gebhart/patrepeval huggingface dataset:
Oxygen Consumption, Ammonia-N Excretion, and Growth Rate in Juvenile Green-Neon Shrimp (Neocaridina denticulata) Exposed to Chlordane and Lindane (2004)

The purpose of this study was to investigate the chronic toxicity of chlordane and lindane as well as their sublethal concentration effects on green-neon shrimp (Neocaridina denticulata), a common habitant of freshwater systems of eastern Asia and Hawaii. In this study, the effects of experimental concentrations of 1 and 10 ng/L of chlordane and 0.1 and 1 μg/L of lindane on the growth rate, the duration of the molt cycle, oxygen consumption (QO2), ammonia-N excretion (ENH4(superscript +)), and the O:N ratio were examined. Results indicated that growth rates of the were lower than those of the control group, and the molt cycle duration times had also been altered. In all treatments, we also observed that QO2 increased in the first few days, then it gradually returned to normal during the latter part of the experiment from days 14 to 28. Furthermore, a decrease in ENH4(superscript +) and an increase in the O:N ratio were observed in chlordane-treated groups, while lindane showed significantly increased ENH4(superscript +) and a decreased O:N ratio compared to the control. Accordingly, the results of this study demonstrate that lower concentrations of both chlordane and lindane toxicity to N. denticulate, even though their effects varied.
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model (2017)

http://raptorx.uchicago.edu/ContactMap/.
Construction and expression of a bispecific single-chain antibody that penetrates mutant p53 colon cancer cells and binds p53. (2004)

A bispecific, single-chain antibody Fv fragment (Bs-scFv) was constructed from a single-chain Fv fragment of mAb 3E10 that penetrates living cells and localizes in the nucleus, and a single-chain Fv fragment of a non-penetrating antibody, mAb PAb421 that binds the C-terminal of p53. PAb421 binding restores wild-type functions of some p53 mutants, including those of SW480 human colon cancer cells. The Bs-scFv penetrated SW480 cells and was cytotoxic, suggesting an ability to restore activity to mutant p53. COS-7 cells (monkey kidney cells with wild-type p53) served as a control since they are unresponsive to PAb421 due to the presence of SV40 large T antigen that inhibits binding of PAb421 to p53. Bs-scFv penetrated COS-7 cells but was not cytotoxic, thereby eliminating non-specific toxicity of Bs-scFv unrelated to binding p53. A single mutation in CDR1 of PAb421 VH eliminated binding of the Bs-scFv to p53 and abrogated cytotoxicity for SW480 cells without altering cellular penetration, further supporting the requirement of PAb421 binding to p53 for cytotoxicity. Our study demonstrates the use of an antibody that penetrates living cells in the design of a bispecific single chain antibody to target and restore the function of an intracellular protein.
Controlling the Permeability of Multilayered Polyelectrolyte Films through Derivatization, Cross-Linking, and Hydrolysis (2001)

Partial Fischer esterification of poly(acrylic acid) allows tailoring of the hydrophobicity and charge density of multilayered films containing poly(allylamine hydrochloride) (PAH) and derivatized poly(acrylic acid) (d-PAA). As hydrophobicity and charge density strongly affect film permeability, control over these properties is vital for possible applications of PAH/d-PAA films as ion-separation membranes and sensors. The hydrophobicity of these films depends on both the extent of esterification and the nature of the derivatizing alcohol. Even though PAH/d-PAA films are composed of polyelectrolytes, the presence of hydrophobic ester groups results in advancing water contact angles as high as 101°. The hydrophobicity of these coatings allows them to effectively passivate underlying electrodes as shown by minimal peak currents in cyclic voltammograms (CVs) of Ru(NH3)63+ and Fe(CN)63-. Cross-linking of hydrophobic PAH/d-PAA films via heat-induced amidation stabilizes coatings over a wide pH range but does not significantly decrease the already low film permeability to Ru(NH3)63+ and Fe(CN)63-. Stabilization due to cross-linking does, however, allow base-promoted hydrolysis of the ester groups of PAH/d-PAA coatings. After hydrolysis, films are extremely hydrophilic and selectively permeable to Ru(NH3)63+ over Fe(CN)63- due to the high density of newly formed −COO- groups. In the case of some hydrolyzed films, the presence of small concentrations of Ca2+ results in dramatic current decreases in CVs of Ru(NH3)63+, suggesting possible use of these films in sensing applications.
Membrane Protein Insertion: The Biology–Physics Nexus (2007)

