gebhart/patrepeval huggingface dataset:
Mechanistically different catalytic antibodies obtained from immunization with a single transition-state analog. (1995)

The variable-region peptide sequence and steady-state kinetic behavior are compared for a family of catalytic antibodies that arose from the same immune response to a transition-state analog. The crystal structure of the most catalytically active member of the family (17E8) has been solved to 2.5 A resolution and shows that the antibody active site contains a SerH99-HisH35 (H = heavy chain) catalytic dyad analogous to the Ser-His-Asp catalytic triad of serine proteases. The variable-region peptide sequence of the next most active antibody (29G11) differs from that of 17E8 by nine heavy-chain point mutations, and results from computer modeling suggest that the three-dimensional structure of 29G11 is similar to that of 17E8. In addition, 29G11 is an efficient catalytic antibody; it possesses 26% of the hydrolytic activity of 17E8. There is one active-site mutation in 29G11 compared to 17E8; position 99 of the heavy chain of 29G11 contains a glycine residue in place of the nucleophilic serine at this position in 17E8. Consistent with this mutation, results from pH-rate studies and hydroxylamine partitioning experiments indicate that in contrast to the catalytic mechanism of 17E8, the mechanism of 29G11-catalyzed esterolysis does not feature nucleophilic catalysis.
Transfer of Specificity for Human Immunodeficiency Virus Type 1 into Primary Human T Lymphocytes by Introduction of T-Cell Receptor Genes (2000)

The introduction of genes encoding T-cell receptor (TCR) chains specific for human immunodeficiency virus into T cells of infected patients represents a means to quantitatively and qualitatively improve immunity to the virus. Our results demonstrate that the high level of TCR expression required for physiologic functioning can be reproducibly achieved with retroviral vectors encoding full-length unmodified TCR chains under the control of a strong internal constitutive phosphoglycerate kinase promoter.
Amino-terminal processing of mutant forms of yeast iso-1-cytochrome c. The specificities of methionine aminopeptidase and acetyltransferase. (1985)

Met-Ile-Glu-Phe-Lys- Met-Asn-Lys-Phe-Lys-Ala
Continuous-Time Adaptive Critics (2007)

A continuous-time formulation of an adaptive critic design (ACD) is investigated. Connections to the discrete case are made, where backpropagation through time (BPTT) and real-time recurrent learning (RTRL) are prevalent. Practical benefits are that this framework fits in well with plant descriptions given by differential equations and that any standard integration routine with adaptive step-size does an adaptive sampling for free. A second-order actor adaptation using Newton's method is established for fast actor convergence for a general plant and critic. Also, a fast critic update for concurrent actor-critic training is introduced to immediately apply necessary adjustments of critic parameters induced by actor updates to keep the Bellman optimality correct to first-order approximation after actor changes. Thus, critic and actor updates may be performed at the same time until some substantial error build up in the Bellman optimality or temporal difference equation, when a traditional critic training needs to be performed and then another interval of concurrent actor-critic training may resume.
Critical Role of the C-Terminal Domains of Factor H in Regulating Complement Activation at Cell Surfaces (2006)

The plasma protein factor H primarily controls the activation of the alternative pathway of complement. The C-terminal of factor H is known to be involved in protection of host cells from complement attack. In the present study, we show that domains 19-20 alone are capable of discriminating between host-like and complement-activating cells. Furthermore, although factor H possesses three binding sites for C3b, binding to cell-bound C3b can be almost completely inhibited by the single site located in domains 19-20. All of the regulatory activities of factor H are expressed by the N-terminal four domains, but these activities toward cell-bound C3b are inhibited by isolated recombinant domains 19-20 (rH 19-20). Direct competition with the N-terminal site is unlikely to explain this because regulation of fluid phase C3b is unaffected by domains 19-20. Finally, we show that addition of isolated rH 19-20 to normal human serum leads to aggressive complement-mediated lysis of normally nonactivating sheep erythrocytes and moderate lysis of human erythrocytes, which possess membrane-bound regulators of complement. Taken together, the results highlight the importance of the cell surface protective functions exhibited by factor H compared with other complement regulatory proteins. The results may also explain why atypical hemolytic uremic syndrome patients with mutations affecting domains 19-20 can maintain complement homeostasis in plasma while their complement system attacks erythrocytes, platelets, endothelial cells, and kidney tissue.
Modular Nature of Blimp-1 in the Regulation of Gene Expression during B Cell Maturation (2004)

