gebhart/patrepeval huggingface dataset:
Temperature-sensitive binding of alpha-glucans by Bacillus stearothermophilus (1986)

Bacillus stearothermophilus was found to bind strongly to starch and related alpha-glucans at 25 degrees C but not at 55 degrees C. The binding at the lower temperature could be assayed either by binding of fluorescein-labeled amylopectin to washed cell suspensions or through the reversible retention of bacteria by affinity chromatography in matrices containing immobilized starch. The bacteria exhibited amylopectin-dependent agglutination. The binding and agglutination were highest in bacteria grown on substrates containing alpha-1,4-glucosidic linkages such as maltose or dextrins. The binding affinity of cells was highest for maltohexaose, lower for maltose, and low or undetectable for glucose, isomaltose, cellobiose, or lactose. The reduced binding at the higher temperature was due to the rapid breakdown of the alpha-glucosides. The bacteria exhibited an extracellular alpha-amylase activity as well as a cell-associated alpha-glucosidase with high activity at 55 degrees C but undetectable activity at 25 degrees C. The inducibility, specificity, and protease sensitivity of the thermophilic alpha-glucosidase in whole cells were similar to those of the binding activity assayed at the lower temperature. Further evidence linking the binding and alpha-glucosidase activities came from a mutant, selected through affinity chromatography, which was reduced in starch binding at room temperature and also reduced in membrane-associated alpha-glucosidase activity at 55 degrees C. These results suggest a novel survival mechanism whereby a bacterium attaches to a macromolecular substrate under nonoptimal growth conditions for possible utilization upon a shift to more favorable conditions.
Helicobacter pylorienter and survive within multivesicular vacuoles of epithelial cells (2002)

Although intracellular Helicobacter pylori have been described in biopsy specimens and in cultured epithelial cells, the fate of these bacteria is unknown. Using differential interference contrast (DIC) video and immunofluorescence microscopy, we document that a proportion of cell-associated H. pylori enter large cytoplasmic vacuoles, where they remain viable and motile and can survive lethal concentrations of extracellular gentamicin. Entry into vacuoles occurs in multiple epithelial cell lines including AGS gastric adenocarcinoma, Caco-2 colon adenocarcinoma and MDCK kidney cell line, and depends on the actin cytoskeleton. Time-lapse microscopy over several hours was used to follow the movement of live H. pylori within vacuoles of a single cell. Pulsed, extracellular gentamicin treatments show that the half-life of intravacuolar bacteria is on the order of 24 h. Viable H. pylori repopulate the extracellular environment in parallel with the disappearance of intravacuolar bacteria, suggesting release from the intravacuolar niche. Using electron microscopy and live fluorescent staining with endosomal dyes, we observe that H. pylori-containing vacuoles are similar in morphology to late endosomal multivesicular bodies. VacA is not required for these events, as isogenic vacA- mutants still enter and survive within the intravacuolar niche. The exploitation of an intravacuolar niche is a new aspect of the biological life cycle of H. pylori that could explain the difficulties in eradicating this infection.
Definitive endoderm of the mouse embryo: Formation, cell fates, and morphogenetic function (2006)

The endoderm is one of the primary germ layers but, in comparison to ectoderm and mesoderm, has received less attention. The definitive endoderm forms during gastrulation and replaces the extraembryonic visceral endoderm. It participates in the complex morphogenesis of the gut tube and contributes to the associated visceral organs. This review highlights the role of the definitive endoderm as a source of patterning cues for the morphogenesis of other germ-layer tissues, such as the anterior neurectoderm and the pharyngeal region, and also emphasizes the intricate patterning that the endoderm itself undergoes enabling the acquisition of regionalized cell fates.
A Design of One-Time Password Mechanism Using Public Key Infrastructure (2008)

