gebhart/patrepeval huggingface dataset:
Parathion hydrolase specified by the Flavobacterium opd gene: relationship between the gene and protein (1989)

The sequence of a 1,693-base-pair plasmid DNA fragment from Flavobacterium sp. strain ATCC 27551 containing the parathion hydrolase gene (opd) was determined. Within this sequence, there is only one open reading frame large enough to encode the 35,000-dalton membrane-associated hydrolase protein purified from Flavobacterium extracts. Amino-terminal sequence analysis of the purified Flavobacterium hydrolase demonstrated that serine is the amino-terminal residue of the hydrolase protein. The amino-terminal serine corresponds to a TCG codon located 87 base pairs downstream of the presumptive ATG initiation codon in the nucleotide sequence. The amino acid composition of the purified protein agrees well with that predicted from the nucleotide sequence, using serine as the amino-terminal residue. These data suggest that the parathion hydrolase protein is processed at its amino terminus in Flavobacterium sp. Construction in Escherichia coli of a lacZ-opd gene fusion in which the first 33 amino-terminal residues of opd were replaced by the first 5 residues of lacZ resulted in the production of an active hydrolase identical in molecular mass to the hydrolase isolated from Flavobacterium sp. E. coli cells containing the lacZ-opd fusion showed higher levels of hydrolase activity than did cells containing the parent plasmid.
Transferrin receptors in human tissues: their distribution and possible clinical relevance. (1983)

The distribution of transferrin receptors (TR) has been studied in a range of normal and malignant tissues using four monoclonal antibodies, BK19.9, B3/25, T56/14 and T58/1. In normal tissues TR was found in a limited number of sites, notably basal epidermis, the endocrine pancreas, hepatocytes, Kupffer cells, testis and pituitary. This restricted pattern of distribution may be relevant to the characteristic pattern of iron deposition in primary haemachromatosis. In contrast to this limited pattern of expression in normal tissue, the receptor was widely distributed in carcinomas, sarcomas and in samples from cases of Hodgkin's disease. This malignancy-associated expression of the receptor may play a role in the anaemia of advanced malignancy by competing with the bone marrow for serum iron.
Monoclonal antibody 8H9 targets a novel cell surface antigen expressed by a wide spectrum of human solid tumors. (2001)

Tumor-restricted surface antigens may be targets for diagnosis and immune-based therapies. Monoclonal antibody 8H9 is a murine IgG1 hybridoma derived from the fusion of mouse myeloma SP2/0 cells and splenic lymphocytes from BALB/c mice immunized with human neuroblastoma. By immunohistochemistry, 8H9 was highly reactive with human brain tumors, childhood sarcomas, and neuroblastomas, and less so with adenocarcinomas. Among primary brain tumors, 15 of 17 glioblastomas, 3 of 4 mixed gliomas, 4 of 11 oligodendrogliomas, 6 of 8 astrocytomas, 2 of 2 meningiomas, 3 of 3 schwannomas, 2 of 2 medulloblastomas, 1 of 1 neurofibroma, 1 of 2 neuronoglial tumors, 2 of 3 ependymomas, and 1 of 1 pineoblastoma tested positive. Among sarcomas, 21 of 21 Ewing's/primitive neuroectodermal tumor, 28 of 29 rhabdomyosarcomas, 28 of 29 osteosarcomas, 35 of 37 desmoplastic small round cell tumors, 2 of 3 synovial sarcomas, 4 of 4 leiomyosarcomas, 1 of 1 malignant fibrous histiocytoma, and 2 of 2 undifferentiated sarcomas tested positive with 8H9. Eighty-seven of 90 neuroblastomas, 12 of 16 melanomas, 3 of 4 hepatoblastomas, 7 of 8 Wilms' tumors, 3 of 3 rhabdoid tumors, and 12 of 27 adenocarcinomas also tested positive. In contrast, 8H9 was nonreactive with normal human tissues including bone marrow, colon, stomach, heart, lung, muscle, thyroid, testes, pancreas, and human brain (frontal lobe, cerebellum, pons, and spinal cord). Reactivity with normal cynomolgus monkey tissue was restricted similarly. Indirect immunofluorescence localized the antigen recognized by 8H9 to the cell membrane. The antigen is proteinase sensitive and is not easily modulated off the cell surface. 8H9 immunoprecipitated a M(r) 58,000 band after N-glycanase treatment, most likely a protein with a heterogeneous degree of glycosylation. This novel antibody-antigen system may have potential for tumor targeting.
Stool microflora in extremely low birthweight infants (1999)

