gebhart/patrepeval huggingface dataset:
HMG-1 Stimulates Estrogen Response Element Binding by Estrogen Receptor from Stably Transfected HeLa Cells (1999)

Estrogen receptor (ER) toxicity has hampered the development of vertebrate cell lines stably expressing substantial levels of recombinant wild-type ER. To isolate clonal lines of HeLa cells stably expressing epitope-tagged ER, we used a construction encoding a single bicistronic mRNA, in which FLAG-epitope-tagged human ER alpha (fER) was translated from a 5'-translation initiation site and fused to the neomycin resistance gene, which was translated from an internal ribosome entry site. One stable HeLa-ER-positive cell line (HeLa-ER1) produces 1,300,000 molecules of fER/cell (approximately 20-fold more ER than MCF-7 cells). The HeLa fER is biologically active in vivo, as judged by rapid death of the cells in the presence of either 17 beta-estradiol or trans-hydroxytamoxifen and the ability of the cell line to activate a transfected estrogen response element (ERE)-containing reporter gene. The FLAG-tagged ER was purified to near homogeneity in a single step by immunoaffinity chromatography with anti-FLAG monoclonal antibody. Purified fER exhibited a distribution constant (KD) for 17 beta-estradiol of 0.45 nM. Purified HeLa fER and HeLa fER in crude nuclear extracts exhibit similar KD values for the ERE (0.8 nM and 1 nM, respectively), which are approximately 10 times lower than the KD of 10 nM we determined for purified ER expressed using the baculovirus system. HMG-1 strongly stimulated binding of both crude and purified HeLa fER to the ERE (KD of 0.25 nM). In transfected HeLa cells, HMG-1 exhibited a dose-dependent stimulation of 17 beta-estradiol-dependent transactivation. At high levels of transfected HMG-1 expression plasmid, transactivation by ER became partially ligand-independent, and transactivation by trans-hydroxytamoxifen was increased by more than 25-fold. These data describe a system in which ER, stably expressed in HeLa cells and easily purified, exhibits extremely high affinity for the ERE, and suggest that intracellular levels of HMG-1 may be limiting for ER action.
Pipelining in multi-query optimization (2001)

Database systems frequently have to execute a set of related queries, which share several common subexpressions. Multi-query optimization exploits this, by finding evaluation plans that share common results. Current approaches to multi-query optimization assume that common subexpressions are materialized. Significant performance benefits can be had if common subexpressions are pipelined to their uses, without being materialized. However, plans with pipelining may not always be realizable with limited buffer space, as we show. We present a general model for schedules with pipelining, and present a necessary and sufficient condition for determining validity of a schedule under our model. We show that finding a valid schedule with minimum cost is NP-hard. We present a greedy heuristic for finding good schedules. Finally, we present a performance study that shows the benefit of our algorithms on batches of queries from the TPCD benchmark.
Accelerated marrow recovery following total‐body irradiation after treatment with vincristine, lithium or combined vincristine‐lithium (1991)

Accelerated post-irradiation recovery of hematopoietic marrow has been reported following treatment with lithium (Li) or vincristine (VcR). Because these two agents appear to exert their effects on different, albeit overlapping, hematopoietic populations, it was felt that combining them might lead to a wider spectrum of enhanced post-irradiation marrow regeneration. Results demonstrated that an accelerated recovery, which appeared to be additive in nature, was observed in the marrow following combined VcR-Li/4.5 Gy total-body irradiation. The combined schedule significantly enhanced post-irradiation recovery of white blood cells, 12-day spleen colony-forming units, erythroid burst-forming units, and fibroblastic colony-forming units over radiation alone; and recovery of marrow cellularity, multipotential colony-forming units (CFU-gemm) and granulocytic/monocytic colony-forming units (CFU-gm) over both radiation alone and either drug given singly with the 4.5 Gy. In addition, while data on the ability of regenerating stroma to support CFU-gm and CFU-gemm did not suggest that VcR was acting to enhance post-irradiation marrow recovery by increasing stromal production of hematopoietic growth factors, Li did appear to increase production of one or more of these factors, and this may be part of its mechanism of action.
LDL phospholipid hydrolysis produces modified electronegative particles with an unfolded apoB-100 protein (2004)

