gebhart/patrepeval huggingface dataset:
Metal−Organic Frameworks with Functional Pores for Recognition of Small Molecules (2010)

Molecular recognition, an important process in biological and chemical systems, governs the diverse functions of a variety of enzymes and unique properties of some synthetic receptors. Because molecular recognition is based on weak interactions between receptors and substrates, the design and assembly of synthetic receptors to mimic biological systems and the development of novel materials to discriminate different substrates for selective recognition of specific molecules has proved challenging. The extensive research on synthetic receptors for molecular recognition, particularly on noncovalent complexes self-assembled by hydrogen bonding and metal-organic coordination, has revealed some underlying principles. In particular, these studies have demonstrated that the shapes of the supramolecular receptors play significant roles in their specific and selective recognition of substrates: receptors can offer concave surfaces that complement their convex targets. This Account describes our research to develop a synthetic molecular recognition platform using porous metal-organic frameworks (MOFs). These materials contain functional pores to direct their specific and unique recognition of small molecules through several types of interactions: van der Waals interactions of the framework surface with the substrate, metal-substrate interactions, and hydrogen bonding of the framework surface with the substrate. These materials have potential applications for gas storage, separation, and sensing. We demonstrate a simple strategy to construct a primitive cubic net of interpenetrated microporous MOFs from the self-assembly of the paddle-wheel clusters M(2)(CO(2))(4) (M = Cu(2+), Zn(2+), and Co(2+)) with two types of organic dicarboxylic acid and pillar bidentate linkers. This efficient method allows us to rationally tune the micropores to size-exclusively sort different small gas molecules, leading to the highly selective separation and purification of gases. By optimizing the strong interactions between open metal sites within porous MOFs and gas molecules such as hydrogen and acetylene, we have developed several MOF materials with extraordinary acetylene storage capacity at room temperature. We have also immobilized Lewis acidic and basic sites into luminescent porous MOFs to recognize and sense neutral and ionic species. Using the strategy to systematically immobilize different open metal sites within porous MOFs from the metalloligand precursors, we have developed the first microporous mixed-metal-organic framework (M'MOF) with enhanced affinity for hydrogen molecules, which successfully separated D(2) from H(2) using kinetic isotope quantum molecular sieving. Because we can functionalize the pores to direct their specific recognition of small molecules, the emerging porous MOFs serve as novel functional materials for gas storage, separation, heterogeneous catalysis, and sensing.
A Novel Multi-Biomarker Assay for Non-Invasive Quantitative Monitoring of Kidney Injury (2019)

The current standard of care measures for kidney function, proteinuria, and serum creatinine (SCr) are poor predictors of early-stage kidney disease. Measures that can detect chronic kidney disease in its earlier stages are needed to enable therapeutic intervention and reduce adverse outcomes of chronic kidney disease. We have developed the Kidney Injury Test (KIT) and a novel KIT Score based on the composite measurement and validation of multiple biomarkers across a unique set of 397 urine samples. The test is performed on urine samples that require no processing at the site of collection and without target sequencing or amplification. We sought to verify that the pre-defined KIT test, KIT Score, and clinical thresholds correlate with established chronic kidney disease (CKD) and may provide predictive information on early kidney injury status above and beyond proteinuria and renal function measurements alone. Statistical analyses across six DNA, protein, and metabolite markers were performed on a subset of residual spot urine samples with CKD that met assay performance quality controls from patients attending the clinical labs at the University of California, San Francisco (UCSF) as part of an ongoing IRB-approved prospective study. Inclusion criteria included selection of patients with confirmed CKD and normal healthy controls; exclusion criteria included incomplete or missing information for sample classification, logistical delays in transport/processing of urine samples or low sample volume, and acute kidney injury. Multivariate logistic regression of kidney injury status and likelihood ratio statistics were used to assess the contribution of the KIT Score for prediction of kidney injury status and stage of CKD as well as assess the potential contribution of the KIT Score for detection of early-stage CKD above and beyond traditional measures of renal function. Urine samples were processed by a proprietary immunoprobe for measuring cell-free DNA (cfDNA), methylated cfDNA, clusterin, CXCL10, total protein, and creatinine. The KIT Score and stratified KIT Score Risk Group (high versus low) had a sensitivity and specificity for detection of kidney injury status (healthy or CKD) of 97.3% (95% CI: 94.6-99.3%) and 94.1% (95% CI: 82.3-100%). In addition, in patients with normal renal function (estimated glomerular filtration rate (eGFR) ≥ 90), the KIT Score clearly identifies those with predisposing risk factors for CKD, which could not be detected by eGFR or proteinuria (p &amp;lt; 0.001). The KIT Score uncovers a burden of kidney injury that may yet be incompletely recognized, opening the door for earlier detection, intervention and preservation of renal function.
Macrophages contribute to the initiation of ischaemic acute renal failure in rats (2006)

