gebhart/patrepeval huggingface dataset:
Alternate Translation Occurs within the Core Coding Region of the Hepatitis C Viral Genome (2002)

The majority of hepatitis C virus (HCV) isolates contain an open reading frame (ORF) overlapping with the core coding sequences in the +1 frame, which was assumed to be untranslated. We present evidence supporting the expression of this ORF (designated core+1 ORF) via novel translation mechanisms. First, fusion of the luciferase gene with the HCV-1 core+1 ORF followed by in vitro translation resulted in the synthesis of a chimeric protein (core+1-luciferase) that exhibited approximately 54% luciferase activity relative to the positive control (core-luciferase). Second, antisera raised against two different synthetic core+1 peptides recognized the previously identified p16 (but not p21) core protein band expressed from HCV-1, indicating the presence of epitopes from the core+1 ORF within the p16 protein. Third, HCV-positive sera specifically recognized lysates of Escherichia coli cells expressing recombinant core+1 protein, suggesting the presence of anti-core+1 antibodies in HCV-infected patients. Finally, luciferase tagging experiments designed to assess for -1 frameshifting combined with site-directed mutagenesis experiments supported the presence of +1/-1 ribosomal frameshift translation mechanisms within the core coding region. In conclusion, our data provide evidence for novel translation mechanisms within the core coding region and demonstrate the expression of the core+1 ORF, at least for some HCV isolates.
Uroplakin I: a 27-kD protein associated with the asymmetric unit membrane of mammalian urothelium. (1990)

The luminal surface of mammalian urothelium is covered with numerous plaques (also known as the asymmetric unit membrane or AUM) composed of semi-crystalline, hexagonal arrays of 12-nm protein particles. Despite the presumed importance of these plaques in stabilizing the urothelial surface during bladder distention, relatively little is known about their protein composition. Using a mouse mAb, AE31, we have identified a 27-kD protein that is urothelium-specific and is differentially expressed in superficial umbrella cells. This protein (pI approximately 5.8) partitions into the detergent phase during Triton X-114 phase separation. Pulse-chase experiments using cultured bovine urothelial cells showed that this protein is synthesized as a 32-kD precursor that is processed through a 30-kD intermediate, to the mature 27-kD form. In cytoplasmic vesicles containing immature AUM, the AE31 epitope is detected in patches on the cytoplasmic side, but in mature, apical AUM it is detected exclusively on the luminal side. This suggests an unusual translocation of the AE31 epitope during AUM maturation; more data are required, however, to substantiate this interpretation. Immunoaffinity purification of the 27-kD protein results in the copurification in approximately molar ratio of a 15-kD protein, as well as a small and variable amount of a 47-kD protein. Immunoblotting data indicate that these three proteins are immunologically distinguishable. This copurified 15-kD protein is relative basic (pI approximately 8.0). Like the 27-kD protein, it is urothelium-specific and is present mainly in the umbrella cells. Together, our data indicate that a 27-kD protein is urothelial plaque-associated (uroplakin I). Based on complex formation data, we provisionally name the 15-kD protein uroplakin II; additional data will be required to determine whether this and the 47-kD protein are integral parts of AUM. The identification of these AUM-associated and -related proteins, plus the availability of a culture system capable of synthesizing and processing some of these molecules, offer new opportunities for studying the detailed structure, assembly, and function of asymmetrical unit membrane.
Apolipoprotein E gene and Alzheimer's disease: is tau the link? (2001)

The finding that APOE (the gene encoding apolipoprotein E) polymorphic variation was associated with an altered risk of developing Alzheimer's disease (AD) was a significant advance and immediately prompted a search for the mechanisms responsible for this alteration. Some 6 years later, a number of different hypotheses remain that might account for this influence on pathogenesis with no single mechanism being unequivocally accepted. The different approaches to understanding these mechanisms can be broadly categorized as: those suggesting a remote effect, such as different rates of vascular risk factors in those with the different APOE alleles; those proposing altered neuronal vulnerability, perhaps due to apolipoprotein E (ApoE)-isoform-specific differences in local cholesterol transport; and those hypotheses postulating an ApoE interaction with the two key lesions of AD, plaques and tangles. In this chapter we will review the evidence for and against an interaction between ApoE and the neuronal cytoskeleton, in particular with the microtubule-associated protein tau.
Empirical proof of the empirical line (2007)

