gebhart/patrepeval huggingface dataset:
Antimicrobial Penetration and Efficacy in an In Vitro Oral Biofilm Model (2011)

The penetration and overall efficacy of six mouthrinse actives was evaluated by using an in vitro flow cell oral biofilm model. The technique involved preloading biofilm cells with a green fluorescent dye that leaked out as the cells were permeabilized by a treatment. The loss of green color, and of biomass, was observed by time-lapse microscopy during 60 min of treatment under continuous flow conditions. The six actives analyzed were ethanol, sodium lauryl sulfate, triclosan, chlorhexidine digluconate (CHX), cetylpyridinium chloride, and nisin. Each of these agents effected loss of green fluorescence throughout biofilm cell clusters, with faster action at the edge of a cell cluster and slower action in the cluster center. The time to reach half of the initial fluorescent intensity at the center of a cell cluster, which can be viewed as a combined penetration and biological action time, ranged from 0.6 to 19 min for the various agents. These times are much longer than the predicted penetration time based on diffusion alone, suggesting that anti-biofilm action was controlled more by the biological action time than by the penetration time of the active. None of the agents tested caused any removal of the biofilm. The extent of fluorescence loss after 1 h of exposure to an active ranged from 87 to 99.5%, with CHX being the most effective. The extent of fluorescence loss in vitro, but not penetration and action time, correlated well with the relative efficacy data from published clinical trials.
The catalytic domain of a bacterial lytic transglycosylase defines a novel class of lysozymes (1995)

The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli is a bacterial exo-muramidase that cleaves the cell wall peptidoglycan, producing 1,6-anhydro-muropeptides. The X-ray structure of SLT70 showed that one of its domains is structurally related to lysozyme, although there is no obvious similarity in amino acid sequence. To relate discrete structural features to differences in reaction mechanism and substrate/product specificity, we compared the three-dimensional structure of the catalytic domain of SLT70 with the structures of three typical representatives of the lysozyme superfamily: chicken-type hen egg-white lysozyme, goose-type swan egg-white lysozyme, and phage-type lysozyme from bacteriophage T4. We find a particularly close relationship between the catalytic domain of SLT70 and goose-type lysozyme, with not only a significant similarity in overall structure, but even a weak homology in amino acid sequence. This finding supports the notion that the goose-type lysozyme takes up a central position in the lysozyme superfamily and that it is structurally closest to the lysozyme ancestors. The saccharide-binding groove is the most conserved part in the four structures, but only two residues are absolutely preserved: the "catalytic" glutamic acid and a structurally required glycine. The "catalytic" aspartate is absent in SLT70, a difference that can be related to a different mechanism of cleavage of the beta-1,4-glycosidic bond. The unique composition of amino acids at the catalytic site, and the observation of a number of differences in the arrangements of secondary structure elements, define the catalytic domain of SLT70 as a novel class of lysozymes. Its fold is expected to be exemplary for other bacterial and bacteriophage muramidases with lytic transglycosylase activity.
The effects of metal plates on post-traumatic remodelling and bone mass (1983)

The long-term effect of stainless steel and titanium alloy plates on structural remodelling and bone mass of osteotomised canine femora was studied and the effects of early and late removal of plates were compared in 27 adult Beagles. Radiological, histological, histomorphometric and tetracycline fluorescence studies led to three conclusions. First, the continuous (60 weeks) presence of plates, irrespective of their composition, delays remodelling and leads to a reduction of bone mass. This loss is significantly greater under stainless steel plates. Secondly, the removal of plates at eight weeks leads during the 52 ensuing weeks to a marked and widespread structural remodelling and to a return to normal bone mass, irrespective of the type of plate used. However, remodelling is more intense after titanium alloy plates have been used; it is not complete 60 weeks after osteotomy. Thirdly, removal of plates at 40 weeks activates remodelling during the ensuing 20 weeks to a lesser degree and to a more limited extent than early plate removal. The clinical significance of this study is that less rigid but stable internal fixation permits the radiological assessment of healing and thus the determination of the optimal moment for removal of the plates. It also reduces the degree of bone loss should the plate be left in situ for any reason.
Conducting filament of the programmed metal electrode amorphous silicon antifuse (2002)

