gebhart/patrepeval huggingface dataset:
Urinary Megalin Deficiency Implicates Abnormal Tubular Endocytic Function in Fanconi Syndrome (2002)

Normal reabsorption of glomerular filtrate proteins probably requires recycling of the endocytic receptors megalin (gp330) and cubilin. Both receptors are located on the luminal surface of the renal proximal tubule epithelium. Whether abnormal amounts of receptor are present in the urine of patients with Dent's disease, Lowe's syndrome, or autosomal dominant idiopathic Fanconi syndrome was explored. They are all forms of the renal Fanconi syndrome and are associated with tubular proteinuria. Urine samples of equal creatinine contents were dialyzed, lyophilized, and subjected to electrophoresis on nonreducing sodium dodecyl sulfate-5% polyacrylamide gels. Proteins were blotted and probed with anti-megalin IgG, anti-cubilin IgG, or receptor-associated protein. Megalin and cubilin levels detected by immunochemiluminescence were measured as integrated pixels and expressed as percentages of the normal mean values. A striking deficiency of urinary megalin, compared with normal individuals (n = 42), was observed for eight of nine families with Dent's disease (n = 10) and for the two families with Lowe's syndrome (n = 3). The family with autosomal dominant idiopathic Fanconi syndrome (n = 2) exhibited megalin levels within the normal range. The measured levels of cubilin were normal for all patients. These results are consistent with defective recycling of megalin to the apical cell surface of the proximal tubules and thus decreased loss into urine in Dent's disease and Lowe's syndrome. This defect would interfere with the normal endocytic function of megalin, result in losses of potential ligands into the urine, and produce tubular proteinuria.
Development of high-performance stent: Gelatinous photogel-coated stent that permits drug delivery and gene transfer (2001)

Hydrogel-coated metallic stents may provide supplementary functions such as local drug delivery and gene transfer in addition to mechanical dilation function. To this end, we used a photoreactive material consisting of gelatin macromer (multiple styrene-derivatized gelatin) and carboxylated camphorquinone (photo-initiator). A few minutes of visible light irradiation of a stent after dip-coating of an aqueous solution of the photoreactive material resulted in the formation of a homogeneously crosslinked gelatinous layer on the entire exterior surface of the stent. As the metal stent, gold stents under development were used. Rhodamine-conjugated albumin as a model drug or adenoviral vector expressing bacterial beta-galactosidase (AdLacZ) as a model gene were photo-immobilized in the gelatinous gel layer. In vitro experiments using hybrid tubular tissue, which is a self-shrinkaged, vascular smooth muscle cell-incorporated type-I collagen gel, as a vascular model, showed that the immobilized dye-derivatized albumin was released on and permeated into tissues, as observed by confocal laser microscopy, and that the cells transfected with immobilized AdLacZ produced beta-galactosidase up to almost 3 weeks, as observed by x-gal staining. In preliminary in vivo experiments these drug- or adenovirus-immobilized stents were implanted in rabbit common carotid arteries. Within 3 weeks of implantation, drug permeation and gene expression in the vascular tissues were observed, indicating that the gelatinous photogel effectively serves as a matrix or coating for a bioactive stent,which permits drug release as well as gene transfer. This intraluminal approach has the potential to realize drug and gene therapy in atherosclerotic plaque.
An In Vivo Immunotherapy Screen of Costimulatory Molecules Identifies Fc-OX40L as a Potent Reagent for the Treatment of Established Murine Gliomas (2012)

These data show that Fc-OX40L has unique and potent activity against experimental gliomas and warrants further testing.
Synthesis and antiviral evaluation of β‐L‐Xylo‐fuanosyl nucleosides of the five naturally occurring nucleic acid bases (1993)

Abstract The β‐L‐ xylo ‐furanosyl analogues of the naturally occurring nucleosides have been synthesized and their antiviral properties examined. All these compounds were hitherto unknown and they were stereospecifically prepared by glycosylation of pyrimidine and purine aglycons with a suitably peracyl‐L‐ xylo ‐furanose (specially synthesized from L‐xylose for our present purpose), followed by removal of the protecting groups. All the prepared compounds were tested for their activity against a variety of DNA and RNA viruses (including HIV), but they did not show significant antiviral activity.
Grammar-based codes: a new class of universal lossless source codes (2000)

