gebhart/patrepeval huggingface dataset:
Molecular Cloning and Characterization of a Plasma Membrane-associated Sialidase Specific for Gangliosides (1999)

Gangliosides are plasma membrane components thought to play important roles in cell surface interactions, cell differentiation, and transmembrane signaling. A mammalian sialidase located in plasma membranes is unique in specifically hydrolyzing gangliosides, suggesting crucial roles in regulation of cell surface functions. Here we describe the cloning and expression of a cDNA for the ganglioside sialidase, isolated from a bovine brain cDNA library based on the amino acid sequence of the purified enzyme from bovine brain. This cDNA encodes a 428-amino acid protein containing a putative transmembrane domain and the three Asp boxes characteristic of sialidases and sharing 19-38% sequence identity with other sialidases. Northern blot and polymerase chain reaction analyses revealed a general distribution of the gene in mammalian species, including man, and the mouse. In COS-7 cells transiently expressing the sialidase, the activity was found to be 40-fold that of the control level with ganglioside substrates in the presence of Triton X-100, and the hydrolysis was almost specific to gangliosides other than GM1 and GM2, both alpha2-->3 and alpha2-->8 sialyl linkages being susceptible. The major subcellular localization of the expressed sialidase was assessed to be plasma membrane by Percoll density gradient centrifugation of cell homogenates and by immunofluorescence staining of the transfected COS-7 cells. Analysis of the membrane topology by protease protection assay suggested that this sialidase has a type I membrane orientation with its amino terminus facing to the extracytoplasmic side and lacking a signal sequence.
Signals required for programming effector and memory development by CD8+ T cells (2006)

Stimulation of naïve CD8+ T cells with antigen and costimulation results in proliferation and weak clonal expansion, but the cells fail to develop effector functions and are tolerant long term. Initiation of the program leading to the strong expansion and development of effector functions and memory requires a third signal that can be provided by interleukin-12 (IL-12) or interferon-alpha (IFN-alpha). CD4+ T cells condition dendritic cells (DCs) to effectively present antigen to CD8+ T cells, and this conditioning involves, at least in part, CD40-dependent upregulation of the production of these signal 3 cytokines by the DCs. Upon being fully activated, the cytotoxic T lymphocytes develop activation-induced non-responsiveness (AINR), a form of split anergy characterized by an inability to produce IL-2 to support continued expansion. If antigen remains present, IL-2 provided by CD4+ T cells can reverse AINR to allow further expansion of the effector population and conversion to responsive memory cells following antigen clearance. If IL-2 or potentially other proliferative signals are not available, persistent antigen holds cells in the AINR state and prevents the development of a responsive memory population. Thus, in addition to antigen and costimulation, CD8+ T cells require cytokine signals at distinct stages of the response to be programmed for optimal generation of effector and memory populations.
Two years of replacement therapy in adults with growth hormone deficiency (1997)

We confirmed in a large group of patients the beneficial effects of rhGH therapy on body composition, metabolic parameters and general well-being and found a consistent drop in number of sick days and hospitalization rate. These effects were maintained during two years of therapy, except for an attenuation in body composition changes after 24 months. The high incidence of fluid-related adverse events suggests that it may be better to start with lower doses of rhGH and to increase the dose more slowly over a number of weeks. The finding of suboptimal high or low IGF-1 levels in many patients reinforces guidelines not to give rhGH in a weight-dependent dose but to titrate it individually for each patient.
Cultured pancreatic ductal cells undergo cell cycle re-distribution and beta-cell-like differentiation in response to glucagon-like peptide-1 (2002)