Calibrating remotely sensed data to reflectance maximizes their quantitative utility. Many approaches exist for calibrating to reflectance (ρ), one of which is the empirical line (EL) method. It offers high‐quality results, often to within a few per cent, but is demanding in terms of field work and analysis. The method assumes there is a linear relationship between raw digital numbers (DNs) (or radiance) and reflectance spectra of ground targets. While the EL technique is widely accepted, we have not found an exhaustive demonstration that there is a truly linear relationship between radiance/DN and reflectance factors. In this paper we present an empirical demonstration of the EL method using a data set that consists of 5304 ground spectra paired with Landsat Thematic Mapper (TM) pixels.
A Low-Complexity Screen Compression Scheme for Interactive Screen Sharing (2013)

Interactive screen sharing requires extremely low latency end-to-end transmission, which in turn requires highly efficient and low-complexity screen compression. In this paper, we present a block-based low-complexity screen compression scheme, in which multiple block modes are adopted to exploit the intra- and inter-frame redundancies. In particular, we classify the intra-coded blocks to pictorial blocks and textual blocks using a proposed fast block classification algorithm, which exploits the discriminative features between the pictorial and the textual blocks. Then, we design a low-complexity, yet efficient, algorithm to compress the textual blocks. We use base colors and escape colors to represent and quantize the textual pixels, which not only achieves high compression ratios but also preserves a high quality on textual pixels. The two-dimensionally predictive index coding and hierarchical pattern coding technologies are used to exploit local spatial correlations and global pattern correlation, respectively. To further utilize the correlation between the luminance and chrominance channels, we propose a joint-channel index coding method. We compare the coding efficiency and the computational complexity of the proposed scheme against the standard image coding schemes such as JPEG, JPEG2000, and PNG, the compound image compressor HJPC, and the popular video coding standard H.264. We also compare the visual quality of the proposed scheme against H.264 intra coding, JPEG2000, and HJPC. The evaluation results show that the proposed scheme achieves superior or comparable compression efficiency with much lower complexity than other schemes in most of the cases.
The Efficacy and Tolerability of Inhaled Montelukast Plus Inhaled Mometasone Compared with Mometasone Alone in Patients with Chronic Asthma (2011)

Inhaled montelukast plus inhaled mometasone was significantly more effective than placebo plus inhaled mometasone in improving FEV(1), symptoms, asthma control, and blood eosinophil count.
Disulfide Bond Structure of the AVR9 Elicitor of the Fungal Tomato PathogenCladosporium fulvum:  Evidence for a Cystine Knot (2001)

Disease resistance in plants is commonly activated by the product of an avirulence (Avr) gene of a pathogen after interaction with the product of a matching resistance (R) gene in the host. In susceptible plants, Avr products might function as virulence or pathogenicity factors. The AVR9 elicitor from the fungus Cladosporium fulvum induces defense responses in tomato plants carrying the Cf-9 resistance gene. This 28-residue beta-sheet AVR9 peptide contains three disulfide bridges, which were identified in this study as Cys2-Cys16, Cys6-Cys19, and Cys12-Cys26. For this purpose, AVR9 was partially reduced, and the thiol groups of newly formed cysteines were modified to prevent reactions with disulfides. After HPLC purification, the partially reduced peptides were sequenced to determine the positions of the modified cysteines, which originated from the reduced disulfide bridge(s). All steps involving molecules with free thiol groups were performed at low pH to suppress disulfide scrambling. For that reason, cysteine modification by N-ethylmaleimide was preferred over modification by iodoacetamide. Upon (partial) reduction of native AVR9, the Cys2-Cys16 bridge opened selectively. The resulting molecule was further reduced to two one-bridge intermediates, which were subsequently completely reduced. The (partially) reduced cysteine-modified AVR9 species showed little or no necrosis-inducing activity, demonstrating the importance of the disulfide bridges for biological activity. Based on peptide length and cysteine spacing, it was previously suggested that AVR9 isa cystine-knotted peptide. Now, we have proven that the bridging pattern of AVR9 is indeed identical to that of cystine-knotted peptides. Moreover, NMR data obtained for AVR9 show that it is structurally closely related to the cystine-knotted carboxypeptidase inhibitor. However, AVR9 does not show any carboxypeptidase inhibiting activity, indicating that the cystine-knot fold is a commonly occurring motif with varying biological functions.
Application of olefin metathesis in oleochemistry: an example of green chemistry (2002)

