gebhart/patrepeval huggingface dataset:
Patterns of transgene inheritance in rainbow trout (Oncorhynchus mykiss) (1991)

There have been very few studies of the inheritance of introduced genes (transgenes) in fish. We have followed the inheritance of the mammalian fusion gene MTrGH from founder generation transgenics (originating from eggs microinjected with the MTrGH DNA) to offspring in crosses with control fish. Initial screening of the founder generation transgenics was by analysing DNA from blood samples. Only three out of six fish which carried the novel gene in blood DNA transmitted it to their offspring, despite the presence of the gene in DNA extracted from the sperm of all four male fish in this group. The frequency of transgenics in the progeny groups from the three fish which transmitted the gene varied widely: in one of these groups more than one type of MTrGH restriction pattern was found. These results suggest widespread mosaicism in founder generation transgenics.
Immunization with Recombinant Brucella Species Outer Membrane Protein Omp16 or Omp19 in Adjuvant Induces Specific CD4 + and CD8 + T Cells as Well as Systemic and Oral Protection against Brucella abortus Infection (2008)

Available vaccines against Brucella spp. are live attenuated Brucella strains. In order to engineer a better vaccine to be used in animals and humans, our laboratory aims to develop an innocuous subunit vaccine. Particularly, we are interested in the outer membrane proteins (OMPs) of B. abortus: Omp16 and Omp19. In this study, we assessed the use of these proteins as vaccines against Brucella in BALB/c mice. Immunization with lipidated Omp16 (L-Omp16) or L-Omp19 in incomplete Freund's adjuvant (IFA) conferred significant protection against B. abortus infection. Vaccination with unlipidated Omp16 (U-Omp16) or U-Omp19 in IFA induced a higher degree of protection than the respective lipidated versions. Moreover, the level of protection induced after U-Omp16 or U-Omp19 immunization in IFA was similar to that elicited by live B. abortus S19 immunization. Flow cytometric analysis showed that immunization with U-Omp16 or U-Omp19 induced antigen-specific CD4(+) as well as CD8(+) T cells producing gamma interferon. In vivo depletion of CD4(+) or CD8(+) T cells in mice immunized with U-Omp16 or U-Omp19 plus IFA resulted in a loss of the elicited protection, indicating that both cell types are mediating immune protection. U-Omp16 or U-Omp19 vaccination induced a T helper 1 response, systemic protection in aluminum hydroxide formulation, and oral protection with cholera toxin adjuvant against B. abortus infection. Both immunization routes exhibited a similar degree of protection to attenuated Brucella vaccines (S19 and RB51, respectively). Overall these results indicate that U-Omp16 or U-Omp19 would be a useful candidate for a subunit vaccine against human and animal brucellosis.
Just say no: benefits of early cache miss determination (2003)

As the performance gap between the processor cores and the memory subsystem increases, designers are forced to develop new latency hiding techniques. Arguably, the most common technique is to utilize multi-level caches. Each new generation of processors is equipped with higher levels of memory hierarchy with increasing sizes at each level. In this paper, we propose 5 different techniques that will reduce the data access times and power consumption in processors with multi-level caches. Using the information about the blocks placed into and replaced from the caches, the techniques quickly determine whether an access at any cache level will be a miss. The accesses that are identified to miss are aborted. The structures used to recognize misses are much smaller than the cache structures. Consequently the data access times and power consumption are reduced. Using the SimpleScalar simulator, we study the performance of these techniques for a processor with 5 cache levels. The best technique is able to abort 53.1% of the misses on average in SPEC2000 applications. Using these techniques, the execution time of the applications is reduced by up to 12.4% (5.4% on average), and the power consumption of the caches is reduced by as much as 11.6% (3.8% on average).
Methoxyestradiols Mediate the Antimitogenic Effects of 17β-Estradiol (2003)

These data provide strong evidence that the vascular antimitogenic effects of estradiol are estrogen receptor-independent and involve the sequential conversion of estradiol to hydroxyestradiols and then to methoxyestradiols.
Joint turbo coding and modulated coding for channel with intersymbol interference (2000)

