gebhart/patrepeval huggingface dataset:
Passive droplet sorting using viscoelastic flow focusing (2012)

We present a study of passive hydrodynamic droplet sorting in microfluidic channels based on intrinsic viscoelastic fluid properties. Sorting is achieved by tuning the droplets' intrinsic viscous and viscoelastic properties relative to the continuous oil phase to achieve a positive or negative lateral migration toward high or low shear gradients in the channel. In the presence of weakly viscoelastic fluid behavior, droplets with a viscosity ratio, κ, between 0.5-10 were found to migrate toward a high shear gradient near the channel walls. For all other κ-values, or Newtonian fluids, droplets would migrate toward a low shear gradient at the channel centerline. It was also found that for strongly viscoelastic fluids with low interfacial tension, droplets would migrate toward the edge even with κ-values lower than 0.5. The resulting bi-directional lateral droplet migration between different droplets allows size-independent sorting. Still, their sorting efficiencies are dependent on droplet size, intrinsic fluid elasticity, viscosity, droplet deformability, and overall fluid shear rates. Based on these findings, we demonstrate >200 Hz passive droplet sorting frequencies and achieve >100 fold enrichment factors without the need to actively sense and/or control active mechanisms. Using a low viscosity oil phase of 6.25 cPs, we demonstrate sorting discrimination of 1 cPs and 5 cPs aqueous droplets with κ-values of 0.2 and 0.8 respectively.
Raf-1 Physically Interacts with Rb and Regulates Its Function: a Link between Mitogenic Signaling and Cell Cycle Regulation (1998)

Cells initiate proliferation in response to growth factor stimulation, but the biochemical mechanisms linking signals received at the cell surface receptors to the cell cycle regulatory molecules are not yet clear. In this study, we show that the signaling molecule Raf-1 can physically interact with Rb and p130 proteins in vitro and in vivo and that this interaction can be detected in mammalian cells without overexpressing any component. The binding of Raf-1 to Rb occurs subsequent to mitogen stimulation, and this interaction can be detected only in proliferating cells. Raf-1 can inactivate Rb function and can reverse Rb-mediated repression of E2F1 transcription and cell proliferation efficiently. The region of Raf-1 involved in Rb binding spanned residues 1 to 28 at the N terminus, and functional inactivation of Rb required a direct interaction. Serum stimulation of quiescent human fibroblast HSF8 cells led to a partial translocation of Raf-1 into the nucleus, where it colocalized with Rb. Further, Raf-1 was able to phosphorylate Rb in vitro quite efficiently. We believe that the physical interaction of Raf-1 with Rb is a vital step in the growth factor-mediated induction of cell proliferation and that Raf-1 acts as a direct link between cell surface signaling cascades and the cell cycle machinery.
Common Genetic Variation and Human Traits (2009)

The human genome has been cracked wide open in recent years and is spilling many of its secrets. More than 100 genomewide association studies have been conducted for scores of human diseases, identifying hundreds of polymorphisms that are widely seen to influence disease risk. After many years in which the study of complex human traits was mired in false claims and methodologic inconsistencies, genomics has brought not only comprehensive representation of common variation but also welcome rigor in the interpretation of statistical evidence. Researchers now know how to properly account for most of the multiple hypothesis testing involved in mining . . .
The Tir‐binding region of enterohaemorrhagic Escherichia coli intimin is sufficient to trigger actin condensation after bacterial‐induced host cell signalling (1999)

Enterohaemorrhagic Escherichia coli (EHEC) has emerged as an important agent of diarrhoeal disease. Attachment to host cells, an essential step during intestinal colonization by EHEC, is associated with the formation of a highly organized cytoskeletal structure containing filamentous actin, termed an attaching and effacing (A/E) lesion, directly beneath bound bacteria. The outer membrane protein intimin is required for the formation of this structure, as is Tir, a bacterial protein that is translocated into the host cell and is thought to function as a receptor for intimin. To understand intimin function better, we fused EHEC intimin to a homologous protein, Yersinia pseudotuberculosis invasin, or to maltose-binding protein. The N-terminal 539 amino acids of intimin were sufficient to promote outer membrane localization of the C-terminus of invasin and, conversely, the N-terminal 489 amino acids of invasin were sufficient to promote the localization of the C-terminus of intimin. The C-terminal 181 residues of intimin were sufficient to bind mammalian cells that had been preinfected with an enteropathogenic E. coli strain that expresses Tir but not intimin. Binding of intimin derivatives to preinfected cells correlated with binding to recombinant Tir protein. Finally, the 181-residue minimal Tir-binding region of intimin, when purified and immobilized on latex beads, was sufficient to trigger A/E lesions on preinfected mammalian cells.
Haemodynamic responses and renin release during stimulation of afferent renal nerves in the cat. (1976)