The metathesis of natural oils and fats and their derivatives is a clean catalytic reaction that can be considered as an example of green chemistry. Using this reaction, oleochemical feedstocks can be converted into valuable chemical products, directly or in only a few reaction steps. With the development of catalysts that are active and highly selective under mild reaction conditions, there are favourable perspectives for the application of the metathesis reaction in the oleochemical industry.
The effect of morphine on formalin‐evoked behaviour and spinal release of excitatory amino acids and prostaglandin E2 using microdialysis in conscious rats (1995)

1. In the present study, the object was to examine the effects of morphine on spinal release in vivo of excitatory amino acids (EAA), prostaglandin E2 (PGE2), and a marker for nitric oxide (NO) synthesis, citrulline (Cit), evoked by a protracted noxious stimulus produced by the injection of formalin into the paw. Spinal release was monitored in conscious rats using a microdialysis probe implanted into the subarachnoid space with the active site placed at the level of the lumbar enlargement. In split dialysate samples. EAAs were measured by high performance liquid chromatography (h.p.l.c.) and PGE2 was determined by radioimmunoassay. 2. Resting concentrations in nmol ml-1 for the amino acids (mean +/- s.e.mean, n = 21) were: 4.8 +/- 0.4 for glutamate (Glu), 0.8 +/- 0.1 for aspartate (Asp), 8.8 +/- 0.8 for taurine (Tau), 24 +/- 3 for glycine (Gly), 19 +/- 3 for serine (Ser), 5.2 +/- 0.8 for asparagine (Asn), 64 +/- 4 for glutamine (Gln) and 5.2 +/- 0.4 for Cit. Mean basal release for PGE2 was 12 +/- 1 pmol ml-1. 3. Subcutaneous (s.c.) injection of 5% formalin evoked a biphasic flinching behaviour (phase 1: 0-9 min and phase 2: 10-60 min) of the injected paw. Corresponding to phase 1 behaviour, there was a significant increase (50-100%) in spinal levels of Glu, Asp, Tau, Gly, Cit and PGE2, but not Ser, Asn and Gln. A significant (P < 0.01) second phase increase in release was observed only for Cit and PGE2. However, Glu and Asp levels were increased by approximately 45%. 4. Injection of morphine sulphate (3 mg kg-1, s.c.) had no effect on resting release, but produced a significant suppression of the formalin-evoked behaviour and release of Glu, Asp, Tau, Gly, Cit and PGE2. The effect of morphine was reversed by pretreatment with 1 mg kg-1 naloxone. Naloxone by itself did not change the release or behaviour of the formalin test.5. This study demonstrates that both spinal EAA and PGE2 release patterns correlate with behavioural nociceptive responses in the formalin test and that morphine suppresses the formalin-evoked behaviours and spinal release. The reversal by naloxone of the morphine effect indicates mediation via an opioid receptor.
Nuclear Fusion by Inertial Confinement: A Comprehensive Treatise (1992)

An Introduction to Nuclear Fusion by Inertial Confinement (J.M. Martinez-Val, G. Velarde, and Y. Ronen). The Physics of Directly Driven Targets (S. Eliezer and H. Hora). Laser-Target Interaction: Laser Energy Absorption and Nonlinear Plasma Phenomena (V. Yu. Bychenkov and V.T. Tikhonchuk). Energy Transfer to the Plasma in Laser Targets (Yu.V. Afanasiev and S.Yu.Gus'kov). Ion Beam-Target Interaction (Z. Zinamon). Atomic Physics in Dense Plasma (R.M. More). Electron Heat Conduction in ICF Targets (J.R. Sanmartin). Radiation Transport in ICF Targets (E. Minguez). Charged Particle Transport (J.J. Honrubia). ICF Neutronics (M. Piera and J.M. Martinez-Val). The Compression Phase in ICF Targets (T. Yabe). Ignition and Burn Propagation in ICF Targets (S. Gus'kov and V. Rozanov). Hydrodynamic Instability of Target Implosion in ICF (E.G. Gamaly). Solid State Lasers (J.M. Soures). Excimer Lasers (L. Rosocha, S.J. Czuchlewski, B.J. Krohn, and J. McLeod). Free Electron Lasers for ICF (W.B. Colson, J. Blau, D. Craun, D. Gillingham, D. Kiel, J.H. Park, and R. Souza). Heavy Ion Accelerators for ICF (R.W. Muller). Light-Ion Accelerators for ICF (J.P. VanDevender and H.-J. Bluhm). Magnetically Imploded Plasma as a Driver for ICF (J.G. Linhart). Diagnostics of Laser-Imploded Plasma (C. Yamanaka). Target Fabrication (Y. Izawa and T. Norimatsu). Laser-Driven ICF Experiments (R.L. McCrory, Jr.). Particle Beam-Driven ICF Experiments (H.U. Karow and J.P. VanDevender). Irradiation Effects and Activation in Structural Materials (J.M. Perlado and J. Sanz). ICF Reactors-Conceptual Design Studies (G. Kessler, G.L. Kulcinski, and R.R. Peterson). Appendix: Units and Physical Constants. Index.
Primary effusion lymphoma: a distinct clinicopathologic entity associated with the Kaposi's sarcoma-associated herpes virus (1996)

