gebhart/patrepeval huggingface dataset:
HPLC: Early and Recent Perspectives (1997)

In this article, we provide personal reflections on the early days of HPLC and recent developments. HPLC has emerged from a technique that could only be imagined in the early 1960's to sales over $1.4 billion in 1994. Key to the advances has been the translation of theory to practice, in the ability to pack small particle diameter matrices of 5 mm to yield high efficiency columns. Chemically bonded phases have become a major separation mode in HPLC, particularly in the reversed phase mode. We note that the ruggedness of such columns are orders of magnitude better today than when they were introduced almost 25 years ago. The contributions of many people to this success is noted. We next turn to a brief look at the role of biochemists and analytical chemists in the development of liquid phase separation methods of biological substances. In the early years, the two communities did not strongly interact; however, today their connection in the field of biopolymer separations is quite significant. Since the future holds even more overlap, the need for analytical chemistry students to know fundamentals in the biological sciences is great.
Enhanced Nanoencapsulation of Sepiapterin within PEG-PCL Nanoparticles by Complexation with Triacetyl-Beta Cyclodextrin (2019)

In this work, we aimed to improve the encapsulation efficiency of sepiapterin (SP), the natural precursor of the essential cofactor tetrahydrobiopterin (BH4) that displays mild water-solubility and a short biological half-life, within methoxy-poly(ethylene-glycol)-poly(epsilon-caprolactone)(mPEG-PCL) nanoparticles (NPs) by means of its complexation and hydrophobization with 2,3,6-triacetyl-β-cyclodextrin (TAβCD). For this, SP/TAβCD complexes were produced by spray-drying of SP/TAβCD binary solutions in ethanol using the Nano Spray Dryer B-90 HP. Dry powders were characterized by differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FTIR), and transmission and scanning electron microscopy (TEM and SEM, respectively) and compared to the pristine components and their physical mixtures (PMs). Next, SP was encapsulated within mPEG-PCL NPs by nano-precipitation of an SP/TAβCD complex/mPEG-PCL solution. In addition to the nano-encapsulation of a preformed complex within the polymeric NPs, we assessed an alternative encapsulation approach called drying with copolymer (DWC) in which pristine SP, TAβCD, and mPEG-PCL were co-dissolved in a mixture of acetone and methanol at the desired weight ratio, dried under vacuum, re-dissolved, and nano-precipitated in water. The dissolution-drying step was aimed to promote the formation of molecular hydrophobic interactions between SP, TAβCD, and the PCL blocks in the copolymer. SP-loaded mPEG-PCL NPs were characterized by dynamic light scattering (DLS) and SEM. NPs with a size of 74-75 nm and standard deviation (S.D., a measure of the peak width) of 21-22 nm were obtained when an SP:TAβCD (1:1 molar ratio) spray-dried complex was used for the nano-encapsulation and SEM analysis revealed the absence of free SP crystals. The encapsulation efficiency (<i>%EE</i>) and drug loading (<i>%DL</i>) were 85% and 2.6%, respectively, as opposed to the much lower values (14% and 0.6%, respectively) achieved with pristine SP. Moreover, the NPs sustained the SP release with relatively low burst effect of 20%. Overall, our results confirmed that spray-drying of SP/TAβCD solutions at the appropriate molar ratio leads to the hydrophobization of the relatively hydrophilic SP molecule, enabling its encapsulation within mPEG-PCL NPs and paves the way for the use of this strategy in the development of novel drug delivery systems of this vital biological precursor.
Immunogenic proteins of feline rhinotracheitis virus (1984)

Feline rhinotracheitis virus is an upper-respiratory-tract pathogen of cats. It may also cause generalized infections or abortions. Antigens present in [35S]methionine- or [14C]glucosamine-labeled purified virions, in Nonident P-40 (NP-40) extracts of a mixture of virions and infected cells, and in virion-free cell culture medium, along with mock-infected Crandell -Rees feline kidney cell controls, were analyzed by direct sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) or by SDS-PAGE preceded by Staphylococcus aureus protein A immunoprecipitation. The direct SDS-PAGE analysis revealed at least 17 virus-specific peptides with molecular weights ranging from less than 200,000 ( 200K ) to more than 30K . Three of these peptides were glycosylated and had molecular weights of 105K , 68K , and 60K. Immunoprecipitates of purified virions and NP-40 extracts contained three major glycoproteins with the same estimated molecular weights as those found by the direct analysis. A prominent 105K glycoprotein was present in virion-free cell culture medium immunoprecipitates. In addition, a number of nonglycosylated feline rhinotracheitis virus-specific polypeptides (eight in virions, three in NP-40 extracts, and nine in virion-free cell culture medium), ranging in molecular weight from 145K to 32K, were present in the various immunoprecipitates.
Endothelial cell GlcNAc beta 1-4GlcNAc epitopes for outer membrane protein A enhance traversal of Escherichia coli across the blood-brain barrier (1996)