### Introduction

Membrane proteins are a greasy lot. Thrown into water without detergents, they form intractable aggregates, which minimize exposure of their nonpolar transmembrane surfaces to water. Aggregation would be their certain fate if membrane proteins were translated on the ribosome in the
Differential accumulation of callose, arabinoxylan and cellulose in nonpenetrated versus penetrated papillae on leaves of barley infected with Blumeria graminis f. sp. hordei (2014)

In plants, cell walls are one of the first lines of defence for protecting cells from successful invasion by fungal pathogens and are a major factor in basal host resistance. For the plant cell to block penetration attempts, it must adapt its cell wall to withstand the physical and chemical forces applied by the fungus. Papillae that have been effective in preventing penetration by pathogens are traditionally believed to contain callose as the main polysaccharide component. Here, we have re-examined the composition of papillae of barley (Hordeum vulgare) attacked by the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) using a range of antibodies and carbohydrate-binding modules that are targeted to cell wall polysaccharides. The data show that barley papillae induced during infection with Bgh contain, in addition to callose, significant concentrations of cellulose and arabinoxylan. Higher concentrations of callose, arabinoxylan and cellulose are found in effective papillae, compared with ineffective papillae. The papillae have a layered structure, with the inner core consisting of callose and arabinoxylan and the outer layer containing arabinoxylan and cellulose. The association of arabinoxylan and cellulose with penetration resistance suggests new targets for the improvement of papilla composition and enhanced disease resistance.
AN ULTRA-WIDEBAND QUASI-PLANAR ANTENNA WITH ENHANCED GAIN (2014)

A new ultra-wideband antenna with enhanced and nearly constant gain is presented. This quasi-planar antenna is composed of a CPW-fed printed monopole and a short horn, both made out of a single substrate. The measurements demonstrate an almost ∞at peak gain of 5:5dBi § 0:7dB from 2.5GHz to 15GHz with the average gain difierence in XZ plane is roughly 2dB up to 8GHz, which further rise to 6dB at 10GHz. The antenna also has a nearly linear phase response in this band. Well tested performance both in frequency and time domains, along with broad azimuth pattern, results in minimal ringing of a radiated pulse. The new antenna is suitable for establishing good line of sight link for UWB transmission and other broadband applications.
ChemInform Abstract: Reactions of Three Bis(viologen) Tetraquaternary Salts and Their Reduced Radicals. (1986)

Abstract The electrochemical, spectral, and equilibria characteristics of the bis(viologens) (I) and its reduction products ‐ the monoradical trications (II) and the diradical dications (III) ‐ are reported.
MIME (Multipurpose Internet Mail Extensions) Part Three: Message Header Extensions for Non-ASCII Text (1996)

This memo describes an extension to the message format defined in RFC 1521 [1], to allow the representation of character sets other than ASCII in RFC 822 (STD 11) message headers. The extensions described were designed to be highly compatible with existing Internet mail handling software, and to be easily implemented in mail readers that support RFC 1521.
Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1 (1991)

Plasmid pRO1957 contains a 26.5-kb BamHI restriction endonuclease-cleaved DNA fragment cloned from the chromosome of Pseudomonas pickettii PKO1 that allows P. aeruginosa PAO1c to grow on toluene, benzene, phenol, or m-cresol as the sole carbon source. The genes encoding enzymes for meta cleavage of catechol or 3-methylcatechol, derived from catabolism of these substrates, were subcloned from pRO1957 and were shown to be organized into a single operon with the promoter proximal to tbuE. Deletion and analysis of subclones demonstrated that the order of genes in the meta cleavage operon was tbuEFGKIHJ, which encoded catechol 2,3-dioxygenase, 2-hydroxymuconate semialdehyde hydrolase, 2-hydroxymuconate semialdehyde dehydrogenase, 4-hydroxy-2-oxovalerate aldolase, 4-oxalocrotonate decarboxylase, 4-oxalocrotonate isomerase, and 2-hydroxypent-2,4-dienoate hydratase, respectively. The regulatory gene for the tbuEFGKIHJ operon, designated tbuS, was subcloned into vector plasmid pRO2317 from pRO1957 as a 1.3-kb PstI fragment, designated pRO2345. When tbuS was not present, meta pathway enzyme expression was partially derepressed, but these activity levels could not be fully induced. However, when tbuS was present in trans with tbuEFGKIHJ, meta pathway enzymes were repressed in the absence of an effector and were fully induced when an effector was present. This behavior suggests that the gene product of tbuS acts as both a repressor and an activator. Phenol and m-cresol were inducers of meta pathway enzymatic activity. Catechol, 3-methylcatechol, 4-methylcatechol, o-cresol, and p-cresol were not inducers but could be metabolized by cells previously induced by phenol or m-cresol.
Wound dressings of the nineties: indications and contraindications. (1991)

