gebhart/patrepeval huggingface dataset:
A Review of the pharmacokinetics, Electrophysiology and Clinical Efficacy of Dronedarone (2005)

The results of major clinical trials and advances in pharmacologic and nonpharmacologic therapies are continuing to alter treatment approaches for both atrial and ventricular arrhythmias. Originally developed as an antianginal medication, amiodarone serves as the most effective antiarrhythmic drug in the treatment of both atrial and life-threatening ventricular arrhythmias. However, amiodarone has complex pharmacokinetics and is associated with serious extracardiac side effects, partially due to the presence of an iodine moiety. With a better understanding of the mechanisms of arrhythmias and antiarrhythmic drugs, new antiarrhythmic agents are currently under development with the hope that they will be more effective and safer than currently available drugs. One such drug that might potentially fulfill this hope is dronedarone. This amiodarone-like compound lacks the iodine moiety, and is similar in structure and electrophysiologic mechanisms of action to amiodarone, to date no evidence of liver, thyroid or pulmonary toxicity has been reported. Three clinical trials demonstrate efficacy in suppressing recurrences of atrial fibrillation and there is also evidence of a rate-slowing benefit during atrial fibrillation/flutter. However, the ANtiarrhythmic trial with DROnedarone in Moderate-to-severe congestive heart failure Evaluating morbidity Decrease (ANDROMEDA) study, performed in patients with left ventricular dysfunction, demonstrated excess noncardiac mortality in patients treated with dronedarone. Although effective in the treatment of atrial fibrillation, the future of this novel amiodarone-like drug remains uncertain until further clarification of the excess mortality in heart failure patients is better studied.
Interspecies Molecular Chimeras of Kit Help Define the Binding Site of the Stem Cell Factor (1993)

The extracellular portion of the kit-encoded receptor for the stem cell factor (SCF) comprises five immunoglobulin (Ig)-like domains. To localize the ligand recognition site, we exploited the lack of binding of human SCF to the murine receptor by using human-mouse hybrids of Kit and species-specific monoclonal antibodies (MAbs) that inhibit ligand binding. Replacement of the three N-terminal Ig-like domains of the murine Kit with the corresponding portion of the human receptor conferred upon the chimeric receptor high-affinity binding of the human ligand as well as of human-specific ligand-inhibitory MAbs. By constructing five chimeric murine Kit proteins which individually contain each of these three human Ig-like units or pairs of them, we found that the second human domain confers upon the mouse Kit high-affinity binding of the human ligand and also binding of species-specific SCF-competitive MAbs. Nevertheless, the flanking Ig-like domains also affect high-affinity recognition of SCF. Moreover, it appears that the determinants that define ligand specificity of the murine and the human receptors do not structurally coincide. This observation allowed us to identify a chimeric receptor that displayed a dual specificity; namely, it bound with high affinity either the human or the murine SCF molecules and reacted with mouse- as well as human-specific ligand-inhibitory MAbs. Conversely, another chimera, which included all of the five Ig-like domains, bound neither ligand. In conclusion, interdomain packing involving the second Ig-like domain of human Kit and noncontiguous structural motifs of the receptor are involved in SCF recognition.
Individualizing neuro-anatomical atlases using a massively parallel computer (1996)

An anatomical atlas is an annotated volume of images, charts or tables that systematically illustrate an anatomical part. Atlas annotations often include structure names, descriptions, locations and functions, as well as other information specific to the atlas anatomy. Individualized digital atlases can be generated by using a computer to transform the shape of the atlas into the shape of images taken of the individual. Generalized electronic atlases of the head, created from MRI scans and labeled by experts, are currently available. The algorithms in this research create individualized, subject-specific atlases.
Role of Gender and Anatomical Region on Induction of Osteogenic Differentiation of Human Adipose-derived Stem Cells (2008)

