gebhart/patrepeval huggingface dataset:
Liposome-encapsulated alginate: controlled hydrogel particle formation and release (1995)

Large unilamellar liposomes of dipalmitoyl phosphatidylcholine have been employed as reaction sites for calcium alginate gelation. Encapsulation of sodium alginate was accomplished by extrusion of phospholipid dispersions through polycarbonate filter of uniform pore size followed by incubation with high concentrations of calcium chloride. The diffusion of calcium into the liposome interior resulted in alginate gelatin within the liposome. Detergent treatment of the liposomes resulted in solubilization of the lipid bilayer with subsequent release of the alginate beads which were measured by laser light scattering and electron microscopy. The release profiles of both the liposomes with entrapped alginate beads and the alginate beads (released by detergent treatment of the liposomes) were determined using cytochrome-c as a marker for release. The release profiles show a rapid release of cytochrome-c over the first 2 for both preparations with slower subsequent release rates for the liposomes with encapsulated alginate beads. The similar early profile may be due to the release of cytochrome-c from bound calcium alginate adsorbed to the outer leaflet of the liposome. This is also supported by calorimetric results which indicate a marked reduction in the enthalpy of the main gel to liquid crystalline phase transition of multilamellar and large unilamellar dispersions of the lipid. This method results in the fabrication of easily controlled, unimodal submicron hydrogel particles which may be used for controlled-release applications.
Nitroxyl and its anion in aqueous solutions: Spin states, protic equilibria, and reactivities toward oxygen and nitric oxide (2002)

The thermodynamic properties of aqueous nitroxyl (HNO) and its anion (NO(-)) have been revised to show that the ground state of NO(-) is triplet and that HNO in its singlet ground state has much lower acidity, pKa((1)HNO/(3)NO(-)) approximately 11.4, than previously believed. These conclusions are in accord with the observed large differences between (1)HNO and (3)NO(-) in their reactivities toward O(2) and NO. Laser flash photolysis was used to generate (1)HNO and (3)NO(-) by photochemical cleavage of trioxodinitrate (Angeli's anion). The spin-allowed addition of (3)O(2) to (3)NO(-) produced peroxynitrite with nearly diffusion-controlled rate (k = 2.7 x 10(9) M(-1) x s(-1)). In contrast, the spin-forbidden addition of (3)O(2) to (1)HNO was not detected (k << 3 x 10(5) M(-1) x s(-1)). Both (1)HNO and (3)NO(-) reacted sequentially with two NO to generate N(3)O as a long-lived intermediate; the rate laws of N(3)O formation were linear in concentrations of NO and (1)HNO (k = 5.8 x 10(6) M(-1) x s(-1)) or NO and (3)NO(-) (k = 2.3 x 10(9) M(-1) x s(-1)). Catalysis by the hydroxide ion was observed for the reactions of (1)HNO with both O(2) and NO. This effect is explicable by a spin-forbidden deprotonation by OH(-) (k = 4.9 x 10(4) M(-1) x s(-1)) of the relatively unreactive (1)HNO into the extremely reactive (3)NO(-). Dimerization of (1)HNO to produce N(2)O occurred much more slowly (k = 8 x 10(6) M(-1) x s(-1)) than previously suggested. The implications of these results for evaluating the biological roles of nitroxyl are discussed.
Catumaxomab – trifunctional anti-EpCAM antibody used to treat malignant ascites (2010)

Catumaxomab i.p. treatment results in a significant and clinically relevant improvement of puncture-free survival time and time to first need for puncture compared with paracentesis alone. The related side effects of catumaxomab treatment are predictable and related to the antibody's mode of action.
Extending Quine-McCluskey for Exclusive-Or logic synthesis (1996)

Various forms of Boolean minimization have been used within electronic engineering degrees as a key part of the syllabus. Typically, Karnaugh maps and Quine-McCluskey methods are the principal exhaustive search techniques for digital minimization at the undergraduate level as they are easy to use and simple to understand. Despite the popularity of these methods, they are not well suited to typical digital circuits. Simple examples of such circuits are parity, adders, gray code generators, and so on. The common factor among these is the Exclusive-Or logic gate. This problem is exacerbated by the increasing importance of Exclusive-Or in modern design. This paper proposes an extension to the Quine-McCluskey method which successfully incorporates Exclusive-Or gates within the minimization process. A number of examples are given to demonstrate the effectiveness of this approach. This technique is easy to master as it can be considered to be an extension to the Quine-McCluskey method.
Quantification of immunohistochemistry—issues concerning methods, utility and semiquantitative assessment II (2006)

