gebhart/patrepeval huggingface dataset:
Risk factors for acute non-A, non-B hepatitis in the United States and association with hepatitis C virus infection (1990)

The Centers for Disease Control conducted intensive surveillance for acute non-A, non-B hepatitis in four sentinel counties over a 7-year period. Testing for antibody to hepatitis C virus was performed with the newly developed enzyme immunoassay. The incidence of non-A, non-B hepatitis remained relatively stable (average, 7.1 cases per 100 000), but there were significant changes in disease transmission patterns. The proportion of patients with a history of blood transfusion declined from 17% to 6%, but the proportion with a history of parenteral drug use increased from 21% to 42%. The proportion of patients with histories of sexual exposure (6%), household exposure (3%), occupational exposure to blood (2%), or hemodialysis (0.6%) did not change over time. Antibody to hepatitis C virus was found in 45% of patients within 6 weeks of onset of illness and in 68% of patients followed up for at least 6 months. Patients with no history of transfusions were just as likely to be positive for antibody to hepatitis C virus as patients with transfusion-associated hepatitis, indicating that hepatitis C virus is the major causative agent of all non-A, non-B hepatitis in the United States. (<i>JAMA</i>. 1990;264:2231-2235)
Baff Binds to the Tumor Necrosis Factor Receptor–Like Molecule B Cell Maturation Antigen and Is Important for Maintaining the Peripheral B Cell Population (2000)

The tumor necrosis factor (TNF) family member B cell activating factor (BAFF) binds B cells and enhances B cell receptor-triggered proliferation. We find that B cell maturation antigen (BCMA), a predicted member of the TNF receptor family expressed primarily in mature B cells, is a receptor for BAFF. Although BCMA was previously localized to the Golgi apparatus, BCMA was found to be expressed on the surface of transfected cells and tonsillar B cells. A soluble form of BCMA, which inhibited the binding of BAFF to a B cell line, induced a dramatic decrease in the number of peripheral B cells when administered in vivo. Moreover, culturing splenic cells in the presence of BAFF increased survival of a percentage of the B cells. These results are consistent with a role for BAFF in maintaining homeostasis of the B cell population.
Understanding electrochemical potentials of cathode materials in rechargeable batteries (2015)

Presently, sustainable energy as well as efficient and economical energy conversion and storage technologies has become important work in light of the rising environmental issues and dependence on portable and uninterrupted power sources. Increasingly more researchers are focusing on harvesting and converting solar energy, mechanical vibration, waste heat, and wind to electricity. Electrical energy storage technologies play a significant role in the demand for green and sustainable energy. Rechargeable batteries or secondary batteries, such as Li-ion batteries, Na-ion batteries, and Mg-ion batteries, reversibly convert between electrical and chemical energy via redox reactions, thus storing the energy as chemical potential in their electrodes. The energy density of a rechargeable battery is determined collectively by the specific capacity of electrodes and the working voltage of the cell, which is the differential potential between the cathode and the anode. Over the past decades, a significant number of studies have focused on enhancing this specific capacity; however, studies to understand and manipulate the electrochemical potential of the electrode materials are limited. In this review, the material characteristics that determine and influence the electrochemical potentials of electrodes are discussed. In particular, the cathode materials that convert electricity and chemical potential through electrochemical intercalation reactions are investigated. In addition, we summarize the selection criteria for elements or compounds and the effect of the local atomic environment on the discharge potential, including the effects of site energy, defects, crystallinity, and microstructure, using LiMn2O4, V2O5, Mo6S8, LiFePO4, and LiCoO2 as model samples for discussion.
Cell‐mediated cytotoxicity against ectromelia virus‐infected target cells. II. Identification of effector cells and analysis of mechanisms (1974)

