gebhart/patrepeval huggingface dataset:
Hidden Markov model for Mandarin lexical tone recognition (1988)

A case of lexical tone recognition for Mandarin speech is discussed using a combination of vector quantization and hidden Markov modelling techniques. The observation sequence was a sequence of vectorized parameters consisting of a logarithmic pitch interval and its first derivative. The vector quantization was applied to convert the observation sequence into a symbol sequence for Hidden Markov modeling. The speech database was provided by seven male and seven female college students, with each pronouncing 72 isolated monosyllabic utterances. A probabilistic model for each of the four tones was generated. A series of tonal recognition tests were then conducted to evaluate the effects of pitch reference base, codebook size, and tonal model topology. Future consideration of Mandarin speech recognition is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A stochastic learning-to-rank algorithm and its application to contextual advertising (2011)

This paper is concerned with the problem of learning a model to rank objects (Web pages, ads and etc.). We propose a framework where the ranking model is both optimized and evaluated using the same information retrieval measures such as Normalized Discounted Cumulative Gain (NDCG) and Mean Average Precision (MAP). The main difficulty in direct optimization of NDCG and MAP is that these measures depend on the rank of objects and are not differentiable. Most learning-to-rank methods that attempt to optimize NDCG or MAP approximate such measures so that they can be differentiable. In this paper, we propose a simple yet effective stochastic optimization algorithm to directly minimize any loss function, which can be defined on NDCG or MAP for the learning-to-rank problem. The algorithm employs Simulated Annealing along with Simplex method for its parameter search and finds the global optimal parameters. Experiment results using NDCG-Annealing algorithm, an instance of the proposed algorithm, on LETOR benchmark data sets show that the proposed algorithm is both effective and stable when compared to the baselines provided in LETOR 3.0. In addition, we applied the algorithm for ranking ads in contextual advertising. Our method has shown to significantly improve relevance in offline evaluation and business metrics in online tests in a real large-scale advertising serving system. To scale our computations, we parallelize the algorithm in a MapReduce framework running on Hadoop.
Total synthesis of prostaglandin-F2? through homoconjugate addition of an organocuprate reagent to a tricyclo[3.2.0.02,7]heptanone (1978)

Prostaglandin-F2α has been synthesised from cyclopentadiene in a highly stereoselective ten-step sequence of reactions. The key step involves the coupling of a protected 3-hydroxyoct-1-enyl unit to 3-dimethyl-t-butylsilyloxytricyclo[3.2.0.02,7]heptan-6-one through the use of a mixed organocuprate reagent.
Friendship modeling for cooperative co-evolutionary fuzzy systems: a hybrid GA-GP algorithm (2004)

A novel approach is proposed to combine the strengths of GA and GP to optimize rule sets and membership functions of fuzzy systems in a co-evolutionary strategy in order to avoid the problem of dual representation in fuzzy systems. The novelty of proposed algorithm is twofold. One is that GP is used for the structural part (Rule sets) and GA for the string part (Membership functions). The goal is to reduce/eliminate the problem of competing conventions by co-evolving pieces of the problem separately and then in combination. Second is exploiting the synergism between rules sets and membership functions by imitating the effect of "matching" and friendship in cooperating teams of humans, thereby significantly reducing the number of function evaluations necessary for evolution. The method is applied to a chaotic time series prediction problem and compared with the standard fuzzy table look-up scheme. demonstrate several significant improvements with the proposed approach; specifically, four times higher fitness and more steady fitness improvements as compared with epochal improvements observed in GP.
Generation of Monoclonal Antibodies against Autologous Proteins in Gene-inactivated Mice (1995)

