gebhart/patrepeval huggingface dataset:
Expanded Breadth of the T-Cell Response to Mosaic Human Immunodeficiency Virus Type 1 Envelope DNA Vaccination (2008)

An effective AIDS vaccine must control highly diverse circulating strains of human immunodeficiency virus type 1 (HIV-1). Among HIV-1 gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV-1 Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential T-cell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining in inbred mice with a standardized panel of highly conserved 15-mer PTE peptides. One-, two-, and three-mosaic sets that increased theoretical epitope coverage were developed. The breadth and magnitude of T-cell immunity stimulated by these vaccines were compared to those for natural strain Envs; additional comparisons were performed on mutant Envs, including gp160 or gp145 with or without V regions and gp41 deletions. Among them, the two- or three-mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the three-mosaic set elicited responses to an average of eight peptide pools, compared to two pools for a set of three natural Envs. Synthetic mosaic HIV-1 antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T-cell-based HIV-1 vaccines.
Boosting image retrieval (2002)

We present an approach for image retrieval using a very large number of highly selective features and efficient online learning. Our approach is predicated on the assumption that each image is generated by a sparse set of visual "causes" and that images which are visually similar share causes. We propose a mechanism for computing a very large number of highly selective features which capture some aspects of this causal structure (in our implementation there are over 45,000 highly selective features). At query time a user selects a few example images, and a technique known as "boosting" is used to learn a classification function in this feature space. By construction, the boosting procedure learns a simple classifier which only relies on 20 of the features. As a result a very large database of images can be scanned rapidly, perhaps a million images per second. Finally we will describe a set of experiments performed using our retrieval system on a database of 3000 images.
Crystal Structure of a Self-Spliced Group II Intron (2008)

Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.
Frequency Modulation of Cavity Stabilized Solid State Diode Oscillators (1973)

A coupled cavity technique for frequency modulation of cavity stabilized solid state diode sources is described. This technique provides FM deviations suitable for communications system applications while still retaining low FM noise.
Solid-phase direct DNA sequencing of allele-specific polymerase chain reaction-amplified HLA-DR genes. (1991)

We describe in this report a new strategy to directly sequence polymerase chain reaction-amplified human leucocyte antigen DRB genes using biotinylated allele-specific synthetic oligonucleotide primers coupled to streptavidin-coated magnetic beads. The use of allele-specific primers in the polymerase chain reaction allows for selective amplification of DNA from one haplotype, which when combined with the direct sequencing technique circumvents the need for DNA cloning prior to sequencing. We demonstrate here that this method can be used to characterize human leucocyte antigen DRB genes among heterozygous individuals. This method can be used for the rapid analysis of highly polymorphic genes among individuals heterozygous at the gene of interest.
Human T-lymphocyte activation is associated with changes in O-glycan biosynthesis. (1988)

The activation of human T-lymphocytes by anti-CD3 antibodies and interleukin-2 results in a marked increase in apparent molecular weight of the major cell-surface sialoglycoprotein. Both forms of the sialoglycoprotein were identified as leukosialin by a monospecific antiserum, and the differences in molecular weight were found to be due to changes in the carbohydrate structures. Our results suggest that resting T-lymphocytes express on leukosialin the disialotetrasaccharides NeuNAc alpha 2----3Gal beta 1----3(NeuNAc alpha 2----6)Gal-NAc-Ser/Thr, whereas activated human T-cells carry on leukosialin exclusively the more complex structures NeuNAc alpha 2----3Gal beta 1----3(NeuNAc alpha 2----3Gal beta 1----4GlcNAc beta 1----6)GalNAc-Ser/Thr. The radical shift in the biosynthetic pathway of O-glycans in activated T-lymphocytes compared to resting cells is apparently caused by a decrease of alpha 2----6 sialyltransferase activity and by the parallel dramatic stimulation of the beta 1----6GlcNAc-transferase. Since both enzymes compete for the same precursor substrate, the coordinate changes in their activities are most likely responsible for the complete change of the carbohydrate structures on leukosialin during the activation of human T-lymphocytes.
Dose fractionation of radiolabeled antibodies in patients with metastatic colon cancer. (1992)