The intestinal hormone glucagon-like peptide-1 (GLP-1) has been shown to promote an increase in pancreatic beta-cell mass via proliferation of islet cells and differentiation of non-insulin-secreting cells. In this study, we have characterized some of the events that lead to the differentiation of pancreatic ductal cells in response to treatment with human GLP-1. Rat pancreatic ductal (ARIP) cells were cultured in the presence of GLP-1 and analyzed for cell counting, cell cycle distribution, expression of cyclin-dependent-kinase (Cdk) inhibitors, transcription of beta-cell-specific genes, loss of ductal-like phenotype and acquisition of beta-cell-like gene expression profile. Exposure of ARIP cells to 10 nM GLP-1 induced a significant reduction in the cell replication rate and a significant decrease in the percentage of cells in S phase of the cell cycle. This was associated with an increase in the number of cells in G0-G1 phase and a reduction of cells in G2-M phase. Western blot analysis for the Cdk inhibitors, kinase inhibitor protein 1 (p27(Kip1)) and Cdk-interacting protein 1 (p21(Cip1)), demonstrated a significant increase in p27(Kip1) and p21(Cip1) levels within the first 24 h from the beginning of GLP-1 treatment. As cells slowed down their proliferation rate, GLP-1 also induced a time-dependent expression of various beta-cell-specific mRNAs. The glucose transporter GLUT-2 was the first of those factors to be expressed (24 h treatment), followed by insulin (44 h) and finally by the enzyme glucokinase (56 h). In addition, immunocytochemistry analysis showed that GLP-1 induced a time-dependent down-regulation of the ductal marker cytokeratin-20 (CK-20) and a time-dependent induction of insulin expression. Finally, GLP-1 promoted a glucose-dependent secretion of insulin, as demonstrated by HPLC and RIA analyses of the cell culture medium. The present study has demonstrated that GLP-1 induces a cell cycle re-distribution with a decrease in cell proliferation rate prior to promoting the differentiation of cells towards an endocrine-like phenotype.
The molecular defect of albumin Tagliacozzo: 313 Lys → Asn (1986)

Albumin Tagliacozzo is a fast-moving genetic variant of human serum albumin found in 19 unrelated families. The protein was isolated from the serum of a heterozygous healthy subject. Analysis of CNBr fragments by isoelectric focusing allowed us to localize the mutation to CNBr fragment IV (residues 299-329). This fragment was isolated on a preparative scale and subjected to tryptic digestion. Sequential analysis of the abnormal tryptic peptide, purified by RP-HPLC, revealed the variant was caused by 313 Lys----Asn substitution, probably due to a point mutation in the structural gene. The lack of a lysine residue accounts for the electrophoretic behavior of albumin Tagliacozzo.
Acquired itraconazole resistance in Aspergillus fumigatus (2001)

The antifungal susceptibility profiles of four ASPERGILLUS: fumigatus isolates, recovered at different times from a patient treated with itraconazole for a pulmonary ASPERGILLUS: infection, were evaluated. Itraconazole MICs against two pre-treatment isolates were 0.5 mg/L, whilst two later isolates, recovered after at least 4 months of itraconazole therapy, had itraconazole MICs of >16 mg/L. In vivo susceptibilities to itraconazole and amphotericin B were tested in a murine model of disseminated aspergillosis. Treatment efficacy was evaluated by examining mortality rates and qualitative cultures of brain and kidneys. Itraconazole therapy significantly prolonged survival of mice infected with the initial isolates as compared with untreated controls. The third isolate was only partially susceptible to itraconazole in vivo, and the fourth isolate was highly resistant. The four isolates were typed by random amplified polymorphic DNA (RAPD) with four different primers. RAPD patterns obtained with each of them were identical, suggesting that the same strain was recovered over time and had acquired resistance to itraconazole.
Glycine, a simple physiological compound protecting by yet puzzling mechanism(s) against ischaemia–reperfusion injury: current knowledge (2011)

Ischaemia is amongst the leading causes of death. Despite this importance, there are only a few therapeutic approaches to protect from ischaemia-reperfusion injury (IRI). In experimental studies, the amino acid glycine effectively protected from IRI. In the prevention of IRI by glycine in cells and isolated perfused or cold-stored organs (tissues), direct cytoprotection plays a crucial role, most likely by prevention of the formation of pathological plasma membrane pores. Under in vivo conditions, the mechanism of protection by glycine is less clear, partly due to the physiological presence of the amino acid. Here, inhibition of the inflammatory response in the injured tissue is considered to contribute decisively to the glycine-induced reduction of IRI. However, attenuation of IRI recently achieved in experimental animals by low-dose glycine treatment regimens suggests additional/other (unknown) protective mechanisms. Despite the convincing experimental evidence and the large therapeutic width of glycine, there are only a few clinical trials on the protection from IRI by glycine with ambivalent results. Thus, both the mechanism(s) behind the protection of glycine against IRI in vivo and its true clinical potential remain to be addressed in future experimental studies/clinical trials.
Structural and Mechanistic Insight into the Inhibition of Aspartic Proteases by a Slow-Tight Binding Inhibitor from an ExtremophilicBacillussp.:  Correlation of the Kinetic Parameters with the Inhibitor Induced Conformational Changes (2001)