We recently discovered the Kaposi's sarcoma-associated herpes virus (KSHV/HHV-8) in an uncommon and unusual subset of AIDS-related lymphomas that grow mainly in the body cavities as lymphomatous effusions without an identifiable contiguous tumor mass. The consistent presence of KSHV and certain other distinctive features of these body cavity-based lymphomas suggest that they represent a distinct entity. We tested this hypothesis by investigating 19 malignant lymphomatous effusions occurring in the absence of a contiguous tumor mass for their clinical, morphologic, immunophenotypic, viral, and molecular characteristics, KSHV was present in 15 of 19 lymphomas. All four KSHV-negative lymphomatous effusions exhibited Burkitt or Burkitt-like morphology and c-myc gene rearrangements and, therefore, appeared to be Burkitt-type lymphomas occurring in the body cavities. In contrast, all 15 KSHV-positive lymphomatous effusions exhibited a distinctive morphology bridging large-cell immunoblastic lymphoma and anaplastic large-cell lymphoma, and all 12 cases studied lacked c-myc gene rearrangements. In addition, these lymphomas occurred in men (15/15), frequently but not exclusively in association with HIV infection (13/15), in which homosexuality was a risk factor (13/13), presented initially as a lymphomatous effusion (14/15), remained localized to the body cavity of origin (13/15), expressed CD45 (15/15) and one or more activation-associated antigens (9/10) in the frequent absence of B-cell-associated antigens (11/15), exhibited clonal immunoglobulin gene rearrangements (13/13), contained Epstein-Barr virus (14/15), and lacked bcl-2, bcl-6, ras and p53 gene alterations (13/15). These findings strongly suggest that the KSHV-positive malignant lymphomatous effusions represent a distinct clinicopathologic and biologic entity and should be distinguished from other malignant lymphomas occurring in the body cavities. Therefore, we recommend that these malignant lymphomas be designated primary effusion lymphomas (PEL), rather than body cavity-based lymphomas, since this term describes them more accurately and avoids their confusion with other malignant lymphomas that occur in the body cavities. We further recommend that these PEL be considered for inclusion as a new entity in the Revised European-American Lymphoma Classification.
Differentiation-dependent expression of phosphatidylserine in mammalian plasma membranes: quantitative assessment of outer-leaflet lipid by prothrombinase complex formation. (1989)

Phosphatidylserine (PS) is asymmetrically distributed in mammalian cell membranes, being preferentially localized in the inner leaflet. Some studies have suggested that a disturbance in the normal asymmetric distribution of PS--e.g., PS exposure in the outer leaflet of the cell membrane, which can occur upon platelet activation as well as in certain pathologic red cells--serves as a potent procoagulant surface and as a signal for triggering their recognition by macrophages. These studies suggest that the regulation of PS distribution in cell membranes may be critical in controlling coagulation and in determining the survival of pathologic cells in the circulation. In this paper we describe a sensitive technique, based on PS-dependent prothrombinase complex activity, for assessing the amount of PS on the external leaflet of intact viable cells. Our results indicate that tumorigenic, undifferentiated murine erythroleukemic cells express 7- to 8-fold more PS in their outer leaflet than do their differentiated, nontumorigenic counterparts. Increased expression of PS in the tumorigenic cells directly correlated with their ability to be recognized and bound by macrophages.
Layered tunnel barriers for nonvolatile memory devices (1998)

