gebhart/patrepeval huggingface dataset:
Structure of the membrane proximal oxidoreductase domain of human Steap3, the dominant ferrireductase of the erythroid transferrin cycle (2008)

The daily production of 200 billion erythrocytes requires 20 mg of iron, accounting for nearly 80% of the iron demand in humans. Thus, erythroid precursor cells possess an efficient mechanism for iron uptake in which iron loaded transferrin (Tf) binds to the transferrin receptor (TfR) at the cell surface. The Tf:TfR complex then enters the endosome via receptor-mediated endocytosis. Upon endosomal acidification, iron is released from Tf, reduced to Fe(2+) by Steap3, and transported across the endosomal membrane by divalent metal iron transporter 1. Steap3, the major ferrireductase in erythrocyte endosomes, is a member of a unique family of reductases. Steap3 is comprised of an N-terminal cytosolic oxidoreductase domain and a C-terminal heme-containing transmembrane domain. Cytosolic NADPH and a flavin are predicted cofactors, but the NADPH/flavin binding domain differs significantly from those in other eukaryotic reductases. Instead, Steap3 shows remarkable, although limited homology to FNO, an archaeal oxidoreductase. We have determined the crystal structure of the human Steap3 oxidoreductase domain in the absence and presence of NADPH. The structure reveals an FNO-like domain with an unexpected dimer interface and substrate binding sites that are well positioned to direct electron transfer from the cytosol to a heme moiety predicted to be fixed within the transmembrane domain. Here, we discuss possible gating mechanisms for electron transfer across the endosomal membrane.
Antitumor Activity with CYP17 Blockade Indicates That Castration-Resistant Prostate Cancer Frequently Remains Hormone Driven (2009)

Abiraterone acetate is a potent, selective, and orally bioavailable small molecule inhibitor of CYP17, an enzyme that catalyzes two key serial reactions (17 alpha hydroxylase and 17,20 lyase) in androgen and estrogen biosynthesis. Clinical trials have confirmed that specific inhibition of CYP17 is safe and results in clinically important antitumor activity in up to 70% of castrate patients with advanced prostate cancer resistant to currently available endocrine therapies. These clinical data indicate that castration-resistant prostate cancer frequently remains hormone dependent and has confirmed that this disease should no longer be described as "hormone resistant or refractory". Biomarker studies, including the analysis of ETS gene fusion status, on patients treated with abiraterone acetate may allow enrichment of patients with a sensitive phenotype in future studies of therapeutics targeting CYP17.
Measurement of Circulating Cell‐Free DNA in Relation to 18F‐Fluorocholine PET/CT Imaging in Chemotherapy‐Treated Advanced Prostate Cancer (2012)

Chemotherapy is associated with significant changes in plasma cfDNA content and FCH PET/CT-detected tumor activity. These interrelated measures are potential candidate markers of therapeutic response in HRPC.
Introduction to the CoNLL-2005 shared task (2005)

In this paper we describe the CoNLL-2005 shared task on Semantic Role Labeling. We introduce the specification and goals of the task, describe the data sets and evaluation methods, and present a general overview of the 19 systems that have contributed to the task, providing a comparative description and results.
Performance of STBC with turbo code in HARQ scheme for mobile communication systems (2003)

The performance of STBC (space time block codes) concatenated with turbo codes in an HARQ (hybrid automatic repeat request) scheme is analyzed. When two transmitter antennas are used, up to 5dB and 10dB gains are obtained in AWGN and Rayleigh fading channels, respectively, as compared to the conventional one antenna system. Gain in the fading channel is much larger than in the AWGN channel. Therefore, STBC with turbo codes may be a suitable HARQ scheme for future third generation mobile communication systems such as cdma2000 and W-CDMA.
Use of Protein Antigens for Early Serological Diagnosis of Leprosy (2007)

