gebhart/patrepeval huggingface dataset:
The construction of cosmid libraries of eukaryotic DNA using the Homer series of vectors (1982)

We have constructed and characterised a series of approved, disabled cosmid vectors which we call Homer cosmids and have examined the optimal conditions for the construction of libraries of eukaryotic DNA segments using these vectors. Analysis of these libraries shows that most of the sequences we have tested for are present at the expected frequency and that the libraries can be stably propagated. We have also directly tested the stability of cosmid clones carrying tandemly repeated inserts. This work shows that it should be possible to clone most eukaryotic genes using cosmid vectors and that such cloning systems have considerable advantages over those more commonly used.
Rate-limiting steps in the DNA polymerase I reaction pathway (1985)

The initial rates of incorporation of dTTP and thymidine 5'-O-(3-thiotriphosphate) (dTTP alpha S) into poly(dA) X oligo(dT) during template-directed synthesis by the large fragment of DNA polymerase I have been measured by using a rapid-quench technique. The rates were initially equal, indicating a nonrate-limiting chemical step. However, the rate of thionucleotide incorporation steadily diminished to 10% of its initial value as the number of consecutive dTMP alpha S residues in the primer strand increased. This anomalous behavior can be attributed to the helix instability inherent in phosphorothioate-containing duplexes. Positional isotope exchange experiments employing the labeled substrate [alpha-18O2]dATP have revealed negligible alpha, beta-bridging----beta-nonbridging isotope exchange in template-directed reactions of Escherichia coli DNA polymerase I (Pol I) both in the presence and in the absence of added inorganic pyrophosphate (PPi), suggesting rapid PPi release following the chemical step. These observations are consistent with a rate-limiting step that is tentatively assigned to a conformational change of the E X DNA X dNTP complex immediately preceding the chemical step. In addition, the substrate analogue (Sp)-dATP alpha S has been employed to examine the mechanism of the PPi exchange reaction catalyzed by Pol I. The net retention of configuration at the alpha-P is interpreted in terms of two consecutive inversion reactions, namely, 3'-hydroxyl attack, followed by PPi attack on the newly formed primer terminus. Kinetic analysis has revealed that while alpha-phosphorothioate substitution has no effect upon the initial rate of polymerization, it does attenuate the PPi exchange reaction by a factor of 15-18 fold.(ABSTRACT TRUNCATED AT 250 WORDS)
Surface Passivation of Bare Aluminum Nanoparticles Using Perfluoroalkyl Carboxylic Acids (2005)

Surface passivation of unpassivated Al nanoparticles has been realized using self-assembled monolayers (SAMs). Nanoscale Al particles were prepared in solution by catalytic decomposition of H3Al·NMe3 or H3Al·N(Me)Pyr by Ti(OiPr)4 and coated in situ using a perfluoroalkyl carboxylic acid SAM. Because the Al particles are prepared using wet chemistry techniques and coated in solution, they are free of oxygen passivation. This SAM coating passivates the aluminum and appears to prevent the oxidation of the particles in air and renders the composite material, to some extent, soluble in polar organic solvents such as diethyl ether. Characterization data including scanning electron microscopy , transmission electron microscopy, thermogravimetric analysis, and attenuated total reflectance-Fourier transform infrared spectroscopy of prepared materials are presented.
A Zinc Clasp Structure Tethers Lck to T Cell Coreceptors CD4 and CD8 (2003)

The T cell coreceptors CD4 and CD8 both associate via their cytoplasmic tails with the N-terminus of the Src-family tyrosine kinase Lck. These interactions require zinc and are critical for T cell development and activation. We examined the folding and solution structures of ternary CD4-Lck-Zn2+ and CD8alpha-Lck-Zn2+ complexes. The coreceptor tails and the Lck N-terminus are unstructured in isolation but assemble in the presence of zinc to form compactly folded heterodimeric domains. The cofolded complexes have similar "zinc clasp" cores that are augmented by distinct structural elements. A dileucine motif required for clathrin-mediated endocytosis of CD4 is masked by Lck.
Two-port network analyzer calibration using an unknown 'thru' (1992)

A procedure performed by using a genuine two-port reciprocal network instead of a standard 'thru' in a full two-port error correction of an automatic network analyzer is presented. Although it can be applied to any type of waveguide system, the proposed technique is particularly useful with noninsertable coaxial or one-wafer devices. Experimental comparisons show that the suggested procedure provides a great degree of accuracy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Properties of an insulin receptor with an IGF‐1 receptor loop exchange in the cysteine‐rich region (2000)

