gebhart/patrepeval huggingface dataset:
Strategy for Recombinant Multichain Protein Synthesis:  Fibrinogen Bβ-Chain Variants as Thrombin Substrates (1996)

Thrombotic disease has been found in patients with congenital dysfibrinogens that have abnormalities in the amino terminal domain of the fibrinogen B beta-chain. Surprisingly, these fibrinogens are poor substrates for thrombin. In order to examine the molecular basis for this impaired thrombin-fibrinogen interaction, we synthesized three fibrinogens with single amino acid substitutions in this domain: B beta A68T, B beta P70S, and B beta L72S. B beta-chain expression vectors were altered by PCR-directed mutagenesis of the B beta cDNA. The altered vectors were transfected into a Chinese hamster ovary (CHO) cell line that was constructed as a first step in recombinant fibrinogen synthesis, this CHO line synthesizes fibrinogen A alpha- and gamma-chains. More than 86% of the stably selected clones expressed significant levels of fibrinogen, confirming that a two-step strategy permitted efficient synthesis of variant fibrinogens. In large-scale cultures variant fibrinogen accumulation in serum-free medium fluctuated between 1 and 15 micrograms/mL. Normal and variant recombinant fibrinogens were compared to plasma fibrinogens by following the time course of thrombin-catalyzed release of fibrinopeptides. Only the variant B beta A68T, a change identified in a congenital dysfibrinogen, showed significantly impaired kinetics. The rate of fibrinopeptide A release was decreased 27-fold, and the rate of fibrinopeptide B release was decreased 45-fold relative to normal fibrinogen. Fibrinopeptide release was not significantly altered by the substitutions B beta P70S or B beta L72S. These results suggest that B beta residue Ala68 has a novel and critical role in the interaction between thrombin and fibrinogen.
Atlas of the prenatal mouse brain (1992)

Introduction. Methods. Alphabetical List of Abbreviations. Alphabetical List of Structures. Acknowledgement. References. Gestational Day 12 (GD 12). Gestational Day 14 (GD 14). Gestational Day 16 (GD 16). Gestational Day 18 (GD 18). Each Chapter Includes References. Index.
Metabolic Flux Control at the Pyruvate Node in an AnaerobicEscherichia coliStrain with an Active Pyruvate Dehydrogenase (2010)

During anaerobic growth of Escherichia coli, pyruvate formate-lyase (PFL) and lactate dehydrogenase (LDH) channel pyruvate toward a mixture of fermentation products. We have introduced a third branch at the pyruvate node in a mutant of E. coli with a mutation in pyruvate dehydrogenase (PDH*) that renders the enzyme less sensitive to inhibition by NADH. The key starting enzymes of the three branches at the pyruvate node in such a mutant, PDH*, PFL, and LDH, have different metabolic potentials and kinetic properties. In such a mutant (strain QZ2), pyruvate flux through LDH was about 30%, with the remainder of the flux occurring through PFL, indicating that LDH is a preferred route of pyruvate conversion over PDH*. In a pfl mutant (strain YK167) with both PDH* and LDH activities, flux through PDH* was about 33% of the total, confirming the ability of LDH to outcompete the PDH pathway for pyruvate in vivo. Only in the absence of LDH (strain QZ3) was pyruvate carbon equally distributed between the PDH* and PFL pathways. A pfl mutant with LDH and PDH* activities, as well as a pfl ldh double mutant with PDH* activity, had a surprisingly low cell yield per mole of ATP (Y(ATP)) (about 7.0 g of cells per mol of ATP) compared to 10.9 g of cells per mol of ATP for the wild type. The lower Y(ATP) suggests the operation of a futile energy cycle in the absence of PFL in this strain. An understanding of the controls at the pyruvate node during anaerobic growth is expected to provide unique insights into rational metabolic engineering of E. coli and related bacteria for the production of various biobased products at high rates and yields.
The absolute configurations and pharmacological activities of the optical isomers of fluoxetine, a selective serotonin-uptake inhibitor (1988)