Abstract Cell‐mediated cytotoxicity of ectromelia‐immune spleen cells against ectromelia‐infected L929 target cells was abrogated by treatment of the spleen cells with anti‐Θ antibody and complement. Treatment of spleen cells with anti‐immunoglobulin serum and complement, or removal of macrophages had little or no effect on cytotoxicity. Specific or nonspecific soluble cytotoxic factors were not detected, and exogenous interferon did not enhance cytotoxicity. No blocking of cytotoxicity was detected with either hyperimmune or 9‐day immune anti‐ectromelia serum. By varying the spleen cell‐target cell ratio from 3: 1 to 400: 1, it was shown that the efficiency of cytotoxicity was inversely related to spleen cell density. These results were interpreted to mean that thymus‐derived (T) cells, probably acting alone, were responsible for cytotoxicity and that the mechanism involved contact between T cell and target cell.
DIVE A multi-user virtual reality system (2002)

The Distributed Interactive Virtual Environment (DIVE) is a heterogeneous distributed virtual reality system based on UNIX and Internet networking protocols. Each participating process has a copy of a replicated database and changes are propagated to the other processes with reliable multicast protocols. DIVE provides a dynamic virtual environment where applications and users can enter and leave the environment on demand. Several user-related abstractions have been introduced to ease the task of application and user interface construction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Implicit state minimization of non-deterministic FSMs (2002)

This paper addresses state minimization problems of different classes of non-deterministic finite state machines (NDFSMs). We present a theoretical solution to the problem of exact state minimization of general NDFSMs, based on the proposal of generalized compatibles. This gives an algorithmic frame to explore behaviors contained in a general NDFSM. Then we describe a fully implicit algorithm for state minimization of pseudo non-deterministic FSMs (PNDFSMs). The results of our implementation are reported and shown to be superior to a previous explicit formulation. We could solve exactly all but one problem of a published benchmark, while an explicit program could complete approximately one half of the examples, and in those cases with longer run times.
Sortase-Tag Expressed Protein Ligation: Combining Protein Purification and Site-Specific Bioconjugation into a Single Step (2013)

Efficient labeling of protein-based targeting ligands with various cargos (drugs, imaging agents, nanoparticles, etc.) is essential to the fields of molecular imaging and targeted therapeutics. Many common bioconjugation techniques, however, are inefficient, nonstoichiometric, not site-specific, and/or incompatible with certain classes of protein scaffolds. Additionally, these techniques can result in a mixture of conjugated and unconjugated products, which are often difficult to separate. In this study, a bacterial sortase enzyme was utilized to condense targeting ligand purification and site-specific conjugation at the C-terminus into a single step. A model was produced to determine optimal reaction conditions for high conjugate purity and efficient utilization of cargo. As proof-of-principle, the sortase-tag expressed protein ligation (STEPL) technique was used to generate tumor-specific affinity ligands with fluorescent labels and/or azide modifications at high purity (>95%) such that it was not necessary to remove unconjugated impurities. Click chemistry was then used for the highly efficient and site-specific attachment of the azide-modified targeting ligands onto nanoparticles.
Ultrabithorax and Antennapedia 5′ Untranslated Regions Promote Developmentally Regulated Internal Translation Initiation (1997)

The 5' untranslated regions (UTRs) of the Drosophila Ubx and Antp genes were tested for their ability to promote cap-independent translation initiation. The Ubx and the Antp 5' UTR were inserted between the CAT and lacZ coding sequences in a dicistronic gene and tested for IRES activity in transgenic Drosophila. Northern analysis of the mRNAs showed the presence of the predicted full-length dicistronic mRNAs. High CAT activity was expressed from the first cistron from all of the dicistronic constructs introduced into the fly genome. The dicistronic transgenic strains bearing the Ubx and Antp IRES elements expressed significant levels of beta-galactosidase (betaGAL) from the second cistron whereas little or no betaGAL was expressed in the controls lacking the IRESs. In situ analysis of betaGAL expression in the transgenic strains indicates that expression of the second cistron is spatially and temporally regulated. Although the developmental patterns of expression directed by the Antp and Ubx IRESs overlap, they exhibit several differences indicating that these IRESs are not functionally equivalent.
Influence of Molecular Weight on Intracameral Dextran Movement to the Posterior Segment of the Mouse Eye (2004)