Antifuses in PROM and FPGA applications have used silicon and/or polycrystalline silicon electrodes. Metal electrode antifuses have the lowest resistance and lowest capacitance among programmable interconnect structures. The ViaLink, a metal electrode amorphous silicon antifuse, has been used as a programmable interconnect device for a FPGA. This paper describes for the first time, the composition, structure, electrical characteristics, and temperature dependence of the conducting filament in the programmed TiW electrode amorphous silicon antifuse.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Half‐Life Modulating Strategies–An Introduction (2012)

This chapter contains sections titled: Therapeutic Proteins Renal Clearance and FcRn-Mediated Recycling Strategies to Modulate Plasma Half-Life Half-Life Extension Strategies Applied to a Bispecific Single-Chain Diabody–A Case Study Conclusion References
Platelet-derived growth factor ligands and receptors immunolocalized in proliferative retinal diseases. (1994)

PDGF ligands and receptors are widespread in proliferative retinal membranes of different origin. Because PDGFR beta and PDGF-B were colocalized in many of the same cells, the potential for autocrine and paracrine stimulation of cell migration and growth exists. These results are consistent with a role for PDGF ligands and receptors in the pathogenesis of different proliferative retinopathies.
Current understanding of meningeal and cerebral vascular function underlying migraine headache (2018)

We discuss the anatomy of the cranial meninges, their associated vasculature, innervation and immune cell population. We then debate the meningeal neurogenic inflammation hypothesis of migraine and its putative contribution to migraine pain. Finally, we provide insights into potential sources of meningeal inflammation and nociception beyond neurogenic inflammation, and their potential contribution to migraine headache.
Chronic Antidepressants Reduce Depolarization-Evoked Glutamate Release and Protein Interactions Favoring Formation of SNARE Complex in Hippocampus (2005)

Glutamate neurotransmission was recently implicated in the action of stress and in antidepressant mechanisms. We report that chronic (not acute) treatment with three antidepressants with different primary mechanisms (fluoxetine, reboxetine, and desipramine) markedly reduced depolarization-evoked release of glutamate, stimulated by 15 or 25 mm KCl, but not release of GABA. Endogenous glutamate and GABA release was measured in superfused synaptosomes, freshly prepared from hippocampus of drug-treated rats. Interestingly, treatment with the three drugs only barely changed the release of glutamate (and of GABA) induced by ionomycin. In synaptic membranes of chronically treated rats we found a marked reduction in the protein-protein interaction between syntaxin 1 and Thr286-phosphorylated alphaCaM kinase II (alpha-calcium/calmodulin-dependent protein kinase II) (an interaction previously proposed to promote neurotransmitter release) and a marked increase in the interaction between syntaxin 1 and Munc-18 (an interaction proposed to reduce neurotransmitter release). Furthermore, we found a selective reduction in the expression level of the three proteins forming the core SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex. These findings suggest that antidepressants work by stabilizing glutamate neurotransmission in the hippocampus and that they may represent a useful tool for the study of relationship between functional and molecular processes in nerve terminals.
AMPKα2 exerts its anti-inflammatory effects through PARP-1 and Bcl-6 (2013)

B-cell lymphoma-6 protein (Bcl-6) is a corepressor for inflammatory mediators such as vascular cell adhesion molecule-1 and monocyte chemotactic protein-1 and -3, which function to recruit monocytes to vascular endothelial cells upon inflammation. Poly [ADP ribose] polymerase 1 (PARP-1) is proinflammatory, in part through its binding at the Bcl-6 intron 1 to suppress Bcl-6 expression. We investigated the mechanisms by which PARP-1 dissociates from the Bcl-6 intron 1, ultimately leading to attenuation of endothelial inflammation. Analysis of the PARP-1 primary sequence suggested that phosphorylation of PARP-1 Serine 177 (Ser-177) by AMP-activated protein kinase (AMPK) is responsible for the induction of Bcl-6. Our results show that AMPK activation with treatment of 5-aminoimidazole-4-carboxamide ribonucleotide, metformin, or pulsatile shear stress induces PARP-1 dissociation from the Bcl-6 intron 1, increases Bcl-6 expression, and inhibits expression of inflammatory mediators. Conversely, AMPKα suppression or knockdown produces the opposite effects. The results demonstrate an anti-infamatory pathway linking AMPK, PARP-1, and Bcl-6 in endothelial cells.
Improvement of bilateral motor functions in patients with Parkinson disease through the unilateral intraputaminal infusion of glial cell line—derived neurotrophic factor (2005)

