gebhart/patrepeval huggingface dataset:
A LOW WEAR, HIGH IMPACT STRENGTH, SURFACE CROSS-LINKED UHMWPE BY LOW ENERGY IRRADIATION (2013)

Introduction: Irradiated ultra-high molecular weight polyethylene (UHMWPE), used in the fabrication of joint implants, has increased wear resistance [1]. But, increased crosslinking decreases the mechanical strength of the polymer [2], thus limiting the crosslinking to the surface is desirable. Here, we usedelectron beam irradiation with low energy electrons to limit the penetration of the radiation exposure and achieve surface cross-linking. Methods: Medical grade 0.1 wt% vitamin E blended UHMWPE (GUR1050) was consolidated and irradiated using an electron beam at 0.8 and 3 MeV to 150 kGy. Fourier Transform Infrared Spectroscopy (FTIR) was used from the surface along the depth at an average of 32 scans and a resolution of 4 cm −1 . A transvinylene index (TVI) was calculated by normalizing the absorbance at 965 cm −1 (950–980 cm −1 ) against 1895 cm −1 (1850–1985 cm −1 ). TVI in irradiated UHMWPE is linearly correlated with the radiation received [3]. Vitamin E indices were calculated as the ratio of the area under 1265 cm −1 (1245–1275 cm −1 ) normalized by the same. Pin-on-disc (POD) wear testing was conducted on cylindrical pins (9 mm dia., 13 mm length, n = 3) as previously described at 2 Hz [4] for 1.2 million cycles (MC). Wear rate was measured as the linear regression of gravimetric weight change vs. number of cycles from 0.5 to 1.2 MC. Double notched IZOD impact testing was performed (63.5 × 12.7 × 6.35 mm) in accordance with ASTM F648. Cubes (1 cm) from 0.1 wt% blended and 150 kGy irradiated pucks (0.8 MeV) were soaked in vitamin E at 110°C for 1 hour followed by homogenization at 130°C for 48 hours. Results: The penetration of the electron beam for cross-linking was limited at low beam energy and cross-linking of the surface 2 mm was achieved (Fig 1). The wear rate of samples irradiated at 0.8 and 3 MeV was 1.12 ± 0.15, and 0.98 ± 0.11, respectively ( p > 0.5). In addition, the wear rate of the surface (0.8 MeV) irradiated UHMWPE was 0.33 ± 0.02 mg/MC 1 mm below the surface. The impact strength of UHMWPE irradiated at 0.8 MeV was 73 kJ/m 2 and 54.2 kJ/m 2 for that irradiated at 3 MeV ( p = 0.001). Doping with vitamin E and homogenization increased the surface vitamin E concentration from undetectable levels to 0.11 ± 0.01. Discussion: The wear rate of this surface cross-linked UHMWPE was comparable to uniformly cross-linked UHMWPEs irradiated at higher electron beam energies. Even lower wear rate subsurface suggested the feasibility of machining 1 mm from the surface in implant fabrication. Limiting cross-linking to the surface resulted in higher impact strength compared to a uniformly cross-linked UHMWPE. Vitamin E was optionally replenished by additional doping after cross-linking; an advantage of this method may be increased oxidation resistance. Significance: Low energy irradiation of vitamin E blended UHMWPE is feasible to fabricate total joint implants with high wear resistance and impact strength.
Decoupling stability and release in disulfide bonds with antibody-small molecule conjugates (2016)

Disulfide bonds provide a bioactivatable connection with applications in imaging and therapy. The circulation stability and intracellular release of disulfides are problematically coupled in that increasing stability causes a corresponding decrease in cleavage and payload release. However, an antibody offers the potential for a reversible stabilization. We examined this by attaching a small molecule directly to engineered cysteines in an antibody. At certain sites this unhindered disulfide was stable in circulation yet cellular internalization and antibody catabolism generated a disulfide catabolite that was rapidly reduced. We demonstrated that this stable connection and facile release is applicable to a variety of payloads. The ability to reversibly stabilize a labile functional group with an antibody may offer a way to improve targeted probes and therapeutics.
(Invited) Axial Silicon-Germanium Nanowires: Properties and Device Applications (2020)

