gebhart/patrepeval huggingface dataset:
Effects of growth factors on the growth and differentiation of mouse fetal liver epithelial cells in primary cultures (2005)

Hepatocyte growth factor, HB-EGF, bFGF, EGF and TGF-alpha increased DNA synthesis of FLEC. HGF, HB-EGF, bFGF and EGF led to an increase in liver-specific gene expressions; and their effects on differentiation differ as a function of gestation age.
Trimethylsilylpotassium. Deoxygenation of epoxides with inversion of stereochemistry (1976)

The reactions of silyl anions with appropriately substituted epoxides are potential stereospecific routes to diastereomerically pure erythro and threo-/3-alkoxysilanes. We report here that some mono-, di-, and trisubstituted epoxides can be deoxygenated in good yields stereospecifically with inversion of stereochemistry by trimethylsilylpotassium generated in situ. Reaction of cis and trans epoxides with hexamethyldisilane and potassium methoxide (KOMe) in anhydrous hexamethylphosphoric triamide (HMPT) at 65° under argon for 3 h affords the corresponding trans and cis olefins, respectively. Since olefins can be epoxidized with retention of stereochemistry, this constitutes a new olefin inversion procedure. The yields and stereospecificity of this deoxygenation reaction for several isomerically pure (&gt;99%) epoxides5 are listed in Table I.
Correlation between clinicopathology and expression of heat shock protein 70 and glucose-regulated protein 94 in human colonic adenocarcinoma (2005)

The HSP70 and grp94 expression rates in colonic cancer groups are significantly higher than that in their adjacent mucous membrane. The HSP70 and grp94 expression in poorly-differentiated colonic cancers with metastasis is significantly higher than well-differentiated cancers without metastasis. The overexpression of HSP70 and grp94 can be used as diagnostic or prognostic markers for colonic cancer.
R.I.P.: The Complete Book of Death and Dying (1997)

Did you know that American burial traditions include aerial burial, in which the body is placed in tree branches? Have you ever wondered which religions believe in afterlife or reincarnation? Ever been curious about exactly what the embalming process entails? The answers all lie in R.I.P.: The Complete Book of Death Dying by Constance Jones. Reminding us that almost no subject in the world elicits such universal fascination as death, Jones has masterfully collected information from diverse sources to explore, illuminate, demystify and enrich our understanding of the myriad issues related to death and dying. Publishers Weekly has praised Jones' approach as clear-sighted and fearlessly inquisitive and calls R.I.P.: The Complete Book of Death Dying invaluable and oddly uplifting. The book is divided into two parts and is equipped with a resource list of organizations, a bibliography and an index. Part One explores the cultural dimensions of death and dying, with chapters and sections on myths and legends explaining death, cultural traditions, the scientific study of death, demographic statistics, funerary customs, religious beliefs and historical anecdotes. Jones provides wide-ranging, informative, and occasionally humorous material that is thoughtfully and clearly organized. Topics covered include descriptions of the physiological changes at the moment of death, a history of cremation, and summaries of legal and ethical issues associated with death, such as capital punishment, euthanasia and suicide. A comprehensive survey of the many aspects of death and dying. Its how-to section is useful and efficacious...yet itpales in comparison to the entertainment section....a reader's delight. --A. L. A. Booklist
Pain and Poppies: The Good, the Bad, and the Ugly of Opioid Analgesics (2015)

Chronic pain is pervasive and afflicts >100 million Americans. Treating pain in these individuals is notoriously difficult and often requires opioids, one of the most powerful and effective classes of drugs used for controlling pain. However, their use is plagued by major side effects, such as a loss of pain-relieving effects (analgesic tolerance), paradoxical pain (hyperalgesia), and addiction. Despite the potential side effects, opioids remain the pharmacological cornerstone of modern pain therapy. This review highlights recent breakthroughs in understanding the key causes of these adverse effects and explores the cellular control of opioid systems in reward and aversion. The findings will challenge traditional views of the good, the bad, and the ugly of opioids.
Distribution of the Bowman Birk protease inhibitor in mice following oral administration (1992)