The gut of extremely low birthweight infants is colonised by a paucity of bacterial species. Breast milking and reduction of antibiotic exposure are critical to increasing fecal microbial diversity.
Identification of post‐mortem cerebrospinal fluid proteins as potential biomarkers of ischemia and neurodegeneration (2004)

Only few biological markers are currently available for the routine diagnosis of brain damage-related disorders including cerebrovascular, dementia, and other neurodegenerative diseases. In this study, post-mortem cerebrospinal fluid samples were used as a model of massive brain insult to identify new markers potentially relevant for neurodegeneration. The protein pattern of this sample was compared to the one of cerebrospinal fluid from healthy subjects by two-dimensional gel electrophoresis. Using gel imaging, N-terminal microsequencing, mass spectrometry, and immunodetection techniques, we identified 13 differentially expressed proteins. Most of these proteins have been previously reported to be somehow associated with brain destruction or with the molecular mechanisms underlying certain neurodegenerative conditions. These data indicate that the identified proteins indeed represent potential biomarkers of brain damage. We recently showed that H-FABP, a protein highly homologous to E-FABP and A-FABP identified in this study, is a potential marker of Creutzfeldt-Jakob disease and stroke.
Addressing the challenges of cellular delivery and bioavailability of peptide nucleic acids (PNA) (2005)

Recent results on the cellular delivery of antisense peptide nucleic acids (PNA) via peptide conjugation is briefly discussed, in particular in the context of endosomal entrapment and escape.
Solution Structure and Interaction with Basic and Acidic Fibroblast Growth Factor of a 3-kDa Human Platelet Factor-4 Fragment with Antiangiogenic Activity (2001)

Platelet factor-4 is a protein belonging to the family of ELR-negative CXC chemokines which binds to fibroblast growth factor and inhibits its mitogenic activity. Platelet factor-4 also inhibits tumor growth by mechanisms involving antiangiogenesis. Antiangiogenic activity in vitro has also been shown for the 24-residue C-terminal fragment of the protein, which decreases the affinity between basic fibroblast growth factor and its cell-surface receptor. In this study, the preferential conformation of this fragment in solution has been determined and has been found to be composed of two helical subdomains. In addition, we show that the fragment forms a specific 1:1 complex with acidic and basic fibroblast growth factors and that both subdomains are probably required for inhibition of fibroblast growth factor-driven mitogenesis. Finally, we show that the binding of the fragment alters the structure of the fibroblast growth factors, although some of such alterations do not seem related with the inhibition of mitogenic activity. Since this fragment has recently been shown to inhibit fibroblast growth factor-induced angiogenesis in vivo when injected intraperitoneally, these results are relevant for developing new antiangiogenic treatments.
Logic synthesis speeds ASIC design (1989)

An explanation is given of logic synthesis, a design methodology whereby the designer begins by describing a design's behavior in high-level code, and capturing its intended functionality rather than its implementation. Once the functionality has been thoroughly verified through simulation, the designer reformulates the design in terms of large structural blocks. The resulting description is called register-transfer level (RTL) since the equations describe how the data is transferred from one register to another. The designer simulates the RTL description and revises it as necessary to arrive at an acceptable high-level design. Logic synthesis provides two fundamental capabilities: automatic translation of high-level descriptions into logic designs, and optimization to decrease the circuit's area and increase its speed. The capabilities and present limitations of the approach are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Twenty-Four Hour Profile of the Anti-hypertensive Action of Isradipine in Essential Hypertension (1993)

Isradipine, 2.5 mg twice daily and placebo were administered for 4 weeks to 11 untreated essential hypertensives in a double-blind, random order, crossover study. At the end of each phase patients were assessed by 36 h of continuous intra-arterial blood pressure monitoring, surface electrocardiography, and measurement of endogenous creatinine clearance, serum biochemistry and plasma renin activity. Arterial pressure was significantly reduced by isradipine, with mean reduction in systolic blood pressure of 11.0 mmHg and diastolic pressure of 13.2 mmHg over 24 h. There was no significant change in heart rate, endogenous creatinine clearance, serum biochemistry or plasma renin activity.
Oral Testosterone, a Reappraisal (1978)

