gebhart/patrepeval huggingface dataset:
Recent advances in the study of a long pulse relativistic backward wave oscillator (2003)

Laser interferometry was recently used to diagnose plasma formation and evolution in the slow wave structure (SWS) of a relativistic backward wave oscillator (BWO) during the course of microwave generation. The results indicated that plasma from the cutoff neck inlet contributed to the termination of the high power microwave pulse. In an effort to mitigate this pulse shortening effect, the authors have replaced the cutoff neck with a Bragg reflector. As part of these studies, they have observed the cross-excitation instability because of the particularly shallow-ripple SWS used. They present results from recent experiments performed with the long pulse relativistic BWO, including the implementation of a hybrid-hard tube BWO at the University of New Mexico (UNM).
Real-time 3D body reconstruction for immersive TV (2016)

In this work, a novel and fast algorithm for real-time 3D body reconstruction from stereo sequences is proposed. The main contributions of this work consist of a novel approach for a statistically guided stereo processing and a data parallel iteration scheme for 3D estimation that includes temporal predecessors from a local spatial neighborhood. A purely GPU based implementation is provided that exhibits a nearly linear scaling of the runtime with respect to the number of GPUs. This leads to an inherent sub-pixel processing due to the availability of hardware supported texture lookups. Our implementation is able to process 4K (UHD) stereo streams on a 4×4 grid with 30 fps on a single state-of-the-art consumer graphics card. The algorithmic performance of our approach is demonstrated in the context of an immersive TV application.
The Metric Matters (2019)

Electronic hardware trust is an emerging concern for all stakeholders in the semiconductor industry. Trust issues in electronic hardware span all stages of its life cycle - from creation of intellectual property (IP) blocks to manufacturing, test and deployment of hardware components and all abstraction levels - from chips to printed circuit boards (PCBs) to systems. The trust issues originate from a horizontal business model that promotes reliance of third-party untrusted facilities, tools, and IPs in the hardware life cycle. Today, designers are tasked with verifying the integrity of third-party IPs before incorporating them into system-on-chip (SoC) designs. Existing trust metric frameworks have limited applicability since they are not comprehensive. They capture only a subset of vulnerabilities such as potential vulnerabilities introduced through design mistakes and CAD tools, or quantify features in a design that target a particular Trojan model. Therefore, current practice uses ad-hoc security analysis of IP cores. In this paper, we propose a vector-based comprehensive coverage metric that quantifies the overall trust of an IP considering both vulnerabilities and direct malicious modifications. We use a variable weighted sum of a design's functional coverage, structural coverage, and asset coverage to assess an IP's integrity. Designers can also effectively use our trust metric to compare the relative trustworthiness of functionally equivalent third-party IPs. To demonstrate the applicability and usefulness of the proposed metric, we utilize our trust metric on Trojan-free and Trojan-inserted variants of an IP. Our results demonstrate that we are able to successfully distinguish between trusted and untrusted IPs.
Backbone Modification of a Parathyroid Hormone Receptor-1 Antagonist/Inverse Agonist (2016)

A backbone-modified peptide derived from parathyroid hormone (PTH) is shown to function as an inhibitor and inverse agonist of parathyroid hormone receptor-1 (PTHR1) signaling. This receptor acts to regulate calcium and phosphate homeostasis, as well as bone turnover and development. PTH is a natural agonist of PTHR1, and PTH(1-34) displays full activity relative to the natural 84-residue hormone. PTH(1-34) is used clinically to treat osteoporosis. N-terminally truncated derivatives of PTH(1-34), such as PTH(7-34), are known to bind to PTHR1 without initiating intracellular signaling and can thus act as competitive antagonists of PTH-induced signaling at PTHR1. In some cases, N-terminally truncated PTH derivatives also act as inverse agonists of PTHR1 variants that display pathologically high levels of signaling in the absence of PTH. Many analogues of PTH, however, are rapidly degraded by proteases, which may limit biomedical application. We show that backbone modification via periodic replacement of α-amino acid residues with homologous β-amino acid residues leads to an α/β-PTH(7-34) peptide that retains the antagonist and inverse agonist activities of the prototype α-peptide while exhibiting enhanced stability in the presence of aggressive proteases. These findings highlight the value of backbone-modified peptides derived from PTH as tools for investigating determinants of PTH metabolism and provide guidance for designing therapeutic agents for diseases arising from excessive ligand-dependent or ligand-independent PTHR1 activity.
On the electromagnetic fields induced by oceanic internal waves (1984)

