gebhart/patrepeval huggingface dataset:
Exploiting Metal–Ligand Bifunctional Reactions in the Design of Iron Asymmetric Hydrogenation Catalysts (2015)

This is an Account of our development of iron-based catalysts for the asymmetric transfer hydrogenation (ATH) and asymmetric pressure hydrogenation (AH) of ketones and imines. These chemical processes provide enantiopure alcohols and amines for use in the pharmaceutical, agrochemical, fragrance, and other fine chemical industries. Fundamental principles of bifunctional reactivity obtained by studies of ruthenium catalysts by Noyori's group and our own with tetradentate ligands with tertiary phosphine and secondary amine donor groups were applied to improve the performance of these first iron(II) catalysts. In particular the correct positioning of a bifunctional H-Fe-NH unit in an iron hydride amine complex leads to exceptional catalyst activity because of the low energy barrier of dihydrogen transfer to the polar bond of the substrate. In addition the ligand structure with this NH group along with an asymmetric array of aryl groups orients the incoming substrate by hydrogen-bonding, and steric interactions provide the hydrogenated product in high enantioselectivity for several classes of substrates. Enantiomerically pure diamines or diphenylphosphino-amine compounds are used as the source of the asymmetry in the tetradentate ligands formed by the condensation of the amines with dialkyl- or diaryl-phosphinoaldehydes, a synthesis that is templated by Fe(II). The commercially available ortho-diphenylphosphinobenzaldehyde was used in the initial studies, but then diaryl-phosphinoacetaldehydes were found to produce much more effective ligands for iron(II). Once the mechanism of catalysis became clearer, the iron-templated synthesis of (S,S)-PAr2CH2CH2NHCHPhCHPhNH2 ligand precursors was developed to specifically introduce a secondary amine in the precatalyst structures. The reaction of a precatalyst with strong base yields a key iron-amido complex that reacts with isopropanol (in ATH) or dihydrogen (in AH) to generate an iron hydride with the Fe-H bond parallel to the secondary amine N-H. In the AH reactions, the correct acidity of the intermediate iron-dihydrogen complex and correct basicity of the amide are important factors for the heterolytic splitting of the dihydrogen to generate the H-Fe-N-H unit; the acidity of dihydrogen complexes including those found in hydrogenases can be estimated by a simple additive ligand acidity constant method. The placement of the hydridic-protonic Fe-H···HN interaction in the asymmetric catalyst structure influences the enantioinduction. The sense of enantioinduction is predictable from the structure of the H-Fe-N-H-containing catalyst interacting with the ketone in the same way as related H-Ru-N-H-containing catalysts. The modular construction of the catalysts permits large variations in order to produce alcohol or amine products with enantiomeric excess in the 90-100% range in several cases.
Complete coverage path planning and guidance for cleaning robots (2002)

This paper describes a complete coverage path planning and guidance methodology for a mobile robot, having the automatic floor cleaning of large industrial areas as a target application. The proposed algorithms rely on the a priori knowledge of a 2D map of the environment and cope with unexpected obstacles not represented on the map. A template based approach is used to control the path execution, thus incorporating, in a natural way, the kinematic and the geometric model of the mobile robot on the path planning procedure. The novelty of the proposed approach is the capability of the path planner to deal with a priori mapped or unexpected obstacles in the middle of the working space. If unmapped obstacles permanently block the planned trajectory, the path tracking control avoids these obstacles. The paper presents experimental results with a LABMATE mobile robot, confirming the feasibility of the total coverage path and the robustness of the path tracking behaviour based control.
Integration and preliminary evaluation of an Insertable Robotic Effectors Platform for Single Port Access Surgery (2012)

