. This effect was reversible within 48 h of removing the drugs. Treatment with either drug resulted in both cell lines being more resistant to the cytotoxic effects of the lectin leukoagglutinin (PHA-L) and more sensitive to the lectin concanavalin A which indirectly indicated a change in the cell surface oligosaccharide composition and structure consistent with the known effects of these drugs on N-linked oligosaccharide processing. A 25-33% decrease was noted in the adhesion of treated cells to either a reconstituted basement membrane or human umbilical vein endothelial cell monolayer while no change was measured in the cells' proliferative rates. A correlative decrease was observed, however, in the expression of human type IV collagenase mRNA which was recovered within 48 h of removing the drugs. These results suggest that a correlation exists between the drug-induced changes in the cell surface oligosaccharide composition and structure with a concomitant decrease in the mRNA and secreted levels of type IV collagenase and the ability of these cells to invade.
Preparation and structure of porous dielectrics by plasma enhanced chemical vapor deposition (2007)

The preparation of ultralow dielectric constant porous silicon, carbon, oxygen, hydrogen alloy dielectrics, called “pSiCOH,” using a production 200mm plasma enhanced chemical vapor deposition tool and a thermal treatment is reported here. The effect of deposition temperature on the pSiCOH film is examined using Fourier transform infrared (FTIR) spectroscopy, dielectric constant (k), and film shrinkage measurements. For all deposition temperatures, carbon in the final porous film is shown to be predominantly Si–CH3 species, and lower k is shown to correlate with increased concentration of Si–CH3. NMR and FTIR spectroscopies clearly detect the loss of a removable, unstable, hydrocarbon (CHx) phase during the thermal treatment. Also detected are increased cross-linking of the Si–O skeleton, and concentration changes for three distinct structures of carbon. In the as deposited films, deposition temperature also affects the hydrocarbon (CHx) content and the presence of CO and CC functional groups.
Image Coding Via a Nearest Neighbors Image Model (1975)

A two-dimensional interpolative model for coding of images is presented. It is shown that this model leads to three different coding algorithms, each algorithm defining a specific transmitter-receiver architecture. Simulation examples on a 255 × 255 image are given. Computational aspects and possible extensions are discussed.
Patent strategies in the antisense oligonucleotide based therapeutic approach (1997)

Antisense oligonucleotides represent a new approach to therapeuric treatment of a variety of diseases.Due to unique aspects of this new approach, the opportunity to protect inventions via patenting is potentially greater than for small molecule pharmaceutical products.Strategies for protecting antisense technology include developing a multiple layered patent portfolio covering a range of compositions of matter having improved pharmacological properties.Such patentable new compositions of matter arise from exploitation of pharmacological properties discobered in preclinical and clinical trials, and from new synthetic and manufacturing processes, which provide new chemical entities.In addition,advances in manufacturing technology reduce the cost of antisense oligonucleotides and are independently patentable.In this article, the general strategic approach to patenting antisense technology will be presented, together with illustrative examples of the implemantation of such a strategy.For this purpose,primarily numerous illustrations will be taken from selected patents from the patent portfolio of Hybridon, Inc., and relevant literature with which the authors have the greatest familiarity.
Risk Factors for Cytomegalovirus Infection after Human Marrow Transplantation (1986)

The records of 545 patients were reviewed for risk factors associated with cytomegalovirus (CMV) infection after marrow transplant. CMV infection occurred among 36% of seronegative patients and 69% of seropositive patients. Among seronegative patients, significant risk factors for CMV infection included positive serology of the marrow donor (relative rate, 2.3) and the use of granulocyte transfusions from seropositive donors (relative rate, 2.5). Among both seronegative and seropositive patients, the occurrence of acute graft-versus-host disease (GVHD) significantly increased the risk of CMV infection (average relative rate, 1.8) and of subsequent CMV pneumonia (average relative rate, 2.6). CMV excretion and viremia were each associated with subsequent pneumonia, but the positive predictive values were low. One-third of long-term survivors excreted CMV at greater than 250 days after transplantation. The only risk factor for late excretion was CMV infection that occurred in the first 150 days after transplantation. In contrast to the effect of acute GVHD on CMV infection, CMV infection did not increase the risk of either acute or chronic GVHD.
Amblyomma americanum : a Potential Vector of Lyme Disease in New Jersey (1984)

Amblyomma americanum is a likely secondary vector of Lyme disease in New Jersey. Ticks of this species were removed from the site of the characteristic skin lesion known as erythema chronicum migrans on two patients with the disease, and the Lyme disease spirochete was isolated from nymphs and adults of this species. That A. americanum is a potential vector is supported by its similarities to Ixodes dammini, the known tick vector, in seasonal distribution and host utilization. The extensive range of A. americanum may have great implications for potential Lyme disease transmission outside known endemic areas.
Blockade of PD‐L1 (B7‐H1) augments human tumor‐specific T cell responses in vitro (2006)

