gebhart/patrepeval huggingface dataset:
Activity of purified hepatitis C virus protease NS3 on peptide substrates (1996)

The protease domain of the hepatitis C virus (HCV) protein NS3 was expressed in Escherichia coli, purified to homogeneity, and shown to be active on peptides derived from the sequence of the NS4A-NS4B junction. Experiments were carried out to optimize protease activity. Buffer requirements included the presence of detergent, glycerol, and dithiothreitol, pH between 7.5 and 8.5, and low ionic strength. C- and N-terminal deletion experiments defined a peptide spanning from the P6 to the P4' residue as a suitable substrate. Cleavage kinetics were subsequently measured by using decamer P6-P4' peptides corresponding to all intermolecular cleavage sites of the HCV polyprotein. The following order of cleavage efficiency, in terms of kcat/Km, was determined: NS5A-NS5B > NS4A-NS4B >> NS4B-NS5A. A 14-mer peptide containing residues 21 to 34 of the protease cofactor NS4A (Pep4A 21-34), when added in stoichiometric amounts, was shown to increase cleavage rates of all peptides, the largest effect (100-fold) being observed on the hydrolysis of the NS4B-NS5A decamer. From the kinetic analysis of cleavage data, we conclude that (i) primary structure is an important determinant of the efficiency with which each site is cleaved during polyprotein processing, (ii) slow cleavage of the NS4B-NS5A site in the absence of NS4A is due to low binding affinity of the enzyme for this site, and (iii) formation of a 1:1 complex between the protease and Pep4A 21-34 is sufficient and required for maximum activation.
Online Blind Source Separation Using Incremental Nonnegative Matrix Factorization With Volume Constraint (2011)

Online blind source separation (BSS) is proposed to overcome the high computational cost problem, which limits the practical applications of traditional batch BSS algorithms. However, the existing online BSS methods are mainly used to separate independent or uncorrelated sources. Recently, nonnegative matrix factorization (NMF) shows great potential to separate the correlative sources, where some constraints are often imposed to overcome the non-uniqueness of the factorization. In this paper, an incremental NMF with volume constraint is derived and utilized for solving online BSS. The volume constraint to the mixing matrix enhances the identifiability of the sources, while the incremental learning mode reduces the computational cost. The proposed method takes advantage of the natural gradient based multiplication updating rule, and it performs especially well in the recovery of dependent sources. Simulations in BSS for dual-energy X-ray images, online encrypted speech signals, and high correlative face images show the validity of the proposed method.
Molecular cloning and characterization of a novel splicing variant of the Kir3.2 subunit predominantly expressed in mouse testis (1999)

1. One of the features of weaver mutant mice is male infertility, which suggests that Kir3.2, a G-protein-gated inwardly rectifying K+ channel subunit, may be involved in spermatogenesis. Therefore, we have characterized the Kir3.2 isoform in mouse testis using immunological, molecular biological and electrophysiological techniques. 2. Testicular membrane contained a protein that was recognized by the antibody specific to the C-terminus of Kir3.2c (aG2C-3). Its molecular mass was approximately 45 kDa, which was smaller than that of Kir3.2c ( approximately 48 kDa). The immunoprecipitant obtained from testis with aG2C-3 contained a single band of the 45 kDa protein, which could not be detected by the antibody to the N-terminus common to the known Kir3.2 isoforms (aG2N-2). 3. A novel alternative splicing variant of Kir3.2, designated Kir3.2d, was isolated from a mouse testis cDNA library. The cDNA had an open reading frame encoding 407 amino acids, whose molecular mass was calculated to be approximately 45 kDa. Kir3.2d was 18 amino acids shorter than Kir3.2c at its N-terminal end, which was the only difference between the two clones. The 18 amino acid region possesses the epitope for aG2N-2. 4. In heterologous expression systems of both Xenopus oocytes and mammalian cells (HEK 293T), Kir3.2d either alone or with Kir3.1 exhibited G-protein-gated inwardly rectifying K+ channel activity. 5. Prominent Kir3.2d immunoreactivity in the testis was detected exclusively in the acrosomal vesicles of spermatids, while Kir3.1 immunoreactivity was diffuse in the spermatogonia and spermatocytes. These results indicate the possibility that the testicular variant of Kir3.2, Kir3. 2d, may assemble to form a homomultimeric G-protein-gated K+ channel and be involved in the development of the acrosome during spermiogenesis.
A Role for Lipid Rafts in B Cell Antigen Receptor Signaling and Antigen Targeting (1999)