The transcription factor Blimp-1 induces the maturation of B cells into Ab-secreting plasma cells. DNA microarrays were used to analyze the transcription profiles of both Blimp-1-transduced murine B cell lines and the inducible B cell line BCL(1). Hundreds of genes were differentially regulated, showing how Blimp-1 both restricts affinity maturation and promotes Ab secretion, homeostasis, migration, and differentiation. Strikingly, when different modes of plasma cell induction are used, very different genetic programs are used, suggesting that the transition from a B cell to plasma cell can occur in multiple ways, perhaps accounting for the different types of Ab-secreting cells observed in vivo. Furthermore, mutagenesis of Blimp-1 reveals multiple effector domains, which regulate distinct genes. This indicates that Blimp-1 subdivides the maturation program into select and tunable pathways.
Determination of aliphatic alcohols, squalene, α-tocopherol and sterols in olive oils: direct method involving gas chromatography of the unsaponifiable fraction following silylation (2001)

In general, analyses for aliphatic alcohols, sterols and tocopherols in vegetable oils are performed separately. A simple and reliable procedure is presented for the quantification of the alkanols, squalene, alpha-tocopherol and sterols in olive oils by a direct method involving gas chromatographic (GC) analysis of the unsaponifiable fraction after silylation. The method eliminates the need for a preliminary thin-layer chromatographic (TLC) fractionation prior to GC. External standard calibration with reference substances was used for the quantification of squalene, alpha-tocopherol and sterols and internal standard calibration for the quantification of aliphatic alcohols. The analyte recovery and the repeatability of the quantitative results were evaluated and were acceptable for routine use.
A hybrid-PWM based DC-link voltage balancing algorithm for a 3-level neutral-point-clamped (NPC) DC/AC traction inverter drive (2015)

This paper presents a hybrid pulse-width modulation (PWM) technique, for a 3-level neutral point clamped (NPC) electric vehicle (EV) traction inverter drive. In this strategy both the advantages from the SV-PWM and carrier-based PWM strategies are introduced. The duty cycles for the switches are calculated using carrier based PWM, to reduce the computational time and complexity. The redundancies of the switching states are used to balance the two DC-link capacitor voltages, as in the SV-PWM based strategies. The proposed scheme is capable of maintaining the difference between the two DC-link capacitor voltages stable for a wider range of machine speed-torque variations. Moreover, a single carrier is used instead of multiple carriers, which also reduces the computational complexities. A detailed simulation studies are carried out in MATLAB/SIMULINK® platform to verify the controllability of the proposed control scheme. Experimental studies are carried out with a 6.0 kW surface permanent magnet synchronous machine (SPMSM). The simulation and experimental results show the desired performance of the proposed scheme.
Organizational Capital, Innovation Climate, and Service Innovation Behavior (2018)

Along with the knowledge economy era, the concept of organizational capital increasingly receives many attentions. Many previous studies have emphasized the influence of organizational capital on innovation at the organizational level. The present study is trying to explore the impact of organizational capital on service innovation behavior and examine the mediating effect of organizational innovation climate on the relationship between organizational capital and service innovation behavior. The researchers conducted a survey to collect data from Taiwan Top 500 service businesses based on CommonWealth magazine’s survey. We expect to profoundly understand the relationships between organizational capital, innovation climate, and service innovation behaviors as well as provide meaningful implications for academics and practitioners.
Revascularization of occluded haemodialysis fistulae with the Hydrolyser® thrombectomy catheter: description of the technique and report of six cases (1995)

