gebhart/patrepeval huggingface dataset:
Effectiveness of different types of clay for reducing the detrimental effects of aflatoxin-contaminated diets on performance and serum profiles of weanling pigs (1993)

Three trials were conducted with recently weaned pigs (n = 198) to determine the effects of feeding different types of clay in conjunction with aflatoxin-contaminated diets. In Trial 1, pigs (n = 54; trial length 4 wk) were assigned to either an uncontaminated treatment (NC), 800 ppb of aflatoxin from contaminated corn (AC), or AC with one of four clays. In Trial 2 (n = 81; trial length 5 wk), pigs were assigned to NC, AC (500 ppb of aflatoxin from rice starch), or AC with one of seven types of clay. In both trials, pigs fed AC had decreased ADG and gain:feed ratios (P < .05) compared with controls. The clays differed in their ability to produce gains similar to those of controls. The clays did reduce changes in the serum measurements normally affected by aflatoxin, including albumin, total protein, gamma glutamyltransferase (GGT), and alkaline phosphatase (ALP) levels, in a manner similar to their effect on ADG. In Trial 3, pigs (n = 63) were assigned to one of seven diets for 4 wk: NC, AC (800 ppb of aflatoxin) with no clay, AC with one of four levels of a treated Ca bentonite (.25, .5, 1, and 2%), or AC and .5% hydrated sodium calcium aluminosilicate. The addition of treated Ca bentonite to AC improved ADG (P < .05) and ADFI (P < .01) linearly. Gain:feed ratios were not affected by treatments. The inclusion of treated Ca bentonite to the AC diet linearly decreased aspartate aminotransferase (AST) levels and quadratically decreased ALP and GGT levels (P < .05).(ABSTRACT TRUNCATED AT 250 WORDS)
Sorting nexin 9 differentiates ligand-activated Smad3 from Smad2 for nuclear import and transforming growth factor β signaling (2015)

Transforming growth factor β (TGFβ) is a pleiotropic protein secreted from essentially all cell types and primary tissues. While TGFβ's actions reflect the activity of a number of signaling networks, the primary mediator of TGFβ responses are the Smad proteins. Following receptor activation, these cytoplasmic proteins form hetero-oligomeric complexes that translocate to the nucleus and affect gene transcription. Here, through biological, biochemical, and immunofluorescence approaches, sorting nexin 9 (SNX9) is identified as being required for Smad3-dependent responses. SNX9 interacts with phosphorylated (p) Smad3 independent of Smad2 or Smad4 and promotes more rapid nuclear delivery than that observed independent of ligand. Although SNX9 does not bind nucleoporins Nup153 or Nup214 or some β importins (Imp7 or Impβ), it mediates the association of pSmad3 with Imp8 and the nuclear membrane. This facilitates nuclear translocation of pSmad3 but not SNX9.
Online Filtering, Smoothing and Probabilistic Modeling of Streaming data (2008)

In this paper, we address the problem of extending a relational database system to facilitate efficient real-time application of dynamic probabilistic models to streaming data. We use the recently proposed abstraction of model-based views for this purpose, by allowing users to declaratively specify the model to be applied, and by presenting the output of the models to the user as a probabilistic database view. We support declarative querying over such views using an extended version of SQL that allows for querying probabilistic data. Underneath we use particle filters, a class of sequential Monte Carlo algorithms, to represent the present and historical states of the model as sets of weighted samples (particles) that are kept up-to-date as new data arrives. We develop novel techniques to convert the queries on the model-based view directly into queries over particle tables, enabling highly efficient query processing. Finally, we present experimental evaluation of our prototype implementation over several synthetic and real datasets, that demonstrates the feasibility of online modeling of streaming data using our system and establishes the advantages of tight integration between dynamic probabilistic models and databases.
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs (2002)