Leprosy is a chronic and debilitating human disease caused by infection with the Mycobacterium leprae bacillus. Despite the marked reduction in the number of registered worldwide leprosy cases as a result of the widespread use of multidrug therapy, the number of new cases detected each year remains relatively stable. This indicates that M. leprae is still being transmitted and that, without earlier diagnosis, M. leprae infection will continue to pose a health problem. Current diagnostic techniques, based on the appearance of clinical symptoms or of immunoglobulin M (IgM) antibodies that recognize the bacterial phenolic glycolipid I, are unable to reliably identify early-stage leprosy. In this study we examine the ability of IgG within leprosy patient sera to bind several M. leprae protein antigens. As expected, multibacillary leprosy patients provided stronger responses than paucibacillary leprosy patients. We demonstrate that the geographic locations of the patients can influence the antigens they recognize but that ML0405 and ML2331 are recognized by sera from diverse regions (the Philippines, coastal and central Brazil, and Japan). A fusion construct of these two proteins (designated leprosy IDRI diagnostic 1 [LID-1]) retained the diagnostic activity of the component antigens. Upon testing against a panel of prospective sera from individuals who developed leprosy, we determined that LID-1 was capable of diagnosing leprosy 6 to 8 months before the onset of clinical symptoms. A serological diagnostic test capable of identifying and allowing treatment of early-stage leprosy could reduce transmission, prevent functional disabilities and stigmatizing deformities, and facilitate leprosy eradication.
Post-bond testing of 2.5D-SICs and 3D-SICs containing a passive silicon interposer base (2011)

Through-Silicon Vias (TSVs) enable high-density, low-latency, and low-power interconnects for system chips that consist of multiple dies. In “2.5D” Stacked ICs (2.5D-SICs), multiple dies without TSVs are stacked side-by-side on top of a passive silicon interposer base containing TSVs. In true 3D-SICs, multiple dies containing TSVs themselves are vertically stacked; one or multiple of such stacks are possibly placed on a passive silicon interposer. This paper proposes a post-bond test and design-for-test (DfT) strategy for 2.5D- and 3D-SICs containing a passive silicon interposer base. Functional interconnects in the interposer are reused as much as possible in order to keep the interposer cost low.
Bacterial Communities in Neonatal Feces are Similar to Mothers’ Placentae (2015)

These results may provide new directions for the study of infant gut microbial formation.
High-throughput functional genomics using CRISPR–Cas9 (2015)

Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.
Interactions of Amyloid β-Protein with Various Gangliosides in Raft-Like Membranes:  Importance of GM1 Ganglioside-Bound Form as an Endogenous Seed for Alzheimer Amyloid (2002)

GM1 ganglioside-bound amyloid beta-protein (GM1-Abeta), found in brains exhibiting early pathological changes of Alzheimer's disease (AD) plaques, has been suggested to accelerate amyloid fibril formation by acting as a seed. We have previously found using dye-labeled Abeta that Abeta recognizes a GM1 cluster, the formation of which is facilitated by cholesterol [Kakio, A., Nishimoto, S., Yanagisawa, K., Kozutsumi, Y., and Matsuzaki, K. (2001) J. Biol. Chem. 276, 24985-24990]. In this study, we investigated the ganglioside species-specificity in its potency to induce a conformational change of Abeta, by which ganglioside-bound Abeta acts as a seed for Abeta fibrillogenesis, using a major ganglioside occurring in brains (GM1, GD1a, GD1b, and GT1b) in raft-like membranes composed of cholesterol and sphingomyelin. Abeta recognized ganglioside clusters, the density of which increased with the number of sialic acid residues. Interestingly, however, mixing of gangliosides inhibited cluster formation. In contrast, the affinities of the protein for the clusters were similar irrespective of lipid composition and of the order of 10(6) M(-)(1) at 37 degrees C. Abeta underwent a conformational transition from an alpha-helix-rich structure to a beta-sheet-rich structure with the increase in protein density on the membrane. Ganglioside-bound Abeta proteins exhibited seeding abilities for amyloid formation. GM1-Abeta exhibited the strongest seeding potential, especially under beta-sheet-forming conditions. This study suggested that lipid composition including gangliosides and cholesterol strictly controls amyloid formation.
Recombinant V antigen protects mice against pneumonic and bubonic plague caused by F1-capsule-positive and -negative strains of Yersinia pestis (1996)

The purified recombinant V antigen from Yersinia pestis, expressed in Escherichia coli and adsorbed to aluminum hydroxide, an adjuvant approved for human use, was used to immunize outbred Hsd:ND4 mice subcutaneously. Immunization protected mice from lethal bubonic and pneumonic plague caused by CO92, a wild-type F1+ strain, or by the isogenic F1- strain C12. This work demonstrates that a subunit plague vaccine formulated for human use provides significant protection against bubonic plague caused by an F1- strain (C12) or against substantial aerosol challenges from either F1+ (CO92) or F1-(C12) Y. pestis.
Induction of 15-lipoxygenase by interleukin-13 in human blood monocytes. (1994)