These results suggest that macrophages are an important mediator in the initiation period of ischaemia/reperfusion injury and strategies that limit initial macrophage infiltration or activation can be useful in the treatment of acute renal failure.
Liquid Metal Walls, Lithium, And Low Recycling Boundary Conditions In Tokamaks (2010)

At present, the only solid material believed to be a viable option for plasma‐facing components (PFCs) in a fusion reactor is tungsten. Operated at the lower temperatures typical of present‐day fusion experiments, tungsten is known to suffer from surface degradation during long‐term exposure to helium‐containing plasmas, leading to reduced thermal conduction to the bulk, and enhanced erosion. Existing alloys are also quite brittle at temperatures under 700°C. However, at a sufficiently high operating temperature (700 – 1000 °C), tungsten is self‐annealing and it is expected that surface damage will be reduced to the point where tungsten PFCs will have an acceptable lifetime in a reactor environment.The existence of only one potentially viable option for solid PFCs, though, constitutes one of the most significant restrictions on design space for DEMO and follow‐on fusion reactors. In contrast, there are several candidates for liquid metal‐based PFCs, including gallium, tin, lithium, and tin‐lithium eutectics. We will discuss options for liquid metal walls in tokamaks, looking at both high and low recycling materials. We will then focus in particular on one of the candidate liquids, lithium.Lithium is known to have a high chemical affinity for hydrogen, and has been shown in test stands and fusion experiments to produce a low recycling surface, especially when liquid. Because it is also low‐Z and is usable in a tokamak over a reasonable temperature range (200 – 400 °C), it has been now been used as a PFC in several confinement experiments (TFTR, T11‐M, CDX‐U, NSTX, FTU, and TJ‐II), with favorable results. The consequences of substituting low recycling walls for the traditional high recycling variety on tokamak equilibria are very extensive. We will discuss some of the expected modifications, briefly reviewing experimental results, and comparing the results to expectations.
Effect of a high-fat meal on thalidomide pharmacokinetics and the relative bioavailability of oral formulations in healthy men and women (2000)

