gebhart/patrepeval huggingface dataset:
Online Targeted Learning (2014)

We consider the case that the data comes in sequentially and can be viewed as sample of independent and identically distributed observations from a fixed data generating distribution. The goal is to estimate a particular path wise target parameter of this data generating distribution that is known to be an element of a particular semi-parametric statistical model. We want our estimator to be asymptotically efficient, but we also want that our estimator can be calculated by updating the current estimator based on the new block of data without having to revisit the past data, so that it is computationally much faster to compute than recomputing a fixed estimator each time new data comes in. We refer to such an estimator as an online estimator. These online estimators can also be applied on a large fixed data base by dividing the data set in many subsets and enforcing an ordering of these subsets. The current literature provides such online estimators for parametric models, where the online estimators are based on variations of the stochastic gradient descent algorithm.\nFor that purpose we propose a new online one-step estimator, which is proven to be asymptotically efficient under regularity conditions. This estimator takes as input online estimators of the relevant part of the data generating distribution and the nuisance parameter that are required for efficient estimation of the target parameter. These estimators could be an online stochastic gradient descent estimator based on large parametric models as developed in the current literature, but we also propose other online data adaptive estimators that do not rely on the specification of a particular parametric model.\nWe also present a targeted version of this online one-step estimator that presumably minimizes the one-step correction and thereby might be more robust in finite samples. These online one-step estimators are not a substitution estimator and might therefore be unstable for finite samples if the target parameter is borderline identifiable.\nTherefore we also develop an online targeted minimum loss-based estimator, which updates the initial estimator of the relevant part of the data generating distribution by updating the current initial estimator with the new block of data, and estimates the target parameter with the corresponding plug-in estimator. The online substitution estimator is also proven to be asymptotically efficient under the same regularity conditions required for asymptotic normality of the online one-step estimator.\nThe online one-step estimator, targeted online one-step estimator, and online TMLE is demonstrated for estimation of a causal effect of a binary treatment on an outcome based on a dynamic data base that gets regularly updated, a common scenario for the analysis of electronic medical record data bases.\nFinally, we extend these online estimators to a group sequential adaptive design in which certain components of the data generating experiment are continuously fine-tuned based on past data, and the new data generating distribution is then used to generate the next block of data.
20% System-performance Gain of 3D Charge-trap TLC NAND Flash over 2D Floating-gate MLC NAND Flash for SCM/NAND Flash Hybrid SSD (2018)

This paper analyzes the system-level performance of Storage Class Memory (SCM) / NAND flash hybrid solid-state drive (SSD). Four types of NAND flash, 1) 3-dimentional (3D) charge-trap (CT) Triple-Level Cell (TLC) [1], 2) 3D floating-gate (FG) TLC [2], 3) 2-dimentional (2D) FG TLC, and 4) 2D FG Multi-Level Cell (MLC) NAND flash are compared for various applications. For both read-and write-intensive workloads, the low cost 3D CT TLC NAND flash realizes the best performance that is 20% higher than 2D FG MLC NAND flash. This result is very encouraging for NAND flash communities because the low cost high capacity TLC NAND flash can be used at many applications. Especially, low cost 3D CT TLC NAND flash can be extensively used at data centers that requires the high performance SSD, while in 2D FG NAND flash, high cost MLC NAND flash was necessary. The performance gain of 3D CT TLC NAND flash is obtained by the short read/write latency and the smaller write unit which is the word-lines, not the block. Disadvantage of 130% larger block size of 3D CT TLC NAND flash over 2D FG MLC NAND flash is overcome by storing frequently accessed hot data in SCM. On the other hand, in 3D FG TLC NAND flash, the large write unit (block) seriously degrades the performance by 54%. Thus, in 3D FG NAND flash, high cost MLC NAND flash is still necessary at data centers. Finally, this paper shows that in the future 3D CT TLC NAND flash, the stacked layers may increase from 48 to 512. Although the block size increases from 9.4 MBytes to 100 MBytes, the system-level performance of 3D CT TLC NAND flash-based SSD does not degraded by utilizing SCM.
Supplementary Table S2 from Sex Differences in Cancer Driver Genes and Biomarkers (2023)

