gebhart/patrepeval huggingface dataset:
Polymer supports for solid-phase organic synthesis (1998)

The solid-phase synthesis of small organic molecules has received renewed attention since the first reports of the polymer-supported synthesis of compounds of therapeutic interest. Solid-phase synthesis is now a key component of the high-throughput synthesis and screening approach to drug discovery. The recent rapid growth in the number of organic transformations that have been successfully demonstrated on solid supports has involved both the use of the established amine, halide, and hydroxyl supports developed originally for peptide synthesis, and the design and synthesis of new supports to permit the anchoring and releasing of other functional groups. In this article, resins and linkers are subdivided according to the functional group on the solid support to which the first building block is anchored. The chemistry of these supports is illustrated by a relatively small but representative selection from the many recent examples of potential therapeutic agents synthesized on solid supports. © 1999 John Wiley & Sons, Inc. Biopoly 47: 311–351, 1998
A rapid, large scale purification procedure for gibbon interleukin 2. (1983)

Interleukin 2 (IL 2) was purified from the conditioned medium of a gibbon T cell line, MLA144, which releases IL 2 constitutively. The IL 2 was obtained free of contaminating proteins by a simple process consisting of an initial batch purification on trimethylsilyl-controlled pore glass followed by reversed phase high pressure liquid chromatography. Overall recovery of IL 2 activity ranged from 70 to 100% of initial activity and yielded 2 X 10(6) or greater units of IL 2 per 15 liters of serum-free MLA144 conditioned medium. The specific activity of purified IL 2 ranged from 0.5 to 1 X 10(8) IL 2 U/mg protein. The purified IL 2 showed four molecular species when analyzed by two-dimensional isoelectric focusing-SDS-polyacrylamide gel electrophoresis. Each of the four molecular forms was active in the bioassay for IL 2 activity. Three molecular forms had apparent m.w. of 16,000 but different isoelectric points of 5.9, 6.3, and 6.7. One molecular form had an apparent m.w. of 15,000 and an isoelectric point of 7.2. The most abundant form of IL 2 had an apparent m.w. of 16,000 and an isoelectric point of 6.3. The purified IL 2 supported the growth of IL 2-dependent lymphocytes to a greater extent than did the same level of crude IL 2-containing MLA144 conditioned medium. The ability to purify large amounts of IL 2 by a rapid and efficient procedure will be of great help in both biochemical and immunologic studies of this lymphokine.
Micromirror arrays using KOH:H2O micromachining of silicon for lens templates, geodesic lenses, and other applications (1994)

Micromirrors having diameters from a few micrometers to several millimeters have been produced on (100) silicon by wet-chemical etching in KOH:H2O. The <i>f</i>/#'s range from about 2.5 to at least 10. The microroughness of an etched mirror with diameter 550 μm and 9.6-μm sagitta is less than 5 nm and its surface figure is within 0.5 μm of a perfect sphere. Data over a wide range of diameters are presented and a semiempirical model is developed to explain the behavior. The concordance of the normalized etched profiles for all diameter mirrors demonstrates that the etching is dominated by surface reaction rather than diffusion limitation. Design and fabrication schemes are presented for making a wide range of mirror diameters and focal lengths, for both single micromirrors and arrays. The etched depressions can be used as templates for microlenses and as substrates for geodesic waveguide lenses and arrays. Chem-mechanical polishing on the etched structures reduces the edge curvature and produces oblate spheroidal surfaces, both of which should improve geodesic lens behavior. The etched structures can also be used as variable crystal orientation substrates for epitaxial nucleation and various surface analysis studies.
Rational HIV Immunogen Design to Target Specific Germline B Cell Receptors (2013)

Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.
Temporal Trends in Litter Dynamics at a Pebble Pocket Beach (2001)

A pocket beach in South Wales (Tresilian), UK, was studied over a five year period (1994 1998) to assess amounts, types and accumulation of litter. At low spring tide, the beach was sub-divided into 5m transects and all litter recorded prior to removal. At the subsequent low spring tide, roughly 15 days after the initial survey, the beach was revisited and the litter recording repeated. The study established that at least 19% of the total amount of pre clean up beach litter, returned within two weeks; in one year this figure was as high as 46%. Trends in the amounts and composition of the litter were also apparent. The litter standing stock fell by almost 50% between 1995 and 1998, with plastics being the dominant litter material. Plastic containers increased in proportion over the survey period, making up some 30% of the litter in 1998 compared with 12% in 1996. Litter was distributed across the beach at varying levels, with the largest accumulations occurring at the eastern end of the beach, this was especially so in 1997. The litter distribution across this pocket beach brings into question the validity of using selected small transects to give a true assessment of the amounts of litter present.
Verification of a Retractable Solar Sail in a Thermal-Vacuum Environment (2010)