15-Lipoxygenase (15-LO) catalyzes hydroperoxidation of fatty acids, a reaction of potential relevance to inflammation, membrane remodeling, and atherosclerosis. In human leukocytes, 15-lipoxygenation of arachidonic acid produces 15-(S)-hydroxyeicosatetraenoic acid and lipoxin A4, which suppress white cell chemotaxis, adherence, and activation, and antagonize proinflammatory leukotrienes. Interleukin (IL)-13, produced by T-helper subset 2 (TH-2) lymphocytes, specifically and potently induced 15-LO gene expression and enzyme activity in human monocytes. Among other TH-2 lymphokines, this induction of 15-LO is shared by IL-4 but not by IL-10. Interferon-gamma, a product of TH-1 lymphocytes, blocked IL-13-mediated induction of 15-LO. The induction of the anti-inflammatory 15-LO pathway by IL-13 reveals a new facet of IL-13 biology that supports its role as a cytokine with potential to down-regulate inflammatory pathways. The contrasting effects of interferon-gamma and IL-13 on 15-LO induction demonstrate mechanisms by which T-lymphocyte subsets may modulate macrophage/monocyte function in inflammation or atherosclerosis.
Gunshot detection in audio streams from movies by means of dynamic programming and Bayesian networks (2008)

This paper treats gunshot detection in audio streams from movies as a maximization task, where the solution is obtained by means of dynamic programming. The proposed method seeks the sequence of segments and respective class labels, i.e., gunshots vs. all other audio types, that maximize the product of posterior class label probabilities, given the segments' data. The required posterior probabilities are estimated by combining soft classification decisions from a set of Bayesian Network combiners. Tests that have been performed on a large set of audio streams indicate that the proposed method yields high performance in terms of both precision and recall of detected gunshot events.
Synthesis and Pharmacology of Combined Histamine H1‐/H2‐Receptor Antagonists Containing Diphenhydramine and Cyproheptadine Derivatives (1996)

The classical histamine H1-receptor antagonists diphenhydramine (3a) and cyproheptadine (9) and their derivatives (3b-d, 10) were connected with a 2-guanidinothiazole containing structure (28) derived from the H2-receptor antagonist tiotidine in order to obtain combined H1-/H2-receptor antagonists. The two moieties were not directly linked together, but were separated by a polymethylene spacer and a polar group (nitroethenediamine or urea). Thus 12 compounds were obtained that proved in vitro to possess high H1- and H2-receptor antagonist activity at the isolated guinea-pig ileum (H1) and the isolated guinea-pig right atrium (H2), respectively. The incorporation of the diphenhydramine as well as the cyproheptadine component provides high affinity to H1-receptors. The tricyclic cyproheptadine and its 10,11-dihydro derivative (30-32, 34), however, cause a decrease of H2-receptor antagonist potency compared to the diphenhydramines (29a-d, 33a-d). Using nitroethenediamine as the polar group is apparently more favourable to H1- and H2-receptor affinity as the urea function. All compounds elicit a dual mode of competitive and noncompetitive antagonism. Among the novel compounds the nitroethenediamines with 4-fluoro- or 4-methyl-substituted diphenhydramine as H1-receptor antagonist moiety (29c, d) display the most potent H1- and H2-receptor antagonist effects. The presented concept is a very promising way to combine H1- and H2-receptor antagonist properties in one molecule.
Multilevel codes based on partitioning (1989)

Following V.V. Ginzburg (1984), a hierarchy of codes is proposed to match the geometric partitioning of a signal set. The authors show that coset codes (including Ungerboeck, lattice, and binary codes) and indeed any codes which rely on partitioning of the signal set are all subclasses of the proposed coding scheme. The combination of such codes in a multilevel scheme often leads to reduced complexity in comparison with previously published schemes. A variety of decoder structures is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Efficacy of type‐5 phosphodiesterase inhibitors in the drug treatment of premature ejaculation: a systematic review (2006)