Modulated codes as an effective technique to mitigate intersymbol interference (ISI) have been studied previously which can transfer the multipath interference into implicit diversity and provide a certain coding gain compared with the ideal additive white Gaussian noise (AWGN) channel. Turbo codes have been proved as an extremely powerful error correction coding technique for AWGN, which can be used to approach the channel capacity. In this paper, we propose a joint turbo coding and modulated coding for the ISI channels with AWGN and investigate its performance by simulation. Simulation results show that the proposed joint coding method is an effective technique to mitigate the ISI and strong noise simultaneously. In addition, it can approach the limit of ISI channel information rate.
UV-Driven Reversible Switching of a Roselike Vanadium Oxide Film between Superhydrophobicity and Superhydrophilicity (2007)

We report the fabrication of a roselike nanostructured vanadium oxide (V2O5) film with photoinduced surface wettability switching by carrying out the drop-casting of a suspension of V2O5 particles synthesized with the sol−gel method. Although a pure V2O5 film is slightly hydrophilic, the addition of alkylamine renders the nanostructured V2O5 film superhydrophobic owing to the intercalation of alkyl chains between the V2O5 layers. UV exposure switches the wettability of the V2O5 surface to superhydrophilic with a water contact angle of almost 0°, and storage in the dark reconverts the irradiated surface back to its initial superhydrophobic state. This extraordinary wetting transition is ascribed to the cooperation between the photosensitivity of V2O5 and the surface roughness of its nanostructure, which has submicron- to micron-scale apertures. Our approach provides not only the possibility of producing large homogeneous or patterned surfaces with tunable wettability, but also potential uses in catalysts, electrodes, switchable smart devices, etc., in various fields for future industrial applications.
All-trans-retinoic acid in acute promyelocytic leukemia and its potential in other hematologic malignancies. (1994)

Several phase II clinical studies of all-trans-retinoic acid (ATRA) have been conducted in acute promyelocytic leukemia (APL), an uncommon subtype of acute myeloid leukemia (AML). ATRA has been shown to induce complete remission (CR) in 64% to 96% of patients with APL, and with rapid resolution of the coagulopathy, which is a major cause of early morbidity and mortality. Although CRs induced with ATRA alone are usually not sustained and intensive antileukemic consolidation therapy is required to prolong remission, these findings indicate that a new approach of differentiation therapy is effective in treating patients with APL and may potentially be effective in other malignancies. The presence of the PML/retinoic acid receptor-alpha (PML/RAR-alpha) fusion gene, produced as a result of the unique chromosomal translocation in APL, is a marker of sensitivity to ATRA. Aside from the complications of hyperleukocytosis and the retinoic acid syndrome, ATRA therapy is generally well tolerated. An international study (Intergroup 0129), headed by the Eastern Cooperative Oncology Group, is currently under way to determine further the role of ATRA in the treatment of patients with APL. Given its success in APL, studies of ATRA in other hematologic malignancies are also being conducted. A better understanding of how retinoids modulate carcinogenesis will help determine if the results in APL can be realized in other malignancies treated with ATRA or other retinoids.
[Gene expression of bFGF and intimal hyperplasia of autologous vein grafts in rats]. (1996)

bFGF released from dead and damaged cells of autologous vein graft not only is an important factor that promotes SMC proliferation, but also is a potent stimulator of endothelial regrowth.
Protease-Activated Receptor 2 Deficiency Reduces Cardiac Ischemia/Reperfusion Injury (2010)

PAR-2 deficiency reduces myocardial infarction and heart remodeling after I/R injury.
The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1β (2015)

Interleukin-1β (IL-1β) plays a key role in autoinflammatory diseases, such as systemic juvenile idiopathic arthritis (sJIA) or cryopyrin-associated periodic syndrome (CAPS). Canakinumab, a human monoclonal anti-IL-1β antibody, was recently approved for human use under the brand name Ilaris®. Canakinumab does not cross-react with IL-1β from mouse, rat, rabbit, or macaques. The crystal structure of the canakinumab Fab bound to human IL-1β was determined in an attempt to rationalize the species specificity. The X-ray analysis reveals a complex surface epitope with an intricate network of well-ordered water molecules at the antibody-antigen interface. The canakinumab paratope is largely pre-organized, as demonstrated by the structure determination of the free Fab. Glu 64 of human IL-1β is a pivotal epitope residue explaining the exquisite species specificity of canakinumab. We identified marmoset as the only non-human primate species that carries Glu 64 in its IL-1β and demonstrates full cross-reactivity of canakinumab, thereby enabling toxicological studies in this species. As demonstrated by the X-ray structure of the complex with IL-1β, canakinumab binds IL-1β on the opposite side with respect to the IL-1RAcP binding site, and in an approximately orthogonal orientation with respect to IL-1RI. However, the antibody and IL-1RI binding sites slightly overlap and the VH region of canakinumab would sterically interfere with the D1 domain of IL-1RI, as shown by a structural overlay with the IL-1β:IL-1RI complex. Therefore, direct competition with IL-1RI for IL-1β binding is the molecular mechanism of neutralization by canakinumab, which is also confirmed by competition assays with recombinant IL-1RI and IL-1RII.
Nephrotoxicity of 4-Aminophenol Glutathione Conjugate (1991)