We investigate a type of lossless source code called a grammar-based code, which, in response to any input data string x over a fixed finite alphabet, selects a context-free grammar G/sub x/ representing x in the sense that x is the unique string belonging to the language generated by G/sub x/. Lossless compression of x takes place indirectly via compression of the production rules of the grammar G/sub x/. It is shown that, subject to some mild restrictions, a grammar-based code is a universal code with respect to the family of finite-state information sources over the finite alphabet. Redundancy bounds for grammar-based codes are established. Reduction rules for designing grammar-based codes are presented.
Fetal Cell-free Plasma DNA Concentrations in Maternal Blood Are Stable 24 Hours after Collection: Analysis of First- and Third-Trimester Samples (2003)

The discovery of intact fetal cells in maternal blood has led to the possibility of noninvasive prenatal genetic testing. Although extensive work has been performed on maternal blood in the hope of developing a reliable method for the recovery of intact fetal cells, the total number of recoverable cells is quite small, averaging 19 nucleated fetal cells in 16 mL of blood (1)(2). This is contrasted by a relatively large amount of cell-free fetal DNA detectable in maternal plasma (3). Recent studies suggest that cell-free fetal DNA in maternal plasma can be used as a diagnostic tool for diseases of pregnancy, such as preeclampsia or preterm labor, or for fetal anomalies, such as Down syndrome (4)(5)(6)(7). Because of these potential applications, it is of great importance to determine whether cell-free fetal DNA concentrations remain stable in a test tube after phlebotomy.

In this report we evaluate the effects of time after phlebotomy on the quantity of cell-free fetal DNA in blood samples from a pregnant woman and a woman who has just undergone termination of pregnancy. The post-termination samples were used because in the first trimester, there are relatively few fetal cells present in maternal blood. The termination procedure increases fetomaternal transfusion (8). We hypothesized that after phlebotomy, apoptotic fetal cells that die in the venipuncture tube would release their DNA. We also asked whether more fetal cells undergo apoptosis as a result of exposure to the maternal bloodstream and cytokines. In both cases, we hypothesized that cell-free fetal DNA concentrations would increase in the blood samples over time.

This study was performed with Institutional Review Board approval and with informed consent from participants at Tufts-New England Medical Center. For early-gestation samples, 29 women who were 6–17 weeks pregnant were recruited from …
Modified guanidines as chiral superbases: the first example of asymmetric silylation of secondary alcohols (2001)

Modified guanidines could effectively mediate asymmetric silylation of secondary alcohols as recyclable bases under simple and mild conditions.
LIPOPROTEIN PIGMENTS—THEIR RELATIONSHIP TO AGEING IN THE HUMAN NERVOUS SYSTEM (1974)

Journal Article LIPOPROTEIN PIGMENTS—THEIR RELATIONSHIP TO AGEING IN THE HUMAN NERVOUS SYSTEM: II. THE MELANIN CONTENT OF PIGMENTED NERVE CELLS Get access D. M. A. MANN, D. M. A. MANN Department of Neuropathology, Manchester UniversityM13 9PT Search for other works by this author on: Oxford Academic PubMed Google Scholar P. O. YATES P. O. YATES Department of Neuropathology, Manchester UniversityM13 9PT Search for other works by this author on: Oxford Academic PubMed Google Scholar Brain, Volume 97, Issue 1, 1974, Pages 489–498, https://doi.org/10.1093/brain/97.1.489 Published: 01 January 1974 Article history Published: 01 January 1974 Received: 06 February 1974
Bevacizumab Plus Irinotecan in Recurrent Glioblastoma Multiforme (2007)

Bevacizumab and irinotecan is an effective treatment for recurrent glioblastoma multiforme and has moderate toxicity.
Synovial fluid CD146 (MUC18), a marker for synovial membrane angiogenesis in rheumatoid arthritis (1999)

Since CD146 is expressed almost exclusively by vascular endothelium, high levels of soluble CD146 found in RA synovial fluid, particularly in patients with early disease, could reflect increased activity of endothelial cells and angiogenesis.
ABT-888, an Orally Active Poly(ADP-Ribose) Polymerase Inhibitor that Potentiates DNA-Damaging Agents in Preclinical Tumor Models (2007)