In this study, the distribution of the soybean-derived Bowman Birk inhibitor (BBI) in mice was examined. Mice received [125I]BBI by oral gavage and three hours later, the mice were sacrificed, the organs of interest were carefully removed and the distribution of the inhibitor was determined. The bulk of labeled BBI was present in the luminal contents of the small and large bowel, urine and feces. Significant amounts of label were also observed in the serum, esophagus, stomach and intestine, kidney, liver and lung. Analysis of tissue homogenates by gel filtration chromatography revealed that the radioactivity eluted from the column at the same position as the BBI standard indicating that the iodinated BBI was still intact. The chromatographically purified BBI was able to inhibit chymotrypsin indicating that functional protease inhibitory activity was present. These results indicate that the BBI becomes widely distributed in mice 3 h after oral administration and that intact protease inhibitor is present in internal organs.
Modulation of biofilms of Pseudomonas aeruginosa by quinolones (1995)

The interaction between four fluoroquinolones (ciprofloxacin, norfloxacin, pefloxacin, and ofloxacin) and biofilms of Pseudomonas aeruginosa in wells of microtiter plates and on segments of vascular catheters were studied in an in vitro model of vascular catheter colonization. Subinhibitory concentrations (one-half, one-fourth, and one-eight of the MIC) of the fluoroquinolones reduced the adherence of P. aeruginosa to 30 to 33, 44 to 47, and 61 to 67% of that of controls, respectively. The addition of high concentrations of the fluoroquinolones (12.5 and 400 micrograms/ml) to preformed biofilms (grown for 48 h at 37 degrees C) decreased the adherence of P. aeruginosa to 69 to 77 and 39 to 60% of that of controls, respectively. In an in vitro model of vascular catheter colonization, subinhibitory concentrations (one-half, one-fourth, and one-eight of the MIC) of fluoroquinolones reduced the number of adherent bacteria to 21 to 23, 40 to 46, and 55 to 70% of that of the controls, respectively. Scanning electron microscopy demonstrated a significant reduction in glycocalyx formation and adherent bacteria in the presence of pefloxacin at one-half to one-eight of the MIC. Vascular catheter segments precolonized with P. aeruginosa for 24 h and exposed to the fluoroquinolones at 4 to 25 times the MIC (50 micrograms/ml) for 2 h showed <5% growth of adherent cells compared with controls. No adherent organisms were cultured in the presence of 8 to 50 times the MIC (100 micrograms/ml). Scanning electron microscopy studies of preformed biofilms exposed to pefloxacin verified the results obtained by culture. These data show that subinhibitory concentrations of ciprofloxacin, norfloxacin, pefloxacin, and ofloxacin inhibit the adherence of P. aeruginosa to plastic surfaces and vascular catheters. Clinically achievable concentrations of fluoroquinolones (50 to 100 micrograms/ml) were able to eradicate preformed biofilms on vascular catheters.
Dynamic Equilibrium Mechanism for Surface Nanobubble Stabilization (2008)

Recent experiments have convincingly demonstrated the existence of surface nanobubbles on submerged hydrophobic surfaces. However, classical theory dictates that small gaseous bubbles quickly dissolve because their large Laplace pressure causes a diffusive outflux of gas. Here we suggest that the bubbles are stabilized by a continuous influx of gas near the contact line, due to the gas attraction towards hydrophobic walls [Dammer and Lohse, Phys. Rev. Lett. 96, 206101 (2006); 10.1103/PhysRevLett.96.206101Zhang, Phys. Rev. Lett.10.1103/PhysRevLett.98.136101 98, 136101 (2007); 10.1103/PhysRevLett.98.136101Mezger, J. Chem. Phys. 128, 244705 (2008)10.1063/1.2931574]. This influx balances the outflux and allows for a metastable equilibrium, which, however, vanishes in thermodynamic equilibrium. Our theory predicts the equilibrium radius of the surface nanobubbles, as well as the threshold for surface nanobubble formation as a function of hydrophobicity and gas concentration.
Systems of Privilege: Intersections, Awareness, and Applications (2012)