Model spectra for the electric and magnetic fields induced by oceanic internal waves are obtained by combining Green function solutions to the two electromagnetic modal equations with the Garrett‐Munk kinematic description of the internal wave field. The poloidal magnetic mode is dominant at frequencies above 3 f , where f is the local Coriolis frequency, and self and mutual induction are not important over this range. The toroidal magnetic mode is increasingly important at frequencies below 3 f and is sensitive to the conductivity structure below the seafloor for nearinertial frequencies. The moored electric field is shown to be largely a measure of the local velocity field at high frequencies. The vertical electric field is sensitive to the horizontal velocity field, while the horizontal electric field primarily reflects the vertical velocity field and is quite small at the seaearth and sea‐air interfaces. The magnetic field is a measure of the spatially averaged velocity field and is dominated by the poloidal magnetic mode. Electromagnetic boundary effects reduce the horizontal magnetic spectrum by decades at the seafloor and sea surface. At the seafloor and sea surface, internal wave‐induced magnetic fields are within an order of magnitude of their externally induced counterparts, while in the ocean's interior, internal waves are probably the largest source of magnetic signals in the period range one day to one hour. The internal wave‐induced electric field is not measurable except in the vertical component.
Clostridium difficile Infection after Adult Autologous Stem Cell Transplantation: A Multicenter Study of Epidemiology and Risk Factors (2013)

We sought to describe the epidemiology of Clostridium difficile infection (CDI) among adult recipients of autologous hematopoietic stem cell transplantation (auto-HSCT) within the first year after HSCT in centers with variable epidemiology of hypertoxigenic strains. A multicenter, retrospective nested case-control study was conducted among 873 auto-HSCT recipients at Johns Hopkins Hospital (JHH) and Hôpital Maisonneuve-Rosemont (HMR) between January 2003 and December 2008. Despite center differences in the prevalence of NAP-1 strains during the study period (21% to 43% at JHH versus 80% to 84% in HMR), the 1-year incidence of CDI was similar in the 2 hospitals (6.2% at JHH versus 5.7% at HMR). The median time to infection was 11 days (interquartile range, 1 to 27 days). In case-control analyses, grade ≥2 mucositis (odds ratio [OR], 3.00; P = .02) and receipt of a fourth-generation cephalosporin (OR, 2.76; P = .04) were identified as predictors for CDI. Mucositis was the strongest predictor of risk for CDI in multivariate analysis (adjusted OR, 2.77; P = .03). CDI is a common and early complication of auto-HSCT. Treatment-related gastrointestinal mucosal damage, along with the potentially modifiable risk of antimicrobial exposure, influence the risk for CDI early after auto-HSCT.
SIGCHI Social Impact Award Talk -- Ability-Based Design (2017)

The term "disability" connotes an absence of ability, but is like saying "dis-money" or "dis-height." All living people have some abilities [2]. Unfortunately, history is filled with examples of a focus on dis-ability, on what is missing, and on ensuing attempts to replace lost function to make people match a rigid world. Although often well intended, such a focus assumes humans must be adapted, and that interfaces, devices, and environments get to remain as they are. At the same time, our built things embody numerous "ability assumptions" imparted by their designers, and yet our built things remain unaware of their users' abilities. They also remain unaware of the situations their users are in, or how those situations affect their users' abilities [2,3]. An important shift in perspective comes by allowing people to "remain as they are," asking instead how interfaces, devices, and environments can bear the burden of becoming more suitable to their users' situated abilities. I call this perspective and the principles that accompany it "Ability-Based Design" [4,5], where the human abilities required to use a technology in a given context are questioned, and systems are made operable by or adaptable to alternative abilities. From this perspective, all people have varying degrees of ability, and different situations lead to different ability limitations, some long-term and some momentary. Some ability limitations come mostly from within the self, others from mostly outside the self. Ability-Based Design considers this whole "landscape of ability," respecting the human at its center and asking more of our technologies. In this talk, I will cover a decade's worth of projects related to Ability-Based Design, some directed at "people with disabilities" and others directed at "people in disabling situations." Rather than dive into any one project, I will convey a space of explored possibilities. I will also put forth a grand challenge: that anyone, anywhere, at any time can interact with technologies ideally suited to their specific situated abilities, and that our technologies do the work to achieve this fit.
Supplementary Appendix from Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors (2023)