Over the last 15 years a wealth of linkage maps and quantitative trait loci (QTL) mapping results have become available. The pace of generating this genetic information is accelerating owing to advances in molecular marker technology and the development of software for linkage analysis and QTL mapping. A graphical presentation of this information is often needed, both for publication purposes and for easy and intuitive interpretation. However, the development of tools for the graphical presentation of linkage maps and QTLs has lagged behind. DrawMap (Van Ooijen 1994) was an early program capable of drawing genetic linkage maps. However, the output of this program was not very well suited for use in modern word processors and presentation software. Authors in this field have therefore, of necessity, resorted to the use of general graphics software to compose charts of their linkage and QTL maps. This is always a laborious process, with sometimes disappointing results. Also, each time a map is recalculated when new data become available, this process has to be repeated. For this reason I developed MapChart, a software package that takes as input the linkage and QTL data and generates charts of linkage maps and QTLs. These charts can easily be exported to word processing or presentation software. The charts are exported as vector graphics (Windows enhanced metafiles) rather than bitmaps, which makes them easy to rescale and to edit further if desired.
The Bcl-2/Bcl-XL/Bcl-w Inhibitor, Navitoclax, Enhances the Activity of Chemotherapeutic Agents In Vitro and In Vivo (2011)

The ability of a cancer cell to avoid apoptosis is crucial to tumorigenesis and can also contribute to chemoresistance. The Bcl-2 family of prosurvival proteins (Bcl-2, Bcl-X(L), Bcl-w, Mcl-1, and A1) plays a key role in these processes. We previously reported the discovery of ABT-263 (navitoclax), a potent small-molecule inhibitor of Bcl-2, Bcl-X(L), and Bcl-w. While navitoclax exhibits single-agent activity in tumors dependent on Bcl-2 or Bcl-X(L) for survival, the expression of Mcl-1 has been shown to confer resistance to navitoclax, most notably in solid tumors. Thus, therapeutic agents that can downregulate or neutralize Mcl-1 are predicted to synergize potently with navitoclax. Here, we report the activity of navitoclax in combination with 19 clinically relevant agents across a panel of 46 human solid tumor cell lines. Navitoclax broadly enhanced the activity of multiple therapeutic agents in vitro and enhanced efficacy of both docetaxel and erlotinib in xenograft models. The ability of navitoclax to synergize with docetaxel or erlotinib corresponded to an altered sensitivity of the mitochondria toward navitoclax, which was associated with the downmodulation of Mcl-1 and/or upregulation of Bim. These data provide a rationale to interrogate these combinations clinically.
Effect of photobleaching on calibration model development in biological Raman spectroscopy (2011)

A major challenge in performing quantitative biological studies using Raman spectroscopy lies in overcoming the influence of the dominant sample fluorescence background. Moreover, the prediction accuracy of a calibration model can be severely compromised by the quenching of the endogenous fluorophores due to the introduction of spurious correlations between analyte concentrations and fluorescence levels. Apparently, functional models can be obtained from such correlated samples, which cannot be used successfully for prospective prediction. This work investigates the deleterious effects of photobleaching on prediction accuracy of implicit calibration algorithms, particularly for transcutaneous glucose detection using Raman spectroscopy. Using numerical simulations and experiments on physical tissue models, we show that the prospective prediction error can be substantially larger when the calibration model is developed on a photobleaching correlated dataset compared to an uncorrelated one. Furthermore, we demonstrate that the application of shifted subtracted Raman spectroscopy (SSRS) reduces the prediction errors obtained with photobleaching correlated calibration datasets compared to those obtained with uncorrelated ones.
Characterization of an Extracellular Lipase Encoded by LIP2 in Yarrowia lipolytica (2000)

We isolated the LIP2 gene from the lipolytic yeast Yarrowia lipolytica. It was found to encode a 334-amino-acid precursor protein. The secreted lipase is a 301-amino-acid glycosylated polypeptide which is a member of the triacylglycerol hydrolase family (EC 3.1.1.3). The Lip2p precursor protein is processed by the KEX2-like endoprotease encoded by XPR6. Deletion of the XPR6 gene resulted in the secretion of an active but less stable proenzyme. Thus, the pro region does not inhibit lipase secretion and activity. However, it does play an essential role in the production of a stable enzyme. Processing was found to be correct in LIP2(A) (multiple LIP2 copy integrant)-overexpressing strains, which secreted 100 times more activity than the wild type, demonstrating that XPR6 maturation was not limiting. No extracellular lipase activity was detected with the lip2 knockout (KO) strain, strongly suggesting that extracellular lipase activity results from expression of the LIP2 gene. Nevertheless, the lip2 KO strain is still able to grow on triglycerides, suggesting an alternative pathway for triglyceride utilization in Y. lipolytica.
Pentafluoro-λ6-sulfanyl-Terminated Chlorosilanes:  New SF5-Containing Films and Polysiloxane Materials (2000)