As research on privilege increased in the last two decades, a clear need for a social psychological perspective to examine the topic has emerged. In this special issue of JSI, scholars provide a framework for understanding the psychology of privilege, considering the policy implications of privilege, and imagining the future of privilege studies. The contributors emphasize multidisciplinary approaches, mixed methods, and the benefits of intersectional theory for studying privilege.
The Allelic Context of the C797S Mutation Acquired upon Treatment with Third-Generation EGFR Inhibitors Impacts Sensitivity to Subsequent Treatment Strategies (2015)

Mutation of C797S in EGFR is a novel mechanism of acquired resistance to third-generation TKIs. The context in which the C797S develops with respect to the other EGFR alleles affects the efficacy of subsequent treatments.
A database perspective on Lotus Domino/Notes (1999)

In this one-page summary, I introduce the database aspects of Lotus Domino/Notes. These database features are covered in detail in the corresponding SIGMOD99 tutorial available at www.almaden.ibm.com/u/mohan/domino_sigmod99.ps.
Three-kinase inhibitor combination recreates multipathway effects of a geldanamycin analogue on hepatocellular carcinoma cell death (2009)

Multitarget compounds that act on a diverse set of regulatory pathways are emerging as a therapeutic approach for a variety of cancers. Toward a more specified use of this approach, we hypothesize that the desired efficacy can be recreated in terms of a particular combination of relatively more specific (i.e., ostensibly single target) compounds. We test this hypothesis for the geldanamycin analogue 17-Allylamino-17-demethoxygeldanamycin (17AAG) in hepatocellular carcinoma cells, measuring critical phosphorylation levels that indicate the kinase pathway effects correlating with apoptotic responsiveness of the Hep3B cell line in contrast to the apoptotic resistance of the Huh7 cell line. A principal components analysis (PCA) constructed from time course measurements of seven phosphoprotein signaling levels identified modulation of the AKT, IkappaB kinase, and signal transducer and activator of transcription 3 pathways by 17AAG treatment as most important for distinguishing these cell-specific death responses. The analysis correctly suggested from 17AAG-induced effects on these phosphoprotein levels that the FOCUS cell line would show apoptotic responsiveness similarly to Hep3B. The PCA also guided the inhibition of three critical pathways and rendered Huh7 cells responsive to 17AAG. Strikingly, in all three hepatocellular carcinoma lines, the three-inhibitor combination alone exhibited similar or greater efficacy to 17AAG. We conclude that (a) the PCA captures and clusters the multipathway phosphoprotein time courses with respect to their 17AAG-induced apoptotic responsiveness and (b) we can recreate, in a more specified manner, the cellular responses of a prospective multitarget cancer therapeutic.
An extended transmission/disequilibrium test (TDT) for multi‐allele marker loci (1995)

The transmission/disequilibrium test (TDT) was recently introduced by Spielman et al. (1993) as a test for linkage and linkage disequilibrium. The test is based on the unequal probability of transmission of two different marker alleles from parents to affected offspring, when the marker locus and the hypothetical disease locus are linked and are in linkage disequilibrium. The probabilities of marker allele transmission to affected offspring conditional on parental genotype have been derived by Ott (1989) for a biallelic marker and a recessive disorder with no phenocopies. Here, we derive the transmission probabilities for a multi-allele marker locus and a generalized single locus disease model in a random sample of affected individuals from a randomly mating population. The form of these transmission probabilities suggests an extension of the TDT to multi-allele marker loci, in which the alternative hypothesis is restricted to take account of the likely pattern of unequal transmission when the recombination fraction is near 0. We show how our extended TDT can be implemented by standard software for logistic regression, although we have also written our own program which is available on request. We have evaluated the approximate power of the test under a range of realistic assumptions, and it appears that the test will often have good power when linkage disequilibrium is strong and if the disease is recessive.
Light-Induced Conformational Changes of Polymers in Solution and Gel Phase (1987)

Attempts have been made to control the polymer chain conformation reversibly by photoirradiation. The aim is attained by incorporating photochromic chromophores into the pendant groups or main chain. It was found from the results in solution that the intramolecular electrostatic force of repulsion between photogenerated pendant cations is a more effective driving force for the conformational change than trans-cis geometrical isomerization of unsaturated linkages in the polymer backbone. The large conformational change at the molecular level is amplified into the shape change of polymer gels at the visible macro level. Polyacrylamide gels having photoionizable triphenylmethane leucocyanide groups dilated 2.2 times in each dimension by ultraviolet irradiation. Electric field effect on the gel was also examined. By applying alternating electric field(0.5 Hz), the rod-shaped gel showed oscillating motion.
An Introduction to Biometric Recognition (2004)