&lt;p&gt;This file contains additional details on the supplementary methods, plus supplementary tables and legends.&lt;/p&gt;
NMR Reciprocity: A Simple(r) Description (2018)

In the context of NMR spectroscopy and MRI, the principle of reciprocity provides a convenient method for determining the reception sensitivity from the transmitted rf field pattern. The reciprocity principle for NMR was originally described by Hoult et al. [J. Magn. Reson. (1976),24, 71], and can be seen as being based on the broader Lorentz reciprocity principle, and similar theorems from antenna theory. One frequent application of the reciprocity principle is that for a single coil used for both transmission and detection, the transmit and receive fields can be assumed to be equal. This aspect is also where some of the conceptual difficulty of applying the theorem may be encountered. For example, the questions of whether one should use the complex conjugate field for detection, or whether one should apply the theorem in the rotating frame or the laboratory frame are often where considerable confusion may arise, and incorrect results may be derived. We attempt here to provide a helpful discussion of the application of the reciprocity principle in such a way as to clarify some of the confounding questions. In particular, we avoid the use of the `negatively rotating frame', which is frequently mentioned in this context, since we consider it to unnecessarily complicate the matter. In addition, we also discuss the implications of the theorem for magnetic resonance experiments on conducting samples, and metals, in particular.
Characterization of Lanthanum Zirconate Formation at the A‐Site‐Deficient Strontium‐Doped Lanthanum Manganite Cathode/Yttrium‐Stabilized Zirconia Electrolyte Interface of Solid Oxide Fuel Cells (2008)

Lanthanum zirconate (LZO) formation and growth kinetics between 1273–1673 K at the A‐site (La, Sr)‐deficient Sr‐doped lanthanum manganite (LSM)/yttrium‐stabilized zirconia (YSZ) interface were studied using high‐resolution transmission electron microscopy–energy‐dispersive X‐ray spectrometry (HRTEM–EDS). A cross‐section TEM sample preparation technique was developed using a dual‐beam focused ion beam and an in situ Omniprobe manipulator. The LZO pyrochlore phase was identified at the LSM/YSZ interface by TEM. The LZO is epitaxial with respect to the YSZ phase but not to the LSM phase. EDS results coupled with structural analysis suggest that La diffusion is a critical step in LZO formation. This study shows that LZO formation can occur even for A‐site‐deficient LSM with a La composition of 78 mol% (&lt;86 mol%). The activation energy for LZO formation was found to be 168±8 KJ/mol.
Comparison of 2DEG density and mobility increase by annealing AlGaN/GaN heterostructures deposited with Ti/Al, Ti/Au, V/Au, and Ni/Au (2013)

Abstract Temperature dependence of sheet electron density ( n s ) and mobility ( µ) of the two dimensional electron gas has been investigated in AlGaN/GaN hetero‐ structures deposited with different metal stacks such as Ti/Al, Ti/Au, V/Au, and Ni/Au. It was found that a sudden increase in n s and a hump in µ were observed with the temperature increase corresponding to the onset of reaction between the bottom metal (Ti, V, or Ni) and the AlGaN layer. At room temperature, Ti/Al showed an order of magnitude higher n s and 50% higher µ by annealing, while the amount of increase was much less for other metal stacks, indicating that Al played a key role for the increase in n s and µ . (© 2013 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Data from Selective Down-Regulation of Glioma-Associated Oncogene 2 Inhibits the Proliferation of Hepatocellular Carcinoma Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;The sonic hedgehog (Shh) pathway contributes to the initiation and progression of tumors with various origins when aberrantly activated. In this study, we investigated if the Shh pathway is important for the proliferation of hepatocellular carcinoma (HCC) cells and also began to identify which components of the pathway play a pivotal role in the biology of HCC. Expression levels of components in the pathway were measured, and glioma-associated oncogene (Gli) 2 levels were found to be considerably higher in human HCC lines compared with normal liver. Gli2 levels were also higher in tumor tissue from HCC patients compared with normal liver. Antisense oligonucleotides (ASO) were used to specifically down-regulate Gli2, and this led to decreased proliferation of various HCC cell lines. However, inhibition of Gli1 and Gli3 with ASOs did not decrease proliferation in most HCC cell lines and inhibitors targeting the upstream components of the pathway, including smoothened (Smo), displayed antiproliferative effects in only a subset of HCC cell lines. Moreover, in cancer cells harboring &lt;i&gt;Smo&lt;/i&gt; mutations or unresponsive to the Smo inhibitor 3-keto-&lt;i&gt;N&lt;/i&gt;-aminoethylaminoethylcaproyldihydrocinnamoyl cyclopamine, the Gli2 ASO was still able to inhibit proliferation. The importance of Gli2 in HCC proliferation was further confirmed by the changes in expression levels of genes, such as &lt;i&gt;Bcl-2, c-Myc&lt;/i&gt;, and &lt;i&gt;p27&lt;/i&gt;, following suppression of Gli2 expression. Taken together, these results suggest that, among the Gli transcription factors, Gli2 plays a predominant role in the proliferation of HCC cells and the suppression of Gli2 expression may provide a useful therapeutic option for the treatment of HCC. [Cancer Res 2007;67(8):3583–93]&lt;/p&gt;&lt;/div&gt;
SRH based trap model for GaN MMIC power switches (2013)

