gebhart/patrepeval huggingface dataset:
Reversible Extrusion and Uptake of HCl Molecules by Crystalline Solids Involving Coordination Bond Cleavage and Formation (2006)

Yellow crystalline salts (3-XpyH)2[CuCl4] (3-XpyH = 3-halopyridinium, X = Cl, Br) lose HCl upon exposure to air in an open vessel, yielding quantitatively blue crystalline coordination compounds [CuCl2(3-Xpy)2]. The reaction is prevented if the vessel is sealed, but can be driven forward under such conditions by providing a trapping agent for HCl, such as an aqueous solution of AgNO3. The reaction requires cleavage of Cu-Cl and N-H bonds and formation of Cu-N bonds. The metal coordination geometry also changes from distorted tetrahedral to square planar. Remarkably, the reaction is fully reversible upon exposure of the blue coordination compound to vapor from a concentrated aqueous solution of HCl, and the initial yellow crystalline salt results. The structural changes occurring in these reactions have been followed by X-ray powder diffraction, including Rietveld refinement, of the crystal structures.
Specifying the Treatment Process (1978)

With a focus on the implications for effectiveness research, This paper presents a conceptualization of the treatment process, some distinctions among types of outcomes, and a framework in which the effectiveness of specific interventive approaches may be evaluated. Variables characterizing the treatment situation are delineated in terms of (a) their defining referents, (b) the specificity and rigor of their definition, and (c) the complexity of their formulation. Three general types of outcomes are also distinguished: ultimate, intermediate, and instrumental. In order to meet the proposed requisites of practice knowledge, a number of areas for future research are outlined, emphasizing the identification of specific interventive variables and the investigation of causal hypotheses linking those interventions to specific types of outcomes.
Properties of the Equilibrium State in Transportation Networks (1978)

The Wardrop equilibrium problem for urban road networks is considered. It is shown that the (unique) equilibrium total flow vector is a continuous function of the input traffic flows. Under fairly weak conditions it is proven that the total origin to destination travel costs are also continuous functions of the input traffic flows. It is then shown that each origin to destination cost is a monotonically nondecreasing function of its own input flow when other inputs are held fixed. Finally, it is demonstrated by means of simple examples that the equilibrium total flow vector and origin to destination travel cost functions are not differentiable at certain (possibly difficult to predict) points in the set of feasible input flow vectors and that the cost functions do not in general possess such other potentially useful properties as convexity or concavity. These results are important to an understanding of the sensitivity of the equilibrium state to variations in input data.
An Extracellular Polysaccharide Locus Required for Transmission of Bordetella bronchiseptica (2017)

These results have important implications for potential roles of polysaccharides in the pathogenesis and transmission of Bordetella species as well as other respiratory pathogens. Cases of pertussis (whooping cough) caused by Bordetella pertussis are on the rise, and understanding factors that contribute to their spread is critical to its control.
Calcium-induced increase in the radius of gyration and maximum dimension of calmodulin measured by small-angle x-ray scattering (1985)

We have used solution small-angle X-ray scattering to characterize bovine brain calmodulin in the presence and absence of calcium. In the presence of calcium, calmodulin exists in solution as an elongated molecule with a radius of gyration of 21.5 A and a maximum vector length of approximately 62 A. These values are consistent with the dimensions recently determined for the crystal form of rat testis calmodulin. In the absence of calcium, the calmodulin molecule is shorter, the radius of gyration decreases to 20.6 A, and the maximum vector length decreases to approximately 58 A. This change in dimensions is consistent with an overall contraction of the protein through movement of the two lobes closer to each other upon removal of calcium from calmodulin.
Estrogen-Related Receptor α in Human Breast Carcinoma as a Potent Prognostic Factor (2004)

Estrogen-related receptor alpha (ERRalpha) was identified as a gene related to estrogen receptor alpha (ERalpha) and belongs to a class of nuclear orphan receptors. ERRalpha binds to estrogen responsive element(s) (ERE) and is considered to be involved in modulation of estrogenic actions. However, biological significance of ERRalpha remains largely unknown. Therefore, we examined the expression of ERRalpha in human breast carcinoma tissues using immunohistochemistry (n = 102) and real-time reverse transcription-PCR (n = 30). ERRalpha immunoreactivity was detected in the nuclei of carcinoma cells in 55% of breast cancers examined, and relative immunoreactivity of ERRalpha was significantly (P = 0.0041) associated with the mRNA level. Significant associations were detected between ERalpha and ERE-containing estrogen-responsive genes, such as pS2 (P < 0.0001) and EBAG9/RCAS1 (P = 0.0214), in breast carcinoma tissues. However, no significant association was detected between ERalpha and pS2 (P = 0.1415) in the ERRalpha-positive cases (n = 56) or between ERalpha and EBAG9/RCAS1 (P = 0.8271) in the ERRalpha-negative group (n = 46). ERRalpha immunoreactivity was significantly associated with an increased risk of recurrence and adverse clinical outcome by both uni- (P = 0.0097 and P = 0.0053, respectively) and multi- (P = 0.0215 and P = 0.0118, respectively) variate analyses. A similar tendency was also detected in the group of breast cancer patients who received tamoxifen therapy after surgery. Results from our study suggest that ERRalpha possibly modulates the expression of ERE-containing estrogen-responsive genes, and ERRalpha immunoreactivity is a potent prognostic factor in human breast carcinoma.
Processing of synthetic pro‐islet amyloid polypeptide (proIAPP) ‘amylin’ by recombinant prohormone convertase enzymes, PC2 and PC3, <i>in vitro</i> (2000)

