gebhart/patrepeval huggingface dataset:
Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase. (1993)

Sialidases (EC 3.2.1.18 or neuraminidases) remove sialic acid from sialoglycoconjugates, are widely distributed in nature, and have been implicated in the pathogenesis of many diseases. The three-dimensional structure of influenza virus sialidase is known, and we now report the three-dimensional structure of a bacterial sialidase, from Salmonella typhimurium LT2, at 2.0-A resolution and the structure of its complex with the inhibitor 2-deoxy-2,3-dehydro-N-acetylneuraminic acid at 2.2-A resolution. The viral enzyme is a tetramer; the bacterial enzyme, a monomer. Although the monomers are of similar size (approximately 380 residues), the sequence similarity is low (approximately 15%). The viral enzyme contains at least eight disulfide bridges, conserved in all strains, and binds Ca2+, which enhances activity; the bacterial enzyme contains one disulfide and does not bind Ca2+. Comparison of the two structures shows a remarkable similarity both in the general fold and in the spatial arrangement of the catalytic residues. However, an rms fit of 3.1 A between 264 C alpha atoms of the S. typhimurium enzyme and those from an influenza A virus reflects some major differences in the fold. In common with the viral enzyme, the bacterial enzyme active site consists of an arginine triad, a hydrophobic pocket, and a key tyrosine and glutamic acid, but differences in the interactions with the O4 and glycerol groups of the inhibitor reflect differing kinetics and substrate preferences of the two enzymes. The repeating "Asp-box" motifs observed among the nonviral sialidase sequences occur at topologically equivalent positions on the outside of the structure. Implications of the structure for the catalytic mechanism, evolution, and secretion of the enzyme are discussed.
The Demise and Rebirth of Polio—A Modern Phoenix? (2008)

In 1991, one of us wrote in a commentary that eradication of polio by the year 2000 would be a magnificent gift from the 20th century to future generations of children [1]. That remains no less true today. However, although the burden ofpolio has been dramatically lowered by the intense effort to enact its ultimate demise, the goal of eradication has not yet been achieved. The polio-eradication effort is led by a dedicated team at the World Health Organization that has repeatedly examined the reasons for the delay in achieving the eradication goal and modified its operational strategies-although the primary tool remains repeated mass immunization with live Sabin strain oral
Polycrystalline Carbon: A Novel Material for Gate Electrodes in MOS Technology (1993)

Polycrystalline carbon is proposed as a potential candidate for the gate material for submicron VLSI devices. Fine grained polycarbon films with significantly lower resistivity than polysilicon have been deposited on silicon dioxide. Well behaved capacitance-voltage and oxide breakdown characteristics are observed. Tunneling current measurements on these films indicate lower depletion effects in polycarbon compared to polysilicon. PMOSFETs have been fabricated with carbon gates in a conventional silicon process line to demonstrate the compatibility of polycrystalline carbon with existing silicon processes.
Recombinant human macrophage colony-stimulating factor reduces plasma cholesterol and carrageenan granuloma foam cell formation in Watanabe heritable hyperlipidemic rabbits. (1994)

Previous studies have demonstrated that short-term administration of recombinant human macrophage colony-stimulating factor (rhM-CSF) reduces plasma cholesterol in rabbits, nonhuman primates, and human subjects. This study extended the dose schedule of rhM-CSF to 8 weeks of continuous intravenous infusion (CIV) in the Watanabe heritable hyperlipidemic (WHHL) rabbit and expanded the scope to include an assessment of macrophage-derived foam cell development. Ten male WHHL rabbits were injected subcutaneously with 1% carrageenan to promote formation of a macrophage-rich foam cell granuloma. Rabbits were infused with either vehicle or rhM-CSF at 100 micrograms/kg per day (weeks 1 through 5) followed by 300 micrograms/kg per day (weeks 6 through 8). rhM-CSF (100 micrograms/kg per day) decreased total plasma cholesterol by 45% at 2 weeks compared with controls. The gradual return of plasma cholesterol toward control concentrations over the subsequent 3 weeks correlated with the appearance of circulating antibodies specific to rhM-CSF. Granuloma weights at harvest (8 weeks after infusion) were significantly lower (2.8 +/- 0.7 g, mean +/- SEM) in rhM-CSF-treated rabbits relative to controls (7.1 +/- 1.5 g, P < .05). Granulomas from rabbits treated with rhM-CSF contained lower concentrations of cholesterol (2.0 +/- 0.7 versus 6.1 +/- 1.5 micrograms/mg, P < .03) and cholesteryl ester (0.7 +/- 0.4 versus 3.9 +/- 1.2 micrograms/mg, P < .03) than controls. Histological evaluation revealed that granulomas from the rhM-CSF-treated rabbits were more fibrous and contained fewer foam cells than those from controls.(ABSTRACT TRUNCATED AT 250 WORDS)
Chimeric Chickens and Their Use in Manipulation of the Chicken Genome (1993)

