gebhart/patrepeval huggingface dataset:
Five-Coordinate Rearrangements of Metallacyclobutane Intermediates during Ring-Opening Metathesis Polymerization of 2,3-Dicarboalkoxynorbornenes by Molybdenum and Tungsten Monoalkoxide Pyrrolide Initiators (2012)

Addition of rac-DCENBE (2,3-dicarboethoxynorbornene) or rac-DCBNBE (2,3-dicarbo-tert-butoxynorbornene) to Mo(NAd)(CHCMe2Ph)(Pyr)(OHMT) (1a) (Ad = 1-adamantyl, OHMT = 2,6-dimesitylphenoxide, Pyr– = NC4H4–) led to the formation of polymers that have a cis,syndiotactic,alt structure analogous to the structure observed for the polymer obtained from rac-DCMNBE (2,3-dicarbomethoxynorbornene). The PDI of cis,syndio,alt-poly(DCBNBE) is low and decreases as the polymer length increases, and there is a linear relationship between the number of equivalents of monomer employed and the molecular weight of the polymers measured in THF versus polystyrene standards. In contrast, polymerization of (+)-DCMNBE by 1a at 25, 0, −25, and −40 °C yields a polymer that contains ∼25% trans,isotactic dyads and 75% cis,syndiotactic dyads. A similar polymerization by Mo(NAd)(CHCMe2Ph)(Pyr)(OHIPT) (1b) (OHIPT = 2,6-(2,4,6-i-Pr3)2C6H3) gives a polymer that contains cis,syndiotactic and trans,isotactic dyads in a ratio of ∼8:92, respectively. This is the first report of synthesis of a norbornene polymer that has primarily a trans,isotactic structure. Addition of 100 equiv of (+)-DCMNBE, (−)-DCENBE, or (−)-DCBNBE to a toluene solution of W(O)(CH-t-Bu)(2,5-Me2NC4H2)(OHMT)(PMe2Ph) (5) led to formation of ∼99% cis,syndiotactic polymer. Cis,syndiotactic dyads arise through a mechanism that consists of a syn approach of the monomer to a syn alkylidene isomer followed by inversion of configuration at the metal center as a consequence of an exchange of aryloxide and pyrrolide ligands. The mechanism for formation of trans,isotactic dyads is one in which the monomer approaches in an anti fashion to the syn isomer followed by a “turnstile” rotation in the five-coordinate intermediate metallacyclobutane that allows the metallacylic ring to open productively with retention of configuration at the metal center. The metallacyclobutane intermediate that gives rise to trans,isotactic dyads in the copolymer could be regarded as a relatively high energy species with a “nonideal” structure compared to a trigonal bipyramidal or a square pyramidal structure.
Structural studies of L10 FePt nanoparticles (2002)

We have studied the lattice parameter changes of L10 FePt nanoparticles annealed to near equilibrium as a function of composition by x-ray diffraction. We have found that the (111) diffraction peak shifts linearly with composition, however, the c parameter mostly changes in the Pt rich compositions and the a parameter mostly changes in the Fe rich compositions with respect to the equiatomic composition. This causes the tetragonality of the L10 structure to be maximized near the Fe 50%/Pt 50% composition. The magnetic properties were measured at room temperature and at 5 K and are correlated to the structural changes occurring as a function of composition.
Analysis of the Crosslinking Components in Collagen and Elastin (1982)

This chapter contains sections titled: Introduction Historical Background Crosslinking of Collagen Detailed Methods of Analysis Crosslinking of Elastin Concluding Remarks
Identification and assessment of markers of biotin status in healthy adults (2013)