The effect of food on the oral pharmacokinetics of thalidomide and the relative bioavailability of two oral thalidomide formulations were determined in an open label, single dose, randomized, three-way crossover study. Five male and eight female healthy volunteers received a single oral dose of 200 mg Celgene thalidomide capsules under fasted and non-fasted conditions, and a single dose of 200 mg tablets of Serral thalidomide under fasted conditions. The high-fat meal resulted in a 0.5-1.5 h absorption lag time, an increased mean C(max), a decreased mean AUC and a delay in mean T(max). The Serral tablet formulation resulted in a lower mean C(max), and slower terminal decline in plasma thalidomide concentrations compared with both Celgene treatments. Mean C(max) concentrations were 1.99+/-0.41 microg/mL (range 1.28-2.76) within 4.00+/-1.13 h (2-5) for the Celgene formulation fasted, 2.17+/-0.51 microg/mL (1.43-3.01) within 6.08+/-2.33 h (3-12) for the Celgene formulation with food, and 1. 05+/-0.31 microg/mL (0.62-1.65) within 6.23+/-1.88 h (5-10) for the Serral formulation fasted. Mean terminal half-lives were 13.50+/-6. 77 h for the Serral product, compared with 5.80+/-1.72 h and 5. 09+/-1.03 h for Celgene fasted and fed, respectively. Celgene's formulation exhibited slightly greater bioavailability than Serral's formulation, with mean ratios of 122% and 110% for Ln-transformed AUC(0-t) and AUC(0-infinity), respectively. The mean C(max) for the Celgene formulation was approximately two times greater than Serral's. Food delayed the onset of absorption of by 0.5-1.5 h, but had little effect on the extent of absorption from the Celgene capsule. Under fasted conditions, the Celgene thalidomide resulted in a two-fold greater C(max) and 10% greater AUC(0-infinity) than the Serral formulation.
Differential effect of oleic and palmitic acid on lipid accumulation and apoptosis in cultured hepatocytes (2009)

Oleic acid is more steatogenic but less apoptotic than palmitic acid in hepatocityc cell cultures. These data may provide a biological basis for clinical findings on dietary patterns and pathogenetic models of nonalcoholic fatty liver disease.
Identification of androgen receptors in normal human osteoblast-like cells. (1989)

The sex steroids, androgens and estrogens, are major regulators of bone metabolism. However, whether these hormones act on bone cells through direct or indirect mechanisms has remained unclear. A nuclear binding assay recently used to demonstrate estrogen receptors in bone [Eriksen, E.F., Colvard, D.S., Berg, N.J., Graham, M.L., Mann, K.G., Spelsberg, T.C. & Riggs, B.L. (1988) Science 241, 84-86] was used to identify specific nuclear binding of a tritiated synthetic androgen, [3H]R1881 (methyltrienolone), in 21 of 25 (84%) human osteoblast-like cell strains and a concentration of bound steroid receptors of 821 +/- 140 (mean +/- SEM) molecules per cell nucleus. Binding was saturable and steroid-specific. Androgen receptor gene expression in osteoblasts was confirmed by RNA blot analysis. Relative concentrations of androgen and estrogen receptors were compared by measuring specific nuclear estrogen binding. Nuclear binding of [3H]estradiol was observed in 27 of 30 (90%) cell strains; the concentration of bound estradiol receptor was 1537 +/- 221 molecules per cell nucleus. The concentrations of nuclear binding sites were similar in males and females for both [3H]R1881 and [3H]estradiol. We conclude that both androgens and estrogens act directly on human bone cells through their respective receptor-mediated mechanisms.
Diabetic nephropathy (1989)

Journal Article Diabetic nephropathy Get access P L Drury, P L Drury Departments of Diabetes, King's College HospitalLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar P J Watkins, P J Watkins Departments of Diabetes, King's College HospitalLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar G C Viberti, G C Viberti Unit for Metabolic Medicine, Guy's HospitalLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar J D Walker J D Walker Unit for Metabolic Medicine, Guy's HospitalLondon Search for other works by this author on: Oxford Academic PubMed Google Scholar British Medical Bulletin, Volume 45, Issue 1, 1989, Pages 127–147, https://doi.org/10.1093/oxfordjournals.bmb.a072308 Published: 01 January 1989
Comparison of Serum Galactomannan Antigen Detection and Competitive Polymerase Chain Reaction for Diagnosing Invasive Aspergillosis (1998)