Germline chimeric chickens can be made by injecting dispersed cells from Stage X blastoderms into recipient embryos at an equivalent stage of development. Colonization of the chimera by donor-derived cells is facilitated when the recipient embryo is compromised by exposure to irradiation prior to injection of the donor cells. Donor cells can be genetically manipulated by lipofection-mediated gene transfer before they are introduced into the recipient. The genetic modification is expressed in the ectoderm, mesoderm, and endoderm of the chimera after incubation for 96 h. Donor cells can also be cultured as dispersed cells in a monolayer or as whole-embryo explants for at least 48 h before transfer into recipients and retain the ability to enter both somatic and germline tissues in the resulting chimera. A strategy is proposed for the production of transgenic chickens using lipofection-mediated gene transfer to blastoderm cells isolated from Stage X embryos, which are subsequently injected into compromised recipients to yield a germline chimera.
Electronic structures and magnetic properties of Fe2P, Co2P and CoMnP (1988)

The electronic structures of the compounds Fe2P, Co2P and CoMnP are calculated by the LMTO method within the LSD approximation, not only for the orthorhombic structure but also for the hexagonal structure. The paramagnetic DOS are very similar for both structures. The values of the paramagnetic DOS at the Fermi level allow us to predict that Co2P exhibits ferromagnetism only in the hexagonal structure and that Fe2P exhibits ferromagnetism in both crystal structures. The theoretical results for the magnetic properties of CoMnP are in agreement with the experimental results. The site preference is also discussed together with the electron transfer from P atoms to 3d atoms.
Real-Time Urban Monitoring Using Cell Phones: A Case Study in Rome (2010)

This paper describes a new real-time urban monitoring system. The system uses the Localizing and Handling Network Event Systems (LocHNESs) platform developed by Telecom Italia for the real-time evaluation of urban dynamics based on the anonymous monitoring of mobile cellular networks. In addition, data are supplemented based on the instantaneous positioning of buses and taxis to provide information about urban mobility in real time, ranging from traffic conditions to the movements of pedestrians throughout the city. This system was exhibited at the Tenth International Architecture Exhibition of the Venice Biennale. It marks the unprecedented monitoring of a large urban area, which covered most of the city of Rome, in real time using a variety of sensing systems and will hopefully open the way to a new paradigm of understanding and optimizing urban dynamics.
Adaptive routing and load balancing of ephemeral connections (2002)

In order to deliver quality of service and/or load balancing in the broadband communication networks, new routing solutions are required that must be capable to adapt to both topology and network traffic changes. For this purpose, we have designed a new routing scheme, and in this paper we present how it inserts itself into the integrated communication networks routing tool-box. Furthermore, we have verified some of its features and properties by simulation.
Jun is phosphorylated by several protein kinases at the same sites that are modified in serum-stimulated fibroblasts. (1992)

c-jun is a member of the family of immediate-early genes whose expression is induced by factors such as serum stimulation, phorbol ester, and differentiation signals. Here we show that increased Jun synthesis after serum stimulation is accompanied by a concomitant increase in phosphorylation. Several serine-threonine kinases were evaluated for their ability to phosphorylate Jun in vitro. p34cdc2, protein kinase C, casein kinase II, and pp44mapk phosphorylated Jun efficiently, whereas cyclic AMP-dependent protein kinase and glycogen synthase kinase III did not. The sites phosphorylated by p34cdc2 were similar to those phosphorylated in vivo after serum induction. The major sites of phosphorylation were mapped to serines 63, 73, and 246. Phosphorylation of full-length Jun with several kinases did not affect the DNA-binding activity of Jun homodimers or Fos-Jun heterodimers. Comparison of the DNA binding and in vitro transcription properties of wild-type and mutated proteins containing either alanine or aspartic acid residues in place of Ser-63, -73, and -246 revealed only minor differences among homodimeric complexes and no differences among Fos-Jun heterodimers. Thus, phosphorylation of Jun did not produce a significant change in dimerization, DNA-binding, or in vitro transcription activity. The regulatory role of phosphorylation in the modulation of Jun function is likely to be considerably more complex than previously suggested.
Studies on Absorption of Eutectic Mixture. I. A Comparison of the Behavior of Eutectic Mixture of Sulfathiazole and that of Ordinary Sulfathiazole in Man. (1961)