A microparticulate form of free testosterone was given orally to 6 hypogonadal men. Plasma levels were followed after a 200-mg dose, and a double-peak effect was observed. This suggests that particles of different sizes were absorbed at different rates. The clinical and biochemical effects were observed over a 2-month period, on a dose of 200 mg twice daily, taken in place of the usual androgen replacement. The results indicate that absorption is not sufficiently reliable for routine use. The large doses required to achieve therapeutic levels, make oral administration of free testosterone impractical.
Generation of superoxide and hydrogen peroxide during interaction of nitrite with human hemoglobin. (1981)

Generation of superoxide and hydrogen peroxide during interaction of nitrite with human hemoglobin was detected by chemiluminescence of luminol. Luminol chemiluminescence was inhibited by the addition of superoxide dismutase (SOD) and catalase. Methemoglobin formation induced by nitrite was also inhibited by the addition of SOD and catalase. The mechanism of methemoglobin formation by nitrite was discussed in regard to the oxidation of hemoglobin by superoxide and hydrogen peroxide as generated by the interaction of nitrite with hemoglobin.
Transient detection of audio signals based on an adaptive comb filter in the frequency domain (2004)

This paper presents a transient detection algorithm suitable for rhythm detection in music signals. In many audio signals, low energy transients are masked by high energy stationary sounds. These masked transients, as well as higher energy and more visible transients, convey important information on the rhythm and time segmentation of the music signal. The proposed segmentation algorithm uses a sinusoidal model combined with adaptive comb filtering in the frequency domain to remove the stationary component of a sound signal. After filtering, the time envelope of the residual signal is analyzed to locate the transient components. Results show that the proposed algorithm can accurately detect most low energy transients.
Broadband signals for electrical impedance measurements of long bone fractures (2002)

The use of broadband signals in a multifrequency electric impedance tomography system for observation of long bone fracture healing and the characterisation of electrical bioimpedance is presented. Digital signal processing methods for signal generation, system control and data acquisition enable the investigation of broadband measurement methods for bioelectrical spectroscopy. The generation of multifrequency signals and the application of maximum length sequences in impedance measurement systems are proposed. Broadband methods may deliver additional information which promises to indicate nonunion of long bone fractures at an early stage.
Techniques for collecting saliva from awake, unrestrained, adult monkeys for cortisol assay (2000)

Cortisol levels serve as an index of pituitary-adrenal activity in nonhuman primates. In adult monkeys, cortisol is normally measured in blood (typically requiring restraint or sedation) or urine (reflecting a state rather than point estimate). In contrast, saliva collection is less invasive than drawing blood and allows for repeated sampling within a short period of time. Although protocols exist for collecting saliva from young monkeys, these procedures are inadequate for awake, unrestrained adult animals. Our laboratory has developed two methods for collecting saliva from adult rhesus monkeys: a “screen” method, which involves licking screen-covered gauze, and a “pole” method, which involves sucking and chewing on an attached rope. Twenty-three adult male rhesus monkeys were used to evaluate these two methods. After a period of adaptation, saliva samples were collected from 21 of 23 subjects. Saliva collection was faster with the pole than with the screen method (P < 0.01), but the pole method was not suitable for some animals because of their tendency to bite off the attached rope. An analysis of 19 saliva samples revealed a mean cortisol concentration of 0.84 μg/dl (range 0.27–1.77 μg/dl). There was no statistically significant difference in cortisol value between methods used (P > 0.22). The influence of the flavoring on the cortisol assay was tested, and was found to have no significant effect (P > 0.28). Our results indicate that either technique can be used to safely collect saliva from unrestrained adult monkeys. Choice of technique will depend on the proclivities of individual monkeys. Am. J. Primatol. 52:93–99, 2000. © 2000 Wiley-Liss, Inc.
Physicochemical Characterization of Casein Phosphopeptide-Amorphous Calcium Phosphate Nanocomplexes (2005)