Analysis of the data in this open-label study demonstrates the safety and potential efficacy of unilateral intraputaminal GDNF infusion. Unilateral administration of the protein resulted in significant, sustained bilateral effects.
Overview of the Retrovirus Transduction System (1996)

A retrovirus vector is an infectious virus used to introduce a nonviral gene into mitotic cells in vivo or in vitro. The efficient and precise integration machinery of naturally occurring retroviruses is utilized to produce either a single copy or a few copies of the viral genome stably integrated into a host chromosome. This unit presents an overview of the retrovirus life cycle and a description of vector designs and packaging cell lines.
Dehydroepiandrosterone feeding prevents aortic fatty streak formation and cholesterol accumulation in cholesterol-fed rabbit. (1989)

The concentration of dehydroepiandrosterone sulfate (DHEA-S) in human plasma is higher than any other steroid. Recent evidence has suggested an inverse relationship between plasma DHEA levels and the development of coronary atherosclerosis in humans. We used the cholesterol-fed rabbit model to investigate whether DHEA feeding would diminish aortic fatty streak formation in this model. Fifteen New Zealand White rabbits were fed rabbit chow supplemented with 0.5% cholesterol (wt/wt). Seven animals were, in addition, fed DHEA, 0.5% of diet (wt/wt). Animals were sacrificed after 2 months, and the aortic involvement with fatty streaks was evaluated by computerized planimetry of Sudan IV-stained aortas and by chemical analysis of aortic wall lipids. Compared to controls, DHEA-fed animals had similar plasma levels of total, very low density lipoprotein (VLDL), low density lipoprotein (LDL), and high density lipoprotein (HDL) cholesterol, corticoids, and estrogens. DHEA-fed animals had higher plasma levels of total, VLDL, and LDL triglycerides and lower HDL triglycerides than did controls. DHEA feeding resulted in 30% and 40%, respectively, inhibition of fatty streak formation by chemical analysis and planimetry. We conclude that DHEA feeding inhibits the development of aortic fatty streaks in cholesterol-fed rabbits, independent of changes in plasma total and LDL cholesterol levels of DHEA conversion to estrogens or corticoids.
Evidence for two heat-stable enterotoxins produced by enterotoxigenic Escherichia coli (1979)

Heat-stable enterotoxins from a bovine and porcine strain of Escherichia coli were isolated and showed significant differences in amino acid composition and heat stability.
Investigating the stereochemistry of binding to HIV-1 protease with inhibitors containing isomers of 4-amino-3-hydroxy-5-phenylpentanoic acid (1991)

A series of inhibitors containing all possible isomers of 4-amino-3-hydroxy-5-phenylpentanoic acid was synthesized and tested for inhibition of HIV-1 protease. Incorporation of the (3S,4S) isomer of the t-butyloxycarbonyl protected amino acid into the sequence Glu-Phe resulted in a potent inhibitor of HIV-1 protease (Ki = 63 nM). This inhibitor is at least 47-times more potent than the inhibitors containing other isomers of 4-amino-3-hydroxy-5-phenylpentanoic acid, indicating that the (3S,4S) isomer is the preferred isomer for binding to HIV-1 protease.
Resolving Created, Propped, and Effective Hydraulic-Fracture Length (2009)