Two new SF5-terminated perfluoroalkylsilanesSF5(CF2CF2)nCH2CH2SiCl3 (n = 1 and 2)were synthesized by addition of trichlorosilane to the corresponding synthetic SF5-terminated perfluoroalkenes by hydrosilylation. Thin films of these SF5-silanes on clean silicon oxide substrates were characterized by ellipsometry, aqueous contact angle, and X-ray photoelectron spectroscopy (XPS) methods. The shorter SF5-silane film shows a hydrophobic interface with minimal angle dependence in depth-dependent XPS analysis, suggesting a poorly organized film. The longer SF5-silane exhibits a high aqueous static contact angle (106°) and angular-dependent XPS compositional variance consistent with improved film assembly (fewer defects and more vertical chain orientation). Bulk SF5-bearing materials were fabricated by silane hydrolysis, producing SF5-polymers and cross-linked networks bearing the unique SF5 perfluoroalkyl chemistry.
Shear, Bond and Torsion (1976)

This chapter deals with the theory and derivation of the design equations for shear, bond and torsion. Some of the more practical factors governing the choice and arrangement of the reinforcement are dealt with in the chapters on member design, particularly chapter 7, which contains examples of the design and detailing of shear and torsion reinforcement in beams. Punching shear caused by concentrated loads on slabs is covered in section 8.1 of the chapter on slab design.
NMOS SPDT Switch MMIC with >44 dB Isolation and 30 dBm IIP3 for Applications within GSM and UMTS bands (2001)

This paper describes the first reported, fully integrated, 0.25摯瑬敳獩m NMOS SPDT switch MMIC, for GSM and UMTS applications, fabricated on 10 Ωcm silicon substrate. This switch has the highest reported isolation, >44 dB below 2.2GHz, for a NMOS switch and high IIP3 (30 dBm at 900 MHz) for a 3V control voltage. Good RF port matches and <2.3 dB insertion loss are demonstrated over the whole frequency band.
A material sensitivity study on the accuracy of deformable organ registration using linear biomechanical modelsa) (2006)

Model-based deformable organ registration techniques using the finite element method (FEM) have recently been investigated intensively and applied to image-guided adaptive radiotherapy (IGART). These techniques assume that human organs are linearly elastic material, and their mechanical properties are predetermined. Unfortunately, the accurate measurement of the tissue material properties is challenging and the properties usually vary between patients. A common issue is therefore the achievable accuracy of the calculation due to the limited access to tissue elastic material constants. In this study, we performed a systematic investigation on this subject based on tissue biomechanics and computer simulations to establish the relationships between achievable registration accuracy and tissue mechanical and organ geometrical properties. Primarily we focused on image registration for three organs: rectal wall, bladder wall, and prostate. The tissue anisotropy due to orientation preference in tissue fiber alignment is captured by using an orthotropic or a transversely isotropic elastic model. First we developed biomechanical models for the rectal wall, bladder wall, and prostate using simplified geometries and investigated the effect of varying material parameters on the resulting organ deformation. Then computer models based on patient image data were constructed, and image registrations were performed. The sensitivity of registration errors was studied by perturbating the tissue material properties from their mean values while fixing the boundary conditions. The simulation results demonstrated that registration error for a subvolume increases as its distance from the boundary increases. Also, a variable associated with material stability was found to be a dominant factor in registration accuracy in the context of material uncertainty. For hollow thin organs such as rectal walls and bladder walls, the registration errors are limited. Given 30% in material uncertainty, the registration error is limited to within 1.3 mm. For a solid organ such as the prostate, the registration errors are much larger. Given 30% in material uncertainty, the registration error can reach 4.5 mm. However, the registration error distribution for prostates shows that most of the subvolumes have a much smaller registration error. A deformable organ registration technique that uses FEM is a good candidate in IGART if the mean material parameters are available.
A High-Throughput HERG Potassium Channel Function Assay: An Old Assay with a New Look (2002)