Human biotin requirements are unknown and the identification of reliable markers of biotin status is necessary to fill this knowledge gap. Here, we used an outpatient feeding protocol to create states of biotin deficiency, sufficiency and supplementation in sixteen healthy men and women. A total of twenty possible markers of biotin status were assessed, including the abundance of biotinylated carboxylases in lymphocytes, the expression of genes from biotin metabolism and the urinary excretion of biotin and organic acids. Only the abundance of biotinylated 3-methylcrotonyl-CoA carboxylase (holo-MCC) and propionyl-CoA carboxylase (holo-PCC) allowed for distinguishing biotin-deficient and biotin-sufficient individuals. The urinary excretion of biotin reliably identified biotin-supplemented subjects, but did not distinguish between biotin-depleted and biotin-sufficient individuals. The urinary excretion of 3-hydroxyisovaleric acid detected some biotin-deficient subjects, but produced a meaningful number of false-negative results and did not distinguish between biotin-sufficient and biotin-supplemented individuals. None of the other organic acids that were tested were useful markers of biotin status. Likewise, the abundance of mRNA coding for biotin transporters, holocarboxylase synthetase and biotin-dependent carboxylases in lymphocytes were not different among the treatment groups. Generally, datasets were characterised by variations that exceeded those seen in studies in cell cultures. We conclude that holo-MCC and holo-PCC are the most reliable, single markers of biotin status tested in the present study.
Integrated optical frequency domain reflectometry device for characterization of complex integrated devices (2018)

Because of the demand for advanced measurement systems in the field of modern photonic integrated circuits, optical frequency domain reflectometry (OFDR) is a robust technique for characterizing design-to-fabrication deviations. In this paper we report an OFDR device where the interferometric part is monolithically integrated along with the device under test. We discuss the advantages in terms of compactness and performance, and the importance of the incorporated dispersion de-embedding mechanism. Experimental validation is carried out by interrogating an arrayed waveguide grating on a silicon nitride platform. The results establish the proposed device as a first step in the quest for a universal test structure for integrated devices.
A phase I clinical study of vaccination of melanoma patients with dendritic cells loaded with allogeneic apoptotic/necrotic melanoma cells. Analysis of toxicity and immune response to the vaccine and of IL-10 -1082 promoter genotype as predictor of disease progression (2008)

Clinicaltrials.gov (NHI) NCT00515983.
Role of Aspartate 70 and Tryptophan 82 in Binding of Succinyldithiocholine to Human Butyrylcholinesterase (1997)

The atypical variant of human butyrylcholinesterase has Gly in place of Asp 70. Patients with this D70G mutation respond abnormally to the muscle relaxant succinyldicholine, experiencing hours of apnea rather than the intended 3 min. Asp 70 is at the rim of the active site gorge 12 A from the active site Ser 198. An unanswered question in the literature is why the atypical variant has a 10-fold increase in Km for compounds with a single positive charge but a 100-fold increase in Km for compounds with two positive charges. We mutated residues Asp 70, Trp 82, Trp 231, Glu 197, and Tyr 332 and expressed mutant enzymes in mammalian cells. Steady-state kinetic parameters for hydrolysis of butyrylthiocholine, benzoylcholine, succinyldithiocholine, and o-nitrophenyl butyrate were determined. The wild type and the D70G mutant had identical k(cat) values for all substrates. Molecular modeling and molecular dynamics suggested that succinyldicholine could bind in two consecutive orientations in the active site gorge; formation of one complex caused a conformational change in the omega loop involving Asp 70 and Trp 82. We propose the formation of three enzyme-substrate intermediates preceding the acyl-enzyme intermediate; kinetic data support this contention. Substrates with a single positive charge interact with Asp 70 just once, whereas substrates with two positive charges, for example succinyldithiocholine, interact with Asp 70 in two complexes, thus explaining the 10- and 100-fold increases in Km in the D70G mutant.
Activation mediated by RP105 but not CD40 makes normal B cells susceptible to anti-IgM-induced apoptosis: a role for Fc receptor coligation. (1996)