Islet amyloid polypeptide (IAPP), amylin, is the constituent peptide of pancreatic islet amyloid deposits which form in islets of Type 2 diabetic subjects. Human IAPP is synthesized as a 67-residue propeptide in islet beta-cells and colocalized with insulin in beta-cell granules. The mature 37-amino acid peptide is produced by proteolysis at pairs of basic residues at the C- and N-termini of the mature peptide. To determine the enzymes responsible for proteolysis and their activity at the potential cleavage sites, synthetic human proIAPP was incubated (0.5-16 h) with recombinant prohormone convertases, PC2 or PC3 at appropriate conditions of calcium and pH. The products were analysed by MS and HPLC. Proinsulin was used as a control and was cleaved by both recombinant enzymes resulting in intermediates. PC3 was active initially at the N-terminal-IAPP junction and later at the C-terminus, whereas initial PC2 activity was at the IAPP-C-terminal junction. Processing at the basic residues within the C-terminal flanking peptide rarely occurred. There was no evidence for substantial competition for the processing enzymes when the combined substrates proinsulin and proIAPP were incubated with both PC2 and PC3. As proinsulin cleavage is sequential in vivo (PC3 active at the B-chain-C-peptide junction, followed by PC2 at A chain-C-peptide junction), these data suggest that proteolysis of proIAPP and proinsulin is coincident in secretory granules and increased proinsulin secretion in diabetes could be accompanied by increased production of proIAPP.
Investigation into the use of C‐ and N‐terminal GFP fusion proteins for subcellular localization studies using reverse transfection microarrays (2004)

Abstract Reverse transfection microarrays were described recently as a high throughput method for studying gene function. We have investigated the use of this technology for determining the subcellular localization of proteins. Genes encoding 16 proteins with a variety of functions were placed in Gateway expression constructs with 3′ or 5′ green fluorescent protein (GFP) tags. These were then packaged in transfection reagent and spotted robotically onto a glass slide to form a reverse transfection array. HEK293T cells were grown over the surface of the array until confluent and GFP fluorescence visualized by confocal microscopy. All C‐terminal fusion proteins localized to cellular compartments in accordance with previous studies and/or bioinformatic predictions. However, less than half of the N‐terminal fusion proteins localized correctly. Of those that were not in concordance with the C‐terminal tagged proteins, half did not exhibit expression and the remainder had differing subcellular localizations to the C‐terminal fusion protein. This data indicates that N‐terminal tagging with GFP adversely affects the protein localization in reverse transfection assays, whereas tagging with GFP at the C‐terminal is generally better in preserving the localization of the native protein. We discuss these results in the context of developing high‐throughput subcellular localization assays based on the reverse transfection array technology. Copyright © 2004 John Wiley & Sons, Ltd.
Lactate Dehydrogenase, Serum Protein, and Immunoglobulin G Content of Uncured Turkey Thigh Rolls As Influenced by Endpoint Cooking Temperature (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLactate Dehydrogenase, Serum Protein, and Immunoglobulin G Content of Uncured Turkey Thigh Rolls As Influenced by Endpoint Cooking TemperatureCheng-Hsin Wang, James J. Pestka, Alden M. Booren, and Denise M. SmithCite this: J. Agric. Food Chem. 1994, 42, 8, 1829–1833Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/jf00044a049https://doi.org/10.1021/jf00044a049research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Removal of perfluoalkyl acids (PFAAs) through fluorochemical industrial and domestic wastewater treatment plants and bioaccumulation in aquatic plants in river and artificial wetland (2019)

