gebhart/patrepeval huggingface dataset:
The Three Dimensional Structure of the Lysozyme from Bacteriophage T4 (1974)

The three dimensional structure of the lysozyme from bacteriophage T4 has been determined from a 2.5 Å resolution electron density map. About 60% of the molecule is in a helical conformation and there is one region consisting of antiparallel β-structure. The polypeptide backbone folds into two distinct lobes linked in part by a long helix. In the region between the two lobes, there is a cleft which deepens into a hole or cavity, about 6-8 Å in diameter, extending from one side of the molecule to the other. This opening is closed off by side chains which extend to within 3-5 Å of each other. A number of mutant lysozymes in which residues in the vicinity of the opening are modified have markedly reduced catalytic activity, suggesting that this region of the molecule may be catalytically important. The three dimensional structure of T4 phage lysozyme is quite different from that of hen egg-white lysozyme although it is not clear at this time whether or not the mechanisms of catalysis of the respective enzymes are related.
Dangling bonds and the Urbach tail in silicon (1985)

Electron spin resonance (ESR) and highly sensitive optical-absorption measurements have been performed on plastically deformed silicon, polycrystalline silicon, and high interface state density, oxidized silicon samples. In the first two cases, the response of the Urbach-like subgap optical absorption and the ‘‘dangling bond’’ ESR signal following thermal and atomic hydrogen anneals is found to be distinctly different from that reported previously for polycrystalline silicon. These data suggest that transitions of the dangling bond are not responsible for this Urbach-like behavior. In addition, we find that removal of the interfacial silicon dangling bond by oxide stripping results in no measurable sample absorptance decreases, implying a considerably lower optical cross section than has been previously estimated for dangling bonds in the bulk.
Neuropeptide Y modulates neurotransmitter release and Ca2+ currents in rat sensory neurons (1988)

Using 125I-labeled neuropeptide Y (NPY) and peptide YY (PYY), we demonstrated the existence of specific receptors for these peptides on rat dorsal root ganglion (DRG) cells grown in primary culture. Scatchard analysis of membrane homogenates indicated that the peptides bound to 2 populations of sites, with approximate affinities of 0.08 and 6.5 nM. Only low levels of binding were detected on sympathetic neurons cultured from the same animals or on a variety of neuronal clonal cell lines. The binding of 125I-NPY and 125I-PYY to DRG cell membranes was considerably reduced by the nonhydrolyzable analog of GTP, Gpp(NH)p. The major effect of Gpp(NH)p was to reduce the number of lower-affinity NPY binding sites without altering the number of high-affinity binding sites. NPY potently inhibited Ca2+ currents recorded under voltage clamp in rat DRG cells. Both the transient and sustained portions of the Ca2+ current were inhibited. The inhibitory effects of NPY were completely blocked following treatment of the cells with pertussis toxin. Depolarization elicited a large influx of Ca2+ into DRG neurons as assessed using fura-2-based microspectrofluorimetry. This influx of Ca2+ could be partially inhibited by NPY. Furthermore, NPY effectively inhibited the depolarization-induced release of substance P from DRG cells in vitro. Thus, NPY may be an important regulator of sensory neuron function in vivo.
Lanthanide Macrocyclic Quinolyl Conjugates as Luminescent Molecular-Level Devices (2001)

The Eu(III) tetraazamacrocyclic complexes [Eu.1] and [Eu.2], and the Tb(III) and Yb(III) complexes [Tb.1] and [Yb.2], have been synthesized as luminescent molecular-level devices. The Eu complexes exhibit unique dual pH switching behavior in water under ambient conditions. The delayed Eu emission is reversibly switched on in acid, with an enhancement factor of several hundred for [Eu.1]. These observations are consistent with the protonation of the quinoline aryl nitrogen moiety (pK(a) approximately equal to 5.9 for [Eu.1]). The fluorescence emission spectra of these complexes are unaffected by acid, but pronounced changes occur in alkaline solution due to the deprotonation of the aryl amide nitrogen (pK(a) approximately 9.4 for [Eu.1]). [Tb.1] shows a more intriguing pH dependence; Tb emission is switched "on" only in the presence of H+ and in the absence of molecular oxygen, whereas the fluorescence emission properties are similar to those observed with [Eu.1]. This behavior can be conveniently described as a molecular-level logic gate, corresponding to a two-input INHIBIT function, A wedge B'. The analogous [Yb.2] complex shows no such pH or O(2) dependence.
'Normal'-pressure Hydrocephalus and the Saga of the Treatable Dementias (1989)

