gebhart/patrepeval huggingface dataset:
A Human Parvovirus, Adeno-Associated Virus, as a Eucaryotic Vector: Transient Expression and Encapsidation of the Procaryotic Gene for Chloramphenicol Acetyltransferase (1984)

We have used the defective human parvovirus adeno-associated virus (AAV) as a novel eucaryotic vector (parvector) for the expression of a foreign gene in human cells. The recombinant, pAV2, contains the AAV genome in a pBR322-derived bacterial plasmid. When pAV2 is transfected into human cells together with helper adenovirus particles, the AAV genome is rescued from the recombinant plasmid and replicated to produce infectious AAV particles at high efficiency. To create a vector, we inserted a procaryotic sequence coding for chloramphenicol acetyltransferase (CAT) into derivatives of pAV2 following either of the AAV promoters p40 (pAVHiCAT) and p19 (pAVBcCAT). When transfected into human 293 cells or HeLa cells, pAVHiCAT expressed CAT activity in the absence of adenovirus. In the presence of adenovirus, this vector produced increased amounts of CAT activity and the recombinant AAV-CAT genome was replicated. In 293 cells, pAVBcCAT expressed a similar amount of CAT activity in the absence or presence of adenovirus and the recombinant AAV-CAT genome was not replicated. In HeLa cells, pAVBcCAT expressed low levels of CAT activity, but this level was elevated by coinfection with adenovirus particles or by cotransfection with a plasmid which expressed the adenovirus early region 1A (E1A) product. The E1A product is a transcriptional activator and is expressed in 293 cells. Thus, expression from two AAV promoters is differentially regulated: expression from p19 is increased by E1A, whereas p40 yields high levels of constitutive expression in the absence of E1A. Both AAV vectors were packaged into AAV particles by complementation with wild-type AAV and yielded CAT activity when subsequently infected into cells in the presence of adenovirus.
Fetal hemoglobin in acute and chronic states of erythroid expansion (1993)

Physiologic principles underlying the differences in fetal hemoglobin (HbF) induction between acute and chronic states of erythroid expansion are poorly understood. Whereas abrupt erythroid expansion is characterized by a high proportion of reticulocytes coexpressing adult and fetal globin (F reticulocytes), HbF levels wane with chronic erythropoietic stimulation. To investigate this phenomenon, we used various schedules of erythropoietin (epo) administration in primates. Acute intravenous epo administration promoted a 2- to 10-fold preferential induction of F reticulocytes compared with total reticulocytes. Total reticulocyte and F reticulocyte production were significantly correlated (correlation coefficient .41 to .74). With chronic epo administration, preferential F reticulocyte production was lost, and there was no correlation between reticulocyte and F reticulocyte production (correlation coefficient -.03). The mean percentage of F reticulocytes did not change between acute and chronic schedules of epo administration. The subcutaneous route of high-dose (3,000 U/kg) epo administration was as effective as intravenous administration in the induction of HbF. Reticulocyte and F reticulocyte responses to increasing epo doses were found to be saturable. These results suggest that the kinetics rather than absolute levels of reticulocyte and F reticulocyte response form the basis for preferential F reticulocyte induction with acute erythropoietic stimulation, and they support the hypothesis that F reticulocytes arise from a relatively rapid pathway of erythroid maturation.
p53-Independent and -Dependent Requirements for E1B-55K in Adenovirus Type 5 Replication (1999)

The adenovirus type 5 mutant dl1520 was engineered previously to be completely defective for E1B-55K functions. Recently, this mutant (also known as ONYX-015) has been suggested to replicate preferentially in p53(-) and some p53(+) tumor cell lines but to be attenuated in primary cultured cells (C. Heise, A. Sampson-Johannes, A. Williams, F. McCormick, D. D. F. Hoff, and D. H. Kirn, Nat. Med. 3:639-645, 1997). It has been suggested that dl1520 might be used as a "magic bullet" that could selectively lyse tumor cells without harm to normal tissues. However, we report here that dl1520 replication is independent of p53 genotype and occurs efficiently in some primary cultured human cells, indicating that the mutant virus does not possess a tumor selectivity. Although it was not the sole host range determinant, p53 function did reduce dl1520 replication when analyzed in a cell line expressing temperature-sensitive p53 (H1299-tsp53) (K. L. Fries, W. E. Miller, and N. Raab-Traub, J. Virol. 70:8653-8659, 1996). As found earlier for other E1B-55K mutants in HeLa cells (Y. Ho, R. Galos, and J. Williams, Virology 122:109-124, 1982), dl1520 replication was temperature dependent in H1299 cells. When p53 function was restored at low temperature in H1299-tsp53 cells, it imposed a modest defect in viral DNA replication and accumulation of late viral cytoplasmic mRNA. However, in both H1299 and H1299-tsp53 cells, the defect in late viral protein synthesis appeared to be much greater than could be accounted for by the modest defects in late viral mRNA levels. We therefore propose that in addition to countering p53 function and modulating viral and cellular mRNA nuclear transport, E1B-55K also stimulates late viral mRNA translation.
Definition of a nonlinear conformational epitope for the apolipoprotein B-100-specific monoclonal antibody, MB47. (1994)

