gebhart/patrepeval huggingface dataset:
Principled Hybrids of Generative and Discriminative Models (2006)

When labelled training data is plentiful, discriminative techniques are widely used since they give excellent generalization performance. However, for large-scale applications such as object recognition, hand labelling of data is expensive, and there is much interest in semi-supervised techniques based on generative models in which the majority of the training data is unlabelled. Although the generalization performance of generative models can often be improved by ‘training them discriminatively’, they can then no longer make use of unlabelled data. In an attempt to gain the benefit of both generative and discriminative approaches, heuristic procedure have been proposed [2, 3] which interpolate between these two extremes by taking a convex combination of the generative and discriminative objective functions. In this paper we adopt a new perspective which says that there is only one correct way to train a given model, and that a ‘discriminatively trained’ generative model is fundamentally a new model [7]. From this viewpoint, generative and discriminative models correspond to specific choices for the prior over parameters. As well as giving a principled interpretation of ‘discriminative training’, this approach opens door to very general ways of interpolating between generative and discriminative extremes through alternative choices of prior. We illustrate this framework using both synthetic data and a practical example in the domain of multi-class object recognition. Our results show that, when the supply of labelled training data is limited, the optimum performance corresponds to a balance between the purely generative and the purely discriminative.
The exoenzyme S regulon of Pseudomonas aeruginosa (1997)

Pseudomonas aeruginosa can cause severe life-threatening infections in which the bacterium disseminates rapidly from epithelial colonization sites to the bloodstream. In experimental models, the ability of P. aeruginosa to disseminate is linked to epithelial injury, in vitro cytotoxicity and expression of the exoenzyme S regulon. Using the expression of ExoS as a model, a series of genes that are important for regulation, secretion and, perhaps, intoxication of eukaryotic cells have been identified. Proteins encoded by the exoenzyme S regulon and the Yersinia Yop virulon show a high level of amino acid homology, suggesting that P. aeruginosa may use a contact-mediated translocation mechanism to transfer anti-host factors directly into eukaryotic cells. Potential anti-host factors that may disrupt eukaryotic signal transduction through ADP-ribosylation include ExoS and ExoT. Expression of ExoU, another candidate anti-host factor, has been correlated with acute cytotoxicity and lung epithelial injury. Members of the exoenzyme S regulon represent only a portion of the virulence factor arsenal possessed by P. aeruginosa. It will be important to understand how the exoenzyme S regulon contributes to pathogenesis and whether these factors could serve as potential therapeutic targets.
Optical FDM transmission technique (1987)

This paper surveys the present state of optical frequency-division multiplexing (optical FDM) technologies. Utilizing a broad optical frequency bandwidth up to several hundred terahertz, optical FDM is expected to find applications in large-capacity trunking and local distribution networks. The present state of the related technologies and the future prospects for these applications are discussed.
Restoration strategies and spare capacity requirements in self-healing ATM networks (1999)

This paper studies the capacity and flow assignment problem arising in the design of self-healing asynchronous transfer mode (ATM) networks using the virtual path concept. The problem is formulated here as a linear programming problem which is solved using standard methods. The objective is to minimize the spare capacity cost for the given restoration requirement. The spare cost depends on the restoration strategies used in the network. We compare several restoration strategies quantitatively in terms of spare cost, notably: global versus failure-oriented reconfiguration, path versus link restoration, and state-dependent versus state-independent restoration. The advantages and disadvantages of various restoration strategies are also highlighted. Such comparisons provide useful guidance for real network design. Further, a new heuristic algorithm based on the minimum cost route concept is developed for the design of large self-healing ATM networks using path restoration. Numerical results illustrate that the heuristic algorithm is efficient and gives near-optimal solutions for the spare capacity allocation and flow assignment for tested examples.
Structure of a DNA Duplex Containing a Single 2‘-O-Methyl-β-d-araT:  Combined Use of NMR, Restrained Molecular Dynamics, and Full Relaxation Matrix Refinement (1996)

Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.
Interaction of CD154 with different receptors and its role in bidirectional signals (2014)

In addition to its classical receptor, CD40, it is now well established that CD154 also binds αIIbβ3, α5β1, and αMβ2 integrins. Although these integrins are all members of the same family, they bind CD154 differently. The current investigation aims to analyze the interaction of CD154 with α5β1 and αMβ2 and investigate its role in bidirectional signals in various human cell lines. Results obtained herein indicate that the CD154 residues involved in the interaction with α5β1 are N151 and Q166, whereas those involved in αMβ2 binding are common to residues required for CD40, namely Y145 and R203. Soluble CD40/CD154 or αMβ2/CD154 complexes do not interfere with the binding of CD154 to α5β1-positive cells, but inhibit the binding of CD154 to CD40- or αMβ2-positive cells, respectively. Ligation of CD154 on CD154-positive cells with soluble CD40, αIIbβ3, α5β1, or αMβ2 stimulates intracellular signaling, including MAPK phosphorylation. Given that CD154 exists as a trimer, our data strongly suggest that CD154 may bind concomitantly to two receptors of the same or different family, and biologically activate cells expressing both receptors. The characterization of CD154/receptor interactions helps the identification of new therapeutic targets for the prevention and/or treatment of CD154-associated autoimmune and inflammatory diseases.
Nuclear analogs of β-lactam antibiotics. I. Synthesis of O-2-isocephams (1977)

The preparation by total synthesis of a saturated cephalosporin analog 7-β-phenoxyacet-amido-3-ethoxy-O-2-isocepham-4-α-carboxylic acid 30, is described. Compound 30 was prepared via cycloaddition of azidoacetyl chloride to the cinnamylidene Schiff base of ethyl 2-amino-3, 3-diethoxypropionate 13b to give the cis-3-azido-4-styryl β-lactam 15b. Ozonolysis of 15b followed by sodium borohydride reduction gave the alcohol 18b. Boron trifluoride treatment of 18b gave ethyl 7-β-azido-3- β-ethoxy-O-2-isocephem-4-carboxylate 27. Reduction of the azido group followed by coupling with phenoxyacetic acid and saponification of the ester gave 30. The mechanism of the cycloaddition reaction and the stereochemical assignments are also discussed.
Roots of Acceptance: The Intercultural Communication of Religious Meanings. By William E. Biernatzki, S.J. (Inculturation: Working Papers on Living Faith and Cultures, No. XIII. Rome: Gregorian University Press for the Cultures and Religions Centre, Gregorian University, 1991. 186 pp. 23,000 Lira; $19.50 (paper). (1992)

Roots of Acceptance: The Intercultural Communication of Religious Meanings. By William E. Biernatzki, S.J. (Inculturation: Working Papers on Living Faith and Cultures, No. XIII. Rome: Gregorian University Press for the Cultures and Religions Centre, Gregorian University, 1991. 186 pp. 23,000 Lira; $19.50 (paper). - Volume 51 Issue 2
Tet repressor-tet operator interaction (1989)

Tetracycline resistance genes are widespread among gram-negative aerobic bacteria. A large number of independent isolates have been characterized and most of them shown to belong to five different classes of determinants, named classes A to E. They are usually plasmid- or transposon-encoded and share several genetic and mechanistic features (Chopra et al., 1981; Izaki et al., 1966; Levy and McMurray, 1978; Mendez et al., 1980; Marshall et al., 1986; Levy, 1988). Resistance against the drug is achieved by an active export mechanism of tetracycline from the resistant cell. This is mediated by a membrane associated resistance protein (McMurray et al., 1980; Waters et al., 1983; Hillen and Schollmeier, 1983; Nguyen et al., 1983). The expression of this protein is inducible by subinhibitory amounts of tetracycline (Mendez et al., 1980). This regulation of expression occurs at the level of transcription. It is brought about by a repressor protein, which under non-inducing conditions represses expression of the resistance gene, as well as that of its own gene. Induction of tetracycline resistance is achieved by binding of tetracycline to the repressor, thereby inactivating the operator-binding function of the protein and allowing expression of both genes. The regulated genes termed tetA for resistance and tetR for repressor are arranged adjacent to each other with opposite polarity and share common regulatory sequences comprising at least two promotors and two operators per determinant (Beck et al., 1982; Wray et al., 1981; Jorgensen and Reznikoff, 1979; Hillen et al., 1984; Hillen et al., 1982a; Bertrand et al., 1983; Altenbuchner et al., 1983; Unger et al., 1984a; Unger et al., 1984b; Tovar et al., 1988).
Polyisoprenyl phosphate specificity of UDP-GIcNAc:undecaprenyl phosphate N-acetylglucosaminyl 1-P transferase from E.coli (1997)