In this paper, we present the integration and preliminary evaluation of a novel Insertable Robotic Effectors Platform (IREP) for Single Port Access Surgery (SPAS). The unique design of the IREP includes planar parallel mechanisms, continuum snake-like arms, wire-actuated wrists, and passive flexible components. While this design has advantages, it presents challenges in terms of modeling, control, and telemanipulation. The complete master-slave resolved-rates telemanipulation framework of the IREP along with its actuation compensation is presented. Experimental evaluation of the capabilities of this new surgical system include bi-manual exchange of rings, pick-and-place tasks, suture passing and knot tying. Results show that the IREP meets the minimal workspace and dexterity requirements specified for laparoscopic surgery, it allows for dual-arm operations such as tool exchange and knot tying in confined spaces. Although it was possible to tie a surgeon's knot with minimal training, suture passing was difficult due to the limited axial rotation of the distal wrists.
Utilizing the adjuvant properties of CD1d-dependent NK T cells in T cell–mediated immunotherapy (2004)

Activation of invariant CD1d-dependent NK T cells (iNKT cells) in vivo through administration of the glycolipid ligand alpha-galactosylceramide (alpha-GalCer) or the sphingosine-truncated alpha-GalCer analog OCH leads to CD40 signaling as well as the release of soluble molecules including type 1 and gamma interferons that contribute to DC maturation. This process enhances T cell immunity to antigens presented by the DC. The adjuvant activity is further amplified if APCs are stimulated through Toll-like receptor 4, suggesting that iNKT cell signals can amplify maturation induced by microbial stimuli. The adjuvant activity of alpha-GalCer enhances both priming and boosting of CD8(+) T cells to coadministered peptide or protein antigens, including a peptide encoding the clinically relevant, HLA-A2-restricted epitope of the human tumor antigen NY-ESO-1. Importantly, alpha-GalCer was used to induce CD8(+) T cells to antigens delivered orally, despite the fact that this route of administration is normally associated with blunted responses. Only T cell responses induced in the presence of iNKT cell stimulation, whether by the i.v. or oral route, were capable of eradicating established tumors. Together these data highlight the therapeutic potential of iNKT cell ligands in vaccination strategies, particularly "heterologous prime-boost" strategies against tumors, and provide evidence that iNKT cell stimulation may be exploited in the development of oral vaccines.
Mechanisms of Vasodilatation Induced by Nitrite Instillation in Intestinal Lumen: Possible Role of Hemoglobin (2005)

It has been shown that nitrite can be reduced to nitric oxide (NO) in intestine and a number of other tissues and released into the blood to form nitrosylhemoglobin (NO-Hb), existing in an equilibrium with S-nitrosohemoglobin. The latter has been suggested to be an NO transporter to distant organs. The aim of this study was to define the pathway of nitrite reduction to form NO in intestinal wall and to estimate whether this pathway has an effect on peripheral circulation. We have shown that in rat intestine at pH 7.0 70% of nitrite is converted to NO in mitochondria. At pH 6.0, nonenzymatic nitrite reduction becomes as efficient as the mitochondrial pathway. To prove whether the NO formed from nitrite in intestine can induce vasodilatation, sodium nitrite was instilled into intestinal lumen and the concentration of NO formed and diffused into the blood was followed by measuring of NO-Hb complex formation. We found that the concentration of NO-Hb gradually increases with the increase of nitrite concentration in intestinal lumen. However, it was not always accompanied by a decrease in systemic blood pressure. Blood pressure dropped down only after NO-Hb reached a threshold concentration of approximately 10 microM. These data show that NO-Hb cannot provide enough NO for vasodilatation if the concentration of NO bound to Hb is < 10 microM. The exact mechanism underlying vasodilatation observed when the concentration of NO-bound Hb was > 10 microM is, however, not clear yet and requires further studies.
L-696,474, a novel cytochalasin as an inhibitor of HIV-1 protease. II. Isolation and structure. (1992)

A novel HIV-1 protease inhibitor, L-696,474 (C30H39NO4, 477), was isolated from the fermentations of the fungus Hypoxylon fragiforme (ATCC 20995, MF5511) and purified by silica gel chromatography followed by crystallization. Spectroscopic studies have shown the competitive inhibitor L-696,474 to be a novel cytochalasin. Two related novel cytochalasins were also isolated and had no effect on the enzyme.
Identification of variations in SzP proteins of Streptococcus equi subspecies zooepidemicus and the relationship between protein variants and clinical signs of infection in horses (2003)

