gebhart/patrepeval huggingface dataset:
Critical problems in very-large-scale computer systems. Semiannual technical report, 1 April-30 September 1989 (1989)

The research vehicle for this contract is the largest possible computer that could be conceived for the mid to late 1990's. The technical challenges of such a machine serve as our guiding stimulus for the research carried out and reported here. We imagine this machine to occupy a 14-story building, to cost upward of $1 billion, and to be so colossal that the nation could only afford one or two of them. The available chip technology and machine size are consistent with 10 to the 15th power FLOPS and 10 to the 15th power bytes of memory. The machine will be used to solve large-scale scientific problems having both military and civilian applications. This investigation addresses the hardware technology, software techniques, algorithms, communications, processing elements, and applications. The study will determine the plausibility (not feasibility) of the machine. Progress in these various areas are highlighted in the forthcoming sections. (rrh)
Protein Engineering with Biosynthesized Libraries from Bordetella bronchiseptica Bacteriophage (2013)

Phage display offers a powerful approach to engineer protein affinity. A naturally occurring analog to phage display, the Bordetella bronchiseptica bacteriophage (BP) employs a highly variable protein termed the major tropism determinant (Mtd) to recognize its dynamic host. Propagation of BP provides a self-made phage library (SMPL) with vast numbers of phage particles, each displaying a single Mtd variant. We report applying the diversity of the BP-SMPL to access a tyrosine-rich library of Mtd variants. Expression of the SMPL-engineered Mtd variant as a GST-bound fusion protein demonstrated specific binding to the target T4 lysozyme with dissociation constants in the sub-micromolar range. The results guide future experiments with SMPLs applied to protein engineering.
NCHRP Report 350 Test 3-11 of the Modified T8 Bridge Rail (2009)

A new flexible bridge rail system, referred to as the T8 rail, was designed as a replacement for the T6 rail in high-speed applications on culverts and thin deck structures. The T8 rail failed a crash test when the breakaway posts failed the thin deck to which it was attached rather than breakaway as designed. After analysis of the test results, the system was modified in an effort to address the identified failure mechanism. The modifications included increasing the length of the breakaway slot in the tension flange of the steel support posts and incorporating a 1-inch thick offset block between the post and upper portion of the tubular thrie beam rail to raise the point of force application on the post. The impact performance of the modified T8 bridge rail system was evaluated through a full-scale crash test. The crash testing was performed in accordance with the requirements of NCHRP Report 350 Test Level 3 (TL-3). Despite the modifications to the rail system, the posts once again failed the thin concrete deck prior to breakaway activation. Because the posts did not release from their baseplates as designed, their rotation lowered the rail height and permitted snagging of the wheel of the pickup truck. These behaviors combined to destabilize the pickup truck, causing it to roll as it exited the barrier. Consequently, the modified T8 bridge rail is NOT suitable for implementation in its present form.
N-Terminus to Arginine Side-Chain Cyclization of Linear Peptidic Neuropeptide Y Y4 Receptor Ligands Results in Picomolar Binding Constants (2021)

The family of neuropeptide Y (NPY) receptors comprises four subtypes (Y<sub>1</sub>R, Y<sub>2</sub>R, Y<sub>4</sub>R, Y<sub>5</sub>R), which are addressed by at least three endogenous peptides, i.e., NPY, peptide YY, and pancreatic polypeptide (PP), the latter showing a preference for Y<sub>4</sub>R. A series of cyclic oligopeptidic Y<sub>4</sub>R ligands were prepared by applying a novel approach, i.e., N-terminus to arginine side-chain cyclization. Most peptides acted as Y<sub>4</sub>R partial agonists, showing up to 60-fold higher Y<sub>4</sub>R affinity compared to the linear precursor peptides. Two cyclic hexapeptides (<b>18</b>, <b>24</b>) showed higher Y<sub>4</sub>R potency (Ca<sup>2+</sup> aequorin assay) and, with p<i>K</i><sub>i</sub> values >10, also higher Y<sub>4</sub>R affinity compared to human pancreatic polypeptide (hPP). Compounds such as <b>18</b> and <b>24</b>, exhibiting considerably lower molecular weight and considerably more pronounced Y<sub>4</sub>R selectivity than PP and previously described dimeric peptidic ligands with high Y<sub>4</sub>R affinity, represent promising leads for the preparation of labeled tool compounds and might support the development of drug-like Y<sub>4</sub>R ligands.
Homophymines B–E and A1–E1, a family of bioactive cyclodepsipeptides from the sponge Homophymia sp. (2009)