The B cell antigen receptor (BCR) serves both to initiate signal transduction cascades and to target antigen for processing and presentation by MHC class II molecules. How these two BCR functions are coordinated is not known. Recently, sphingolipid- and cholesterol-rich plasma membrane lipid microdomains, termed lipid rafts, have been identified and proposed to function as platforms for both receptor signaling and membrane trafficking. Here we show that upon cross-linking, the BCR rapidly translocates into ganglioside G(M1)-enriched lipid rafts that contain the Src family kinase Lyn and exclude the phosphatase CD45R. Both Igalpha and Lyn in the lipid rafts become phosphorylated, and subsequently the BCR and a portion of G(M1) are targeted to the class II peptide loading compartment. Entry into lipid rafts, however, is not sufficient for targeting to the antigen processing compartments, as a mutant surface Ig containing a deletion of the cytoplasmic domain is constitutively present in rafts but when cross-linked does not internalize to the antigen processing compartment. Taken together, these results provide evidence for a role for lipid rafts in the initial steps of BCR signaling and antigen targeting.
Recognition by Human V γ 9/V δ 2 T Cells of a GroEL Homolog on Daudi Burkitt's Lymphoma Cells (1990)

All human gamma delta T cells coexpressing the products of the variable (V) region T cell receptor (TCR) gene segments V gamma 9 and V delta 2 recognize antigens from mycobacterial extracts and Daudi cells. Exogenous and endogenous ligands on the cell surface, homologous to the groEL heat shock family, induced reactivities that resembled superantigen responses in this major subset of human peripheral blood gamma delta T cells. Stimulation of human V gamma 9/V delta 2 T cells is not restricted by human leukocyte antigens (HLA), including nonpolymorphic beta 2-microglobulin (beta 2M)-associated class Ib molecules. These data may be important for understanding the role of gamma delta T cells in autoimmunity and in responses to microorganisms and tumors.
Quantitative analysis of trophoblast invasion in preeclampsia (2003)

This study demonstrates restricted invasion of the trophoblastic cells in preeclampsia. This inadequate invasion may influence vascular remodeling required for delivering adequate volumes of maternal blood to the placenta.
Autophagy Defends Cells Against Invading Group A Streptococcus (2004)

We found that the autophagic machinery could effectively eliminate pathogenic group A Streptococcus (GAS) within nonphagocytic cells. After escaping from endosomes into the cytoplasm, GAS became enveloped by autophagosome-like compartments and were killed upon fusion of these compartments with lysosomes. In autophagy-deficient Atg5-/- cells, GAS survived, multiplied, and were released from the cells. Thus, the autophagic machinery can act as an innate defense system against invading pathogens.
Fluorescent Derivatization Method of Proteins for Characterization by Capillary Electrophoresis- Sodium Dodecyl Sulfate with Laser-Induced Fluorescence Detection (2007)

A fast and improved sample preparation scheme was developed for protein analysis using capillary electrophoresis-sodium dodecyl sulfate (CE-SDS) with laser-induced fluorescence detection. This CE-SDS method was developed as a purity assay for recombinant monoclonal antibodies (rMAbs). In this assay, rMAbs are derivatized with the fluorogenic reagent 3-(2-furoyl)-quinoline-2-carboxaldehyde (FQ) in the presence of a nucleophile (CN-), which fluoresces only upon covalent binding to the protein. Purification after labeling is therefore not necessary to remove unreacted reagents. Proteins are incubated at 75 degrees C for 5 min to facilitate denaturation and labeling. For nonreduced preparation, rMAbs are labeled at pH 6.5 with a dye-to-protein (D/P) molar ratio of 50:1, which forms conjugates having 6 +/- 4 FQ labels. For reduced preparation, rMAbs are labeled at pH 9.3 with a D/P molar ratio of 10:1, which generates light chain conjugates incorporated with 3 +/- 2 FQ labels. Labeling artifacts such as fragmentation or aggregation are absent with use of alkylation reagents. This efficient labeling scheme generates detection limits for FQ-labeled rMAbs as low as 10 ng/mL. In comparison to other labeling strategies, labeling proteins with FQ has the advantage of speed, ease of use, and robust quantification.
Artificial lantipeptides from in vitro translations (2011)

