gebhart/patrepeval huggingface dataset:
Mouse CD99 participates in T-cell recruitment into inflamed skin (2004)

Human CD99 is a small highly O-glycosylated cell-surface protein expressed on most leukocytes. It was recently found to be expressed at endothelial cell contacts and to participate in the transendothelial migration (TEM) of monocytes in vitro. In order to analyze the physiologic relevance of CD99 in vivo we searched for the mouse homolog. We cloned a mouse cDNA coding for a protein 45% identical in its sequence with human CD99. Based on the cDNA, we generated antibodies against this mouse homolog of CD99, which detected the antigen on most leukocytes, on endothelia of various tissues, and at cell contacts of cultured endothelial cells. Cell aggregation of CD99-transfected Chinese hamster ovary (CHO) cells was completely blocked by anti-CD99 antibodies. The same antibodies inhibited TEM of lymphocytes in vitro, independent of whether T cells or endothelial cells were preincubated with antibodies. In a cutaneous delayed-type hypersensitivity (DTH) reaction, anti-CD99 antibodies inhibited the recruitment of in vivo-activated T cells into inflamed skin as well as edema formation. We conclude that mouse CD99 participates in the TEM of lymphocytes and in their recruitment to inflamed skin in vivo. This establishes CD99 as a valid target for interference with cutaneous inflammatory processes.
The influence of wafer dimensions on the contact wave velocity in silicon wafer bonding (1996)

The contact wave velocity in silicon wafer bonding is experimentally found to decrease with wafer thickness and to be only weakly dependent on wafer diameter. Wafers of different thicknesses ranging from 270 to 5000 μm, were dipped in HF:H2O before bonding to give the surfaces hydrophobic properties. A model based on energy conservation can explain the main characteristics of the experimental results. The contact wave velocity is determined by the amount of energy available as kinetic energy for the entrapped gas in the gap between the wafers. By increasing wafer thickness, the elastic energy stored in the material is increased, and the contact wave velocity is decreased.
Synthesis and Structure−Activity Relationship Study of Potent Trypanocidal Thio Semicarbazone Inhibitors of the Trypanosomal Cysteine Protease Cruzain (2002)

American trypanosomiasis, or Chagas' disease, is the leading cause of heart disease in Latin America. Currently there is an urgent need to develop antitrypanosomal therapy due to the toxicity of existing agents and emerging drug resistance. A novel series of potent thio semicarbazone small-molecule inhibitors of the Trypanosoma cruzi cysteine protease cruzain have been identified. Some of these inhibitors have been shown to be trypanocidal. We initially discovered that 3'-bromopropiophenone thio semicarbazone (1i) inhibited cruzain and could cure mammalian cell cultures infected with T. cruzi. 3'-Bromopropiophenone thio semicarbazone showed no toxicity for mammalian cells at concentrations that were trypanocidal. Following this lead, more than 100 compounds were designed and synthesized. A specific structure-activity relationship (SAR) was established, and many potent analogues with IC(50) values in the low nanomolar range were identified. Eight additional analogues were trypanocidal in a cell culture assay, and this indicates that aryl thio semicarbazone is a productive scaffold for killing the parasites. Kinetic studies show that these are time-dependent inhibitors. Molecular modeling studies of the enzyme-inhibitor complex have led to a proposed mechanism of interaction as well as insight into the SAR of the thio semicarbazone series. The nonpeptide nature of this series, small size, and extremely low cost of production suggest this is a promising direction for the development of new antitrypanosome chemotherapy.
Differential regulation of transcription factor gene expression and phenotypic markers in developing sympathetic neurons (1995)