Signals through the B cell antigen receptor lead to a variety of cellular events such as activation, anergy, and apoptosis. B cells select these outcomes to establish and maintain self-tolerance, and to mount adequate antibody responses. However, it is not fully understood how one and the same signal causes such different consequences. In the present study, we have studied the effect of activation signals on the outcome of responses to antigen receptor ligation. Two distinct growth-promoting signals were used to activate B cells. Ligation of either RP105, a newly discovered B cell surface molecule, or the CD40 molecule, drove B cells to proliferate. Resultant blastic cells were then exposed to anti-immunoglobulin M (IgM). Blast cells that had been stimulated with anti-RP105 ceased growing and underwent apoptosis after cross-linking of surface IgM. Coligation of the Fc gamma receptor IIB with surface IgM augmented, rather than aborted, this response. In contrast to RP105-activated B cells, blast cells that had been activated by CD40 ligation were unaltered by anti-IgM. On the other hand, CD40-activated B cells became extremely susceptible to Fas-mediated apoptosis, whereas RP105-activated B cells were much less sensitive. Anti-IgM-induced apoptosis in RP105 blasts was independent of Fas, because it was demonstrable with Fas-deficient MRL-lpr/lpr mice. These results demonstrate that the nature of an initial activation signal has a great influence on the fate of activated B cells after (re)engagement of the antigen receptor. RP105, as well as CD40, may be important in this life/death decision.
Reactions of metal carbonyls. Part III. Steric and stereochemical limitations of higher substitution of manganese carbonyl bromide (1973)

The reaction of [Mn(CO)5Br] with the ligands, L [L = P(OMe)3, P(OEt)3, P(OMe)2Ph, PMe3, PMe2Ph, and AsMe2Ph] have given fac- and trans-[Mn(CO)3L2Br] and terminated with mer-[Mn(CO)2L3Br]. The complex trans-[Mn(CO)2{P(OMe)3}3Br], prepared by hydrazine reduction of trans-[Mn(CO)2{P(OMe)3}3Br]PF6, further reacts with P(OMe)3 to give the tetra substituted compound trans-[Mn(CO){P(OMe)3}4Br]. Factors influencing the substitution reactions of [Mn(CO)5Br] with monodentate tertiary phosphorus and arsenic ligands are discussed in terms of incoming ligand size and the stereochemistry of the manganese carbonyl complexes. The i.r. and 1H n.m.r. spectra of these complexes are discussed.
Structural Characterization of Proteins with an Attached ATCUN Motif by Paramagnetic Relaxation Enhancement NMR Spectroscopy (2001)

The use of a short, three-residue Cu(2+)-binding sequence, the ATCUN motif, is presented as an approach for extracting long-range distance restraints from relaxation enhancement NMR spectroscopy. The ATCUN motif is prepended to the N-termini of proteins and binds Cu(2+) with a very high affinity. Relaxation rates of amide protons in ATCUN-tagged protein in the presence and absence of Cu(2+) can be converted into distance restraints and used for structure refinement by using a new routine, PMAG, that has been written for the structure calculation program CNS. The utility of the approach is demonstrated with an application to ATCUN-tagged ubiquitin. Excellent agreement between measured relaxation rates and those calculated on the basis of the X-ray structure of the protein have been obtained.
Construir e legitimar a a autoridade paterna e comunal em um processo em São Severino na metade do século XV (2013)

Construire et légitimer l’autorité paternelle et communale dans un procès à San Severino (Marche) au milieu du XVe siècle
Interferon, double-stranded RNA, and protein phosphorylation. (1976)

We reported earlier that the addition of double-stranded RNA and ATP increases the endonuclease activity more in an extract of Ehrlich ascites tumor cells which have been treated with an interferon preparation than in a comparable extract from control cells. We report here that the addition of double-stranded RNA to an extract from Ehrlich ascites tumor cells which have been treated with an interferon preparation [or with the interferon inducer poly(I)-poly(C)] promotes the phosphorylation by [gamma-32P]ATP of at least two proteins: P1 (molecular weight of 64,000) and P2 (molecular weight of 37,000). Double-stranded RNA also promotes the phosphorylation of at least one (i.e., P1) of these two proteins in an extract from cells which have not been treated with interferon, but the extent of phosphorylation is much smaller. Double-stranded RNA which has been degraded by RNase III, or DNA, does not promote the phosphorylation.
Total Synthesis and Cloning of a Gene Coding for the Ribonuclease S Protein (1984)