Dense nanowire films can be considered as quasi-porous structures with a high surface-to-volume ratio. From this perspective, structural, optical and electrical properties of axial Si-Ge nanowire heterojunctions produced by the vapor-liquid-solid growth method using Au nanoclusters as catalysts are analyzed. The lattice mismatch induced strain is partially relieved due to spontaneous SiGe intermixing at the heterointerface and lateral expansion of the Ge segment of the nanowire. The mismatch in Ge and Si coefficients of thermal expansion and low thermal conductivity of Si-Ge nanowire heterojunctions are found to be responsible for the thermally induced stress detected under intense laser radiation in photoluminescence and Raman scattering measurements. In electrical measurements, the observed non-linear current-voltage characteristics, strong flicker noise, and damped current oscillations with frequencies of 20-30 MHz are explained using a proposed Si-Ge nanowire heterojunction energy band diagram that includes energy states associated with structural imperfections at the nanowire surface.
Coordinated Regulation of Cell Cycle Transcripts by p53-Inducible microRNAs, miR-192 and miR-215 (2008)

Cell cycle arrest in response to DNA damage is an important antitumorigenic mechanism. MicroRNAs (miRNAs) were recently shown to play key regulatory roles in cell cycle progression. For example, miR-34a is induced in response to p53 activation and mediates G(1) arrest by down-regulating multiple cell cycle-related transcripts. Here we show that genotoxic stress promotes the p53-dependent up-regulation of the homologous miRNAs miR-192 and miR-215. Like miR-34a, activation of miR-192/215 induces cell cycle arrest, suggesting that multiple miRNA families operate in the p53 network. Furthermore, we define a downstream gene expression signature for miR-192/215 expression, which includes a number of transcripts that regulate G(1) and G(2) checkpoints. Of these transcripts, 18 transcripts are direct targets of miR-192/215, and the observed cell cycle arrest likely results from a cooperative effect among the modulations of these genes by the miRNAs. Our results showing a role for miR-192/215 in cell proliferation combined with recent observations that these miRNAs are underexpressed in primary cancers support the idea that miR-192 and miR-215 function as tumor suppressors.
Addressing the ethical issues raised by synthetic human entities with embryo-like features (2017)

The "14-day rule" for embryo research stipulates that experiments with intact human embryos must not allow them to develop beyond 14 days or the appearance of the primitive streak. However, recent experiments showing that suitably cultured human pluripotent stem cells can self-organize and recapitulate embryonic features have highlighted difficulties with the 14-day rule and led to calls for its reassessment. Here we argue that these and related experiments raise more foundational issues that cannot be fixed by adjusting the 14-day rule, because the framework underlying the rule cannot adequately describe the ways by which synthetic human entities with embryo-like features (SHEEFs) might develop morally concerning features through altered forms of development. We propose that limits on research with SHEEFs be based as directly as possible on the generation of such features, and recommend that the research and bioethics communities lead a wide-ranging inquiry aimed at mapping out solutions to the ethical problems raised by them.
Towards the Multidimensional Measurement of Library Performance (2021)

The User Experience Index (IUX) is a composite index aimed to measure the overall user experience of services supplied by a library. The user satisfaction is evaluated by calculating the sum of the selected attributes coming from the (scaled) responses to user surveys and weighted by the coefficients assigned by experts. The reason for using the composite index approach is to capture the aggregate effect of multiple factors influencing the overall user experience. The attributes of the IUX were derived from the responses to the National User Survey conducted in Finland over several years in the same format. Altogether seven attributes were selected. The weights of these attributes in relation to each other were defined in a library directors’ workshop. The proposed composite index allows the libraries to follow a long-term development of the selected attributes through a single number encompassing their aggregate effect. At the same time, analysis of the individual attributes of the composite index can reveal components of the user experience that require special attention.
Organic Thin-Film Transistors: Part I—Compact DC Modeling (2009)

