gebhart/patrepeval huggingface dataset:
A study of the mechanism of T4 DNA polymerase with diastereomeric phosphorothioate analogues of deoxyadenosine triphosphate. (1982)

T4 DNA polymerase copolymerizes the SP isomers of 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) and 5'-O-(2-thiotriphosphate) with dTTP onto a poly(d(A-T) template in the presence of various metal ions. The corresponding RP diastereomers are inactive, independent of the metal ion used. The polymer resulting from the polymerization of the SP diastereomer of 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) and dTTP can be degraded by the 5' leads to 3' exonuclease activity of Escherichia coli DNA polymerase I and alkaline phosphatase (Brody, R. S., and Frey, P. A. (1981) Biochemistry 20, 1245-1252) to d(Tp(S)A). This material has the RP configuration as determined by comparison with the RP and SP diastereomers obtained by chemical synthesis and preparative separation by high performance liquid chromatography. This result indicates inversion of configuration at the alpha-phosphorus in the nucleotidyl transfer reaction and is compatible with the absence of a covalent enzyme intermediate.
LXIII.—A synthesis of tropinone (1917)

R. Robinson, J. Chem. Soc., Trans., 1917, 111, 762 DOI: 10.1039/CT9171100762
Lodderomyces elongisporus Masquerading as Candida parapsilosis as a Cause of Bloodstream Infections (2007)

Ten yeast bloodstream isolates identified as Candida parapsilosis by conventional methods grew as turquoise blue colonies on Chromagar media. Subsequent sequence analysis showed that these isolates were the species Lodderomyces elongisporus. To our knowledge, this is the first published report of L. elongisporus as a cause of human disease.
Computer‐aided baker's yeast fermentations (1977)

The economics of yeast production depend heavily upon the cellular yield coefficient on the carbon source and the volumetric productivity of the process. The application of an on-line computer to maximize these two terms during the fermentation requires a continuous method of measuring cell density and growth rate. Unfortunately, a direct sensor for biomass concentration suitable for use in industrial fermentations is not available. Material balancing, with the aid of on-line computer monitoring, offers an indirect method of measurement. Laboratory results from baker's yeast production in a 14-liter fermentor (with a PDP-11/10 computer for on-line analyses) show this indirect measurement technique to be a viable alternative. From the oxygen uptake and carbon dioxide production data, gas flow rate, and ammonia addition rate, the cell density during the fermentation has been estimated and found to compare well with actual fermentation data.
Human dural replacement with acellular dermis: Clinical results and a review of the literature (2000)

We contend that AlloDerm is a safe and viable option for dural replacement in cases in which autogenous tissues are either unavailable or insufficient for proper reconstruction.
Dipeptidyl Peptidase IV in the Immune System. Effects of Specific Enzyme Inhibitors on Activity of Dipeptidyl Peptidase IV and Proliferation of Human Lymphocytes (1991)

Dipeptidyl peptidase IV (DP IV) is a membrane peptidase playing a significant role in the process of activation and proliferation of human thymus-derived lymphocytes. This conclusion is drawn from (1) the induction of this enzyme on mitogen-activated T lymphocytes (cf. Schön, E. & Ansorge, S. (1990) Biol. Chem. Hoppe-Seyler 371, 699-705) and (2) the impairment of different functions of activated T cells in the presence of specific inhibitors and antibodies against DP IV (Schön, E. & al. (1987) Eur. J. Immunol 17, 1821-1826). This paper is aimed at testing new active site-specific peptide inhibitors for their efficiency as inhibitors of lymphocyte DP IV and DNA synthesis of mitogen-stimulated lymphocytes. These inhibitors comprise (i) diacylhydroxylamine derivatives of Xaa-Pro or Xaa-Ala peptides, (ii) different oligopeptides with N-terminal Xaa-Pro-sequences, and (iii) amino-acid amides of the pyrrolidide and the thiazolidide type. The thiazolidides of epsilon-(4-nitrobenzyloxycarbonyl)-L-lysine and of L-isoleucine as well as Ala-Pro-nitrobenzoylhydroxylamine are the most effective inhibitors in both test systems, yielding half-maximal inhibitory concentrations in the micromolar range. Cell viability was not impaired in this effective concentration range. Other inhibitors of DP IV are one to two orders of magnitude less efficient in the suppression of lymphocyte proliferation.
Synergism between ammonia, lactic acid and carboxylic acids as kairomones in the host-seeking behaviour of the malaria mosquito Anopheles gambiae sensu stricto (Diptera: Culicidae) (2005)