We have devised a protocol for enzyme-free insertion of dehydroalanine, dehydrobutyrine and thioether crosslinks into translated peptides. In vitro translation using 4-selenalysine and 4-selenoisoleucine as substitutes for lysine and isoleucine yields peptides that can be converted to polycyclic structures using mild chemistry in water. This methodology presents a gateway for exploring the potential of artificial lantipeptides as scaffolds for drug development.
Introns in histone genes alter the distribution of 3′ ends (1990)

Chimeric genes were constructed which contained either a histone or globin promoter, a human alpha-globin coding region as a cDNA or containing one or both intervening sequences, and the 3' end of a mouse histone H2a gene. The genes were introduced into mouse L cells or Chinese Hamster Ovary cells. The genes containing at least one intervening sequence produced two mRNAs in about equal amounts, one which ended at a cryptic polyadenylation site 33 nucleotides 3' to the normal histone mRNA 3' end and one which ended at the normal histone 3' end. In contrast, the same construct containing a globin cDNA yielded mRNA ending only at the correct histone 3' end. Similar proportions of polyadenylated and non-polyadenylated mRNA were obtained when the cryptic polyadenylation signal was replaced with the globin polyadenylation signal. More than 90% of the transcripts were accurately spliced. All of the unspliced transcripts had histone 3' ends.
Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. (1995)

The CCAAT-binding factor is a conserved heteromeric transcription factor that binds to CCAAT box-containing upstream activation sites (UASs) within the promoters of numerous eukaryotic genes. The CCAAT-binding factor of Saccharomyces cerevisiae activates the transcription of these genes in response to growth in a nonfermentable carbon source. Previous studies have demonstrated that the HAP2, HAP3, and HAP4 subunits of the yeast CCAAT-binding factor are required for the transcriptional activation of genes containing a CCAAT box. Using the two-hybrid screening method, we have identified an additional component of the CCAAT-binding factor. We present the identification and characterization of a novel gene, HAP5, that encodes an additional subunit of the CCAAT-binding factor required for the assembly and DNA-binding activity of the complex. In a hap5 mutant, we show that CCAAT-binding activity is abolished in vitro. Furthermore, we demonstrate that purified recombinant HAP2, HAP3, and HAP5 are able to reconstitute CCAAT-binding activity in mobility shift analysis. These data suggest that the HAP2/3/5 heterotrimer represents a unique DNA-binding factor in which all three subunits of the complex are absolutely required for DNA-binding activity.
Synthesis and reaction of 5‐amino‐3‐trifluoromethylisoxazole and ‐pyrazole‐4‐carboxylic acids (1986)

Abstract 5‐Amino‐3‐trifluoromethylisoxazole‐ and ‐pyrazole‐4‐carboxylic acids were prepared by the reactions ot trifluoroacetonitrile oxide or ‐imines with cyanoacetic acid derivatives, respectively. The behavior of thus obtained aminoazole‐4‐carboxylic acids toward some electrophiles was examined. In acylation with acyl chlorides, the aminoisoxazole‐4‐carboxylate 2a was diacylated to give the (diacylamino)isoxazole‐4‐carboxylate 7 , whereas the analogous aminopyrazole 5a produced the cyclized pyrazolooxazinone 13 . Moreover, carbamoylation of 2a with isocyanates gave the trifluoromethylisoxazolouracils 10 .
Repression of Wnt/β-catenin signaling in the anterior endoderm is essential for liver and pancreas development (2007)

The liver and pancreas are specified from the foregut endoderm through an interaction with the adjacent mesoderm. However, the earlier molecular mechanisms that establish the foregut precursors are largely unknown. In this study, we have identified a molecular pathway linking gastrula-stage endoderm patterning to organ specification. We show that in gastrula and early-somite stage Xenopus embryos, Wnt/beta-catenin activity must be repressed in the anterior endoderm to maintain foregut identity and to allow liver and pancreas development. By contrast, high beta-catenin activity in the posterior endoderm inhibits foregut fate while promoting intestinal development. Experimentally repressing beta-catenin activity in the posterior endoderm was sufficient to induce ectopic organ buds that express early liver and pancreas markers. beta-catenin acts in part by inhibiting expression of the homeobox gene hhex, which is one of the earliest foregut markers and is essential for liver and pancreas development. Promoter analysis indicates that beta-catenin represses hhex transcription indirectly via the homeodomain repressor Vent2. Later in development, beta-catenin activity has the opposite effect and enhances liver development. These results illustrate that turning Wnt signaling off and on in the correct temporal sequence is essential for organ formation, a finding that might directly impact efforts to differentiate liver and pancreas tissue from stem cells.
ANDROID A PROGRAMMERS GUIDE (2008)