The SzP protein appears to be limited to a selected number of types. Variations in the SzP protein are frequently determined on the basis of different motifs rather than random amino acid substitutions. There does not appear to be any association of SzP protein variations and clinical manifestations of infection in horses.
Optimized production of transgenic buffalo embryos and offspring by cytoplasmic zygote injection (2015)

Our cytoplasmic injection protocol improved generation of transgenic embryos and resulted in the first transgenic buffalo calves produced by this method.
Surface peptide mapping of protein I and protein III of four strains of Neisseria gonorrhoeae (1982)

Whole cells and isolated outer membranes (OMs) of four strains of gonococci were surface radioiodinated with either lactoperoxidase or Iodogen (Pierce Chemical Co., Rockford, Ill.). These preparations were solubilized in sodium dodecyl sulfate and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Surface-radioiodinated protein I (PI) and PIII bands were excised from the sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels and digested with alpha-chymotrypsin, and the resultant 125I-peptide fragments were resolved by high-voltage electrophoresis and thin-layer chromatography (i.e., surface peptide mapping). Radioemitting peptidic fragments were visualized by autoradiography. Results demonstrated that the PI molecule of each gonococcal strain studied had unique iodinatable peptides exposed on the surface of whole cells and OMs, whereas PIIIs appeared to have the same portion of the molecule exposed on the surface of bacteria or OMs, regardless of the gonococcal strain from which they were isolated. Many more radiolabeled peptides were seen in surface peptide maps of PIs from radiolabeled OMs than in those from radioiodinated whole cells, whereas different peptidic fragments were seen in the surface peptide maps of PIIIs from radiolabeled OMs than were seen in those from radiolabeled whole cells. These data suggest that PI may contribute strain-specific antigenic determinants and PIII may contribute cross-reactive determinants and that the surface exposure of PI and PIII is different in isolated OMs than in the OM of intact gonococci.
DNS Security Extension Clarification on Zone Status (2001)

The definition of a secured zone is presented, clarifying and updating sections of RFC 2535. RFC 2535 defines a zone to be secured based on a per algorithm basis, e.g., a zone can be secured with RSA keys, and not secured with DSA keys. This document changes this to define a zone to be secured or not secured regardless of the key algorithm used (or not used). To further simplify the determination of a zone's status, experimentally secure status is deprecated.
A Hidden Trajectory Model with Bi-directional Target-Filtering: Cascaded vs. Integrated Implementation for Phonetic Recognition (2006)

We present a novel acoustic model of speech, based on statistical hidden trajectory modeling (HTM) with bi-directional vocal tract resonance (VTR) target filtering, for speech recognition. The HTM consists of two stages of the generative process of speech: from the phone sequence to VTR dynamics and then to the cepstrum-based acoustic observation. Two types of model implementation are detailed, one with straightforward two-stage cascading, and another which integrates over the statistical distribution of VTR in model construction and in computing acoustic likelihood. With the use of first-order Taylor series approximation to the nonlinearity in the VTR-to-cepstrum prediction component of HTM, the acoustic likelihood is established in an analytical form. It is a Gaussian with the time-varying mean that gives structured long-span context dependence over the entire utterance, and with the dynamically adjusted variance proportional to the squared "local slope" in the nonlinear mapping function from VTR to cepstrum. When the HTM parameters are trained via maximizing this "integrated" likelihood, dramatic reduction of an upper error bound is achieved in the standard TIMIT phonetic recognition task using a large-scale N-best rescoring paradigm.
Epitope mapping of a monoclonal antibody against human thrombin by H/D‐exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein (2002)

The epitope of a monoclonal antibody raised against human thrombin has been determined by hydrogen/deuterium exchange coupled to MALDI mass spectrometry. The antibody epitope was identified as the surface of thrombin that retained deuterium in the presence of the monoclonal antibody compared to control experiments in its absence. Covalent attachment of the antibody to protein G beads and efficient elution of the antigen after deuterium exchange afforded the analysis of all possible epitopes in a single MALDI mass spectrum. The epitope, which was discontinuous, consisting of two peptides close to anion-binding exosite I, was readily identified. The epitope overlapped with, but was not identical to, the thrombomodulin binding site, consistent with inhibition studies. The antibody bound specifically to human thrombin and not to murine or bovine thrombin, although these proteins share 86% identity with the human protein. Interestingly, the epitope turned out to be the more structured of two surface regions in which higher sequence variation between the three species is seen.
Internal electric field and charge distribution in multilayer organic light-emitting diodes (2003)