4-Aminophenol (p-aminophenol, PAP) causes selective necrosis to the pars recta of the proximal tubule in Fischer 344 rats. The basis for this selective toxicity is not known, but PAP can undergo oxidation in a variety of systems to form the 4-aminophenoxy free radical. Oxidation or disproportionation of this radical will form 1,4-benzoquinoneimine which can covalently bind to tissue macromolecules. Recent studies have shown that certain benzoquinol-glutathione conjugates can cause renal necrosis in rats. We have synthesized a putative glutathione conjugate of PAP. The effect on the kidney of this conjugate and the sulphate and N-acetyl conjugates, known metabolites of PAP, have been examined in Fischer 344 rats. 4-Amino-3-S-glutathionylphenol produced a dose-dependent (92-920 mumol kg-1) necrosis of the proximal tubular epithelium and altered renal excretory function. The lesion at the low dose was restricted to the pars recta of the proximal tubule in the medullary rays, while at the higher doses it affected the pars recta region of all nephrons. In contrast, PAP-O-sulphate and N-acetyl-4-aminophenol (paracetamol) caused no histological or functional alteration to the kidney at 920 mumol kg-1. The renal necrosis produced by 4-amino-3-S-glutathionylphenol was very similar to that produced by PAP (367-920 mumol kg-1), both functionally and histologically, except that smaller doses of the glutathione conjugate were required. These studies indicate that glutathione conjugation of PAP generates a metabolite that is more toxic to the kidney than the parent compound. A possible mechanism of toxicity (analogous to that reported for glutathione conjugates of certain quinones) involving oxidation to form a 1,4-benzoquinoneimine thioether that could redox cycle is discussed.
ESCHERICHIA COLI SINGLE-STRANDED DNA-BINDING PROTEIN: Multiple DNA-Binding Modes and Cooperativities (1994)

There are now several well-documented SSBs from both prokaryotes and eukaryotes that function in replication, recombination, and repair; however, no "consensus" view of their interactions with ssDNA has emerged. Although these proteins all bind preferentially and with high affinity to ssDNA, their modes of binding to ssDNA in vitro, including whether they bind with cooperativity, often differ dramatically. This point is most clear upon comparing the properties of the phage T4 gene 32 protein and the E. coli SSB protein. Depending on the solution conditions, Eco SSB can bind ssDNA in several different modes, which display quite different properties, including cooperativity. The wide range of interactions with ssDNA observed for Eco SSB is due principally to its tetrameric structure and the fact that each SSB protomer (subunit) can bind ssDNA. This reflects a major difference between Eco SSB and the T4 gene 32 protein, which binds DNA as a monomer and displays "unlimited" positive cooperativity in its binding to ssDNA. The Eco SSB tetramer can bind ssDNA with at least two different types of nearest-neighbor positive cooperativity ("limited" and "unlimited"), as well as negative cooperativity among the subunits within an individual tetramer. In fact, this latter property, which is dependent upon salt concentration and nucleotide base composition, is a major factor influencing whether ssDNA interacts with all four or only two SSB subunits, which in turn determines the type of intertetramer positive cooperativity. Hence, it is clear that the interactions of Eco SSB with ssDNA are quite different from those of T4 gene 32 protein, and the idea that all SSBs bind to ssDNA as does the T4 gene 32 protein must be amended. Although it is not yet known which of the Eco SSB-binding modes is functionally important in vivo, it is possible that some of the modes are used preferentially in different DNA metabolic processes. In any event, the vastly different properties of the Eco SSB-binding modes must be considered in studies of DNA replication, recombination, and repair in vitro. Since eukaryotic mitochondrial SSBs as well as SSBs encoded by prokaryotic conjugative plasmids are highly similar to Eco SSB, these proteins are likely to show similar complexities. However, based on their heterotrimeric subunit composition, the eukaryotic nuclear SSBs (RP-A proteins) are significantly different from either Eco SSB or T4 gene 32 proteins. Further subclassification of these proteins must await more detailed biochemical and biophysical studies.
Theoretical investigations of superlattice band structure in the envelope-function approximation (1982)