To improve the diagnosis of invasive aspergillosis (IA), we retrospectively compared competitive polymerase chain reaction (PCR) and sandwich ELISA for detection of serum galactomannan (GM) antigen. We studied 281 serum samples collected weekly during the period at risk for IA from 41 selected hematology patients. Twenty-two patients had confirmed, probable, or suspected IA, according to clinical and mycologic data. Fifteen of them had positive GM titers (87 samples) and 12 had positive PCRs (20 samples). Nineteen of the 20 PCR-positive samples were also GM-positive. Of the 19 patients without IA (83 samples), one had 3 GM-false-positive samples. Neither test anticipated the initiation of antifungal therapy on the basis of clinical suspicion. Both tests were more likely to be positive before death. This study suggests that PCR on serum samples is not more sensitive than GM detection. However, PCR can improve the specificity of the GM test. Together, these noninvasive tests should improve the diagnosis of IA.
Service overlay networks: slas, qos, and bandwidth provisioning (2003)

We advocate the notion of service overlay network (SON) as an effective means to address some of the issues, in particular, end-to-end quality of service (QoS), plaguing the current Internet, and to facilitate the creation and deployment of value-added Internet services such as VoIP, Video-on-Demand, and other emerging QoS-sensitive services. The SON purchases bandwidth with certain QoS guarantees from the individual network domains via bilateral service level agreement (SLA) to build a logical end-to-end service delivery infrastructure on top of the existing data transport networks. Via a service contract, users directly pay the SON for using the value-added services provided by the SON. In this paper, we study the bandwidth provisioning problem for a SON which buys bandwidth from the underlying network domains to provide end-to-end value-added QoS sensitive services such as VoIP and Video-on-Demand. A key problem in the SON deployment is the problem of bandwidth provisioning, which is critical to cost recovery in deploying and operating the value-added services over the SON. The paper is devoted to the study of this problem. We formulate the bandwidth provisioning problem mathematically, taking various factors such as SLA, service QoS, traffic demand distributions, and bandwidth costs. Analytical models and approximate solutions are developed for both static and dynamic bandwidth provisioning. Numerical studies are also performed to illustrate the properties of the proposed solutions and demonstrate the effect of traffic demand distributions and bandwidth costs on SON bandwidth provisioning.
Staying FIT: efficient load shedding techniques for distributed stream processing (2007)

In distributed stream processing environments, large numbers of continuous queries are distributed onto multiple servers. When one or more of these servers become overloaded due to bursty data arrival, excessive load needs to be shed in order to preserve low latency for the query results. Because of the load dependencies among the servers, load shedding decisions on these servers must be well-coordinated to achieve end-to-end control on the output quality. In this paper, we model the distributed load shedding problem as a linear optimization problem, for which we propose two alternative solution approaches: a solver-based centralized approach, and a distributed approach based on metadata aggregation and propagation, whose centralized implementation is also available. Both of our solutions are based on generating a series of load shedding plans in advance, to be used under certain input load conditions. We have implemented our techniques as part of the Borealis distributed stream processing system. We present experimental results from our prototype implementation showing the performance of these techniques under different input and query workloads. 1.
Constituents of Cannabis sativa L. XVII. A Review of the Natural Constituents (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConstituents of Cannabis sativa L. XVII. A Review of the Natural ConstituentsCarlton E. Turner, Mahmoud A. Elsohly, and Edward G. BoerenCite this: J. Nat. Prod. 1980, 43, 2, 169–234Publication Date (Print):March 1, 1980Publication History Published online1 July 2004Published inissue 1 March 1980https://pubs.acs.org/doi/10.1021/np50008a001https://doi.org/10.1021/np50008a001research-articleACS PublicationsRequest reuse permissionsArticle Views5326Altmetric-Citations435LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Antisense Phosphorodiamidate Morpholino Oligomers Targeted to an Essential Gene Inhibit Burkholderia cepacia Complex (2010)

AcpP PPMO is active against Bcc infections in vitro and in vivo.
Designing Optically Tracked Instruments for Image-Guided Surgery (2004)