A full-scale, 10m, flight-like, retractable solar sail prototype has recently undergone environmental deployment testing, shape surveys, deployment kinematic measurements, and structural analysis predictions in an effort to demonstrate that this payload can be qualified for flight. The large deformation, elastic strain-energy mechanics used to enforce the deterministic unfurling and refurling of the Flexible Unfurlable and Refurlable Lightweight (FURL) solar sail were predicted using finite element structural analysis techniques. These structural models were validated by comparison to shape surveys of the EDU2 system and by comparison to component level strength testing. The EDU2 system was verified to meet driving functional requirements by enduring four thermal cycles and 50 deploymentretraction lifecycles in a thermal-vacuum environment and an additional 25 hands-off cycles in an ambient environment. This testing and analysis activities have established confidence that the flight system will endure dozens of deployment-retraction cycles on-orbit. Overall these efforts have demonstrated the robustness of this FURL solar sail system to serve as a propellant-free thrust source for small satellites.
Preclinical evidence for the potential of a bivalent fHBP vaccine to preventNeisseria meningitidisSerogroup C Disease (2011)

A bivalent factor H binding protein (fHBP) vaccine for the prevention of disease caused by Neisseria meningitidis serogroup B is currently in clinical development. Since fHBP is also expressed by other meningococcal serogroups, anti-fHBP antibodies may have bactericidal activity against meningococci independent of serogroup. To begin examining the susceptibility of other meningococcal serogroups to anti-fHBP antibodies, meningococcal serogroup C invasive isolates (n = 116) were collected from the Centers for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) sites during 2000-2001. These isolates were analyzed for the presence of the fhbp gene. All serogroup C isolates contained the gene, and sequence analysis grouped the proteins into two subfamilies, A and B. Flow cytometry analysis demonstrated that fHBP was expressed on the surface of ~70% of isolates in vitro with varying levels of expression. fHBP was accessible to antibodies on the cell surface even in the presence of the polysaccharide capsule. Nine isolates from different geographic regions were identified which harboured an identical single nucleotide deletion that could result in a truncated subfamily B fHBP. Analysis by flow cytometry using a polyclonal fHBP antibody preparation revealed that a subpopulation of each of these isolates expressed fHBP. Rabbit and non-human primate immune sera generated with bivalent fHBP vaccine were tested for bactericidal activity against a panel of diverse serogroup C clinical isolates using human complement. Sera from both species demonstrated serum bactericidal antibody activity against the serogroup C isolates tested. These promising findings suggest that a bivalent fHBP vaccine may be capable of providing protection against meningococcal disease caused by both serogroup C and B.
Tyrosine Sulfation of Chemokine Receptor CCR2 Enhances Interactions with Both Monomeric and Dimeric Forms of the Chemokine Monocyte Chemoattractant Protein-1 (MCP-1) (2013)

Chemokine receptors are commonly post-translationally sulfated on tyrosine residues in their N-terminal regions, the initial site of binding to chemokine ligands. We have investigated the effect of tyrosine sulfation of the chemokine receptor CCR2 on its interactions with the chemokine monocyte chemoattractant protein-1 (MCP-1/CCL2). Inhibition of CCR2 sulfation, by growth of expressing cells in the presence of sodium chlorate, significantly reduced the potency for MCP-1 activation of CCR2. MCP-1 exists in equilibrium between monomeric and dimeric forms. The obligate monomeric mutant MCP-1(P8A) was similar to wild type MCP-1 in its ability to induce leukocyte recruitment in vivo, whereas the obligate dimeric mutant MCP-1(T10C) was less effective at inducing leukocyte recruitment in vivo. In two-dimensional NMR experiments, sulfated peptides derived from the N-terminal region of CCR2 bound to both the monomeric and dimeric forms of wild type MCP-1 and shifted the equilibrium to favor the monomeric form. Similarly, MCP-1(P8A) bound more tightly than MCP-1(T10C) to the CCR2-derived sulfopeptides. NMR chemical shift mapping using the MCP-1 mutants showed that the sulfated N-terminal region of CCR2 binds to the same region (N-loop and β3-strand) of both monomeric and dimeric MCP-1 but that binding to the dimeric form also influences the environment of chemokine N-terminal residues, which are involved in dimer formation. We conclude that interaction with the sulfated N terminus of CCR2 destabilizes the dimerization interface of inactive dimeric MCP-1, thus inducing dissociation to the active monomeric state.
A Liquid-Phase Process Suitable for Large-Scale Synthesis of Phosphorothioate Oligonucleotides (2000)