We extend our previous investigations on the band structure of superlattices by applying the envelope-function approximation to four distinct problems. We calculate the band structure of HgTe-CdTe superlattices and show that these materials can be either semiconducting or zero-gap semiconductors, i.e., behave exactly like the ternary ${\mathrm{Hg}}_{1\ensuremath{-}x}{\mathrm{Cd}}_{x}$ Te random alloys. We analyze the superlattice dispersion relations in the layer planes (Landau superlattice subbands) and we compare the longitudinal and transverse effective masses of semiconducting InAs-GaSb superlattices. We calculate the general equation for the bound states due to aperiodic layers, taking account of the band structure of the host materials. We finally derive the dispersion relations of polytype ($\mathrm{ABC}$ or $\mathrm{ABCD}$) superlattices.
Kinetic evolution during the laser/thermal preparation of Mn3O4from MnCO3 (1986)

An investigation was performed of the decomposition of MnCO3 by both CW CO2 laser heating and controlled thermal heating in a derivatograph. The process was shown to have different kinetic evolutions in the two cases even though the final product was the same.
Real-time detection technique for Doppler optical coherence tomography (2000)

We propose and demonstrate a novel detection technique, based on a modified electronic phase-locked loop, for Doppler optical coherence tomography. The technique permits real-time simultaneous reflectivity and continuous, bidirectional velocity mapping in turbid media over a wide velocity range with minimal sensitivity penalty compared with conventional optical coherence tomography, which is a major advance over current postprocessing and discrete parallel detection techniques.
Building and Managing Virtual Private Networks (1998)

THE INTERNET AND BUSINESS. Business on the Internet. Virtual Private Networks. A Closer Look at Internet VPNs. SECURING AN INTERNET VPN. Security: Threats and Solutions. Using IPSec to Build a VPN. Using PPTP to Build a VPN. Using L2TP to Build a VPN. Designing Your VPN. BUILDING BLOCKS OF A VPN. The ISP Connection. Firewalls and Routers. VPN Hardware. VPN Software. MANAGING A VPN. Security Management. IP Address Management. Performance Management. LOOKING AHEAD. Extending VPNs to Extranets. Future Directions. Appendices. Glossary. Index.
Determination of plasma soluble fibrin using a new ELISA method in patients with disseminated intravascular coagulation (1996)

We measured plasma levels of soluble fibrin (SF) in 98 patients suspected of having disseminated intravascular coagulation (DIC) using a newly developed enzyme-linked immunosorbent assay (ELISA) and investigated the correlations between SF determinations and measurements of other hemostatic molecular markers to determine the diagnostic usefulness of determinations of SF. Patients were classified into four groups according to their clinical and laboratory findings: overt DIC (n = 33), subclinical DIC (n = 23), hypercoagulability (n = 22), and non-DIC (n = 20). SF levels were significantly higher in patients with overt DIC compared with the other three groups and were significantly higher in the subclinical DIC and hypercoagulability groups compared with the non-DIC patients. SF levels increased significantly with each increase in the clinical stage. Although levels of thrombin-antithrombin III complex (TAT), prothrombin fragment 1 + 2 (PF1+2), cross-linked fibrin degradation products (XDP), and plasmin-antiplasmin complex (PAP) were significantly increased in patients with overt DIC compared with non-DIC patients, the values of these hemostatic molecular markers did not consistently show an increase in association with advances in the disease stage. Plasma levels of SF in patients with overt DIC showed a positive correlation with levels of TAT, XDP, and FDP(E), but not with PF1+2 and PAP. Analysis of receiver-operating characteristic curves showed that the sensitivity and specificity of SF were similar to those of XDP for diagnosis of DIC. The sensitivity and specificity of SF for diagnosis of overt DIC were both above 90% when the cut-off value was set at 65 μg/ml. Plasma levels of SF were also increased in patients with extravascular fibrin formation without DIC. Our findings suggest that measurement of plasma levels of SF by this ELISA method is useful for the diagnosis of DIC and the evaluation of the patient's clinical status. © 1996 Wiley-Liss, Inc.
Assessing the Reversibility of the Anaplerotic Reactions of the Propionyl-CoA Pathway in Heart and Liver (2003)