Gallium Nitride (GaN) HEMTs have increasingly been used in high frequency switching power converters. The combination of high voltage, high current, high temperature and low-on resistance enables higher efficiency and lower form factor as compared to Silicon devices. FET switch operate in the linear ohmic region. However, the presence of trap centres in GaN HEMTs alter the on-resistance and shifts the threshold voltage, causing current collapse and degrades the efficiency. Pulsed I-V measurements of a commercial foundry GaN MMIC HEMT revealed drain current collapse and on-resistance modulation in the ohmic region of the HEMT loadline. A trap model based on SRH theory was used to characterize trapping effects that alter the drain current in the linear region of operation.
Long-term efficiency preservation for gradient phase metasurface diffraction gratings in the visible (2018)

Metal-dielectric metasurfaces with an engineered phase response provide a versatile technology for the next generation of optical systems. However, metal oxidation is detrimental to the performance and lifespan of these devices. Here we demonstrate the design and fabrication of a 1200 lp/mm coated reflective metal-dielectric metasurface grating for use with 650 nm illumination. An 80 nm PMMA coating protects the sample from metal oxidation and sample degradation. The fabricated samples exhibit ~45% efficiency in the first diffractive order over 0-50° angle of incidence consistent with the electromagnetic simulations. The coated samples preserve the performance over 25 weeks in standard room temperature and humidity while the unprotected samples show over an 80% drop in efficiency.
Synthesis and Anti-HIV Activities of Glutamate and Peptide Conjugates of Nucleoside Reverse Transcriptase Inhibitors (2012)

Mono-, di-, and trinucleoside conjugates of glutamate or peptide scaffolds containing nucleoside reverse transcriptase inhibitors were synthesized. Among dinucleoside glutamate ester derivatives, N-myristoylated derivatives showed significantly higher anti-HIV activity than the corresponding N-acetylated conjugates against cell-free virus. Myristoyl-Glu(3TC)-FLT (46, EC(50) = 0.3-0.6 μM) and myristoyl-Glu(FTC)-FLT (47, EC(50) = 0.1-0.4 μM) derivatives were the most active glutamate-dinucleoside conjugates. A trinucleoside glutamate derivative containing AZT, FLT, and 3TC (34, EC(50) = 0.9-1.4 μM) exhibited higher anti-HIV activity than AZT and 3TC against cell-free virus. Compound 34 also exhibited higher anti-HIV activity against multidrug (IC(50) = 5.9 nM) and NNRTI (IC(50) = 12.9 nM) resistant viruses than parent nucleosides. The physical mixture containing FLT-succinate, AZT, 3TC, and glutamic acid exhibited 115-fold less activity against cell associated virus (EC(50) = 91.9 μM) when compared to 34 (EC(50) = 0.8 μM). Other conjugates showed less or comparable potency to that of the corresponding physical mixtures.
An array of insulin-activated, proline-directed serine/threonine protein kinases phosphorylate the p70 S6 kinase. (1992)