Inadequate knowledge of pathogenesis and pathophysiology has contributed to the high mortality and morbidity associated with neonatal Escherichia coli meningitis. We have shown previously that outer membrane protein A (OmpA) contributes to E. coli K1 membrane invasion of brain microvascular endothelial cells. In this study we report that this OmpA+ K1 E. coli invasion of brain microvascular endothelial cells was inhibited by wheat germ agglutinin and chitooligomers prepared from the polymer of 1,4-linked GlcNAc, chitin. The specificity of the interaction between OmpA and GlcNAc beta 1-4GlcNAc epitopes was verified by the demonstration that chitotriose-bound OmpA and wheat germ agglutinin-bound brain microvascular endothelial cell membrane proteins inhibit E. coli K1 invasion. Of interest, OmpA+ E. coli invasion into systemic endothelial cells did not occur, but invasion similar to that of brain microvascular endothelial cells was observed when systemic cells were treated with alpha-fucosidase, suggesting that the GlcNAc beta 1-4GlcNAc moieties might be substituted with L-fucose on these cells. More importantly, the chitooligomers prevented entry of E. coli K1 into the cerebrospinal fluid of newborn rats with experimental hematogenous E. coli meningitis, suggesting that the GlcNAc beta 1-4GlcNAc epitope of brain microvascular endothelial cells indeed mediates the traversal of E. coli K1 across the blood-brain barrier. A novel strategy with the use of soluble receptor analog(s) may be feasible in the prevention of devastating neonatal E. coli meningitis.
The Diagnosis and Prognosis of Autosomal Dominant Polycystic Kidney Disease (1990)

At present, in most persons with a 50 percent risk of autosomal dominant polycystic kidney disease, imaging techniques are the only mode of reaching a diagnosis before symptoms appear. In such persons a negative ultrasonographic study during early adult life indicates that the likelihood of inheriting a PKD1 mutation is small. In the few who inherit a non-PKD1 mutation for polycystic kidney disease, renal failure is likely to occur relatively late in life.
Visualization and debugging in a heterogeneous environment (1993)

The authors' experiences with visualization and debugging of parallel virtual machine (PVM) applications and two of the tools they have devised to facilitate these tasks are described. One of the tools is a graphical monitoring package called Xab that can visually display PVM activities inside an application running across a network. The other is a graphical programming environment called Hence, which helps the user write, compile, execute, and trace heterogeneous distributed programs. The authors discuss their early work, the present research, and the future directions of these experimental projects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Experimental and Clinical Study of Cobra Venom as an Analgesic (1936)

Introduction.-Reptiles were used empirically in the primitive medicine of the ancients.Eminent physicians of the Middle Ages used different portions of various snakes as medicinal agents.Thus, for instance, Moses Maimonides, the Osler of medieval Hebrew and Arabic medicine, states in his treatise entitled, Pirqut Mosheh,I that certain parts of poisonous snakes were useful in the treatment of leprosy and cancer.2Even in the old English dispensatories of modem times, reptiles, including serpents, are classified under materia medica as, for instance, in the fascinating Pharmacopoeia Londinensis' of William Salmon.Parenteral ad inistra- tion of snake venom for medicinal purposes, however, is an achievement of recent years.Venoms or poisons of various species of snakes have thus been introduced into therapeutics in largely an empirical way within the last decade or two.Thus Crotalus or rattlesnake venom has been empiricallr employed in the treatment of epilepsy by Mays,4 Fackenheim,5 Prevost,6 Jenkins and Pendleton,7 Thom8 and others; and the venom of the moccasin, Ancistrodon piscivorus, has been recommended for treatment of certain TABLE 1
Learning with Whom to Share in Multi-task Feature Learning (2011)