A revolution in wound management has occurred over the past 3 decades. A plethora of wound care dressings appear to enhance the wound repair process in acute and chronic wounds. However, extensive research is needed to discriminate between the beneficial effects of increased attention to all aspects of patient care, including wound management, and the salutary effects of dressing materials.
Optical painting and fluorescence activated sorting of single adherent cells labelled with photoswitchable Pdots (2016)

The efficient selection and isolation of individual cells of interest from a mixed population is desired in many biomedical and clinical applications. Here we show the concept of using photoswitchable semiconducting polymer dots (Pdots) as an optical 'painting' tool, which enables the selection of certain adherent cells based on their fluorescence, and their spatial and morphological features, under a microscope. We first develop a Pdot that can switch between the bright (ON) and dark (OFF) states reversibly with a 150-fold contrast ratio on irradiation with ultraviolet or red light. With a focused 633-nm laser beam that acts as a 'paintbrush' and the photoswitchable Pdots as the 'paint', we select and 'paint' individual Pdot-labelled adherent cells by turning on their fluorescence, then proceed to sort and recover the optically marked cells (with 90% recovery and near 100% purity), followed by genetic analysis.
Novel Technique of Quantitative Nested Real-Time PCR Assay for Mycobacterium tuberculosis DNA (2006)

The diagnosis of tuberculous meningitis (TBM) remains a complex issue because the most widely used conventional diagnostic tools, such as culture and PCR assay for cerebrospinal fluid (CSF) samples, are unable to rapidly detect Mycobacterium tuberculosis with sufficient sensitivity in the acute phase of TBM. Based on TaqMan PCR, we designed a novel technique consisting of an internally controlled quantitative nested real-time (QNRT) PCR assay that provided a marked improvement in detection sensitivity and quantification. We applied this novel technique to quantitatively detect M. tuberculosis DNA in CSF samples from patients with suspected TBM. For use as the internal control in the measurement of the M. tuberculosis DNA copy numbers in the QNRT-PCR assay, the original mutation (M) plasmid, which included an artificial random 22-nucleotide sequence within an inserted DNA fragment of the MPB64 gene of M. tuberculosis, was prepared. The QNRT-PCR assay showed high sensitivity and specificity that were approximately equivalent to those of the conventional nested PCR assay. Moreover, the QNRT-PCR assay made it possible to precisely and quantitatively detect the initial copy number of M. tuberculosis DNA in CSF samples. Therefore, compared to the conventional PCR assay, the QNRT-PCR assay can be considered a more useful and advanced technique for the rapid and accurate diagnosis of TBM. To establish the superiority of this novel technique in TBM diagnosis, it will be necessary to accumulate data from a larger number of patients with suspected TBM.
Competitive Fitness of Nevirapine-Resistant Human Immunodeficiency Virus Type 1 Mutants (2003)