While a number of studies underline the importance of anaplerotic pathways for hepatic biosynthetic functions and cardiac contractile activity, much remains to be learned about the sites and regulation of anaplerosis in these tissues. As part of a study on the regulation of anaplerosis from propionyl-CoA precursors in rat livers and hearts, we investigated the degree of reversibility of the reactions of the propionyl-CoA pathway. Label was introduced into the pathway via NaH13CO3, [U-13C3]propionate, or [U-13C3]lactate + [U-13C3]pyruvate, under various concentrations of propionate. The mass isotopomer distributions of propionyl-CoA, methylmalonyl-CoA, and succinyl-CoA revealed that, in intact livers and hearts, (i) the propionyl-CoA carboxylase reaction is slightly reversible only at low propionyl-CoA flux, (ii) the methylmalonyl-CoA racemase reaction keeps the methylmalonyl-CoA enantiomers in isotopic equilibrium under all conditions tested, and (iii) the methylmalonyl-CoA mutase reaction is reversible, but its reversibility decreases as the flow of propionyl-CoA increases. The thermodynamic dis-equilibrium of the combined reactions of the propionyl-CoA pathway explains the effectiveness of anaplerosis from propionyl-CoA precursors such as heptanoate.
Peptide-Labeled Quantum Dots for Imaging GPCRs in Whole Cells and as Single Molecules (2007)

We report a robust and practical method for the preparation of water-soluble luminescent quantum dots (QDs) selectively coupled through an amine or thiol linkage to peptide ligands targeted to G-protein coupling receptors (GPCRs) and demonstrate their utility in whole-cell and single-molecule imaging. We utilized a low molecular weight ( approximately 1200 Da) diblock copolymer with acrylic acids as hydrophilic segments and amido-octyl side chains as hydrophobic segments for facile encapsulation of QDs (QD 595 and QD 514) in aqueous solutions. As proof of principle, these QDs were targeted to the human melanocortin receptor (hMCR) by chemoselectively coupling the polymer-coated QDs to either a hexapeptide analog of alpha-melanocyte stimulating hormone or to the highly potent MT-II ligand containing a unique amine. To label QDs with ligands lacking orthogonal amines, the diblock copolymers were readily modified with water-soluble trioxa-tridecanediamine to incorporate freely available amine functionalities. The amine-functionalized QDs underwent facile reaction with the bifunctional linker NHS-maleimide, allowing for covalent coupling to GPCR-targeted ligands modified with unique cysteines. We demonstrate the utility of these maleimide-functionalized QDs by covalent conjugation to a highly potent Deltorphin-II analog that allowed for selective cell-surface and single-molecule imaging of the human delta-opioid receptor (hDOR).
Anterior Cruciate Ligament Graft Fixation (1994)

This study assessed the tensile properties of hamstring and patellar tendon anterior cruciate ligament reconstructions in older cadaveric knees (age range, 48 to 79 years). Mechanical testing to failure was conducted by translating the tibia anteriorly at 1 mm/sec with the knee in 20 degrees of flexion. The strongest gracilis-semitendinosus graft fixation technique (103% of intact anterior cruciate ligament) had the tendons doubled and secured with soft tissue washers (P < 0.01). However, all reconstructions using gracilis-semitendinosus grafts were significantly less stiff than the intact anterior cruciate ligament specimens regardless of fixation technique (P < 0.01). The highest strength patellar tendon graft fixation technique (84% of intact anterior cruciate ligament) was obtained with a combination interference screw and suture technique. The difference in stiffness between a patellar tendon graft and an intact anterior cruciate ligament was not significant when interference screws were placed at both ends of the graft (P > 0.05). Both types of grafts failed most often on the tibial side. With appropriate fixation, both grafts approximated the intact anterior cruciate ligament in strength, but only patellar tendon grafts secured with interference screws were comparable in stiffness.