&lt;p&gt;Summary of mutation load and percentage genome altered analysis&lt;/p&gt;
A control point for reducing root abuse of file-system privileges (2010)

We address the problem of restricting root's ability to change arbitrary files on disk, in order to prevent abuse on most current desktop operating systems. The approach first involves recognizing and separating out the ability to configure a system from the ability to use the system to perform tasks. The permission to modify configuration of the system is then further subdivided in order to restrict applications from modifying the file-system objects of other applications. We explore the division of root's current ability to change arbitrary files on disk and discuss a prototype that proves out the viability of the approach for designated system-wide file-system objects. Our architecture exposes a control point available for use to enforce policies that prevent one application from modifying another's file-system objects. In addition, we review in detail the permissions given to current installers, and alternative approaches for secure software installation.
Tag-Free Site-Specific BMP-2 Immobilization with Long-Acting Bioactivities via a Simple Sugar–Lectin Interaction (2020)

The construction of a biomaterial matrix with biological properties is of great importance to developing functional materials for clinical use. However, the site-specific immobilization of growth factors to endow materials with bioactivities has been a challenge to date. Considering the wide existence of glycosylation in mammalian proteins or recombinant proteins, we establish a bioaffinity-based protein immobilization strategy (bioanchoring method) utilizing the native sugar-lectin interaction between concanavalin A (Con A) and the oligosaccharide chain on glycosylated bone morphogenetic protein-2 (GBMP-2). The interaction realizes the site-specific immobilization of GBMP-2 to a substrate modified with Con A while preserving its bioactivity in a sustained and highly efficient way, as evidenced by its enhanced ability to induce osteodifferentiation compared with that of the soluble GBMP-2. Moreover, the surface with Con A-bioanchored GBMP-2 can be reused to stimulate multiple batches of C2C12 cells to differentiate almost to the same degree. Even after 4 month storage at 4 °C in phosphate-buffered saline (PBS), the Con A-bioanchored GBMP-2 still maintains the bioactivity to stimulate the differentiation of C2C12 cells. Furthermore, the ectopic ossification test proves the in vivo bioactivity of bioanchored GBMP-2. Overall, our results demonstrate that the tag-free and site (i.e., sugar chain)-specific protein immobilization strategy represents a simple and generic alternative, which is promising to apply for other glycoprotein immobilization and application. It should be noted that although the lectin we utilized can only bind to d-mannose/d-glucose, the diversity of the lectin family assures that a specific lectin could be offered for other sugar types, thus expanding the applicable scope further.
Sensitivity to a Nonpeptidic Compound (RPR103611) Blocking Human Immunodeficiency Virus Type 1 Env-Mediated Fusion Depends on Sequence and Accessibility of the gp41 Loop Region (2000)

The triterpene RPR103611 is an efficient inhibitor of membrane fusion mediated by the envelope proteins (Env, gp120-gp41) of CXCR4-dependent (X4) human immunodeficiency virus type 1 (HIV-1) strains, such as HIV-1(LAI) (LAI). Other X4 strains, such as HIV-1(NDK) (NDK), and CCR5-dependent (R5) HIV-1 strains, such as HIV-1(ADA) (ADA), were totally resistant to RPR103611. Analysis of chimeric LAI-NDK Env proteins identified a fragment of the NDK gp41 ectodomain determining drug resistance. A single difference at position 91, leucine in LAI and histidine in NDK, apparently accounted for their sensitivity or resistance to RPR103611. We had previously identified a mutation of isoleucine 84 to serine in a drug escape LAI variant. Both I84 and L91 are located in the "loop region" of gp41 separating the proximal and distal helix domains. Nonpolar residues in this region therefore appear to be important for the antiviral activity of RPR103611 and are possibly part of its target. However, another mechanism had to be envisaged to explain the drug resistance of ADA, since its gp41 loop region was almost identical to that of LAI. Fusion mediated by chimeric Env consisting of LAI gp120 and ADA gp41, or the reciprocal construct, was fully blocked by RPR103611. The gp120-gp41 complex of R5 strains is stable, relative to that of X4 strains, and this stability could play a role in their drug resistance. Indeed, when the postbinding steps of ADA infection were performed under mildly acidic conditions (pH 6.5 or 6.0), a treatment expected to favor dissociation of gp120, we achieved almost complete neutralization by RPR103611. The drug resistance of NDK was partially overcome by preincubating virus with soluble CD4, a gp120 ligand inducing conformational changes in the Env complex. The antiviral efficacy of RPR103611 therefore depends on the sequence of the gp41 loop and the stability of the gp120-gp41 complex, which could limit the accessibility of this target.
Swelling Behavior of γ-Irradiation Cross-Linked Elastomeric Polypentapeptide-Based Hydrogels (2001)