SELECTED CASE A 74-YEAR-OLD widow presented to the Laboratory of Neurosciences of the National Institute on Aging in February 1985 with a 4-year history of progressive cognitive impairment. She had experienced gradual onset of memory loss, with occasional urinary incontinence. There was no history of hypertension, cardiovascular disease, diabetes, head trauma, stroke, or intracranial bleeding or infection. She was not taking any medications. Social and family histories were not contributory. Findings from a general physical examination were normal. Neurological examination disclosed a mild dementia, with impaired memory, calculations, and constructions. Her score on the Mini-Mental State Examination 1 was 22 (23 to 30 is normal), and her score on the Blessed Memory and Information Concentration Test was 22 (normal score is 37). 2 She had poor balance but normal gait. Results from routine laboratory tests of blood and urine were normal, as was an electroencephalogram. Cerebrospinal fluid protein level, glucose
Applications of GRIN-rod lenses in optical fiber communication systems (1980)

Graded-refractive-index-rod lenses (GRIN-rod lenses) have a number of features that make them particularly suitable for use in optical devices for manipulating and processing the optical signals in fiber communication systems. Such lenses can be cemented directly to the other elements of a device, thus giving a structure that is compact, solid, stable, and rugged. They also have significantly smaller aberrations than equivalent simple homogeneous lenses, and this results in lower insertion losses. Designs for various GRIN-rod lens devices, including connectors, attenuators, directional couplers, switches, isolators and wavelength-division multiplexers are reviewed. A consistent set of loss estimates is provided for all the device designs considered.
Gamma-Ray Excitation of the 15.1-Mev Level inC12 (1959)

The parameters of the 15.1-Mev level in ${\mathrm{C}}^{12}$ have been determined. The angular distribution of scattered photons has been determined to be dipole. A scatter-associated background to the scattering from this level has been demonstrated. The peak absorption cross section of 29.7\ifmmode\pm\else\textpm\fi{}1.1 barns has been determined from a self-absorption experiment. The self-absorption measurement and a production experiment combine to give values of 64.5\ifmmode\pm\else\textpm\fi{}10.4 ev and 59.2\ifmmode\pm\else\textpm\fi{}9.7 ev for the total level width and radiative width to the ground state, respectively. The combination of the value of the integrated elastic scattering cross section from the absolute measurement, and those values calculated from the self-absorption and production experiments gives for this integrated cross section the value 2.33\ifmmode\pm\else\textpm\fi{}0.19 mb-Mev. The radiation width to the 4.43-Mev state of ${\mathrm{C}}^{12}$ is determined to be 3.2\ifmmode\pm\else\textpm\fi{}2.5 ev by fitting the detector resolution function to observed pulse-height spectra. A value for the inelastic scattering in the giant resonance region of ${\mathrm{C}}^{12}$ is determined.
Lack of outcome benefit and clopidogrel “resistance” (2009)