We have examined the regulation of transcription factor gene expression and phenotypic markers in developing chick sympathetic neurons. Sympathetic progenitor cells first express the bHLH transcriptional regulator Cash-1 (a chicken achaete-scute homologue), followed by coordinate expression of Phox2, a paired homeodomain protein, and GATA-2, a zinc finger protein. SCG10, a pan-neuronal membrane protein, is first detected one stage later, followed by the catecholaminergic neurotransmitter enzyme tyrosine hydroxylase (TH). We have used these markers to ask two questions: (1) is their expression dependent upon inductive signals derived from the notochord or floor plate?; (2) does their sequential expression reflect a single linear pathway or multiple parallel pathways? Notochord ablation experiments indicate that the floor plate is essential for induction of GATA-2, Phox2 and TH, but not for that of Cash-1 and SCG10. Taken together these data suggest that the development of sympathetic neurons involves multiple transcriptional regulatory cascades: one, dependent upon notochord or floor plate-derived signals and involving Phox2 and GATA-2, is assigned to the expression of the neurotransmitter phenotype; the other, independent of such signals and involving Cash-1, is assigned to the expression of pan-neuronal properties. The parallel specification of different components of the terminal neuronal phenotype is likely to be a general feature of neuronal development.
Pinocchio: Nearly Practical Verifiable Computation (2013)

To instill greater confidence in computations outsourced to the cloud, clients should be able to verify the correctness of the results returned. To this end, we introduce Pinocchio, a built system for efficiently verifying general computations while relying only on cryptographic assumptions. With Pinocchio, the client creates a public evaluation key to describe her computation; this setup is proportional to evaluating the computation once. The worker then evaluates the computation on a particular input and uses the evaluation key to produce a proof of correctness. The proof is only 288 bytes, regardless of the computation performed or the size of the inputs and outputs. Anyone can use a public verification key to check the proof. Crucially, our evaluation on seven applications demonstrates that Pinocchio is efficient in practice too. Pinocchio's verification time is typically 10ms: 5-7 orders of magnitude less than previous work; indeed Pinocchio is the first general-purpose system to demonstrate verification cheaper than native execution (for some apps). Pinocchio also reduces the worker's proof effort by an additional 19-60x. As an additional feature, Pinocchio generalizes to zero-knowledge proofs at a negligible cost over the base protocol. Finally, to aid development, Pinocchio provides an end-to-end toolchain that compiles a subset of C into programs that implement the verifiable computation protocol.
Human transforming growth factor type .beta.2: production by a prostatic adenocarcinoma cell line, purification, and initial characterization (1987)

Human type beta 2 transforming growth factor (hTGF-beta 2) was purified from tamoxifen-supplemented, serum-free medium conditioned by the human prostatic adenocarcinoma cell line PC-3. The purification of hTGF-beta 2 was monitored in a growth inhibition assay and was achieved by batch purification on methylsilyl-controlled pore glass, followed by gel permeation chromatography and reversed-phase high-performance liquid chromatography. The overall recovery of hTGF-beta 2 was 75% of the initial activity and yielded 22 micrograms of hTGF-beta 2/L of conditioned medium. The concentration of hTGF-beta 2 required for half-maximal inhibition of Mv 1 Lu mink lung epithelial cells (CCl-64) was approximately 5 pM when assayed in the presence of 10% fetal bovine serum. The purified hTGF-beta 2 has a molecular weight of 24,000 when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and consists of two disulfide-linked, apparently identical polypeptide chains, with a molecular weight of 13,000. The amino-terminal sequence of hTGF-beta 2 was determined. Alignment of the amino acid sequences of hTGF-beta 2 and hTGF-beta reveals statistically significant sequence homology. On the basis of the extensive amino acid sequence homology, we propose the term TGF-beta 2 for this newly isolated polypeptide. The reported results suggest that TGF-beta (TGF-beta 1) and TGF-beta 2 may have evolved from a common progenitor.
Characterization of the Interaction Between L-Ficolin/P35 and Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 (2002)