The dynamic and equilibrium swelling behavior are reported for four γ-irradiation cross-linked elastic protein-based polymers comprised of repeating pentapeptide sequences. The elastomeric polypentapeptides, previously prepared using recombinant DNA technology, are (GVGVP)251, (GVGIP)260, (GVGVP GVGVP GEGVP GVGVP GVGVP GVGVP)35](GVGVP), and (GVGVP GVGFP GEGFP GVGVP GVGFP GFGFP)35](GVGVP), where G = glycine, V = valine, P = proline, I = isoleucine, F = phenyalanine, and E = glutamic acid. These polymers had been γ-irradiation cross-linked into elastic matrices using doses ranging from 6 to 34 Mrad. Fick's law was able to explain their initial dynamic swelling behavior. Thermal history was found to be a variable affecting dynamic swelling. The equilibrium swelling ratio was dependent on both temperature and pH (for the E-containing polymers) and analyzed using the Flory−Huggins interaction parameter. The interaction parameter could be related with the Tt mechanism developed for polypeptides. Different continuities found in the phase transitions of these polymers and poly(N-isopropylacrylamide) were discussed in terms of cooperative units.
Reduced viscous damping in high frequency Piezoelectric Resonant Nanochannels for sensing in fluids (2011)

This work reports on the demonstration of a new class of high frequency piezoelectric aluminum nitride resonant sensors, dubbed Piezoelectric Resonant Nanochannels (PRNs), for operation in liquid environment with reduced viscous damping. A novel process consisting of 7 lithographic steps was developed to fabricate the PRNs of this work. The new resonant devices operating at high frequencies (278 and 458 MHz) show an unchanged value of the electromechanical coupling, k <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (about 0.7 and 0.8%), whether the channel is filled with air or a liquid. A quality factor in fluid, Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> , as high as 464 and 340 is recorded when the 278 MHz PRN is filled with DI-water and 25% glycerol solution, respectively.
Precision heterodyne oxygen-corrected spectrometry: vertical profiling of water and carbon dioxide in the troposphere and lower stratosphere (2019)

We describe the development of a near-infrared laser heterodyne radiometer: the precision heterodyne oxygen-corrected spectrometer (PHOCS). The prototype instrument is equipped with two heterodyne receivers for oxygen and water (measured near 1278 nanometers) and carbon dioxide (near 1572 nanometers) concentration profiles, respectively. The latter may be substituted by a heterodyne receiver module equipped with a laser to monitor atmospheric methane near 1651 nanometers. Oxygen measurements are intended to provide dry gas corrections and-more importantly-determine accurate temperature and pressure profiles that, in turn, improve the precision of the ${{\rm CO}_2}$CO<sub>2</sub> and ${{\rm H}_2}{\rm O}$H<sub>2</sub>O column retrievals. Vertical profiling is made feasible by interrogating the very low-noise absorption lines shapes collected at $ \approx {0.0067}\;{{\rm cm}^{ - 1}}$≈0.0067cm<sup>-1</sup> resolution. PHOCS complements the results from the Orbiting Carbon Observatory (OCO-2), Active Sensing of ${{\rm CO}_2}$CO<sub>2</sub> Emissions over Nights, Days, and Seasons (ASCENDS), and ground-based Fourier transform spectrometers. In this paper, we describe the development of the instrument by Mesa Photonics and present the results of initial tests in the vicinity of Washington, DC.
Targeting the TNFR2 oncogene on tumor cells and tregs of the tumor microenvironment via dominant TNFR2 antagonism. (2017)