Nine new cyclodepsipeptides, homophymines B-E (2-5) and A1-E1 (1a-5a), were isolated from the polar extracts of the sponge Homophymia sp. The new structures, featuring new polyketide-derived end groups, were determined by interpretation of NMR and MS data. The configurations of the new end groups was secured by the application of J-based configurational analysis. Homophymines displayed very potent antiproliferative activity (IC(50) in the nM range) against a panel of human cancer cell lines.
Population and alignment of N2 scattered from Ag(111) (1987)

A well-characterized Ag(111) surface in an ultrahigh vacuum system is bombarded with supersonically cooled N2 and the scattered molecules are detected near the specular angle using 2+2 resonance enhanced multiphoton ionization. The first three even spatial moments of the angular momentum distribution have been measured. The zeroth moment is the population of a given rotational level, while the second and fourth moments describe the quadrupole and hexadecapole alignment of the J vector with respect to the surface normal. The relative population distribution shows an excess at high J characteristic of rotational rainbow scattering. For J&amp;gt;7, the second and fourth moments closely approach their limiting values expected when the J vector lies in the plane of the surface. It is concluded that the N2/Ag(111) system closely approaches the ideal of a rigid rotor colliding with a flat surface.
Molecular Profiling of Cancer Testis Antigens in Chronic Lymphocytic Leukemia. (2009)

Abstract Abstract 4701 Background Chronic Lymphocytic Leukemia (CLL) is characterized by the progressive accretion of long-lived mature B-lymphocytes. Although the classical Rai and Binet staging is still commonly used, a new molecular understanding has identified specific signatures which could help predict disease progression and survival. Given the recent success of immunotherapeutic strategies and immunomodulatory drugs in the treatment of CLL we sought to identify potentially immunologically relevant targets and their relation to well known disease criterion. Methods Our study characterized the mRNA expression of 29 known cancer-testis antigens (CTAs) in 66 patients with CLL at varying stages of disease using a RT-PCR based expression panel. Relevant clinical criterion such as RAI stage, B2m, ZAP-70, IGVH mutational status, CD38, cytogenetics by FISH analysis, WBC count, age, gender, and treatment among others were then taken into account. The binary RNA expression data associated with the clinical and demographic factors were evaluated using chi-square or Wilcoxon rank sum analysis. Results Of the cancer-testis antigens tested, the MAGE family of CTAs revealed statistically significant correlations with multiple clinical criteria. Our analysis reveals a correlation between previous chemo-immunotherapy treatment and MAGE-A1, B2, E1, MAD-CT-2, SPA-17, and PAGE-5 expression. Beyond treatment, total white blood cell count was shown to have a significant association with MAGE family members A1, A3, and B2 expression. In addition, MAD-CT-2 and MAGE-B2 were significantly correlated with the expression of FMC-7 and SSX-4 and LAGE-1 correlated with the presence of B-cell symptomatology. Conclusions Preliminary RT-PCR based CTA phenotyping has unveiled interesting correlations to clinical criteria, opening multiple avenues for future immunotherapeutic interventions as well as possible prognostic value in CLL. Further investigation to better understand the biological value of this information in warranted. Disclosures: Pinilla: Novartis: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Research Funding; exelixis: Research Funding.
Third-order optical susceptibilities and their temperature dependence in polysilane and polygermane materials (1988)

We report the first measurements of the third-order nonlinear susceptibilities of an important new class of polymer, polysilane, and polygermane with planar zigzag backbones. Thermally induced phase changes between the planar trans structure and other backbone disordered structures were found to result in dramatic and reversible changes in the nonlinearity. A significant enhancement of the nonlinear susceptibility was observed to result from the optimal sigma bonded conjugation in the low-temperature all-trans structure.
Optimal parameters for clinical implementation of breast cancer patient setup using Varian DTS software (2012)