N-Acetyl-D-glucosaminylpyrophosphorylundecaprenol (GlcNAc-P-P-Und), an intermediate in the biosynthesis of the enterobacterial common antigen in E.coli and some O-antigen chains in gram-negative bacteria, is formed by the transfer of GlcNAc 1-P from UDP-GlcNAc to Und-P, analogous to the reaction forming GlcNAc-P-P-dolichol (GlcNAc-P-P-Dol) in mammalian cells. Since the microsomal enzyme from animal cells exhibits a strong preference for Dol-P, which contains a saturated alpha-isoprene unit, the polyisoprenyl phosphate specificity of the homologous bacterial enzyme was characterized. The enzyme remained bound to the membrane fraction when spheroplasts, formed by lysozyme-EDTA treatment, were lysed in hypotonic buffer. GlcNAc-P-P-Und synthase (GPT) activity was elevated in a strain of E.coli bearing the rfe gene, which encodes GPT on a multicopy plasmid, and virtually absent from rfe null mutants. GPT actively utilized fully unsaturated polyprenyl phosphate (Poly-P) substrates with maximal activity seen with (C55) Und-P, but was unable to utilize (C55)Dol-P. This substrate specificity contrasts with the microsomal GPT from pig brain, which actively utilized (C55)Dol-P, but not Und-P, as substrate. GPT activity bound to particulate fractions from three strains of bacilli also exhibited a strict preference for fully unsaturated Poly-P substrates. Unexpectedly, E.coli GPT activity cofractionated with the cytosolic marker enzyme, beta-galactosidase, and not the membrane-bound enzyme, D-lactate dehydrogenase, in cells disrupted in a French pressure cell. The properties and polyisoprenyl phosphate specificity of the soluble form of GPT were identical to the activity associated with the membrane preparations obtained from spheroplasts. The evolutionary and functional significance of the use of polyisoprenyl glycosyl carrier lipids with saturated alpha-isoprene units in eukaryotes remains uncertain.
Boxfishes (Teleostei: Ostraciidae) as a model system for fishes swimming with many fins: kinematics (2001)

Swimming movements in boxfishes were much more complex and varied than classical descriptions indicated. At low to moderate rectilinear swimming speeds (<5 TL s(-1), where TL is total body length), they were entirely median- and paired-fin swimmers, apparently using their caudal fins for steering. The pectoral and median paired fins generate both the thrust needed for forward motion and the continuously varied, interacting forces required for the maintenance of rectilinearity. It was only at higher swimming speeds (above 5 TL s(-1)), when burst-and-coast swimming was used, that they became primarily body and caudal-fin swimmers. Despite their unwieldy appearance and often asynchronous fin beats, boxfish swam in a stable manner. Swimming boxfish used three gaits. Fin-beat asymmetry and a relatively non-linear swimming trajectory characterized the first gait (0--1 TL s(-1)). The beginning of the second gait (1--3 TL s(-1)) was characterized by varying fin-beat frequencies and amplitudes as well as synchrony in pectoral fin motions. The remainder of the second gait (3--5 TL s(-1)) was characterized by constant fin-beat amplitudes, varying fin-beat frequencies and increasing pectoral fin-beat asynchrony. The third gait (>5 TL s(-1)) was characterized by the use of a caudal burst-and-coast variant. Adduction was always faster than abduction in the pectoral fins. There were no measurable refractory periods between successive phases of the fin movement cycles. Dorsal and anal fin movements were synchronized at speeds greater than 2.5 TL s(-1), but were often out of phase with pectoral fin movements.
Loss of stromal caveolin-1 expression in malignant melanoma metastases predicts poor survival (2011)