This review examines the role of nitric oxide (NO) as a neurotransmitter involved in the central and peripheral control of ejaculation, the methods of phosphodiesterase type 5 inhibitor (PDE5I) drug treatment studies for premature ejaculation (PE), the adherence of methods to the contemporary consensus of ideal PE drug trial design, the impact of methods on treatment outcomes and the role of PDE5Is in the treatment of PE. NO/cGMP transduction is involved in both the central and peripheral control of emission, but evidence for a direct central or peripheral effect of PDE5Is on ejaculation is speculative. Thirteen of the 14 studies reviewed failed to fulfil the evidence-based medicine criteria for ideal PE drug trial design. Limitations of the studies include inadequately defined study populations, the lack of a double-blind placebo-controlled study design, and the absence of consistent objective physiological measures or sensitive, validated outcome assessment instruments as study endpoints. The broad range of intravaginal ejaculatory latency time (IELT) fold-increases reported with PDE5Is, on-demand selective serotonin re-uptake inhibitor (SSRI) drugs, and combined PDE5I/on-demand SSRIs is testament to the unreliability of data and conclusions from methodologically flawed studies. The one study that fulfilled the evidence-based medicine criteria of an ideal clinical trial design reported that treatment with sildenafil failed to significantly increase baseline IELT, supporting our conclusion that there is no convincing evidence to support any role for PDE5Is in the treatment of men with lifelong PE and normal erectile function. However, there is limited evidence to support a potential role for PDE5Is alone or combined with daily or on-demand SSRIs in the treatment of acquired PE in men with comorbid erectile dysfunction. Further controlled studies adhering to the contemporary consensus of ideal clinical trial design are required to clarify the role of PDE5Is in this subgroup of men with acquired PE.
Additive inhibitory effects of an androgen and the antiestrogen EM-170 on estradiol-stimulated growth of human ZR-75-1 breast tumors in athymic mice. (1991)

The effects of the androgen dihydrotestosterone (DHT) and of the androgenic steroid medroxyprogesterone acetate were studied on the growth of human ZR-75-1 breast carcinoma in athymic mice. The possibility of additive inhibitory effects of DHT and the new steroidal antiestrogen N-n-butyl, N-methyl-11-[16' alpha-chloro-3',17' alpha-dihydroxyestra-1',3',5'(10')trien-7' alpha-yl]undecanamide (EM-170) was also investigated on tumor growth. Removal of the high dose 17 beta-estradiol (E2) implants used to optimally stimulate initial ZR-75-1 tumor development in ovariectomized mice led to a progressive decrease in tumor area to 50.2 +/- 8% (SEM) of original tumor size 40 days after E2 deprivation. Additional treatment with the androgen DHT led to a more rapid fall in tumor volume, which already reached 57% of pretreatment values at 11 days. Whereas physiological implants of E2 led to a progressive increase in tumor size to about 180% above original size after 40 days, physiological plasma levels (205 +/- 37.2 pg/ml or approximately 0.67 nM) of DHT completely reversed the stimulatory effect of E2. Similar inhibitory effects on E2-stimulated tumor growth were achieved with the synthetic androgenic steroid medroxyprogesterone acetate. When the steroidal antiestrogen EM-170 at the dose of 30 micrograms/day was used simultaneously with DHT, tumor area was further reduced from 99.0 +/- 9.5% (DHT alone) to 58.8 +/- 18% when both DHT and EM-170 were administered together for 40 days compared with 169 +/- 22.2% in control E2-stimulated animals. The present data show that the androgen DHT as well as medroxy-progesterone acetate are potent inhibitors of E2-stimulated human ZR-75-1 breast cancer cell growth in vivo. Moreover, the inhibitory effect of DHT can be further increased by addition of the antiestrogen EM-170, thus suggesting the interest of combining these 2 classes of compounds acting, at least partially, through different mechanisms, in order to improve breast cancer therapy in women.
Combination mTOR and IGF-1R Inhibition: Phase I Trial of Everolimus and Figitumumab in Patients with Advanced Sarcomas and Other Solid Tumors (2010)

Combination figitumumab plus everolimus at full doses appears safe and well tolerated with no unexpected toxicities. Dose reductions in everolimus may be required after prolonged drug administration. This regimen exhibits interesting antitumor activity warranting further investigation.
Ribavirin is not a functional mimic of the 7-methyl guanosine mRNA cap (2005)