We present here the first report of a hydrophilic peptidic inhibitor, ATBI, from an extremophilic Bacillus sp. exhibiting a two-step inhibition mechanism against the aspartic proteases, pepsin and F-prot from Aspergillus saitoi. Kinetic analysis shows that these proteases are competitively inhibited by ATBI. The progress curves are time-dependent and consistent with slow-tight binding inhibition: E + I ⇄ (k3, k4) EI ⇄ (k5, k6) EI*. The Ki values for the first reversible complex (EI) of ATBI with pepsin and F-prot were (17 ± 0.5) × 10-9 M and (3.2 ± 0.6) × 10-6 M, whereas the overall inhibition constant Ki* values were (55 ± 0.5) × 10-12 M and (5.2 ± 0.6) × 10-8 M, respectively. The rate constant k5 revealed a faster isomerization of EI for F-prot [(2.3 ± 0.4) × 10-3 s-1] than pepsin [(7.7 ± 0.3) × 10-4 s-1]. However, ATBI dissociated from the tight enzyme−inhibitor complex (EI*) of F-prot faster [(3.8 ± 0.5) × 10-5 s-1] than pepsin [(2.5 ± 0.4) × 10-6 s-1]. Comparative analysis of the kinetic parameters with pepstatin, the known inhibitor of pepsin, revealed a higher value of k5/k6 for ATBI. The binding of the inhibitor with the aspartic proteases and the subsequent conformational changes induced were monitored by exploiting the intrinsic tryptophanyl fluorescence. The rate constants derived from the fluorescence data were in agreement with those obtained from the kinetic analysis; therefore, the induced conformational changes were correlated to the isomerization of EI to EI*. Chemical modification of the Asp or Glu by WRK and Lys residues by TNBS abolished the antiproteolytic activity and revealed the involvement of two carboxyl groups and one amine group of ATBI in the enzymatic inactivation.
Tissue-Engineered Lungs for in Vivo Implantation (2010)

Because adult lung tissue has limited regeneration capacity, lung transplantation is the primary therapy for severely damaged lungs. To explore whether lung tissue can be regenerated in vitro, we treated lungs from adult rats using a procedure that removes cellular components but leaves behind a scaffold of extracellular matrix that retains the hierarchical branching structures of airways and vasculature. We then used a bioreactor to culture pulmonary epithelium and vascular endothelium on the acellular lung matrix. The seeded epithelium displayed remarkable hierarchical organization within the matrix, and the seeded endothelial cells efficiently repopulated the vascular compartment. In vitro, the mechanical characteristics of the engineered lungs were similar to those of native lung tissue, and when implanted into rats in vivo for short time intervals (45 to 120 minutes) the engineered lungs participated in gas exchange. Although representing only an initial step toward the ultimate goal of generating fully functional lungs in vitro, these results suggest that repopulation of lung matrix is a viable strategy for lung regeneration.
Immune alterations and immunotherapy prospects in head and neck cancer (2013)

Important and severe immune defects including T-cell dysfunction, cytokine alterations and antigen presentation defects are present in patients with HNSCC. In addition, tumor microenvironment was shown to play a critical role in the HNSCC progression. These discoveries have triggered a growing interest in immunotherapy as a potential treatment strategy for HNSCC. Effective immunotherapy could avoid the toxic side effects plaguing the current management of HNSCC. It is also hoped that immunotherapy will have long-lasting effects due to induction of immunologic memory. Promising directions include nonspecific immune stimulation, targeting specific HNSCC tumor antigens and therapeutic vaccines among others. These new agents may expand the existing therapy options for HNSCC in future.
Formation of a Complex between Nucleolin and Replication Protein a after Cell Stress Prevents Initiation of DNA Replication (2000)

