gebhart/patrepeval huggingface dataset:
Standardizing CYP2D6 Genotype to Phenotype Translation: Consensus Recommendations from the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group (2019)

Translating CYP2D6 genotype to metabolizer phenotype is not standardized across clinical laboratories offering pharmacogenetic (PGx) testing and PGx clinical practice guidelines, such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). The genotype to phenotype translation discordance between laboratories and guidelines can cause discordant cytochrome P450 2D6 (CYP2D6) phenotype assignments and, thus lead to inconsistent therapeutic recommendations and confusion among patients and clinicians. A modified-Delphi method was used to obtain consensus for a uniform system for translating CYP2D6 genotype to phenotype among a panel of international CYP2D6 experts. Experts with diverse involvement in CYP2D6 interpretation (clinicians, researchers, genetic testing laboratorians, and PGx implementers; n = 37) participated in conference calls and surveys. After completion of 7 surveys, a consensus (> 70%) was reached with 82% of the CYP2D6 experts agreeing to the final CYP2D6 genotype to phenotype translation method. Broad adoption of the proposed CYP2D6 genotype to phenotype translation method by guideline developers, such as CPIC and DPWG, and clinical laboratories as well as researchers will result in more consistent interpretation of CYP2D6 genotype.
Threshold Levels of Fluid Shear Promote Leukocyte Adhesion through Selectins (CD62L,P,E) (1997)

Leukocyte adhesion through L-selectin to peripheral node addressin (PNAd, also known as MECA-79 antigen), an L-selectin ligand expressed on high endothelial venules, has been shown to require a minimum level of fluid shear stress to sustain rolling interactions (Finger, E.B., K.D. Puri, R. Alon, M.B. Lawrence, V.H. von Andrian, and T.A. Springer. 1996. Nature (Lond.). 379:266-269). Here, we show that fluid shear above a threshold of 0.5 dyn/cm2 wall shear stress significantly enhances HL-60 myelocyte rolling on P- and E-selectin at site densities of 200/microm2 and below. In addition, gravitational force is sufficient to detach HL-60 cells from P- and E-selectin substrates in the absence, but not in the presence, of flow. It appears that fluid shear-induced torque is critical for the maintenance of leukocyte rolling. K562 cells transfected with P-selectin glycoprotein ligand-1, a ligand for P-selectin, showed a similar reduction in rolling on P-selectin as the wall shear stress was lowered below 0.5 dyn/cm2. Similarly, 300.19 cells transfected with L-selectin failed to roll on PNAd below this level of wall shear stress, indicating that the requirement for minimum levels of shear force is not cell type specific. Rolling of leukocytes mediated by the selectins could be reinitiated within seconds by increasing the level of wall shear stress, suggesting that fluid shear did not modulate receptor avidity. Intravital microscopy of cremaster muscle venules indicated that the leukocyte rolling flux fraction was reduced at blood centerline velocities less than 1 mm/s in a model in which rolling is mediated by L- and P-selectin. Similar observations were made in L-selectin-deficient mice in which leukocyte rolling is entirely P-selectin dependent. Leukocyte adhesion through all three selectins appears to be significantly enhanced by a threshold level of fluid shear stress.
Nickel and Palladium Complexes with New Phosphinito-Imine Ligands and Their Application as Ethylene Oligomerization Catalysts (2012)

Phosphinito-imines, a new class of P,N donors, are readily generated by reaction of bulky arylamide anions [R2CONAr]− (R2 = Me or t-Bu; Ar = 2,6-i-Pr2C6H4) with chlorophosphines ClP(R1)2. In solution, free phosphinito-imines exist in equilibrium with the corresponding amidophosphine tautomers, containing a nitrogen-bound P(R1)2 group. However, reacting the tautomer mixtures with metal precursor complexes, such as NiBr2(dme) or PdCl2(cod), selectively affords stable phosphinito-imine complexes MX2(P-N) (M = Ni, Pd) in excellent yields. These complexes are diamagnetic and exhibit square-planar structures in the solid state, but in solution, the Ni derivatives exchange with a small amount of the corresponding high-spin tetrahedral isomers. On treatment with MMAO or DEAC, NiX2(P-N) complexes become active ethylene oligomerization catalysts, affording mainly butenes along with smaller amounts of hexenes and octenes. The activity and the selectivity of these catalysts depend on the structure of the phosphinito-imine ligand and the cocatalyst used. When activated with DEAC, complexes containing the P(i-Pr)2 moiety are extremely active, achieving TOFs over 106 mol C2H4/mol Ni·h and high selectivity for butenes.
Antitumor Efficacy Testing in Rodents (2008)

