gebhart/patrepeval huggingface dataset:
Regulation of dihydrodipicolinate synthase and aspartate kinase in Bacillus subtilis (1975)

The regulation of dihydrodipicolinate synthase (EC 4.2.1.52) and aspartate kinase (EC 2.7.2.4) was studied in Bacillus subtilis 168. Starvation for lysine gave depression of one aspartate kinase isoenzyme but not of dihydrodipicolinate synthase. Strains resistant to growth inhibition by the lysine analogue thiosine exhibited constitutively derepressed synthesis of one aspartate kinase isoenzyme but had normal levels of dihydrodipicolinate synthase. The data provide strong evidence that lysine is not the signal for derepression of dihydrodipicolinate synthase. Nevertheless, dihydrodipicolinate synthase specific activity increased during sporulation, and it is suggested that this increase may result, in part, from resistance to proteolysis of that enzyme.
The Epitopes Targeted by the Rheumatoid Arthritis-Associated Antifilaggrin Autoantibodies are Posttranslationally Generated on Various Sites of (Pro)Filaggrin by Deimination of Arginine Residues (1999)

Antifilaggrin autoantibodies (AFA) are a population of IgG autoantibodies associated to rheumatoid arthritis (RA), which includes the so-called "antikeratin" Abs and antiperinuclear factor. AFA are the most specific serological markers of RA. We previously showed that they recognize human epidermal filaggrin and other profilaggrin-related proteins of various epithelial tissues. Here, we report further characterization of the protein Ags and epitopes targeted by AFA. All the Ags that exhibit numerous neutral/ acidic isoelectric variants were immunochemically demonstrated to be deiminated proteins. In vitro deimination of a recombinant human filaggrin by a peptidylarginine deiminase generated AFA epitopes on the protein. Moreover, two of three filaggrin-derived synthetic peptides with a citrulline in the central position were specifically and widely recognized by AFA affinity-purified from a series of RA sera. These results indicate that citrulline residues are constitutive of the AFA epitopes, but only in the context of specific amino acid sequences of filaggrin. In competition experiments, the two peptides abolished the AFA reactivity of RA sera, showing that they present major AFA epitopes. These data should help in the identification of a putative deiminated AFA-inducing or cross-reactive articular autoantigen and provide new insights into the pathogenesis of RA. They could also open the way toward specific immunosuppressive and/or preventive therapy of RA.
Analysis of vitamin D‐regulated gene expression in LNCaP human prostate cancer cells using cDNA microarrays (2003)

The putative 1,25(OH)2D3 target genes appear to be involved in a variety of cellular functions including growth regulation, differentiation, membrane transport, cell-cell and cell-matrix interactions, DNA repair, and inhibition of metastasis. The up-regulation of IGFBP-3 gene has been shown to be crucial in 1,25(OH)2D3-mediated inhibition of LNCaP cell growth. 1,25(OH)2D3 regulation of androgen-responsive genes as well as genes involved in androgen catabolism suggests that there are interactions between 1,25(OH)2D3 and androgen signaling pathways in LNCaP cells. Further studies on the role of these genes and others in mediating the anti-cancer effects of 1,25(OH)2D3 may lead to better approaches to the prevention and treatment of prostate cancer.
Developmental regulation of hexosamine biosynthesis by protein phosphatases 2A and 2C in Blastocladiella emersonii (1993)