The fluorochemical industry has shifted to the production of short chain homologues of perfluoalkyl acids (PFAAs) in recent years. Yet the effective removal of short-chain PFAAs from wastewater is still a major challenge. In this study, the removal efficiencies (RM) of short- and long-chain PFAAs emitted from two fluorochemical industrial parks were evaluated in one industrial and two domestic waste water treatment plants (WWTPs), and bioaccumulation factors (BAF) of PFAAs in various emerged and submerged aquatic plants in adjacent river and an artificial wetland were also calculated. Perfluorobutanoic acid (PFBA), perfluorobutane sulfonic acid (PFBS) and perfluorooctanoic acid (PFOA) were dominant in the whole area. The source water of the fluorochemical industrial WWTP (F-WWTP) gathered from the facilities in Park 2 contained total PFAAs (∑PFAAs) of 5,784 ng/L. Among the four main technologies, the biological aerated filter, combined with upflow sludge bed processes presented the greatest RM of ∑PFAAs in the F-WWTP, respectively. The source water of the wetland from the river brought ∑PFAAs to 21,579 ng/L, emerged plants showed higher BAF of PFBA and PFBS, while lower BAF of PFOA and PFOS than submerged plants. J. serotinus showed both the highest ∑PFAAs and the highest BAF for short chain PFAAs. With the increasing production capacity, this study provided valuable information for risk assessment and management of PFAA emission from point sources.
Plant lipid biosynthesis in 1959 and 1984 (1984)

Twenty-five years ago information concerning the synthesis of fatty acids was at a primitive stage.It was known from the work of Wakil, Brady and Gurin that in animal systems the &oxidation enzymes were not involved, citrate stimulated synthesis remarkably, and COP had a similar effect.The mechanism of these effects was not known (1).
Dissociation of analyte oxide ions in inductively coupled plasma mass spectrometry (1994)

Analyte oxide ions have been studied in inductively coupled plasma mass spectrometry as a function of the sampling position, the carrier gas flow rate and the efficiency of the energy transfer from the plasma to the sample, in order to support the hypothesis of analyte oxide formation in the plasma. Lanthanum was selected as the test species owing to its high oxide bond strength, and its behaviour was compared to that of Pb as this element has a low oxide bond strength. A prototype ICP mass spectrometer was used. The LaO+: La+ ratio was found to be in the 0.2–13 000% range under the operating conditions used. Energy transfer was either degraded by adding a sheathing gas or improved by adding hydrogen. The LaO+: La+ ratio was minimized for low carrier gas flow rates and an efficient energy transfer. This was corroborated by temperature optical measurements. The results are in good agreement with those found in other recent work. In any instance, the role of the sampling position was found to be crucial in studying analyte oxide ion behaviour and optimizing analytical performance.
An <i>Arabidopsis thaliana</i> Pectin Acetylesterase Gene Is Upregulated in Nematode Feeding Sites Induced by Root-knot and Cyst Nematodes (2002)

By using differential display, gene expression was investigated in Arabidopsis thaliana roots shortly after nematode infection, and a putative pectin acetylesterase (PAE) homolog (DiDi 9C-12) was found to be upregulated. PAEs catalyze the deacetylation of pectin, a major compound of primary cell walls. mRNA in situ hybridization experiments showed that the expression of DiDi 9C-12 was enhanced very early after infection in initiating giant-cells and in cells surrounding the nematodes. Later on, the level of DiDi 9C-12 mRNA was lower in giant-cells and transcripts were mainly found in parenchyma, endodermis, and pericycle cells of the root gall. Twenty days after infection, DiDi 9C-12 transcripts could no longer be detected. DiDi 9C-12 transcripts were also found in young syncytia and in the cells surrounding the expanding syncytium. Our results suggest that plant parasitic nematodes can modulate the rapid growth of the feeding cells and the expansion of the root gall by triggering the expression of DiDi 9C-12. PAEs, which probably act together with a range of other pectin-degrading enzymes, could be involved in softening and loosening the primary cell wall in nematode-infected plant roots.
Step Smoothing by Radical and Ion Assisted Chemical Vapor Deposition (1986)

A novel step smooting method called radical and ion assisted chemical vapor deposition (RID), is proposed. In this method, plasma chemical vapor deposition and reactive ion etching occur simultaneously on the surface. The bias sputtering and RID methods are compared and RID is found to provide better step coverage. A silicon oxide deposition experiment is performed in a planar diode-type reactor to verify this method. Experimentation shows that smooth step coverage with rounded edges is obtained for films at room temperature, while high quality films are fabricated at 400°C.
Resistance of digital watermarks to collusive attacks (2002)

In digital watermarking (also called digital fingerprinting), extra information is embedded imperceptibly into digital content (such as an audio track, a still image, or a movie). This extra information can be read by authorized parties, and other users attempting to remove the watermark cannot do so without destroying the value of the content by making perceptible changes to the content. This provides a disincentive to copying by allowing copies to be traced to their original owner. Unlike cryptography, digital watermarking provides protection to content that is in the clear. It is not easy to design watermarks that are hard to erase, especially if an attacker has access to several differently marked copies of the same base content. Cox et al. (see IEEE Trans. on Image Processing, vol.6, no.12, p.1673-87, 1997) have proposed the use of additive normally distributed values as watermarks, and have sketched an argument showing that, in a certain theoretical model, such watermarks are resistant to collusive attacks. Here, we fill in the mathematical justification for this claim.
Some Improved Diagnostics for Failure of the Rasch Model (1983)