In this paper, we describe an assay using radioactive rubidium (86Rb) efflux to screen functional human ether-a go-go-related gene (HERG) K+ channels in a high-throughput screening (HTS) format. This assay offers an alternative way to examine junctional interactions between chemical compounds and HERG K+ channels. Follow-up experiments and discussions were carried out to address a variety of factors that affect potency evaluation within the Rb efflux assay. Factors that can affect the assay results, such as assay time, efflux rate, and compound blocking kinetics, are discussed in detail. Our results provide some explanations for the variances of the assay results and offer some guidelines for using the Rb efflux assay to evaluate compound interactions with HERG K+ channels in the pharmaceutical industry.
of Mouse Mammary Tumor Virus RNA: a System for Studying Glucocorticoid Action" (1975)

Gordon M. Ringold, Keith R. Yamamoto, Gordon M. Tomkins, J. Michael Bishop, and Harold E. Varmus Departments of Microbiology and Biochemistry and Biophysics University of California San Francisco, California 94143 Summary We have investigated the mechanisms by which dexamethasone (a synthetic glucocorticoid) stimu- lates the production of mouse mammary tumor virus (MMTV) by cell cultures derived from mam- mary carcinomas of GR mice. Treatment of these cells with dexamethasone stimulates a rapid accu- mulation of intracellular virus-specific RNA which is dependent upon RNA synthesis but not upon DNA or protein synthesis. The effect of dexametha- sone is probably mediated by a specific and satura- ble glucocorticoid receptor. We conclude that the accumulation of MMTV RNA is a primary response to dexamethasone and that the rate of synthesis of MMTV RNA is probably accelerated by treatment with dexamethasone. Introduction Steroid hormones have an important role in regulat- ing specific gene expression in metazoan orga- nisms. It is commonly believed that the various steroids function via a unified mechanism (for re- view, see King and Mainwaring, 1974) in which the hormone diffuses into the target cell and becomes tightly associated with a soluble, steroid-specific re- ceptor protein; the complex then binds to DNA- containing nuclear sites (Harris, 1971; Yamamoto and Alberts, 1972) to initiate the biological response. Thus steroids may act as allosteric effec- tors, altering receptor properties to increase the af- finity of the steroid-receptor complex for the nu- clear binding sites (Jensen et al., 1969; Samuels and Tomkins, 1970). Although evidence consistent with this model has been reported, the initial molecular events subse- quent to interaction of the steroid-receptor complex with the nuclear sites remain obscure. In no case has it been unambiguously shown that the first event detected biochemically actually represents the primary biological effect of the hormone. In fact, in several systems, there is evidence that the pri- mary event is not being directly monitored. For example, the induction of specific proteins by glu-
Expression of herpes simplex virus beta and gamma genes integrated in mammalian cells and their induction by an alpha gene product. (1983)

The proteins of herpes simplex virus type 1 (HSV-1) form three kinetic groups termed alpha, beta, and gamma, whose synthesis is regulated in a cascade fashion. alpha products are synthesized first during infection, and they are required for synthesis of beta and gamma proteins. To examine the expression of several HSV-1 beta and gamma genes in the absence of alpha functions, we transferred into mammalian cells a plasmid containing a region of the HSV-1 genome that codes for only beta and gamma genes (0.315 to 0.421 map units). We found stable integration of at least one copy of the intact plasmid in each cell line. Four HSV-1 transcripts of the beta and gamma classes were transcribed constitutively in the cells, including the genes for glycoprotein B and DNA-binding protein. No constitutive synthesis of these two proteins could be demonstrated, however. The integrated HSV-1 genes responded to viral regulatory signals in that they could be induced by infection with HSV-1 mutants resulting in a high level of synthesis of both glycoprotein B and DNA-binding protein. The HSV-1 alpha gene product ICP4 was necessary for this induction, and it was found to be most efficient at a low multiplicity of infection. Functional expression of four genes was demonstrated in that the cell lines complemented infecting HSV-1 temperature-sensitive mutants. The same genes were not available for homologous recombination with infecting virus, however, since no recombinant wild-type virus could be detected. These data demonstrate that HSV-1 beta and gamma genes can be transcribed in the absence of alpha functions in mammalian cells, but that they still respond to HSV-1 regulatory signals such as the alpha gene product ICP4.
Scalable Generation of Universal Platelets from Human Induced Pluripotent Stem Cells (2014)