Extracts of the aquatic fungus Blastocladiella emersonii were found to contain protein phosphatases type 1, type 2A, and type 2C with properties analogous to those found in mammalian tissues. The activities of all three protein phosphatases are developmentally regulated, increasing during sporulation, with maximum level in zoospores. Protein phosphatases 2A and 2C, present in zoospore extracts, catalyze the dephosphorylation of L-glutamine:fructose-6-phosphate amidotransferase (EC 2.6.1.16, amidotransferase), a key regulatory enzyme in hexosamine biosynthesis. The protein phosphatase inhibitor okadaic acid induces encystment and inhibits germ tube formation but does not affect the synthesis of the chitinous cell wall. These results strongly suggest that phosphatase 2C is responsible for the dephosphorylation of amidotransferase in vivo. This dephosphorylation is inhibited by uridine-5'-diphospho-N-acetylglucosamine, the end product of hexosamine synthesis and the substrate for chitin synthesis. This result demonstrates a dual role of uridine-5'-diphospho-N-acetylglucosamine by inhibiting the activity of the phosphorylated form of amidotransferase and by preventing its dephosphorylation by protein phosphatases.
Oncolytic Vaccinia Virotherapy of Anaplastic Thyroid Cancer in Vivo (2008)

GLV-1h68 efficiently infects, expresses transgenes within, and inhibits the growth of ATC in vivo. These promising findings support future clinical trials for patients with ATC.
A study of language models for exploiting user feedback in information retrieval (2009)

Feedback is an important technique in Information Retrieval to have users provide contextual information about their search needs, with the goal of improving retrieval accuracy and achieving personalization. Relevance feedback has been studied extensively, and in recent years new types of feedback such as implicit feedback and collective feedback have attracted much research interest. However, there are not many works exploring language modeling techniques for feedback. In this thesis, I study how to use language models to exploit user feedback, including long-term implicit feedback and short-term explicit term-based feedback. I show that language models have unique advantages in modeling users search interests and preferences in the long-term, as well as capturing term and sub-topic relevance in the short-term. 
In particular, I first study exploiting implicit feedback from a user’s long-term search log. Language models are constructed to represent both information needs in past searches and history context for new searches. These history language models capture the user’s search interests and preferences, thus can help personalize search results for new queries. Not only that, by selecting topics in a user’s long-term search history that represent their long-lasting exploratory interests and building language models for these topics, the user can receive personalized recommendation of new information without a query. 
I also study term-based explicit feedback that deviates from traditional document-based relevant feedback. By modeling query sub-topics using language models and asking the user for term-level relevance judgments, both term and sub-topic level relevance can be incorporated into a new query model that improves retrieval accuracy. 
Finally, I have designed the UCAIR system to support development, deployment and evaluation of feedback algorithms for personalized search and recommendation. The system not only implements some of the previously proposed algorithms but also provides a highly reusable and easily extensible platform for designing and testing new feedback algorithms in the language modeling framework. It is hoped that this system will help reduce the difficulty of building personalized feedback systems and generating feedback evaluation data sets.
The line absorption coefficient (2005)

The strengths and shapes of spectral lines contain a great deal of information about the stars, and the line absorption coefficient plays a fundamental role here. The situation in this regard is similar to the effect the continuous absorption coefficient has on the shape of the continuum. Lines are more interesting, however, because several different physical effects can enter the structuring of the final absorption coefficient. Each of these has its own variation with wavelength across the line, that is, its own absorption coefficient. The main processes we consider in this chapter are: (1) natural atomic absorption, (2) pressure broadening, of which there are several, and (3) thermal Doppler broadening. The final combined absorption coefficient is the multiple convolution of these individual absorption coefficients. One of the remarkable results of these studies is that the natural atomic absorption and all the significant pressure broadenings have the same wavelength dependence in their individual absorption coefficients (with the notable exception of the hydrogen lines), namely the dispersion profile. This leads to a tremendous simplification, as we shall see, since the convolution of dispersion profiles is a dispersion profile with a half-width equal to the sum of the individual half-widths of the contributing processes. The thermal broadening, on the other hand, reflects the Maxwellian velocity distribution of the absorbing atoms and ions via the Doppler effect, so its wavelength shape is a Gaussian. The final absorption coefficient is therefore a convolution of the dispersion profile with the Gaussian profile.
Benzyl and Naphthalene Methylphosphonic Acid Inhibitors of Autotaxin with Anti‐invasive and Anti‐metastatic Activity (2011)