Fluoxetine is a potent and selective inhibitor of the neuronal serotonin-uptake carrier and is a clinically effective antidepressant. Although fluoxetine is used therapeutically as the racemate, there appears to be a small but demonstrable stereospecificity associated with its interactions with the serotonin-uptake carrier. The goals of this study were to determine the absolute configurations of the enantiomers of fluoxetine and to examine whether the actions of fluoxetine in behavioral tests were enantiospecific. (S)-Fluoxetine was synthesized from (S)-(-)-3-chloro-1-phenylpropanol by sequential reaction with sodium iodide, methylamine, sodium hydride, and 4-fluorobenzotrifluoride. (S)-Fluoxetine is dextrorotatory (+1.60) in methanol, but is levorotatory (-10.85) in water. Fluoxetine enantiomers were derivatized with (R)-1-(1-naphthyl)ethyl isocyanate, and the resulting ureas were assayed by 1H NMR or HPLC to determine optical purities of the fluoxetine samples. Both enantiomers antagonized writhing in mice; following sc administration of (R)- and (S)-fluoxetine, ED50 values were 15.3 and 25.7 mg/kg, respectively. Moreover, both enantiomers potentiated a subthreshold analgesic dose (0.25 mg/kg) of morphine, and ED50 values were 3.6 and 5.7 mg/kg, respectively. Following ip administration to mice, the two stereoisomers antagonized p-chloroamphetamine-induced depletion of whole brain serotonin concentrations. ED50 values for (S)- and (R)-fluoxetine were 1.2 and 2.1 mg/kg, respectively. The two enantiomers decreased palatability-induced ingestion following ip administration to rats; (R)- and (S)-fluoxetine reduced saccharin-induced drinking with ED50 values of 6.1 and 4.9 mg/kg, respectively. Thus, in all biochemical and pharmacological studies to date, the eudismic ratio for the fluoxetine enantiomers is near unity.
A comparison of T cell memory against the same antigen induced by virus versus intracellular bacteria (1999)

Cytotoxic T cell (CTL) memory was analyzed after infection with lymphocytic choriomeningitis virus (LCMV) and recombinant Listeria monocytogenes (rLM) expressing the complete nucleoprotein of LCMV (rLM-NP(actA)) or only the immunodominant epitope of H-2(d) mice (rLM-NP(118-126)). Immunization with LCMV and rLM induced a long-lived increased CTL precursor (CTLp) frequency specific for the viral (NP(118-126)) and for the bacterial (LLO(91-99)) epitope, respectively. However, after infection with rLM memory, CTLs were less protective against an intravenous LCMV challenge infection than a comparable number of LCMV-induced memory T cells. LCMV, but not recombinant Listeria-induced memory T cells were able to protect against lethal choriomeningitis by LCMV or a subsequent peripheral infection with recombinant vaccinia virus expressing LCMV-NP. The protective memory after viral and after rLM immunization was paralleled by evidence of LCMV but not rLM antigen persistence on day 15 and 30 after vaccination. These results document a striking difference in protective T cell memory between viral and bacterial vaccines and indicate that rapid T cell-dependent immune protection correlates with antigen persistence.
Benchmarking Quantum Hardware for Training of Fully Visible Boltzmann Machines (2016)

Quantum annealing (QA) is a hardware-based heuristic optimization and sampling method applicable to discrete undirected graphical models. While similar to simulated annealing, QA relies on quantum, rather than thermal, effects to explore complex search spaces. For many classes of problems, QA is known to offer computational advantages over simulated annealing. Here we report on the ability of recent QA hardware to accelerate training of fully visible Boltzmann machines. We characterize the sampling distribution of QA hardware, and show that in many cases, the quantum distributions differ significantly from classical Boltzmann distributions. In spite of this difference, training (which seeks to match data and model statistics) using standard classical gradient updates is still effective. We investigate the use of QA for seeding Markov chains as an alternative to contrastive divergence (CD) and persistent contrastive divergence (PCD). Using $k=50$ Gibbs steps, we show that for problems with high-energy barriers between modes, QA-based seeds can improve upon chains with CD and PCD initializations. For these hard problems, QA gradient estimates are more accurate, and allow for faster learning. Furthermore, and interestingly, even the case of raw QA samples (that is, $k=0$) achieved similar improvements. We argue that this relates to the fact that we are training a quantum rather than classical Boltzmann distribution in this case. The learned parameters give rise to hardware QA distributions closely approximating classical Boltzmann distributions that are hard to train with CD/PCD.
Content-Aware Master Data Management (2010)