Impaired response to clopidogrel, or "resistance" is a cornerstone concept for justification of more aggressive antiplatelet regimens, and development of new more potent drugs. There are over 1,000 citations (although predominantly reviews, or case reports) in MEDLINE related to clopidogrel "resistance", while about 100 of them attempted to link low response to adverse clinical outcomes. However, most of these studies are woefully small, and not randomised. The TRITON trial assessed head-to-head novel antiplatelet agent prasugrel versus clopidogrel in patients with acute coronary syndromes. This study was the first in a decade to challenge clopidogrel monopoly, and to indirectly test the "resistance" hypothesis. The primary endpoint was the rate of cardiovascular death, non-fatal myocardial infarction, or stroke, and occurred in 12.1% of patients treated with clopidogrel, and 9.9% of patients randomised to prasugrel, suggesting impressive vascular outcome benefit of prasugrel over clopidogrel. However, the Food and Drug Administration (FDA) presented more balanced, and realistic outlook on TRITON. While very early periprocedural benefit exists, long-term prasugrel therapy yielded identical to clopidogrel vascular outcomes among 13,608 TRITON patients challenging the postulate that clopidogrel "resistance" phenomenon is clinically relevant. Despite the fact that prasugrel 10 mg/daily cause 2.5 times more potent platelet inhibition than conventional clopidogrel 75 mg/daily, with fewer patients exhibiting broad response variability, and/or antiplatelet "resistance", the vascular benefit beyond acute phase was identical. Keeping in mind growing over time bleeding, cancer, and mortality risks associated with chronic prasugrel use, small observational studies should be judged with skepticism as hypothesis-generating, pending confirmation in randomised trials.
Tumor-associated macrophages (TAM) as major players of the cancer-related inflammation (2009)

The microenvironment of solid tumors is characterized by a reactive stroma with an abundance of inflammatory mediators and leukocytes, dysregulated vessels and proteolytic enzymes. TAM, major players in the connection between inflammation and cancer, summarize a number of functions (e.g., promotion of tumor cell proliferation and angiogenesis, incessant matrix turnover, repression of adaptive immunity), which ultimately have an important impact on disease progression. Thus, together with other myeloid-related cells present at the tumor site (Tie2 macrophages and MDSCs), TAM represent an attractive target of novel biological therapies of tumors.
A unified theory of garbage collection (2004)

Tracing and reference counting are uniformly viewed as being fundamentally different approaches to garbage collection that possess very distinct performance properties. We have implemented high-performance collectors of both types, and in the process observed that the more we optimized them, the more similarly they behaved - that they seem to share some deep structure. We present a formulation of the two algorithms that shows that they are in fact duals of each other. Intuitively, the difference is that tracing operates on live objects, or "matter", while reference counting operates on dead objects, or "anti-matter". For every operation performed by the tracing collector, there is a precisely corresponding anti-operation performed by the reference counting collector. Using this framework, we show that all high-performance collectors (for example, deferred reference counting and generational collection) are in fact hybrids of tracing and reference counting. We develop a uniform cost-model for the collectors to quantify the trade-offs that result from choosing different hybridizations of tracing and reference counting. This allows the correct scheme to be selected based on system performance requirements and the expected properties of the target application.
Peptide Fragmentation Assisted by Surfaces Treated with a Low‐Temperature Plasma in NanoESI (2008)

A softy toughens up: When a nanoelectrospray (nanoESI) emitter was exposed first to a helium plasma (see illustration of experimental setup), ESI, a widely accepted “soft” ionization technique, caused significant and useful peptide fragmentation. The appearance of abundant peptide-fragment ions in the mass spectrum was ascribed to electrolyte release into the solution. Labile phosphate groups on the peptide were preserved during fragmentation. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Enhancing Medical Device Training with Hybrid Physical-Virtual Simulators: Smart Peripherals for Virtual Devices (2013)

We introduce a novel platform for medical device training: hybrid physical-virtual simulators of medical devices, combining touchscreen-enabled virtual emulations of real devices with sensorized physical peripherals to enable tactile, hands-on interaction between the trainee, simulated device and standardized patients or mannequins. The system enables objective measurement and recording of trainee performance, including interactions with both the virtual device elements and the physical components, and can include metrics and feedback not available in the real device. The system also includes an integrated wireless signaling device for use with standardized patients. We present the implementation of an example system, a virtual defibrillator with sensorized paddles and wireless signaling of successful defibrillator operation.
Asymmetric transfer hydrogenation of ketones : Catalyst development and mechanistic investigation (2011)