Host odours play a major role in the orientation and host location of blood-feeding mosquitoes. Anopheles gambiae Giles sensu stricto, which is the most important malaria vector in Africa, is a highly anthropophilic mosquito species, and the host-seeking behaviour of the females of this mosquito is guided by volatiles of human origin. Ammonia, lactic acid and several carboxylic acids are known to be present in the human odour blend. We investigated the effect of these compounds on naive female mosquitoes using a dual-port olfactometer. Ammonia was an attractant on its own, whereas lactic acid was not attractive. Carboxylic acids, offered as a mixture of 12 compounds, were repellent at the concentration tested. The addition of ammonia to the carboxylic acid mixture overruled the repellent effect of the latter. Combining ammonia with either lactic acid or the carboxylic acids did not enhance the attractiveness of ammonia alone. However, a synergistic effect was found when ammonia, lactic acid and the carboxylic acids were applied as a blend. Our findings indicate that An. gambiae s.s. relies on the combination of ammonia, lactic acid and carboxylic acids in its orientation to human hosts. The role of lactic acid in this tripartite synergism differs from that reported for the yellow fever mosquito Aedes aegypti.
Molecular evolution of ruminant lysozymes (1996)

The evolution of a new digestive enzyme, stomach lysozyme, from an antibacterial host defense enzyme provides a link between molecular evolution and organismal evolution. Lysozymes have been recruited at least three times (twice from a conventional lysozyme c and once from a calcium-binding lysozyme c) in vertebrates for functioning in the stomach. The recruitment of lysozyme for its new biological function involved many molecular changes, beyond those required to adapt the protein to function in the stomach. The evolution of the stomach lysozyme gene has been extensively studied in ruminant artiodactyls. In ruminants, the lysozyme c gene has duplicated to yield a family of about ten genes. These duplications allowed: (1) specialization of gene function and (2) increased levels of expression. The ruminant stomach lysozyme genes have evolved in an episodic fashion - there was a period of rapid adaptive sequence evolution, driven by positive selection in the early ruminant, that was followed by an increase in purifying selection upon the well-adapted stomach lysozyme sequence among modern species. Recombination of small portions (exons) of the genes between members of the lysozyme gene family may have aided in adaptive evolution. Evolution to a stomach lysozyme is not irreversible; at least one member of the ruminant stomach lysozyme gene family appears to have reverted to a more ancestral function, yet retains hallmarks of its history as a stomach lysozyme.
Real-Time Intensity-Image Reconstruction for Event Cameras Using Manifold Regularisation (2016)

Event cameras or neuromorphic cameras mimic the human perception system as they measure the per-pixel intensity change rather than the actual intensity level. In contrast to traditional cameras, such cameras capture new information about the scene at MHz frequency in the form of sparse events. The high temporal resolution comes at the cost of losing the familiar per-pixel intensity information. In this work we propose a variational model that accurately models the behaviour of event cameras, enabling reconstruction of intensity images with arbitrary frame rate in real-time. Our method is formulated on a per-event-basis, where we explicitly incorporate information about the asynchronous nature of events via an event manifold induced by the relative timestamps of events. In our experiments we verify that solving the variational model on the manifold produces high-quality images without explicitly estimating optical flow.
Electrolyte Transistors:  Ionic Reaction−Diffusion Systems with Amplifying Properties (1998)

The problem of constructing chemoelectric amplifying devices based on acid−base reactions is discussed. It is shown that the construction of a direct analogue of the semiconductor transistor (that is, when the p- and n-doped semiconductors are replaced by ion exchange membranes in the H+ and OH- forms, respectively) is technically not feasible. The new amplifying device reported here is based exclusively on mobile ions migrating in a hydrogel arrangement that contains no fixed charges. The polarization curve of an acid−base interface in this medium has a diode characteristic. When two of such “electrolyte diodes” are connected appropriately, a transistor action can be observed: the electric current flowing in one (reverse biased) diode is affected not only by the voltage applied there but also by the current flowing through the other (forward biased) diode. The common emitter current gain of an acid−base−acid transistor studied here was between 4 and 5. The active mode characteristics of this device can be explained by the appearance of an acidic tunnel across the alkaline middle section. Although the acid−base−acid transistor is a stable amplifying device, the base−acid−base transistor is unstable in its active mode and displays complex oscillations. The underlying bistable behavior was also demonstrated with this transistor when its acidic feedstream was contaminated with KCl.
Pulmonary Surface Tension and the Mucus Lining of the Lungs: Some Theoretical Considerations (1958)