A wide variety of systems requires reliable personal recognition schemes to either confirm or determine the identity of an individual requesting their services. The purpose of such schemes is to ensure that the rendered services are accessed only by a legitimate user and no one else. Examples of such applications include secure access to buildings, computer systems, laptops, cellular phones, and ATMs. In the absence of robust personal recognition schemes, these systems are vulnerable to the wiles of an impostor. Biometric recognition, or, simply, biometrics, refers to the automatic recognition of individuals based on their physiological and/or behavioral characteristics. By using biometrics, it is possible to confirm or establish an individual's identity based on "who she is", rather than by "what she possesses" (e.g., an ID card) or "what she remembers" (e.g., a password). We give a brief overview of the field of biometrics and summarize some of its advantages, disadvantages, strengths, limitations, and related privacy concerns.
Prokineticin 2 Is a Target Gene of Proneural Basic Helix-Loop-Helix Factors for Olfactory Bulb Neurogenesis (2007)

Prokineticin 2, a cysteine-rich secreted protein, regulates diverse biological functions including the neurogenesis of olfactory bulb. Here we show that the PK2 gene is a functional target gene of proneural basic helix-loop-helix (bHLH) factors. Neurogenin 1 and MASH1 activate PK2 transcription by binding to E-box motifs on the PK2 promoter with the same set of E-boxes critical for another pair of bHLH factors, CLOCK and BMAL1, in the regulation of circadian clock. Our results establish PK2 as a common functional target gene for different bHLH transcriptional factors in mediating their respective functions.
Interleukin‐10 suppression of myeloid cell activation — a continuing puzzle (2004)

Efforts to identify the signal transduction pathways used by interleukin-10 (IL-10) have resulted in limited success. The anti-inflammatory effects elicited by IL-10, and the mechanisms by which these are mediated, are still relatively unknown. Understanding the signalling mechanisms behind the suppression of cytokine expression by IL-10 could be of potential therapeutic interest. Although the consensus is that the Janus kinase, Jak1, as well as the signal transducer and activator of transcription STAT3 are central, much controversy exists about the participation and roles of many other signalling pathways targeted by IL-10. The mechanisms of cytokine suppression proposed by various groups have included transcriptional, post-transcriptional and post-translational regulation of IL-10 target genes; nevertheless no unifying model has emerged thus far. Here we would like to highlight novel findings and discuss their implications in the context of current understanding of IL-10 signalling.
High refractive index polyimide–nanocrystalline-titania hybrid optical materials (2008)

In this study, a new synthetic route was developed to prepare polyimide–nanocrystalline-titania hybrid materials with a relatively high titania content (up to 90 wt%). A soluble polyimide with carboxylic acid end groups (6FDA–6FpDA–COOH) was first synthesized from 4,4′-(hexafluoroisopropylidene) diphthalic anhydride (6FDA), 4,4′-(hexafluoroisopropylidene) dianiline (6FpDA), and 4-aminobenzoic acid (4ABA). Such end groups could undergo an esterification reaction with titanium butoxide and provide organic–inorganic bonding. A homogeneous hybrid solution was obtained through the mole ratio of titanium butoxide/carboxylic acid, water/acid content, and a mixed solvent system. HRTEM and XRD results indicated the formation of nanocrystalline-titania domains of around 3–4 nm in the hybrid films. The spin-coated hybrid films had relatively good surface planarity, high thermal stability, tunable refractive index (1.571 < n < 1.993), and optical transparency in the visible range. The achieved refractive index of 1.943 is the highest among the polymer–titania based hybrid materials as far as we know. A three-layer anti-reflection coating based on the prepared hybrid films was designed and possessed a reflectance of less than 0.5% in the visible range. Our study demonstrates a new route for preparing high refractive index polyimide–nanocrystalline-titania hybrid materials for potential optical applications.
100% spin accumulation in non-half-metallic ferromagnet–semiconductor junctions (2007)