A gene for ribonuclease S protein, has been chemically synthesized and cloned. The gene is designed to have 25 specific restriction endonuclease sites spaced at short intervals, permitting its structure to be rapidly modified. This flexibility facilitates tests of hypotheses relating the primary structure of the enzyme to its physical and catalytic behavior.
Lessons Learned from Marketed and Investigational Prodrugs. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Probabilistic roadmaps for path planning in high-dimensional configuration spaces (1996)

A new motion planning method for robots in static workspaces is presented. This method proceeds in two phases: a learning phase and a query phase. In the learning phase, a probabilistic roadmap is constructed and stored as a graph whose nodes correspond to collision-free configurations and whose edges correspond to feasible paths between these configurations. These paths are computed using a simple and fast local planner. In the query phase, any given start and goal configurations of the robot are connected to two nodes of the roadmap; the roadmap is then searched for a path joining these two nodes. The method is general and easy to implement. It can be applied to virtually any type of holonomic robot. It requires selecting certain parameters (e.g., the duration of the learning phase) whose values depend on the scene, that is the robot and its workspace. But these values turn out to be relatively easy to choose, Increased efficiency can also be achieved by tailoring some components of the method (e.g., the local planner) to the considered robots. In this paper the method is applied to planar articulated robots with many degrees of freedom. Experimental results show that path planning can be done in a fraction of a second on a contemporary workstation (/spl ap/150 MIPS), after learning for relatively short periods of time (a few dozen seconds).
Metabolomic insights into the intricate gut microbial–host interaction in the development of obesity and type 2 diabetes (2015)

Gut microbiota has recently been proposed as a crucial environmental factor in the development of metabolic diseases such as obesity and type 2 diabetes, mainly due to its contribution in the modulation of several processes including host energy metabolism, gut epithelial permeability, gut peptide hormone secretion, and host inflammatory state. Since the symbiotic interaction between the gut microbiota and the host is essentially reflected in specific metabolic signatures, much expectation is placed on the application of metabolomic approaches to unveil the key mechanisms linking the gut microbiota composition and activity with disease development. The present review aims to summarize the gut microbial-host co-metabolites identified so far by targeted and untargeted metabolomic studies in humans, in association with impaired glucose homeostasis and/or obesity. An alteration of the co-metabolism of bile acids, branched fatty acids, choline, vitamins (i.e., niacin), purines, and phenolic compounds has been associated so far with the obese or diabese phenotype, in respect to healthy controls. Furthermore, anti-diabetic treatments such as metformin and sulfonylurea have been observed to modulate the gut microbiota or at least their metabolic profiles, thereby potentially affecting insulin resistance through indirect mechanisms still unknown. Despite the scarcity of the metabolomic studies currently available on the microbial-host crosstalk, the data-driven results largely confirmed findings independently obtained from in vitro and animal model studies, putting forward the mechanisms underlying the implication of a dysfunctional gut microbiota in the development of metabolic disorders.
Identification of Arabidopsis Loci Required for Susceptibility to the Downy Mildew Pathogen Hyaloperonospora parasitica (2005)

Plants are susceptible to a limited number of pathogens. Most infections fail due to active defense or absence of compatibility. Many components of the plant's surveillance system and defense arsenal have been identified in the last decades. However, knowledge is limited on compatibility; in particular, the role of plant factors in the infection process. To gain insight into these processes, we have initiated an Arabidopsis thaliana mutant screen for reduced susceptibility to the downy mildew pathogen Hyaloperonospora parasitica. Ethyl methane sulfonate (EMS) mutants were generated in the highly susceptible Arabidopsis line Ler eds1-2. Eight downy mildew-resistant (dmr) mutants were analyzed in detail, corresponding to six different loci. Microscopic analysis showed that, in all mutants, H. parasitica growth was severely reduced. Resistance of dmr3, dmr4, and dmr5 was associated with constitutive expression of PR-1. Furthermore, dmr3 and dmr4, but not dmr5, also were resistant to Pseudomonas syringae and Golovinomyces orontii, respectively. However, enhanced activation of plant defense was not observed in dmr1, dmr2, and dmr6. We postulate that, in these susceptibility mutants, cellular processes are disrupted which are required for H. parasitica infection. This interesting new set of mutants provides a basis to elucidate the molecular processes underlying susceptibility to downy mildew in Arabidopsis.
Petal (1996)