Twelve patients with metastatic colon cancer were treated with 131I-chimeric B72.3 (IgG-4) at total doses of 28 or 36 mCi/m2 in two or three weekly fractions. Bone marrow suppression was the only significant side effect. The degree of bone marrow suppression adjusted for whole-body dose was modestly but statistically significantly (p = 0.04) less than that seen with identical doses given as a single infusion for the total dose of 36 mCi/m2. Nine of twelve patients developed an antibody response to ch B72.3, which altered the kinetics of radiolabeled antibody in four patients given a second course of therapy. One patient had a minor response that lasted 4 mo. Fractionation of this particular radiolabeled antibody at the dose schedule used produced a modest increase in the therapeutic window in regard to administered dose.
Antithrombotic Therapy To Prevent Stroke in Patients with Atrial Fibrillation (1999)

Adjusted-dose warfarin and aspirin reduce stroke in patients with atrial fibrillation, and warfarin is substantially more efficacious than aspirin. The benefit of antithrombotic therapy was not offset by the occurrence of major hemorrhage among participants in randomized trials. Judicious use of antithrombotic therapy, tailored according to the inherent risk for stroke, importantly reduces stroke in patients with atrial fibrillation.
Spherical Clay Conglomerates:  A Novel Stationary Phase for Solid-Phase Extraction and “Reversed-Phase” Liquid Chromatography (1999)

A new solid phase is presented to be used for the solid-phase extraction (SPE) of organic compounds from aqueous solutions and as a stationary phase for the separation of organic compounds in "reversed-phase" HPLC. The material consists of spherical clay conglomerates (SCCs) in the size ranges of 2-5, 5-10, and 10-20 μm. SCCs are especially well suited for the extraction and separation of aromatic compounds with electron-withdrawing substituents, because of the formation of specific electron donor-acceptor (EDA) complexes of such compounds with natural clay minerals. A series of nitroaromatic compounds (NACs), e.g., nitrophenols, and nitrotoluenes, served as probe substances for the characterization of the SPE with SCCs online coupled to a C18-HPLC-DAD system. Breakthrough volumes were > 1 L and method detection limits (MDLs) < 100 ng/L for compounds with moderate to high affinity towards clay minerals. The performance of the material is hardly affected by matrix effects and because of its excellent physical properties, i.e., regenerability and pressure-resistance, it meets the requirements for fully automated routine trace analysis of several primary pollutants, such as 6-methyl-2,4-dinitrophenol (DNOC) or 2,4,6-trinitrotoluene (TNT), in various natural waters. Offline SPE with SCCs was superior or equivalent to commercial SPE products for analysis of such compounds. Finally, SCCs are shown to be well suited as a stationary phase in reversed-phase HPLC. This opens a wide range of applications, e.g., as an easy and fast separation technique that is orthogonal to C18 reversed-phase HPLC.
The cognitive power meter: Looking beyond the smart meter (2013)

The smart meter is often heralded as the key component supporting energy displays that can notify home occupants of their energy usage. But, a smart meter is only a digital power meter with enhanced communications capabilities - it is not actually smart. We need to look beyond the smart meter and define what intelligence is needed to actually make a meter smart. One area with promise is load disaggregation. Load disaggregation can be used to determine what loads contributing to the consumption reading at the smart meter. A smart meter incorporating load disaggregation intelligence can be seen as going beyond the traditional smart meter - what we call a cognitive power meter (c-meter). However, using load disaggregation, in its current form, is not feasible. We critically review the requirements for a c-meter and provide insights as to how load disaggregation research needs to change to make the c-meters a reality.
Glutamatergic approaches in major depressive disorder: focus onketamine, memantine and riluzole (2012)