The development of ligands derived from natural amino acids for asymmetric transfer hydrogenation (ATH) of prochiral ketones is described herein. In the first part, reductions performed in alcoholic media are examined, where it is found that amino acid-derived hydroxamic acids and thioamides, respectively, are simple and versatile ligands that in combination with [RhCp*Cl2]2 efficiently catalyze this particular transformation. Selectivities up to 97% ee of the corresponding secondary alcohols are obtained, and it is furthermore observed that the two different ligand classes, albeit based on the same amino acid scaffold, give rise to products of opposite configuration. The highly interesting enantioswitchable nature of the two abovementioned catalysts is studied in detail by mechanistic investigations. A structure/activity correlation analysis is performed, which reveals that the diverse behavior of the catalysts arise from different interactions between the ligands and the metal. Kinetic studies furthermore stress the catalyst divergence, since a difference in the rate determining step is established from initial rate measurements. In addition, rate constants are determined for each step of the overall reduction process. In the last part, catalyst development for ATH executed in water is discussed. The applicability of hydroxamic acid ligands is further extended, and catalysts based on these compounds are found to be efficient and compatible with aqueous conditions. The structurally even simpler amino acid amide is also evaluated as a ligand, and selectivities up to 90% ee are obtained in the reduction of a number of aryl alkyl ketones. The very challenging reduction of dialkyl ketones is moreover examined in the Rh-catalyzed aqueous ATH, where a modified surfactant-resembling sulfonylated diamine is used as ligand, and the reaction is carried out in the presence of SDS-micelles. A positive effect is to some extent found on the catalyst performance upon addition of phase-transfer components, especially regarding the catalytic activity in the reduction of more hydrophobic substrates.
Role of hypoxia and glycolysis in the development of multi-drug resistance in human tumor cells and the establishment of an orthotopic multi-drug resistant tumor model in nude mice using hypoxic pre-conditioning (2011)

Hypoxic pre-conditiong and xenografting may be used to develop a multitude of orthotopic models for MDR cancer aiding in the study and treatment of the disease.
Requirement of ATM-Dependent Phosphorylation of Brca1 in the DNA Damage Response to Double-Strand Breaks (1999)

The Brca1 (breast cancer gene 1) tumor suppressor protein is phosphorylated in response to DNA damage. Results from this study indicate that the checkpoint protein kinase ATM (mutated in ataxia telangiectasia) was required for phosphorylation of Brca1 in response to ionizing radiation. ATM resides in a complex with Brca1 and phosphorylated Brca1 in vivo and in vitro in a region that contains clusters of serine-glutamine residues. Phosphorylation of this domain appears to be functionally important because a mutated Brca1 protein lacking two phosphorylation sites failed to rescue the radiation hypersensitivity of a Brca1-deficient cell line. Thus, phosphorylation of Brca1 by the checkpoint kinase ATM may be critical for proper responses to DNA double-strand breaks and may provide a molecular explanation for the role of ATM in breast cancer.
Using and Porting the GNU Compiler Collection (2000)

this document under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation; with the Invariant Sections being \\GNU General Public License&amp;quot;, the Front-Cover texts being (a) (see below), and with the Back-Cover Texts being (b) (see below). A copy of the license is included in the section entitled \\GNU Free Documentation License&amp;quot;
Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis of Thalidomide Analogues as Angiogenesis Inhibitors (2004)

Thalidomide, 2-(2,6-dioxo-3-piperidinyl)-1H-isoindole-1,3(2H)-dione, has been shown to inhibit angiogenesis, the formation of new blood vessels from existing vasculature. As a result, there is renewed interest in this drug as a potential therapy for solid tumors. Thalidomide forms a number of metabolites and has been shown to require metabolic activation for antiangiogenic activity. A series of 39 compounds, based upon the structure of some of these metabolites, was synthesized and tested for their ability to inhibit microvessel growth in the rat aortic ring assay. The results of this testing have been used as the basis for a three-dimensional quantitative structure-activity relationship (3D-QSAR) study, utilizing comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) procedures. The best resulting CoMFA and CoMSIA models have conventional r(2) values of 0.924 and 0.996, respectively. The cross-validated q(2) values are 0.666 and 0.635, respectively. These models offer insight into the structural requirements for activity of thalidomide analogues as angiogenesis inhibitors, since there is only speculative knowledge of the target. Additionally, it appears as though there is more than one active site or mechanism of action.
Predicting motor outcome and death in term hypoxic-ischemic encephalopathy (2011)