In multi-task learning (MTL), multiple tasks are learnt jointly. A major assumption for this paradigm is that all those tasks are indeed related so that the joint training is appropriate and beneficial. In this paper, we study the problem of multi-task learning of shared feature representations among tasks, while simultaneously determining “with whom ” each task should share. We formulatetheproblemasamixedintegerprogramming and provide an alternating minimization technique to solve the optimization problem of jointly identifying grouping structures and parameters. The algorithm monotonicallydecreasesthe objectivefunction and converges to a local optimum. Compared to the standard MTL paradigm where all tasks are in a single group, our algorithm improves its performance with statistical significance for three out of the four datasets we have studied. We also demonstrate its advantage over other task grouping techniques investigated in literature. 1.
Dual Effect of β-Adrenergic Receptors on Mitogen-activated Protein Kinase (1995)

The enzymatic activity of mitogen-activated protein kinases (MAP kinases) increases in response to agents acting on a variety of cell surface receptors, including receptors linked to heterotrimeric G proteins of the Gi and Gq family. Recently, it has been shown that stimulation of beta-adrenergic receptors, which are typical of those that act through Gs to activate adenylyl cyclases, potently activates MAP kinases in the heart, resulting in the hypertrophy of the cardiac muscle (Lazou, A., Bogoyevitch, M.A., Clerk, A., Fuller, S.J., Marshall, C.J., and Sudgen, P.H. (1994) Circ. Res. 75, 938-941). We have observed that exposure of COS-7 cells to a beta-adrenergic agonist, isoproterenol, raises intracellular levels of cAMP and effectively activates protein kinase A (PKA) and an epitope-tagged MAP kinase. However, MAP kinase stimulation by isoproterenol was neither mimicked by expression of an activated mutant of G alpha s, nor by treatment with PKA-stimulating agents. Moreover, pretreatment of COS-7 with a permeable cAMP analog, 8-Br-cAMP, markedly decreased MAP kinase activation by either isoproterenol or epidermal growth factor. Thus, in COS-7 cells cAMP and PKA do not appear to mediate MAP kinase activation by beta-adrenergic receptors. Signaling from beta-adrenergic receptors to MAP kinase was inhibited by transfection of a chimeric molecule consisting of the CD8 receptor and the carboxyl terminus of the beta-adrenergic receptor kinase, which includes the beta gamma-binding domain. MAP kinase activation by isoproterenol was not affected by depletion of protein kinase C, but it was completely abolished by expression of Ras-inhibiting molecules. We conclude that signaling from beta-adrenergic receptors to MAP kinase involves an activating signal mediated by beta gamma subunits acting on a Ras-dependent pathway and a G alpha s-induced inhibitory signal mediated by cAMP and PKA. The balance between these two opposing mechanisms of regulation would be expected to control the MAP kinase response to beta-adrenergic agonists as well as to other biologically active agents known to act on Gs coupled receptors, including a number of hormones, neurotransmitters, and lipid mediators.
Abstract B267: AR-mTOR-1: A potent, selective mTORC 1/2 kinase inhibitor for the treatment of malignancy (2009)

Abstract Through alterations in the PTEN and PI3K genes, the PI3K / Akt pathway is constitutively activated in human cancers. mTOR kinase plays an unique role in this pathway as the key component of two independent signaling complexes (mTORC1 (raptor - rapamycin sensitive) and mTORC2 (rictor - rapamycin insensitive)) that are involved at multiple branch points in this signaling cascade. As such, inhibition of mTOR kinase inactivates both mTOR complexes and therefore serves as an attractive means to target this integral pathway for the treatment of human malignancy. We report the biological and pharmaceutical evaluation of our selective mTOR 1/2 kinase inhibitor AR-mTOR-1. AR-mTOR-1 inhibits mTOR kinase with an IC50 of &amp;lt; 10 nM while maintaining selectivity against PI3K as well as a panel of additional lipid kinases, serine/threonine kinases and cytoplasmic and receptor tyrosine kinases. In mechanistic cellular assays, AR-mTOR-1 inhibits pAkt (Ser473), 4E-BP1 (Thr36/46) and pS6 (Ser235/6) with nanomolar potency, thus demonstrating inhibition of signaling from both mTORC1 and mTORC2 complexes. In line with its enzymatic selectivity over PI3K , AR-mTOR-1 does not significantly inhibit pAkt (Thr308) in cells. AR-mTOR-1 is broadly anti-proliferative in both epithelial and hematologic cancer cell lines, irrespective of mutational status, with IC50's ranging from 30 to 550 nM across 20 cell lines, suggesting the potential for broad clinical activity. Once daily dosing of AR-mTOR-1 in several mouse xenograft models, including PC3 prostate, U87 glioblastma, and H460 lung, results in robust anti-tumor activity. Finally, AR-mTOR-1 possesses desired in vitro and in vivo preclinical ADME properties including low clearance, high permeability and good absorption in three preclinical species. In total these data demonstrate that selectively targeting mTORC1 and mTORC2 with AR-mTOR-1 holds promise for broad spectrum clinical utility as a single agent across a wide array of cancer types. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B267.
Size-Dependent Localization and Penetration of Ultrasmall Gold Nanoparticles in Cancer Cells, Multicellular Spheroids, and Tumors in Vivo (2012)