We used a biochemical screen to identify nucleolin, a key factor in ribosome biogenesis, as a high-affinity binding partner for the heterotrimeric human replication protein A (hRPA). Binding studies in vitro demonstrated that the two proteins physically interact, with nucleolin using an unusual contact with the small hRPA subunit. Nucleolin significantly inhibited both simian virus 40 (SV-40) origin unwinding and SV-40 DNA replication in vitro, likely by nucleolin preventing hRPA from productive interaction with the SV-40 initiation complex. In vivo, use of epifluorescence and confocal microscopy showed that heat shock caused a dramatic redistribution of nucleolin from the nucleolus to the nucleoplasm. Nucleolin relocalization was concomitant with a tenfold increase in nucleolin-hRPA complex formation. The relocalized nucleolin significantly overlapped with the position of hRPA, but only poorly with sites of ongoing DNA synthesis. We suggest that the induced nucleolin-hRPA interaction signifies a novel mechanism that represses chromosomal replication after cell stress.
Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry with pulsed in-source collision gas and in-source ion accumulation (2000)

A new matrix-assisted laser desorption/ionization (MALDI) source for Fourier transform ion cyclotron resonance mass spectrometry (FTMS) has been developed. The new source is equipped with a hexapole ion guide. The sample on the laser target is one millimeter from the hexapole ion guide, so that ions are desorbed directly into the guide. A device for pulsing collision gas in direct proximity to the laser target makes it possible to cool the ions, which have a kinetic energy spread of several electron volts when produced by the MALDI process. These ions are trapped in the hexapole where positive potentials at the laser target and at an extraction plate help trap ions along the longitudinal axis. After a pre-defined trapping time the voltage of the extraction plate is reversed and the trapped ions are extracted for transmission to the ion cyclotron resonance cell. Accumulation of ions from multiple laser shots in the hexapole before mass spectrometric analysis increases sensitivity. Preliminary sensitivity studies with substance P show that 10 attomoles of analyte applied on the target can be detected with a signal-to-noise (S/N) ratio >15.
Reinforcement of poly(dimethylsiloxane) networks by blended and in-situgenerated silica fillers having various sizes, size distributions, and modified surfaces (1999)

Elastomeric networks of poly(dimethylsiloxane) (PDMS) were reinforced with silica particles introduced in two rather different ways. The first was by the simple blending of separately-prepared particles into hydroxyl-terminated PDMS chains that were subsequently end-linked, and the second was by in-situ precipitation through the catalyzed "sol-gel" hydrolysis and condensation of a tetraalkoxysilane. Both approaches permitted control of particle sizes and particle-size distributions. Strongly bimodal size distributions in which there were equal weights of small and large particles were of particular interest, and were achieved in the in-situ approach by using two consecutive steps for generating the two sizes of particles. In addition, some in-situ generated particles were treated to make their surfaces more hydrophobic using co-hydrolyses of dialkoxysilanes with the tetraalkoxysilane. X-ray scattering measurements and electron microscopy were used to characterize the particles and their dispersion within the PDMS matrix. In the in-situ approach, an increased amount of catalyst gave larger particles, but in smaller amounts. It also gave better dispersions, both with regard to the particles within the matrix in general, and in the mixing of the two sizes of particles amongst themselves. The resulting composites were also characterized with regard to their mechanical properties in elongation, both in continuous extension and in near-equilibrium measurements. In the latter case, the extents of stress relaxation were also measured and found to be smaller for the in-situ reinforced systems. The bimodal size distributions did not give mechanical properties superior to those of the unimodal ones, with most of the improvements in mechanical properties coming from the smaller particles. The surface-modified silica particles, however, did seem to give improved mechanical properties, presumably through stronger polymer-filler interfacial interactions.
A novel method to isolate cells with conditional gene expression using fluorescence activated cell sorting (1997)

An inducible expression system using control elements of the tetracycline resistance operon has recently shown promise for conditional gene expression of any gene of interest. However, intensive screening of multiple independent clones is often required to find cell lines with optimal induction characteristics. By coupling expression of the gene of interest with a fluorescent marker, we have developed a novel fluorescence activated cell sorting (FACS) based strategy to isolate cells with desirable expression characteristics, thus alleviating the laborious isolation and analysis of multiple independent clones.
The transactivation potential of variant hepatocyte nuclear factor 1 is modified by alternative splicing. (1993)