The influence of molecular weight on the redistribution of macromolecules from the anterior chamber to the posterior globe in the mouse eye appears to be similar to primate eyes. These similarities include passage of all size dextrans through the proximal uveoscleral pathway, the dependence of the extent of posterior movement on the size of the dextran, and the absence of large dextran entry into the distal uveoscleral pathway.
Predicting system performance for multi-tenant database workloads (2011)

Database consolidation is gaining wide acceptance as a means to reduce the cost and complexity of managing database systems. However, this new trend poses many interesting challenges for understanding and predicting system performance. The consolidated databases in multi-tenant settings share resources and compete with each other for these resources. In this work we present an experimental study to highlight how these interactions can be fairly complex. We argue that individual database staging or workload profiling is not an adequate approach to understanding the performance of the consolidated system. Our initial investigations suggest that machine learning approaches that use monitored data to model the system can work well for important tasks.
Use of a yeast site‐specific recombinase to generate embryonic mosaics in Drosophila (1992)

An efficient method for generating embryonic mosaics using a yeast site-specific recombinase (FLP), under the control of a heat shock promoter, is described. FLP-recombinase can promote mitotic exchange between homologous chromosomes that contain FRT (FLP Recombination Target) sequences. To demonstrate the efficiency of FLP-recombinase to generate embryonic mosaics, clones of the recessive and cell autonomous mutation armadillo (arm), detected by their ability to differentiate ectopic denticles in the naked cuticle of each abdominal segment, have been induced. We have analyzed the parameters of FLP-recombinase induced embryonic mitotic recombination and have demonstrated that clones can be efficiently induced during the postblastoderm mitotic divisions. We discuss applications of this technique for the analyses of the roles of various mutations during embryonic patterning.
Expression levels of functional folate receptors α and β are related to the number of N-glycosylated sites (1997)

In a previous study with inhibitors of N-glycosylation, it was proposed that core glycosylation of the folate receptor (FR) is required for the proper folding of the protein [Luhrs (1991) Blood 77, 1171-1180]. The human FR isoforms type alpha and type beta have three and two candidate sites for N-glycosylation respectively, only one of which is conserved. The significance of N-glycosylation at each of these loci in the expression and function of FR was examined by eliminating the sites both individually and in combination by introducing Asn-->Gln substitutions. Translation experiments in vitro showed that the mutations did not alter the synthetic rates of the polypeptides. The recombinant proteins were expressed in human 293 fibroblasts. Treatment with N-glycanase and analysis by Western blotting of the wild-type and mutant proteins revealed that all of the candidate sites in both FR-alpha and FR-beta are glycosylated. When all of the N-glycosylation sites were abolished, 2% and 8% of FR-alpha and FR-beta respectively were expressed on the cell surface compared with the corresponding wild-type proteins; the residual FR polypeptides in the cell lysates were unable to bind [3H]folic acid. In both the proteins, the inclusion of each additional N-glycosylation site partly contributed to restoration of cell surface [3H]folic acid binding and receptor-mediated folate transport. Further, in FR-beta the introduction of an additional unnatural site of N-glycosylation resulted in the enhancement of the expression of the cell surface receptor compared with the wild-type protein. The results indicate that the total mass of N-glycosylation, not a specific locus of the modification, is critical for the efficient folding and optimal expression of functional FR-alpha and FR-beta.
Biosynthesis and secretion of factor VII, protein C, protein S, and the Protein C inhibitor from a human hepatoma cell line (1986)

Using specific radioimmunoassays, 8 day cultures of Hep G2 cells were shown to contain in their supernatants 16, 74, and 828 ng/mL and in their cell lysates, 8, 55, and 48 ng/2 X 10(8) cells of factor VII, protein C, and protein S, respectively. These proteins and the protein C inhibitor were functionally active, and each of these activities was neutralized by their respective polyclonal antibodies. Although vitamin K had a modest effect, warfarin decreased the activity of secreted factor VII, protein C, and protein S by 50% to 90%. Protein C and protein S antigens were reduced three- to fourfold by warfarin. The protein C inhibitor antigen and activity were unaffected by vitamin K or warfarin treatment. Intrinsic labeling and immunoprecipitation indicated that factor VII, protein S, and the protein C inhibitor were secreted as 52,000, 77,000, and 58,000 molecular weight (mol wt) proteins, respectively. Protein C was secreted as a single-chain protein of about 65,000 mol wt, indicating that all of the vitamin K-dependent proteins are translated and secreted as single-chain molecules. Each of the four proteins studied represented their plasma protein counterparts structurally, functionally, and immunochemically. Thus, all of the known soluble components of the protein C pathway are produced by liver parenchymal cells.
Prediction of prognosis in patients with uveal melanoma using fluorescence in situ hybridisation (2001)