Determining the fitness of drug-resistant human immunodeficiency virus type 1 (HIV-1) strains is necessary for the development of population-based studies of resistance patterns. For this purpose, we have developed a reproducible, systematic assay to determine the competitive fitness of HIV-1 drug-resistant mutants. To demonstrate the applicability of this assay, we tested the fitness of the five most common nevirapine-resistant mutants (103N, 106A, 181C, 188C, and 190A), with mutations in HIV-1 reverse transcriptase (RT), singly and in combination (for a total of 31 variants) in a defined HIV-1 background. For these experiments, the 27 RT variants that produced viable virus were cocultured with wild-type virus without nevirapine. The ratios of the viral species were determined over time by utilization of a quantitative real-time RT-PCR-based assay. These experiments revealed that all of the viable variants were less fit than the wild type and demonstrated that the order of relative fitness of the single mutants tested was as follows: 103N > 181C > 190A > 188C > 106A. This order correlated with the commonality of these mutants as a result of nevirapine monotherapy. These investigations also revealed that, on average, the double mutants were less fit than the single mutants and the triple mutants were less fit than the double mutants. However, the fitness of the single and double mutants was often not predictive of the fitness of the derivative triple mutants, suggesting the presence of complex interactions between the closely aligned residues that confer nevirapine resistance. This complexity was also evident from the observation that all three of the replication-competent quadruple mutants were fitter than most of the triple mutants, and in some cases, even the double mutants. Our data suggest that, in many cases, viral fitness is the determining factor in the evolution of nevirapine-resistant mutants in vivo, that interactions between the residues that confer nevirapine resistance are complex, and that these interactions substantially affect reverse transcriptase structure and/or function.
Rational Design of a Plasmid Origin That Replicates Efficiently in Both Gram-Positive and Gram-Negative Bacteria (2010)

Our results demonstrate the efficiency of pBAV1K-T5 replication in different bacterial species, thereby facilitating the study of proteins that don't fold well in E. coli and pathogens not amenable to existing genetic tools.
Structure of the CD59-encoding gene: further evidence of a relationship to murine lymphocyte antigen Ly-6 protein. (1992)

The gene for CD59 [membrane inhibitor of reactive lysis (MIRL), protectin], a phosphatidylinositol-linked surface glycoprotein that regulates the formation of the polymeric C9 complex of complement and that is deficient on the abnormal hematopoietic cells of patients with paroxysmal nocturnal hemoglobinuria, consists of four exons spanning 20 kilobases. The untranslated first exon is preceded by a G+C-rich promoter region that lacks a consensus TATA or CAAT motif. The second exon encodes the hydrophobic leader sequence of the protein, and the third exon encodes the amino-terminal portion of the mature protein. The fourth exon encodes the remainder of the mature protein, including the hydrophobic sequence necessary for glycosyl-phosphatidylinositol anchor attachment. The structure of the CD59 gene is very similar to that encoding Ly-6, a murine glycoprotein with which CD59 has some structural similarity. The striking similarity in gene structure is further evidence that the two proteins belong to a superfamily of proteins that may also include the urokinase plasminogen-activator receptor and a squid glycoprotein of unknown function.
Monoclonal antibody humanness score and its applications (2013)

Our results reveal that in most cases humanizing an antibody and confirming the humanness of the final form may be sufficient to eliminate immunogenicity issues to the same extent as using fully human antibodies. We created a public website to calculate the humanness score of any input antibody sequence based on our human antibody database. This tool will be of great value during the preclinical drug development process for new monoclonal antibody therapeutics.
Identification of isomeric flavonoid glucuronides in urine and plasma by metal complexation and LC‐ESI‐MS/MS (2006)

Noncovalent complexes were used for structural determination and isomer differentiation of flavonoid glucuronides. Several flavonoid glucuronides including naringenin-7-O-glucuronide, synthesized here for the first time, were used as test compounds. Electrospray ionization quadrupole ion trap mass spectrometry with collision-induced dissociation (CID) was used to analyze complexes of the form [Co(II) (L-H) (Aux)]+ and [Co(II) (L-H) (Aux)2]+, in which L is the flavonoid glucuronide and Aux is a phenanthroline-based ligand. These complexes yielded characteristic fragmentation patterns that facilitated assignment of the substitution position of the glucuronides. The methods were adapted to liquid chromatography/tandem mass spectrometry (LC-MS/MS) with postcolumn cobalt complexation and were tested on extracts from biological fluids. The metabolites naringenin-7-O-glucuronide and naringenin-4'-O-glucuronide were detected in human urine following the consumption of grapefruit juice. Isomeric quercetin glucuronides were identified and differentiated after spiking rat plasma at the 1 microM level, proving that the new methods are effective at biologically relevant concentrations.
Multiplexed DNA Detection Using Spectrally Encoded Porous SiO2 Photonic Crystal Particles (2009)