The insulin receptor (IR) and the insulin-like growth factor-I receptor (IGF-1R) show differential binding of insulin and IGFs. The specificity determinants for IGF-1 binding are known to be located in the cysteine-rich (Cys-rich) region between residues 223 and 274 of human IGF-1R, which includes a loop that protrudes into the putative ligand binding site. In this report we have replaced residues 260-277 of human IR with residues 253-266 of the human IGF-1R to produce an IR-based, cysteine loop exchange chimaera, termed hIR-Cys loop exchange (CLX), in which all 14 amino acid residues in the exchanged loop differ from wild-type insulin receptor. This loop exchange had a detrimental effect on the efficiency of pro-receptor processing and on the binding of the mouse monoclonal antibody 83-7. However, this antibody, which binds hIR but not hIGF-1R, was still capable of immunoprecipitating the mature chimaeric receptor, indicating that the conformational epitope recognised by this antibody is not primarily determined by the loop region exchanged. The loop exchange did not significantly affect the ability of insulin to displace bound radiolabelled insulin, but increased the capacity of IGF-1 to competitively displace labelled insulin by at least 10 fold.
Reconstitution of Human Base Excision Repair with Purified Proteins (1997)

Base excision repair is a major mechanism for correcting aberrant DNA bases. We are using an in vitro base excision repair assay to fractionate and purify proteins from a human cell extract that are involved in this type of repair. Three fractions are required to reconstitute base excision repair synthesis using a uracil-containing DNA as a model substrate. We previously showed that one fraction corresponds to DNA polymerase beta. A second fraction was extensively purified and found to possess uracil-DNA glycosylase activity and was identified as the product of the UNG gene. A neutralizing antibody to the human UNG protein inhibited base excision repair in crude extract by at least 90%. The third fraction was highly purified and exhibited apurinic/apyrimidinic (AP) endonuclease activity. Immunoblot analysis identified HAP1 as the major polypeptide in fractions possessing DNA repair activity. Recombinant versions of UNG, HAP1, and DNA polymerase beta were able to substitute for the proteins purified from human cells. Addition of DNA ligase I led to ligated repair products. Thus, complete base excision repair of uracil-containing DNA was achieved by a combination of UNG, HAP1, DNA polymerase beta, and DNA ligase I. This is the first complete reconstitution of base excision repair using entirely eukaryotic proteins.
Kinetics of hydralazine elimination (1977)

Hydralazine was given orally in single doses of 10, 25, and 50 mg to 2 slow-acetylating subjects, while 2 rapid-acetylating subjects also received 100- and 150-mg doses on different occasions. Administration of the 50-mg dose to the subjects who were slow acetylators and the 150-mg dose to those who were rapid acetylators caused a disproportionately large increase in the amount of unchanged drug appearing in the systemic circulation as judged from the increases in the ratios of areas under concentration-time curves (AUC) to dose. A modification of the gas-liquid chromatographic hydralazine assay allowed the simultaneous determination of hydralazine and its acetylated metabolite, 3-methyl-s-triazolo-3,4,a-phthalazine (MTP), in serum. It was found that the disproportionately large increases in the AUC/dose ratio of hydralazine upon intake of 50 or 150-mg doses by the slow and rapid-acetylating subjects, respectively, were paralleled by a decrease in the ratio AUCMTP/AUChydralazine during a 6-hr observation period. It is concluded that the acetylation of hydralazine in man is a capacity-limited process.
T-Cell-Independent Immunoglobulin G Responses In Vivo Are Elicited by Live-Virus Infection but Not by Immunization with Viral Proteins or Virus-Like Particles (1998)

Immunoglobulin G (IgG) responses to viruses are generally assumed to be T-cell dependent (TD). Recently, however, polyomavirus (PyV) infection of T-cell-deficient (T-cell receptor beta chain [TCR-beta] -/- or TCR-betaxdelta -/-) mice was shown to elicit a protective, T-cell-independent (TI) antiviral IgM and IgG response. A repetitive, highly organized antigenic structure common to many TI antigens is postulated to be important in the induction of antibody responses in the absence of helper T cells. To test whether the repetitive structure of viral antigens is essential and/or sufficient for the induction of TI antibodies, we compared the abilities of three forms of PyV antigens to induce IgM and IgG responses in T-cell-deficient mice: soluble capsid antigens (VP1), repetitive virus-like particles (VLPs), and live PyV. Immunization with each of the viral antigens resulted in IgM production. VLPs and PyV elicited 10-fold-higher IgM titers than VP1, indicating that the highly organized, repetitive antigens are more efficient in IgM induction. Antigen-specific TI IgG responses, however, were detected only in mice infected with live PyV, not in VP1- or VLP-immunized mice. These results suggest that the highly organized, repetitive nature of the viral antigens is insufficient to account for their ability to elicit TI IgG response and that signals generated by live-virus infection may be essential for the switch to IgG production in the absence of T cells. Germinal centers were not observed in T-cell-deficient PyV-infected mice, indicating that the germinal center pathway of B-cell differentiation is TD even in the context of a virus infection.
Experimental study of variant KJA in ulcerative colitis rat model (2008)