This work demonstrated that ultrasmall gold nanoparticles (AuNPs) smaller than 10 nm display unique advantages over nanoparticles larger than 10 nm in terms of localization to, and penetration of, breast cancer cells, multicellular tumor spheroids, and tumors in mice. Au@tiopronin nanoparticles that have tunable sizes from 2 to 15 nm with identical surface coatings of tiopronin and charge were successfully prepared. For monolayer cells, the smaller the Au@tiopronin NPs, the more AuNPs found in each cell. In addition, the accumulation of Au NPs in the ex vivo tumor model was size-dependent: smaller AuNPs were able to penetrate deeply into tumor spheroids, whereas 15 nm nanoparticles were not. Owing to their ultrasmall nanostructure, 2 and 6 nm nanoparticles showed high levels of accumulation in tumor tissue in mice after a single intravenous injection. Surprisingly, both 2 and 6 nm Au@tiopronin nanoparticles were distributed throughout the cytoplasm and nucleus of cancer cells in vitro and in vivo, whereas 15 nm Au@tiopronin nanoparticles were found only in the cytoplasm, where they formed aggregates. The ex vivo multicellular spheroid proved to be a good model to simulate in vivo tumor tissue and evaluate nanoparticle penetration behavior. This work gives important insights into the design and functionalization of nanoparticles to achieve high levels of accumulation in tumors.
Soluble Egg Shell Membrane Protein as a Regulating Material for Collagen Matrix Reconstruction (1996)

Soluble egg shell membrane protein (SEP) was prepared from egg shell membrane by the combined treatment of performic acid oxidation (4 or 25 degrees C for 24 h) and pepsin digestion (25 degrees C for 24-72 h) before dialyzing against water and lyophilizing. The yield of SEP was about 16-39%. SEP had high contents of acidic amino acids (320-340 residues/1000 residues) containing cysteic acid (101-108 residues) converted from cystine, a small amount of saccharides, a main molecular weight of 12,000-22,000 and pI 4.2-4.8. SEP accelerated the reconstruction of collagen matrix with ordered molecular rearrangement and reduced redissolution of the collagen matrix under several solvent conditions. SEP elevated the denaturation temperature of the matrix.
Criteria for the classification of monoclonal gammopathies, multiple myeloma and related disorders: a report of the International Myeloma Working Group (2003)

Summary. The monoclonal gammopathies are a group of disorders associated with monoclonal proliferation of plasma cells. The characterization of specific entities is an area of difficulty in clinical practice. The International Myeloma Working Group has reviewed the criteria for diagnosis and classification with the aim of producing simple, easily used definitions based on routinely available investigations. In monoclonal gammopathy of undetermined significance (MGUS) or monoclonal gammopathy, unattributed/unassociated (MG[u]), the monoclonal protein is &lt; 30 g/l and the bone marrow clonal cells &lt; 10% with no evidence of multiple myeloma, other B‐cell proliferative disorders or amyloidosis. In asymptomatic (smouldering) myeloma the M‐protein is ≥ 30 g/l and/or bone marrow clonal cells ≥ 10% but no r elated o rgan or t issue i mpairment (ROTI)(end‐organ damage), which is typically manifested by increased c alcium, r enal insufficiency, a naemia, or b one lesions (CRAB) attributed to the plasma cell proliferative process. Symptomatic myeloma requires evidence of ROTI. Non‐secretory myeloma is characterized by the absence of an M‐protein in the serum and urine, bone marrow plasmacytosis and ROTI. Solitary plasmacytoma of bone, extramedullary plasmacytoma and multiple solitary plasmacytomas (± recurrent) are also defined as distinct entities. The use of these criteria will facilitate comparison of therapeutic trial data. Evaluation of currently available prognostic factors may allow better definition of prognosis in multiple myeloma.
Salivary markers of oxidative stress and Salivette collection systems (2011)