Master data management (MDM) provides a means to link data from various structured data sources and to generate a consolidated master record for entities such as customers or products. However, a large amount of valuable information about entities exists as un-structured content in documents. In this paper, we show how MDM can be made aware of information from unstructured content by automatically extract-ing valuable information from documents. We demon-strate for an example application that it is possible to make MDM content-aware without compromising MDM’s premise to be the one trusted source for all entity-related information. 1
Fatal cadmium-induced pneumonitis. (1993)

A previously relatively healthy 78-year-old man was exposed to cadmium fumes during brazing with cadmium-containing silver solder. He developed severe chemical pneumonitis and died 25 d after exposure.
Isosterism and molecular modification in drug design (1979)

The first page of this article is displayed as the abstract.
Multiplexed Elimination of Wild-Type DNA and High-Resolution Melting Prior to Targeted Resequencing of Liquid Biopsies (2017)

Closed-tube homogeneous ND-NaME-PrO combined with multiplexed HRM is a convenient approach to efficiently enrich for mutations on multiple DNA targets and to enable prescreening before targeted resequencing.
Validity and reliability of Swedish WOMAC osteoarthritis index: A self-administered disease-specific questionnaire (WOMAC) versus generic instruments (SF-36 and NHP) (2000)

We assessed whether a disease-specific, self-administered questionnaire could replace a generic instrument as an outcome tool after total hip replacement, and tested the validity and reliability of the Swedish WOMAC osteoarthritis index. 58 patients operated on with total hip arthroplasty 2-10 years ago were randomized to the study. All patients were asked to answer one disease-specific questionnaire (WOMAC osteoarthritis index) and two generic instruments (NUP and SF-36) in the same week. The procedure was repeated after 4 weeks. We tested content validity, construct validity, criterion validity, test-retest reliability and internal consistency reliability according to total score, domains and items. We found that both the generic instruments (NHP and SF-36) and the disease-specific test (WOMAC) had a high validity, i.e., measuring what they were supposed to measure (high validity). The questionnaires were also reproducible over time (high reliability). We suggest the Swedish WOMAC to be used after total hip arthroplasty in future studies.
Low-Dose Vaccinia Virus-Mediated Cytokine Gene Therapy of Glioma (2001)

Recombinant viruses can produce cytokines in tumors mobilizing an immune response to tumor cells. In this study, the authors investigated gene expression, in vivo antitumor efficacy, and safety of attenuated recombinant vaccinia virus (rVV) carrying murine cytokine genes interleukin (IL)-2 (rVV-mIL-2), IL-12 (rVV-mIL-12), and both IL-2 and IL-12 (rVV-2-12) in an athymic nude mice model. Significant tumor inhibition (p < 0.05) was observed in a preestablished subcutaneously implanted C6 glioma model using rVVs at doses ranging from 10(2) to 10(7) plaque forming units (PFU). An antitumor effect did not depend on the dose of the rVV-mIL-2 and rVV-mIL-12 viruses. All constructed rVVs induced a high level of cytokine expression in vitro and in vivo. Most groups injected with high doses of recombinant viruses encoding cytokine genes (10(5) to 10(7) PFU) showed signs of cytokine toxicity, whereas in the low-dose treatment groups (10(2) to 10(3) PFU) toxicity was greatly reduced. The antitumor activity of rVV-mIL-12 was associated with increases in both the percentage and number of natural killer T cells in the spleen. Local detection of interferon-y and tumor necrosis factor-alpha was also correlated with tumor growth arrest induced by the treatment. High-dose VV control vector per se induced tumor inhibition by activating Mac-1+ cells in blood, but the antitumor effect was less pronounced compared with rVV-carrying cytokine genes (p < 0.05). These results suggest that attenuated recombinant strains of VV at low doses may potentially be efficient vectors for cancer immunotherapy.
Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding (2009)