Human tumors frequently escape immune destruction, despite the presence of cytotoxic T cells (CTL) recognizing tumor-associated antigens (TAA). We have previously shown that programmed death ligand-1 (PD-L1), a recently identified ligand of the B7 superfamily, is expressed on murine tumors and can inhibit antitumor immune responses. To evaluate the clinical relevance of our animal model findings, we examined human tumors and tumor-specific T cells. We found PD-L1 to be constitutively expressed on human renal cell carcinoma (RCC) cell lines and upregulated on human melanoma cell lines upon exposure to interferon-gamma. Similarly, we found binding of anti-PD-L1 monoclonal antibody (mAb) on frozen sections from RCC and melanomas, but not on normal tissues. The corresponding inhibitory receptor of PD-L1, PD-1, revealed a higher expression on tumor-infiltrating lymphocytes than on peripheral blood lymphocytes (PBL) from melanoma patients upon specific antigen stimulation. Stimulation of PBL from healthy donors with peptide-loaded dendritic cells in the presence of anti-PD-L1 mAb altered neither the total T cell numbers after expansion, nor the percentage of peptide-specific CTL, when providing a T cell help by addition of cytokines. However, when stimulating TAA-specific CTL and T helper cells with Ag-pulsed dendritic cells in the absence of exogenous cytokines, PD-L1 blockade increased the cytokine production. Similar to the data achieved in the murine system, the blockade of PD-L1 on human tumors resulted in enhanced cytolytic activity of TAA-specific CTLs and cytokine production of TAA-specific T helper cells when interacting directly with the tumor. In summary, our data suggest that PD-L1/PD-1 interactions negatively regulate T cell effector functions predominantly in the absence of exogenous cytokine support, indicating an important role for this pathway in tumor evasion.
microRNAs outwit immune limitations in gene therapy (2007)

In this issue of Blood, Brown and colleagues deliver lentiviral vectors that express human factor IX from the livers of mice.
Prostaglandins, leukotrienes and perennial rhinitis (2004)

Prostaglandins and leukotrienes are implicated in conditions of both the upper and lower airways. In the former they are deranged in nasal polyposis, intrinsic rhinitis and allergic rhinitis while in the latter they are involved in the pathogenesis of asthma. The aim of the present study was to measure mucosal eicosanoid levels in the three types of rhinitis and compare with controls. In addition, the effect of topical steroids on eicosanoid levels in rhinitis was examined. The levels of prostaglandins E(2) (PGE(2)) and D(2) (PGD(2)) and of leukotrienes E(4) (LTE(4)) and B(4) (LTB(4)) were measured in nasal biopsies from the inferior turbinates of patients suffering from perennial rhinitis and a control group. Rhinitis patients were classified into three categories: perennial allergic rhinitis (PAR), non-allergic rhinitis with eosinophilia (NARES) and noneosinophilic non-allergic rhinitis (NENAR) on the basis of symptoms, secretion eosinophilia, nasal resistance and allergy testing. Patients with rhinitis were randomized into two groups. One received fluticasone propionate nasal spray (FPANS) and the other a placebo (PNS) over a period of six weeks prior to the biopsies. One hundred and one patients with PAR, NARES or NENAR were recruited sequentially and the control group consisted of 21 patients with no evidence of rhinitis but with nasal obstruction due to septal deviation. Untreated rhinitics had significantly lower levels of PGE(2), PGD(2) and LTE(4) than non-rhinitic controls. Six-weeks' treatment with FPANS significantly increased the levels of those eicosanoids in patients with PAR and NARES but they were still significantly below normal. Levels of LTB(4) in all three rhinitis groups were not significantly different from controls and treatment with topical steroids had no effect. Their findings are contrary to current thinking that increased levels of eicosanoids, in particular cysteinyl-leukotrienes, play an important role in the pathogenesis of chronic, non-infective upper airway inflammation.
Streptomycin-resistance ofEuglena gracilischloroplasts: identification of a point mutation in the 16S rRNA gene in an invariant position (1985)

We sequenced the chloroplast 16S rRNA gene of two Euglena gracilis mutants which contain streptomycin-resistant chloroplasts (Smr 139.12/4 and Smr 139.20/2). These mutants are known to contain a single intact rrn operon per circular chloroplast genome. Nucleotide sequence comparison between a 16S rRNA gene of wild type Euglena gracilis, strain Z, with streptomycin-sensitive chloroplasts, and the 16S rRNA gene of both Smr-strains reveals a single base change (C to T) at position 876. This position is equivalent to the invariant position 912 of the E. coli 16S rRNA gene. The analogous position is also conserved in all chloroplast small subunit RNA genes from lower and higher plants sequenced so far. Light dependent protein synthesis with purified chloroplasts from streptomycin-resistant cells is not inhibited by streptomycin. Based on the results reported here we postulate linkage between the observed point mutation on the 16S rRNA gene and streptomycin-resistance of chloroplast 70S ribosomes.
A herbicide antidote (safener) induces the activity of both the herbicide detoxifying enzyme and of a vacuolar transporter for the detoxified herbicide (1994)