Ficolins are oligomeric lectins comprising a collagen-like and a fibrinogen-like domain, with a binding specificity for N-acetylglucosamine. It has been reported recently that L-ficolin/P35 associates with mannan-binding lectin (MBL)-associated serine proteases (MASP-1 and -2) and MBL-associated protein 19 (MAp19) in serum and forms complexes able to activate complement. Using surface plasmon resonance spectroscopy we have shown that recombinant MASP-1 and -2, their N-terminal CUB1 (module originally found in complement proteins C1r/C1s, Uegf, and bone morphogenetic protein-1)-epidermal growth factor (EGF)-CUB2 and CUB1-EGF segments, and MAp19 bind to immobilized L-ficolin/P35 in the presence of Ca(2+) ions. Comparable K(d) values were obtained for the full-length proteases and their CUB1-EGF-CUB2 segments (9.2 and 10 nM for MASP-1 and 4.6 and 5.4 nM for MASP-2, respectively), whereas higher values were obtained for the CUB1-EGF segments (26.7, 15.6, and 14.3 nM for MASP-1, MASP-2, and MAp19). These values are in the same range as those determined for the interaction of these proteins with MBL. Binding was Ca(2+) dependent and was only partly sensitive to EDTA for MASP-1, MASP-2, and MASP-2 CUB1-EGF-CUB2. Half-maximal binding was obtained at comparable Ca(2+) concentrations for MASP-1 and MASP-2 (0.45 and 0.47 micro M, respectively), their CUB1-EGF-CUB2 segments (0.37 and 0.72 micro M), and their CUB1-EGF segments (0.31 and 0.79 micro M). These values are lower than those determined in the case of MBL, indicating a difference between MBL and L-ficolin/P35 with respect to the Ca(2+) dependence of their interaction with the MASPs. Preincubation of the MASPs with soluble MBL inhibited subsequent binding to immobilized L-ficolin/P35 and, conversely, suggesting that these lectins compete with each other for binding to the MASPs in vivo.
Physician recommendations regarding tamoxifen and patient utilization of tamoxifen after surgery for ductal carcinoma in situ (2004)

Physicians and patients remain cautious regarding the use of tamoxifen after local treatment for DCIS. The current findings have implications for current trials evaluating aromatase inhibitors and other chemopreventive agents for this disease.
Plasminogen Activator Inhibitor-1 and Vitronectin Promote the Cellular Clearance of Thrombin by Low Density Lipoprotein Receptor-related Proteins 1 and 2 (1996)

Thrombin is a multifunctional protein that has both proteinase and growth factor-like activities. Its regulation is largely mediated by interaction with a host of inhibitors including antithrombin III (ATIII), heparin cofactor II (HCII), alpha2-macroglobulin (alpha2-M), protease nexin I, and plasminogen activator inhibitor-1 (PAI-1). ATIII, HCII, and alpha2-M are all abundant in blood and can inactivate blood-borne thrombin leading to rapid hepatic clearance of the thrombin-inhibitor complex. PAI-1 alone, a poor solution phase inhibitor of thrombin, can efficiently inhibit thrombin in the presence of native vitronectin (VN). In this study, active thrombin was found to be efficiently endocytosed and degraded by cultured pre-type II pneumocyte cells, and both processes could be blocked by polyclonal antibodies to PAI-1. When the relative efficiency of cellular endocytosis of thrombin in complex with a number of inhibitors was examined, 125I-thrombin-PAI-1 complexes were most efficiently cleared compared to 125I-thrombin in complex with the serpins ATIII, HCII, alpha1-proteinase inhibitor, or d-phenylalanyl-l-prolyl-l-arginine chloromethyl ketone. Low density lipoprotein receptor-related proteins 1 (LRP) and 2 (gp330/megalin) mediate the endocytosis of thrombin-PAI-1, since antagonists of receptor function such as LRP-1 and LRP-2 antibodies and the 39-kDa receptor-associated protein blocked 125I-thrombin-PAI-1 endocytosis and degradation. The LRP-mediated clearance of exogenously added 125I-thrombin by cultured cells was found to be enhanced 5-fold by inclusion of wild-type PAI-1 but by only 2-fold when a mutant form of PAI-1 that is unable to bind VN was included. This wild-type PAI-1 enhancement of 125I-thrombin clearance was found to occur only in the presence of native VN and not with its conformationally altered form. The results highlight a novel mechanism for cellular clearance of thrombin involving native VN promoting the interaction of thrombin and PAI-1 and the subsequent endocytosis of the complex by LRP-1 or LRP-2. This pathway is potentially important for the regulation of the potent biological activities of thrombin, particularly at sites of vascular injury.
Evaluation of a polyester collagen-coated heparin bonded vascular graft. (1997)