1) Sulfathiazole forms eutectic mixtures with urea, l-ascorbic acid, acetamide, nicotinic acid, nicotinamide, or succinimide. It was observed that a eutectic mixture of sulfathiazole and urea produces a microcrystalline suspension of sulfathiazole in water. 2) Sulfathiazole in a eutectic mixture with urea shows higher absorption and excretion after oral administration than ordinary sulfathiazole. 3) Since urea does not possess solubilizing action on sulfathiazole and also it does not enhance absorption of the drug physiologically, the accelerated absorption or excretion must be attributed to the physical state of sulfathiazole in its eutectic mixture with easily soluble compound, such as urea. 4) It is assumed that this new form of preparation will give a means of adjusting therapeutic effect of medical compounds.
Reflectance spectroscopy for in vivo characterization of ovarian tissue (2000)

Reflectance spectroscopy should be further investigated for ovarian cancer screening.
Recombinations between IRP and cystic fibrosis. (1988)

A candidate gene for cystic fibrosis was recently isolated by selective cloning of HpaII-tiny-fragment islands; it maps considerably closer to CF than does MET or D7S8 (pJ3.11), and DNA polymorphisms from this region are in marked disequilibrium with CF. cDNA cloning has shown that this protein has a growth factor-like structure and shows homology to the murine and human proto-oncogene int-1; it is designated IRP (int-1-related protein). DNA sequences from the IRP locus that recognize RFLPs are proving to be highly informative for prenatal diagnosis. We report five crossovers that have been identified which occur either within the IRP locus or between IRP and CF; these recombinants demonstrate that CF maps between the DNA markers D7S8 and KM.19.
Google news personalization (2007)

Several approaches to collaborative filtering have been studied but seldom have studies been reported for large (several millionusers and items) and dynamic (the underlying item set is continually changing) settings. In this paper we describe our approach to collaborative filtering for generating personalized recommendations for users of Google News. We generate recommendations using three approaches: collaborative filtering using MinHash clustering, Probabilistic Latent Semantic Indexing (PLSI), and covisitation counts. We combine recommendations from different algorithms using a linear model. Our approach is content agnostic and consequently domain independent, making it easily adaptable for other applications and languages with minimal effort. This paper will describe our algorithms and system setup in detail, and report results of running the recommendations engine on Google News.
Treatment regimens including the multitargeted antifolate LY231514 in human tumor xenografts. (2000)

The scheduling of antifolate antitumor agents, including the new multitargeted autofolate LY231514 (MTA), with 5-fluorouracil was explored in the human MX-1 breast carcinoma and human H460 and Calu-6 non-small cell lung carcinoma xenografts to assess antitumor activity and toxicity (body weight loss). Administration of the antifolate (methotrexate, MTA, or LY309887) 6 h prior to administration of 5-fluorouracil resulted in additive growth delay of the MX-1 tumor when the antifolate was methotrexate or LY309887 and greater-than-additive tumor growth delay (TGD) when the antifolate was MTA. In the H460 tumor, the most effective regimens were a 14-day course of MTA or LY309887 along with 5-fluorouracil administered on the final 5 days. In addition, the simultaneous combination of MTA administered daily for 5 days for 2 weeks with administration of gemcitabine resulted in greater-than-additive H460 TGD. MTA was additive with fractionated radiation therapy in the H460 tumor when the drug was administered prior to each radiation fraction. MTA administered along with paclitaxel produced greater-than-additive H460 TGD and additive responses along with vinorelbine and carboplatin. In the Calu-6 non-small cell lung carcinoma xenograft, MTA administered in combination with cisplatin or oxaliplatin was highly effective, whereas MTA administered in combination with cyclophosphamide, gemcitabine, or doxorubicin produced additive responses. Administration of MTA along with paclitaxel or doxorubicin resulted in additive MX-1 TGD. Thus, MTA appears to be especially effective in combination therapies including 5-fluorouracil or an antitumor platinum complex.
Linear Precoding and Decoding for Multiple Input Multiple Output (MIMO) Wireless Channels (2001)