One-time password mechanism solves password problems like password conjecture and wiretapping that can occur by using the same password several times repeatedly. However, such one-time password mechanism also is exposed to various attacks, and is vulnerable in matters of confidentiality and security protection, the most important elements of security depending on mechanism. This paper solves user disguise problem by authenticating users with the use of public key infrastructure, and guarantees integrity by generating password by applying session identifier L and random value R to hash function in every applicable session. Additionally, to enhance security while transferring the generated password, the mechanism digital signature the password with user's private key, encode it again with service provider's public key, and guarantee denial prevention by requesting the server authentication while being able to verify the identity of user. Therefore in this paper proposes one-time password mechanism that has enhanced security using public key infrastructure to prevent integrity problem due to birthday attack and hash collision problem occurring from hash function. Comparison and analysis of existing one-time password mechanism will tell of the excellence of this paper.
High-resolution dose–response screening using droplet-based microfluidics (2011)

A critical early step in drug discovery is the screening of a chemical library. Typically, promising compounds are identified in a primary screen and then more fully characterized in a dose-response analysis with 7-10 data points per compound. Here, we describe a robust microfluidic approach that increases the number of data points to approximately 10,000 per compound. The system exploits Taylor-Aris dispersion to create concentration gradients, which are then segmented into picoliter microreactors by droplet-based microfluidics. The large number of data points results in IC(50) values that are highly precise (± 2.40% at 95% confidence) and highly reproducible (CV = 2.45%, n = 16). In addition, the high resolution of the data reveals complex dose-response relationships unambiguously. We used this system to screen a chemical library of 704 compounds against protein tyrosine phosphatase 1B, a diabetes, obesity, and cancer target. We identified a number of novel inhibitors, the most potent being sodium cefsulodine, which has an IC(50) of 27 ± 0.83 μM.
Measurement of the Seebeck coefficient and the thermal conductivity of SiC/Cu by AC method. (1996)

An AC method of simultaneous measurment for the Seebeck coefficient and the thermal conductivity is proposed. This method shortens measurement time compared with conventional methods. In this work, the thermoelectric properties of the SiC/Cu are measured by this method at room temperature. The Seebeck coefficient obtained by the AC method (1.4-4.9×10-4V/K) is comparable to the data obtained by the DC method (1.8-3.8×10-4V/K). The thermal conductivity obtained by the AC method (78-86W/mK) is in good agreement with the data obtained by the photo pyro electric (PPE) method using the poly vinyliden difloride (PVF2) as the transducer (53-80W/mK).
Centromere Satellites From Arabidopsis Populations: Maintenance of Conserved and Variable Domains (2003)

The rapid evolution of centromere sequences between species has led to a debate over whether centromere activity is sequence-dependent. The Arabidopsis thaliana centromere regions contain approximately 20,000 copies of a 178-bp satellite repeat. Here, we analyzed satellites from 41 Arabidopsis ecotypes, providing the first broad population survey of satellite variation within a species. We found highly conserved segments and consistent sequence lengths in the Arabidopsis satellites and in the published collection of human alpha-satellites, supporting models for a functional role. Despite this conservation, polymorphisms are significantly enriched at some sites, yielding variation that could restrict binding proteins to a subset of repeat monomers. Some satellite regions vary considerably; at certain bases, consensus sequences derived from each ecotype diverge significantly from the Arabidopsis consensus, indicating substitutions sweep through a genome in less than 5 million years. Such rapid changes generate more variation within the set of Arabidopsis satellites than in genes from the chromosome arms or from the recombinationally suppressed centromere regions. These studies highlight a balance between the mechanisms that maintain particular satellite domains and the forces that disperse sequence changes throughout the satellite repeats in the genome.
Critical Role for TrkB Kinase Function in Anoikis Suppression, Tumorigenesis, and Metastasis (2007)