Electronegative low density lipoprotein (LDL(-)) formation that structurally resembles LDL(-) isolated from plasma was evaluated after LDL treatment with snake venom phospholipase A(2) (PLA(2)). PLA(2) treatment of LDL increased its electrophoretic mobility in proportion to the amount of LDL(-) formed without evidence of lipid peroxidation. These changes dose-dependently correlated with the degree of phospholipid hydrolysis. Strong immunoreactivity of LDL(-) subfraction from plasma and PLA(2)-treated LDL (PLA(2)-LDL) to amyloid oligomer-specific antibody was observed. Higher beta-strand structural content and unfolding proportionate to the loss of alpha-helical structure of apolipoprotein B-100 (apoB-100) of LDL(-) isolated from both native and PLA(2)-LDLs was demonstrated by circular dichroism (CD) spectropolarimetry. These structural changes resembled the characteristics of some oxidatively modified LDLs and soluble oligomeric aggregates of amyloidogenic proteins. PLA(2)-LDL was also more susceptible to nitration by peroxynitrite, likely because of exposure of otherwise inaccessible hydrophilic and hydrophobic domains arising from apoB-100 unfolding. This was also demonstrated for plasma LDL(-). In contrast, PLA(2)-LDL was more resistant to copper-mediated oxidation that was reversed upon the addition of small amounts of unsaturated fatty acids. The observed similarities between PLA(2)-LDL(-)-derived LDL(-) and plasma LDL(-) implicate a role for secretory PLA(2) in producing modified LDL(-) that is facilitated by unfolding of apoB-100.
Trabecular Meshwork Length in Men and Women by Histological Assessment (2012)

There was no statistically significant difference between the average trabecular meshwork length in men and women. Among the angles evaluated, 25.3-28.5% were graded as difficult to identify the scleral spur.
In-fiber Mach-Zehnder interferometer based on a pair of long-period gratings (1996)

A new type of in-fiber Mach-Zehnder interferometer based on a pair of long-period gratings is proposed. This interferometer can be used to measure the refractive index induced in fibers and that of the surrounding medium.
Antioxidant properties of flavonol glycosides from tea (1999)

We have determined the antioxidant activity of the major flavonols found in tea: a monoglycoside, a diglycoside and two triglycosides of kaempferol and three monoglycosides, a diglycoside and two triglycosides of quercetin. The Trolox equivalent antioxidant capacity (TEAC) and inhibition of iron/ascorbate-induced lipid peroxidation of phosphatidyl choline vesicles were measured. In the aqueous phase TEAC assay, the quercetin monoglycosides and diglycoside were approximately half as effective as quercetin aglycone. The quercetin triglycosides were much less effective than the monoglycosides and the diglycoside. The kaempferol glycosides were 32-39% less effective in the aqueous phase antioxidant assay compared to the kaempferol aglycone. Quercetin monoglycosides and diglycoside were potent inhibitors of lipid peroxidation, in contrast to the triglycoside which was much less effective. All the kaempferol glycosides were significantly less potent inhibitors of lipid peroxidation compared to the kaempferol aglycone. The compounds described herein demonstrate the antioxidant activity of the major flavonols in tea and indicate the effect of substituting a range of sugar moieties in the phenolic C ring.
Trifluoroacetyl Hypofluorite1 (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTrifluoroacetyl Hypofluorite1George H. Cady and K. B. KelloggCite this: J. Am. Chem. Soc. 1953, 75, 10, 2501–2502Publication Date (Print):May 1, 1953Publication History Published online1 May 2002Published inissue 1 May 1953https://pubs.acs.org/doi/10.1021/ja01106a504https://doi.org/10.1021/ja01106a504research-articleACS PublicationsRequest reuse permissionsArticle Views76Altmetric-Citations12LEARN 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
Beyond C, H, O, and N! Analysis of the Elemental Composition of U.S. FDA Approved Drug Architectures (2014)

The diversity of elements among U.S. Food and Drug Administration (FDA) approved pharmaceuticals is analyzed and reported, with a focus on atoms other than carbon, hydrogen, oxygen, and nitrogen. Our analysis reveals that sulfur, chlorine, fluorine, and phosphorous represent about 90% of elemental substitutions, with sulfur being the fifth most used element followed closely by chlorine, then fluorine and finally phosphorous in the eighth place. The remaining 10% of substitutions are represented by 16 other elements of which bromine, iodine, and iron occur most frequently. The most detailed parts of our analysis are focused on chlorinated drugs as a function of approval date, disease condition, chlorine attachment, and structure. To better aid our chlorine drug analyses, a new poster showcasing the structures of chlorinated pharmaceuticals was created specifically for this study. Phosphorus, bromine, and iodine containing drugs are analyzed closely as well, followed by a discussion about other elements.
A Lack of Premature Termination Codon Read-Through Efficacy of PTC124 (Ataluren) in a Diverse Array of Reporter Assays (2013)