In plants potentially toxic compounds are ultimately deposited in the large central vacuole. In this report we show that isolated barley mesophyll vacuoles take up the glucoside conjugate of the herbicide derivate [5-hydroxyphenyl]primisulfuron. Transport is stimulated by Mg-ATP and is distinct from that previously described for glutathione conjugates. Treatment of barley with different herbicide antidotes (safeners) revealed that the safener cloquintocet-mexyl doubles the vacuolar transport activities for both the glutathione and glucoside conjugates. Stimulation of the uptake of the metolachlor-glutathione conjugate was the result of an increased uptake velocity whereas the Km remained unaltered, suggesting that the higher activity was due to a higher expression of the transporter. These results indicate that modulation of vacuolar transport activities are an integral part of the detoxification mechanism of plants.
CMOS single-chip multisensor gas detection system (2003)

We present a novel single-chip smart chemical microsensor system fabricated using industrial CMOS technology and post-CMOS micro machining. It combines three different micromachined transducers (mass-sensitive, capacitive, and calorimetric) all of which rely on polymeric coatings as sensitive layers to detect airborne volatile organic compounds (VOC). A temperature sensor is included to account for the strong temperature dependence of volatile absorption in polymers. Integration of microelectronics and micromechanical components on the same chip allows for controlling of the sensor functions, and enables on-chip signal conditioning that drastically improves the sensor performance. The circuitry includes biasing, amplification, and a serial interface to transmit data to off-chip recording units. The chip forms an integral part of a handheld chemical sensor unit to discriminate and quantify VOC's.
Robust Object Detection via Soft Cascade (2005)

We describe a method for training object detectors using a generalization of the cascade architecture, which results in a detection rate and speed comparable to that of the best published detectors while allowing for easier training and a detector with fewer features. In addition, the method allows for quickly calibrating the detector for a target detection rate, false positive rate or speed. One important advantage of our method is that it enables systematic exploration of the ROC surface, which characterizes the trade-off between accuracy and speed for a given classifier.
Dually Responsive Janus Composite Nanosheets (2015)

Janus composite nanosheets of PNIPAM/silica/PDEAEMA are synthesized by sequential ATRP grafting two polymers from the corresponding sides of the Janus silica nanosheets. They are dually responsive to pH and temperature since wettability of the two sides is tunable accordingly. The nanosheets can serve as a responsive solid emulsifier. Type and stability of the emulsions are triggered by simply changing pH and temperature.
Transplantation of human fetal retinal pigment epithelium rescues photoreceptor cells from degeneration in the Royal College of Surgeons rat retina. (1996)

The Royal College of Surgeons (RCS) rat suffers from a well-characterized, early-onset, and relentless form of photoreceptor cell degeneration. It has been shown that allografts of retinal pigment epithelial cells from normal perinatal rats have rescue effects in this condition. In preparation for human application, the authors determined whether human fetal retinal pigment epithelium (RPE) grafts have a photoreceptor rescue effect in RCS dystrophic rat retinas.Sheets of RPE from human fetal eyes (10 to 16 weeks gestational age) were isolated according to the authors' recently described method. Fragments of the RPE sheets were transplanted to the subretinal space within the superior hemisphere. Transplants were performed within the superior equatorial region of five dystrophic RCS rats, one eye per animal. A similar volume of vehicle was injected into the subretinal space of five age-matched control rats, again one eye per rat. All rats were immunosuppressed with daily injections of cyclosporine. Using light microscopy, photoreceptor cell nuclear profiles of superior equatorial (SE) and inferior equatorial (IE) regions of transplanted and sham-injected control animals were counted.Four weeks after transplantation, a dramatic rescue effect was observed. Microscopically, presumptive donor RPE cells were seen as single pigmented cells and as cell clusters in the subretinal space. An outer nuclear layer three to four profiles thick was present in the area of the RPE transplant but was nearly absent in the rest of the retina, as well as in the retinas of control rats. The number of photoreceptor nuclear profiles per 100 microns was 34.7 +/- 2.2 (mean +/- SEM) in the SE region of transplanted rats and 3.5 +/- 1.4 in the same region of sham-injected rats. There were 3.0 +/- 1.0 photoreceptor nuclear profiles in the IE region of transplanted rats and 3.5 +/- 1.2 in the IE region of sham-injected eyes. No evidence of graft rejection was seen.This study provides the first indication that transplanted human fetal RPE cells are able to rescue photoreceptor cells in a model of hereditary retinal degeneration.
Antidepressant efficacy and cognitive effects of repetitive transcranial magnetic stimulation in vascular depression: an open trial (2004)

Our preliminary observations prompt to perform a subsequent controlled study to examine if rTMS may constitute an alternative to electroconvulsive therapy.
In silico panning for a non-competitive peptide inhibitor (2007)

We demonstrate an effective methodology of in silico panning for the selection of a non-competitive peptide inhibitor from small virtual peptide library. This study is the first to demonstrate the usefulness of in silico evolution using experimental data. Our study highlights the usefulness of this strategy for structure-based screening of enzyme inhibitors.