Anoikis, or cell death induced by cell detachment, provides protection against the metastatic spread of tumor cells. We have previously shown that the neurotrophic receptor tyrosine kinase TrkB suppresses anoikis in rat intestinal epithelial cells and renders them highly tumorigenic and metastatic. Because TrkB is overexpressed in several aggressive human cancers, first attempts are being made to target TrkB in cancer therapy. However, the mechanisms underlying TrkB-mediated anoikis suppression, tumorigenesis, and metastasis still remain largely elusive. Although, to date, most attempts to neutralize TrkB in tumors aim to inactivate its kinase activity, it is unclear whether TrkB kinase activity is required for its oncogenic functions. Indeed, it has been suggested that also other properties of the receptor contribute to functions that are relevant to tumor cell survival. Specifically, several adhesion motifs reside within the extracellular domains of TrkB. In line with this, TrkB-expressing epithelial cells form large cellular aggregates in suspension cultures, possibly facilitating tumor cell survival. Therefore, we set out to study the relative contributions of TrkB's kinase activity and its adhesion domains to anoikis suppression and oncogenicity. On the basis of a structure-function analysis, we report that TrkB kinase activity is required and, unexpectedly, also sufficient for anoikis suppression, tumor formation, and experimental metastasis. Thus, TrkB can act tumorigenically independent of its adhesion motifs. These results suggest that targeting the enzymatic activity of TrkB might be beneficial in cancer therapy.
Senneville et al. (Clin Infect Dis 2009; 48:888-93) (2006)

We report an unusual cluster of Burkholderia cepacia in patients. Environmental cultures identified indigo-carmine dye used in enteral feeding as the reservoir. Compared with the controls, the cases were significantly more likely to have received tube feedings tinted with this dye. This outbreak was terminated with the removal of the dye from hospital inventory.
A new algorithm to correct fish-eye- and strong wide-angle-lens-distortion from single images (2002)

The use of super-wide angle and fish-eye lenses causes strong distortions in the resulting images. A methodology for the correction of distortions in these cases using only single images and linearity of imaged objects is presented. Contrary to most former algorithms, the algorithm discussed here does not depend on information about the real world co-ordinates of matching points. Moreover reference points determination and camera calibration is not required in this case. The algorithm is based on circle fitting. It requires only the possibility of the extraction of distorted image points from straight lines in the 3D scene. Further, the actual distortion must approximately fit the chosen distortion model. For most fish-eye lenses appropriate distortion correction results can be obtained.
Tandem chirped quasi-phase-matching grating optical parametric amplifier design for simultaneous group delay and gain control (2005)

We present a broadband optical parametric amplifier design using tapered gain and tandem chirped quasi-phase-matching gratings to obtain flat gain and group-delay spectra suitable for applications such as ultrashort-pulse amplification and fiber-optic communication systems. Although a tapered-gain amplifier consisting of a single chirped grating can provide constant gain over a wide frequency range, it cannot be used to control the group delay across the spectrum. We propose controlling both the gain and the group delay profiles using a two-stage amplifier configuration, in which the idler of the first is used as the input signal of the second.
Functional Characterization of Three Mutations of the Endothelin B Receptor Gene in Patients With Hirschsprung’s Disease: Evidence for Selective Loss of Gi Coupling (2001)

The absence of the P383L mutant receptor from the membrane clearly indicates that this mutation could be involved in HSCR. The G57S and R319W mutant receptors, despite their normal coupling to Gaq, have a defect in the Galphai signaling pathway and the G57S mutation couples to Galphas. These observations allow us to hypothesize that cAMP signaling might be involved in the differenciation of neural cells in the bowel.
Foveated 3D graphics (2012)