The drug molecule PTC124 (Ataluren) has been described as a read-through agent, capable of suppressing premature termination codons (PTCs) and restoring functional protein production from genes disrupted by nonsense mutations. Following the discovery of PTC124 there was some controversy regarding its mechanism of action with two reports attributing its activity to an off-target effect on the Firefly luciferase (FLuc) reporter used in the development of the molecule. Despite questions remaining as to its mechanism of action, development of PTC124 continued into the clinic and it is being actively pursued as a potential nonsense mutation therapy. To thoroughly test the ability of PTC124 to read through nonsense mutations, we conducted a detailed assessment comparing the efficacy of PTC124 with the classical aminoglycoside antibiotic read-through agent geneticin (G418) across a diverse range of in vitro reporter assays. We can confirm the off-target FLuc activity of PTC124 but found that, while G418 exhibits varying activity in every read-through assay, there is no evidence of activity for PTC124.
Treatment of Ulcerative Colitis Using Fecal Bacteriotherapy (2003)

Colonic infusion of donor human intestinal flora can reverse UC in selected patients. These anecdotal results support the concept of abnormal bowel flora or even a specific, albeit unidentified, bacterial pathogen causing UC.
Comparative Analysis of Small Molecules and Histone Substrate Analogues as LSD1 Lysine Demethylase Inhibitors (2010)

LSD1 is a flavin-dependent histone demethylase that oxidatively removes methyl groups from Lys-4 of histone H3. LSD1 belongs to the amine oxidase enzyme superfamily which utilize molecular oxygen to transform amines to imines that are hydrolytically cleaved to formaldehyde. In prior studies, it has been shown that monoamine oxidase inhibitory scaffolds such as propargylamines and cyclopropylamines can serve as mechanism-based inactivators of LSD1. Propargylamine-histone H3 peptide analogues are potent LSD1 inhibitors, whereas small molecule antidepressant MAO acetylenic inhibitors like pargyline do not inhibit LSD1. In contrast, the small molecule MAO cyclopropylamine inhibitor tranylcypromine is a time-dependent LSD1 inhibitor but exo-cyclopropylamine-peptide substrate analogue is not. To provide further insight into small molecule versus peptide relationships in LSD1 inhibition, herein we further our analysis of warheads in peptide scaffolds to include the chlorovinyl, endo-cyclopropylamine, and hydrazine-functionalities as LSD1 inactivators. We find that chlorovinyl-H3 is a mechanism-based LSD1 inactivator whereas endo-cyclopropylamine-H3 does not show time-dependent inactivation. The hydrazine-H3 was shown to be the most potent LSD1 suicide inhibitor yet reported, more than 20-fold more efficient in inhibiting demethylation than propargylamine-H3 derivatives. We re-explored MAO antidepressant agent phenelzine (phenethylhydrazine), previously reported to be a weak LSD1 inhibitor, and found that it is far more potent than previously appreciated. We show that phenelzine can block histone H3K4Me demethylation in cells, validating it as a pharmacologic tool and potential lead structure for anticancer therapy.
On Optimal Frequency-Domain Multichannel Linear Filtering for Noise Reduction (2009)

Several contributions have been made so far to develop optimal <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">multichannel</i> linear filtering approaches and show their ability to reduce the acoustic noise. However, there has not been a clear <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">unifying theoretical</i> analysis of their performance in terms of both noise reduction and speech distortion. To fill this gap, we analyze the frequency-domain (non-causal) multichannel linear filtering for noise reduction in this paper. For completeness, we consider the noise reduction constrained optimization problem that leads to the parameterized multichannel non-causal Wiener filter (PMWF). Our contribution is fivefold. First, we formally show that the minimum variance distortionless response (MVDR) filter is a particular case of the PMWF by properly formulating the constrained optimization problem of noise reduction. Second, we propose new simplified expressions for the PMWF, the MVDR, and the generalized sidelobe canceller (GSC) that depend on the signals' statistics only. In contrast to earlier works, these expressions are explicitly independent of the channel transfer function ratios. Third, we quantify the theoretical gains and losses in terms of speech distortion and noise reduction when using the PWMF by establishing new simplified closed-form expressions for three performance measures, namely, the signal distortion index, the noise reduction factor (originally proposed in the paper titled ldquoNew insights into the noise reduction Wiener filter,rdquo by J. Chen ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">IEEE Transactions on Audio, Speech, and Language Processing</i> , Vol. 15, no. 4, pp. 1218-1234, Jul. 2006) to analyze the single channel time-domain Wiener filter), and the output signal-to-noise ratio (SNR). Fourth, we analyze the effects of coherent and incoherent noise in addition to the benefits of utilizing multiple microphones. Fifth, we propose a new proof for the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a posteriori</i> SNR improvement achieved by the PMWF. Finally, we provide some simulations results to corroborate the findings of this work.
Multimedia information broadcasting using digital TV channels (1997)