Immunohistochemistry is entering its fourth decade of use on formalin-fixed paraffin-embedded tissues. Over this period the method has evolved to become a major part of the practice of diagnostic surgical pathology worldwide. From the beginning immunohistochemistry has been adapted to provide a range of markers of cell lineage and tissue type, with particular application to the diagnosis and classification of tumours. In this modality immunohistochemical methods were employed simply as 'special stains', the results of which were evaluated qualitatively by the pathologist, as for any other stain. More recently, attention has shifted to the demonstration of prognostic markers in tumour cells, driven by the advent of molecular biology and the discovery of numerous regulatory molecules, coupled with manufacture of the corresponding specific antibodies. Immunohistochemistry has rapidly adapted to this new use, but in so doing the demand for quantification has become paramount; it is no longer enough that the 'stain' is there; rather it is a question of 'How much is there?'. This review explores the limitations of immunohistochemistry when employed in a semiquantitative mode, and explores the possibility of fulfilling the full potential of immunohistochemistry, as a true quantitative immunoassay applied in a tissue section environment.
Use of Biological Markers and Pharmacokinetics in Human Health Risk Assessment (1991)

There are two reasons to connect discussions ofbiolo a markers and phacokinetics.irst, both tend to open up the black box between exposure and effect.Doing thi promisesmorecomplete nding than simple input- output analysis, the possibility of better mechanim-based projection of risk beyond the range of possible direct obser- vations, and the possibility ofgreater sensitivity ofanalysis, in some cases going from the or to the cell as the unit ofanalysis.Second, pharmacokinetic (or simlnar pharmacodynamic) analysis will often be essential for appropriate interpretation of biologia marker information.One needs some sort of dynamic model ofthe generation and loss of the marker in relation to exposure in order to use a biological marker, either to form a better measure of dosage (either ac- cumulated past dose, or biologically relevant dose), or to make an improved predition of effect. (For eample, the use ofa blood c level alone to pdit kidney effects might beinfrior to e ns based on pastaccumutionof uminthe kidny, based on the pt history ofc I blod leve x time).Several eamples wi be d of the use of biomarkers and pharmacokinetics in risk assessments for both carcinogenesis and other effects.
Prevention of platelet alloimmunization in dogs with systemic cyclosporine and by UV-irradiation or cyclosporine-loading of donor platelets (1987)

To study the immunosuppressive effects of three different treatments, 30 dogs received at weekly intervals eight platelet transfusions from a single random donor dog. The three experimental protocols were daily oral cyclosporine (Cs) treatment of recipients; in vitro ultraviolet (UV)-irradiation of donor platelets; and Cs-loading of donor platelets. All nine recipients of Cs, 11/12 (92%) recipients of UV-irradiated platelets, and 5/9 (56%) recipients of Cs-loaded donor platelets remained nonimmunized to repeated transfusions of donor platelets. In contrast, only 3 of 21 untreated controls (14%) were not alloimmunized by donor platelets. Moreover, 44% to 67% of the nonimmunized recipients remained tolerant to continued platelet transfusions from their original donor even after experimental therapy was discontinued. Forty- three percent to 100% of transfusions from secondary donors were also accepted without causing alloimmunization, suggesting that tolerance induced by prior treatment was not specific for the primary donor. However, survival of both the original and secondary donor platelets was reduced to about half the starting level, suggesting that some immune response to platelets had occurred. Also, recipients immunized by their original donor's platelets frequently developed refractoriness to platelets from other donors.
The major heat‐modifiable outer membrane protein CD is highly conserved among strains of Branhamella catarrhalis (1993)