Summary Recent advances in hydraulic-fracture-mapping technologies have provided a wealth of information on the created fracture length in numerous geologic settings. Before having such measurements, fracture length was estimated using "uncalibrated" fracture-propagation models, but there was significant uncertainty in the results that cascaded into subsequent production analyses. However, we also need to understand how the created fracture length relates to the location of proppant in the fracture and to the producing or effective length to evaluate well performance and improve stimulation designs. Unfortunately, the advanced fracture-mapping technologies that provide accurate measurements of the created fracture length cannot provide any insights (yet) into the propped and effective fracture lengths. Advanced production-data analyses (PDAs), pressure-transient testing, and/or numerical reservoir modeling are required to determine the effective fracture length. This paper begins with a comparison of the strengths, weaknesses, and limitations of fracture modeling, PDA, pressure-transient analysis (PTA), and numerical reservoir modeling to estimate effective fracture length and conductivity. This work also evaluates how the complexities (in the hydraulic fracture) associated with non-Darcy flow, multiphase flow, and complex fracture geometries affect the results from the various techniques. This work documents the significant differences in "effective" fracture length that, in many cases, can result from each technique and how these uncertainties can impact fracture treatment designs and field-development decisions. The paper concludes with several field case histories that illustrate the integration of multiple technologies to determine the created, propped, and effective fracture length. The case histories illustrate the dramatic differences in created and effective fracture length that can occur in some reservoirs, while also showing that in some cases, effective fracture lengths can be very similar to the created length (and quite long). Integrating the results from multiple diagnostic techniques in a consistent and coherent manner can provide significant insights into created, propped, and effective fracture length that are otherwise unattainable from each technique alone.
Replacing creatinine measurements with specific gravity values to adjust urine cotinine concentrations (1994)

Creatinine and specific gravity (relative density) measurements both allow differences in urine concentration to be taken into account in determining urine cotinine concentrations. In this study we demonstrate that the variance of urine cotinine measurements is reduced comparably when either creatinine or specific gravity measurements are used for correction. This reduction in variability improves the correlation between urine cotinine measurements and clinical endpoints. In this study, the clinical endpoints were pulmonary function in a population of nonsmoking children with asthma, 42% of whom were reported to have been exposed to environmental tobacco smoke. When corrected by either creatinine measurements or specific gravity values, the urine cotinine measurements performed as well or better than reported exposure (and comparably with each other) in assessments of lung function. A dose-response relationship was also more consistently apparent. Specific gravity values can be used reliably in place of creatinine values to adjust urine cotinine measurements for both research and clinical purposes.
Antibodies to Bradykinin and Angiotensin: A Use of Carbodiimides in Immunology (1964)

Antibodies to bradykinin and angiotensin have been produced in rabbits by the use of conjugates containing albumin and the hapten, covalently bound. The use of water-soluble carbodiimide reagents provided an easy and rapid method of synthesis of the antigenic conjugates.
The synthesis of compounds with potential anti-folic acid activity. Part I. 7-Amino- and 7-hydroxy-pteridines (1954)

R. G. W. Spickett and G. M. Timmis, J. Chem. Soc., 1954, 2887 DOI: 10.1039/JR9540002887
Cytoprotective effects of ferritin on doxorubicin-induced breast cancer cell death (2015)

Ferritin is a major iron storage protein and essential for iron homeostasis. It has a wide range of functions in the body including iron delivery, immunosuppression, angiogenesis, and cell proliferation. Ferritin is overexpressed in many cancer cells, but its precise role in cancer is unclear. In the present study, we examined the functional roles of ferritin in protecting the MCF-7 breast cancer cell line against treatment with the chemotherapeutic agent doxorubicin. The effects of ferritin (human liver ferritin) and doxorubicin on the human MCF-7 breast cancer cell line were evaluated using the cell viability assay. The impact of decreasing ferritin light chain (FTL) and ferritin heavy chain (FTH) expression on doxorubicin sensitivity was assessed using siRNA. Reactive oxygen species (ROS) was also measured using the fluorescence probe CM-H2DCFDA. The mechanism of modulated chemosensitivity was evaluated by western blot analysis. Ferritin treatment activated MCF-7 cell proliferation in a concentration- and time-dependent manner. While treatment with doxorubicin alone significantly increased intracelullar ROS production, the addition of ferritin decreased this ROS formation, thereby reducing doxorubicin‑induced MCF-7 cell death. The inhibition of FTL and FTH by siRNA sensitized cells to doxorubicin. Treatment with doxorubicin alone significantly induced the cell cycle‑dependent kinase inhibitor protein p21, whereas ferritin reduced p21 expression. Thus, ferritin plays a critical role in protecting MCF-7 cells against the chemotherapeutic drug doxorubicin. A targeted reduction of ferritin may be a useful strategy for overcoming chemoresistance in breast cancer.
Web Queries as a Source for Syndromic Surveillance (2009)