In this paper, the structure of a new system to broadcast multimedia information within a digital TV channel is outlined. The proposed scheme is based on the DSM-CC (digital storage media command and control) functions, and uses a newly developed protocol that allows to efficiently convey multimedia information. Such information has the same characteristics of HTML files used in WWW environments, as it may contain text, images, sounds and animation organized as hypertext. The transport structure used is the MPEG-2 transport stream, which is the most popular standardized platform for the development of new digital TV services. Prototype software was developed to encode the file system by means of DSM-CC operations and include it in a MPEG-2 compatible transport system.
Stretching and unzipping nucleic acid hairpins using a synthetic nanopore (2008)

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA.
A high-density NAND EEPROM with block-page programming for microcomputer applications (1990)

A high-density, 5-V-only, 4-Mb CMOS EEPROM with a NAND-structured cell using Fowler-Nordheim tunneling for programming is discussed. The block-page mode is utilized for high-speed programming and easy microprocessor interface. On-chip test circuits for shortening test time and for evaluating cell characteristics yield highly reliable EEPROMs. The NAND EEPROM has many applications for microcomputer systems that require small size and large nonvolatile storage systems with low power consumption.
Biochemical Diagnosis of Vaginitis: Determination of Diamines in Vaginal Fluid (1982)

To assess correlations between the content of the diamines putrescine and cadaverine in vaginal fluid and the clinical manifestations of vaginitis, a rapid procedure for the determination of diamines has been developed. The procedure involves thin-layer chromatography of the dansylated vaginal washings; then the fluorescence of dansyl diamines is compared with that of dansyl alanine. For 520 college women, the result of the test for diamines was positive in 173 (88%) of 197 women with nonspecific vaginitis or vaginitis due to Trichomonas vaginalis and was negative in 291 (90%) of 323 women without nonspecific vaginitis or vaginitis due to T. vaginalis. The diamine content of vaginal fluid specimens after therapy with metronidazole was correlated with the clinical response to treatment.
Lysosomal Dysfunction Promotes Cleavage and Neurotoxicity of Tau In Vivo (2010)

Expansion of the lysosomal system, including cathepsin D upregulation, is an early and prominent finding in Alzheimer's disease brain. Cell culture studies, however, have provided differing perspectives on the lysosomal connection to Alzheimer's disease, including both protective and detrimental influences. We sought to clarify and molecularly define the connection in vivo in a genetically tractable model organism. Cathepsin D is upregulated with age in a Drosophila model of Alzheimer's disease and related tauopathies. Genetic analysis reveals that cathepsin D plays a neuroprotective role because genetic ablation of cathepsin D markedly potentiates tau-induced neurotoxicity. Further, generation of a C-terminally truncated form of tau found in Alzheimer's disease patients is significantly increased in the absence of cathepsin D. We show that truncated tau has markedly increased neurotoxicity, while solubility of truncated tau is decreased. Importantly, the toxicity of truncated tau is not affected by removal of cathepsin D, providing genetic evidence that modulation of neurotoxicity by cathepsin D is mediated through C-terminal cleavage of tau. We demonstrate that removing cathepsin D in adult postmitotic neurons leads to aberrant lysosomal expansion and caspase activation in vivo, suggesting a mechanism for C-terminal truncation of tau. We also demonstrate that both cathepsin D knockout mice and cathepsin D-deficient sheep show abnormal C-terminal truncation of tau and accompanying caspase activation. Thus, caspase cleavage of tau may be a molecular mechanism through which lysosomal dysfunction and neurodegeneration are causally linked in Alzheimer's disease.
Cell Type Regulates Selective Segregation of Mouse Chromosome 7 DNA Strands in Mitosis (2006)

After chromosome replication, sister chromatid copies are generally thought to segregate randomly to daughter cells. However, sister chromatids differ in their DNA strands, with each chromatid inheriting one older strand that is paired to a newly synthesized strand. Genetic analysis with a homologous chromosome pair indicated nonrandom chromatid distribution in embryonic stem cells. Biased segregation pattern was also found in all 100 endoderm cells examined, but not in any of the 165 neuroectoderm cells. In contrast, the mesoderm, cardiomyocyte, and pancreatic cells exhibited a random mode of segregation. Strand distribution mechanisms regulated by cell type may have consequences for cellular differentiation and for evolving strategies for developmental mechanisms.
Digital steganography: hiding data within data (2001)

Digital steganography is the art of inconspicuously hiding data within data. Steganography's goal in general is to hide data well enough that unintended recipients do not suspect the steganographic medium of containing hidden data. The software and links mentioned in this article are just a sample of the steganography tools currently available. As privacy concerns continue to develop along with the digital communication domain, steganography will undoubtedly play a growing role in society. For this reason, it is important that we are aware of digital steganography technology and its implications. Equally important are the ethical concerns of using steganography and steganalysis. Steganography enhances rather than replaces encryption. Messages are not secure simply by virtue of being hidden. Likewise, steganography is not about keeping your message from being known - it's about keeping its existence from being known.