Autotaxin (ATX, NPP2) is a member of the nucleotide pyrophosphate phosphodiesterase enzyme family. ATX catalyzes the hydrolytic cleavage of lysophosphatidylcholine (LPC) by lysophospholipase D activity, which leads to generation of the growth-factor-like lipid mediator lysophosphatidic acid (LPA). ATX is highly upregulated in metastatic and chemotherapy-resistant carcinomas and represents a potential target to mediate cancer invasion and metastasis. Herein we report the synthesis and pharmacological characterization of ATX inhibitors based on the 4-tetradecanoylaminobenzylphosphonic acid scaffold, which was previously found to lack sufficient stability in cellular systems. The new 4-substituted benzylphosphonic acid and 6-substituted naphthalen-2-ylmethylphosphonic acid analogues block ATX activity with K(i) values in the low micromolar to nanomolar range against FS3, LPC, and nucleotide substrates through a mixed-mode inhibition mechanism. None of the compounds tested inhibit the activity of related enzymes (NPP6 and NPP7). In addition, the compounds were evaluated as agonists or antagonists of seven LPA receptor (LPAR) subtypes. Analogues 22 and 30 b, the two most potent ATX inhibitors, inhibit the invasion of MM1 hepatoma cells across murine mesothelial and human vascular endothelial monolayers in vitro in a dose-dependent manner. The average terminal half-life for compound 22 is 10±5.4 h and it causes a long-lasting decrease in plasma LPA levels. Compounds 22 and 30 b significantly decrease lung metastasis of B16-F10 syngeneic mouse melanoma in a post-inoculation treatment paradigm. The 4-substituted benzylphosphonic acids and 6-substituted naphthalen-2-ylmethylphosphonic acids described herein represent new lead compounds that effectively inhibit the ATX-LPA-LPAR axis both in vitro and in vivo.
Fluorescent Whole-Cell Hybridization with 16S rRNA-Targeted Oligonucleotide Probes To Identify Brucella spp. by Flow Cytometry (2000)

A whole-cell hybridization assay with fluorescent oligonucleotide probes derived from the 16S rRNA sequence of Brucella abortus in combination with flow cytometry has been developed. With the three fluorescent probes selected, a positive signal was observed with all the representative strains of the species and biovars of Brucella and with a total of nine different Brucella clinical isolates. Using the B9 probe in the hybridization assay, it was possible to discriminate between Brucella suis biovars 2, 3, 4, and 5 and almost all the other Brucella spp. On the basis of differences in fluorescence intensities, no discrimination was established between Brucella spp. and other phylogenetically related microorganisms. No positive fluorescence signals were detected with any of the bacteria showing serological cross-reactions with Brucella spp. and with a total of 17 clinical isolates not belonging to the genus Brucella. These results suggest that the 16S rRNA whole-cell hybridization technique could be a valuable diagnostic tool for the detection and identification of Brucella spp.
A fast and area efficient 2-D convolver for real time image processing (2008)

Two dimentional (2-D) convolver is a basic processing unit used in real time video and image processing algorithms. VLSI chip area and external memory bus bandwidth are two major concerns of efficient and fast 2-D convolver. Till now people have considered both of these parameters separately. Achieving low complexity and high packing density at the same time is a difficult task. This paper proposes a new FPGA oriented architecture which uses a multiplierless 2-D convolver with area efficient buffering scheme which achieves high speed and saves up to 80% of chip area at the same time.
PNA FISH: an intelligent stain for rapid diagnosis of infectious diseases (2003)

Fluorescence in situ hybridization using peptide nucleic acid probes (PNA FISH) is a novel diagnostic technique combining the simplicity of traditional staining procedures with the unique performance of PNA probes to provide rapid and accurate diagnosis of infectious diseases; a feature that makes PNA FISH well suited for routine application and enables clinical microbiology laboratories to report important information for patient therapy within a time frame not possible using classic biochemical methods. Having transitioned from an academic curiosity into an advanced diagnostic tool, PNA probes are now debuting on the infectious disease stage, representing the new generation of therapy-directing diagnostics.
Crystal Engineering Using Anilic Acids and Dipyridyl Compounds through a New Supramolecular Synthon (2001)