ABT-888 is a potent inhibitor of PARP, has good oral bioavailability, can cross the blood-brain barrier, and potentiates temozolomide, platinums, cyclophosphamide, and radiation in syngeneic and xenograft tumor models. This broad spectrum of chemopotentiation and radiopotentiation makes this compound an attractive candidate for clinical evaluation.
A Capacitorless Twin-Transistor Random Access Memory (TTRAM) on SOI (2007)

We propose a novel capacitorless twin-transistor random access memory (TTRAM). The 2Mb test device has been fabricated on 130nm SOI-CMOS process. We demonstrate the TTRAM cell has two data-storage states and confirm the data retention time of 100 ms at 80°C. TTRAM process is compatible with the conventional SOI-CMOS and never requires any additional processes. A 6.1 ns row-access time is achieved and 250 MHz operation can be realized by using 2 bank 8 b-burst mode.
Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein (1993)

Electrostatic interactions are among the key factors determining the structure and function of proteins. Here we report experimental results that illuminate the functional importance of local dipoles to these interactions. The refined 1.7-A X-ray structure of the liganded form of the sulfate-binding protein, a primary sulfate active transport receptor of Salmonella typhimurium, shows that the sulfate dianion is completely buried and bound by hydrogen bonds (mostly main-chain peptide NH groups) and van der Waals forces. The sulfate is also closely linked, via one of these peptide units, to a His residue. It is also adjacent to the N-termini of three alpha-helices, of which the two shortest have their C-termini "capped" by Arg residues. Site-directed mutagenesis of the recombinant Escherichia coli sulfate receptor had no effect on sulfate-binding activity when an Asn residue was substituted for the positively charged His and the two Arg (changed singly and together) residues. These results, combined with other observations, further solidify the idea that stabilization of uncompensated charges in a protein is a highly localized process that involves a collection of local dipoles, including those of peptide units confined to the first turns of helices. The contribution of helix macrodipoles appears insignificant.
Efficacy of microdermabrasion preceding ALA application in reducing the incubation time of ALA in laser PDT. (2007)

Topical 5-aminolevulinic acid (ALA) and various light sources have been used to treat actinic keratoses and acne. Many of these regimens have required long incubation times due to the penetration qualities of ALA. This study tested the effectiveness of ALA in producing erythema when applied for 10 minutes after 2 passes of microdermabrasion versus an incubation time of one hour without microdermabrasion. The areas were treated with a 595-nm pulsed dye laser at 15 J/cm2 or 22.5 J/cm2. Photographs were taken at 24 and 48 hours after the treatment. The data indicated consistent superior results with the use of microdermabrasion prior to the application of ALA for 10 minutes. It appears that incubation of ALA with microdermabrasion for 10 minutes is as effective as, or more so than, ALA applied alone for one hour in producing erythema.
Listeria Protein ActA Mimics WASP Family Proteins:  It Activates Filament Barbed End Branching by Arp2/3 Complex (2001)

Actin-based propulsion of the bacteria Listeria and Shigella mimics the forward movement of the leading edge of motile cells. While Shigella harnesses the eukaryotic protein N-WASp to stimulate actin polymerization and filament branching through Arp2/3 complex, the Listeria surface protein ActA directly activates Arp2/3 complex by an unknown mechanism. Here we show that the N-terminal domain of ActA binds one actin monomer, in a profilin-like fashion, and Arp2/3 complex and mimics the C-terminal domain of WASp family proteins in catalyzing filament barbed end branching by Arp2/3 complex. No evidence is found for side branching of filaments by ActA-activated Arp2/3 complex. Mutations in the conserved acidic (41)DEWEEE(46) and basic (146)KKRRK(150) regions of ActA affect Arp2/3 binding but not G-actin binding. The motility properties of wild-type and mutated Listeria strains in living cells and in the medium reconstituted from pure proteins confirm the conclusions of biochemical experiments. Filament branching is followed by rapid debranching. Debranching is 3-4-fold faster when Arp2/3 is activated by ActA than by the C-terminal domain of N-WASp. VASP is required for efficient propulsion of ActA-coated beads in the reconstituted motility medium, but it does not affect the rates of barbed end branching/debranching by ActA-activated Arp2/3 nor the capping of filaments. VASP therefore affects another still unidentified biochemical reaction that plays an important role in actin-based movement.
Structural and Functional Aspects of Chloride Binding to Alteromonas haloplanctis α-Amylase (1996)