The preclinical research and human clinical trials necessary for developing anticancer therapeutics are costly. One contributor to these costs is preclinical rodent efficacy studies, which, in addition to the costs associated with conducting them, often guide the selection of agents for clinical development. If inappropriate or inaccurate recommendations are made on the basis of these preclinical studies, then additional costs are incurred. In this commentary, I discuss the issues associated with preclinical rodent efficacy studies. These include the identification of proper preclinical efficacy models, the selection of appropriate experimental endpoints, and the correct statistical evaluation of the resulting data. I also describe important experimental design considerations, such as selecting the drug vehicle, optimizing the therapeutic treatment plan, properly powering the experiment by defining appropriate numbers of replicates in each treatment arm, and proper randomization. Improved preclinical selection criteria can aid in reducing unnecessary human studies, thus reducing the overall costs of anticancer drug development.
A recombinant HIV provirus is synergistically activated by the HIV Tat protein and the HSV IE1 protein but not by the HSV IE3 protein (1991)

To study the effects of regulatory proteins encoded by herpes viruses on the HIV long terminal repeat (LTR) in the presence or absence of HIV-encoded regulatory products, we prepared a proviral construct containing 5' and 3' HIV LTR, but lacking the coding sequences of any HIV proteins. This construct allowed the effects of herpesvirus regulatory proteins on the HIV LTR to be assessed in a construct similar to the HIV provirus whilst also allowing their interactions with HIV-encoded regulatory proteins to be studied. In this system, the herpes simplex virus (HSV) protein IE1 (ICPO) but not the IE3 (ICP4) protein can activate the HIV LTR, whereas both proteins are active on a single plasmid-bone HIV LTR. Although the activation of the LTR by IE1 is strongly stimulated by the HIV Tat protein, it can also be observed in the absence of Tat, indicating that HSV infection via IE1 has the potential to activate an entirely silent, latent HIV provirus.
Dataflow anomaly detection (2006)

Beginning with the work of Forrest et al, several researchers have developed intrusion detection techniques based on modeling program behaviors in terms of system calls. A weakness of these techniques is that they focus on control flows involving system calls, but not their arguments. This weakness makes them susceptible to several classes of attacks, including attacks on security-critical data, race-condition and symbolic link attacks, and mimicry attacks. To address this weakness, we develop a new approach for learning dataflow behaviors of programs. The novelty in our approach, as compared to previous system-call argument learning techniques, is that it learns temporal properties involving the arguments of different system calls, thus capturing the flow of security-sensitive data through the program. An interesting aspect of our technique is that it can be uniformly layered on top of most existing control-flow models, and can leverage control-flow contexts to significantly increase the precision of dataflows captured by the model. This contrasts with previous system-call argument learning techniques that did not leverage control-flow information, and moreover, were focused on learning statistical properties of individual system call arguments. Through experiments, we show that temporal properties enable detection of many attacks that aren't detected by previous approaches. Moreover, they support formal reasoning about security assurances that can be provided when a program follows its dataflow behavior model, e.g., tar would read only files located within a directory specified as a command-line argument.
Human TLRs and IL-1Rs in Host Defense: Natural Insights from Evolutionary, Epidemiological, and Clinical Genetics (2011)

Toll-like receptors (TLRs) and interleukin-1 receptors (IL-1Rs) have TIR intracellular domains that engage two main signaling pathways, via the TIR-containing adaptors MyD88 (which is not used by TLR3) and TRIF (which is used only by TLR3 and TLR4). Extensive studies in inbred mice in various experimental settings have attributed key roles in immunity to TLR- and IL-1R-mediated responses, but what contribution do human TLRs and IL-1Rs actually make to host defense in the natural setting? Evolutionary genetic studies have shown that human intracellular TLRs have evolved under stronger purifying selection than surface-expressed TLRs, for which the frequency of missense and nonsense alleles is high in the general population. Epidemiological genetic studies have yet to provide convincing evidence of a major contribution of common variants of human TLRs, IL-1Rs, or their adaptors to host defense. Clinical genetic studies have revealed that rare mutations affecting the TLR3-TRIF pathway underlie herpes simplex virus encephalitis, whereas mutations in the TIR-MyD88 pathway underlie pyogenic bacterial diseases in childhood. A careful reconsideration of the contributions of TLRs and IL-1Rs to host defense in natura is required.
Cross-talk of WNT and FGF signaling pathways at GSK3ß to regulate ß-catenin and SNAIL signaling cascades (2006)