The apolipoprotein (apo) B-100-specific monoclonal antibody MB47 has been widely used in lipoprotein metabolism and atherosclerosis research. When bound to apoB-100 on low density lipoproteins (LDL), antibody MB47 completely blocks the binding of LDL to the LDL receptor. The epitope for antibody MB47 has previously been mapped to the vicinity of apoB-100 amino acid (aa) residue 3500. To map the epitope for antibody MB47 more precisely, we used recombinant bacterial fusion proteins. Antibody MB47 bound strongly to a fusion protein containing apoB-100 aa 3214-3728, but no specific binding was observed to fusion proteins containing aa 3214-3351, 3214-3506, 3351-3506, or a fusion protein containing aa 3214-3351 and 3506-3728. Although antibody MB47 did not bind to aa 3214-3506, it did bind to aa 3214-3510. Further fusion protein studies revealed that antibody MB47 bound to aa 3429-3510, but bound only very weakly to aa 3453-3510, indicating that aa 3429-3453 constitute an important part of the MB47 epitope. Subsequent fusion protein studies revealed that MB47 bound much more strongly to aa 3429-3523, 3429-3544, 3429-3565, and 3429-3590 than to aa 3429-3510. Thus, aa 3507-3523 also constitute an important part of the MB47 epitope. In summary, the fusion protein data indicated that two nonlinear domains of apoB-100 separated by approximately 53 aa (the 25 residues from aa 3429 to 3453 and the 17 residues from aa 3507 to 3523) form key parts of the MB47 epitope.(ABSTRACT TRUNCATED AT 250 WORDS)
Genetic modification of cells by receptor-mediated adenovirus-augmented gene delivery: a new approach for immunotherapy of cancer. (1994)

Most concepts of gene therapy of cancer are based on the generation of an enhanced immune response against the cancer by means of vaccination with gene-modified cancer cells. We have investigated the applicability of a new gene transfer technique which uses the receptor-mediated endocytosis pathway and the endosome disruption activity of adenovirus for the generation of a cancer vaccine consisting of interleukin-2 (IL-2)-transfected, irradiated murine melanoma cells (clone M-3). This technique resulted in very high IL-2 expression (in the range of 30,000 Units IL-2/10(6) cells/24 hrs) in the transfected cells without the need to selection of stably expressing cell clones. We found that this high IL-2 expression of the melanoma cells correlates with high efficacy of the vaccine. Immunization of animals with this vaccine elicits a systemic T-cell-mediated immune response which protects from tumor development after implantation of highly tumorigenic doses of wild-type melanoma cells.
Directed placement of suspended carbon nanotubes for nanometer-scale assembly (2002)

Single-wall carbon nanotubes (SWNTs) suspended in an aqueous solution have been placed selectively between two metal electrodes separated by a few tens of nanometers. After the initial patterning of the metal electrodes by electron beam lithography, no further fine-line lithography steps are necessary to achieve directed placement of SWNTs at these dimensions. An ac bias is applied between the two electrodes and the “nanoscale wiring” is completed within seconds. An additional advantage of using ac bias is the enhancement for selectively placing SWNTs between the electrode gap over competing contaminant species in the solution.
CD56brightCD16− NK Cells Produce Adenosine through a CD38-Mediated Pathway and Act as Regulatory Cells Inhibiting Autologous CD4+ T Cell Proliferation (2015)