The internal electric field in multilayer organic light-emitting diodes (OLEDs) is investigated using a combination of experimental measurement and numerical device modeling. This approach results in a detailed understanding of the functioning of a multilayer OLED. The method is applied to a standard device structure that has received broad attention in literature. From the experimental part, we have demonstrated that the average electric field inside the hole transport layer is larger than or equal to the average field in the emission layer over the entire current range. Device simulations fully clarify the situation, giving an insight into the space charge effects as well as the hole and the electron current distributions in the device. In particular, we find that there is a leakage of unrecombined holes towards the cathode at low voltages. We also find a strong variation of the electric field in the tris(8-hydroxyquinolinato)aluminum layer.
Social networks for creative collaboration (2005)

The Authors are colleagues within the User Experience Discipline at Avenue A | Razorfish, a services consulting firm that designs user centered applications and solutions for business and consumer brands.The User Experience discipline employs approximately 50 interface designers, information architects and experience designers across the United States. A social networking application has been developed in-house to promote creative collaboration within the organization. The organizational problem we were solving for was a need to create greater visibility in to the work of each information designer as well as the opportunity to support smarter collaboration and drive innovation within the organization.
Evidence for HIV-associated B cell exhaustion in a dysfunctional memory B cell compartment in HIV-infected viremic individuals (2008)

Human immunodeficiency virus (HIV) disease leads to impaired B cell and antibody responses through mechanisms that remain poorly defined. A unique memory B cell subpopulation (CD20(hi)/CD27(lo)/CD21(lo)) in human tonsillar tissues was recently defined by the expression of the inhibitory receptor Fc-receptor-like-4 (FCRL4). In this study, we describe a similar B cell subpopulation in the blood of HIV-viremic individuals. FCRL4 expression was increased on B cells of HIV-viremic compared with HIV-aviremic and HIV-negative individuals. It was enriched on B cells with a tissuelike memory phenotype (CD20(hi)/CD27(-)/CD21(lo)) when compared with B cells with a classical memory (CD27(+)) or naive (CD27(-)/CD21(hi)) B cell phenotype. Tissuelike memory B cells expressed patterns of homing and inhibitory receptors similar to those described for antigen-specific T cell exhaustion. The tissuelike memory B cells proliferated poorly in response to B cell stimuli, which is consistent with high-level expression of multiple inhibitory receptors. Immunoglobulin diversities and replication histories were lower in tissuelike, compared with classical, memory B cells, which is consistent with premature exhaustion. Strikingly, HIV-specific responses were enriched in these exhausted tissuelike memory B cells, whereas total immunoglobulin and influenza-specific responses were enriched in classical memory B cells. These data suggest that HIV-associated premature exhaustion of B cells may contribute to poor antibody responses against HIV in infected individuals.
Etiology of community-acquired pneumonia in a population-based study: Link between etiology and patients characteristics, process-of-care, clinical evolution and outcomes (2012)

Our study provides information about the etiology of CAP in the general population. The microbiology of CAP remains stable: infections by conventional bacteria result in higher severity, and the S. pneumoniae remains the most important pathogen. However, atypical pathogens could also infect patients in a wide spectrum of severity and age.
Tyrosines 868, 966, and 972 in the Kinase Domain of JAK2 Are Autophosphorylated and Required for Maximal JAK2 Kinase Activity (2010)