Salivette and Salivette cortisol collection systems significantly altered the determined concentrations of several markers of oxidative stress in comparison to measurements in whole unstimulated saliva samples.
Transcriptional analysis and regulatory signals of the hom-thrB cluster of Brevibacterium lactofermentum (1994)

Two genes, hom (encoding homoserine dehydrogenase) and thrB (encoding homoserine kinase), of the threonine biosynthetic pathway are clustered in the chromosome of Brevibacterium lactofermentum in the order 5' hom-thrB 3', separated by only 10 bp. The Brevibacterium thrB gene is expressed in Escherichia coli, in Brevibacterium lactofermentum, and in Corynebacterium glutamicum and complements auxotrophs of all three organisms deficient in homoserine kinase, whereas the Brevibacterium hom gene did not complement two different E. coli auxotrophs lacking homoserine dehydrogenase. However, complementation was obtained when the homoserine dehydrogenase was expressed as a fusion protein in E. coli. Northern (RNA) analysis showed that the hom-thrB cluster is transcribed, giving two different transcripts of 2.5 and 1.1 kb. The 2.5-kb transcript corresponds to the entire cluster hom-thrB (i.e., they form a bicistronic operon), and the short transcript (1.1 kb) originates from the thrB gene. The promoter in front of hom and the hom-internal promoter in front of thrB were subcloned in promoter-probe vectors of E. coli and corynebacteria. The thrB promoter is efficiently recognized both in E. coli and corynebacteria, whereas the hom promoter is functional in corynebacteria but not in E. coli. The transcription start points of both promoters have been identified by primer extension and S1 mapping analysis. The thrB promoter was located in an 87-bp fragment that overlaps with the end of the hom gene. A functional transcriptional terminator located downstream from the cluster was subcloned in terminator-probe vectors.
A Cellular MicroRNA Mediates Antiviral Defense in Human Cells (2005)

In eukaryotes, 21- to 24-nucleotide-long RNAs engage in sequence-specific interactions that inhibit gene expression by RNA silencing. This process has regulatory roles involving microRNAs and, in plants and insects, it also forms the basis of a defense mechanism directed by small interfering RNAs that derive from replicative or integrated viral genomes. We show that a cellular microRNA effectively restricts the accumulation of the retrovirus primate foamy virus type 1 (PFV-1) in human cells. PFV-1 also encodes a protein, Tas, that suppresses microRNA-directed functions in mammalian cells and displays cross-kingdom antisilencing activities. Therefore, through fortuitous recognition of foreign nucleic acids, cellular microRNAs have direct antiviral effects in addition to their regulatory functions.
Novel Replication-Incompetent Vector Derived from Adenovirus Type 11 (Ad11) for Vaccination and Gene Therapy: Low Seroprevalence and Non-Cross-Reactivity with Ad5 (2004)

A novel plasmid-based adenovirus vector system that enables manufacturing of replication-incompetent (DeltaE1) adenovirus type 11 (Ad11)-based vectors is described. Ad11 vectors are produced on PER.C6/55K cells yielding high-titer vector batches after purification. Ad11 seroprevalence proves to be significantly lower than that of Ad5, and neutralizing antibody titers against Ad11 are low. Ad11 seroprevalence among human immunodeficiency virus-positive (HIV(+)) individuals is as low as that among HIV(-) individuals, independent of the level of immune suppression. The low level of coinciding seroprevalence between Ad11 and Ad35 in addition to a lack of correlation between high neutralizing antibody titers towards either adenovirus strongly suggest that the limited humoral cross-reactive immunity between these two highly related B viruses appears not to preclude the use of both vectors in the same individual. Ad11 transduces primary cells including smooth muscle cells, synoviocytes, and dendritic cells and cardiovascular tissues with higher efficiency than Ad5. Ad11 and Ad35 appear to have a similar tropism as judged by green fluorescent protein expression levels determined by using a panel of cancer cell lines. In addition, Ad5 preimmunization did not significantly affect Ad11-mediated transduction in C57BL/6 mice. We therefore conclude that the Ad11-based vector represents a novel and useful candidate gene transfer vehicle for vaccination and gene therapy.
Adaptive statistical language modeling (1994)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.