Recent studies suggested that human CD56(bright)CD16(-) NK cells may play a role in the regulation of the immune response. Since the mechanism(s) involved have not yet been elucidated, in the present study we have investigated the role of nucleotide-metabolizing enzymes that regulate the extracellular balance of nucleotides/nucleosides and produce the immunosuppressive molecule adenosine (ADO). Peripheral blood CD56(dim)CD16(+) and CD56(bright)CD16(-) NK cells expressed similar levels of CD38. CD39, CD73, and CD157 expression was higher in CD56(bright)CD16(-) than in CD56(dim)CD16(+) NK cells. CD57 was mostly expressed by CD56(dim)CD16(+) NK cells. CD203a/PC-1 expression was restricted to CD56(bright)CD16(-) NK cells. CD56(bright)CD16(-) NK cells produce ADO and inhibit autologous CD4(+) T cell proliferation. Such inhibition was 1) reverted pretreating CD56(bright)CD16(-) NK cells with a CD38 inhibitor and 2) increased pretreating CD56(bright)CD16(-) NK cells with a nucleoside transporter inhibitor, which increase extracellular ADO concentration. CD56(bright)CD16(-) NK cells isolated from the synovial fluid of juvenile idiopathic arthritis patients failed to inhibit autologous CD4(+) T cell proliferation. Such functional impairment could be related to 1) the observed reduced CD38/CD73 expression, 2) a peculiar ADO production kinetics, and 3) a different expression of ADO receptors. In contrast, CD56(bright)CD16(-) NK cells isolated from inflammatory pleural effusions display a potent regulatory activity. In conclusion, CD56(bright)CD16(-) NK cells act as "regulatory cells" through ADO produced by an ectoenzymes network, with a pivotal role of CD38. This function may be relevant for the modulation of the immune response in physiological and pathological conditions, and it could be impaired during autoimmune/inflammatory diseases.
Results of the First Phase I/II Clinical Vaccination Trial With Direct Injection of mRNA (2008)

Vaccination against tumor antigens has been shown to be a safe and efficacious prophylactic and therapeutic antitumor treatment in many animal models. Clinical studies in humans indicate that specific immunotherapy can also result in clinical benefits. The active pharmaceutical ingredient in such vaccines can be DNA, RNA, protein, or peptide and can be administered naked, encapsulated, or after delivery in vitro into cells that are then adoptively transferred. One of the easiest, most versatile and theoretically safest technologies relies on the direct injection of naked messenger RNA (mRNA) that code for tumor antigens. We and others have shown in mice that intradermal application of naked mRNA results in protein expression and the development of an immune response. We used this protocol to vaccinate 15 melanoma patients. For each patient a growing metastasis was removed, total RNA was extracted, reverse-transcribed, amplified, and cloned. Libraries of cDNA were transcribed to produce unlimited amounts of copy mRNA. Autologous preparations were applied intradermally in combination with granulocyte macrophage colony-stimulating factor as adjuvant. We demonstrate here that such treatment is feasible and safe (phase 1 criteria). Furthermore, an increase in antitumor humoral immune response was seen in some patients. However, a demonstration of clinical effectiveness of direct injection of copy mRNA for antitumor immunotherapy was not shown in this study and must be evaluated in subsequent trials.
Sequences affecting the regulation of solvent production in Clostridium acetobutylicum (2003)

The high solvent phenotype of Clostridium acetobutylicum mutants B and H was complemented by the introduction of a plasmid that contains either an intact or partially-deleted copy of solR, restoring acetone and butanol production to wild-type levels. This demonstrates that the solR open reading frame on pSOLThi is not required to restore solvent levels. The promoter region upstream of alcohol dehydrogense E (adhE) was examined in efforts to identify sites that play major roles in the control of expression. A series of adhE promoter fragments was constructed and the expression of each in acid- and solvent-phases of growth was analyzed using a chloramphenicol acetyl-transferase reporter system. Our results show that a region beyond the 0A box is needed for full induction of the promoter. Additionally, we show that the presence of sequences around a possible processing site designated S2 may have a negative role in the regulation of adhE expression.
Regulation of Programmed Death Ligand 1 (PD-L1) Expression in Breast Cancer Cell Lines In Vitro and in Immunodeficient and Humanized Tumor Mice (2018)