The authors have shown that FISH analysis for chromosome 3 and 8 is a reliable and efficient technique in the analysis of fresh frozen tumour specimens and is valuable in the prediction of prognosis in individuals with uveal melanomas.
Simplified enzymatic assay of angiotensin-converting enzyme in serum (1993)

We report a simple, enzymatic method for determining angiotensin-converting enzyme (ACE; EC 3.4.15.1) in serum. The proposed method features coupling an established reaction catalyzed by gamma-glutamyltransferase (GGT; EC 2.3.2.2) to the ACE reaction, which releases glycylglycine from the artificial substrate hippuryl-glycyl-glycine. The glycyl-glycine released by the ACE reaction becomes rate-limiting in the GGT reaction, in which it participates as a receptor substrate for a gamma-glutamyl group transferred from a donor substrate, L-gamma-glutamyl-3-carboxy-4-nitroanilide. The reaction releases 3-carboxy-4-nitroaniline, which is monitored spectrophotometrically at 410 nm. The resulting rate of change in absorbance is linearly related to the glycyl-glycine concentration and therefore to the activity of ACE. The linear range of the method extends from ACE values < 50 to at least 1300 U/L of serum. Good precision is indicated by a low CV for replicate analyses (3.6% and 4.6% for within-run and day-to-day assays, respectively, for normal ACE activity, and 3.1% within-run for high ACE activity). Results also correlate well with those of an established colorimetric method (r = 0.978). The major advantages of the method are its procedural simplicity, limited cost, use of readily available reagents, applicability to isoenzyme studies, and adaptability to automation.
Kalman Filtering: Theory and Practice (1993)

1. General Information. 2. Linear Dynamic Systems. 3. Random Processes and Stochastic Systems. 4. Linear Optimal Filters and Predictors. 5. Nonlinear Applications. 6. Implementation Methods. 7. Practical Considerations. Appendix A: Software. Appendix B: A Matrix Refresher.
Recent Advances in the Treatment of Malignant Astrocytoma (2006)

Malignant gliomas, including the most common subtype, glioblastoma multiforme (GBM), are among the most devastating of neoplasms. Their aggressive infiltration in the CNS typically produces progressive and profound disability--ultimately leading to death in nearly all cases. Improvement in outcome has been elusive despite decades of intensive clinical and laboratory research. Surgery and radiotherapy, the traditional cornerstones of therapy, provide palliative benefit, while the value of chemotherapy has been marginal and controversial. Limited delivery and tumor heterogeneity are two fundamental factors that have critically hindered therapeutic progress. A novel chemoradiotherapy approach, consisting of temozolomide administered concurrently during radiotherapy followed by adjuvant systemic temozolomide, has recently demonstrated a meaningful, albeit modest, improvement in overall survival for newly diagnosed GBM patients. As cell-signaling alterations linked to the development and progression of gliomas are being increasingly elucidated, targeted therapies have rapidly entered preclinical and clinical evaluation. Responses to therapies that function via DNA damage have been associated with specific mediators of resistance that may also be subject to targeted therapies. Other approaches include novel locoregional delivery techniques to overcome barriers of delivery. The simultaneous development of multiple advanced therapies based on specific tumor biology may finally offer glioma patients improved survival.
Selective H/D Exchange at Vinyl and Methylidene Groups with D2O Catalyzed by an Iridium Complex (2016)