An attempt is made to clarify the dependence of static pressure-volume characteristics of the lung on internal surface forces. The theoretical development is based on two premises: a) the lung is lined with surface-denaturable mucus; b) alveolar sizes deviate significantly from the mean. The surface forces in a single unit are computed from the surface tension and changes in tension with area of a mucoprotein film. The effects of surface forces in the lung as a whole are obtained by summation, using the distribution of sizes. The major outlines of the pulmonary pressure-volume diagram are quantitatively deduced, including opening pressures, hysteresis and residual volumes. The role of surface compressibility in the structural stability of the lung is explored. Submitted on August 12, 1957
THE ENZYMATIC PREPARATION OF ISOLATED INTACT PARENCHYMAL CELLS FROM RAT LIVER (1967)

Suspensions of isolated parenchymal cells were prepared from rat liver by incubation with collagenase and hyaluronidase followed by mechanical treatment. Utilization of 0.15% collagenase together with 0.15% hyaluronidase yielded adequate numbers of cells for experimental purposes. As shown by light and electron microscopy, approximately 75% of the isolated cells retain their structural integrity. The cell suspensions are capable of maintaining endogenous respiration in the presence of 1% albumin for periods of time up to 8 hr. These cell preparations consist almost entirely of parenchymal cells and offer a unique tissue preparation for the study of hepatic metabolism.
Treating COPD with PDE 4 inhibitors. (2007)

While the pathogenesis of chronic obstructive pulmonary disease (COPD) is incompletely understood, chronic inflammation is a major factor. In fact, the inflammatory response is abnormal, with CD8+ T-cells, CD68+ macrophages, and neutrophils predominating in the conducting airways, lung parenchyma, and pulmonary vasculature. Elevated levels of the second messenger cAMP can inhibit some inflammatory processes. Theophylline has long been used in treating asthma; it causes bronchodilation by inhibiting cyclic nucleotide phosphodiesterase (PDE), which inactivates cAMP. By inhibiting PDE, theophylline increases cAMP, inhibiting inflammation and relaxing airway smooth muscle. Rather than one PDE, there are now known to be more than 50, with differing activities, substrate preferences, and tissue distributions. Thus, the possibility exists of selectively inhibiting only the enzyme(s) in the tissue(s) of interest. PDE 4 is the primary cAMP-hydrolyzing enzyme in inflammatory and immune cells (macrophages, eosinophils, neutrophils). Inhibiting PDE 4 in these cells leads to increased cAMP levels, down-regulating the inflammatory response. Because PDE 4 is also expressed in airway smooth muscle and, in vitro, PDE 4 inhibitors relax lung smooth muscle, selective PDE 4 inhibitors are being developed for treating COPD. Clinical studies have been conducted with PDE 4 inhibitors; this review concerns those reported to date.
Cancer stem cells: a reality, a myth, a fuzzy concept or a misnomer? An analysis (2009)

The concept of cancer stem cells (CSC) embodies two aspects: the stem cell as the initial target of the oncogenic process and the existence of two populations of cells in cancers: the CSC and derived cells. The second is discussed in this review. CSC are defined as cells having three properties: a selectively endowed tumorigenic capacity, an ability to recreate the full repertoire of cancer cells of the parent tumor and the expression of a distinctive repertoire of surface biomarkers. In operational terms, the CSC are among all cancer cells those able to initiate a xenotransplant. Other explicit or implicit assumptions exist, including the concept of CSC as a single unique infrequent population of cells. To avoid such assumptions, we propose to use the operational term tumor-propagating cells (TPC); indeed, the cells that initiate transplants did not initiate the cancer. The experimental evidence supporting the explicit definition is analyzed. Cancers indeed contain a fraction of cells mainly responsible for the tumor development. However, there is evidence that these cells do not represent one homogenous population. Moreover, there is no evidence that the derived cells result from an asymmetric, qualitative and irreversible process. A more general model is proposed of which the CSC model could be one extreme case. We propose that the TPC are multiple evolutionary selected cancer cells with the most competitive properties [maintained by (epi-)genetic mechanisms], at least partially reversible, quantitative rather than qualitative and resulting from a stochastic rather than deterministic process.
Enhanced synthesis of choline and glycine betaine in transgenic tobacco plants that overexpress phosphoethanolamine N -methyltransferase (2001)