1. Experiments were done on anaesthetized cats to study the effect of electrical stimulation of afferent renal nerves on the circulatory system and on the release of renin from the kidney. 2. Stimulation of afferent renal nerves over a wide range of parameters consistently elicited an increase in arterial pressure and heart rate. This response was still present in paralysed animals and was not accompanied by changes in respiration or in sympathetic autonomic activity usually associated with painful stimulation. Mesenteric and iliac vasoconstriction was observed concomitantly with the increase in arterial pressure. 3. Release of renin from the contralateral innervated kidney was not significantly changed by stimulation of afferent renal nerves. 4. The existence of renal vascular mechanoreceptors was investigated by altering renal circulation. Stenosis of the renal artery or a marked reduction in renal perfusion pressure elicited an increase in arterial pressure while stenosis of the renal vein elicited a decrease in arterial pressure. These responses, however, were not affected by denervation of the kidney and were therefore interpreted as not being due to neural mechanisms. 5. The precise nature, location and physiological role of renal receptors involved in the cardiovascular responses observed during electrical stimulation of afferent renal nerves remain to be determined.
Aptamer-Functionalized Microgel Particles for Protein Detection (2011)

Highly sensitive and multiplexed detection of clinically relevant proteins in biologically complex samples is crucial for the advancement of clinical proteomics. In recent years, aptamers have emerged as useful tools for protein analysis due to their specificity and affinity for protein targets as well as their compatibility with particle-based detection systems. In this study, we demonstrate the highly sensitive detection of human α-thrombin on encoded hydrogel microparticles functionalized with an aptamer capture sequence. We use static imaging and microfluidic flow-through analysis techniques to evaluate the detection capabilities of the microgels in sandwich-assay formats that utilize both aptamers and antibodies for the reporting of target-binding events. Buffers and reagent concentrations were optimized to provide maximum reaction efficiency while still maintaining an assay with a simple workflow that can be easily adapted to the multiplexed detection of other clinically relevant proteins. The three-dimensional, nonfouling hydrogel immobilization scaffold used in this work provides three logs of dynamic range, with a limit of detection of 4 pM using a single aptamer capture species and without the need for spacers or signal amplification.
6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer (2018)

Metastasis is the cause of death in the majority (∼90%) of malignant cancers. The oral potassium-sparing diuretic amiloride and its 5-substituted derivative 5 -N, N-(hexamethylene)amiloride (HMA) reportedly show robust antitumor/metastasis effects in multiple in vitro and animal models. These effects are likely due, at least in part, to inhibition of the urokinase plasminogen activator (uPA), a key protease determinant of cell invasiveness and metastasis. This study reports the discovery of 6-substituted HMA analogs that show nanomolar potency against uPA, high selectivity over related trypsin-like serine proteases, and minimal inhibitory effects against epithelial sodium channels (ENaC), the diuretic and antikaliuretic target of amiloride. Reductions in lung metastases were demonstrated for two analogs in a late-stage experimental mouse metastasis model, and one analog completely inhibited formation of liver metastases in an orthotopic xenograft mouse model of pancreatic cancer. The results support further evaluation of 6-substituted HMA derivatives as uPA-targeting anticancer drugs.
A Self-Assembly Approach to the Fabrication of Patterned, Two-Dimensional Arrays of Microlenses of Organic Polymers (2001)

Arrayed microlenses are used in a variety of applications that involve miniaturized optical components, such as optical communications systems, facsimile machines, laser printers, and other digitized information storage or processing devices. Here, a self-assembly method is presented which facilitates the production of 2D arrays of monodispersed polystyrene beads (microlenses) with well-controlled lateral dimensions in the range of 1–10 μm (see Figure).
Antiretroviral Drug Resistance Testing in Adults Infected with Human Immunodeficiency Virus Type 1: 2003 Recommendations of an International AIDS Society–USA Panel (2003)