Caveolins are the principal protein component of caveolae, plasma membrane invaginations found in most cell types. Caveolin-1 (Cav-1) plays a major role in oncogenesis through its various functions in lipid transport, membrane trafficking, and signal transduction. Increased expression of Cav-1 in tumor cells has been associated with aggressiveness and poor survival. More recently, loss of stromal Cav-1 expression was linked to poor survival and increased metastatic potential in breast and prostate cancer. To date, there is no study addressing the clinical significance of Cav-1 expression in malignant melanoma (MM). Our study consisted of 44 cases of MM: 12 MM lymph node metastases from patients with short survival, 12 MM lymph node metastases from patients with long survival and 20 primary MM. All cases were stained with Cav-1 antibodies. Cav-1 expression in melanoma and stromal cells was quantified using a 3 point scale: 0 = no staining, 1 = diffuse weak staining or strong staining in < 30% of cells, and 2 = diffuse strong staining. A score of 0-1 represented low Cav-1 expression and a score of 2 represented high Cav-1 expression. In patients with MM lymph node metastases, a low stromal Cav-1 expression was associated with shorter survival when compared to the high stromal Cav-1 expression group (median survival 252 days versus 3,508 days, p value 0.0054). Conversely, high Cav-1 expression in melanoma cells was associated with a longer survival in primary MM (p < 0.0001). In conclusion, high expression of stromal Cav-1 correlates with longer survival in malignant melanoma metastases, and high expression of Cav-1 in melanoma cells correlates with longer survival in primary malignant melanoma.
Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protien (1995)

We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are essential for recognition by the phage coat protein. These experiments have been complemented with modification-binding interference assays. The results confirm that the complexes which form between TR and RNA-free phage capsids, the X-ray structure of which has recently been reported at 3.0 A, are identical to those which form in solution between TR and a single coat protein dimer. There are also effects on operator affinity which cannot be explained simply by the alteration of direct RNA-protein contacts and may reflect changes in the conformational equilibrium of the unliganded operator. The results also provide support for the approach of using modified oligoribonucleotides to investigate the details of RNA-ligand interactions.
Structure of N‐glycosidic Carbohydrates of Secretory Proteins of Tetrahymena thermophila (2003)

Glycoproteins secreted by Tetrahymena into the culture medium were isolated and the N-glycosidic oligosaccharides analyzed using lectin blots and fluorophore-assisted carbohydrate gel electrophoresis (FACE). Lectin blots showed that the glycoproteins secreted by Tetrahymena contain only N-glycosidic structures of the high mannose type. Further analysis using the FACE technology revealed the presence of four different N-glycosidic structures differing only in the number of mannose residues attached to the core chitobiose unit.
Meta-Analysis and Meta-Review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers (2006)

Our approach represents a useful method for identifying consistent gene expression markers when raw data are unavailable. A review of the top 12 candidates revealed well known thyroid cancer markers such as MET, TFF3, SERPINA1, TIMP1, FN1, and TPO as well as relatively novel or uncharacterized genes such as TGFA, QPCT, CRABP1, FCGBP, EPS8 and PROS1. These candidates should help to develop a panel of markers with sufficient sensitivity and specificity for the diagnosis of thyroid tumors in a clinical setting.
Neuropilin-1 Binds Vascular Endothelial Growth Factor 165, Placenta Growth Factor-2, and Heparin via Its b1b2 Domain (2002)