Chloride is the allosteric effector of vertebrate pancreatic and salivary alpha-amylases and of the bacterial alpha-amylase from Alteromonas haloplanctis. Activation experiments of A. haloplanctis alpha-amylase by several monovalent anions show that a negative charge, not restricted to that of Cl-, is essential for the amylolytic reaction. Engineering of the chloride binding site reveals that a basic residue is an essential component of the site. The mutation K337R alters the Cl--binding properties, whereas the mutation K337Q produces an active, chloride-independent enzyme. Comparison of the Kd values for Cl- in three homologous alpha-amylases also indicates that the binding affinity is dependent on the chloride coordination mode by this basic residue. Analysis of substrate and chloride binding according to the allosteric kinetic model shows that the chloride effector is not involved in substrate binding. By contrast, the pH dependence of activity and experiments of chemical modifications and Ca2+ inhibition show that the chloride ion is responsible for the pKa shift of catalytic groups and interacts with active site carboxyl groups.
Discovery of Alogliptin:  A Potent, Selective, Bioavailable, and Efficacious Inhibitor of Dipeptidyl Peptidase IV (2007)

Alogliptin is a potent, selective inhibitor of the serine protease dipeptidyl peptidase IV (DPP-4). Herein, we describe the structure-based design and optimization of alogliptin and related quinazolinone-based DPP-4 inhibitors. Following an oral dose, these noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and a lowering of blood glucose in animal models of diabetes. Alogliptin is currently undergoing phase III trials in patients with type 2 diabetes.
Leishmanicidal, Antiplasmodial, and Cytotoxic Activity of Novel Diterpenoid 1,2-Quinones from Perovskia abrotanoides:  New Source of Tanshinones (2001)

Cryptotanshinone (1), a quinoid diterpene with a nor-abietane skeleton, and three new natural products, 1beta-hydroxycryptotanshinone (2), 1-oxocryptotanshinone (3), and 1-oxomiltirone (4), were isolated from roots of the Iranian medicinal plant Perovskia abrotanoides. Their structures were established using homo- and heteronuclear two-dimensional NMR experiments, supported by HRMS. The total amount of tanshinones isolated from dry roots of Perovskia abrotanoides was about 1.5%. The compounds exhibited leishmanicidal activity in vitro (IC(50) values in the range 18-47 microM). These findings provide a rationale for traditional use of the roots in Iran as a constituent of poultices for treatment of cutaneous leishmaniasis. The isolated tanshinones also inhibited growth of cultured malaria parasites (3D7 strain of Plasmodium falciparum), drug-sensitive KB-3-1 human carcinoma cell line, multidrug-resistant KB-V1 cell line, and human lymphocytes activated with phytohaemagglutinin A (IC(50) values in the range 5-45 microM). The toxicity of tanshinones toward the drug-sensitive KB-3-1 and the multidrug-resistant KB-V1 cells was the same, indicating that the compounds are not substrates for the P-glycoprotein drug efflux pump.
Contactin Associates with Na+Channels and Increases Their Functional Expression (2001)

Contactin (also known as F3, F11) is a surface glycoprotein that has significant homology with the beta2 subunit of voltage-gated Na(+) channels. Contactin and Na(+) channels can be reciprocally coimmunoprecipitated from brain homogenates, indicating association within a complex. Cells cotransfected with Na(+) channel Na(v)1.2alpha and beta1 subunits and contactin have threefold to fourfold higher peak Na(+) currents than cells with Na(v)1.2alpha alone, Na(v)1.2/beta1, Na(v)1.2/contactin, or Na(v)1.2/beta1/beta2. These cells also have a correspondingly higher saxitoxin binding, suggesting an increased Na(+) channel surface membrane density. Coimmunoprecipitation of different subunits from cell lines shows that contactin interacts specifically with the beta1 subunit. In the PNS, immunocytochemical studies show a transient colocalization of contactin and Na(+) channels at new nodes of Ranvier forming during remyelination. In the CNS, there is a particularly high level of colocalization of Na(+) channels and contactin at nodes both during development and in the adult. Contactin may thus significantly influence the functional expression and distribution of Na(+) channels in neurons.
Lipids and Fatty Acid Compositions of Chlorella (1997)