Objective:To establish ulcerative colitis model in rats by DNCB+acetic acid and observe the therapeutic effect of KuiJieAn(KJA)decoction on ulcerative colitis rats.Methods:After preparation of the ulcerative colitis rat models were induced by DNCB+acetic acid,the animals were divided into 5 groups randomly,which was individually normal group,model group,3 variant KJA treatment group included large dose group,medium and little dose group,the group was treated with physiological saline.The whole condition and pathomorphism were observed in all groups after 20 days treatment with KJA.Results:General conditions:The rats' general conditions of normal group and all treatment groups after 20 days treatment are better than that of model group.Observation by optical microscope:The structure of colon in normal group is clear and no inflammation.The structure of colon in model group show obvious inflammation and even forms severe ulcer.There is inflammation improvement in all treatment group.Conclusion:KJA has conspicuous treatment effect in ulcerative colitis rat.
The outer membranes of Brucella spp. are resistant to bactericidal cationic peptides (1995)

The actions of polymyxin B, rabbit polymorphonuclear lysosome extracts, 14 polycationic peptides (including defensin NP-2, cecropin P1, lactoferricin B, and active peptides from cationic protein 18 and bactenecin), EDTA, and Tris on Brucella spp. were studied, with other gram-negative bacteria as controls. Brucella spp. were comparatively resistant to all of the agents listed above and bound less polymyxin B, and their outer membranes (OMs) were neither morphologically altered nor permeabilized to lysozyme by polymyxin B concentrations, although both effects were observed for controls. EDTA and peptides increased or accelerated the partition of the hydrophobic probe N-phenyl-naphthylamine into Escherichia coli and Haemophilus influenzae OMs but had no effect on Brucella OMs. Since Brucella and H. influenzae OMs are permeable to hydrophobic compounds (G. Martínez de Tejada and I. Moriyón, J. Bacteriol. 175:5273-5275, 1993), the results show that such unusual permeability is not necessarily related to resistance to polycations. Although rough (R) B. abortus and B. ovis were more resistant than the controls were, there were qualitative and quantitative differences with smooth (S) brucellae; this may explain known host range and virulence differences. Brucella S-lipopolysaccharides (LPSs) had reduced affinities for polycations, and insertion of Brucella and Salmonella montevideo S-LPSs into the OM of a Brucella R-LPS mutant increased and decreased, respectively, its resistance to cationic peptides. The results show that the core lipid A of Brucella LPS plays a major role in polycation resistance and that O-chain density also contributes significantly. It is proposed that the features described above contribute to Brucella resistance to the oxygen-independent systems of phagocytes.
The hyphomyceteTeberdinia hygrophilagen. nov., sp. nov. and related anamorphs ofPseudeurotiumspecies (2005)

A hyphomycetous fungus isolated from montane fen soil in the Caucasus Mountains, Russia, had obscurely sympodial conidiogenous cells that suggested a link to the heterogeneous genus Leptodontidium. Sequence analysis of the nuclear ribosomal small subunit and internal transcribed spacer region, however, disclosed that the fungus was an anamorphic member of a clade containing the cleistothecial ascomycetous genus Pseudeurotium. Teberdinia, gen. nov., is proposed for the blastic, generally sympodially proliferating anamorphs in this group, and Teberdinia hygrophila, sp. nov., is proposed for the species from upland fens. Binomials are not proposed for the remaining Teberdinia anamorphs of Pseudeurotium species. Purely anamorphic isolates in this clade are difficult to recognize using current morphological keys and might be more widely distributed and ecologically significant than is currently evident.
Product Quantization for Nearest Neighbor Search (2010)

This paper introduces a product quantization-based approach for approximate nearest neighbor search. The idea is to decompose the space into a Cartesian product of low-dimensional subspaces and to quantize each subspace separately. A vector is represented by a short code composed of its subspace quantization indices. The euclidean distance between two vectors can be efficiently estimated from their codes. An asymmetric version increases precision, as it computes the approximate distance between a vector and a code. Experimental results show that our approach searches for nearest neighbors efficiently, in particular in combination with an inverted file system. Results for SIFT and GIST image descriptors show excellent search accuracy, outperforming three state-of-the-art approaches. The scalability of our approach is validated on a data set of two billion vectors.
Kv4.2 mRNA Abundance and A-Type K+Current Amplitude Are Linearly Related in Basal Ganglia and Basal Forebrain Neurons (2000)