Our purpose was to describe initial experience with a new mechanical thrombectomy catheter for treating haemodialysis fistulae. The Hydrolyser thrombectomy catheter combines thrombus fragmentation by a saline jet with simultaneous low-pressure aspiration. This catheter was used in six cases of dialysis-fistula occlusion. In four instances this was a polytetrafluoroethylene loop, in two cases a Brescia-Cimino fistula. In all cases rapid revascularization was obtained without complications. Reocclusion occurred in one patient, immediate reintervention being successful. Our initial results suggest that the Hydrolyser is a quick, minimally invasive, and useful alternative to the presently accepted methods of revascularizing occluded haemodialysis fistulae.
Design of N-substituted Peptomer Ligands for EVH1 Domains (2003)

Ena/VASP proteins are implicated in cytoskeletal reorganization during actin-dependent motility processes. Recruitment to subcellular sites of actin polymerization is mediated by the highly conserved N-terminal EVH1 domain, which interacts with target proteins containing proline-rich motifs. The VASP EVH1 domain specifically binds peptides with the consensus motif FPPPP present in all its binding partners, including the Listerial ActA protein. Previous studies have shown that the Phe and first and final Pro residues are highly conserved and cannot be substituted with any other natural amino acid without significant loss of binding affinity. We have incorporated peptoid building blocks (sarcosine derived, non-natural amino acids) into the peptide SFEFPPPPTEDEL from the Listerial ActA protein and were able to substitute the most highly conserved residues of this motif while maintaining binding to the VASP EVH1 domain with affinities in the range of 45-180 microm. We then used NMR chemical shift perturbations to locate specific domain residues involved in particular interactions. These studies may open up the way for designing selective modulators of VASP function for biological studies and for the development of novel therapeutics for diseases involving pathologically altered cell adhesion or cell motility.
In Defense of Safe Spaces: A Phenomenological Account (2019)

The notion of “safe space” is one example of a theoretical and pedagogical resource grounded in studies of marginalized experiences that has recently undergone backlash in dominant culture and the academy. In this essay, I offer a defense of safe spaces using the theoretical resources of phenomenology and offer suggestions for moving past the dichotomy of safe versus unsafe space. I argue that safe space should be understood not as static and acontextual, as truly “safe” or “unsafe,” but through the relational work of cultivating such spaces. Furthermore, far from restricting dialogue in the classroom, safe spaces encourage dialogue through requiring students to utilize critical thinking in their exchanges and through supporting marginalized students whose positions and humanity often fail to be recognized in dominant spaces.
LSD1 and pluripotency: A new player in the network (2011)

Comment on: Adamo A, et al. Nat Cell Biol 2011; 13:652-60.
A Simple and Scalable Process for the Differentiation of Retinal Pigment Epithelium From Human Pluripotent Stem Cells (2013)

Age-related macular degeneration (AMD), the leading cause of irreversible vision loss and blindness among the elderly in industrialized countries, is associated with the dysfunction and death of the retinal pigment epithelial (RPE) cells. As a result, there has been significant interest in developing RPE culture systems both to study AMD disease mechanisms and to provide substrate for possible cell-based therapies. Because of their indefinite self-renewal, human pluripotent stem cells (hPSCs) have the potential to provide an unlimited supply of RPE-like cells. However, most protocols developed to date for deriving RPE cells from hPSCs involve time- and labor-consuming manual steps, which hinder their use in biomedical applications requiring large amounts of differentiated cells. Here, we describe a simple and scalable protocol for the generation of RPE cells from hPSCs that is less labor-intensive. After amplification by clonal propagation using a myosin inhibitor, differentiation was induced in monolayers of hPSCs, and the resulting RPE cells were purified by two rounds of whole-dish single-cell passage. This approach yields highly pure populations of functional hPSC-derived RPE cells that display many characteristics of native RPE cells, including proper pigmentation and morphology, cell type-specific marker expression, polarized membrane and vascular endothelial growth factor secretion, and phagocytic activity. This work represents a step toward mass production of RPE cells from hPSCs.
Putative human male germ cells from bone marrow stem cells. (2007)