Programmed death ligand 1 (PD-L1) expression is an efficient strategy of tumor cells to escape immunological eradiation. However, only little is known about the factors that affect the cellular expression levels. Here we assessed the PD-L1 expression on different breast cancer cell lines under standard in vitro culture conditions and as a function of Epirubicin or Paclitaxel treatment. Moreover, we evaluated the expression in immunodeficient tumor mice as well as in humanized tumor mice (i.e., in the presence of a human immune system). We found highest PD-L1 levels in JIMT-1 and MDA-MB-231 cells. Epirubicin treatment caused a decrease and Paclitaxel treatment an increased PD-L1 expression in MDA-MB-231 cells. In addition, we identified nuclear PD-L1 in MDA-MB-231 cells. All in vivo transplanted breast cancer cell lines downregulated PD-L1 expression compared to their in vitro counterpart. Neither the gene copy number nor the presence of human immune system in humanized tumor mice had an effect on the PD-L1 content. We demonstrate that the degree of PD-L1 expression amongst breast cancer cell lines varies considerably. In addition, cytotoxic treatments and other extrinsic parameters differentially affect the expression. Hence, further investigations including in vivo evaluations are necessary to understand PD-L1 regulation for advanced breast cancer stratification.
Enzyme-assisted Purification of two Phloem-limited Plant Viruses: Tobacco Necrotic Dwarf and Potato Leafroll (1979)

SUMMARY Tobacco necrotic dwarf (TNDV) and potato leafroll (PLRV), viruses which are normally phloem-limited and are transmitted by aphids in the persistent manner, were successfully purified using Driselase, an enzyme that macerates plant tissue. Frozen tissue of Physalis floridana infected with TNDV or PLRV was homogenized in buffer containing Driselase and incubated with shaking. The virus particles were then purified by clarifying extracts with chloroform and n-butanol, precipitation of virus with polyethylene glycol, differential centrifugation and density-gradient sedimentation. The average yield of TNDV purified without the enzyme was 0.5 mg/kg of fresh tissue and of that purified with the enzyme was 4.7 mg. Yield of PLRV purified using the enzyme was 1.3 mg/kg. The sedimentation coefficients of both TNDV and PLRV were s 20, w = 115S. Enzyme treatment had no influence on the infectivity of the viruses, assessed either using tobacco mesophyll protoplasts or using aphids fed through membranes. The enzyme method described here may be useful for purification of other phloem-limited viruses.
Image Retrieval for Image-Based Localization Revisited (2012)

To reliably determine the camera pose of an image relative to a 3D point cloud of a scene, correspondences between 2D features and 3D points are needed. Recent work has demonstrated that directly matching the features against the points outperforms methods that take an intermediate image retrieval step in terms of the number of images that can be localized successfully. Yet, direct matching is inherently less scalable than retrievalbased approaches. In this paper, we therefore analyze the algorithmic factors that cause the performance gap and identify false positive votes as the main source of the gap. Based on a detailed experimental evaluation, we show that retrieval methods using a selective voting scheme are able to outperform state-of-the-art direct matching methods. We explore how both selective voting and correspondence computation can be accelerated by using a Hamming embedding of feature descriptors. Furthermore, we introduce a new dataset with challenging query images for the evaluation of image-based localization.
Biosynthesis of heparan sulfate. Coordination of polymer-modification reactions in a Chinese hamster ovary cell mutant defective in N-sulfotransferase (1991)

A previous study identified a Chinese hamster ovary cell mutant, pgsE-606, which is defective in the N-sulfotransferase that catalyzes one of the initial polymer-modification reactions in the biosynthesis of heparan sulfate (Bame, K. J., and Esko, J. D. (1989) J. Biol. Chem. 264, 8059-8065). The structure of heparan sulfate generated by these cells reflects a 3-5-fold reduction in enzyme activity. The mutant produces heparan sulfate with half the content of N-sulfated glucosamine residues of that produced by wild-type cells and a more sparse distribution of N-sulfated residues. The present study demonstrates corresponding reductions in the proportion of 6-O-sulfated glucosamine residues (41% reduction) and the content of L-iduronic acid (51% reduction). The amount of 2-O-sulfated L-iduronic acid declines more dramatically (from 25% of total L-iduronic acid in the wild type to 8.4% in the mutant). Enzymatic assay of mixed O-sulfotransferases showed that the mutant has more activity than the wild type. Previous studies on the biosynthesis of heparin/heparan sulfate in cell-free systems point to a pivotal role of N-sulfation in determining the extent of the subsequent polymer-modification reactions. The present study shows that this concept also applies to heparan sulfate biosynthesis in the intact cell.
Improved Catalysts for the Palladium-Catalyzed Synthesis of Oxindoles by Amide α-Arylation. Rate Acceleration, Use of Aryl Chloride Substrates, and a New Carbene Ligand for Asymmetric Transformations (2001)