The role of glutamate in modulating various mood states is being increasingly recognized and researched. Existing antidepressants have been shown to exert effects on various glutamatergic mechanisms, even if such agents are traditionally classified as working via other mechanisms, such as selective serotonin reuptake inhibitors. The NMDA receptor antagonist ketamine has been investigated in various mood disorders, especially major depressive disorder (MDD). It was found to produce a rapid, robust and persistent antidepressant effect. Although it can produce cognitive, dissociative and perceptual disturbances, these tend to be transient and do not outlast the antidepressant effect. Trials with memantine and riluzole, agents with actions broadly similar to and different from ketamine on the glutamatergic system, are also reviewed in MDD and prospects for future research in the area are discussed. Although preclinical studies are discussed, the main focus of the review is on clinical outcomes.
Inhibition of Fatty Acyl Desaturase by Cyclopropene Fatty Acids (1967)

Abstract Comparisons were made of the ratios of the specific activities of stearic acid to oleic acid in adipose tissue and liver triglycerides of rats given methyl stearate-1-14C dissolved in 0.25 ml of corn oil and Sterculia foetida oil. The ratios were about 3 in the corn oil control animals compared to 31 to 43 in adipose tissue and 44 to 246 in liver triglycerides of the S. foetida test animals. When the labeled stearate was administered in 0.5 ml of S. foetida oil almost no label appeared in tissue oleic acid. The inhibition was also shown to be affected by sterculic acid in vitro with rat liver preparations. Evidence was obtained that the mechanism of inhibition is the irreversible binding of enzyme sulfhydryl groups by the cyclopropene group.
Restoration of telomeres in human papillomavirus-immortalized human anogenital epithelial cells. (1994)

Loss of telomeres has been hypothesized to be important in cellular senescence and may play a role in carcinogenesis. In this study, we have measured telomere length in association with the immortalization and transformation of human cervical and foreskin epithelial cells by the human papillomavirus type 16 or 18 E6 and E7 open reading frames. By using a telomeric TTAGGG repeat probe, it was shown that the telomeres of precrisis normal and E6-, E7-, and E6/E7-expressing cells gradually shortened with passaging (30 to 100 bp per population doubling). Cells that expressed both E6 and E7 went through a crisis period and gave rise to immortalized lines. In contrast to precrisis cells, E6/E7-immortalized cells generally showed an increase in telomere length as they were passaged in culture, with some later passage lines having telomeres that were similar to or longer than the earliest-passage precrisis cells examined. No consistent association could be made between telomere length and tumorigenicity of cells in nude mice. However, of the three cell lines that grew in vivo, two had long telomeres, thus arguing against the hypothesis that cancer cells favor shortened telomeres. Our results indicate that arrest of telomere shortening may be important in human papillomavirus-associated immortalization and that restoration of telomere length may be advantageous to cells with regard to their ability to proliferate.
[Design of recombinant plasmids for effective Zymomonas mobilis pyruvate decarboxylase (pdk) gene expression in Bacillus subtilis cells]. (1994)

The pdk gene from Z. mobilis localized on the 4.7-kb SpHI DNA fragment in plasmid pB201 was subcloned using DraI restriction endonuclease into the SmaI site of the phage cloning vector M13mp19. The derivatives of M13mp19 obtained, containing 1.8-kb inserts of the pdk gene in two opposite orientations, were used for DNA sequencing and site-directed mutagenesis. The latter was performed using polymerase chain reaction (PCR) and synthetic deoxyribonucleotides of appropriate structure as primers. In this way a BamHI site near the initial (formylmethionine) codon of the pdk gene was created. After amplification the pdk gene was treated by restriction endonuclease BamHI and cloned into pUC19, and then recloned into shuttle vector pCB20 capable of replicating in both Gram negative and Gram positive bacteria. A recombinant plasmid pCB20pdkI--a derivative of pCB20 carrying the pdk gene under control of the "expression unit" EU19035 containing a bacillar vegetative promoter and an RBS site was obtained. The properties of the pCB20pdkI in E. coli and Bac. subtilis cells were studied. It was shown that pCB20pdkI determines a high level of PDK synthesis in Bac. subtilis. At the same time, it strongly inhibits E. coli cell growth and segregates rapidly from this host.
Formation and elimination of 7-hydroxymethotrexate in the rat in vivo after methotrexate administration. (1989)