We have shown that in term newborns with HIE and BGT injury, early MRI can be used to predict death and specific motor outcomes.
Sheep and goats: pastoral imagery in the bible and today (2008)

The bible makes frequent use of the imagery of sheep and shepherds, both to illustrate God’s care for his people and also in relation to human leaders of the nation (Old Testament) and the church (New Testament). This article suggests some ways in which an informed awareness of the reality of a shepherd’s life may enrich our understanding of such imagery. It also draws attention to some limitations of the metaphor, and warns against sentimental misconceptions of the ‘pastoral’ role.
On the amine oxidases of Klebsiella aerogenes strain W70 (2006)

Klebsiella aerogenes W70 was reported previously to produce a membrane-associated tyramine oxidase (TynA) that did not act on 2-phenylethylamine. Subsequently, a gene cloned from K. aerogenes W70 produced a soluble amine oxidase (MaoA) that acted readily on 2-phenylethylamine and tyramine. This enzyme appeared to be equivalent to a 2-phenylethylamine oxidase of Escherichia coli K-12 (MaoA) but was assumed to be the originally described K. aerogenes W70 tyramine oxidase (TynA). However, as described here, whole cells and cell-free extracts of K. aerogenes W70 showed only the tyramine oxidase (TynA) that is inactive against 2-phenylethylamine and not the maoA gene product. It seems that the organism has two amine oxidase genes, tynA and maoA, but only tynA is expressed. Hence, data relating to the expression of the K. aerogenes W70 tynA gene cannot be assumed to apply to the maoA gene of E. coli K-12 because they encode different enzymes.
The natural killer cell‐mediated killing of autologous dendritic cells is confined to a cell subset expressing CD94/NKG2A, but lacking inhibitory killer Ig‐like receptors (2003)

The cognate NK-DC interaction in inflamed tissues results in NK cell activation and acquisition of cytotoxicity against immature DC (iDC). This may represent a mechanism of DC selection required for the control of downstream adaptive immune responses. Here we show that killing of monocyte-derived iDC is confined to the NK cell subset that expresses CD94/NKG2A, but not killer Ig-like receptors (KIR). Consistent with these data, the expression of HLA-E (i.e. the cellular ligand of CD94/NKG2A) was down-regulated in iDC. On the other hand, HLA-B and HLA-C down-regulation in iDC was not sufficient to induce cytotoxicity in NK cells expressing KIR3DL1 or KIR2DL. Remarkably, CD94/NKG2A(+)KIR(-) NK cells were heterogeneous in their ability to kill iDC and an inverse correlation existed between their CD94/NKG2A surface density and the magnitude of their cytolytic activity. It is conceivable that the reduced CD94/NKG2A surface density enables these cells to efficiently sense the decrease of HLA-E surface expression in iDC. Finally, most NK cells that lysed iDC did not kill mature DC that express higher amounts of HLA class I molecules (including HLA-E)as compared with iDC. However, a small NK cell subset was capable of killing not only iDC but also mature DC.
Depletion of eosinophils in mice through the use of antibodies specific for C-C chemokine receptor 3 (CCR3) (1999)

We have generated rat monoclonal antibodies specific for the mouse eotaxin receptor, C-C chemokine receptor 3 (CCR3). Several anti-CCR3 mAbs proved to be useful for in vivo depletion of CCR3-expressing cells and immunofluorescent staining. In vivo CCR3 mAbs of the IgG2b isotype substantially depleted blood eosinophil levels in Nippostrongyus brasiliensis-infected mice. Repeated anti-CCR3 mAb treatment in these mice significantly reduced tissue eosinophilia in the lung tissue and bronchoalveolar lavage fluid. Flow cytometry revealed that mCCR3 was expressed on eosinophils but not on stem cells, dendritic cells, or cells from the thymus, lymph node, or spleen of normal mice. Unlike human Th2 cells, mouse Th2 cells did not express detectable levels of CCR3 nor did they give a measurable response to eotaxin. None of the mAbs were antagonists or agonists of CCR3 calcium mobilization. To our knowledge, the antibodies described here are the first mAbs reported to be specific for mouse eosinophils and to be readily applicable for the detection, isolation, and in vivo depletion of eosinophils.