We exploit the falloff of acuity in the visual periphery to accelerate graphics computation by a factor of 5-6 on a desktop HD display (1920x1080). Our method tracks the user's gaze point and renders three image layers around it at progressively higher angular size but lower sampling rate. The three layers are then magnified to display resolution and smoothly composited. We develop a general and efficient antialiasing algorithm easily retrofitted into existing graphics code to minimize "twinkling" artifacts in the lower-resolution layers. A standard psychophysical model for acuity falloff assumes that minimum detectable angular size increases linearly as a function of eccentricity. Given the slope characterizing this falloff, we automatically compute layer sizes and sampling rates. The result looks like a full-resolution image but reduces the number of pixels shaded by a factor of 10-15. We performed a user study to validate these results. It identifies two levels of foveation quality: a more conservative one in which users reported foveated rendering quality as equivalent to or better than non-foveated when directly shown both, and a more aggressive one in which users were unable to correctly label as increasing or decreasing a short quality progression relative to a high-quality foveated reference. Based on this user study, we obtain a slope value for the model of 1.32-1.65 arc minutes per degree of eccentricity. This allows us to predict two future advantages of foveated rendering: (1) bigger savings with larger, sharper displays than exist currently (e.g. 100 times speedup at a field of view of 70° and resolution matching foveal acuity), and (2) a roughly linear (rather than quadratic or worse) increase in rendering cost with increasing display field of view, for planar displays at a constant sharpness.
Cellular Therapies for Myocardial Infarct Repair (2002)

Despite significant advances in prevention, diagnosis,and treatment, myocardial infarction remains the numberone cause of death in the United States and other industrialized nations. Myocardial infarctions almost alwaysresult from complications of atherosclerosis, typicallyarising when an atherosclerotic plaque ruptures, leadingto thrombotic occlusion of a major coronary artery. Myocardium has one of the highest metabolic rates of anytissue in the body, making it very susceptible to injury byischemia (deprivation of blood flow). Irreversible ischemic injury (defined as cell death occurring despitereperfusion) begins within 20 minutes of severe ischemiain vivo in all species studied. A wavefront of cell deaththen progresses from subendocardium to subepicardium(Reimer et al. 1977; Reimer and Jennings 1979). Thetime to completion of irreversible injury varies withspecies, from 1–2 hours in the mouse (Michael et al.1999) to 3–6 hours in the dog (Reimer and Jennings1979). Although cardiac myocytes are the most ischemiasensitive cell population, prolonged ischemia also killsmost of the fibroblasts and vascular cells in the tissue...
A Toolkit and Methods for Internet Firewalls. (1994)

As the number of businesses and government agencies connecting to the Internet continues to increase, the demand for Internet firewalls — points of security guarding a private network from intrusion — has created a demand for reliable tools from which to build them. We present the TIS Internet Firewall Toolkit, which consists of software modules and configuration guidelines developed in the course of a broader ARPAsponsored project. Components of the toolkit, while designed to work together, can be used in isolation or can be combined with other firewall components. The Firewall Toolkit software runs on UNIX ® systems using TCP/IP with the Berkeley socket interface. We describe the Firewall Toolkit and the reasoning behind some of its design decisions, discuss some of the ways in which it may be configured, and conclude with some observations as to how it has served in practice. Overview Computer networks by their very nature are designed to allow the flow of information. Network technology is such that, today, you can sit at a workstation in Maryland, and have a process connected to a system in London, with files mounted from a system in California, and be able to do your work just as if all of the systems were in the same room as your computer. Impeding the free flow of data is contrary to the basic functionality of the network, but the free flow of information is contrary to the rules by which companies and governments need to conduct business. Proprietary information and sensitive data must be kept insulated from unauthorized access yet security must have a minimal impact on the overall useability of the network.
Live Simian Immunodeficiency Virus Vaccine Correlate of Protection: Local Antibody Production and Concentration on the Path of Virus Entry (2014)

We sought design principles for a vaccine to prevent HIV transmission to women by identifying correlates of protection conferred by a highly effective live attenuated SIV vaccine in the rhesus macaque animal model. We show that SIVmac239Δnef vaccination recruits plasma cells and induces ectopic lymphoid follicle formation beneath the mucosal epithelium in the rhesus macaque female reproductive tract. The plasma cells and ectopic follicles produce IgG Abs reactive with viral envelope glycoprotein gp41 trimers, and these Abs are concentrated on the path of virus entry by the neonatal FcR in cervical reserve epithelium and in vaginal epithelium. This local Ab production and delivery system correlated spatially and temporally with the maturation of local protection against high-dose pathogenic SIV vaginal challenge. Thus, designing vaccines to elicit production and concentration of Abs at mucosal frontlines could aid in the development of an effective vaccine to protect women against HIV-1.
Neutrophil‐Derived Oxidative Stress After Myocardial Ischemia Induced by Incremental Atrial Pacing (1998)