Choline (Cho) is the precursor of the osmoprotectant glycine betaine and is itself an essential nutrient for humans. Metabolic engineering of Cho biosynthesis in plants could therefore enhance both their resistance to osmotic stresses (drought and salinity) and their nutritional value. The key enzyme of the plant Cho-synthesis pathway is phosphoethanolamine N-methyltransferase, which catalyzes all three of the methylations required to convert phosphoethanolamine to phosphocholine. We show here that overexpressing this enzyme in transgenic tobacco increased the levels of phosphocholine by 5-fold and free Cho by 50-fold without affecting phosphatidylcholine content or growth. Moreover, the expanded Cho pool led to a 30-fold increase in synthesis of glycine betaine via an engineered glycine betaine pathway. Supplying the transgenics with the Cho precursor ethanolamine (EA) further enhanced Cho levels even though the supplied EA was extensively catabolized. These latter results establish that there is further scope for improving Cho synthesis by engineering an increased endogenous supply of EA and suggest that this could be achieved by enhancing EA synthesis and/or by suppressing its degradation.
A recombinant human papillomavirus (HPV) type 16 L1–vaccinia virus murine challenge model demonstrates cell-mediated immunity against HPV virus-like particles (1999)

Human papillomavirus (HPV) virus-like particles (VLP) are emerging as the immunogen of choice for prophylactic vaccines. The inability to infect animals with HPV has prevented the testing of potential vaccines such as these in animal systems. This study describes the development of a recombinant vaccinia virus (VV)-HPV type 16 (HPV-16) VLP challenge model to evaluate the efficacy of the cell-mediated immune response following HPV-16 VLP immunization in mice. Inoculation of BALB/c and C57 BL/6 mice with HPV-16 VLP resulted in HPV VLP-specific T cell proliferative responses characterized by the production of both Th1 and Th2 cytokines, and afforded protection against virus challenge from recombinant VV expressing HPV-16 L1 (VVL1R-16). Protection was demonstrated by a 4.6 log10 reduction in ovarian titres of VVL1R-16 in vaccinated BALB/c mice and a 2.3 log10 reduction in vaccinated C57 BL/6 mice, compared with unvaccinated mice.
Parallel and distributed simulation: traditional techniques and recent advances (2006)

This tutorial on parallel and distributed simulation systems reviews some of the traditional synchronization techniques and presents some recent advances.
Aglycosylantibody. Effects of exoglycosidase treatments on autochthonous antibody survival time in the circulation. (1976)

Rabbit anti-hapten antibodies were purified by affinity chromatography and characterized immunochemical for in vivo studies of their blood clearance rate and organ distribution after treatment with various glycosidases. Following sequential removal of sialic acid, galactose, and N-acetylglucosamine with the appropriate cellulose-immobilized exoglycosidases, the antibody populations were recharacterized, radiolabeled, and introduced intravenously into the original animals. Using double radioiodine lables it was possible to demonstrate alterations in purified antibody survival times in the circulation and altered organ distribution after glycolytic cleavage. Removal of terminal sialic acid resulted in rapid blood clearance and enhanced localization of asialoantibody in the liver. Subsequent removal of penultimate galactose residues returned both antibody survival time in the circulation and organ distribution to near normal. Removal of subpenultimate N-acetylglucosamine moieties resulted in aglycosylantibody survival values which were intermediate between asialo- and asialoagalactoantibodies. Removal of the three saccharide also increased kidney localization. The results are evaluated based on current concepts of the biological roles of protein-linked carbohydrate and plasma glycoprotein survival time in the circulation.
PCR을 이용한 국내시장에 유통중인 유전자재조합 콩 및 가공식품의 모니터링 (2003)

본 연구에서는 PCR을 이용하여 국내시장에 유통중인 원료콩과 가공식품에 epsps 또는 pat 유전자가 삽입된 유전자재조합 콩(GMS)의 사용여부를 모니터링하였다. 이러한 GMS의 검출을 위해 3쌍의 primer set을 제작하였고, 각각의 primer들은 GMS에 삽입된 유전자와 특이적으로 반응하여 PCR산물을 생성하였다. 2001년 표시제가 시행되기 이전에 생산된 총 가공식품과 이후의 제품에 대해 각각 모니터링을 수행하였으며, 표시제 이전에 생산된 제품의 경우 대부분의 미국산 원료에서 esps가 삽입된 GMS가 검출되었으나, 표시제 이후에는 검출되지 않았다.
Dual-wavelength ratiometric fluorescence measurements of membrane potential (1989)