Adipose-derived stem cells (ASCs) display multilineage plasticity and, under appropriate conditions, can mineralize their extracellular matrix and undergo osteogenesis. The aims of this study are to examine in vitro osteogenic differentiation properties of ASCs to assess the role of gender, fat depot, and optimal duration as variables for differentiation. Human ASCs were isolated from superficial and deep adipose layers of the abdominoplasty specimens obtained from patients undergoing elective surgeries. ASCs were cultured in osteogenic media (OM). After 1, 2, and 4 weeks of differentiation, cultures were assessed for markers of osteogenesis. Alkaline phosphatase (AP), alizarin red (AR) and Masson trichrome (MT) stainings for osteoblastic transformation, matrix mineralization, and collagen production; enzyme-linked immunosorbent assay (ELISA) for Gla-osteocalcin; and Western blot analysis for osteonectin protein expression were performed. Osteogenic differentiation began as early as 1 week. Cells exhibited a vertical growth pattern, lacunae formed in the cultures, matrix volume increased, and mineralization was observed. Differences in AP staining were most evident during the first week. AR activity progressively increased over 4 weeks, and collagen was secreted only by differentiated ASCs. There was no significant difference in the degree of osteogenic differentiation between the ASCs from both depots in the female. In the male, the superficial depot ASCs differentiated faster and more efficiently than those of the deep depot. Male ASCs from both depots differentiated more effectively than female ASCs from both depots. We describe a hierarchy of osteogenic differentiation potential based on gender and anatomic harvest site by layering adipose tissues of the abdominal wall. ASCs derived from male superficial layer were most efficient in achieving osteogenesis. In future clinical applications using stem cells for osseous healing, these gender and depot differences will guide our clinical methods.
Metalloenzymes involving amino acid-residue and related radicals (1994)

Free Radicals and Metalloenzymes. General Considerations * Peroxidases: Structure, Function, and Engineering * Photosystem II * Ribonucleotide Reductase in Mammalian Systems * Manganese-Dependent Ribonucleotide Reduction and Overproduction of Nucleotides in Coryneform Bacteria * Prostaglandin Endoperoxide Synthases * Diol Dehydrase from Clostridium Glycolicum: The Non-B12-Dependent Enzyme * Diol Dehydrase and Glycerol Dehydrase, Coenzyme B12-Dependent Isozymes * Adenosyl (Cobalamin) Vitamin B12 Coenzyme)-Dependent Enzymes * S-Adenosylmethionine-Dependent Radical Formation in Anaerobic Systems * The Free Radical Coupled Copper Active Site of Galactose Oxidase * Amine Oxidases * Bacterial Transport of and Resistance to Copper.
Metamaterial Apertures for Computational Imaging (2013)

By leveraging metamaterials and compressive imaging, a low-profile aperture capable of microwave imaging without lenses, moving parts, or phase shifters is demonstrated. This designer aperture allows image compression to be performed on the physical hardware layer rather than in the postprocessing stage, thus averting the detector, storage, and transmission costs associated with full diffraction-limited sampling of a scene. A guided-wave metamaterial aperture is used to perform compressive image reconstruction at 10 frames per second of two-dimensional (range and angle) sparse still and video scenes at K-band (18 to 26 gigahertz) frequencies, using frequency diversity to avoid mechanical scanning. Image acquisition is accomplished with a 40:1 compression ratio.
Denaturation of proteins during heat shock. In vivo recovery of solubility and activity of reporter enzymes (1991)

Using beta-galactosidase and luciferase as reporter enzymes, we have previously shown that enzymatic inactivation occurring during a heat shock is concomitant with protein insolubilization (Nguyen, V. T., Morange, M., and Bensaude, O. (1989) J. Biol. Chem. 264, 10487-10492). In this paper, we observe that pretreatment of cells with D2O and glycerol, compounds known to stabilize protein structure, leads to a parallel decrease of protein inactivation and insolubilization, suggesting that these two phenomena result most probably from heat-induced protein denaturation. We found that heat shock-promoted inactivation and insolubilization are not irreversible processes, since even in the absence of protein synthesis, beta-galactosidase solubility and luciferase solubility and activity are recovered in vivo after a heat treatment. Cognate heat shock proteins might be involved in this renaturation process.
Method of growing vaginal mucosal cells on a collagen sponge matrix. Results of preliminary studies. (1990)

A method of obtaining and growing vaginal mucosal epithelial cells in culture on plastic and on a collagen sponge was developed. The results indicate that simultaneous culture of skin and vaginal epithelial cells from the same donor showed morphologically similar growth potential in culture on plastic and on a collagen sponge. Vaginal cells grown on a collagen sponge formed elongated clumps of cells similar to those observed for skin epithelial cells. The results suggest that vaginal cells grown in culture on a collagen matrix may be a suitable biomaterial for use in reconstructive surgery on women with the Rokitansky syndrome or in those who have had a malignancy.
Neutralization of membrane complement regulators improves complement-dependent effector functions of therapeutic anticancer antibodies targeting leukemic cells (2015)