The lipids profile of Chlorella vulgaris grown on an organic medium and inorganic medium were examined.1) The neutral lipid on the organic medium was 2.8 g/100 g and inorganic medium was 1.88 g/100 g of the total dry weight, which composed of 80% waxesters and 20% triacylglycerols on both medium.2) The phospholipid on the organic medium was 8.6 g/100 g and on the inorganic medium was 6.2 g/100 g of the total dry weight, those composition (PG, PC, PE, PI) on the both medium were similar but those distribution of the fatty acid were different.3) The glycolipid were contained on the both medium about 5.7 g/100 g of the total dry weight, those composition (MGDG, DGDG, SQDG) and fatty acid composition of each glycolipid on the both medium were different. 4) Both hexadecatetraenoic acid (C16 : 4) and octadecatetraenoic acid (C18 : 4) were observed in the glycolipid and phospholipids except PG which was absent, while triacylglycerols were not present.5) Trans-hexadecenoic acid was present only in the PG, which contained 1.6% on organic medium and 2.3% on inorganic medium.
Planar three-dimensional constrained lenses (1986)

A new design for a beamforming lens is presented. Both faces are planar arrays of radiating elements interconnected by transmission lines whose length varies as a function of radius. While the front face elements are regularly spaced, the back face elements are displaced radially from their corresponding front face elements, the amount of displacement also being a function of radius. We show that such a lens is capable of forming low sidelobe beams over an angular sector 36 beamwidths across in all planes of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\phi</tex> by switching between clusters of only seven feed elements. Because both faces are planar, construction of lightweight lenses for multibeam antennas should be feasible.
Insulin-Like Growth Factor System in Neuroblastoma Tumorigenesis and Apoptosis: Potential Diagnostic and Therapeutic Perspectives (1999)

Apoptosis is a cell death program which is modulated by a variety of factors including growth factors, signal transduction molecules and inducers of gene expression or DNA replication. Of particular interest is Type I insulin-like growth factor receptor which contains a tyrosine kinase domain linked to the ras-raf-MAPK cascade. This receptor has antiapoptotic effects in a number of in vivo and in vitro models, thus making IGF-I-R a potential target for gene therapy. Particularly the growth of neuroblastoma depends on IGFs which exert their effect through the Type I IGF receptor. This review highlights the role of the IGF-system in neuroblastoma and points at possible modulators with the aim of inducing differentiation or apoptosis of tumor cells.
A Pair of Related Genes with Antagonistic Roles in Mediating Flowering Signals (1999)

Flowering in Arabidopsis is promoted via several interacting pathways. A photoperiod-dependent pathway relays signals from photoreceptors to a transcription factor gene, CONSTANS (CO), which activates downstream meristem identity genes such as LEAFY (LFY). FT, together with LFY, promotes flowering and is positively regulated by CO. Loss of FT causes delay in flowering, whereas overexpression of FT results in precocious flowering independent of CO or photoperiod. FT acts in part downstream of CO and mediates signals for flowering in an antagonistic manner with its homologous gene, TERMINAL FLOWER1 (TFL1).
Aerobic biodegradation of benzene, toluene and ethylbenzene in liquid medium by a bacterial consortium, isolated from non-history clay soil, and their interrelation effect (2000)

The present study was carried out in order to investigate the ability of isolated subsurface bacteria, from a non-history clay soil, to biodegrade the non-aqueous phase-liquids (NAPLs), monoaromatic hydrocarbons: benzene, toluene and ethylbenzene. First stage of the study was focussed on stand-alone biodegradation of each contaminant under described conditions. Benzene (100, 260 and 500 mg/l) exposed to isolated soil bacteria for 14 days, was biodegraded 100, 70 and 50%, respectively, ethylbenzene (100, 260 and 500 mg/l) at 85, 87 and 90%, respectively and toluene (100, 260 and 500 mg/l) revealed the lowest rate of 45, 50 and 52%. Toluene and ethylbenzene showed a direct increase in biodegradation associated with increase in their concentration. The second stage was the biodegradation of benzene, toluene and ethylbenzene admixture (all three compounds at the very same concentrations, w/v) in glucose absence and supplemented with Tween 80 (10 and 15 mg/l). The overall biodegradation improved when contaminants were mixed together.
Evaluation of a Novel 18 F-Labeled Positron-Emission Tomography Perfusion Tracer for the Assessment of Myocardial Infarct Size in Rats (2009)

Myocardial (18)F BMS747158-02 PET imaging provides excellent image quality and uptake properties, enabling accurate evaluation of MI size and left ventricular function in rats. It is a promising technique for evaluation of MI size in clinical trials.