The anilic acids, 2,5-dihydroxy-1,4-benzoquinone (1a), 2,5-dibromo-3,6-dihydroxy-1,4-benzoquinone (bromanilic acid; 1b), 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone (chloranilic acid; 1c), and 2,5-dicyano-3,6-dihydroxy-1,4-benzoquinone (cyananilic acid; 1d), were cocrystallized with rigid organic ligands containing two pyridine rings, 2,4-bipyridine (2a), 4,4'-bipyridine (2b), 1,2-bis(2-pyridyl)ethylene (3a), 1,2-bis(4-pyridyl)ethylene (3b), 2,2'-dipyridylacetylene (4a), 3,3'-dipyridylacetylene (4b), and 4,4'-dipyridylacetylene (4c). Fourteen complexes 5-18 were obtained as single crystals, and their crystal structures were successfully determined by X-ray analysis. All complexes except those with 2a are 1:1 and are composed of an infinite linear or zigzag tape structure, the formation of which is ascribed to intermolecular O-H...N, N(+)-H...O, or N(+)-H...O(-) hydrogen bonds or a combination of these between the anilic acids and the dipyridyl compounds. In the complexes 5 and 6, no infinite tape structure is observed although the molecular units connected by a similar hydrogen-bonding pattern are formed. For the 1:1 complexes, we have found two types of stacking arrangements, segregated stacks (7, 9, 12-15, 18) and alternated ones (8, 10, 11, 16, 17). In the complexes of 1c with the series of dipyridylacetylenes 4 (14, 15, 17), the neutral, dication, and monocaction states are formed depending on the nitrogen positions, which can be attributed to the different basicity of the pyridyl groups.
Age and gender detection in the I-DASH project (2011)

This article presents a description of the INESC-ID Age and Gender classification systems which were developed for aiding the detection of child abuse material within the scope of the European project I-DASH. The Age and Gender classification systems are composed respectively by the fusion of four and six individual subsystems trained with short- and long-term acoustic and prosodic features, different classification strategies, Gaussian Mixture Models-Universal Background Model (GMM-UBM), Multi-Layer Perceptrons (MLP) and Support Vector Machines (SVM), trained over five different speech corpus. The best results obtained by the calibration and linear logistic regression fusion back-end show an absolute improvement of 2% on the unweighted accuracy value for the Age and 1% for the Gender when compared to the best individual frontend systems in the development set. The final age/gender detection system evaluated using a six-hour child abuse (CA) test set achieved promising results given the extremely difficult conditions of this type of video material. In order to further improve the performance in the CA domain, the classification modules were adapted using unsupervised selection of training data. An automatic data selection algorithm using frame-level posterior probabilities was developed. Performance improvement after adapting the classification modules was around 10% relative when compared with the baseline classifiers.
Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing (2016)

Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants.
Mediators of inflammation and blood-brain barrier permeability in cerebral ischemia (2001)

Secondary brain damage is tissue injury that is not apparent immediately after an insult, but develops after a delay of hours or days and has typically been observed after ischemia, trauma or subarachnoidal haemorrhage [1]. Secondary ischemic brain damage develops as a consequence of: (a) brain edema, (b) post-ischemic microvascular stasis and vasomotor/hemodynamic deficits leading to hypoperfusion, and (c) post-ischemic inflammation involving activation of microglia and brain infiltration of peripheral inflammatory cells [1–3]. It is believed that damage to the tissues surrounding the ischemic core, known as the penumbra, can be reduced by therapeutic measures designed to prevent or minimize molecular events contributing to the development of secondary brain damage [3].
EpCAM an immunotherapeutic target for gastrointestinal malignancy: current experience and future challenges (2007)