A particle-based multiplexed DNA assay based on encoded porous SiO(2) photonic crystal disks is demonstrated. A "spectral barcode" is generated by electrochemical etch of a single-crystal silicon wafer using a programmed current-time waveform. A lithographic procedure is used to isolate cylindrical microparticles 25 microm in diameter and 10 microm thick, which are then oxidized, modified with a silane linker, and conjugated to various amino-functionalized oligonucleotide probes via cyanuric chloride. It is shown that the particles can be decoded based on their reflectivity spectra and that a multiple analyte assay can be performed in a single sample with a modified fluorescence microscope. The homogeneity of the reflectivity and fluorescence spectra, both within and across the microparticles, is also reported.
Synthesis of Imides, N‐Acyl Vinylogous Carbamates and Ureas, and Nitriles by Oxidation of Amides and Amines with Dess–Martin Periodinane (2005)

Expanding our synthetic tool repertoire: The DMP-mediated oxidation of a range of amide substrates has been demonstrated, affording the corresponding imides and N-acyl vinylogous carbamates and ureas. Likewise, an array of benzylic and related amines have also been successfully converted into their nitrile counterparts (see scheme; DMP=Dess–Martin periodinane).
Antitumor effect of actinomycin D entrapped in liposomes bearing subunits of tumor-specific monoclonal immunoglobulin M antibody. (1983)

Sonicated liposomes containing actinomycin D in the membranes were chemically coated with the subunits of monoclonal immunoglobulin M (IgM) antibody against a mouse mammary tumor-associated antigen (MM antigen) and examined for their in vitro and in vivo antitumor effects against MM46 (MM+) and MM48 (MM-) tumors of C3H/He mouse origin. The antibody-bearing, actinomycin D-containing liposomes (chemoimmunoliposomes) were selectively bound to MM+ tumor cells and showed much more in vitro cytotoxicity against the tumor cells than that shown by free actinomycin D. The in vivo antitumor effect of the chemoimmunoliposomes was tested on the mammary tumor cells (5 X 10(4) to 5 X 10(6) transplanted i.p. into syngeneic mice. A single i.p. injection of the chemoimmunoliposomes containing 0.3, 0.5, or 1 microgram of actinomycin D into MM46 tumor-bearing mice resulted in the cure of some mice and a prolonged survival time in the rest of the mice as compared to results in controls. In this test, free actinomycin D, anti-MM IgM antibody, and bovine serum albumin-coated liposomes containing actinomycin D were marginally effective or ineffective. To examine a systemic antitumor effect of chemoimmunoliposomes, mice were inoculated with MM46 tumor cells and then treated with a single i.v. injection of liposomes 4 days later. If the mice were pretreated with an i.v. injection of unmodified multilamellar liposomes, an injection of the chemoimmunoliposomes containing 1 microgram of actinomycin D resulted in a significant inhibition of tumor growth. Both free actinomycin D and bovine serum albumin-coated liposomes containing actinomycin D were ineffective against the s.c. tumor. These results indicate that an antitumor drug entrapped in the membranes of small sonicated liposomes bearing antitumor monoclonal antibodies can be delivered to antigenic tumor cells and exert more efficient antitumor activity than does the free drug.
Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system. (1993)

Interferon (IFN) regulatory factor 1 (IRF-1) and IRF-2 were originally identified as transcription factors involved in the regulation of the IFN system. IRF-1 functions as a transcriptional activator, while IRF-2 represses IRF-1 function. More recently, evidence has been provided that IRF-1 and IRF-2 manifest antioncogenic and oncogenic properties, respectively, and that loss of one or both of the IRF-1 alleles may be critical for the development of human hematopoietic neoplasms. Both factors show a high degree of structural similarity in their N-terminal DNA-binding domains, and previous studies suggested that IRF-1 and IRF-2 bind to similar or identical cis elements within type I IFN (IFN-alpha and -beta) and IFN-inducible genes. However, the exact recognition sequences of these two factors have not yet been determined; hence, the spectrum of the IRF-responsive genes remains unclear. In this study, we determined the DNA sequences recognized by IRF-1 and IRF-2, using a polymerase chain reaction-assisted DNA-binding site selection method. We report that sequences selected by this method and the affinities for each sequence were virtually indistinguishable between IRF-1 and IRF-2. We confirm the presence of two contiguous IRF recognition sequences within the promoter region of the IFN-beta gene and of at least one such sequence in all of the IFN-inducible genes examined. Furthermore, we report the presence of potential IRF sequences in the upstream region of several genes involved in cell growth control.