Complement-dependent cytotoxicity (CDC) is one of the effector mechanisms mediated by therapeutic anticancer monoclonal antibodies (mAbs). However, the efficacy of antibodies is limited by the resistance of malignant cells to complement attack, primarily due to the over-expression of one or more membrane complement regulatory proteins (mCRPs) CD46, CD55, and CD59. CD20-positive Burkitt lymphoma Raji cells and primary CLL cells are resistant to rituximab (RTX)-induced CDC whereas ofatumumab (OFA) proved to be more efficient in cell killing. Primary CLL cells but not CD52-positive acute lymphoblastic leukemia (ALL) REH cells were sensitive to alemtuzumab (ALM)-induced CDC. Upon combined inhibition on Raji and CLL cells by mCRPs-specific siRNAs or neutralizing antibodies, CDC induced by RTX and by OFA was augmented. Similarly, CDC of REH cells was enhanced after mCRPs were inhibited upon treatment with ALM. All mAbs induced C3 opsonization, which was significantly augmented upon blocking mCRPs. C3 opsonization led to enhanced cell-mediated cytotoxicity of leukemia cells exposed to PBLs or macrophages. Furthermore, opsonized CLL cells were efficiently phagocytized by macrophages. Our results provide conclusive evidence that inhibition of mCRPs expression sensitizes leukemic cells to complement attack thereby enhancing the therapeutic effect of mAbs targeting leukemic cells.
Fast 3D imaging using variable‐density spiral trajectories with applications to limb perfusion (2003)

Variable-density k-space sampling using a stack-of-spirals trajectory is proposed for ultra fast 3D imaging. Since most of the energy of an image is concentrated near the k-space origin, a variable-density k-space sampling method can be used to reduce the sampling density in the outer portion of k-space. This significantly reduces scan time while introducing only minor aliasing artifacts from the low-energy, high-spatial-frequency components. A stack-of-spirals trajectory allows control over the density variations in both the k(x)-k(y) plane and the k(z) direction while fast k-space coverage is provided by spiral trajectories in the k(x)-k(y) plane. A variable-density stack-of-spirals trajectory consists of variable-density spirals in each k(x)-k(y) plane that are located in varying density in the k(z) direction. Phantom experiments demonstrate that reasonable image quality is preserved with approximately half the scan time. This technique was then applied to first-pass perfusion imaging of the lower extremities which demands very rapid volume coverage. Using a variable-density stack-of-spirals trajectory, 3D images were acquired at a temporal resolution of 2.8 sec over a large volume with a 2.5 x 2.5 x 8 mm(3) spatial resolution. These images were used to resolve the time-course of muscle intensity following contrast injection.
Effect of mutations at Met‐88 and Met‐90 on the biotination of Lys‐89 of the apo 1.3S subunit of transcarboxylase (1988)

The apo 1.3S subunit of transcarboxylase contains the sequence Ala-87-Met-88-Lys-89-Met-90, and it is Lys-89 that is biotinated. This sequence is highly conserved in all the biotin enzymes that have been sequenced (with the exception of acetyl-CoA carboxylase from chicken liver, which has Val in place of Ala). The role of Met-88 and Met-90 in specifying Lys-89 for biotination by synthetase was examined by site-directed mutagenesis. Genes of the 1.3S subunit coding for Thr-88, Leu-88, or Leu-90 were generated by oligonucleotide-directed in vitro mutagenesis and expressed in Escherichia coli. The mutated apo 1.3S subunits were isolated and the biotination by homogeneous synthetase from Propionibacterium shermanii was compared with that of the apo wild-type subunit. The Vmax for the apo mutants was the same as that for the apo wild type, but when Leu was substituted for Met-88 or Met-90, the Km for the mutant was lower than that of the wild-type or mutant Thr-88. The activity of the synthetase of E. coli was determined by an in vivo assay. During the early log phase of growth, a smaller portion of mutants Thr-88 and Leu-90 was biotinated than with the wild-type or mutant Leu-88. When the cultures progressed to stationary phase, mutants and the wild type were biotinated to the same extent. The overall results show that Met-88 and Met-90 are not required for biotination of the apo 1.3S subunit by the synthetases.
Determination of polyamines in urine of normal human and cancer patients by capillary gas chromatography (1990)