106 Background: A major barrier to cancer immunotherapy is lack of selective inhibitors of the regulatory T cells (Tregs) of the cancer microenvironment and methods to directly kill tumors through novel surface oncogenes. Tumor necrosis factor receptor 2 (TNFR2) is a target protein with restricted expression on the most potent Tregs of the tumor infiltrate and newly identified as a broadly expressed oncogene on human tumors. Methods: We characterized the effect of TNFR2 antibody antagonists via TNFR2 in human samples from ovarian ascites compared to healthy controls. Results: TNFR2 antagonists potently inhibited Treg proliferation with exponential potency and selectivity for tumor microenvironment Tregs. Furthermore, common ovarian cancer cell lines such as OVCAR3 expressed the TNFR2 oncogene and were rapidly and completely killed by TNFR2 antagonistic antibodies. TNFR2 antagonistic antibodies were dominant because they succeeded even in the presence of TNF agonism. Remarkably, these antibodies worked as well in killing Treg cells as F(ab’)2 fragments, but not as well as Fc fragments. TNFF2 antagonists were not dependent on ADCC mechanisms for activity. Conclusions: Dominant TNFR2 antagonistic antibodies demonstrate tumor-specific Treg depletion. Blocking TNFR2 signaling with antagonist antibodies also creates a novel tool to possibly eliminate tumors expressing the TNFR2 oncogene and to more potently suppress Tregs of the tumor microenvironment.
Reduced-memory high-throughput fast-SSC polar code decoder architecture (2017)

Polar codes have been selected for use within 5G networks, and are being considered for data and control channel for additional 5G scenarios, like the next generation ultra reliable low latency channel. As a result, efficient fast polar code decoder implementations are essential. In this work, we present a new fast simplified successive cancellation (Fast-SSC) decoder architecture. Our proposed solution is able to reduce the memory requirements and has an improved throughput with respect to state of the art Fast-SSC decoders. We achieve these objectives through a more efficient memory utilization than that of Fast-SSC, which also enables to execute multiple instructions in a single clock cycle. Our work shows that, compared to the state of the art, memory requirements are reduced by 22.2%; at the same time, a throughput improvement of 11.6% is achieved with (1024, 512) polar codes. Comparing equal throughputs, the memory requirements are reduced by up to 60.4%.
Integrated AlGaInAs-silicon evanescent race track laser and photodetector (2007)

Here we report a racetrack resonator laser integrated with two photo-detectors on the hybrid AlGaInAs-silicon evanescent device platform. Unlike previous demonstrations of hybrid AlGaInAs-silicon evanescent lasers, we demonstrate an on-chip racetrack resonator laser that does not rely on facet polishing and dicing in order to define the laser cavity. The laser runs continuous-wave (c.w.) at 1590 nm with a threshold of 175 mA, has a maximum total output power of 29 mW and a maximum operating temperature of 60 C. The output of this laser light is directly coupled into a pair of on chip hybrid AlGaInAs-silicon evanescent photodetectors used to measure the laser output.
A magnetic resonance compatible E4D ultrasound probe for motion management of radiation therapy (2017)

There is recent interest in the use of ultrasound (US) and magnetic resonance (MR) imaging modalities for motion management during radiation therapy treatments. These imaging modalities aim to improve clinical outcomes by tracking tumor motion in order to increase the therapeutic ratio. The objective of this research is to develop an MR-compatible, real-time, three-dimensional ultrasound probe (E4D) for simultaneous MR and US imaging. The probe will be used in a system which leverages the real-time capabilities of ultrasound imaging and the soft-tissue image quality of MR for image guided radiation therapy (IgRT) of moving tumors.
Reliability Considerations in 3D Stacked Strata Systems (2009)