New information about the benefits and limitations of testing for resistance to human immunodeficiency virus (HIV) type 1 (HIV-1) drugs has emerged. The International AIDS Society-USA convened a panel of physicians and scientists with expertise in antiretroviral drug management, HIV-1 drug resistance, and patient care to provide updated recommendations for HIV-1 resistance testing. Published data and presentations at scientific conferences, as well as strength of the evidence, were considered. Properly used resistance testing can improve virological outcome among HIV-infected individuals. Resistance testing is recommended in cases of acute or recent HIV infection, for certain patients who have been infected as long as 2 years or more prior to initiating therapy, in cases of antiretroviral failure, and during pregnancy. Limitations of resistance testing remain, and more study is needed to refine optimal use and interpretation.
Ceramide-mediated growth inhibition and CAPP are conserved in Saccharomyces cerevisiae (1993)

Ceramide is emerging as a potential physiologic regulator of growth and differentiation in mammalian cells. This regulation may be mediated through the action of a serine/threonine ceramide-activated protein phosphatase (CAPP). In this study, the existence of a ceramide-mediated pathway of cell regulation in Saccharomyces cerevisiae was investigated. Incubating exponentially growing S. cerevisiae cells with 1-20 microM cell-permeable ceramide (C2-ceramide) produced a dose-dependent inhibition of proliferation. A number of other lipids and detergents, such as arachidonate, oleate, Triton X-100, dioctanoylglycerol, and phenylaminoalcohol ceramide analogs, were largely ineffective, demonstrating the specificity of the response. Stereospecificity was demonstrated, in that the D enantiomer of erythro-C2-ceramide was more potent than the L enantiomer. More dramatically, a highly specific structural requirement for C2-ceramide was demonstrated, in that 1-12 microM C2-dihydroceramide was completely ineffective at inhibiting growth. Since C2-dihydroceramide lacks the 4-5 trans double bond present in C2-ceramide, this suggests that the antiproliferative properties of C2-ceramide depend upon the presence of the double bond. This raises an interesting possibility; the dehydrogenase responsible for introduction of the double bond during endogenous ceramide synthesis may regulate cell growth by controlling the cellular concentrations of dihydroceramide and ceramide. The oxygenase responsible for introduction of the final hydroxyl group in phytoceramide could provide a similar regulatory function in yeast. The potential role of CAPP in ceramide action in yeast was investigated next. Crude extracts of S. cerevisiae also contained a ceramide-dependent serine/threonine phosphatase activity, which was sensitive to inhibition by okadaic acid. This enzyme exhibited stereospecificity and structural requirements identical to that of the ceramide-induced growth inhibition. We conclude that both the growth-inhibitory response to ceramide and CAPP activity are conserved in S. cerevisiae. The identical stereochemical and structural requirements in both the biological and phosphatase assays suggest that the anti-proliferative effects of ceramide in yeast may be mediated in part through the action of CAPP.
Mechanical ventilation with high tidal volume induces inflammation in patients without lung disease (2010)

NCT00935896.
Expression of Zm13, a pollen specific maize protein, in Escherichia coli reveals IgE‐binding capacity and allergenic potential (1996)

Plant proteins belong to the most frequent elicitors of type I allergic symptoms in industrialized countries. Several relevant plant allergens have been found to be either specifically expressed or highly upregulated in mature pollen. The cDNA coding for a pollen specific maize protein, Zm13, shows significant sequence homology with a number of pollen or anther specific proteins from monocot and dicot plants as well as with recently described allergens from olive and rye grass. To test whether the Zm13 protein might possess IgE-binding capacity, Zm13 was expressed in E. coli. The coding region of Zm13 was PCR amplified from a genomic clone and expressed as a glutathione-S-transferase fusion protein. The recombinant Zm13 fusion protein bound a Zm13 specific rabbit antiserum and reacted with serum IgE from grass pollen allergic patients indicating that Zm13 and homologous proteins represent a family of conserved plant allergens.
Direct deprotected glycosyl–asparagine ligation (2006)