Bile, urine, and serum concentrations of methotrexate (MTX) and 7-hydroxy-methotrexate (7-OH-MTX) were monitored in rats in vivo following a short-time infusion of 10 mg/kg [3H]MTX. The experiments were performed in one group of anesthetized, bile-drained rats and in two control groups, one anesthetized and one unanesthetized, that were not bile-drained. Peak biliary levels of MTX (3.8 x 10(-3) M) and 7-OH-MTX (1.8 x 10(-4) M) appeared within 15 min after cessation of infusions. For two log ranges of serum MTX concentrations, biliary levels remained 180-fold higher. High bile 7-OH-MTX levels appeared few min after start of MTX administration, and were 720 times higher than the peak serum concentrations, indicating that the liver is a major site of 7-OH-MTX formation in the rat. 7-OH-MTX concentrations in bile declined monophasically with a half-life of 29.4 min, while MTX showed a biphasic elimination with initial and second phase half-lives of 23.1 and 86.4 min, respectively. Bile was the major excretory route for MTX and 7-OH-MTX, with 50% of the dose recovered as the parent compound and 3.6% as the metabolite. There was no difference in urinary recovery of MTX in bile-drained and control animals, indicative of insignificant enterohepatic circulation of MTX. This was further corroborated by the finding of just 2.1% urinary recovery of MTX in rats who received previously collected MTX-containing bile through a duodenal catheter. Serum concentration curves were analyzed according to a three-compartment open model with an initial elimination half-life of 1.7-3.3 min, a second phase half-life of 15.4-21.0 min, and a terminal phase half-life of 119-240 min. Our finding of 7-OH-MTX formation and high biliary levels of the metabolite in the rat, can be used as basis for studies of interactions with in vivo MTX conversion to the 7-hydroxy metabolite.
Degradation of mRNA in bacteria: emergence of ubiquitous features (2000)

The amount of a messenger RNA available for protein synthesis depends on the efficiency of its transcription and stability. The mechanisms of degradation that determine the stability of mRNAs in bacteria have been investigated extensively during the last decade and have begun to be better understood. Several endo- and exoribonucleases involved in the mRNA metabolism have been characterized as well as structural features of mRNA which account for its stability have been determined. The most important recent developments have been the discovery that the degradosome-a multiprotein complex containing an endoribonuclease (RNase E), an exoribonuclease (polynucleotide phosphorylase), and a DEAD box helicase (RhlB)-has a central role in mRNA degradation and that oligo(A) tails synthesized by poly(A) polymerase facilitate the degradation of mRNAs and RNA fragments. Moreover, the phosphorylation status and the base pairing of 5' extremities, together with 3' secondary structures of transcriptional terminators, contribute to the stability of primary transcripts. Degradation of mRNAs can follow several independent pathways. Interestingly, poly(A) tails and multienzyme complexes also control the stability and the degradation of eukaryotic mRNAs. These discoveries have led to the development of refined models of mRNA degradation.
Amplification and expression of the epidermal growth factor receptor gene in human glioma xenografts. (1988)