Digital tomosynthesis (DTS) was evaluated as an alternative to cone-beam computed tomography (CBCT) for patient setup. DTS is preferable when there are constraints with setup time, gantry-couch clearance, and imaging dose using CBCT. This study characterizes DTS data acquisition and registration parameters for the setup of breast cancer patients using nonclinical Varian DTS software. DTS images were reconstructed from CBCT projections acquired on phantoms and patients with surgical clips in the target volume. A shift-and-add algorithm was used for DTS volume reconstructions, while automated cross-correlation matches were performed within Varian DTS software. Triangulation on two short DTS arcs separated by various angular spread was done to improve 3D registration accuracy. Software performance was evaluated on two phantoms and ten breast cancer patients using the registration result as an accuracy measure; investigated parameters included arc lengths, arc orientations, angular separation between two arcs, reconstruction slice spacing, and number of arcs. The shifts determined from DTS-to-CT registration were compared to the shifts based on CBCT-to-CT registration. The difference between these shifts was used to evaluate the software accuracy. After findings were quantified, optimal parameters for the clinical use of DTS technique were determined. It was determined that at least two arcs were necessary for accurate 3D registration for patient setup. Registration accuracy of 2 mm was achieved when the reconstruction arc length was > 5° for clips with HU ≥ 1000; larger arc length (≥ 8°) was required for very low HU clips. An optimal arc separation was found to be ≥ 20° and optimal arc length was 10°. Registration accuracy did not depend on DTS slice spacing. DTS image reconstruction took 10-30 seconds and registration took less than 20 seconds. The performance of Varian DTS software was found suitable for the accurate setup of breast cancer patients. Optimal data acquisition and registration parameters were determined.
Synthesis of 1,2‐Diheteroatom‐Substituted Alkenes via Rhodium‐Catalyzed Intramolecular Hydrogen Transfer. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
NO IMPROVEMENT OF PANCREAS TRANSPLANT ENDOCRINE FUNCTION BY EXOGENOUS INSULIN INFUSION (ISLET REST) IN THE POSTOPERATIVE PERIOD (1989)

The concept of islet exhaustion maintains that exposure of pancreatic islets to hyperglycemia and other stresses leads to islet dysfunction and irreparable damage. The process of pancreatic transplantation places many stresses on islets (e.g., counter-regulatory hormones, steroids, cyclosporine toxicity). As practiced by some centers, it may be important to administer exogenous insulin in the postoperative period to provide islet rest. Using a porcine pancreas transplant model that simulates clinical transplantation, we studied 2 groups: 1 group (n = 8) received constant insulin infusion for 7 days after transplantation; the control group (n = 5) received vehicle only. The islets in the insulin infusion group were rested as evidenced by a significantly decreased mean C-peptide level (0.27 +/- 0.04 ng/ml) as compared to the control group (0.66 +/- 0.08 ng/ml) (P less than 0.05). After insulin infusion was discontinued, intravenous glucose tolerance testing found insulin, C-peptide and glucagon responses were not different between groups. Glucose clearance was also comparable; K values were -1.79 and -1.60 in the insulin infusion and control groups, respectively. In conclusion, islet rest by insulin infusion for 7 postoperative days did not improve subsequent pancreas transplant endocrine function.
Comparison Foaming Behaviour of Polylactic Acid and Polypropylene (2019)

Polymer foams have wide application area due to their light weight, resistance to impact, ability of insulation, and damping properties for specific applications. In this study, two different thermoplastic materials, polylactic acid (PLA) and polypropylene (PP), were used to compare their foaming ability in foam injection molding. Chemical foaming agent, azodicarbonamide, was used in foam injection molding and tensile test samples were obtained. Mechanical strength of the polymer foam samples were investigated by tensile test. Scanning electron microscopy was applied in order to observe the differences in cell morphologies of PLA and PP foams. It has been seen that 23.4% higher cell density and 151.2% higher cell size have been seen in the PLA foam when the results were compared with PP foam. This induced sharp reductions in mechanical strength of PLA foam while PP foams gave smooth decreases in the mechanical strength. Weight reduction in PLA was also 366.6% higher than that of PP foam due to its higher cell density.
In-plane orientation of polyimide chains induced by thermal imidization. (1994)