This animal study was designed to compare a collagen coated heparin bonded vascular graft (CHG) versus a collagen coated vascular graft (CG) regarding intraoperative blood loss and healing process. 24 polyester vascular grafts (12 CHG and 12 CG) of 6 mm in diameter and 5 mm in length were implanted between the common iliac and external iliac artery in 12 adult dogs. The grafts were explanted between the first and the sixth months which followed the implantations. The healing process was observed by gross examination, microscopic and scanning electron microscopic examination. Prostaglandin PGE2, TXB2, 6 keto PGF1 alpha and PGF2 alpha were measured by radioimmunologic assay from samples retrieved from the medium part of the graft. During implantation, there was no notable difference in blood loss through the graft. At the time of explantation, 20 grafts were patent (10 CHG, 10 CG). In both grafts, the healing process developed progressively between 2 and 6 months and 90% of the internal surface of the grafts were covered with endothelial like cells. At 6 months, the internal layer was thinner in heparinized graft. PGI2 secretion was found with the two types of grafts. In conclusion, the present study showed no difference in the blood loss or healing characteristic of CHG and CG except for a potentially thinner internal layer with CHG. Comparative studies in humans are necessary to evaluate the potential benefit of heparin bonded graft in clinical practice.
Investigating clearance mechanisms for recombinant activated factor VII in a perfused liver model (2010)

Clearance mechanisms for recombinant activated human FVII (rFVIIa; NovoSeven), a heterogeneously glycosylated protein, have yet to be fully elucidated, but may involve the liver. The effects of the gamma-carboxy glutamic acid (Gla) domain and the sialic acid content of the protein on rFVIIa clearance were investigated following intravenous administration of rFVIIa lacking the Gla domain, des(1-44) rFVIIa and asialo-rFVIIa in pharmacokinetic (PK) studies and perfused rat livers. PK parameters for both rFVIIa and des(1-44) rFVIIa had similar biphasic clearance profiles, as well as half-lives ([t(1/2)]=80 and 88 minutes, respectively), while asialo-rFVIIa was cleared quickly (t(1/2)=21 minutes) with a linear clearance profile. Perfused liver studies with all proteins (10 nM) mirrored the trends in profiles observed in the PK study. rFVIIa and des(1-44) rFVIIa were cleared to a similar extent, 41% and 35%, respectively, after 1 h, whereas plasma-derived FVII from humans (which has a higher sialylation content than rFVIIa) was cleared to a lesser extent (21%). Asialo-rFVIIa, on the other hand, was almost totally cleared and when an excess of asialo-orosomucoid was added to the perfusate, its clearance was significantly reduced (by 34%) and also for rFVIIa, albeit to a lesser extent (by 14%). Together these data suggest that carbohydrate receptor(s) (e.g. the asialoglycoprotein receptor, ASGPR) play a role in asialo-rFVIIa and rFVIIa clearance. In vivo and liver clearance data correlated well showing similar trends and indicated that rFVIIa clearance is not affected by the Gla domain, but rather by a subpopulation of N-glycosylated structures on rFVIIa.
Application of Belief Theory to Similarity Data Fusion for Use in Analog Searching and Lead Hopping (2008)

A wide variety of computational algorithms have been developed that strive to capture the chemical similarity between two compounds for use in virtual screening and lead discovery. One limitation of such approaches is that, while a returned similarity value reflects the perceived degree of relatedness between any two compounds, there is no direct correlation between this value and the expectation or confidence that any two molecules will in fact be equally active. A lack of a common framework for interpretation of similarity measures also confounds the reliable fusion of information from different algorithms. Here, we present a probabilistic framework for interpreting similarity measures that directly correlates the similarity value to a quantitative expectation that two molecules will in fact be equipotent. The approach is based on extensive benchmarking of 10 different similarity methods (MACCS keys, Daylight fingerprints, maximum common subgraphs, rapid overlay of chemical structures (ROCS) shape similarity, and six connectivity-based fingerprints) against a database of more than 150,000 compounds with activity data against 23 protein targets. Given this unified and probabilistic framework for interpreting chemical similarity, principles derived from decision theory can then be applied to combine the evidence from different similarity measures in such a way that both capitalizes on the strengths of the individual approaches and maintains a quantitative estimate of the likelihood that any two molecules will exhibit similar biological activity.
Increased resistance to oxidative stress in transgenic plants that overexpress chloroplastic Cu/Zn superoxide dismutase. (1993)