Space-time coding and spatial multiplexing are prime candidates for achieving high data rates and link quality in multiple-input multiple-output (MIMO) wireless links. However, both the schemes assume no channel knowledge at the transmitter. In a number of applications, channel knowledge can be made available at the transmitter. A natural question to ask is how to use these channel estimates to further optimize the transmitter. There can be several ways to linearly or non-linearly optimize the transmitter and receiver depending on channel knowledge. In this thesis, we consider linear optimization schemes at the transmitter (precoding) and receiver (decoding) to improve performance of MIMO systems. We consider a number of designs depending on the performance criteria and degree of channel knowledge at the transmitter.
Purification of a branched-chain keto acid dehydrogenase from Pseudomonas putida (1981)

We purified branched-chain keto acid dehydrogenase to a specific activity of 10 mumol/min per mg of protein from Pseudomonas putida grown on valine. The purified enzyme was active with 2-ketoisovalerate, 2-ketoisocaproate, and 2-keto-3-methylvalerate in a ratio of 1.0:0.8:0.7 but showed no activity with either pyruvate or 2-ketoglutarate. There were four polypeptides in the purified enzyme (molecular weights, 49,000, 46,000, 39,000, and 37,000). The purified enzyme was deficient in the specific lipoamide dehydrogenase produced during growth on valine (molecular weight, 49,000). Branched-chain keto acid dehydrogenase required L-valine, oxidized nicotinamide adenine dinucleotide, coenzyme A, thiamine pyrophosphate, and magnesium chloride. A partially purified preparation catalyzed the oxidation of 2-keto-[1-14C]isovalerate to [14C]carbon dioxide, isobutyryl-coenzyme A, and reduced nicotinamide adenine dinucleotide in equimolar amounts. Both the Km and the Vmax for 2-ketoisovalerate were affected by the addition of L-valine to the assay mixture. However, only the Vmax values for oxidized nicotinamide adenine dinucleotide and coenzyme A were affected when L-valine was present. This suggested that valine acted by affecting the binding of branched-chain keto acids to subunit E1 of the complex.
Matrix Metalloproteinases: Discrete Elevations in Essential Hypertension and Hypertensive End-Stage Renal Disease (2009)

The contribution of inflammation to hypertension and target organ damage is under investigation. The matrix metalloproteinase (MMP) enzymes are inflammatory mediators that may contribute to hypertension and its target organ consequences. Here we probe MMPs as inflammatory mediators in hypertension, by studying all three MMP classes in uncomplicated hypertension as well hypertension with profound renal damage, such as hypertensive end-stage renal disease (ESRD). We assayed plasma levels of five MMPs: one collagenase (MMP-1), two gelatinases (MMP-2, MMP-9), and two stromelysins (MMP-3, MMP-10). In hypertension, MMP-9 was elevated versus normotensive controls. Systolic blood pressure (SBP) in all three subject groups positively correlated with MMP-9. In hypertensive-ESRD, MMP-2 and MMP-10 were elevated compared to both hypertensive and normotensive subjects. Several correlations occurred across MMPs, suggesting coordinate biosynthetic control. Our results suggest discrete patterns of MMP overexpression in hypertension, with MMP-9 elevated early, and MMP-2 and MMP-10 linked to target organ damage.
Combinations of Osmolytes, Including Monosaccharides, Disaccharides, and Sugar Alcohols Act in Concert During Cryopreservation to Improve Mesenchymal Stromal Cell Survival (2016)