Two forms of the transcription factor vHNF1 (HNF1 beta or LFB3) have been previously described, derived by alternative splicing from a common premessenger RNA, and have been called vHNF1-A and vHNF1-B. vHNF1 proteins share a homologous homeo-related DNA-binding domain with the HNF1 protein, initially characterized as a liver-restricted transcription factor, and bind to a similar sequence motif. Here we demonstrate that vHNF1-A is a stronger transactivator than vHNF1-B when assayed in transient transfections using two different promoters. vHNF1-A also binds DNA with a higher affinity suggesting that a region of the protein located immediately upstream of the homeodomain can modulate the protein/DNA interaction and transactivation. Both vHNF1 transcripts were found at a constant ratio in every tissue where vHNF1 expression could be detected, using a quantitative reverse transcriptase-polymerase chain reaction.
Human delta-aminolevulinate dehydratase: nucleotide sequence of a full-length cDNA clone. (1986)

Two cDNAs encoding human delta-aminolevulinate dehydratase (ALA-D; porphobilinogen synthase; EC 4.2.1.24), the second enzyme in the heme biosynthetic pathway, were identified, recloned into bacteriophage M13, and sequenced by primer extension. The first clone with an 827-base-pair (bp) pEX-ALA-D cDNA insert, shown to contain DNA sequences that were colinear with four bovine ALA-D peptide sequences, was used to screen a pKT218 human liver library. A second clone containing a 1200-bp insert was identified that contained an open reading frame of 990 bp as well as 5' (66 bp)- and 3' (94 bp)-untranslated regions, the latter terminating in poly(dA). The predicted N-terminal amino acid sequence was colinear with the first 13 residues of microsequenced ALA-D purified from human erythrocytes. The ATG initiation codon was preceded by ACGCC, a functional initiation sequence, while an upstream (position -32), in-phase AACTG ATG sequence was entirely nonhomologous with the initiation consensus sequence and, therefore, presumed to be nonfunctional. The unusual polyadenylylation signal, AGTAAA, has been reported only in the human HRAS1 gene. The nucleotide sequences of the two cDNA clones differed at position 730 or 733 and encoded two differently charged amino acids. This nucleotide difference may be the basis for the polymorphic charge isozymes of human ALA-D. The sequence encoding this zinc metalloenzyme contained a cysteine- and histidine-rich binding site for zinc and an unusual region of charge complementarity surrounding the active lysine residue in the catalytic site.
Assessment of man's thermal comfort in practice (1973)

<b>Fanger, P. O. (1973).</b><i>British Journal of Industrial Medicine,</i><b>30,</b> 313-324. <b>Assessment of man9s thermal comfort in practice.</b> A review is given of existing knowledge regarding the conditions for thermal comfort. Both physiological and environmental comfort conditions are discussed. Comfort criteria are shown diagrammatically, and their application is illustrated by numerous practical examples. Furthermore, the effect on the comfort conditions of age, adaptation, sex, seasonal and circadian rhythm, and unilateral heating or cooling of the body is discussed. The term `climate monotony9 is considered. A method is recommended for the evaluation of the quality of thermal environments in practice.
The Golden Age of GPCR Structural Biology: Any Impact on Drug Design? (2011)

Keep ‘em coming: Seven years after the first G-protein-coupled receptor structure was published (rhodopsin in 2000), the β2-adrenergic receptor was the second GPCR to succumb to crystallization. Since then, a flurry of new structures, now totaling 39 structures of seven receptors, have been reported. Each structure has taught us something new about GPCR structure and activation, and it will be exciting to see what future structures will reveal.
The pulmonary circulation (1992)

Recent studies have emphasized the complex regulation of the pulmonary circulation. This increased understanding should result in new therapeutic approaches in the treatment of hypoxia and pulmonary hypertension. This review will discuss some of the recent advances in our understanding of the pulmonary circulation. The effects of anesthetics on the pulmonary circulation are reviewed, emphasizing the multiple modulatory systems which are altered by specific anesthetic agents. The therapeutic role of inhaled nitric oxide, and the modulatory role of endogenous nitric oxide, on the pulmonary circulation are discussed. New insights into the mechanism of hypoxic pulmonary vasoconstriction (HPV) are presented. Clinical advances in the epidemiology of pulmonary hypertension, the use of vasodilators, the role of single lung transplantation, and the anesthetic management of pulmonary hypertension are discussed. Pulmonary capillary pressure (PCP) and its dependence on the longitudinal distribution of pulmonary vascular resistance are reviewed. Finally, the role of the pulmonary circulation in acute lung injury is emphasized.