Despite advances in surgery and adjuvant regimes, gastrointestinal malignancy remains a major cause of neoplastic mortality. Immunotherapy is an emerging and now successful treatment modality for numerous cancers that relies on the manipulation of the immune system and its effector functions to eradicate tumour cells. The discovery that the pan-epithelial homotypic cell adhesion molecule EpCAM is differentially expressed on gastrointestinal tumours has made this a viable target for immunotherapy. Clinical trials using naked anti EpCAM antibody, immunoconjugates, anti-idiotypic and dendritic cell vaccines have met variable success. The murine IgG2a Edrecolomab was shown to reduce mortality and morbidity at a level slightly lower than treatment with 5FU and Levamisole when administered to patients with advanced colorectal carcinoma in a large randomised controlled trial. Fully human and trifunctional antibodies that specifically recruit CD3-positive lymphocytes are now being tested clinically in the treatment of minimal residual disease and ascites. Although clinical trials are in their infancy, the future may bring forth an EpCAM mediated approach for the effective activation and harnessing of the immune system to destroy a pathological aberrance that has otherwise largely escaped its attention.
Über Diazoanhydride (1,2,3‐Oxydiazole oder Diazoxyde) und Diazoketone (1912)

g e l i die Verbindung in unreinem Zustande schon in Handeir (Gazz.chim.ital.'74, 370 jl694]).amid und 4-Acetyl-5-methyl-l,2,3-triazol.') Diese Auiialen 33h, 253 (1904).
A controlled study of the effects of ferric carboxymaltose on bone and haematinic biomarkers in chronic kidney disease and pregnancy (2017)

Changes in bone and haematinic biomarkers differ between patient groups following IV FCM. For patients with lower serum phosphate concentrations, limiting the dose and measuring levels 7 days after administration may mitigate clinically significant hypophosphataemia.
Maintenance of Stable Heterochromatin Domains by Dynamic HP1 Binding (2003)

One function of heterochromatin is the epigenetic silencing by sequestration of genes into transcriptionally repressed nuclear neighborhoods. Heterochromatin protein 1 (HP1) is a major component of heterochromatin and thus is a candidate for establishing and maintaining the transcriptionally repressive heterochromatin structure. Here we demonstrate that maintenance of stable heterochromatin domains in living cells involves the transient binding and dynamic exchange of HP1 from chromatin. HP1 exchange kinetics correlate with the condensation level of chromatin and are dependent on the histone methyltransferase Suv39h. The chromodomain and the chromoshadow domain of HP1 are both required for binding to native chromatin in vivo, but they contribute differentially to binding in euchromatin and heterochromatin. These data argue against HP1 repression of transcription by formation of static, higher order oligomeric networks but support a dynamic competition model, and they demonstrate that heterochromatin is accessible to regulatory factors.
Antipsychotic Drugs: Direct Correlation Between Clinical Potency and Presynaptic Action on Dopamine Neurons (1975)

Neuroleptic (antipsychotic) drugs inhibited the electrically stimulated release of [3-H] dopamine from rat striatal slices. The concentrations for 50 percent inhibition (ranging from 11.5 nanomolar for spiroperidol to 800 nanomolar for thioridazine) correlated closely with the average daily dosages of 25 neuroleptic drugs used clinically for schizophrenia. The correlation includes butyrophenones, phenothiazines, reserpine, pimozide, clozapine, and (plus)- butaclamol. Clinically inactive isomers [trans-thiothixene, trans-flupenthixol, and (minus)-butaclamol] required 20 to 1000 times higher concentrations than the active isomers to inhibit release. Compared to the inhibition of [3-H] dopamine release, much higher neuroleptic concentrations were needed to inhibit the electrically stimulated release of other neurotransmitters--[3-H] acetylcholine, [3-H-a1 (gamma-aminobutyric acid). The neuroleptic drugs may block the presynaptic coupling between impulse and neurosecretion.
Cryogenic Heat Transfer (1999)

Presents applied heat transfer principles in the range of extremely low temperatures. The specific features of heat transfer at cryogenic temperatures, such as variable properties, near critical convection, and Kapitza resistance, are described. This book includes many example problems, in each section, that help to illustrate the applications of t