Milk caseins stabilize calcium and phosphate ions and make them available to the neonate. Tryptic digestion of the caseins yields phosphopeptides from their polar N-terminal regions that contain clusters of phosphorylated seryl residues. These phosphoseryl clusters have been hypothesized to be responsible for the interaction between the caseins and calcium phosphate that lead to the formation of casein micelles. The casein phosphopeptides stabilize calcium and phosphate ions through the formation of complexes. The calcium phosphate in these complexes is biologically available for intestinal absorption and remineralization of subsurface lesions in tooth enamel. We have studied the structure of the complexes formed by the casein phosphopeptides with calcium phosphate using a range of physicochemical techniques including x-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, and equilibrium binding analyses. The amorphous nature of the calcium phosphate phase was confirmed by two independent methods: x-ray powder diffraction and selected area diffraction. In solution, the ion activity product of a basic amorphous calcium phosphate phase was the only ion product that was a function of bound phosphate independent of pH, consistent with basic amorphous calcium phosphate being the phase stabilized by the casein phosphopeptides. Detailed investigations of calcium and calcium phosphate binding using a library of synthetic homologues and analogues of the casein phosphopeptides have revealed that although the fully phosphorylated seryl-cluster motif is pivotal for the interaction with calcium and phosphate, other factors are also important. In particular, calcium binding and calcium phosphate stabilization by the peptides was influenced by peptide net charge, length, and sequence.
Ligand Docking and Virtual Screening in Structure-based Drug Discovery (2006)

As the number of high‐resolution three‐dimensional protein and nucleic acid structures continues to grow, ligand‐docking—based virtual screening of chemical libraries to a receptor are playing a critical role in the drug discovery process by identifying new ‘drug‐candidates’. The capability to correctly predict ligand‐protein interaction is fundamental to any accurate docking algorithm and the necessary starting point for any reliable virtual screening protocol. Furthermore, explicit consideration of receptor flexibility in computational ligand docking is emerging in many cases as crucial for an accurate prediction of the orientation and interactions of ligands within the binding pocket. The combination of ligand docking with a fast scoring algorithm that can account for the thermodynamics of binding, and discriminate between potential active/inactive compounds, can greatly reduced the number of compounds to be tested experimentally, while predicting a detailed structure of hits bound to the receptor useful enough to help the synthetic elaboration of leads.
Efficient gene activation in mammalian cells by using recombinant adenovirus expressing site-specific Cre recombinase (1995)

A recombinant adenovirus (Ad) expressing Cre recombinase derived from bacteriophage P1 was constructed. To assay the Cre activity in mammalian cells, another recombinant Ad bearing an on/off-switching reporter unit, where a LacZ-expression unit can be activated by the Cre-mediated excisional deletion of an interposed stuffer DNA, was also constructed. Co-infection experiments together with the Cre-expressing and the reporter recombinant Ads showed that the Cre-mediated switching of gene expression was detected in nearly 100% of cultured CV1, HeLa and Jurkat cells. These results suggest that the recombinant Ad efficiently expressed functional Cre and offers a basis for establishing a powerful on/off switching strategy of gene expression in cultured mammalian cells and presumably in transgenic animals. The method is also applicable to construction of recombinant Ad bearing a gene the expression of which is deleterious to propagation of recombinant Ad.
Characterization of chimeras between the ecotropic Moloney murine leukemia virus and the amphotropic 4070A envelope proteins (1996)

A series of 22 chimeric envelope (env) genes were generated between the ecotropic Moloney murine leukemia virus and the amphotropic 4070A isolate. The chimeric envelopes were expressed within the complete, replication-competent provirus and tested for virus viability by transient expression assays. Eleven of the 22 viruses were viable. Five of these chimeric viruses showed an ecotropic host range, and six exhibited an amphotropic host range and viral interference. The host range determinants map to the first half of the surface (SU) protein. The N-terminal 72 amino acids of 4070A (42 of processed SU) are not required for amphotropic receptor usage. Ecotropic and amphotropic viruses differ in their ability to form large, multinucleated syncytia when cocultured with the rat XC cell line. Ecotropic murine leukemia virus forms large syncytia with XC cells, whereas no syncytia are reported for amphotropic virus. All chimeras which contained the N-terminal half of the ecotropic SU protein, encoding the receptor binding domain, formed the large multinucleated syncytia with XC cells.
Study of Interfacial Degradation of the Vapor-Deposited Bilayer of Alq3/TPD for Organic Electroluminescent (EL) Devices by Photoluminescence (1995)