A generic analytical model for the current-voltage characteristics of organic thin-film transistors (OTFTs) is derived. Based on this generic model, a TFT compact dc model that meets the requirements for compact modeling, including for computer circuit simulators, is proposed. The models are fully symmetrical, and the TFT compact dc model covers all regimes of TFT operation-linear and saturation above threshold, subthreshold, and reverse biasing. The empirical fitting parameters are mostly eliminated from the characteristic equations. The developed models are also in close correspondence to several physical, parametric, and limiting models for current-voltage and mobility characteristics. An essential practical feature of the TFT compact dc model is that the model is both upgradable and reducible, allowing for easier implementation and modifications and also simultaneously allowing for separation of characterization techniques. This allows for systematic fitting of experimental data with large scattering in the values, but at the same time, preserving consistently the OTFT behavior in the model.
PhoP–PhoQ homologues in Pseudomonas aeruginosa regulate expression of the outer‐membrane protein OprH and polymyxin B resistance (1999)

Rapid adaptation to environmental challenge is essential for the survival of many bacterial species, and is often effectively mediated by two-component regulatory systems. Part of the adaptive response of Pseudomonas aeruginosa to Mg2+ starvation is overexpression of the outer-membrane protein OprH and increased resistance to the polycationic antibiotic polymyxin B. Two overlapping open reading frames that encoded proteins with high similarities to the PhoP-PhoQ two-component regulatory system of Salmonella typhimurium were identified downstream of the oprH gene. A P. aeruginosa PhoP-null mutant, H851, was constructed by means of a phoP:xylE-GmR transcriptional fusion, and shown to be deficient in OprH expression. In contrast, an analogous PhoQ-null mutant, H854 (phoQ:xylE-GmR), exhibited constitutive overexpression of OprH. Normal Mg2+-regulated OprH expression could be restored in both mutants by complementation with a plasmid carrying the phoP and phoQ genes. Measurement of the catechol-2,3-dioxygenase activity, expressed from the xylE transcriptional fusion in strains H851 and H854, indicated that PhoP-PhoQ is involved in the regulation of phoP-phoQ as well as oprH. Reverse transcription polymerase chain reaction experiments and Northern blot analysis revealed linkage of oprH, phoP and phoQ into an operon that was demonstrated to be under the joint control of PhoP-PhoQ and Mg2+ ion concentration. In addition, studies of the polymyxin B resistance of the two mutant strains, H851 and H854, indicated that PhoP-PhoQ is involved in regulating P. aeruginosa polymyxin resistance in response to external Mg2+ concentrations.
Biopsy needle susceptibility artifacts (1996)

Understanding the appearance of thin metallic structures in magnetic resonance imaging is important for evaluating the potential role of MRI in guiding and monitoring percutaneous interventions. As most MR compatible instruments are made from materials with a susceptibility different from water, their visibility is enhanced beyond what is expected on the grounds of displaced water alone. Unfortunately, this artifactually enhanced visibility is not constant, but instead depends on a variety of factors. This article presents computer simulations of the image distortion resulting from magnetic susceptibility differences between a needle and the surrounding tissue. The simulations show not only an artifact size that is dependent on needle composition, orientation, and pulse sequence, but also a corresponding shift of the artifact center away from the actual center of the needle. These effects place limits on the accuracy of MRI-guided needle tip placement.
Real Java applications in software transactional memory (2010)

Transactional Memory (TM) shows promise as a new concurrency control mechanism to replace lock-based synchronization. However, there have been few studies of TM systems with real applications, and the real-world benefits and barriers of TM remain unknown. In this paper, we present a detailed analysis of the behavior of real applications on a software transactional memory system. Based on this analysis, we aim to clarify what programming work is required to achieve reasonable performance in TM-based applications. We selected three existing Java applications: (1) HSQLDB, (2) the Geronimo application server, and (3) the GlassFish application server, because each application has a scalability problem caused by lock contentions. We identified the critical sections where lock contentions frequently occur, and modified the source code so that the critical sections are executed transactionally. However, this simple modification proved insufficient to achieve reasonable performance because of excessive data conflicts. We found that most of the data conflicts were caused by application-level optimizations such as reusing objects to reduce the memory usage. After modifying the source code to disable those optimizations, the TM-based applications showed higher or competitive performance compared to lock-based applications. Another finding is that the number of variables that actually cause data conflicts is much smaller than the number of variables that can be accessed in critical sections. This implies that the performance tuning of TM-based applications may be easier than that of lock-based applications where we need to take care of all of the variables that can be accessed in the critical sections.
Abstract CT205: Phase 2 study to evaluate the safety, pharmacokinetics, and clinical activity of the PI3K / mTOR inhibitor paxalisib (GDC-0084) in glioblastoma (GBM) with unmethylated O6-methylguanine-methyltransferase (MGMT) promotor status (2020)