Fowler–Nordheim tunneling of electrons through “crested” energy barriers (with the height peak in the middle) is much more sensitive to applied voltage than that through barriers of uniform height. Calculations for trilayer barriers, with layer parameters typical for wide-band-gap semiconductors, have shown that by merely doubling the voltage, the tunnel current may be changed by more than 16 orders of magnitude. It is argued that this effect may be used for the implementation of nonvolatile random-access memories combining a few ns cycle time with a few years retention time and for ultradense electrostatic data storage.
Tumor-infiltrating BRAFV600E-specific CD4+ T cells correlated with complete clinical response in melanoma (2018)

T cells specific for neoantigens encoded by mutated genes in cancers are increasingly recognized as mediators of tumor destruction after immune checkpoint inhibitor therapy or adoptive cell transfer. Unfortunately, most neoantigens result from random mutations and are patient specific, and some cancers contain few mutations to serve as potential antigens. We describe a patient with stage IV acral melanoma who achieved a complete response following adoptive transfer of tumor-infiltrating lymphocytes (TILs). Tumor exome sequencing surprisingly revealed fewer than 30 nonsynonymous somatic mutations, including oncogenic BRAFV600E. Analysis of the specificity of TILs identified rare CD4+ T cells specific for BRAFV600E and diverse CD8+ T cells reactive to nonmutated self-antigens. These specificities increased in blood after TIL transfer and persisted long-term, suggesting they contributed to the effective antitumor immune response. Gene transfer of the BRAFV600E-specific T cell receptor (TCR) conferred recognition of class II MHC-positive cells expressing the BRAF mutation. Therapy with TCR-engineered BRAFV600E-specific CD4+ T cells may have direct antitumor effects and augment CD8+ T cell responses to self- and/or mutated tumor antigens in patients with BRAF-mutated cancers.
Mathematically Modeling Fetal Electrocardiograms (2014)

Some of the most common and fatal birth defects are those related to the heart. In adults, possible heart conditions are often identified through the use of an electrocardiogram (ECG). However, due to the presence of other signals and noise in the recording, fetal electrocardiography has not yet proven effective in diagnosing these defects. This paper develops a mathematical model of three-dimensional heart vector trajectories, which was used to generate synthetic maternal and fetal ECG signals. The dipole model is a useful simplification in which the electrical activity of the heart is viewed as a single time-varying vector originating at the center of the body. A system of ordinary differential equations whose numerical solution approximates this cardiac dipole vector was used. To simulate the cardiac activity of both mother and fetus, two sets of these equations must be implemented. When implementing this model, various physiological factors must be accounted for. After realistic maternal and fetal dipole vectors have been simulated, they are projected onto random unit vectors representing the lead axes of the fECG. Noise is then added to the signal. Using this model a database of realistic, synthetic fECG signals with different parameter values and noise levels has been built. Currently algorithms to extract the fetal signal from the fECG are tested on a database of clinical recordings. Our synthetic database will allow for algorithms to be tested on a broader set of data.
SO-Net: Self-Organizing Network for Point Cloud Analysis (2018)

This paper presents SO-Net, a permutation invariant architecture for deep learning with orderless point clouds. The SO-Net models the spatial distribution of point cloud by building a Self-Organizing Map (SOM). Based on the SOM, SO-Net performs hierarchical feature extraction on individual points and SOM nodes, and ultimately represents the input point cloud by a single feature vector. The receptive field of the network can be systematically adjusted by conducting point-to-node k nearest neighbor search. In recognition tasks such as point cloud reconstruction, classification, object part segmentation and shape retrieval, our proposed network demonstrates performance that is similar with or better than state-of-the-art approaches. In addition, the training speed is significantly faster than existing point cloud recognition networks because of the parallelizability and simplicity of the proposed architecture. Our code is available at the project website. https://github.com/lijx10/SO-Net
Neocortical Neural Sprouting, Synaptogenesis, and Behavioral Recovery After Neocortical Infarction in Rats (1995)

These data support the occurrence of neurite growth followed by synaptogenesis in the neocortex, ipsilateral and contralateral to neocortical ischemia, in a pattern that corresponds both spatially and temporally with behavioral recovery. Thus, neuroanatomical remodeling in the neocortex provides a mechanism for recovery of function.