Abstract The interfacial change of a vapor-deposited TPD (N,N′-diphenyl-N,N′-bis-(3-methylphenyl)-[1,1′-biphenyl]-4,4′-diamine) and Alq3 (Tris-(8-hydroxyquinoline) aluminum) bilayer film was characterized by photoluminescence (PL) in the temperature range from room temperature to 80 °C under an ambient atmosphere. The TPD and the Alq3 film are widely used as a hole transport and an emitter layer, respectively, in organic electroluminescent (EL) devices (ITO/TPD/Alq3/metal). As the substrate plate, a slide glass was used in this work. In an Alq3/TPD bilayered structure, two PL bands from Alq3 and TPD were observed and the relative PL intensity of Alq3 to that of TPD was increased with time. The change was accelerated with increasing temperature. In case of a co-deposited single layer of TPD and Alq3, an Alq3 PL band predominated and, in addition, the PL intensity was not changed remarkably with increasing temperature. These results support that the PL change observed for the Alq3/TPD bilayered structure is ascribed to quenching of photo-excited TPD by Alq3 as a result of diffusion of the components into each other layer.
Reactive species: Ynols and ynamines (1996)

Acetylenic alcohols—ynols—and acetylenic amines—ynamines—have been generated in aqueous solution by flash phololytic decarbonylation of hydroxy- and aminocyclopropenones and their chemistry has been examined in that medium. This has revealed a remarkably strong acid-strengthening effect of the acetylenic group, which ab initio molecular orbital calculations suggest results from a combination of destabilizing inductive effects on the initial state and stabilizing resonance effects on the final state of the acid ionization reaction.
fldA is an essential gene required in the 2‐C‐methyl‐D‐erythritol 4‐phosphate pathway for isoprenoid biosynthesis (2005)

Although flavodoxin I is indispensable for Escherichia coli growth, the exact pathway(s) where flavodoxin I is essential has not been identified. We performed transposon mutagenesis of the flavodoxin I gene, fldA, in an E. coli strain that expressed mevalonate pathway enzymes and that had a point mutation in the lytB gene of the MEP pathway resulting in the accumulation of (E)-4-hydroxy-3-methylbutyl-2-enyl pyrophosphate (HMBPP). Disruption of fldA abrogated mevalonate-independent growth and dramatically decreased HMBPP levels. The fldA- mutant grew with mevalonate indicating that the essential role of flavodoxin I under aerobic conditions is in the MEP pathway. Growth was restored by fldA complementation. Since GcpE (which synthesizes HMBPP) and LytB are iron-sulfur enzymes that require a reducing system for their activity, we propose that flavodoxin is essential for GcpE and possibly LytB activity. Thus, the essential role for flavodoxin I in E. coli is in the MEP pathway for isoprenoid biosynthesis.
Antiangiogenic agents potentiate cytotoxic cancer therapies against primary and metastatic disease. (1992)

The formation of a blood supply (angiogenesis) is critical to the growth of solid tumors. The naturally occurring steroid tetrahydrocortisol, the synthetic cyclodextrin derivative beta-cyclodextrin tetradecasulfate, and the tetracycline derivative minocycline have antiangiogenic activity. Tetrahydrocortisol and beta-cyclodextrin tetradecasulfate in a 1:1 molar ratio by continuous infusion over 14 days and minocycline administered i.p. over 14 days from day 4 to day 18 postimplantation of the Lewis lung carcinoma significantly increased the growth delay of the primary tumor after treatment with cis-diamminedichloroplatinum(II), melphalan, cyclophosphamide, Adriamycin, bleomycin, and radiation therapy administered in standard regimens. Addition of the antiangiogenic agents to treatment with the cytotoxic therapies not only reduced the number of lung metastases formed from the primary tumor but also reduced the number of large metastases. Five of 12 animals treated with the antiangiogenic modulators and cyclophosphamide were long-term survivors (> 120 days). Thus, antiangiogenic therapies can potentiate the efficacy of standard anticancer therapies.
Next-generation tissue microarray (ngTMA) increases the quality of biomarker studies: an example using CD3, CD8, and CD45RO in the tumor microenvironment of six different solid tumor types (2013)

Based on a manual selection criteria, ngTMA is able to precisely capture histological zones or cell types of interest in a precise and accurate way, aiding the pathological study of the tumor microenvironment. This approach would be advantageous for visualizing proteins, DNA, mRNA and microRNAs in specific cell types using in situ hybridization techniques.