The plant genome can respond rapidly and dynamically to stress in a manner that overcomes the restrictions of a highly stable DNA sequence. Abiotic stresses such as chilling, planting density, rubbing, cutting, and successive rounds of subculture generally decrease the levels of DNA methylation. The opposite effect is seen for salt stress, and the effects of heavy-metal stress are species specific. Biotic stresses such as pathogenic infection can lead to two contrasting effects on the levels of methylation in plants: hypermethylation on the genome-wide level and hypomethylation of resistance-related genes. Both phenomena may contribute to the adaptation of plants to stress. Although heritable methylation patterns and phenotypic variations that arise in response to stress are of potential value for plant breeding, their exploitation presents great challenges.
Synthesis and biological evaluation of a fluorescent analog of folic acid (1991)

A fluorescein derivative of the lysine analogue of folic acid, N alpha-pteroyl-N epilson-(4'-fluoresceinthiocarbamoyl)-L-lysine (PLF), was synthesized as a probe for dihydrofolate reductase (DHFR) and a membrane folate binding protein (m-FBP). Excitation of PLF at 282 nm and at 497 nm gave a fluorescence emission maximum at 518 nm. Binding of PLF to human DHFR or human placental m-FBP results in approximately a 20-fold enhancement in the magnitude of the fluorescence emission, suggesting that the ligand interacts with a hydrophobic region on these proteins. Additional evidence suggests that an energy transfer may occur between the pteridine and the fluorescein moieties. PLF binds to the active site of human DHFR since methotrexate (MTX) competes stoichiometrically and the denatured enzyme in the presence of PLF did not exhibit fluorescent enhancement. The dissociation constant for the fluorescein derivative with respect to human DHFR is 115 nM as compared to 111 nM for folic acid. The Ki value for the competitive inhibition of human DHFR by the fluorescent analogue of folic acid is 2.0 microM compared to 0.48 microM for folic acid. PLF was reduced to N alpha-(7,8-dihydropteroyl)-N epilson-(4'-fluoresceinthiocarbamoyl)-L-lysine (H2PLF) and assayed by the enzymatic conversion to the tetrahydro derivative. The Km value for human DHFR for the dihydrofolate analogue is 2.0 microM. The KD value for H2PLF to human DHFR is 47 nM as compared to 44 nM for dihydrofolate. The KD values for both H2PLF and PLF indicate that the fluorescein moiety does not significantly affect folate binding in enzyme binary complexes.(ABSTRACT TRUNCATED AT 250 WORDS)
Large-scale Analysis of in Vivo Phosphorylated Membrane Proteins by Immobilized Metal Ion Affinity Chromatography and Mass Spectrometry (2003)

Global analyses of protein phosphorylation require specific enrichment methods because of the typically low abundance of phosphoproteins. To date, immobilized metal ion affinity chromatography (IMAC) for phosphopeptides has shown great promise for large-scale studies, but has a reputation for poor specificity. We investigated the potential of IMAC in combination with capillary liquid chromatography coupled to tandem mass spectrometry for the identification of plasma membrane phosphoproteins of Arabidopsis. Without chemical modification of peptides, over 75% pure phosphopeptides were isolated from plasma membrane digests and detected and sequenced by mass spectrometry. We present a scheme for two-dimensional peptide separation using strong anion exchange chromatography prior to IMAC that both decreases the complexity of IMAC-purified phosphopeptides and yields a far greater coverage of monophosphorylated peptides. Among the identified sequences, six originated from different isoforms of the plasma membrane H(+)-ATPase and defined two previously unknown phosphorylation sites at the regulatory C terminus. The potential for large-scale identification of phosphorylation sites on plasma membrane proteins will have wide-ranging implications for research in signal transduction, cell-cell communication, and membrane transport processes.
AutoScaler: Scale-Attention Networks for Visual Correspondence (2016)

Finding visual correspondence between local features is key to many computer vision problems. While defining features with larger contextual scales usually implies greater discriminativeness, it could also lead to less spatial accuracy of the features. We propose AutoScaler, a scale-attention network to explicitly optimize this trade-off in visual correspondence tasks. Our network consists of a weight-sharing feature network to compute multi-scale feature maps and an attention network to combine them optimally in the scale space. This allows our network to have adaptive receptive field sizes over different scales of the input. The entire network is trained end-to-end in a siamese framework for visual correspondence tasks. Our method achieves favorable results compared to state-of-the-art methods on challenging optical flow and semantic matching benchmarks, including Sintel, KITTI and CUB-2011. We also show that our method can generalize to improve hand-crafted descriptors (e.g Daisy) on general visual correspondence tasks. Finally, our attention network can generate visually interpretable scale attention maps.
Trop2 identifies a subpopulation of murine and human prostate basal cells with stem cell characteristics (2008)