This study characterizes the insulin-activated serine/threonine protein kinases in H4 hepatoma cells active on a 37-residue synthetic peptide (called the SKAIPS peptide) corresponding to a putative autoinhibitory domain in the carboxyl-terminal tail of the p70 S6 kinase as well as on recombinant p70 S6 kinase. Three peaks of insulin-stimulated protein kinase active on both these substrates are identified as two (possibly three) isoforms of the 40-45-kDa erk/microtubule-associated protein (MAP)-2 kinase family and a 150-kDa form of cdc2. Although distinguishable in their substrate specificity, these protein kinases together with the p54 MAP-2 kinase share a major common specificity determinant reflected in the SKAIPS peptide: the requirement for a proline residue immediately carboxyl-terminal to the site of Ser/Thr phosphorylation. In addition, however, at least one peak of insulin-stimulated protein kinase active on recombinant p70, but not on the SKAIPS peptide, is present although not yet identified. MFP/cdc2 phosphorylates both rat liver p70 S6 kinase and recombinant p70 S6 kinase exclusively at a set of Ser/Thr residues within the putative autoinhibitory (SKAIPS peptide) domain. erk/MAP kinase does not phosphorylate rat liver p70 S6 kinase, but readily phosphorylates recombinant p70 S6 kinase at sites both within and in addition to those encompassed by the SKAIPS peptide sequences. Although the tryptic 32P-peptides bearing the cdc2 and erk/MAP kinase phosphorylation sites co-migrate with a subset of the sites phosphorylated in situ in insulin-stimulated cells, phosphorylation of the p70 S6 kinase by these proline-directed protein kinases in vitro does not reproducibly activate p70 S6 kinase activity. Thus, one or more erk/MAP kinases and cdc2 are likely to participate in the insulin-induced phosphorylation of the p70 S6 kinase. In addition to these kinases, however, phosphorylation of the p70 S6 kinase by other as yet unidentified protein kinases is necessary to recapitulate the multisite phosphorylation required for activation of the p70 S6 kinase.
The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors (1993)

The crystal structure of human immunodeficiency virus (HIV) type 2 protease has been determined in complexes with peptidic inhibitors Noa-His-Cha psi [CH(OH)CH(OH)]Val-Ile-Amp (U75875) and Qnc-Asn-Cha psi [CH(OH)CH2]Val-Npt(U92163) (where Noa is naphthyloxyacetyl, Cha is cyclohexylalanine, Amp is 2-aminomethylpyridine, Qnc is quinoline-2-carbonyl, and Npt is neopentylamine), which have dihydroxyethylene and hydroxyethylene moieties, respectively, in place of the normal scissile bond of the natural ligand. The complexes crystallize in space group P2(1)2(1)2(1), with one dimer-inhibitor complex per asymmetric unit and average cell dimensions of a = 33.28 A, b = 45.35 A, c = 135.84 A. Data were collected to approximately 2.5-A resolution. The model structures were refined with resulting R-factors of around 0.19. As expected, the HIV-2 protease structure is approximately C2-symmetric with a gross structure very similar to that of the HIV-1 enzyme. The inhibitors bind in an extended conformation positioned lengthwise in the binding cleft in a manner similar to that found in the HIV-1 protease-inhibitor complexes previously reported. The substitution of the bulkier Ile82 side chain in the HIV-2 protease may help explain the better ability of HIV-2 protease to bind and hydrolyze ligands with small P1 and P1' side groups. It appears that differences in specificity between the proteases of HIV-1 and HIV-2 are not merely a result of simple side chain substitutions, but may be complicated by differences in main chain flexibility as well.
Phosphorylation of Tristetraprolin, a Potential Zinc Finger Transcription Factor, by Mitogen Stimulation in Intact Cells and by Mitogen-activated Protein Kinase in Vitro (1995)

Tristetraprolin (TTP) is a potential transcription factor that contains three PPPPG repeats and two putative CCCH zinc fingers. TTP is encoded by the early response gene Zfp-36, which is highly expressed in response to growth factors and in several hematopoietic cell lines. In the present studies, we investigated the possibility that TTP is phosphorylated in intact cells. In NIH/3T3 cells that were made to overexpress TTP constitutively, we found that the protein was phosphorylated on serine residues, and that this phosphorylation was rapidly (within 10 min) stimulated by several mitogens. In cell-free assays, recombinant mouse TTP was a substrate for the mitogen-activated protein (MAP) kinase. By a combination of protease digestion experiments and site-directed mutagenesis strategies, we found that serine 220 was phosphorylated by p42 MAP kinase in vitro. Expression of mutant TTP in fibroblasts confirmed that serine 220 was one of the major, mitogen-stimulated phosphorylation sites on the protein in intact cells. These results suggest that TTP may be phosphorylated by MAP kinases in vivo and that this phosphorylation may regulate its function.