Induction of an immune response is strongly dependent on the phylogenetic distance between antigen and recipient. In general, antibodies will not be raised against self-antigens nor against highly conserved domains. In the present study we describe the production and characterization of murine monoclonal "auto-antibodies" against murine tissue-type plasminogen activator (t-PA) raised in "knock-out" mice, homozygously deficient of the functional gene. 203 stable hybridomas were obtained producing murine monoclonal antibodies against murine t-PA. Analysis of the species reactivity revealed that 182 cross-reacted with one or more (t-)PAs originating from other species including rat t-PA, human t-PA, and vampire bat-PA. 121 reacted with epitopes conserved among murine, rat, and human t-PA. In addition, 31 of the monoclonal antibodies were directed against domains present in all four species. Epitope mapping indicated a high frequency of specificity toward diverse epitopes that are highly conserved across species. Comparative analysis of their influence on the enzymatic activity of t-PA and their species cross-reactivity clearly demonstrated that the domains required for the biological activity of plasminogen activators are more conserved (p < 0.02) than non-functional domains. The availability of such unique antibodies against a wide variety of conserved epitopes may facilitate studies on the structural homologies between (t-)PAs isolated from various species. The present approach should also apply to various other classes of proteins, allowing the generation of monoclonal antibodies, against conserved epitopes, which could not be raised in wild-type animals because of their "self-antigen" nature.
Synthesis and Characterization of Silicon-Containing Block Copolymers from Nitroxide-Mediated Living Free Radical Polymerization (2004)

High etch resistance to oxygen plasma for silicon-containing polymers, and the high thermal and mechanical robustness of the etching product, silicon oxide, make it attractive to design novel silicon-containing block copolymers for direct patterning of nanostructures on a desired substrate. Here, we report the synthesis of a series of block copolymers from silicon-containing styrenic monomers and styrene (St) or 4-acetoxystyrene (AcOSt) using living free radical polymerization via a α-hydride nitroxide-mediated unimer (α-H unimer). Controlled polymerization with narrow polydispersity (PDI < 1.25) and high yield (up to 80%) were achieved by optimizing polymerization time and temperature, addition of solvents, use of rate accelerants, monomer addition sequence, and solvent polarity. Block copolymer morphologies before and after O2 plasma were studied using small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). When silicon-containing block formed the major phase and silicon concentration was greater than 12 wt %, the morphology and domain size were maintained after O2 plasma.
Influence of age and gland topography on cell kinetics of normal human breast tissue. (1987)

It has been determined in experimental animal models that the susceptibility of the mammary gland to chemically induced carcinogenesis is directly related to the rate of cell proliferation of the gland at the time of carcinogen exposure and inversely related to its degree of differentiation. Cell proliferation, in turn, depends on the topographic location of cells within the mammary gland tree and is modulated by age, among other factors. To determine whether age and gland topography similarly influence cell kinetic parameters in the breast of human females, the following study was done. Fifteen samples of normal human breast tissue were obtained from areas adjacent to histopathologically proved benign lesions. Tissue fragments were incubated in organ culture dishes containing [3H]thymidine ([3H]dThd) and processed for DNA labeling index (DNA-LI), length of cell cycle (Tc), and growth fraction (GF) determination; double labeling with [3H]dThd and [14C]thymidine was used for length of the S-phase determination. The mean values obtained revealed that both DNA-LI and GF were lower, with a concomitant lengthening of G1 and Tc in older women than in young women. The correlation of these values with the gland's topography revealed that in both young and older women, the highest GF and DNA-LI were observed in intralobular terminal ducts, decreasing in alveoli and ducts.
Codes in Permutations and Error Correction for Rank Modulation (2010)

Codes for rank modulation have been recently proposed as a means of protecting flash memory devices from errors. We study basic coding theoretic problems for such codes, representing them as subsets of the set of permutations of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> elements equipped with the Kendall tau distance. We derive several lower and upper bounds on the size of codes. These bounds enable us to establish the exact scaling of the size of optimal codes for large values of n. We also show the existence of codes whose size is within a constant factor of the sphere packing bound for any fixed number of errors.
A Note on "Modulation Methods Related to Sine Wave Crossings" (1985)

In this correspondence we show that the above paper is a rediscovery of what was known since 1973 [1]. The contents of the paper have been published in various forms in the literature. The more general case of a periodic wave crossing has already been considered, which covers the special case of a sine wave crossing.
The Shape and Dimensions of the Human Vagina as Seen in Three-Dimensional Vinyl Polysiloxane Casts (1996)