WNT and FGF signaling pathways cross-talk during a variety of cellular processes, such as human colorectal carcinogenesis, mouse mammary tumor virus (MMTV)-induced carcinogenesis, E2A-Pbx-induced leukemogenesis, early embryogenesis, body-axis formation, limb-bud formation, and neurogenesis. Canonical WNT signals are transduced through Frizzled receptor and LRP5/6 coreceptor to downregulate GSK3beta (GSK3B) activity not depending on Ser 9 phosphorylation. FGF signals are transduced through FGF receptor to the FRS2-GRB2-GAB1-PI3K-AKT signaling cascade to downregulate GSK3beta activity depending on Ser 9 phosphorylation. Because GSK3beta-dependent phosphorylation of beta-catenin and SNAIL leads to FBXW1 (betaTRCP)-mediated ubiquitination and degradation, GSK3beta downregulation results in the stabilization and the nuclear accumulation of beta-catenin and SNAIL. Nuclear beta-catenin is complexed with TCF/LEF, Legless (BCL9 or BCL9L) and PYGO (PYGO1 or PYGO2) to activate transcription of CCND1, MYC, FGF18 and FGF20 genes for the cell-fate determination. Nuclear SNAIL represses transcription of CDH1 gene, encoding E-cadherin, to induce the epithelial-mesenchymal transition (EMT). Mammary carcinogenesis in MMTV-Wnt1 transgenic mice is accelerated by MMTV infection due to MMTV integration around Fgf3-Fgf4 or Fgf8 loci, and mammary carcinogenesis in MMTV-Fgf3 transgenic mice due to MMTV integration around Wnt1-Wnt10b locus. Coactivation of WNT and FGF signaling pathways in tumors leads to more malignant phenotypes. Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) of WNT and FGF signaling molecules could be utilized as screening method of cancer predisposition. cDNA-PCR, microarray or ELISA reflecting aberrant activation of WNT and FGF signaling pathways could be developed as novel cancer-related biomarkers for diagnosis, prognosis, and therapy. Cocktail therapy using WNT and FGF inhibitors, such as small-molecule compounds and human neutralizing antibodies, should be developed to increase the efficacy of chemotherapy through the inhibition of recurrence by destructing cancer stem cells.
agrExpression Precedes Escape of InternalizedStaphylococcus aureusfrom the Host Endosome (2001)

Staphylococcus aureus is a versatile pathogen capable of causing life-threatening infections. Many of its cell wall and exoproduct virulence determinants are controlled via the accessory gene regulator (agr). Although considered primarily as an extracellular pathogen, it is now recognized that S. aureus can be internalized by epithelial and endothelial cells. Traditional experimental approaches to investigate bacterial internalization are extremely time-consuming and notoriously irreproducible. We present here a new reporter gene method to assess intracellular growth of S. aureus in MAC-T cells that utilizes a gfp-luxABCDE reporter operon under the control of the Bacillus megaterium xylA promoter, which in S. aureus is expressed in a growth-dependent manner. This facilitates assessment of the growth of internalized bacteria in a nondestructive assay. The dual gfp-lux reporter cassette was also evaluated as a reporter of agr expression and used to monitor the temporal induction of agr during the MAC-T internalization process. The data obtained suggest that agr induction occurs prior to endosomal lysis and that agr-regulated exoproteins appear to be required prior to the release and replication of S. aureus within the infected MAC-T cells.
Photoinitiated Polymerization of Selected Thiol-ene Systems (2003)

Thiol-ene based photocurable systems exhibit very rapid rates of polymerization in nitrogen that are comparable to those achieved with traditional nitrogen saturated acrylates. In the presence of air, rates of thiol-ene copolymerization are much greater than are attained by traditional multifunctional acrylates. Even in the absence of an added photoinitiator, rapid copolymerization (thiol-acrylate) and homopolymerization (acrylate) rates of a multifunctional thiol and a difunctional acrylate are recorded in air.
NF-κB p105 Processing via the Ubiquitin-Proteasome Pathway (1998)