Most image-guided surgery (IGS) systems track the positions of surgical instruments in the physical space occupied by the patient. This task is commonly performed using an optical tracking system that determines the positions of fiducial markers such as infrared-emitting diodes or retroreflective spheres that are attached to the instrument. Instrument tracking error is an important component of the overall IGS system error. This paper is concerned with the effect of fiducial marker configuration (number and spatial distribution) on tip position tracking error. Statistically expected tip position tracking error is calculated by applying results from the point-based registration error theory developed by Fitzpatrick et al. Tracking error depends not only on the error in localizing the fiducials, which is the error value generally provided by manufacturers of optical tracking systems, but also on the number and spatial distribution of the tracking fiducials and the position of the instrument tip relative to the fiducials. The theory is extended in two ways. First, a formula is derived for the special case in which the fiducials and the tip are collinear. Second, the theory is extended for the case in which there is a composition of transformations, as is the situation for tracking an instrument relative to a coordinate reference frame (i.e., a set of fiducials attached to the patient). The derivation reveals that the previous theory may be applied independently to the two transformations; the resulting independent components of tracking error add in quadrature to give the overall tracking error. The theoretical results are verified with numerical simulations and experimental measurements. The results in this paper may be useful for the design of optically tracked instruments for image-guided surgery; this is illustrated with several examples.
Endobronchial allergen challenge in asthma. Demonstration of cellular source of granulocyte macrophage colony-stimulating factor by in situ hybridization. (1991)

Airway inflammation is thought to play an important role in the pathogenesis of asthma. We have used in situ hybridization and an immunoassay to determine whether granulocyte macrophage colony-stimulating factor (GM-CSF) (a cytokine capable of eosinophil activation) is present in the airway of asthmatics (n = 6) who have 37.0 +/- 15.1% airway eosinophilia after endobronchial allergen challenge. Levels of immunoreactive GM-CSF (less than 4 pg/ml pre-allergen versus 180.5 +/- 46.9 pg/ml post-allergen) increased significantly 24 h after endobronchial allergen stimulation. The cellular source of bronchoalveolar lavage (BAL) GM-CSF, as determined by in situ hybridization and immunoperoxidase staining, was derived predominantly from UCHL-1 positive BAL lymphocytes, as well as from a smaller population of alveolar macrophages. Before local endobronchial allergen challenge, less than 1% of lymphocytes and alveolar macrophages recovered by BAL expressed GM-CSF mRNA, whereas after allergen stimulation 92.6 +/- 3.4% of lymphocytes and 17.5 +/- 22.7% of alveolar macrophages expressed GM-CSF mRNA. This study provides evidence that in an experimental model of allergen-induced asthma, activation of the immune and inflammatory response (BAL lymphocyte and alveolar macrophage production of GM-CSF) is temporally associated with an inflammatory cell influx of eosinophils into the airway.
Predictions of T-cell receptor- and major histocompatibility complex-binding sites on staphylococcal enterotoxin C1 (1994)

We have focused on regions of staphylococcal enterotoxin C1 (SEC1) causing immunomodulation. N-terminal deletion mutants lacking residues 6 through 13 induced T-cell proliferation similar to that induced by native toxin. However, mutants with residues deleted between positions 19 and 33, although nonmitogenic themselves, were able to inhibit both SEC1-induced T-cell proliferation and binding of the native toxin to major histocompatibility complex (MHC) class II. Presumably, these deletions define a part of SEC1 that interacts with the T-cell receptor. Three synthetic peptides containing residues located in a region analogous to the alpha 5 groove of SEC3 had residual mitogenic activity or blocked T-cell proliferation induced by SEC1 and appear to recognize the same site as SEC1 on a receptor for the toxin, presumably MHC class II. We conclude that isolated portions of the SEC1 molecule can retain residual mitogenic activity but that the entire protein is needed to achieve maximal superantigenic stimulation. Our results, together with the results of other investigators, support a model in which SEC1 binds to an alpha helix of MHC class II through a central groove in the toxin and thereby promotes or stabilizes the interaction between antigen-presenting cells and T cells.