A capillary gas chromatographic method is described for the determination of polyamines (putrescine, spermidine and spermine) in the urine of normal human and cancer patients. Morning urine after acid hydrolysis is cleaned up on a silica gel column and derivatized with trifluoroacetic-anhydride. Creatinine in human urine is used as internal standard. Recoveries of polyamines are 96.7% putrescine, 102.6% spermidine (Spd), and 98.7% spermine. SD of the method for Spd is 1.949 +/- 0.041 (micrograms/mg creatinine, mean +/- SD, n = 5). The results show that the mean level of polyamines in cancer patients urine is much higher than that in normal human urine. The mean of total polyamines in the normal human and the cancer patients is 2.01 and 44.74, respectively (g/mg creatinine).
Recent developments in gene-directed enzyme prodrug therapy (GDEPT) for cancer. (1999)

Gene-directed enzyme prodrug therapy (GDEPT) is a promising two-step treatment for solid malignant tumors. In the first step, the gene for a foreign enzyme is administered and directed to the tumor, where it may be expressed using specific transcriptional elements. In the second step, prodrugs are administered and activated by the foreign enzyme expressed at the tumor. This review focuses on the progress from the end of 1997 to date. Important issues, such as viral and non-viral vectors, new enzyme/prodrug systems, new strategies, advances in the understanding of the bystander effects, the comparison of different systems used in GDEPT and clinical trials are outlined.
The Proximal Tubule and Albuminuria (2014)

Recent data highlight the role of the proximal tubule (PT) in reabsorbing, processing, and transcytosing urinary albumin from the glomerular filtrate. Innovative techniques and approaches have provided exciting insights into these processes, and numerous investigators have shown that selective PT cell defects lead to significant albuminuria, even reaching nephrotic range in animal models. Thus, the mechanisms of albumin reabsorption and transcytosis are undergoing intense study. Working in concert with megalin and cubilin, a nonselective multireceptor complex that predominantly directs proteins for lysosomal degradation, the neonatal Fc receptor (FcRn) located at the brush border of the apical membrane has been implicated as the "receptor" mediating albumin transcytosis. The FcRn pathway facilitates reabsorption and mediates transcytosis by its pH-dependent binding affinity in endosomal compartments. This also allows for selective albumin sorting within the PT cell. This reclamation pathway minimizes urinary losses and catabolism of albumin, thus prolonging its serum half-life. It may also serve as a molecular sorter to preserve and reclaim normal albumin while allowing "altered" albumin to be catabolized via lysosomal pathways. Here, we critically review the data supporting this novel mechanism.
Voltage-Gated Ion Channels and Hereditary Disease (1999)

By the introduction of technological advancement in methods of structural analysis, electronics, and recombinant DNA techniques, research in physiology has become molecular. Additionally, focus of interest has been moving away from classical physiology to become increasingly centered on mechanisms of disease. A wonderful example for this development, as evident by this review, is the field of ion channel research which would not be nearly as advanced had it not been for human diseases to clarify. It is for this reason that structure-function relationships and ion channel electrophysiology cannot be separated from the genetic and clinical description of ion channelopathies. Unique among reviews of this topic is that all known human hereditary diseases of voltage-gated ion channels are described covering various fields of medicine such as neurology (nocturnal frontal lobe epilepsy, benign neonatal convulsions, episodic ataxia, hemiplegic migraine, deafness, stationary night blindness), nephrology (X-linked recessive nephrolithiasis, Bartter), myology (hypokalemic and hyperkalemic periodic paralysis, myotonia congenita, paramyotonia, malignant hyperthermia), cardiology (LQT syndrome), and interesting parallels in mechanisms of disease emphasized. Likewise, all types of voltage-gated ion channels for cations (sodium, calcium, and potassium channels) and anions (chloride channels) are described together with all knowledge about pharmacology, structure, expression, isoforms, and encoding genes.
Eukaryotic Expression of Recombinant Biglycan (1996)