The p50 subunit of NF-kappa B is generated by proteolytic processing of a 105-kDa precursor (p105) in yeast and mammalian cells. Here we show that yeast mutants in the ubiquitin-proteasome pathway inhibit or abolish p105 processing. Specifically, p105 processing is inhibited by a mutation in a 20 S proteasome subunit (pre1-1), by mutations in the ATPases located in the 19 S regulatory complexes of the proteasome (yta1, yta2/sug1, yta5, cim5), and by a mutation in a proteasome-associated isopeptidase (doa4). A ubiquitinated intermediate of the p105 processing reaction accumulates in some of these mutants, strongly suggesting that ubiquitination is required for processing. However, none of the ubiquitin conjugating enzyme mutants tested (ubc1, -2, -3, -4/5, -6/7, -8, -9, -10, -11) had an effect on p105 processing, suggesting that more than one of these enzymes is sufficient for p105 processing. Interestingly, a mutant "N-end rule" ligase does not adversely affect p105 processing, showing that the N-end rule pathway is not involved in degrading the C-terminal region of p105. Unexpectedly, we found that a glycine-rich region of p105 that is required for p105 processing in mammalian cells is not required for processing in yeast. Thus, p105 processing in both yeast and mammalian cells requires the ubiquitin-proteasome pathway, but the mechanisms of processing, while similar, are not identical.
Assessing behavioral toxicity with Caenorhabditis elegans (2004)

Behavior, even in simple metazoans, depends upon integrated processes at the subcellular, cellular, and organismal level, and thus is susceptible to disruption by a broad spectrum of chemicals. Locomotor behavior (movement) of the small free-living nematode Caenorhabditis elegans has proven to be useful in assessing toxicity. Recently reported observations suggest that behavioral change (reduced movement) occurs after 4 h of exposure to heavy metals, and that with abbreviated exposure, the concentration-response relationship for Pb (a known neurotoxic metal) differs from that for Cu. In this study, movement was evaluated after 4-h exposures for nine compounds from three chemical classes: organic pesticides, organic solvents, and heavy metals. Concentration-dependent reduction of movement was observed for all test compounds with the exception of mebendazole, for which test concentrations were limited by solubility. Within each chemical class, movement was more sensitive to the neurotoxic compounds than to substances not believed to be neurotoxic, as evidenced by behavioral effective concentration to reduce average worm movement to 50% of the control movement values (e.g., levamisole and chlorpyrifos < mebendazole, ethanol and acetone < dimethylsulfoxide, and Pb and Al < Cu). These observations are discussed as they relate to the use of acute behavioral tests in assessing general chemical toxicity, and the enhanced value of 4-h testing for the detection of neural toxicants.
Identification of gastrin component I as gastrin‐71 (1994)

Gastrin component I is the largest hormonally active form of gastrin. In order to determine its structure, we isolated progastrin-derived peptides from normal human antral tissue. A radioimmunoassay specific for sequence 20-25 of human progastrin was developed to monitor the purifications. After four or five steps of reverse-phase chromatography, the peptides were pure and could be identified by a combination of microsequence, amino acid and mass spectral analysis as well as by a library of sequence-specific immunoassays. In addition to intact progastrin 1-80, fragments 1-71, 1-35, 6-35, 20-35, and 20-36 of progastrin were identified. Only the 71-amino-acid peptide contained at its C-terminus the alpha-amidated bioactive site (Trp-Met-Asp-Phe-NH2). This unoheptacontapeptide amide (gastrin-71) corresponds to component I and is the largest possible bioactive product of progastrin. Its structure shows that progastrin is used in its entirety for biosynthesis of active peptides. The occurrence of fragments 6-35, 20-35, and 20-36 demonstrate that antral progastrin is partially cleaved at two monobasic sites (Arg5 and Arg19) in addition to processing at the three C-terminal dibasic sites. The results show that both the N- and C-terminal parts of antral progastrin undergo extensive processing. The results also suggest that progastrin may follow two different processing pathways of which the less trafficked releases gastrin-71.
IP-based protocols for mobile internetworking (1991)

We consider the problem of providing network access to hosts whose physical location clianges with time. Such hosts cannot depend on traditional forms of network connectivity and routing because their location, and hence the route to reach them, cannot be deduced from their network address. In this paper, we explore the concept of providing continuous network access to mobile computers, and present a set of IP-based protocols that achieve that goal.
Intraarticular injection of anakinra in osteoarthritis of the knee: A multicenter, randomized, double‐blind, placebo‐controlled study (2009)