Catalysts comprised Pd(OAc)(2) and either PCy(3) or sterically hindered N-heterocyclic carbene ligands provide fast rates for a palladium-catalyzed synthesis of oxindoles by amide alpha-arylation. This catalyst system allowed for room-temperature reactions in some cases and reactions of aryl chlorides at 70 degrees C. Most important, reactions occurred in high yields under mild conditions to form the quaternary carbon in alpha,alpha-disubstituted oxindoles. The combined inter- and intramolecular reaction afforded an efficient synthetic method for formation of alpha-aryloxindole derivatives. Surprisingly, catalysts containing tert-butylphosphine ligands, which have been most reactive for ketone arylations, were less active than those containing PCy(3). Use of new, optically active heterocyclic carbene ligands gave substantial enantioselectivity in formation of an alpha,alpha-disubstituted oxindole. In contrast, a variety of optically active phosphine ligands that were tested gave poor enantioselectivity. Mechanistic studies showed that the reaction involves rate-limiting oxidative addition of aryl halide. Base-induced formation of and reductive elimination from an arylpalladium enolate intermediate were both faster than oxidative addition. Deprotonation of the tethered amide appeared to be faster than reductive elimination of the resulting palladium enolate to form the oxindole product.
Neural network recognition of spelling errors (1998)

One area in which artificial neural networks (ANNs) may strengthen NLP systems is in the identification of words under noisy conditions. In order to achieve this benefit when spelling errors or spelling variants are present, variable-length strings of symbols must be converted to ANN input/output form---fixed-length arrays of numbers. A common view in the neural network community has been that different forms of input/output representations have negligible effect on ANN performance. This paper, however, shows that input/output representations can in fact affect the performance of ANNs in the case of natural language words. Minimum properties for an adequate word representation are proposed, as well as new methods of word representation.To test the hypothesis that word representations significantly affect ANN performance, traditional and new word representations are evaluated for their ability to recognize words in the presence of four types of typographical noise: substitutions, insertions, deletions and reversals of letters. The results indicate that word representations have a significant effect on ANN performance. Additionally, different types of word representation are shown to perform better on different types of error.
Parallel derivation of isogenic human primed and naive induced pluripotent stem cells (2018)

Induced pluripotent stem cells (iPSCs) have considerably impacted human developmental biology and regenerative medicine, notably because they circumvent the use of cells of embryonic origin and offer the potential to generate patient-specific pluripotent stem cells. However, conventional reprogramming protocols produce developmentally advanced, or primed, human iPSCs (hiPSCs), restricting their use to post-implantation human development modeling. Hence, there is a need for hiPSCs resembling preimplantation naive epiblast. Here, we develop a method to generate naive hiPSCs directly from somatic cells, using OKMS overexpression and specific culture conditions, further enabling parallel generation of their isogenic primed counterparts. We benchmark naive hiPSCs against human preimplantation epiblast and reveal remarkable concordance in their transcriptome, dependency on mitochondrial respiration and X-chromosome status. Collectively, our results are essential for the understanding of pluripotency regulation throughout preimplantation development and generate new opportunities for disease modeling and regenerative medicine.
Complexity-Theoretic Foundations of Quantum Supremacy Experiments (2016)

Depending on time, I'll discuss some subset of the following results. (1) There exists an oracle relative to which classical and quantum computers can solve the same approximate sampling problems in polynomial time, and yet the polynomial hierarchy is infinite. This means that any "BosonSampling-type theorem" will need to be non-relativizing. (2) Can P be separated from BQP by an efficiently-computable oracle (one in P/poly)? Yes if quantum-resistant one-way functions exist; no if P=PSPACE. The latter builds on recent results in quantum query complexity by myself and Shalev Ben-David. (3) How hard is it to approximately sample the output distribution of a random quantum circuit? One can do it (and even calculate the probabilities) in polynomial space and m^O(n) time, where m is the number of gates and n is the number of qubits. But if that's essentially optimal for estimating probabilities, then approximate sampling also requires exponential time. Joint work with Lijie Chen (Tsinghua University)