Biglycan is a small chondroitin sulfate proteoglycan found in many tissues and is structurally related to decorin, fibromodulin, and lumican. The biological function of biglycan is poorly understood, although several studies have indicated interaction with other extracellular matrix components. We have initiated studies of structural and functional domains of biglycan by transient eukaryotic expression using the vaccinia virus/T7 bacteriophage expression system. A recombinant vaccinia virus, vBGN4 encoding the mature biglycan core protein as a polyhistidine fusion protein under control of the T7 phage promoter was expressed in HT-1080 cells and UMR106 cells. The structure of the recombinant biglycan secreted by these cells was defined by analyzing molecules labeled in the presence of [35S]sulfate, [3H]glucosamine, and [35S]methionine. Glycoforms of biglycan were separated by imidazole gradient elution, under non-denaturing conditions, and comprised: a large proteoglycan form substituted with two chondroitin sulfate chains of molecular mass approximately 34 kDa (HT-1080 cells) or approximately 40 kDa (UMR106 cells); a small proteoglycan form substituted with two chondroitin sulfate chains with a median molecular mass approximately 28 kDa; and a core protein form secreted devoid of glycosaminoglycan chains. All the glycoforms were substituted with two N-linked oligosaccharides, and the disaccharide composition of the two glycosaminoglycan populations were identical. Approximately 70% of the recombinant biglycan secreted by HT-1080 cells was substituted with chondroitin sulfate chains, whereas about 50% of the biglycan expressed by UMR106 cells was substituted with chondroitin sulfate chains. Infection with vBGN4 in both HT-1080 and UMR106 cells resulted in the production of approximately 10 mg of biglycan/10(9) cells per 24 h. The native recombinant biglycan was shown to bind to collagen type V and the complement protein, C1q. However, when the secondary structure of recombinant biglycan was disrupted by exposure to 4 M guanidine hydrochloride, the affinity for collagen type V was dramatically reduced. These data demonstrate the importance of secondary structure to the function of this small proteoglycan.
3p21.3 tumor suppressor cluster: prospects for translational applications (2005)

Chromosomal abnormalities at the 3p21.3 region, including homozygous deletions and loss of heterozygosity and expressional deficiencies in 3p21.3 genes including transcriptional silences by promoter hypermethylation, altered mRNA splicing and aberrant transcripts, and lost or defect protein translation and post-translational modifications, are frequently found in most human cancers. Inactivation of 3p21.3 genes in primary tumors affects a wide spectrum of key biological processes such as cell proliferation, cell cycle kinetics, signaling transduction, ion exchange and transportation, apoptosis and cell death, and demonstrates the molecular signatures of carcinogenesis. Restoration of defective 3p21.3 genes with several wild-type 3p21.3 genes suppresses tumor cell growth both in vitro and in vivo. These findings suggest several 3p21.3 genes as potential tumor suppressors and implicates these 3p21.3 genes for future development as biomarkers for the early detection and diagnosis of cancer, and as prognostic and therapeutic tools for cancer prevention and molecular cancer therapy.
Collaborative Development of 2-Hydroxypropyl-&#946;-Cyclodextrin for the Treatment of Niemann-Pick Type C1 Disease (2014)

In 2010, the National Institutes of Health (NIH) established the Therapeutics for Rare and Neglected Diseases (TRND) program within the National Center for Advancing Translational Sciences (NCATS), which was created to stimulate drug discovery and development for rare and neglected tropical diseases through a collaborative model between the NIH, academic scientists, nonprofit organizations, and pharmaceutical and biotechnology companies. This paper describes one of the first TRND programs, the development of 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) for the treatment of Niemann-Pick disease type C1 (NPC1). NPC is a neurodegenerative, autosomal recessive rare disease caused by a mutation in either the NPC1 (about 95% of cases) or the NPC2 gene (about 5% of cases). These mutations affect the intracellular trafficking of cholesterol and other lipids, which leads to a progressive accumulation of unesterified cholesterol and glycosphingolipids in the CNS and visceral organs. Affected individuals typically exhibit ataxia, swallowing problems, seizures, and progressive impairment of motor and intellectual function in early childhood, and usually die in adolescence. There is no disease modifying therapy currently approved for NPC1 in the US. A collaborative drug development program has been established between TRND, public and private partners that has completed the pre-clinical development of HP-β-CD through IND filing for the current Phase I clinical trial that is underway. Here we discuss how this collaborative effort helped to overcome scientific, clinical and financial challenges facing the development of new drug treatments for rare and neglected diseases, and how it will incentivize the commercialization of HP-β-CD for the benefit of the NPC patient community.