Anakinra was well tolerated as a single 50-mg or 150-mg intraarticular injection in patients with OA of the knee. However, anakinra was not associated with improvements in OA symptoms compared with placebo.
Cell-Free Co-synthesis of Protein Nanoassemblies:  Tubes, Rings, and Doughnuts (2007)

We used a cell-free transcription/translation system to synthesize structural proteins of the T4 bacteriophage. We focused on two proteins that participate in the formation of the virus tail tube assembly. Synthesized separately, the proteins assembled into their in vivo forms, namely one polymerized into rigid hollow nanotubes approximately 20 nm thick and hundreds of nanometers long, the other assembled into 10 nm tube-capping hexameric rings. Co-synthesis of the two proteins, however, revealed a novel structure of a nanodoughnut with an outer diameter of approximately 50 nm and thickness of approximately 20 nm. Cell-free co-synthesis and assembly of T4 structural proteins can be extended in a combinatorial fashion. The addition of other structural genes offers control of native nanoassemblies and may reveal ones not observable by mixing purified components.
Structural Evidence for Ligand Specificity in the Binding Domain of the Human Androgen Receptor (2000)

The crystal structures of the human androgen receptor (hAR) and human progesterone receptor ligand-binding domains in complex with the same ligand metribolone (R1881) have been determined. Both three-dimensional structures show the typical nuclear receptor fold. The change of two residues in the ligand-binding pocket between the human progesterone receptor and hAR is most likely the source for the specificity of R1881 to the hAR. The structural implications of the 14 known mutations in the ligand-binding pocket of the hAR ligand-binding domains associated with either prostate cancer or the partial or complete androgen receptor insensitivity syndrome were analyzed. The effects of most of these mutants could be explained on the basis of the crystal structure.
Biomolecule‐cell interactions and the regulation of myelopoiesis (1986)

The regulation of myelopoiesis in vivo most likely entails a complex set of interactions between cell-derived biomolecules and their target cells. Much of what we currently know of these interactions has been derived from studies in vitro utilizing techniques for the purification of both the biomolecules and the cells producing and responding to these factors. Stimulating and suppressing influences have been uncovered, and with the cloning and purification of biologically active factors, studies assessing the actions of these molecules in vivo have begun. From studies in vitro it is apparent that many of the purified molecules can have move than one action and that different molecules can collaborate in a synergistic manner to enhance or suppress functional endpoints.
Ligation of E-cadherin on in vitro–generated immature Langerhans-type dendritic cells inhibits their maturation (2000)

Epithelial tissues of various organs contain immature Langerhans cell (LC)-type dendritic cells, which play key roles in immunity. LCs reside for long time periods at an immature stage in epithelia before migrating to T-cell-rich areas of regional lymph nodes to become mature interdigitating dendritic cells (DCs). LCs express the epithelial adhesion molecule E-cadherin and undergo homophilic E-cadherin adhesion with surrounding epithelial cells. Using a defined serum-free differentiation model of human CD34(+) hematopoietic progenitor cells, it was demonstrated that LCs generated in vitro in the presence of transforming growth factor beta1 (TGF-beta1) express high levels of E-cadherin and form large homotypic cell clusters. Homotypic LC clustering can be inhibited by the addition of anti-E- cadherin monoclonal antibodies (mAbs). Loss of E-cadherin adhesion of LCs by mechanical cluster disaggregation correlates with the rapid up-regulation of CD86, neo-expression of CD83, and diminished CD1a cell surface expression by LCs-specific phenotypic features of mature DCs. Antibody ligation of E-cadherin on the surfaces of immature LCs after mechanical cluster disruption strongly reduces the percentages of mature DCs. The addition of mAbs to the adhesion molecules LFA-1 or CD31 to parallel cultures similarly inhibits homotypic LC cluster formation, but, in contrast to anti-E-cadherin, these mAbs fail to inhibit DC maturation. Thus, E-cadherin engagement on immature LCs specifically inhibits the acquisition of mature DC features. E-cadherin-mediated LC maturation suppression may represent a constitutive active epithelial mechanism that prevents the uncontrolled maturation of immature LCs. (Blood. 2000;96:4276-4284)