The outer membrane of Branhamella catarrhalis contains a major, heat-modifiable outer membrane protein called CD which has epitopes on the surface of the intact bacterium. The gene encoding CD was cloned and expressed in Escherichia coli. The protein migrates in gels as a doublet, indicating that CD is encoded by single gene whose gene product has two stable conformations. The nucleotide sequence of the gene encoding CD was determined and shows homology with the OprF outer membrane protein of Pseudomonas species. The CD protein contains a proline-rich region, which appears to account for its aberrant migration in gels. Restriction fragment-length analysis of 30 isolates of B. catarrhalis with oligonucleotide probes corresponding to sequences in the CD gene produced identical patterns in Southern blot assays. The major heat-modifiable outer membrane protein CD shares homology with the OprF protein and is highly conserved among strains of B. catarrhalis.
Living Radical Polymerization with Reversible Addition−Fragmentation Chain Transfer (RAFT Polymerization) Using Dithiocarbamates as Chain Transfer Agents (1999)

Living radical polymerization with reversible addition−fragmentation chain transfer (RAFT polymerization) can be achieved with the use of dithiocarbamate derivatives that have the nonbonded electron pair of the nitrogen included as part of an aromatic system. These compounds have been shown to be highly effective in RAFT polymerization of styrene and (meth)acrylate esters to produce polymers of predetermined molecular weight and narrow polydispersity (usually <1.2). By contrast, simple N,N-dialkyl dithiocarbamates (those compounds previously described as "photoiniferters") are ineffective as RAFT agents. The reasons for the different behavior are discussed.
Wearable mobile augmented reality (2011)

Augmented Reality (AR) technologies offer the potential to aid users in a number of professional areas. However, to date, most studies have been tested in controlled laboratory conditions. This paper outlines a user experience study of a wearable mobile augmented reality system in an outdoor urban environment. We describe the use case of using a see-through monocular head-mounted display (HMD) with augmented imagery for orientation, and the use of gesture input for interacting with information while on-the-move. Participants had to navigate to a target location, whilst receiving information updates, and complete a series of gesture-based tasks. Despite participants managing to complete the tasks after some assistance, it was found that more improvements to the user experience are required for it to be viable in outdoor-use. In particular, better visibility, when see-through HMDs are used in a bright environment, and improved situation awareness. This paper further highlights the difficulties in using gesture input, and points to a number of areas requiring further research into the use of wearable mobile AR systems in the context of this work.
Trill (2014)

This paper introduces Trill -- a new query processor for analytics. Trill fulfills a combination of three requirements for a query processor to serve the diverse big data analytics space: (1) Query Model : Trill is based on a tempo-relational model that enables it to handle streaming and relational queries with early results, across the latency spectrum from real-time to offline; (2) Fabric and Language Integration : Trill is architected as a high-level language library that supports rich data-types and user libraries, and integrates well with existing distribution fabrics and applications; and (3) Performance : Trill's throughput is high across the latency spectrum. For streaming data, Trill's throughput is 2-4 orders of magnitude higher than comparable streaming engines. For offline relational queries, Trill's throughput is comparable to a major modern commercial columnar DBMS. Trill uses a streaming batched-columnar data representation with a new dynamic compilation-based system architecture that addresses all these requirements. In this paper, we describe Trill's new design and architecture, and report experimental results that demonstrate Trill's high performance across diverse analytics scenarios. We also describe how Trill's ability to support diverse analytics has resulted in its adoption across many usage scenarios at Microsoft.
STE2/SCG1‐dependent inhibition of STE4‐induced growth arrest by mutant STE4ΔC6 in the yeast pheromone response pathway (1995)

The yeast pheromone response pathway involves the activation of a heterotrimeric G protein composed by SCG1 (alpha) (also GPA1), STE4 (beta), and STE18 (gamma) subunits by the pheromone-activated receptors STE2 and STE3 in a and alpha cells, respectively. Upon exchange of bound GDP for GTP in the SCG1 subunit, the release of STE4/STE18 dimer occurs which, in turn causes activation of downstream effectors leading growth arrest and mating competence. Over-expression of STE4 also leads to growth arrest in a STE18 dependent manner. Removal of 6 amino acids from the C-terminus of STE4 rendered a subunit incapable of downstream signalling but still able to interact with STE18. This delta C6 mutant acts as a dominant negative because it blocks the growth arresting effect obtained by over-expression of STE4. The inhibitory effect of STE4 delta C6 is dependent on the presence of the SCG1 subunit in a STE2 but not ste2 background. Inhibition of the growth arresting effect of STE4 by the delta C6 mutant is not due to competition at the effector site, but rather involves an intrinsic activity of STE2 that is dependent on SCG1.
Ionic Properties of Membrane Association by Vitamin K-Dependent Proteins:  The Case for Univalency (1997)