The degree of in-plane molecular orientation of the unstretched polyamic acid(PAA) films and the corresponding polyimide (PI) film cured thermally have been quantitatively estimated by measuring the dichroic ratio of a rigid-rod dye (perylenebisimide) dispersed molecularly in their films at an incidence angle. Thermal imidization of PAA(BPDA/PDA) cast on a substrate enhanced markedly the degree of in-plane orientation of the PI chains, meaning that spontaneous in-plane molecular orientation occurred without stretching of the film. However, no spontaneous in-plane orientation was observed for BPDA/ODA system as well as PMDA/ODA system. Thus, it was found that the spontaneous orientation behavior depends strongly on the PI chain rigidity or linearity in contrast to that the degree of in-plane orientation for various PAAs is essentially independent of the chemical structure. PI(BPDA/PDA) cured in free-standing showed the degree of the in-plane orientation much smaller than the PI film imidized on a substrate.
Surface structure and chemical states of a-plane and c-plane InN films (2009)

The surface electron accumulation layer, surface structure, and surface chemical states of a-plane (nonpolar) and c-plane (polar) InN epitaxial films were investigated. Electrical measurements indicated electron accumulation layers on the surface of both the InN films. Angle-resolved x-ray photoelectron spectroscopy (XPS) measurements indicated a strong band bending at both surfaces, thus confirming the surface electron accumulation. Further XPS analysis of the near-surface chemical states indicated an In adlayer at the surface of c-plane InN and an oxygen adsorbed layer on the a-plane InN. These results suggest different ad-layers to cause the surface electron accumulation on c-plane and a-plane InN.
Evaluation of existing methods to extract microplastics from bivalve tissue: Adapted KOH digestion protocol improves filtration at single-digit pore size (2019)

Methods standardisation in microplastics research is needed. Apart from reagent-dependent effects on microplastics, varying target particle sizes can hinder result comparison between studies. Human health concerns warrant recovery of small microplastics. We compared existing techniques using hydrogen peroxide, Proteinase-K, Trypsin and potassium hydroxide to digest bivalve tissue. Filterability, digestion efficacy, recoverability of microplastics and subsequent polymer identification using Raman spectroscopy and a matching software were assessed. Only KOH allowed filtration at ≤25 μm. When adding a neutralisation step prior to filtration, KOH digestates were filterable using 1.2-μm filters. Digestion efficacies were >95.0% for oysters, but lower for clams. KOH destroyed rayon at 60 °C but not at 40 °C. Acrylic fibre identification was affected due to changes in Raman spectra peaks. Despite those effects, we recommend KOH as the most viable extraction method for exposure risk studies, due to microplastics recovery from bivalve tissues of single-digit micrometre size.
The Netivus Manifesto (2021)

We study operational issues faced by Small and Medium Enterprise (SME) network owners and find that SME network management practices have stagnated over the past decade, despite many recent advances in network management. Many of these advances target hyperscalers and ISPs and cannot be directly applied to SME networks that are operated with vastly different constraints. In our work, we outline these constraints and explain how they impact challenges around debugging, namely: representing, reproducing, and remediating network problems. This article takes a fresh look at these challenges in the light of SME practices around collaborative debugging and presents a roadmap aimed to help resolve SME operational issues quickly.
Driving Convergence with Human Diversity (2014)

Convergent science will require human diversity-individuals with different backgrounds and life experiences-to drive it forward.
Stability of the CpG island methylator phenotype during glioma progression and identification of methylated loci in secondary glioblastomas (2014)

This is the first study to have documented genome-wide methylation changes within paired early/late astrocytic gliomas on such a large CpG probe set, revealing a number of genes that maybe relevant to secondary gliomagenesis.
Fabrication and characterization of metal-molecule-silicon devices (2007)