The bonding of multiple silicon strata to form stacked circuits with high bandwidth connections, increased circuit densities, decreased latency and the capability to stack disparate technologies is increasingly gaining interest in the microelectronics industry. Stacking has been demonstrated using bom dielectric‐to‐dielectric and metal‐to‐metal bonds for die and wafer stratum bonding. The considerable thermal, mechanical and electromigration reliability challenges resulting from such bonding has been the focus of some recently reported work. In mis paper, the bond reliability of various bonding types, including wafer‐to‐wafer dielectric bond, die‐to‐wafer Cu/Sn‐to‐Cu bond and a simultaneous organic adhesive with Cu/Sn‐to‐Cu bond is discussed. Thermomechanical and electromigration characterization of the die‐to‐wafer 3D structures is also discussed. Results indicate that the intrinsic reliability of these structures can be as robust as current 2D technologies.
IA Generative Model for True Orthorectification (2008)

Orthographic images compose an efficient and economic way to represent aerial images. This kind of information allows to measure two-dimensional objects and relate these to Geographic Information Systems. This paper deals with the computation of a true orthographic image given a set of overlapping perspective images. These are, together with the internal and external calibration the only input to our approach. These few requirements form a large advantage to systems where the digital surface model (DSM), e.g. provided by LIDAR data, is necessary. We used a Bayesian approach and define a generative model of the input images. In this, the input images are regarded as noisy measurements of an underlying true and hence unknown orthoimage. These measurements are obtained by an image formation process (generative model) that involves apart from the true orthoimage several additional parameters. Our goal is to invert the image formation process by estimating those parameters which make our input images most likely. We present results on aerial images of a complex urban environment.
Effect of finite phonon wavelength on phonon focusing (1983)

The usual theory of phonon focusing assumes the validity of "geometrical optics" for phonons. We consider here the corrections to this theory due to the finite wavelength of thermal phonons. It is found that in a typical heat-pulse experiment these corrections are very small. However, it may be possible to observe these wave optics effects in a suitably designed experiment.
Subretinal Hemorrhage Management By Pars Plana Vitrectomy and Internal Drainage (1990)

We reviewed 14 consecutive cases of subretinal hemorrhage involving the macula, in which surgery to remove the hemorrhage was performed by the authors between February 1984 and January 1989. All patients underwent pars plana vitrectomy and internal subretinal hemorrhage drainage. The causes of subretinal hemorrhages in group 1 were primary rhegmatogenous retinal detachments (three eyes), complications from scleral buckling procedures (three eyes), traumatic retinal detachments (two eyes), and sickle cell retinopathy associated with anticoagulation therapy after a pulmonary embolus (one eye). Group 2 consisted of five eyes with massive subretinal hemorrhage associated with age-related macular degeneration. In group 1, recurrent postoperative retinal detachment occurred in five eyes but reattachment was achieved in eight of the nine eyes, and final visual acuities were 20/400 or better in those eight eyes. In group 2, marked subretinal fibrosis occurred in two eyes. Although three eyes had improved visual acuities, final visual acuities were 5/200 or worse in all five eyes.
c-Maf and JunB Mediation of Th2 Differentiation Induced by the Type 2 G Protein-Coupled Receptor (VPAC2) for Vasoactive Intestinal Peptide (2004)

Vasoactive intestinal peptide and its G protein-coupled receptors, VPAC(1) and VPAC(2), regulate critical aspects of innate and adaptive immunity. T cell VPAC(2)Rs mediate changes in cytokine generation, which potently increase the Th2/Th1 ratio and consequently shift the effector responses toward allergy and inflammation. To examine mechanisms of VPAC(2) promotion of the Th2 phenotype, we analyzed controls of IL-4 transcription in CD4 T cells from T cell-targeted VPAC(2) transgenic (Tg), VPAC(2) knockout, and wild-type (WT) mice. c-maf and junB mRNA, protein, and activity were significantly up-regulated to a higher level in TCR-stimulated CD4 T cells from Tg mice compared with those from knockout and WT C57BL/6 mice. In contrast, GATA3, T-bet, and NFATc levels were identical in WT and Tg CD4 T cells. Vasoactive intestinal peptide binding to VPAC(2) on CD4 T cells specifically induces an up-regulation of the Th2-type transcription factors c-Maf and JunB, which consequently enhances IL-4 and IL-5 production, leading to a Th2-type phenotype.