A-type K(+) currents are key determinants of repetitive activity and synaptic integration. Although several gene families have been shown to code for A-type channel subunits, recent studies have suggested that Kv4 family channels are the principal contributors to A-type channels in the somatodendritic membrane of mammalian brain neurons. If this hypothesis is correct, there should be a strong correlation between Kv4 family mRNA and A-type channel protein or aggregate channel currents. To test this hypothesis, quantitative single-cell reverse transcription-PCR analysis of Kv4 family mRNA was combined with voltage-clamp analysis of A-type K(+) currents in acutely isolated neurons. These studies revealed that Kv4.2 mRNA abundance was linearly related to A-type K(+) current amplitude in neostriatal medium spiny neurons and cholinergic interneurons, in globus pallidus neurons, and in basal forebrain cholinergic neurons. In contrast, there was not a significant correlation between estimates of Kv4.1 or Kv4.3 mRNA abundance and A-type K(+) current amplitudes. These results argue that Kv4.2 subunits are major constituents of somatodendritic A-type K(+) channels in these four types of neuron. In spite of this common structural feature, there were significant differences in the voltage dependence and kinetics of A-type currents in the cell types studied, suggesting that other determinants may create important functional differences between A-type K(+) currents.
Unsupervised Person Image Synthesis in Arbitrary Poses (2018)

We present a novel approach for synthesizing photorealistic images of people in arbitrary poses using generative adversarial learning. Given an input image of a person and a desired pose represented by a 2D skeleton, our model renders the image of the same person under the new pose, synthesizing novel views of the parts visible in the input image and hallucinating those that are not seen. This problem has recently been addressed in a supervised manner [16, 35], i.e., during training the ground truth images under the new poses are given to the network. We go beyond these approaches by proposing a fully unsupervised strategy. We tackle this challenging scenario by splitting the problem into two principal subtasks. First, we consider a pose conditioned bidirectional generator that maps back the initially rendered image to the original pose, hence being directly comparable to the input image without the need to resort to any training image. Second, we devise a novel loss function that incorporates content and style terms, and aims at producing images of high perceptual quality. Extensive experiments conducted on the DeepFashion dataset demonstrate that the images rendered by our model are very close in appearance to those obtained by fully supervised approaches.
Synthesis of Chiral Amines Using α‐Amino Aldehydes (2008)

Abstract If one were to rank chemical reagents on the basis of their “synthetic content”, loosely defined as the density of functional groups per arbitrary unit of molecular space, the α‐amino aldehydes will find themselves close to the very top of that list. The presence of synthetically ubiquitous amine and aldehyde functionalities predisposes α‐amino aldehydes towards highly convergent bond‐forming operations. Such juxtaposition does not come without a price: incompatibility of these functional groups calls for protecting groups. We discuss challenges and recently identified opportunities in this field.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)
Confidence estimation for translation prediction (2003)

The purpose of this work is to investigate the use of machine learning approaches for confidence estimation within a statistical machine translation application. Specifically, we attempt to learn probabilities of correctness for various model predictions, based on the native probabilites (i.e. the probabilites given by the original model) and on features of the current context. Our experiments were conducted using three original translation models and two types of neural nets (single-layer and multilayer perceptrons) for the confidence estimation task.
SODA: A Low-power Architecture For Software Radio (2006)

The physical layer of most wireless protocols is traditionally implemented in custom hardware to satisfy the heavy computational requirements while keeping power consumption to a minimum. These implementations are time consuming to design and difficult to verify. A programmable hardware platform capable of supporting software implementations of the physical layer, or software defined radio, has a number of advantages. These include support for multiple protocols, faster time-to-market, higher chip volumes, and support for late implementation changes. The challenge is to achieve this without sacrificing power. In this paper, we present a design study for a fully programmable architecture, SODA, that supports software defined radio a high-end signal processing application. Our design achieves high performance, energy efficiency, and programmability through a combination of features that include single-instruction multiple- data (SIMD) parallelism, and hardware optimized for 16bit computations. The basic processing element is an asymmetric processor consisting of a scalar and SIMD pipeline, and a set of distributed scratchpad memories that are fully managed in software. Results show that a four processor design is capable of meeting the throughput requirements of theW-CDMA and 802.11a protocols, while operating within the strict power constraints of a mobile terminal.
Towards Designing Secure Online Games (2006)

The multiplayer gaming industry has become very successful in Asia. With the growth of online gaming, there has been an amazing growth in online gamingrelated crime, especially in Massively Multiplayer Online Role-Playing Games (MMORPGs) [1]. In Taiwan, more than 37% of criminal cases relate to online gaming crime with most offenders in the age range of 15-20 years [5]. Most of these crimes can be attributed to the fact that these online games were not designed to be secure. This paper applies a design for security approach to MMORPGs and then examines what crimes could have been avoided if the games were designed to be secure from the beginning. The approach also uncovers some potential new threats and gives countermeasures for them.
The Probability of Duplicate Gene Preservation by Subfunctionalization (2000)

It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 10(5) or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.