Full vaginal casts of 39 caucasian women, 13 each nulliparous, uniparous and multiparous, were made using vinyl polysiloxane impression material. Vaginal lengths were measured with polished acrylic rods inserted by the subjects, and introital diameters were measured with conical polypropylene flasks. Parallel sided, conical, heart, and slug shapes were found. Lengths ranged from 6.86 to 14.81 cm; widths ranged from 4.8 to 6.3 cm; introital diameters ranged from 2.39 to 6.45 cm. No significant differences by parity or shape were found.
Presence of receptors for bombesin/gastrin-releasing peptide and mRNA for three receptor subtypes in human prostate cancers (2000)

The detection of a wide distribution of bombesin/GRP receptors in human prostate carcinomas supports the view that they may be involved in modulation of tumor progression and suggests that approaches based on binding of bombesin receptor antagonists or new targeted cytotoxic bombesin analogs to prostate cancers could be considered for the therapy.
An N -Glycosidase from Escherichia coli That Releases Free Uracil from DNA Containing Deaminated Cytosine Residues (1974)

An enzyme that liberates uracil from single-stranded and double-stranded DNA containing deaminated cytosine residues and from deoxycytidylate-deoxyuridylate copolymers in the absence of Mg(++) has been purified 30-fold from cell extracts of E. coli. The enzyme does not release uracil from deoxyuridine, dUMP, uridine, or RNA, nor does it liberate the normally occurring pyrimidine bases, cytosine and thymine, from DNA. The enzymatic cleavage of N-glycosidic bonds in DNA occurs without concomitant cleavage of phosphodiester bonds, resulting in the formation of free uracil and DNA strands of unaltered chain length that contain apyrimidinic sites as reaction products. The enzyme may be active in DNA repair, converting deaminated dCMP residues to an easily repairable form.
Characterization of soft errors caused by single event upsets in CMOS processes (2004)

Radiation-induced single event upsets (SEUs) pose a major challenge for the design of memories and logic circuits in high-performance microprocessors in technologies beyond 90nm. Historically, we have considered power-performance-area trade offs. There is a need to include the soft error rate (SER) as another design parameter. In this paper, we present radiation particle interactions with silicon, charge collection effects, soft errors, and their effect on VLSI circuits. We also discuss the impact of SEUs on system reliability. We describe an accelerated measurement of SERs using a high-intensity neutron beam, the characterization of SERs in sequential logic cells, and technology scaling trends. Finally, some directions for future research are given.
Specificity of Cytoplasmic Dynein Subunits in Discrete Membrane-trafficking Steps (2009)

The cytoplasmic dynein motor complex is known to exist in multiple forms, but few specific functions have been assigned to individual subunits. A key limitation in the analysis of dynein in intact mammalian cells has been the reliance on gross perturbation of dynein function, e.g., inhibitory antibodies, depolymerization of the entire microtubule network, or the use of expression of dominant negative proteins that inhibit dynein indirectly. Here, we have used RNAi and automated image analysis to define roles for dynein subunits in distinct membrane-trafficking processes. Depletion of a specific subset of dynein subunits, notably LIC1 (DYNC1LI1) but not LIC2 (DYNC1LI2), recapitulates a direct block of ER export, revealing that dynein is required to maintain the steady-state composition of the Golgi, through ongoing ER-to-Golgi transport. Suppression of LIC2 but not of LIC1 results in a defect in recycling endosome distribution and cytokinesis. Biochemical analyses also define the role of each subunit in stabilization of the dynein complex; notably, suppression of DHC1 or IC2 results in concomitant loss of Tctex1. Our data demonstrate that LIC1 and LIC2 define distinct dynein complexes that function at the Golgi versus recycling endosomes, respectively, suggesting that functional populations of dynein mediate discrete intracellular trafficking pathways.
Efficacy with a replication-selective adenovirus plus cisplatin-based chemotherapy: dependence on sequencing but not p53 functional status or route of administration. (2000)