Ribavirin is a guanosine ribonucleoside analog that displays broad-spectrum anti-viral activity and is currently used for the treatment of some viral infections. Ribavirin has recently been proposed to also be a mimic of the 7-methyl guanosine cap found at the 5' end of mRNAs. To obtain supporting functional data for this hypothesis, we assessed the ability of ribavirin triphosphate to interfere with the interaction between eIF4E and 7-methyl guanosine capped mRNA. In chemical cross-linking assays, cap-affinity chromatography, and cap-dependent translation assays, ribavirin was unable to function as a cap analog.
Molecular cloning and expression of a cDNA encoding endothelial cell nitric oxide synthase. (1992)

Endothelium-derived relaxing factor (EDRF), identified as nitric oxide (NO), is derived from a guanidino nitrogen of L-arginine via its metabolism by nitric oxide synthase (NOS). Herein, we report the molecular cloning of a cDNA encoding the constitutive calcium-calmodulin (Ca2+/CaM)-regulated nitric oxide synthase (ECNOS). A full-length ECNOS clone was isolated by screening a bovine aortic endothelial cell cDNA library using a fragment of rat brain NOS (bNOS) cDNA. This cDNA has an open reading frame of 3615 nucleotides encoding a 1205-amino acid protein. Membranes prepared from COS cells transfected with the ECNOS cDNA demonstrated NADPH- and Ca2+/CaM- dependent conversion of L-, but not D-, arginine to NO and citrulline that was inhibited by NG-nitro-L-arginine methyl ester. Comparison of the deduced amino acid sequence of ECNOS to the bNOS and macrophage NOS (Mac-NOS) sequences revealed 57 and 50% identity, respectively. In addition, ECNOS contains a unique N-myristylation consensus sequence (not shared by bNOS or Mac-NOS) that may explain its membrane localization.
Infection Barriers to Successful Xenotransplantation Focusing on Porcine Endogenous Retroviruses (2012)

Xenotransplantation may be a solution to overcome the shortage of organs for the treatment of patients with organ failure, but it may be associated with the transmission of porcine microorganisms and the development of xenozoonoses. Whereas most microorganisms may be eliminated by pathogen-free breeding of the donor animals, porcine endogenous retroviruses (PERVs) cannot be eliminated, since these are integrated into the genomes of all pigs. Human-tropic PERV-A and -B are present in all pigs and are able to infect human cells. Infection of ecotropic PERV-C is limited to pig cells. PERVs may adapt to host cells by varying the number of LTR-binding transcription factor binding sites. Like all retroviruses, they may induce tumors and/or immunodeficiencies. To date, all experimental, preclinical, and clinical xenotransplantations using pig cells, tissues, and organs have not shown transmission of PERV. Highly sensitive and specific methods have been developed to analyze the PERV status of donor pigs and to monitor recipients for PERV infection. Strategies have been developed to prevent PERV transmission, including selection of PERV-C-negative, low-producer pigs, generation of an effective vaccine, selection of effective antiretrovirals, and generation of animals transgenic for a PERV-specific short hairpin RNA inhibiting PERV expression by RNA interference.
Biosorption of phenolic compounds by the brown alga Sargassum muticum (2006)

Abstract Phenol, 2‐chlorophenol (2‐CP), and 4‐chlorophenol (4‐CP) biosorption on Sargassum muticum , an invasive macroalga in Europe, has been investigated. The efficiency of this biosorbent was studied measuring the equilibrium uptake using the batch technique. A chemical pre‐treatment with CaCl 2 has been employed in this study in order to improve the stability as well as the sorption capacity of the algal biomass. The influence of pH on the equilibrium binding and the effect of the algal dose were evaluated. The experimental data at pH = 1 have been analysed using Langmuir and Freundlich isotherms. It was found that the maximum sorption capacity of chlorophenols, q max = 251 mg g −1 for 4‐CP and q max = 79 mg g −1 for 2‐CP, as well as that of a binary mixture of both chlorophenols, q max = 108 mg g −1 , is much higher than that of phenol, q max = 4.6 mg g −1 . Moreover, sorption kinetics have been performed and it was observed that the equilibrium was reached in less than 10 h. Kinetic data have been fitted to the first order Lagergren model, from which the rate constant and the sorption capacity were determined. Finally, biosorption of the phenolic compounds examined in the present study on Sargassum muticum biomass was observed to be correlated with the octanol‐water partitioning coefficients of the phenols. This result allows us to postulate that hydrophobic interactions are the main responsible for the sorption equilibrium binding. Copyright © 2006 Society of Chemical Industry