Germ cells must develop along distinct male or female paths to produce the spermatozoa or oocyte required for sexual reproduction. Male germline stem cells maintain spermatogenesis in the postnatal human testis. Here we show that a small population of bone marrow cells is able to transdifferentiate to male germ cell-like cells. We show expression of early germ cell markers (Oct4, Fragilis, Stella and Vasa) and male germ cell specific markers (Dazl, TSPY, Piwil2 and Stra8) in these cells. Our preliminary findings provide direct evidence that human bone marrow cells can differentiate to putative male germ cells and identify bone marrow as a potential source of male germ cells that could sustain sperm production.
Integrating the UB-Tree into a Database System Kernel (2000)

Multidimensional access methods have shown high potential for significant performance improvements in various application domains. However, only few approaches have made their way into commercial products. In commercial database management systems (DBMSs) the B-Tree is still the prevalent indexing technique. Integrating new indexing methods into existing database kernels is in general a very complex and costly task. Exceptions exist, as our experience of integrating the UB-Tree into TransBase, a commercial DBMS, shows. The UB-Tree is a very promising multidimensional index, which has shown its superiority over traditional access methods in different scenarios, especially in OLAP applications. In this paper we discuss the major issues of a UB-Tree integration. As we will show, the complexity and cost of this task is reduced significantly due to the fact that the UB-Tree relies on the classical B-Tree. Even though commercial DBMSs provide interfaces for index extensions, we favor the kernel integration because of the tight coupling with the query optimizer, which allows for optimal usage of the UB-Tree in execution plans. Measurements on a real-world data warehouse show that the kernel integration leads to an additional performance improvement compared to our prototype implementation and competing index methods.
The Rate and Character of Spontaneous Mutation in an RNA Virus (2002)

Estimates of spontaneous mutation rates for RNA viruses are few and uncertain, most notably due to their dependence on tiny mutation reporter sequences that may not well represent the whole genome. We report here an estimate of the spontaneous mutation rate of tobacco mosaic virus using an 804-base cognate mutational target, the viral MP gene that encodes the movement protein (MP). Selection against newly arising mutants was countered by providing MP function from a transgene. The estimated genomic mutation rate was on the lower side of the range previously estimated for lytic animal riboviruses. We also present the first unbiased riboviral mutational spectrum. The proportion of base substitutions is the same as that in a retrovirus but is lower than that in most DNA-based organisms. Although the MP mutant frequency was 0.02-0.05, 35% of the sequenced mutants contained two or more mutations. Therefore, the mutation process in populations of TMV and perhaps of riboviruses generally differs profoundly from that in populations of DNA-based microbes and may be strongly influenced by a subpopulation of mutator polymerases.
Impaired mucosal antibody response to cholera toxin in vitamin A-deficient rats immunized with oral cholera vaccine (1993)