Replication-selective adenoviruses are being developed as novel anticancer therapeutics. Clinical trials with dl 1520, an E1B-Mr 55,000 gene-deleted adenovirus (ONYX-015), have demonstrated selective viral replication and biological activity in head and neck and ovarian carcinomas, but durable objective responses were not demonstrated. However, clinical results suggested potentially synergistic interactions with platinum-containing chemotherapy. To better characterize and optimize this interaction, we carried out combined modality treatment with ONYX-015 and cisplatin-based chemotherapy in three nude mouse-human tumor xenograft models with differing tumor locations or p53 functional status. Superior efficacy was demonstrated with combination therapy over either agent alone in all three models, independent of the route of ONYX-015 administration (intratumoral or i.p.). Virus replication was not demonstrably inhibited by cisplatin plus 5-fluorouracil chemotherapy. To assess the role of p53 function or cisplatin resistance in this interaction, we treated ovarian carcinomas that were matched except for p53 functional status (A2780, A2780/CP70). Combination therapy led to improved survival over either agent alone in both the p53(-) and the p53(+) carcinomatosis models. Efficacy was highly dependent on the sequencing of the agents; treatment with ONYX-015 prior to, or simultaneously with, chemotherapy was significantly superior to chemotherapy followed by ONYX-015. These results support further evaluation of replication-selective adenoviruses and cisplatin-based chemotherapy in clinical trials.
Molecules making waves in axon guidance. (1997)

The exquisite complexity of neural connectivity depends upon the precise navigation of axons to their targets in the developing nervous system. How is this achieved? Signals from the environment are assumed to impinge on growth cone receptors and thus steer axons in the right direction, but the molecular details of this process have been largely unknown. Recently, impressive progress has been made in identifying families of molecules that may underlie this process. Candidate diffusible guidance molecules include the netrins and semaphorins, whereas membrane-associated Eph receptors and their ligands are proposed to influence guidance by cellcell contact. Characterization of receptors for some of these molecules now promises the dissection of the signalling pathways that dictate axonal responses to pathfinding cues.
Fast and robust three-dimensional best path phase unwrapping algorithm (2007)

What we believe to be a novel three-dimensional (3D) phase unwrapping algorithm is proposed to unwrap 3D wrapped-phase volumes. It depends on a quality map to unwrap the most reliable voxels first and the least reliable voxels last. The technique follows a discrete unwrapping path to perform the unwrapping process. The performance of this technique was tested on both simulated and real wrapped-phase maps. And it is found to be robust and fast compared with other 3D phase unwrapping algorithms.
Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. (2000)

New genomic large-scale screening techniques have made the task of establishing an accurate molecular fingerprint of cancer cells feasible. Here, we have used a two-phase strategy for identification of molecular alterations in gliomas. First, cDNA microarrays (Clontech Laboratories, Inc., Research Genetics) were used to pinpoint differentially expressed genes between normal brain and diffuse astrocytomas (grades II-IV), and between a primary tumor and a later tumor reoccurrence in the same patient. More than 200 gene expression alterations were detected from glioblastomas, whereas relatively few changes were seen in grade II and grade III tumors. The most distinct progression-related expression change was the up-regulation of the insulin-like growth factor binding protein 2 (IGFBP2) gene. Second, a high-density tissue microarray of 418 brain tumors was constructed and used for clinical validation of gene expression changes. Strong expression of IGFBP2 was associated with progression and poor patient survival in diffuse astrocytomas (P < 0.0001). Third, comparisons of the data between (a) multiple spots retrieved from one predefined tumor region (IGFBP2 and vimentin immunohistochemistry, 20 tumors) or between (b) standard slides and arrayed tissues (p53 immunohistochemistry, 42 tumors) revealed very little variation. In conclusion, the combined use of DNA microarrays and tissue microarrays offers a powerful strategy for rapid identification and thorough characterization of differentially expressed genes in gliomas.
Discovery of Human Macrophage Migration Inhibitory Factor (MIF)-CD74 Antagonists via Virtual Screening (2008)