Ionic properties of membrane interaction by prothrombin, protein Z, and other vitamin K-dependent proteins were studied to determine the relevance of a monovalent membrane contact mechanism between one phospholipid headgroup and a calcium-lined pore in the protein [McDonald, J. F., Shah, A. M., Schwalbe, R. A., Kisiel, W., Dahlback, B., and Nelsestuen, G. L. (1997) Biochemistry 36, 5120-5127]. For comparison, multivalent ionic interaction was illustrated by peptides of +3 to +5 net charge and by blood clotting factor V. As expected, the peptides were easily dissociated by salt and gave nominal charge-charge interactions (zazb values) of -13 to -17. Factor V showed much higher binding affinity despite nominal zazb values of about 9. Membrane-bound prothrombin and protein Z showed very low sensitivity to salt as long as calcium was at saturating levels (zazb values of approximately -1.3 to -1.4), appropriate for univalent ionic attraction. Prothrombin contains +3 charge groups (Lys-2, Lys-11, Arg-10) that are absent from the GLA domain (residues 1-35) of protein Z, while protein Z contains -4 charge groups (Gla-11, Asp-34, Asp-35) that are absent in prothrombin. Thus, similar zazb relationships indicated little role for these surface charges in direct membrane contact. Calcium-saturated protein Z bound to phosphatidylcholine (PC) in a manner which indicated the addition of one calcium ion, bringing the total calcium stoichiometry in the protein-membrane complex to at least 8. Protein Z bound to phosphatidic acid (PA) in a manner suggesting the need for a fully ionized phosphate headgroup, a property expected by ion pairing in an isolated environment. Electrostatic calculations showed that the proposed protein site for phosphate interaction was electropositive. The cluster of hydrophobic amino acids (Phe-5, Leu-6, and Val-9) on the surface of prothrombin was electronegative, suggesting a role in the electrostatic architecture of the GLA domain. Overall, membrane binding by vitamin K-dependent proteins appeared consistent with the formation of an ion pair in an isolated environment.
Peroxovanadates have full insulin-like effects on glycogen synthesis in normal and insulin-resistant skeletal muscle (1991)

1. The insulin-like effects of orthovanadate (10 mM) and peroxides of vanadate (peroxovanadates, at 1 mM) on rates of lactate formation, glucose oxidation and glycogen synthesis were measured in incubated soleus-muscle preparations isolated from non-obese Wistar rats and lean (fa/?) or insulin-resistant obese Zucker (fa/fa) rats. 2. The stimulation of the rates of lactate formation and glucose oxidation by either orthovanadate or peroxovanadates was of similar magnitude to the stimulation by a maximally effective concentration of insulin (1000 microunits/ml). 3. Peroxovanadates, but not orthovanadate, maximally stimulated the rate of glycogen synthesis in incubated soleus muscles isolated from Wistar rats. 4. When soleus-muscle preparations were incubated in the presence of both insulin (1000 microunits/ml) and peroxovanadates (1 mM), this did not result in a synergistic increase in the rate of total glucose utilization as compared with either agent alone. 5. Soleus muscles isolated from obese (fa/fa) Zucker rats exhibited a decrease in response to a physiologically relevant concentration of insulin (100 microunits/ml). Peroxovanadates, at 1 mM, maximally stimulated the rate of glycogen synthesis in soleus muscles isolated from obese (fa/fa) Zucker rats. 6. The findings indicate that peroxovanadates are useful and important agents for investigating the mechanism of action of insulin in skeletal muscle.
Rebalanced hemostasis in patients with liver disease: evidence and clinical consequences (2010)