A simple and efficient synthesis of N-linked glycoamino acids and glycopeptides from deprotected sugars using the Staudinger reaction.
Use of A‐type CpG oligodeoxynucleotides as an adjuvant in allergen‐specific immunotherapy in humans: a phase I/IIa clinical trial (2009)

The subcutaneous application of HDM allergen, together with A-type CpG ODN packaged into VLP, was safe. All patients achieved practically complete alleviation of allergy symptoms after 10 weeks of immunotherapy. This promising clinical outcome calls for larger placebo-controlled phase II studies.
Impact of Stress-Dependent Matrix and Fracture Properties on Shale Gas Production (2017)

Unconventional shale gas production is often characterized by a short period of high production followed by a rapid decline in the production rate. Given the high costs of hydraulic fracturing and horizontal drilling, it is critical to identify the mechanisms behind the production loss. The existing shale gas production models often assume constant matrix permeability. However, laboratory observations show that matrix permeability can decrease significantly with increasing effective stress, which highlights the necessity of considering the stress-dependent properties of shale matrix in production analysis. Moreover, the compaction of pore space will also increase the matrix permeability by enhancing the gas-slippage effect. In this paper, a matrix permeability model which couples the effect of pore volume compaction and non-Darcy slip flow is derived. Numerical simulations are conducted to understand the role of matrix permeability evolution during production. Changes of fractures’ permeability and contact area during depletion process are also taken into account. The results indicate that the loss of fracture permeability has a greater impact at the early stage of the depletion process, while matrix permeability evolution is more important for the long-term production.
Intramolecular cyclization of Mannich reaction for synthesis of pyrimido[2,1‐b]‐1,3,5‐tiadiazines (2010)

Abstract magnified image Reaction of 6‐aryl‐5‐cyano‐2‐mercapto‐3,4‐dihydropyrimidin‐4‐ones with formaldehyde and primary amines in suitable solvent via a double Mannich reaction gave the corresponding 8‐aryl‐7‐cyano‐3‐ N ‐substituted‐pyrimido[2,1‐b]‐1,3,5‐thiadiazin‐6‐ones rather than the isomeric products 6‐aryl‐7‐cyano‐3‐N‐substituted‐pyrimido[2,1‐b]‐1,3,5‐thiadiazin‐8‐ones. The cyclization method was found to be the most favored for the formation of the linear products rather than the angular isomers. This was confirmed not only by using spectral analysis and molecular mechanical calculations but also by X‐ray single crystal structure determination. J. Heterocyclic Chem., (2010).
Antiinflammatory effects of bromodomain and extraterminal domain inhibition in cystic fibrosis lung inflammation (2016)

Significant morbidity in cystic fibrosis (CF) results from chronic lung inflammation, most commonly due to <i>Pseudomonas aeruginosa</i> infection. Recent data suggest that IL-17 contributes to pathological inflammation in the setting of abnormal mucosal immunity, and type 17 immunity-driven inflammatory responses may represent a target to block aberrant inflammation in CF. Indeed, transcriptomic analysis of the airway epithelium from CF patients undergoing clinical bronchoscopy revealed upregulation of IL-17 downstream signature genes, implicating a substantial contribution of IL-17-mediated immunity in CF lungs. Bromodomain and extraterminal domain (BET) chromatin modulators can regulate T cell responses, specifically Th17-mediated inflammation, by mechanisms that include bromodomain-dependent inhibition of acetylated histones at the <i>IL17</i> locus. Here, we show that, in vitro<i>,</i> BET inhibition potently suppressed Th17 cell responses in explanted CF tissue and inhibited IL-17-driven chemokine production in human bronchial epithelial cells. In an acute <i>P. aeruginosa</i> lung infection murine model, BET inhibition decreased inflammation, without exacerbating infection, suggesting that BET inhibition may be a potential therapeutic target in patients with CF.
Ghrelin against alendronate-induced gastric damage in rats (2005)