A new process for the preparation of large amounts of thioate oligonucleotides in a quasi-classical solution condition is described. This method takes advantage of the use of poly(ethylene glycol) as a soluble, inert support during the synthesis. The quality and amount of the desired oligonucleotides are improved by the use of pre-formed dimeric phosphoramidite as synthons. The easy intermediate purification from moderate excess of reagents allows obtaining very high coupling yields, and, consequently, the efficient production of quite long sequences as those required for their pharmacological applications.
Attenuation of infarct size in rats and dogs after myocardial infarction by low‐energy laser irradiation (2001)

The results of the present study indicate that delivery of low-energy laser irradiation to infarcted myocardium in rats and dogs has a profound effect on the infarct size after MI.
Teflon-carbon black as new material for the hydrophobic patterning of polymer labs-on-a-chip (2009)

We provide a new method for the selective surface patterning of microfluidic chips with hydrophobic fluoropolymers which is demonstrated by the fabrication of hydrophobic valves. It enables efficient optical quality control for the surface patterning thus permitting the low-cost production of highly reproducible hydrophobic valves. Specifically, a fluoropolymer-solvent-dye solution based on carbon black (CB) is presented which creates superhydrophobic surfaces (contact angle = 157.9°) on chips made from cyclic olefin copolymer (COC). It further provides good visibility for the quality control (QC) in polymer labs-on-a-chip and increases the burst pressure of hydrophobic valves. Finally, an application which aims for the amplification of mRNA on-chip and relies on the defined flow control by hydrophobic valves is presented. Here, the QC in combination with the Teflon-CB coating improves the average standard deviation of the burst pressures from 14.5% down to 6.1 % compared to solely Teflon-coated valves.
Privacy manipulation and acclimation in a location sharing application (2013)

Location sharing is a popular feature of online social networks, but challenges remain in the effective presentation of privacy choices to users, whose location sharing preferences are complex and diverse. One proposed approach for capturing these nuances builds on the observation that key attributes of users' location sharing preferences can be represented by a small number of privacy profiles, which can provide a basis for configuring individual preferences. However, the impact of this approach on how users view their privacy is relatively unknown. We present a study evaluating the impact of this approach on users' location sharing preferences and their satisfaction with the decisions made by their resulting settings. The results suggest that this approach can influence users to share significantly more without a substantial difference in comfort. This further suggests that the provision of profiles for privacy settings must be carefully considered, as they can substantially alter sharing behavior.
The Efficacy of the Novel Dual PI3-Kinase/mTOR Inhibitor NVP-BEZ235 Compared with Rapamycin in Renal Cell Carcinoma (2010)

Dual inhibition of PI3K/mTOR with NVP-BEZ235 induced growth arrest in RCC cell lines both in vitro and in vivo more effectively than inhibition of TORC1 alone. These results provide the rationale for the clinical assessment of agents such as NVP-BEZ235 in patients with advanced RCC.
G-Protein Coupled Receptors, Nitric Oxide, and the IgE Receptor in Asthma (1995)

"G-protein coupled receptors, nitric oxide, and the IgE receptor in asthma.." American journal of respiratory and critical care medicine, 152(1), pp. 394–402
Inflammation and Infections as Risk Factors for Ischemic Stroke (2003)

Inflammation contributes to stroke risk via various interrelated mechanisms. Infectious diseases, traditional risk factors, and genetic susceptibility may cooperate in stimulating inflammatory pathways. Final proof of a causal role of infectious/inflammatory mechanisms in stroke pathogenesis is still lacking and will require interventional studies.
Use of Bacteriophage MS2 as an Internal Control in Viral Reverse Transcription-PCR Assays (2005)

Diagnostic systems based on reverse transcription (RT)-PCR are widely used for the detection of viral genomes in different human specimens. The application of internal controls (IC) to monitor each step of nucleic acid amplification is necessary to prevent false-negative results due to inhibition or human error. In this study, we designed various real-time RT-PCRs utilizing the coliphage MS2 replicase gene, which differ in detection format, amplicon size, and efficiency of amplification. These noncompetitive IC assays, using TaqMan, hybridization probe, or duplex scorpion probe techniques, were tested on the LightCycler and Rotorgene systems. In our approach, clinical specimens were spiked with the control virus to monitor the efficiency of extraction, reverse transcription, and amplification steps. The MS2 RT-PCR assays were applied for internal control when using a second target hepatitis C virus RNA in duplex PCR in blood donor screening. The 95% detection limit was calculated by probit analysis to 44.9 copies per PCR (range, 38.4 to 73.4). As demonstrated routinely, application of MS2 IC assays exhibits low variability and can be applied in various RT-PCR assays. MS2 phage lysates were obtained under standard laboratory conditions. The quantification of phage and template RNA was performed by plating assays to determine PFU or via real-time RT-PCR. High stability of the MS2 phage preparations stored at -20 degrees C, 4 degrees C, and room temperature was demonstrated.
Optical Flatness Metrology for 300 mm Silicon Wafers (2005)