The ideal storage system is globally accessible, always available, provides unlimited performance and capacity for a large number of clients, and requires no management. This paper describes the design, implementation, and performance of Petal, a system that attempts to approximate this ideal in practice through a novel combination of features. Petal consists of a collection of network-connected servers that cooperatively manage a pool of physical disks. To a Petal client, this collection appears as a highly available block-level storage system that provides large abstract containers called virtual disks. A virtual disk is globally accessible to all Petal clients on the network. A client can create a virtual disk on demand to tap the entire capacity and performance of the underlying physical resources. Furthermore, additional resources, such as servers and disks, can be automatically incorporated into Petal.We have an initial Petal prototype consisting of four 225 MHz DEC 3000/700 workstations running Digital Unix and connected by a 155 Mbit/s ATM network. The prototype provides clients with virtual disks that tolerate and recover from disk, server, and network failures. Latency is comparable to a locally attached disk, and throughput scales with the number of servers. The prototype can achieve I/O rates of up to 3150 requests/sec and bandwidth up to 43.1 Mbytes/sec.
Associations between circulating sex steroid hormones and cognition in normal elderly women (2000)

Both estrogen and testosterone showed associations with cognitive performance. Estrogen may enhance, and depress, specific cognitive skills.
OCTANE: Optical Coherence Tomography Advanced Nanophotonic Engine (2013)

We introduce OCTANE, the first product line of chip-based spectrometers using silicon photonics for spectral domain optical coherence tomography (SD-OCT). It is well suited for low-cost, high-volume applications in both the medical and industrial fields.
PIVoT: project insights and visualization toolkit (2012)

An in-process view into a software development project's health is critical for its success. However, in services organizations, a typical software development team employs a heterogeneous set of tools based on client requirements through the different phases of the software project. The use of disparate tools with non-compatible outputs makes it very difficult to extract one coherent picture of the project's health and status. Existing project management tools either work at the process layer and rely on manually entered information, or are activity centric, without a holistic view. In this paper, we present PIVoT, a metric-based framework for automated, non-invasive, and in-process data collection and analysis in heterogeneous software project environments, that provides rich, multi-dimensional insights into the project's health and trajectory. Here, we introduce the different analyses, insights and metrics, and discuss their usage in typical software projects.
Heterodyne detection through rain, snow, and turbid media: effective receiver size at optical through millimeter wavelengths (1983)

Both scattering and turbulence can effect the spatial coherence of short wavelength signals propagating through the open atmosphere. In this paper, the influence of forward scattering on heterodyne receiver performance is investigated, taking into account turbulence. It is shown that the effect of forward scattering is to reduce the effective heterodyne receiver area through spatial coherence degradation. A common approach to scattering as an attenuation phenomenon is not always valid. Generally, this approach underestimates the SNR. The accuracy of the attenuation approach depends on the ratio R of the actual receiver diameter to the scattering particle diameter. If R >100, scattering is essentially large angle and the typical treatment of scattering as an attenuation effect is indeed justified. However, for small R, forward scattering is primarily small angle, field coherence is noticeably affected by forward scattering, and the attenuation approach is not valid. Further, it is shown that the SNR is improved when the ratio of the scattering particulate size to turbulence coherence diameter decreases. From the practical point of view, the most important result of this study is that small receivers use their area more effectively than large receivers. Thus, an array of several small receivers may perform better than one large receiver with the same total area. The treatment here is particularly relevant for coherent detection through clouds, fog, precipitation, and turbid media in general, including liquid media.