Patients with liver disease frequently acquire a complex disorder of hemostasis secondary to their disease. Routine laboratory tests such as the prothrombin time and the platelet count are frequently abnormal and point to a hypocoagulable state. With more sophisticated laboratory tests it has been shown that patients with liver disease may be in hemostatic balance as a result of concomitant changes in both pro- and antihemostatic pathways. Clinically, this rebalanced hemostatic system is reflected by the large proportion of patients with liver disease who can undergo major surgery without any requirement for blood product transfusion. However, the hemostatic balance in the patient with liver disease is relatively unstable as evidenced by the occurrence of both bleeding and thrombotic complications in a significant proportion of patients. Although it is still common practice to prophylactically correct hemostatic abnormalities in patients with liver disease before invasive procedures by administration of blood products guided by the prothrombin time and platelet count, we believe that this policy is not evidence-based. In this article, we will provide arguments against the traditional concept that patients with liver failure have a hemostasis-related bleeding tendency. Consequences of these new insights for hemostatic management will be discussed.
Microscopic measurement of synovial membrane inflammation in rheumatoid arthritis: proposals for the evaluation of tissue samples by quantitative analysis (1998)

Previous studies have used various techniques for microscopic analysis of rheumatoid synovium, ranging from rapid analysis of limited areas of tissue to detailed quantification of extensive areas. The sensitivity and reproducibility of these methods have not been tested. This study sought to determine the minimum area of rheumatoid synovium needed to allow accurate microscopic analysis of synovial inflammation. Multiple synovial tissue samples were obtained from patients with rheumatoid arthritis at knee arthroplasty (n = 10), knee arthroscopy (n = 10) and by blind needle biopsy (n = 23). Lining layer thickness, sublining T-cell infiltration and vascularity were measured in all high-power fields (hpf) throughout every sample obtained from each patient. These complete measured results were compared with estimated results from limited numbers of hpf from each patient. It was observed that lining layer thickness estimated from as few as five readings from 3 samples/patient correlated significantly with the measured results obtained from as many as 85 readings/patient [Tau (T) = 0.70-0.94 for the three groups, all P < or = 0.005). Estimated measures of T-cell infiltration and vascularity derived from only 17 randomly selected hpf from 3 samples/patient (equivalent to 1 mm2) correlated significantly with the measured results obtained from up to 150 hpf/patient (T = 0.65-0.94, all P < or = 0.002). Quantitative analysis of inflammation in synovial tissue samples is both accurate and practical when restricted to an evaluation of a limited number of microscopic fields. It is proposed that lining layer thickness may be confidently quantified from five randomly selected readings from three tissue samples, and that sublining T-cell infiltration and vascularity may be quantified from 17 randomly selected hpf from the same samples.
Governing step of metastasis visualized in vitro (1997)

Metastasis is the ultimate life-threatening stage of cancer. The lack of accurate model systems thwarted studies of the metastatic cell's basic biology. To follow continuously the succeeding stages of metastatic colony growth, we heritably labeled cells from the human lung adenocarcinoma cell line ANIP 973 with green fluorescent protein (GFP) by transfection with GFP cDNA. Labeled cells were then injected intravenously into nude mice, where, by 7 days, they formed brilliantly fluorescing metastatic colonies on mouse lung [Chishima, T., Miyagi, Y., Wang, X., Yang, M., Tan, Y., Shimada, H., Moossa, A. R. & Hoffman, R. M. (1997) Clin. Exp. Metastasis 15, 547-552]. The seeded lung tissue was then excised and incubated in the three-dimensional sponge-gel-matrix-supported histoculture that maintained the critical features of progressive in vivo tumor colonization while allowing continuous access for measurement and manipulation. Tumor progression was continuously visualized by GFP fluorescence in the same individual cultures over a 52-day period, during which the tumors spread throughout the lung. Histoculture tumor colonization was selective for lung cancer cells to grow on lung tissue, because no growth occurred on histocultured mouse liver tissue, which was also observed in vivo. The ability to support selective organ colonization in histoculture and visualize tumor progression by GFP fluorescence allows the in vitro study of the governing processes of metastasis [Kuo, T.-H., Kubota, T., Watanbe, M., Furukawa, T., Teramoto, T., Ishibiki, K., Kitajima, M., Moossa, A. R., Penman, S. & Hoffman, R. M. (1995) Proc. Natl. Acad. Sci. USA 92, 12085-12089]. The results presented here provide significant, new opportunities to understand and to develop treatments that prevent and possibly reverse metastasis.