Janus kinase 2 (JAK2) is activated by a majority of cytokine family receptors including receptors for GH, leptin, and erythropoietin. To identify novel JAK2-regulatory and/or -binding sites, we set out to identify autophosphorylation sites in the kinase domain of JAK2. Two-dimensional phosphopeptide mapping of in vitro autophosphorylated JAK2 identified tyrosines 868, 966, and 972 as sites of autophosphorylation. Phosphorylated tyrosines 868 and 972 were also identified by mass spectrometry analysis of JAK2 activated by an erythropoietin-bound chimeric erythropoietin receptor/leptin receptor. Phosphospecific antibodies suggest that the phosphorylation of all three tyrosines increases in response to GH. Compared with wild-type JAK2, which is constitutively active when overexpressed, JAK2 lacking tyrosine 868, 966, or 972 has substantially reduced activity. Coexpression with GH receptor and protein tyrosine phosphatase1B allowed us to investigate GH-dependent activation of these mutated JAK2s in human embryonic kidney 293T cells. All three mutated JAK2s are activated by GH, although to a lesser extent than wild-type JAK2. The three mutated JAK2s also mediate GH activation of signal transducer and activator of transcription 3 (Stat3), signal transducer and activator of transcription 5b (Stat5b) and ERK1, but at reduced levels. Coexpression with Src-homology 2B1beta (SH2B1beta), like coexpression with GH-bound GH receptor, partially restores the activity of all three JAK2 mutants. Based on these results and the crystal structure of the JAK2 kinase domain, we hypothesize that small changes in the conformation of the regions of JAK2 surrounding tyrosines 868, 966, and 972 due to e.g. phosphorylation, binding to a ligand-bound cytokine receptor, and/or binding to Src-homology 2B1, may be essential for JAK2 to assume a maximally active conformation.
Anti-tumor activities of immunotoxins made of monoclonal antibody B3 and various forms of Pseudomonas exotoxin. (1991)

B3 is a monoclonal antibody that reacts with a carbohydrate epitope present on a variety of proteins located on the surface of many cancer cells and a limited number of normal tissues. We evaluated the cytotoxic activity of immunotoxins composed of monoclonal antibody B3 coupled to native Pseudomonas exotoxin (PE) or two recombinant forms of Pseudomonas exotoxin, PEArg57 or LysPE40, a form of PE with a deletion of the cell binding domain. All three conjugates were cytotoxic to human cell lines expressing the B3 antigen on their surface. The survival of each of the three immunotoxins in the circulation of mice was determined after administering the immunotoxin i.v. The half-life in blood of B3-PE and B3-PEArg57 was 20 hr, whereas the half-life of B3-LysPE40 was 4 hr. The short half-life of B3-LysPE40 may be due to the absence of domain I of PE. To determine the therapeutic effects of the three immunotoxins, they were given intraperitoneally to nude mice bearing subcutaneous A431 tumors. All three immunotoxins caused complete regression of 50-mm3 tumors with no toxic effects to the animals at therapeutic doses. Furthermore, substantial regression was also noted with much larger tumors. Our data indicate that the monoclonal antibody B3, when coupled to PE or recombinant forms of PE, may be useful for the treatment of tumors expressing B3 antigen. The therapeutic window was largest with B3-LysPE40, which can be administered in higher doses because it lacks sequences in domain I of PE that enable PE to bind to nontarget cells.
The Open Services Gateway Initiative: an introductory overview (2001)

The Open Services Gateway Initiative is a consortium of more than 80 companies from around the world working together to create an infrastructure to enable the deployment of services over wide area networks to local networks and devices. In this article we outline the benefits of OSGi, typical markets, and example use cases. The article goes on to discuss the architecture of the system and the capabilities that are afforded by the latest release. The article concludes with a brief glimpse into the future specifications that are expected to result from OSGi.
BHA prediction software improves directional drilling (1989)

Alwyn North platform is a 40-slot multiwell structure that has been an important drilling project in the UK sector of the northern North Sea in recent years. It has been operated by Total (33.3%), in association with its partner, Elf (66.7%). Total has focused on development of field-efficient bottom hole assembly (BHA) software for some time. (See references in bibliography.) This long-term commitment to RandD has paid off in the Alwyn North operations. This paper features some results obtained through use of BHA prediction software at Alwyn North, including some record directional drilling performances. Comparison is also made between rotary drilling and drilling with steerable systems.