Macrophage migration inhibitory factor (MIF) is a cytokine that is involved in the regulation of inflammation as well as cell proliferation and differentiation. Deactivation of MIF by antibodies or inhibition of MIF binding to its receptor, CD74, attenuates tumor growth and angiogenesis. To discover small-molecule inhibitors of MIF's biological activity, virtual screening was performed by docking 2.1 million compounds into the MIF tautomerase active site. After visual inspection of 1200 top-ranked MIF-ligand complexes, 26 possible inhibitors were selected and purchased and 23 of them were assayed. The in vitro binding assay for MIF with CD74 revealed that 11 of the compounds have inhibitory activity in the micromolar regime, including four compounds with IC(50) values below 5 microM. Inhibition of MIF tautomerase activity was also established for many of the compounds with IC(50) values as low as 0.5 microM; Michaelis-Menten analysis was performed for two cases and confirmed the competitive inhibition.
Mechanisms That Contribute to the Development of Lymphoid Malignancies: Roles for Genetic Alterations and Cytokine Production (1996)

Recent studies have defined genetic alterations commonly associated with transformed lymphocytes. This review suggests roles for these alterations in the development of lymphoid neoplasms. Damage to the genes encoding proteins that function in intracellular signaling, transcription, or regulation of the cell cycle has been identified and linked at varying degrees to the progression of certain lymphoid malignancies. An understanding of the mechanistic consequences following such genetic alterations is essential to an understanding of the development of these lymphoid neoplasms. In contrast, it is also becoming clear that the dysregulated expression of proteins that are not genetically altered can also contribute to the progression of lymphoid malignancies. One such example is the excessive expression of "normal" lymphokines of cytokines which accompanies many lymphoproliferative diseases. The dysregulated expression of cytokines during malignancy can result in the augmentation of growth of transformed lymphocytes, as well as an alteration of the anti-tumor immune response. The latter mechanism is especially important because evasion of the impending immune response is a prerequisite for the progression of lymphoproliferative diseases. Taken together, this review supports the notion that the development of lymphoid malignancies is multifactorial, involving genetic alterations as well as dysregulated cytokine expression.
Synthesis and Antibiofilm Activity of a Second‐Generation Reverse‐Amide Oroidin Library: A Structure–Activity Relationship Study (2008)

A second-generation library of 2-aminoimidazole-based derivatives incorporating a "reversed amide" (RA) motif in comparison to the marine natural product oroidin were synthesized and subsequently assayed for antibiofilm activity against the medically relevant Gram-negative proteobacteria P. aeruginosa and A. baumannii. Most notably, an in-depth activity profile is reported for the most active subclass of derivatives that bear linear aliphatic chains off the amide bond. Additionally, further structural modifications of the core template, such as removal of the amide bond or substitution with a triazole isostere, resulted in the discovery of analogues with antibiofilm activities that varied with respect to their inhibition and dispersal properties of P. aeruginosa and A. baumannii biofilms.
Structural investigations of CXCR2 receptor antagonists by CoMFA, CoMSIA and flexible docking studies (2012)

Three-dimensional quantitative structure activity relationship (3D QSAR) analysis was carried out on a et of 56 N,N'-diarylsquaramides, N,N'-diarylureas and diaminocyclobutenediones in order to understand their antagonistic activities against CXCR2. The studies included comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Models with good predictive abilities were generated with CoMFA q² = 0.709, r² (non-cross-validated square of correlation coefficient) = 0.951, F value = 139.903, r² bs = 0.978 with five components, standard error of estimate = 0.144 and the CoMSIA q² = 0.592, r² = 0.955, F value = 122.399, r² bs = 0.973 with six components, standard error of estimate = 0.141. In addition, a homology model of CXCR2 was used for docking based alignment of the compounds. The most active compound then served as a template for alignment of the remaining structures. Further, mapping of contours onto the active site validated each other in terms of residues involved with reference to the respective contours. This integrated molecular docking based alignment followed by 3D QSAR studies provided a further insight to support the structure-based design of CXCR2 antagonistic agents with improved activity profiles. Furthermore, in silico screening was adapted to the QSAR model in order to predict the structures of new, potentially active compounds.