We show that the spin polarization of electron density in non-magnetic degenerate semiconductors can achieve 100%. The effect of 100% spin accumulation does not require a half-metallic ferromagnetic contact and can be realized in ferromagnet-semiconductor FM-n(+)-n junctions even at moderate spin selectivity of the FM-n(+) contact when the electrons with spin 'up' are extracted from n semiconductor through the heavily doped n(+) layer into the ferromagnet and the electrons with spin 'down' are accumulated near the n(+)-n interface. We derived a general equation relating spin polarization of the current to that of the electron density in non-magnetic semiconductors. We found that the effect of complete spin polarization is achieved near the n(+)-n interface when the concentration of the spin 'up' electrons tends to zero in this region while the diffusion current of these electrons remains finite.
Phase Relationships in the Ternary System CaO─P 2 O 5 ─H 2 O at 25°C (1992)

The portion of the stable phase diagram for the ternary system CaO‐P 2 O 5 ‐H 2 O involving calcium phosphate phases more basic than Ca(H 2 PO 4 ) 2 has been constructed. Construction involves plotting concentrations as their fifth roots to allow phases having very different solubilities to be represented on a single diagram. Hydroxyapatite is shown to be congruently soluble. The stability region for hydroxyapatite includes compositions having Ca/P ratios extending between 1.5 and 1.67. Calcium‐deficient hydroxyapatite forms a stable invariant point with CaHPO 4 and a metastable invariant point with CaHPO 4 . 2H 2 O. Inspection of the diagram indicates that the compounds CaHPO 4 and CaPHO 4 .2H 2 O dissolve incongruently. Incongruent dissolution of either CaHPO 4 or CaHPO 4 .2H 2 O results in the formation of hydroxyapatite during the dissolution process. Such incongruency between these compounds and hydroxyapatite influences their microstructural relationships.
Two-dimensional NMR studies of the zinc finger motif: solution structure and dynamics of mutant ZFY domains containing aromatic substitutions in the hydrophobic core (1992)

Solution structures of mutant Zn fingers containing aromatic substitutions in the hydrophobic core are determined by 2D-NMR spectroscopy and distance-geometry/simulated annealing (DG/SA). The wild-type domain (designated ZFY-6) is derived from the human male-associated protein ZFY and represents a sequence motif (Cys-X2-Cys-X-Ar-X7-Leu-X2-His-X4-His) that differs from the consensus (Cys-X2,4-Cys-X3-Phe-X5-Leu-X2-His-X3-His) in the location ("aromatic swap") and diversity (Ar = tyrosine, phenylalanine, or histidine) of the central aromatic residue (underlined). In a given ZFY domain the choice of a particular aromatic residue is invariant among vertebrates, suggesting that alternative "swapped" aromatic residues are functionally inequivalent. 2D-NMR studies of analogues containing tyrosine, phenylalanine, or histidine at the swapped site yield the following results. (i) The three DG/SA structures each retain the beta beta alpha motif and exhibit similar staggered-horizontal packing between the variant aromatic residue and the proximal histidine in the hydrophobic core. (ii) The structures and stabilities of the tyrosine and phenylalanine analogues are essentially identical, differing only by local exposure of polar (Tyr p-OH) or nonpolar (Phe p-H) surfaces. (iii) The dynamic stability of the histidine analogue is reduced as indicated by more rapid protein-deuterium exchange of hydrogen bonds related to secondary structure and amide-sulfur coordination (slowly exchanging amide resonances in D2O) and by more extensive averaging of main-chain dihedral angles (3J alpha NH coupling constants). An aspartic acid in the putative DNA recognition surface, whose configuration is well-defined as a possible helix N-cap in the tyrosine and phenylalanine analogues, exhibits multiple weak main-chain contacts in the NOESY spectrum of the histidine analogue; such NOEs are geometrically inconsistent and so provide complementary evidence for structural fluctuations. (iv) Because the three DG ensembles have similar apparent precision, the finding of reduced dynamic stability in the histidine analogue emphasizes the importance of experiments that directly probe fluctuations at several time scales. Our results provide insight into the design of biological metal-binding sites and the relationship of protein sequence to structure and dynamics.