Alendronate sodium, a primary amino bisphosphonate, is widely used in the treatment of various diseases that are associated with bone resorption, such as postmenopausal osteoporosis and Paget's disease of bone. Although the adverse effects of biphosphonates on the gastrointestinal system have been demonstrated in experimental and clinical studies, the exact mechanisms underlying this damage are not clear yet. Ghrelin, a 28 amino acid peptide produced predominantly by the stomach, was shown to exert a potent protective action on the stomach of rats exposed to ethanol or stress. Our objective was to evaluate the possible anti-oxidant and anti-inflammatory effects of ghrelin against alendronate-induced gastric damage. Wistar albino rats were administered alendronate (20 mg/kg) by gavage for 4 days, along with either ghrelin (10 ng/kg per day) or saline given i.p. After decapitation, stomach tissues were removed for the determination of malondialdehyde (MDA) and glutathione (GSH) levels, myeloperoxidase (MPO) activity and tissue collagen content, while the extent of tissue damage was analyzed microscopically. Formation of reactive oxygen species was determined by chemiluminesence using a luminol probe in fresh gastric tissues. Serum tumor necrosis factor (TNF-alpha) and lactate dehydrogenase levels were assessed in trunk blood. Oral administration of alendronate-induced significant gastric damage, accompanied by increased MPO activity, collagen content, MDA and luminol levels (P < 0.01-P < 0.001), while tissue GSH was decreased (P < 0.01). On the other hand, ghrelin treatment reversed these alterations (P < 0.05-P < 0.001) as well as elevating serum TNF-alpha levels significantly (P < 0.001). The findings of the present study suggest that alendronate induces oxidative gastric damage by a local irritant effect, and ghrelin ameliorates this damage by its possible antioxidant and anti-inflammatory properties.
Textbook of polymer science (1971)

The Science of Large Molecules POLYMERIZATION Step-Reaction (Condensation) Polymerization Radical Chain (Addition) Polymerization Ionic and Coordination Chain (Addition) Polymerization Copolymerization Polymerization Conditions and Polymer Reactions CHARACTERIZATION Polymer Solutions Measurement of Molecular Weight and Size Analysis and Testing of Polymers STRUCTURE AND PROPERTIES Morphology and Order in Crystalline Polymers Rheology and the Mechanical Properties of Polymers Polymer Structure and Physical Properties PROPERTIES OF COMMERICAL POLYMERS Hydrocarbon Plastics and Elastomers Other Carbon-Chain Polymers Heterochain Thermoplastics Thermosetting Resins POLYMER PROCESSING Plastics Technology Fiber Technology Elastomer Technology Appendixes Author and Subject Indexes.
Effects of Fixative and Fixation Time on the Extraction and Polymerase Chain Reaction Amplification of RNA from Paraffin-Embedded Tissue (1994)

A number of reports have indicated that RNA recovered from paraffin-embedded tissue can be used as a substrate in the polymerase chain reaction (PCR). Although it is established that RNA in paraffin-embedded tissue undergoes significant degradation, the specific contributions of different fixatives and fixation times to this degradation are not known. Mouse splenic tissue was harvested and fixed immediately for 2, 8, or 24 h in either formalin, Omnifix II, or Carnoy's fixative and then processed and embedded in paraffin. RNA was extracted from deparaffinized cubes of tissue using an adaptation of the technique described by Chomczynski and Sacchi. RNA was reverse transcribed using a random hexamer primed reaction. PCR amplification for cDNAs of the housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and hypoxanthine phosphoribosyltransferase (HPRT) mRNAs was then performed. Although GAPDH amplification is used routinely on fresh and frozen tissues, we show that the presence of DNA contamination in the RNA preparations limits its usefulness in paraffin-embedded tissue. Amplifiable HPRT mRNA sequences were detected in nine of 12 samples fixed in Omnifix II, in four of 12 samples fixed in Carnoy's fixative, and in none of 12 formalin-fixed samples. Because of primer selection to preclude amplification of genomic HPRT, DNA contamination is not an issue when HPRT is amplified. Thus, HPRT represents the control system of choice for the evaluation of RNA in PET. The techniques described provide a rapid, uniform, and reproducible method of obtaining RNA from PET for molecular analysis, but they indicate limited utility for retrospective analysis of archival tissues.
The effect of hypotonicity, glutamine, and glycine on red cell preservation (1997)

Cell swelling induced in RBCs after collection appears to improve preservation. Ammonia and phosphate enhance RBC ATP maintenance. Glycine decrease the formation of ammonia by RBCs stored in a hypotonic medium.