We studied the effect of atrial pacing-induced myocardial ischemia on the generation of oxygen free radicals (OFR) in 8 patients with verified coronary artery disease (CAD) and in a control group of 4 patients without coronary atherosclerosis. Myocardial ischemia was measured metabolically by simultaneous lactate sampling from coronary sinus (CS) and arterial blood. Generation of OFR from purified viable polymorphonuclear neutrophils (PMN) was assessed by means of the chemiluminescence (CL) method. At peak pacing, 7 of 8 patients with CAD exhibited transient myocardial ischemia (mean lactate extraction ratio at rest: 23.6 +/- 7.7 vs 5.21 +/- 5.1% at peak pacing, p = 0.012). In these patients, unstimulated PMN harvested from the CS depicted a significant increase of luminol-enhanced CL (from 1.06 +/- 0.54 to 2.15 +/- 1.28 cpm x 10(5), p = 0.012) after atrial pacing. There was no additional effect from further ex vivo stimulation with phorbol myristate acetate. This finding underscores the role of myocardial ischemia as a potent endogenous activator of PMN function and may have implications in the pathogenesis and progression of atherosclerosis.
Spontaneous Hypercholesterolemia and Arterial Lesions in Mice Lacking Apolipoprotein E (1992)

Apolipoprotein E (apoE) is a ligand for receptors that clear remnants of chylomicrons and very low density lipoproteins. Lack of apoE is, therefore, expected to cause accumulation in plasma of cholesterol-rich remnants whose prolonged circulation should be atherogenic. ApoE-deficient mice generated by gene targeting were used to test this hypothesis and to make a mouse model for spontaneous atherosclerosis. The mutant mice had five times normal plasma cholesterol, and developed foam cell-rich depositions in their proximal aortas by age 3 months. These spontaneous lesions progressed and caused severe occlusion of the coronary artery ostium by 8 months. The severe yet viable phenotype of the mutants should make them valuable for investigating genetic and environmental factors that modify the atherogenic process.
Bardoxolone methyl analogs RTA 405 and dh404 are well tolerated and exhibit efficacy in rodent models of Type 2 diabetes and obesity (2013)

Bardoxolone methyl and related triterpenoids are well tolerated and efficacious in numerous animal models potentially relevant to patients with Type 2 diabetes and chronic kidney disease. These agents enhance glucose control and regulate lipid accumulation in rodent models of diabetes and obesity, and improve renal function, reduce inflammation, and prevent structural injury in models of renal disease. However, a recent study in Zucker diabetic fatty (ZDF) rats noted poor tolerability with the bardoxolone methyl analog RTA 405 within 1 mo after treatment initiation, although this study was confounded in part by the use of an impure RTA 405 batch. To investigate these discordant observations, the present studies were conducted to further characterize triterpenoids in rodent models of diabetes and obesity. A follow-up study was conducted in ZDF rats with two related triterpenoids (RTA 405 and dh404) for 1.5 mo. Consistent with previous rodent experience, and in contrast to the more recent ZDF report, ZDF rats administered RTA 405 or dh404 exhibited no adverse clinical signs, had laboratory values similar to controls, and exhibited no evidence of adverse liver or kidney histopathology. Additionally, RTA 405 was well tolerated in streptozotocin-induced Type 1 diabetic rats and high-fat-diet-induced obese mice. The present results are consistent with the overall published body of data obtained with triterpenoids and provide further evidence that these molecules are well tolerated without adverse effects on hepatobiliary or renal function in rodent models of diabetes and obesity.