Neuroplin-1 (NRP1), a receptor for vascular endothelial growth factor (VEGF) family members, has three distinct extracellular domains, a1a2, b1b2, and c. To determine the VEGF(165) and placenta growth factor 2 (PlGF-2)-binding sites of NRP1, recombinant NRP1 domains were expressed in mammalian cells as Myc-tagged, soluble proteins, and used in co-precipitation experiments with 125I-VEGF165 and 125I-PlGF-2. Anti-Myc antibodies immunoprecipitated 125I-VEGF165 and 125I-PlGF-2 in the presence of the b1b2 but not of the a1a2 and c domains. Neither b1 nor b2 alone was capable of binding 125I-VEGF165. In competition experiments, VEGF165 competed PlGF-2 binding to the NRP1 b1b2 domain, suggesting that the binding sites of VEGF165 and PlGF-2 overlap. The presence of the a1a2 domain greatly enhanced VEGF165, but not PlGF-2 binding to b1b2. Heparin enhanced the binding of both 125I-VEGF165 and 125I-PlGF-2 to the b1b2 domain by 20- and 4-fold, respectively. A heparin chain of at least 20-24 monosaccharides was necessary for binding. In addition, the b1b2 domain of NRP1 could bind heparin directly, requiring heparin oligomers of at least 8 monosaccharide units. It was concluded that an intact b1b2 domain serves as the VEGF165-, PlGF-2-, and heparin-binding sites in NRP1, and that heparin is a critical component for regulating VEGF165 and PlGF-2 interactions with NRP1 by physically interacting with both receptor and ligands.
Spatial as Deep: Spatial CNN for Traffic Scene Understanding (2018)

Convolutional neural networks (CNNs) are usually built by stacking convolutional operations layer-by-layer. Although CNN has shown strong capability to extract semantics from raw pixels, its capacity to capture spatial relationships of pixels across rows and columns of an image is not fully explored. These relationships are important to learn semantic objects with strong shape priors but weak appearance coherences, such as traffic lanes, which are often occluded or not even painted on the road surface as shown in Fig. 1 (a). In this paper, we propose Spatial CNN (SCNN), which generalizes traditional deep layer-by-layer convolutions to slice-by-slice convolutions within feature maps, thus enabling message passings between pixels across rows and columns in a layer. Such SCNN is particular suitable for long continuous shape structure or large objects, with strong spatial relationship but less appearance clues, such as traffic lanes, poles, and wall. We apply SCNN on a newly released very challenging traffic lane detection dataset and Cityscapse dataset. The results show that SCNN could learn the spatial relationship for structure output and significantly improves the performance. We show that SCNN outperforms the recurrent neural network (RNN) based ReNet and MRF+CNN (MRFNet) in the lane detection dataset by 8.7% and 4.6% respectively. Moreover, our SCNN won the 1st place on the TuSimple Benchmark Lane Detection Challenge, with an accuracy of 96.53%.
From SOMAmer-Based Biomarker Discovery to Diagnostic and Clinical Applications: A SOMAmer-Based, Streamlined Multiplex Proteomic Assay (2011)

Recently, we reported a SOMAmer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated. We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community.
Dissolution profiles of nonprescription extended-release niacin and inositol niacinate products (2006)

Significant variations in dissolution profiles were noted among the 7 nonprescription extended-release and 12 nonprescription inositol niacinate products in vitro, and their dissolution rates were not comparable to that of the prescription extended-release niacin. Further studies are warranted to correlate such dissolution data with their in vivo efficacy.
Study of receptors for vesicular stomatitis virus in vertebrate and invertebrate cells. (1986)

Early interactions between vesicular stomatitis virus (VSV) and susceptible cells were examined in cell lines of mammalian (HeLa), bird (CER), piscine (EPC) and arthropod (Aedes albopictus) origin showing different permissiveness to VSV growth. The chemical nature of receptors was investigated either by modification of cell surfaces with different enzymes or by competition for VSV binding between extracted membrane components and whole cells. Results obtained indicate that in all cell models, membrane lipid components show receptor activity whereas glycid groups participate to the in virus binding to a different extent.