Human induced pluripotent stem cells (iPSCs) provide a potentially replenishable source for the production of transfusable platelets. Here, we describe a method to generate megakaryocytes (MKs) and functional platelets from iPSCs in a scalable manner under serum/feeder-free conditions. The method also permits the cryopreservation of MK progenitors, enabling a rapid "surge" capacity when large numbers of platelets are needed. Ultrastructural/morphological analyses show no major differences between iPSC platelets and human blood platelets. iPSC platelets form aggregates, lamellipodia, and filopodia after activation and circulate in macrophage-depleted animals and incorporate into developing mouse thrombi in a manner identical to human platelets. By knocking out the β2-microglobulin gene, we have generated platelets that are negative for the major histocompatibility antigens. The scalable generation of HLA-ABC-negative platelets from a renewable cell source represents an important step toward generating universal platelets for transfusion as well as a potential strategy for the management of platelet refractoriness.
Preparation of monolithic polymers with controlled porous properties for microfluidic chip applications using photoinitiated free‐radical polymerization (2002)

Abstract A broad variety of monolithic macroporous polymers with both controlled chemistry and porous properties was prepared using UV‐initiated free‐radical polymerization. The chemistry of the monoliths is defined by the composition of the monomer mixture used for the polymerization. The use of functional methacrylate monomers such as glycidyl methacrylate, 2‐hydroxyethyl methacrylate, butyl methacrylate, 2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid, and [2‐(methacryloyloxy) ethyl] trimethylammonium chloride enabled the preparation of monoliths with reactive, hydrophilic, hydrophobic, and ionizable functionalities, respectively. The porous properties of these monoliths were mainly affected by the choice of the porogenic solvent system. Because the UV polymerization was carried out at room temperature, even low molecular weight alcohols and other low boiling point solvents could safely be used to create a versatile series of binary porogenic mixtures. Monoliths were prepared in spatially defined positions using the photolithographic technique within a fused silica capillary and on microfluidic chips, and the former was demonstrated with the separation of derivatized amines by means of capillary electrochromatography in the reversed‐phase mode. Similarly, a monolith prepared in the microchip format was used to demonstrate a microextraction with enrichment of a solution of green fluorescent protein by a factor of 1000. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 755–769, 2002; DOI 10.1002/pola.10155
Anti-Tumor Activity of Synthetic Peptide Fragments of the Human Interferon-α 2 (1997)

We have studied an influence of nine overlapping peptides from the region between amino acid residues 124 and 144 of the human interferon (FIN)-alpha 2 molecule on the growth of human lymphoid tumor cell lines in vitro. It was found that several, but not all, synthetic peptides inhibited proliferation of the same cell lines that IFN did. One of peptides, corresponding to the 124-138 amino acid residues of the IFN molecule (124-138) was most active. Using a human-mouse somatic hybrid cell line, we have shown that antiproliferative activity of the peptide 124-138 and IFN depended on the presence of human chromosome 21. Receptor binding studies also demonstrated that the peptide specifically interacted with membrane receptors on hybrid human-mouse cells carrying human chromosome 21, but not on parental mouse cells. Displacement experiments confirm that IFN and the peptide 124-138 compete for the same binding sites. Taken together, the data presented support a hypothesis that the C-terminal part of the IFN molecule contributes to antiproliferative activity possessed by IFN. Synthetic peptides studied in the present work may serve as a tool for studying tumor cell growth regulation by IFN and may be considered as potential nontoxic anti-tumor agents.