This work shows that the voltage across membranes in two very different preparations, lipid vesicles in suspension and individual HeLa cells under a microscope, is linearly related to the ratio of fluorescence excited from the two wings of the absorption spectrum of a voltage-sensitive dye. The dye di-4-ANEPPS [1-(3-sulfonatopropyl)-4-[beta-[2-(di-n-butylamino)-6-naphthyl] vin yl]pyridinium betaine] is well characterized from earlier investigations and responds via a rapid (less than millisecond) spectral shift to membrane potential changes. The resultant small change in fluorescence intensity monitored at a single wavelength is useful for measurements of temporally well-defined voltage transients such as action potentials. The dual-wavelength approach described in this work extends the usefulness of this fast potentiometric dye by filtering out complex or artifactual changes in fluorescence intensity and providing a voltage-dependent signal that is internally standardized. Thus, rapid measurements of membrane potential are made possible in nonexcitable cells.
The magnetic immuno polymerase chain reaction assay for direct detection of salmonellae in fecal samples (1992)

Direct polymerase chain reaction (PCR)-based detection with fecal specimens is hampered by inhibitory compounds, such as bilirubin and bile salts. These fecal compounds showed significant inhibition of PCR at low concentrations (10 to 50 micrograms/ml). For direct PCR analysis, fecal samples must be diluted 500-fold to overcome inhibition. Therefore, the magnetic immuno PCR assay (MIPA), which combines immunomagnetic separation by using specific monoclonal antibodies and PCR, was used to directly detect salmonellae in feces from humans. Immunomagnetically extracted stool samples needed to be diluted only 10-fold when 1 microgram of T4 gene 32 protein was added to the PCR. The MIPA sensitivity obtained was 10(5) CFU/ml of feces. A panel of monoclonal antibodies specific for Salmonella serogroups A to E was used to extract salmonellae from clinical samples. MIPA detection of salmonellae occurred with 11 out of 14 stool samples stored at 4 degrees C for 2 months. MIPA detection of salmonellae in stool samples is a promising, fast method for detection and identification.
Dual role of the p75 tumor necrosis factor (TNF) receptor in TNF cytotoxicity. (1994)

Whereas there is ample evidence for involvement of the p55 tumor necrosis factor (TNF) receptor (p55-R) in the cytocidal effect of TNF, the role of the p75 TNF receptor (p75-R) in this effect is a matter of debate. In this study, we probed the function of p75-R in cells sensitive to the cytotoxicity of TNF using a wide panel of antibodies (Abs) against the receptor's extracellular domain. Two distinct Ab effects were observed. The Abs triggered signaling for cytotoxicity. This effect: (a) was correlated with the extent of p75-R expression by the cells; (b) was dependent on receptor cross-linking by the Abs; (c) occurred in HeLa cells, but not in A9 cells transfected with human p75-R or in HeLa cells expressing cytoplasmically truncated p75-R mutants, indicating that it involves cell-specific activities of the intracellular domain of the receptor; (d) was synergistic with the cytocidal effect of Abs against p55-R. Moreover, it seemed to reverse induced desensitization to the cytocidal effect of anti p55-R Abs, suggesting that it involves mechanisms different from those of the signaling by the p55 TNF-R. In addition, the Abs affected the response to TNF in a way that does not involve the signaling activity of p75-R. These effects: (a) could be observed also in cells in which only p55-R signaled for the cytocidal effect; (b) were not dependent on receptor cross-linking by the Abs; (c) varied according to the site at which the Abs bound to the receptor; and (d) were correlated inversely with the effects of the Abs on TNF binding to p75-R. That is, Abs binding to the membrane-distal part of the receptor's extracellular domain displaced TNF from the p75 receptor and enhanced cytocidal effect, whereas Abs that bind to the membrane-proximal part of the extracellular domain--a region at which a conformational change seems to take place upon TNF binding--decreased the dissociation of TNF from p75-R and inhibited its cytocidal effect. The above findings suggest that p75-R contributes to the cytocidal effect of TNF both by its own signaling and by regulating the access of TNF to p55-R.
Panel size: how many patients can one doctor manage? (2007)

There are limits to the number of patients you can effectively care for. Here's how to determine that number, improve patient access and better manage your workload.