Xenografts from eight malignant human gliomas were established in athymic mice and were used to study amplification and expression of the epidermal growth factor receptor (EGFR) gene. Tissue identity between biopsy and xenografts was confirmed by karyotypic profiles, which showed that each glioma xenograft retained structural abnormalities, including double minute chromosomes, present in the parent glioma. EGFR gene amplification was found in six of the eight glioma biopsies and their corresponding xenografts. Expression of the EGFR gene was measured by Scatchard analysis, affinity reactions, immunoprecipitations, Western immunoblots, and immunocytochemistry; significant expression of the EGFR gene was only detectable in xenografts with EGFR gene amplification. Moreover, five of the six xenografts with EGFR gene amplification demonstrated structural alterations of the EGFR gene, which was associated with low-molecular-weight EGFR proteins. These xenografts represent an excellent tissue source and in vivo model system for characterizing the epidermal growth factor receptor in malignant human gliomas.
Synthesis of new derivatives of β‐carboline‐hydantoin (1990)

Abstract Reaction of tetrahydro‐β‐carboline‐3‐carboxylic acids 4a‐c with alkyl and phenyl isocyanates in acetone provide the corresponding 2,5‐disubstituted 1,3‐dioxo‐6 H ‐1,2,3,5,11,11a‐hexahydroimidazo[1,5‐ b ]‐β‐carbolines 2a‐r .
A knowledge transfer and boosting approach to the prediction of affect in movies (2017)

Affect prediction is a classical problem and has recently garnered special interest in multimedia applications. Affect prediction in movies is one such domain, potentially aiding the design as well as the impact analysis of movies. Given the large diversity in movies (such as different genres and languages), obtaining a comprehensive movie dataset for modeling affect is challenging while models trained on smaller datasets may not generalize. In this paper, we address the problem of continuous affect ratings with the availability of limited in-domain data resources. We initially setup several baseline models trained on in-domain data, followed by a proposal of a Knowledge Transfer (KT) + Gradient Boosting (GB) approach. KT learns models on a larger (mismatched) data which are then adapted to make predictions on the data of interest. GB further updates these predictions based on models learnt from the in-domain data. We observe that the KT + GB models provide Concordance Correlation Coefficient values of 0.13 and 0.27 for valence and affect prediction on the continuous LIRIS ACCEDE dataset against best baseline prediction values of 0.12 and 0.11. Not only the KT + GB models improve the overall performance metrics, we also observe a more consistent model performance across movies of various genres.
Salophan Complexes of Group IV Metals (2005)

Abstract The coordination chemistry of tetradentate Salophan ligands with titanium and zirconium alkoxides is described for the first time. Three new Salophan ligand precursors featuring different phenolate substituents ( ortho‐ Me, ortho,para‐ di‐Cl, ortho,para‐ di‐ t Bu) were synthesized in addition to the known prototypical Salophan precursor, by a sequence of condensation and reduction. All ligand precursors were reacted with the metal alkoxides Ti(O i Pr) 4 and Zr(O t Bu) 4 . The unsubstituted Salophan led to a complex product mixture for both titanium and zirconium. The methyl‐substituted ligand led to a clean complex only with zirconium, and the other ligands gave well‐defined coordination chemistry with both metals. NMR analysis indicated that these Salophans acted as dianionic ligands, giving rise to hexa‐coordinate complexes of C 2 ‐symmetry. X‐ray analysis of three complexes supported this view, and revealed that the ligands wrapping mode was fac‐fac and that the orientation of the labile groups was cis . A partial hydrolysis of one of the titanium complexes led to a dinuclear bridging oxo complex in which the ligand wrapping mode had changed to fac‐mer , as revealed from its crystal structure. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Texture Networks: Feed-forward Synthesis of Textures and Stylized Images (2016)

Gatys et al. recently demonstrated that deep networks can generate beautiful textures and stylized images from a single texture example. However, their methods requires a slow and memory-consuming optimization process. We propose here an alternative approach that moves the computational burden to a learning stage. Given a single example of a texture, our approach trains compact feed-forward convolutional networks to generate multiple samples of the same texture of arbitrary size and to transfer artistic style from a given image to any other image. The resulting networks are remarkably light-weight and can generate textures of quality comparable to Gatys~et~al., but hundreds of times faster. More generally, our approach highlights the power and flexibility of generative feed-forward models trained with complex and expressive loss functions.