To investigate the importance of vitamin A in the ability to respond to oral antigen administration, rats were fed a vitamin A-free diet. The animals were immunized perorally three times with a mixture of cholera toxin (CT) and a commercial cholera vaccine. The total immunoglobulin A (IgA) concentration as well as the specific IgA anti-CT antibody levels in serum and bile was significantly lower in the vitamin A-deficient animals than in the paired fed controls (animals that were fed a normal commercial diet in an amount equal to the amount the deficient animals consumed), while the levels of total and specific anti-CT IgG were not affected to the same extent by the vitamin A deficiency. The number of IgA anti-CT antibody-producing cells in the mesenteric lymph nodes after immunization was also significantly lower in the vitamin A-deficient rats than in the control rats. Supplementation of the diet with retinyl palmitate restored the ability to mount an IgA antibody response to the antigen, since the level of specific IgA anti-CT antibodies in relation to the total IgA concentration was as high in the vitamin A-supplemented group as in the paired fed control group. Restricted diet intake by itself did not affect the ability to respond adequately to the antigen since there was no difference in IgA anti-CT antibody level between paired fed rats and those being fed ad libitum. Assessment of transforming growth factor beta in cell cultures revealed no difference between vitamin A-deficient and paired fed animals. In summary, vitamin A deficiency resulted in a decreased number of IgA-producing cells, decreased IgA production, and a reduced ability to respond with IgA antibodies to the oral cholera vaccine.
CONCENTRATION OF PANCREOZYMIN AS A DETERMINANT OF THE EXOCRINE-ENDOCRINE PARTITION OF PANCREATIC ENZYMES (1973)

1. Recent evidence suggests that the pancreatic digestive enzymes are secreted not only into the digestive tract via the gland lumen (exocrine), but also into the blood stream (endocrine). This dual secretion has been designated the ‘exocrine-endocrine partition’ of enzymes and their precursors, and was investigated in both the isolated and perfused rat pancreas, and the rat pancreas in situ.2. The release of amylase was accompanied by the release of precursors of proteolytic enzymes either into the common duct or into the portal vein, and it was measured as a representation of release of pancreatic enzymes.3. When the isolated pancreas was perfused with Krebs-Henseleit solution containing pancreozymin 0.2u./ml, the amylase output into the common duct was markedly increased, whereas the output into the vein was slightly increased. When the concentration of pancreozymin was increased up to 1.5u./ml, the output into the vein was markedly increased in contrast to a small increase in the output into duct.4. Corresponding with the increase in output into the vein, acinar cells exhibiting high effective membrane resistances increased in number during perfusion of pancreozymin at a high concentration.5. Enhanced release due to pancreozymin into the vein and into the duct was negated when calcium was omitted from the perfusing medium.6. As a high dose of pancreozymin was injected repeatedly into the rat in situ, the blood concentration of amylase became higher but the increase in the output into the common duct became lower.7. It is concluded that pancreatic enzymes and precursors preserved in zymogen granules may be extruded into the acinar lumen by the common calcium-dependent cellular processes; then, some of the secretory products may leak into the portal vein via enlarged intercellular spaces when a high concentration of pancreozymin is present.
Phase stability of a garnet-type lithium ion conductor Li7La3Zr2O12 (2013)

The phase stability of Li7La3Zr2O12 (LLZ) was investigated using high temperature X-ray diffraction (HT-XRD). An Al-free tetragonal LLZ phase transformed into a non-quenchable cubic phase around 650 °C. The phase transformation process between the tetragonal phase and the new cubic phase showed perfect reversibility. The thermal analysis showed a pair of endothermic and exothermic peaks around 640 °C that is in good agreement with the phase transformation process observed in the HT-XRD study. The non-quenchable high temperature cubic phase showed high ionic conductivity with extraordinarily low activation energy (0.117 eV). The tetragonal phase showed another phase transformation to a low temperature (LT) cubic phase around 150-200 °C in air by absorbing CO2 into the structure. The preferred temperature for the CO2 absorption process was around 200 °C and the absorbed CO2 was extracted once the temperature reached 450 °C or above resulting in the phase transformation back to the tetragonal phase. On the other hand the high temperature (HT) cubic phase which shows high ionic conductivity was stabilized by Al substitution. A Li-poor LLZ containing impurity phases such as La2Zr2O7 and La2O3 effectively reacted with γ-Al2O3 resulting in the formation of a pure Al-stabilized cubic LLZ, while the stoichiometric LLZ took a much longer time to complete the Al-substitution. The result suggested that the formation of Li vacancies is the primary step in the formation of the Al-stabilized cubic phase.