Master the Android mobile development platform

Build compelling Java-based mobile applications using the Android SDK and the Eclipse open-source software development platform. Android: A Programmer's Guide shows you, step-by-step, how to download and set up all of the necessary tools, build and tune dynamic Android programs, and debug your results. Discover how to provide web and chat functions, interact with the phone dialer and GPS devices, and access the latest Google services. You'll also learn how to create custom Content Providers and database-enable your applications using SQLite.

Install and configure Java, Eclipse, and Android plugin
Create Android projects from the Eclipse UI or command line
Integrate web content, images, galleries, and sounds
Deploy menus, progress bars, and auto-complete functions
Trigger actions using Android Intents, Filters, and Receivers
Implement GPS, Google Maps, Google Earth, and GTalk 
Build interactive SQLite databases, calendars, and notepads
Test applications using the Android Emulator and Debug Bridge


Table of contents

Ch 1. What is Android
Ch 2. Downloading and setting up Eclipse
Ch 3. Downloading the Google Android SDK and Eclipse Plugin
Ch 4. Exploring the Google Android SDK 
Ch 5. Application: Hello World!
Ch 6. Using the Google Android Emulator 
Ch 7. Reacting to phone events
Ch 8. Calling the GPS
Ch 9. Application: Note Block
Ch 10. Buttons, Lists, and other Objects
Ch 11. Application: Caller Info
Ch 12. Application: Find Me
Ch 13. Interacting with other Google Services
Ch 14. Troubleshooting and Errors
Single-Site β-Diiminate Zinc Catalysts for the Alternating Copolymerization of CO2 and Epoxides:  Catalyst Synthesis and Unprecedented Polymerization Activity (2001)

Synthetic routes to zinc beta-diiminate complexes are reported. The synthesis of 11 beta-diimine [(BDI)-H] ligands, with varying N-aryl substituents and bridging structures, is described. These ligands are converted to (BDI)ZnX complexes (X = OAc, Et, N(SiMe3)2, Br, Cl, OH, OMe, O(i)Pr). X-ray structural data revealed that all zinc complexes examined exist as micro-X-bridged dimers in the solid state, with the exception of the zinc ethyl and amido complexes which were monomeric. Complexes of the form (BDI)ZnOR (R = alkyl, acyl) and (BDI)ZnN(SiMe3)2 are highly active catalysts for the alternating copolymerization of epoxides and CO2. Copolymerizations of cyclohexene oxide (CHO) and CO2 with (BDI-1)ZnX [(BDI-1) = 2-((2,6-diisopropylphenyl)amido)-4-((2,6-diisopropylphenyl)imino)-2-pentene)] and (BDI-2)ZnX [(BDI-2) = 2-((2,6-diethylphenyl)amido)-4-((2,6-diethylphenyl)imino)-2-pentene)], where X = OAc, Et, N(SiMe3)2, Br, Cl, OH, OMe, O(i)Pr, were attempted at 50 degrees C and 100 psi CO2. Complexes with X = OAc, N(SiMe3)2, OMe, O(i)Pr all produced polycarbonate by the alternated insertion of CHO and CO2 with similar catalytic activities, comparable molecular weights, and narrow molecular weight distributions (MWD approximately 1.1), indicating the copolymerizations are living. Furthermore, ligand effects were shown to dramatically influence the polymerization activity as minor steric changes accelerated or terminated the polymerization activity.
Hypertension Due to 17α‐Hydroxylase Deficiency (1978)