Abstract Introduction: Paxalisib (previously GDC-0084) is a potent, oral, selective, brain-penetrant, small molecule inhibitor of class I phosphoinositide 3-kinase and mammalian target of rapamycin. The PI3K pathway is upregulated in ~85% of GBM cases and paxalisib has shown efficacy in preclinical models. A phase I study (NCT01547546) investigated paxalisib dosed once daily in 47 patients with recurrent high-grade gliomas and established a maximum tolerated dose (MTD) of 45mg once daily. The current phase II study (NCT03522298) aims to explore the safety, tolerability, and clinical activity of paxalisib in newly diagnosed GBM and an unmethylated MGMT promotor following surgery and temozolomide chemoradiation per Stupp regimen. Methods: This study has a 2-part design: an open-label, dose-escalation phase to assess the safety, tolerability and MTD (Part 1), followed by an expansion cohort (Part 2) at the MTD. Dose-escalation started at 60mg and progressed in 15mg increments using a 3+3 design. Part 2 recruits 20 patients who are randomised to administration in fed or fasted states. Results: Part 1 is complete. Nine patients were recruited and an MTD of 60mg was determined. DLTs were hyperglycemia and oral mucositis, with toxicity and patterns of AEs consistent with prior experience and other PI3K-targeting agents. For eight response-evaluable patients in Part 1, the median progression-free survival (PFS) was 8.4 months, and 25% of patients remained progression free after 15 months of follow-up. Part 2 is ongoing. Citation Format: Patrick Y. Wen, John de Groot, James D. Battiste, Samuel A. Goldlust, James S. Garner, Jeremy A. Simpson, Jelle Kijlstra, Alan Olivero, Timothy Cloughesy. Phase 2 study to evaluate the safety, pharmacokinetics, and clinical activity of the PI3K / mTOR inhibitor paxalisib (GDC-0084) in glioblastoma (GBM) with unmethylated O6-methylguanine-methyltransferase (MGMT) promotor status [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT205.
Modular Folding and Evidence for Phosphorylation-induced Stabilization of an hsp90-dependent Kinase (1998)

The <i>de novo</i> folding of the individual domains of the <i>src</i> family kinase p56<sup>lck</sup> was examined within the context of full-length p56<sup>lck</sup> molecules produced in rabbit reticulocyte lysate containing active chaperone machinery. The catalytic domain required geldanamycin-inhibitable heat shock protein 90 (hsp90) function to achieve its active protease-resistant conformation, but the src homology 2 (SH2) domain acquired phosphopeptide-binding competence independently of hsp90 function. The SH2 domain of hsp90-bound p56<sup>lck</sup> was folded and functional. In addition to the facilitation by hsp90 of kinase biogenesis, a conditional role in maintenance folding could be demonstrated; although wild type p56<sup>lck</sup> molecules with a negative-regulatory C-terminal tyrosine matured to a nearly hsp90-independent state, p56<sup>lck</sup> molecules with a mutated C-terminal tyrosine continued to require hsp90-mediated maintenance.<i>De novo</i> folding could be distinguished from maintenance folding on the basis of proteolytic fingerprints and the effects of different temperatures on folding behavior. Results indicate that during p56<sup>lck</sup> biogenesis, the SH2 domain rapidly folds independently of hsp90 function, followed by the slower hsp90-dependent folding of the catalytic domain and suggest the final stabilization of p56<sup>lck</sup> structure by phosphorylation-mediated interdomain interactions.
A designed folded polypeptide model system that catalyses the decarboxylation of oxaloacetate (1998)