The National Institute of Standards and Technology (NIST) is developing two interferometric methods for measuring the thickness, thickness variation, and flatness of free‐standing and chucked silicon wafers with diameters up to 300 mm. The “eXtremely accurate CALIBration InterferometeR” (XCALIBIR) is a precision phase measuring interferometer with an operating wavelength of 633 nm and a test beam of 300 mm diameter. XCALIBIR is used to evaluate the flatness of chucked wafers. NIST’s Infrared Interferometer (IR2) is a phase measuring interferometer that operates at 1.55 μm and is used to measure the thickness variation of free‐standing 300 mm silicon wafers.
A Miniature Membrane-less Biofuel Cell Operating under Physiological Conditions at 0.5 V (2003)

A biofuel cell operating at a power density of 50 μW cm−2 at a 0.5 V cell potential under physiological conditions (air saturated, pH 7.4, 0.14 M NaCl, 37.5°C, 15 mM glucose) is described. The cell had a glucose electro-oxidizing anode and an electroreducing cathode. The anodic electrocatalyst comprised the electrostatic adduct of glucose oxidase (GOx) a polyanion at physiological pH, and the polycationic redox polymer poly (N-vinyl imidazole), partially quarternized with 2-bromoethylamine and partially complexed with vs. Ag/AgCl). The cathode electrocatalyst was the electrostatic adduct of bilirubin oxidase (BOD) also a polyanion at physiological pH, and the polycationic redox copolymer of polyacrylamide and poly (N-vinylimidazole), complexed with where vs. Ag/AgCl). The anode and the cathode were 7 μm diam, 2 cm long carbon fibers, on which the catalytic enzyme-redox polymer adducts were cross-linked. When the miniature cell operated at 0.5 V, its 50 μW cm−2 initial power density decreased to 30 μW cm−2 after 2 days of continuous operation at 37.5°C. © 2003 The Electrochemical Society. All rights reserved.
Guest Editors' Introduction: High-Performance Interconnects (2006)

We are pleased to introduce this special issue of IEEE Micro, featuring articles that capture the latest results on high-performance interconnection networks, including some of the best presentations from last summer's Hot Interconnects 13 at Stanford University. Hot Interconnects provides a unique international forum for researchers and developers of state-of-the-art hardware and software architectures for interconnection networks at all scales, ranging from on-chip processor-memory interconnects to high-performance networks for the largest and most powerfulsupercomputers.
One-week 96-well soft agar growth assay for cancer target validation (2004)

Soft agar growth, used to measure cell anchorage-independent proliferation potential, is one of the most important and most commonly used assays to detect cell transformation. However, the traditional soft agar assay is time-consuming, labor-intensive, and plagued with inconsistencies due to individual subjectivity. It does not, therefore, meet the increasing demands of today's oncology drug target screening or validation processes. This report describes an alternative 96-well soft agar growth assay that can function as a replacement for the traditional method and overcomes the aforementioned limitations. It offers the following advantages: a shortened assay duration (1 week instead of 4 weeks) that makes transient transfection or treatment possible; plate reader quantification of soft agar growth (measuring cloning efficiency and colony size); and a significant reduction in required labor. Higher throughput also makes it possible to process large numbers of samples and treatments simultaneously and in a much more efficient manner, while saving precious workspace and overall cost.
Acupuncture for Chronic Low Back Pain (2010)

A 45-year-old man with a 7-year history of low back pain asks his physician for a referral to a licensed acupuncturist. Acupuncture involves the insertion of fine metallic needles into the body at specific sites. Clinical trials of acupuncture for chronic low back pain have shown higher rates of symptom improvement with either acupuncture or sham acupuncture than with usual care.
Solid‐Phase synthesis of peptide nucleic acids (1995)

Peptide nucleic acids (PNA) were synthesized by a modified Merrifield method using several improvements. Activation by O-[benzotriazol-1-yl]-1,1,3,3-tetramethyluronium hexafluorophosphate in combination with in situ neutralization of the resin allowed efficient coupling of all four Boc-protected PNA monomers within 30 min. HPLC analysis of the crude product obtained from a fully automated synthesis of the model PNA oligomer H-CGGACTAAGTCCATTGC-Gly-NH2, indicated an average yield per synthetic cycle of 97.1%. N1-benzyloxycarbonyl-N6(3)-methylimidazole triflate substantially outperformed acetic anhydride as a capping reagent. The resin-bound PNAs were successfully cleaved by the 'low-high' trifluoromethanesulphonic acid procedure.
Immersive VR decision training (2003)

Based on the premise of a synergy between the interactive storytelling and VR training simulation this paper treats the main issues involved in practical realization of an immersive VR decision training system supporting possibly broad spectrum of scenarios featuring interactive virtual humans. The paper describes a concrete concept of such a system and its practical realization example.