The epithelium of the adult prostate contains 3 distinct cell types: basal, luminal, and neuroendocrine. Tissue-regenerative activity has been identified predominantly from the basal cells, isolated by expression of CD49f and stem cell antigen-1 (Sca-1). An important question for the field is whether all basal cells have stem cell characteristics. Prostate-specific microarray databases were interrogated to find candidate surface antigens that could subfractionate the basal cell population. Tumor-associated calcium signal transducer 2 (TACSTD2/Trop2/M1S1/GA733-1) was identified because it was enriched after castration, in prostate sphere cells and in the basal fraction. In the murine prostate, Trop2 shows progenitor characteristics such as localization to the region of the gland proximal to the urethra and enrichment for sphere-forming and colony-forming cells. Trop2 subfractionates the basal cells into 2 populations, both of which express characteristic basal cell markers by quantitative PCR. However, only the basal cells expressing high levels of Trop2 were able to efficiently form spheres in vitro. In the human prostate, where Sca-1 is not expressed, sphere-forming progenitor cells were also isolated based on high expression of Trop2 and CD49f. Trop2-expressing murine basal cells could regenerate prostatic tubules in vivo, whereas the remaining basal cells had minimal activity. Evidence was found for basal, luminal, and neuroendocrine cells in prostatic tubules regenerated from Trop2(hi) basal cells. In summary, functionally distinct populations of cells exist within the prostate basal compartment and an epithelial progenitor can give rise to neuroendocrine cells in vivo.
Self‐Assembly and Embedding of Nanoparticles by In Situ Reduced Graphene for Preparation of a 3D Graphene/Nanoparticle Aerogel (2011)

A 3D graphene architecture can be prepared via an in situ self-assembly of graphene prepared by a mild chemical reduction. Fe(3) O(4) nanoparticles are homogeneously dispersed into graphene oxide (GO) aqueous suspension and a 3D magnetic graphene/Fe(3) O(4) aerogel is prepared during the reduction of GO to graphene. This provides a general method to prepare 3D graphene/nanoparticle composites for a wide range of applications including catalysis and energy conversion.
Immunity against the opportunistic fungal pathogenPneumocystis (2005)

Species of the genus Pneumocystis exist as opportunistic fungal pathogens and are associated with severe pneumonia and pulmonary complications in immunocompromised individuals. Although prophylactic therapy for Pneumocystis has significantly decreased the overall incidence of infection, more than 80% of cases in current patient populations are considered breakthrough cases. In the HIV-infected population, in the years following the initiation of highly active antiretroviral therapy (HAART), significant reductions in the incidence of Pneumocystis infection were observed, although trends over the last several years suggest that the incidence of Pneumocystis has plateaued rather than decreased. Furthermore, with the more prominent usage of immunosuppressive therapies, the frequency of Pneumocystis infection in the HIV-negative population, such as those with hematologic malignancies and those who have undergone transplantation, has risen significantly. Investigating host defense mechanisms against P. carinii has historically been problematic due to the difficulty in achieving continuous in vitro propagation of proliferating Pneumocytis organisms. Nevertheless, clinical and experimental studies have documented that host defense against Pneumocystis involves a concerted effort between innate, cell-mediated (T lymphocyte) and humoral (B lymphocyte) responses. However, the pulmonary environment is a tissue site where heightened inflammatory responses can often lead to inflammation-mediated injury, thereby contributing to the pathogenesis of Pneumocystis infection. Accordingly, clearance of Pneumocystis from the pulmonary environment is dependent on a delicate equilibrium between the inflammatory response and immune-mediated clearance of the organism. Furthermore, innate and adaptive responses against Pneumocystis are strikingly similar to those against other medically-important fungi, thus providing additional evidence that Pneumocystis exists as a fungal organism.