Selective H/D exchange at vinyl and methylidene groups of alkenes with D2O was promoted by an iridium catalyst generated in situ from a hydroxoiridium complex and N-mesylbenzamide.
Effects of Conformational Stability and Geometry of Guanidinium Display on Cell Entry by β-Peptides (2005)

We have used our ability to control beta-peptide secondary structure in order to explore the effects of conformational stability and geometry of guanidinium display on cell entry. Both of these factors affect the rate and relative amount of beta-peptide accumulation in the cytoplasm and nucleus of live HeLa cells. These beta-peptides do not show significant differences in cell surface binding, implying that structure and guanidinium display are important in a later step in cell entry than initial surface binding.
Magnetocaloric properties of Co/Cr superlattices (2009)

Nanostructured materials for refrigeration applications are experimentally realized by molecular beam epitaxial growth of Co/Cr superlattices using mean-field theoretical concepts as guiding principles. Magnetocaloric properties are deduced from measurements of the temperature and field dependence of the magnetization of our samples. More generally, the potential of artificial antiferromagnets for near room-temperature refrigeration is explored. The effects of intraplane and interplane exchange interactions on the magnetic phase diagram in Ising-type model systems are revisited in mean-field considerations with special emphasis on tailoring magnetocaloric properties. The experimental results are discussed in light of our theoretical findings, and extrapolations for future improved nanostructures are provided.
Sortase Enzyme-Mediated Generation of Site-Specifically Conjugated Antibody Drug Conjugates with High In Vitro and In Vivo Potency (2015)

Antibody drug conjugates (ADCs) have recently been proven to be highly potent anti-tumor drugs, typically exceeding the efficacy of conventional monoclonal antibodies (mAbs). ADCs are currently produced by chemical conjugation of a small-molecule toxin to the mAb through lysine or cysteine side chains. This leads to heterogeneous mixtures of ADCs in which variable numbers of drugs are conjugated to individual antibodies and in which the site of conjugation cannot be defined. Consequently, there is currently significant interest in further development of drug conjugation technologies, with a particular focus on site-specific payload conjugation. Here, we present an enzymatic conjugation platform based on the S. aureus sortase A-mediated transpeptidation reaction, allowing the efficient generation of ADCs with toxins conjugated to pre-defined sites at pre-defined drug-to-antibody ratios. For this, two modifications were introduced: first, immunoglobulin heavy (IgH) and light (IgL) chains were modified at their C-termini by addition of the sortase A recognition motif LPETG, and second, the small molecule tubulin polymerization inhibitors monomethylauristatin E (MMAE) and maytansine were modified by addition of a pentaglycine peptide, thus making them suitable substrates for sortase A-mediated transpeptidation. We demonstrate efficient generation and characterization of the anti-CD30 ADC Ac10-vcPAB-MMAE, an enzymatically conjugated counterpart of brentuximab vedotin (Adcetris), as well as several anti-HER-2 ADCs including trastuzumab-maytansine, the counterpart of trastuzumab emtansine (Kadcyla). ADCs generated in this manner were found to display in vitro cell killing activities indistinguishable from the classic conjugates. Further, when tested in vivo in a HER-2-overexpressing ovarian cancer xenograft mouse model, enzymatically generated trastuzumab-maytansine was found to lead to complete regression of established tumors, similar to Kadcyla.
Recombinant Factor VIla (NovoSeven®) in the Treatment of Internal Bleeding in Patients with Factor VIM and IX Inhibitors (1996)

Recombinant factor VIIa (NovoSeven) was used on a compassionate use basis to treat 51 episodes of internal bleeding in 43 patients. All had become refractory to (or were not candidates for) other therapeutic agents. 26 of the 43 patients had hemophilia A and FVIII inhibitor antibodies, 13 had acquired FVIII inhibitors, 2 had hemophilia B and FIX inhibitors, and 2 had other coagulopathies, of 50 episodes of internal bleeding evaluated 76% had an excellent or effective response to rFVIIa. The average dosage given was 84 mu g/kg; the median number of doses given was 38. rFVIIa appears to be a very valuable addition to one's therapeutic armamentarium for treating serious bleeding episodes in inhibitor patients.