NP-42, a 42-residue polypeptide that folds into a hairpin helix-loop-helix motif and dimerises to form a four-helix bundle, has been designed to catalyse the decarboxylation of oxaloacetate. The residues of the reactive site are Arg-10, Lys-11, Arg-15 and Arg-34. The lysine residue reacts with the carbonyl carbon of the substrate to form the imine intermediate that is decarboxylated to form the pyruvate product. The second-order rate constant of the NP-42 catalysed reaction in aqueous solution at pH 7.0 and 298 K determined by 1H NMR spectroscopy is 0.015 M–1 s–1, which is approximately a factor of 10 larger than that of the butylamine catalysed reaction. The study of the reaction by 1H NMR spectroscopy permits the direct observation of reactants and products and the problem of determining extinction coefficients is thus avoided. The corresponding second-order rate constant determined by UV spectroscopy is 0.010 M–1 s–1. The NP-42 catalysed reaction has been shown not to follow saturation kinetics and the reaction follows pseudo-first-order kinetics over a range of substrate concentrations from 2.5 to 30 mM. NP-42 is thus a well-defined model system for the further development of efficient catalysts capable of substrate recognition.
Panel 3: The Future Visualization Platform (2004)

Advances in graphics hardware and rendering methods are shaping the future of visualization. For example, programmable graphics processors are redefining the traditional visualization cycle. In some cases it is now possible to run the computational simulation and associated visualization side-by-side on the same chip. Moreover, global illumination and non-photorealistic effects promise to deliver imagery which enables greater insight into high resolution, multivariate, and higher-dimensional data. The panelists will offer distinct viewpoints on the direction of future graphics hardware and its potential impact on visualization, and on the nature of advanced visualizationrelated tools and techniques. Presentation of these viewpoints will be followed by audience participation in the form of a question and answer period moderated by the panel organizer.
22 nm Embedded STT-MRAM Macro with 10 ns Switching and >10 14 Endurance for Last Level Cache Applications (2021)

We demonstrate high performance 22 nm embedded STT-MRAM with a distinct combination of 10 ns write speed and >1014 endurance at chip level. This is achieved by developing a unique MTJ free layer that exhibits high H k , low moment and low damping, which dramatically reduced switching current at short pulse widths. We further show that this MTJ design meets data retention requirement of 10 years at 105°C.
The Effects of Sensor Spectral Sensitivity, Pixel Pitch, Photon Shot Noise, and Dark Noise on Perceived Image Quality (2009)

Image sensor noise was estimated in an approximately perceptually uniform space with a color image sensor model. Particularly, the noise level with respect to an image sensor's pixel pitch and the dark noise was investigated. It was shown that the noise level could be about half when spectral sensitivity was optimized considering noise with reduced color reproduction accuracy. It was also shown that for a 2.0µm pixel pitch sensor, the exposure index should be less than 100-150 in order to keep the noise level σ94 less than 5 even if it had no dark noise, whereas the exposure index could reach about 2000-4000 for a 8.0µm pixel pitch sensor depending on the sensor sensitivity and the dark noise level.
Gas-Liquid Packed Bed Reactors in Microgravity (2004)

Bone defects caused by periapical inflammation can be treated and improved by endodontic therapy. However, the mechanism for osseous healing of periapical lesions after root canal treatment is unclear. In this study we examined whether fibroblastic cells from human periapical granulation tissue could produce calcified matrix in vitro. Periapical lesions from three patients were dissected in endodontic surgery, and fibroblastic cells (HFC) migrating from these lesions in vitro were used in this study. The HFC were cultured with or without beta-glycerophosphate (beta-GP) and ascorbic acid (AA), and the expression of human runt-related transcription factor-2 (Runx2), osterix (Osx), osteopontin (Opn), and osteocalcin (Ocn) mRNA, and alkaline phosphatase (ALPase) was examined by reverse transcriptase-polymerase chain reaction (RT-PCR) or by an enzyme-cytochemical technique. Furthermore, calcification in the cells was investigated by von Kossa staining. At the beginning of the culture, HFC expressed Runx2 mRNA faintly, but neither Opn mRNA nor ALPase activity. Immunocytochemical study also showed HFC expressed Runx2 more weakly, compared to SaOS2. However, the expression levels of ALPase, and Runx2, Osx, and Opn mRNA, were stimulated by 2 mM beta-GP and 50 microg/ml AA. After 4 weeks of culture with 2 mM beta-GP and 50 microg/ml AA, HFC formed von Kossa staining-positive calcified deposits on culture dishes, and also expressed Ocn mRNA. These results suggest that inflamed periapical granulation tissue contains osteogenic cells that have the potential to differentiate into mature osteoblastic or cementoblastic cells, and that such cells might contribute to osseous healing after root canal treatment.