In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries submitted to a medical web site, with influenza as a case study. The hypothesis of the work was that queries on influenza and influenza-like illness would provide a basis for the estimation of the timing of the peak and the intensity of the yearly influenza outbreaks that would be as good as the existing laboratory and sentinel surveillance. We calculated the occurrence of various queries related to influenza from search logs submitted to a Swedish medical web site for two influenza seasons. These figures were subsequently used to generate two models, one to estimate the number of laboratory verified influenza cases and one to estimate the proportion of patients with influenza-like illness reported by selected General Practitioners in Sweden. We applied an approach designed for highly correlated data, partial least squares regression. In our work, we found that certain web queries on influenza follow the same pattern as that obtained by the two other surveillance systems for influenza epidemics, and that they have equal power for the estimation of the influenza burden in society. Web queries give a unique access to ill individuals who are not (yet) seeking care. This paper shows the potential of web queries as an accurate, cheap and labour extensive source for syndromic surveillance.
High-speed phase-control of wavefronts with binary amplitude DMD for light control through dynamic turbid media (2013)

The optical imaging depth in biological materials is limited by the scattering of light in tissue. New methods which control light propagation through scattering media have been introduced with the potential to overcome the scattering of light in biological materials. These techniques shape the incident wavefront to pre-compensate for the scattering effects of light propagation in the material and beyond. However, living biological materials have speckle decorrelation times on the millisecond timescale. This fast rate of change makes liquid crystal spatial light modulation (LC-SLM) devices too slow for this task. To achieve the required wavefront control with high modulation speeds we present binary-amplitude off-axis computer-generated holography implemented on a digital micro-mirror device (DMD). Binary amplitude off-axis holography is a method for the generation of arbitrary wavefronts, and in particular uniform-amplitude phase-modulated images. As a result, we are able to simultaneously encode phase modulated wavefronts at the high frame rate of binary amplitude DMDs. This wavefront encoding technique allows for focusing through temporally dynamic turbid materials at a rate which approaches the decorrelation time of living biological tissue. We demonstrate this technique by high speed wavefront optimization for focusing through turbid media as well as through a dynamic, strongly scattering sample with short speckle decorrelation times. With this approach we attain an order of magnitude improvement in measurement speed over the previous fastest wavefront determination method and three orders of magnitude improvement over LC-SLM methods.
Homing endonucleases: keeping the house in order (1997)

Homing endonucleases are rare-cutting enzymes encoded by introns and inteins. They have striking structural and functional properties that distinguish them from restriction enzymes. Nomenclature conventions analogous to those for restriction enzymes have been developed for the homing endonucleases. Recent progress in understanding the structure and function of the four families of homing enzymes is reviewed. Of particular interest are the first reported structures of homing endonucleases of the LAGLIDADG family. The exploitation of the homing enzymes in genome analysis and recombination research is also summarized. Finally, the evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.
High-throughput multiplexed fluorescence-activated droplet sorting (2018)

Fluorescence-activated droplet sorting (FADS) is one of the most important features provided by droplet-based microfluidics. However, to date, it does not allow to compete with the high-throughput multiplexed sorting capabilities offered by flow cytometery. Here, we demonstrate the use of a dielectrophoretic-based FADS, allowing to sort up to five different droplet populations simultaneously. Our system provides means to select droplets of different phenotypes in a single experimental run to separate initially heterogeneous populations. Our experimental results are rationalized with the help of a numerical model of the actuation of droplets in electric fields providing guidelines for the prediction of sorting designs for upscaled or downscaled microsystems.