Although several goodness of fit tests have been developed for the Rasch model for dichotomous items, most of them are of a global, asymptotic, and confirmatory type. This paper, based on ideas from a recent thesis by Van den Wollenberg, offers some suggestions for local, small sample, and exploratory techniques: difficulty plots for person groups scoring right and wrong on a specific item, a slope test per item based on a binomial distribution per score group, and a unidimensionality check based on an extended hypergeometric distribution per score group.
Routes to High Energy Cathodes of Sodium‐Ion Batteries (2015)

Sodium‐ion batteries (SIBs) are now being actively developed as low cost and sustainable alternatives to lithium‐ion batteries (LIBs) for large‐scale electric energy storage applications. In recent years, various inorganic and organic Na compounds, mostly mimicked from their Li counterparts, have been synthesized and tested for SIBs, and some of them indeed demonstrate comparable specific capacity to the presently developed LIB electrodes. However, the lack of suitable cathode materials is still a major obstacle to the commercial development of SIBs. Here, we present a brief review on the recent developments of SIB cathodes, with a focus on low cost and high energy density materials (> 450 Wh kg −1 vs Na) together with discussion of their Na‐storage mechanisms. The considerable differences in the structural requirements for Li‐ and Na‐storage reactions mean that it is not sufficient to design SIB cathode materials by simply mimicking LIB materials, and therefore great efforts are needed to discover new materials and reaction mechanisms to further develop variable cathodes for advanced SIB technology. Some directions for future research and possible strategies for building advanced cathode materials are also proposed here.
Transbilayer Organization of the Chlorophyll‐Proteins of Spinach Thylakoids (1982)

To investigate the transverse bilayer organization of the chlorophyll-proteins of the three intrinsic chlorophyll-protein complexes, the effects of proteolytic enzymes, and an antibody against the light-harvesting complex were compared using right-side-out and inside-out thylakoid vesicles. The vesicles were isolated by aqueous polymer phase partitioning following the fragmentation of spinach thylakoids by passage through a Yeda press. Both vesicle types were agglutinated by an antiserum specific for the light-harvesting complex, although proteolytic degradation of the complex occurred only in right-side-out vesicles. In addition, there are different antigenic sites for the light-harvesting complex on the inner and outer thylakoid surfaces. Polypeptides of the chlorophyll-alpha-protein complex of photosystem II were degraded by proteases at both membrane surfaces. We concluded that both these chlorophyll-protein complexes are membrane spanning and transversely asymmetric, but that the light-harvesting complex polypeptides accessible at the inner thylakoid surface are more resistant to proteolytic attack. In contrast, the main chlorophyll-containing polypeptide (Mr = 64 500) of photosystem I complex was resistant to proteolytic attack at both the outer and inner thylakoid surfaces.
Nucleic Acid Polymers Inhibit Duck Hepatitis B Virus Infection<i>In Vitro</i> (2013)

Nucleic acid polymers (NAPs) utilize the sequence-independent properties of phosphorothioate oligonucleotides (PS-ONs) to target protein interactions involved in viral replication. NAPs are broadly active against a diverse range of enveloped viruses that use type I entry mechanisms. The antiviral activity of NAPs against hepatitis B virus (HBV) infection was assessed in vitro in duck hepatitis B virus (DHBV)-infected primary duck hepatocytes (PDH). NAPs efficiently entered PDH in the absence of any transfection agent and displayed antiviral activity at concentrations of 0.01 to 10 μM, measured by their ability to prevent the intracellular accumulation of DHBV surface antigen, which was independent of their nucleotide sequence and was specifically dependent on phosphorothioation. Higher levels of antiviral activity were observed with NAPs 40 nucleotides in length or longer. The fully degenerate NAP (REP 2006) was active during DHBV infection or when added 12 h after infection. In contrast, an acidic-pH-sensitive NAP (REP 2031) that was broadly active against other viruses displayed antiviral activity when present during DHBV infection but no activity when added 12 h after infection, suggesting that NAPs exert their postentry effect in an acidic environment unique to DHBV infection. Both REP 2006 and REP 2031 displayed negligible cytotoxicity in PDH at concentrations of up to 10 μM, as assessed using an XTT [2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] cytotoxicity assay. The antiviral activity of NAPs against DHBV in vitro was strictly dependent on their amphipathic character, suggesting that NAPs interact with amphipathic target(s) that are important for DHBV entry and postentry mechanisms required for infection.