There is demand for non-dimethyl sulfoxide (DMSO) cryoprotective agents that maintain cell viability without causing poor postthaw function or systemic toxicity. The focus of this investigation involves expanding our understanding of multicomponent osmolyte solutions and their ability to preserve cell viability during freezing. Controlled cooling rate freezing, Raman microscopy, and differential scanning calorimetry (DSC) were utilized to evaluate the differences in recovery and ice crystal formation behavior for solutions containing multiple cryoprotectants, including sugars, sugar alcohols, and small molecule additives. Postthaw recovery of mesenchymal stem cells (MSCs) in solutions containing multiple osmolytes have been shown to be comparable or better than that of MSCs frozen in 10% DMSO at 1°C/min when the solution composition is optimized. Maximum postthaw recovery was observed in these multiple osmolyte solutions with incubation times of up to 2 h before freezing. Raman images demonstrate large ice crystal formation in cryopreserved cells incubated for shorter periods of time (∼30 min), suggesting that longer permeation times are needed for these solutions. Recovery was dependent upon the concentration of each component in solution, and was not strongly correlated with osmolarity. It is noteworthy that the postthaw recovery varied significantly with the composition of solutions containing the same three components and this variation exhibited an inverted U-shape behavior, indicating that there may be a "sweet spot" for different combinations of osmolytes. Raman images of freezing behavior in different solution compositions were consistent with the observed postthaw recovery. Phase change behavior (solidification patterns and glass-forming tendency) did not differ for solutions with similar osmolarity, but differences in postthaw recovery suggest that biological, not physical, methods of protection are at play. Lastly, molecular substitution of glucose (a monosaccharide) for sucrose (a disaccharide) resulted in a significant drop in recovery. Taken together, the information from these studies increases our understanding of non-DMSO multicomponent cryoprotective solutions and the manner by which they enhance postthaw recovery.
Identification of a Bile Acid-responsive Element in the Human Ileal Bile Acid-binding Protein Gene (1999)

Intestinal bile acid-binding protein (I-BABP) is a cytosolic protein that binds bile acids (BAs) with a high affinity. In the small intestine, its expression is restricted to the ileum where it is involved in the enterohepatic circulation of BAs. Using the human enterocyte-like Caco-2 cell line, we have recently shown that BAs increased I-BABP gene expression. To determine whether this regulation occurs in vivo, the effect of BA depletion or supplementation was studied in mice. A dramatic drop in I-BABP mRNA levels was observed in mice treated with the BA-binding resin cholestyramine, whereas an increase was found in animals fed with taurocholic acid. BAs are physiological ligands for the nuclear farnesoid X receptor (FXR). Both FXR and I-BABP are co-expressed along the small intestine and in Caco-2 cells. To determine the role of FXR in the regulation of I-BABP expression, the promoter of the human I-BABP gene was cloned. In Caco-2 cells, cotransfection of FXR and RXRalpha is required to obtain the full transactivation of the I-BABP promoter by BAs. Deletion and mutation analyses demonstrate that the FXR/RXRalpha heterodimer activates transcription through an inverted repeat bile acid responsive element located in position -160/-148 of the human I-BABP promoter. In conclusion, we show that FXR is a physiological BA sensor that is likely to play an essential role in BA homeostasis through the regulation of genes involved in their enterohepatic circulation.
Vision-based multipoint displacement measurement for structural health monitoring (2015)

A novel noncontact vision sensor for simultaneous measurement of structural displacements at multiple points using one camera is developed based on two advanced template matching techniques: the upsampled cross correlation (UCC) and the orientation code matching (OCM). While existing studies on vision sensors are mostly focused on the time-domain performance evaluation, this study investigates the performance in both time and frequency domains through a shaking table test of a three-story frame structure, in which the displacements at all the floors are measured by using one camera to track either high-contrast artificial targets or low-contrast natural targets on the structural surface such as bolts and nuts. Excellent agreements are observed between the displacements measured by the single camera and those measured by high-performance laser displacement sensors. The results of structural modal analysis based on the measurements by the vision sensor and reference accelerometers also agree well. Moreover, the identified modal parameters are used to update the finite element model of the structure, demonstrating the potential of the vision sensor for structural health monitoring applications. This study further examines the robustness of the proposed vision sensor against ill environmental conditions such as dim light, background image disturbance, and partial template occlusion, which is important for future implementation in the field. Significant advantages of the proposed vision sensor include its low cost (a single camera to remotely measure structural displacements at multiple points without installing artificial targets) and flexibility to extract structural displacements at any point from a single measurement. Copyright © 2015 John Wiley & Sons, Ltd.