Transgenic tobacco plants that express a chimeric gene that encodes chloroplast-localized Cu/Zn superoxide dismutase (SOD) from pea have been developed. To investigate whether increased expression of chloroplast-targeted SOD could alter the resistance of photosynthesis to environmental stress, these plants were subjected to chilling temperatures and moderate (500 mumol of quanta per m2 per s) or high (1500 mumol of quanta per m2 per s) light intensity. During exposure to moderate stress, transgenic SOD plants retained rates of photosynthesis approximately 20% higher than untransformed tobacco plants, implicating active oxygen species in the reduction of photosynthesis during chilling. Unlike untransformed plants, transgenic SOD plants were capable of maintaining nearly 90% of their photosynthetic capacity (determined by their photosynthetic rates at 25 degrees C) following exposure to chilling at high light intensity for 4 hr. These plants also showed reduced levels of light-mediated cellular damage from the superoxide-generating herbicide methyl viologen. These results demonstrate that SOD is a critical component of the active-oxygen-scavenging system of plant chloroplasts and indicate that modification of SOD expression in transgenic plants can improve plant stress tolerance.
Sandiness Prevention in Dulce de Leche by Seeding with Lactose Microcrystals (1990)

Sandiness in Dulce de Leche is caused by a high concentration of lactose. In sweetened condensed milk, this defect is prevented by seeding with lactose mier?crystals. Seeding has not been used 10 Dulce de Leche due to its high viscosity and due to contamination problems at the recommended seeding temperature (30"C). Preliminary experiments demonstrated that seeding at 40C with a seeding material concentration of 6 gll00 kg of Dulce de Leche effectively eliminated sandiness for as long as 6 mo. The high sucrose concentration (Ca. 44%) of Dulce de Leche reduced lactose solubility. Experiments demonstrated that a maximum seeding temperature of 54'C was possible using a seed concentration of 30 gll00 kg of Dulce de Leche and agitating at the seeding temperature for 15 min. This was valid for all fonnulations used in current industrial practice.
The attenuation of wireless waves over land (1928)

A description is given of a series of experiments to determine the attenuation of wireless waves over land. The intensity of the signals from the London broadcasting station (2 LO; λ = 364 m) was measured along a number of radial lines in seven different directions up to a maximum distance of 100 miles. From these measurements curves were drawn of the overall attenuation, and derived curves showing only the surface absorption effect. The experimental results were then compared with curves drawn in accordance with Sommerfeld&apos;s theory of attenuation. The results show that the attenuation is not the same in all directions, the difference being quite important, and the comparison with theory shows for all directions a considerably greater attenuation than would be expected from the previously determined value of the earth&apos;s conductivity.It is suggested that both these features of the results could be explained as an effect due largely to the well-wooded nature of the English country-side. To show this, an experimental method was developed by which the energy-absorbing property of individual trees could be directly measured. The results obtained enabled the total energy-absorbing properties of a given tree-covered area to be calculated, thus providing a correction for trees which could be introduced into the theoretical formula.The conclusion arrived at was that the greater part of the discrepancy between Sommerfeld&apos;s theory and experiment could be ascribed to the effect of trees, and also that the same agency offered a satisfactory explanation of the difference of attenuation observed in different directions—the greatest attenuation corresponding to the most-wooded regions, and vice versa.The experimental results show no evidence of any screening or other effect due to hill systems encountered in the region investigated, which included the North and South Downs and the Chiltern and Cotswold ranges.Finally, check-measurements of attenuation on two other wave-lengths gave results satisfactorily confirming the conclusion derived from the main experiments.