A female patient with hypertension, hypogonadism and hypokalaemia due to 17alpha-hydroxylase deficiency is described, in whom the diagnosis was initially based on the finding of low urinary 17-ketosteroids and 17-hydroxycorticosteroids, in the presence of high plasma fluorometric 11-hydroxycorticoids. Later studies confirmed the diagnosis by demonstrating low circulating levels of 17alpha-hydroxyprogesterone and the steroids derived from this precursor: 11-deoxycortisol, cortisol, oestradiol and testosterone. Plasma progesterone, corticosterone and deoxycorticosterone (DOC) were greatly increased, but plasma and urine aldosterone were very low. The initial subnormal cortisol and 11-deoxycortisol levels responded to tetracosactrin administration, suggesting that the adrenal was not maximally stimulated by endogenous ACTH and indicating that the 17alpha-hydroxylase deficiency was incomplete. Plasma and urinary aldosterone levels were still suppressed after 12 months treatment with prednisone despite normalization of the previously suppressed renin levels. The findings indicate that this uncommon cause of medically-controllable juvenile hypertension can be identified without specific steroid assays.
Self-Coherent OFDM With Undersampling Downconversion for Wireless Communications (2016)

In this paper, we introduce self-coherent orthogonal frequency-division multiplexing (OFDM), a well-known non-coherent technique in optical communications, for wireless radio frequency communications. Self-coherent OFDM provides complete immunity against phase noise (PN) using a non-coherent receiver and a significantly higher spectral efficiency than self-heterodyne (self-het) OFDM, which utilizes at most 50% of the available spectrum for communications. We present the performance analysis of self-coherent OFDM over additive white Gaussian noise and frequency selective fading channels, and show by simulations that self-coherent OFDM provides both higher spectral efficiency and better bit error rate performance than self-het OFDM. Considering that filter realization in high-frequency bands is challenging, we adopt the undersampling downconversion technique in conjunction with self-coherent OFDM. We show that with the self-coherent demodulation, the additional PN introduced by undersampling downconversion can be significantly reduced. We compare analytically the system performance of self-coherent OFDM using undersampling downconversion with two other conventional OFDM systems: one with super-heterodyne receiver and the other with undersampling downconversion. We show theoretically and by simulations that both in AWGN and frequency selective fading channels, self-coherent OFDM with undersampling downconversion outperforms the two conventional OFDM systems even when intercarrier interference compensation schemes are applied.
Photonic nanojet enhancement of backscattering of light by nanoparticles: a potential novel visible-light ultramicroscopy technique (2004)

We report what we believe to be the first evidence of localized nanoscale photonic jets generated at the shadow-side surfaces of micronscale, circular dielectric cylinders illuminated by a plane wave. These photonic nanojets have waists smaller than the diffraction limit and propagate over several optical wavelengths without significant diffraction. We have found that such nanojets can enhance the backscattering of visible light by nanometer-scale dielectric particles located within the nanojets by several orders of magnitude. Not involving evanescent fields and not requiring mechanical scanning, photonic nanojets may provide a new means to detect and image nanoparticles of size well below the diffraction limit. This could yield a potential novel ultramicroscopy technique using visible light for detecting proteins, viral particles, and even single molecules; and monitoring molecular synthesis and aggregation processes of importance in many areas of biology, chemistry, material sciences, and tissue engineering.
Organic–Inorganic Perovskites: Structural Versatility for Functional Materials Design (2016)

Although known since the late 19th century, organic-inorganic perovskites have recently received extraordinary research community attention because of their unique physical properties, which make them promising candidates for application in photovoltaic (PV) and related optoelectronic devices. This review will explore beyond the current focus on three-dimensional (3-D) lead(II) halide perovskites, to highlight the great chemical flexibility and outstanding potential of the broader class of 3-D and lower dimensional organic-based perovskite family for electronic, optical, and energy-based applications as well as fundamental research. The concept of a multifunctional organic-inorganic hybrid, in which the organic and inorganic structural components provide intentional, unique, and hopefully synergistic features to the compound, represents an important contemporary target.
Studies on the Synthesis of Tedanolide:  Synthesis of the C(5)−C(21) Segment via a Highly Stereoselective Fragment Assembly Aldol Reaction of a Chiral β,γ-Unsaturated Methyl Ketone (1999)

[formula: see text] A highly diastereoselective synthesis of 3, corresponding to the C(5)-C(21) segment of tedanolide, has been accomplished by a route utilizing the aldol reaction of aldehyde 4 and the beta,gamma-unsaturated methyl ketone 5.