Metal-molecule-silicon (MMSi) devices have been fabricated, electrically characterized, and analyzed. Molecular layers were grafted to n and p+ silicon by electrochemical reduction of para-substituted aryl-diazonium salts and characterized using standard surface analysis techniques; MMSi devices were then fabricated using traditional silicon (Si) processing methods combined with this surface modification. The measured current-voltage characteristics were strongly dependent on both substrate type and molecular head group. The device behavior was analyzed using a qualitative model considering semiconductor depletion effects and molecular dipole moments and frontier orbital energies.
Gutingimycin: ein komplexer Metabolit aus einem marinen Streptomyceten (2004)

Aus dem Meer: Gutingimycin (1) aus dem marinen Streptomyceten B8652 ist ein Konjugat aus Guanin und Trioxacarcin A, wie durch NMR-Untersuchungen und eine Kristallstrukturanalyse gezeigt wurde. Der Naturstoff entsteht wahrscheinlich durch einen selektiven Angriff von Trioxacarcin A auf die bakterielle DNA, was zu Strangbrüchen führt und die hohe Cytotoxizität von Trioxacarcin A erklärt.
The best backbone for HIV prevention, treatment, and elimination: Emtricitabine+tenofovir (2022)

The advent of antiretroviral combination therapy has significantly impacted the HIV/AIDS epidemic. No longer a death sentence, HIV infection can be controlled and suppressed using cocktail therapies that contain two or more small molecule drugs. This review aims to highlight the discovery, development, and impact of one such molecule, namely, emtricitabine (FTC, emtriva), which is one of the most successful drugs in the fight against HIV/AIDS and has been taken by over 94% of individuals infected with HIV in the USA. We also pay tribute to Dr. John C. Martin, former CEO and Chairman of Gilead Sciences, who unexpectedly passed away in 2021. A true visionary, he was instrumental in delivering FTC, as part of combination therapy with TDF (tenofovir, viread) to the global stage. As the fight to eradicate HIV marches on, we honor Dr. Martin's legacy of collaboration, achievement, and hope.
Modeling multimode-input star couplers in polymers (1994)

In this paper, we present the first numerical study of highly multimode-input integrated-optic star couplers. Although the design utilizes the physical quantities appropriate for a polymer device, many of the results are applicable to multimode-input star couplers using a wide range of materials. Design parameters explored include the input-port waveguide width, refractive index difference, and insertion angle. The simulation work is done utilizing the beam propagation method. The statistically based scaling parameters for these highly multimode structures are shown to be compatible with the results of an analytical model which is suitable for initial device design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of macrophage migration inhibitory factor reduces endometriotic implant size in mice with experimentally induced disease. (2011)

Endometriosis is a debilitating disease common in women of reproductive age characterized by pain and infertility. Macrophage migration inhibitory factor (MIF) is a cytokine whose expression is elevated in endometriotic tissue from women with the disease but the functional role of this factor in the pathogenesis of the disease is uncertain. To examine the role of MIF in the pathogenesis of endometriosis, we induced experimental disease in mice and examined the ability of the MIF antagonist, ISO-1, to reduce endometriotic implant size. Administration of ISO-1 resulted in a significant reduction in implant size and vascularity (as assessed by Flk1 mRNA expression) which was not associated with an alteration in the reproductive cycle. These data suggest that inhibition of MIF activity is associated with a significant reduction in endometriotic implant size and leads us to speculate that a similar approach of targeting MIF may prove useful in treating endometriosis in humans.
Direct measurements of anchor damping in MEMS resonators (2017)

The aim of this study is to quantify the energy loss mechanisms for single anchored double-ended tuning forks (DETF) - particularly, gas damping, thermoelastic dissipation (TED) and anchor damping. We performed ring-down measurements of quality factor (Q) as a function of pressure to confirm the absence of air damping. We also measured Q over a wide temperature range including where the coefficient of thermal expansion (CTE) crosses zero, and consequently the effects from thermoelastic dissipation (TED) become negligible. This provides the first opportunity to directly quantify energy losses due to anchor damping and allows us to vary the mounting configuration to explore the impact of the mounting on the loss.