gebhart/patrepeval huggingface dataset:
Covariates Influencing the Exposure-Response Relationship for Certolizumab Pegol During the Induction and Maintenances Phases in Patients with Crohnʼs Disease (2016)

Introduction: Therapeutic drug monitoring during induction ofcertolizumab pegol (CZP) therapy for Crohn's disease (CD) may be a useful tool to predict efficacy outcomes.This analysis examined the effects of covariates that may influence the exposure-response relationship of CZP at the end of induction (Week 6) and maintenance (Week 26) using a previously described population pharmacokinetic model.1Figure 2Methods: Data were available from 2157 adults with moderate to severe CD who were treated with CZP in 1 of 9 trials. Multiple backward logistic regression was carried out to identify covariates associated with outcome to CZP therapy, including age, gender, weight, CZP concentration (log-transformed), antibodies to CZP (categorical), prior anti-TNF treatment, immunomodulator use, disease duration, prior surgery, baseline hematocrit, albumin, C-reactive protein (CRP) and Crohn's Disease Activity Index (CDAI).Endpoints at Weeks 6 and 26 included clinical remission (CDAI plus FC ≤250 μg/g (composite endpoint). Drop-outs were considered failures. Receiver operating characteristic (ROC) analyses were carried out to determine optimal CZP concentrations for various endpoints. Results: CZP concentrations at Week 6 were significantly associated with all Week 6 outcomes (Figure 1a) and the composite outcome at Week 26. CZP concentration at Week 12 was significantly associated with FC ≤250 μg/g and the composite outcome at Week 26 (Figure 1b). Other covariates were significantly associated with various endpoints (Table 1). Youden index thresholds of 36 μg/mL and 15 μg/mL at Week 6 and Week 12, respectively, were associated with Week 6 and 26 outcomes in ROC analyses (Table 2). Thresholds of 44 μg/mL and 48 μg/mL at Week 6 were associated with 90% specificity of achieving CRP ≤5 mg/L or FC ≤250 μg/g and with CDAI remission or the composite endpoint, respectively, at Week 6.Figure 1Conclusion: CZP concentrations at the end of induction and during maintenance are significantly associated with clinically meaningful endpoints at the end of induction and maintenance. Achieving the threshold CZP concentrations may increase the likelihood of attaining these outcomes.Figure 3
Autonomous algorithms for centralized and distributed interference coordination: a virtual layer-based approach (2014)

Interference mitigation techniques are essential for improving the performance of interference limited wireless networks. In this paper, we introduce novel interference mitigation schemes for wireless cellular networks with space division multiple access (SDMA). The schemes are based on a virtual layer that captures and simplifies the complicated interference situation in the network and that is used for power control. We show how optimization in this virtual layer generates gradually adapting power control settings that lead to autonomous interference minimization. Thereby, the granularity of control ranges from controlling frequency sub-band power via controlling the power on a per-beam basis, to a granularity of only enforcing average power constraints per beam. In conjunction with suitable short-term scheduling, our algorithms gradually steer the network towards a higher utility. We use extensive system-level simulations to compare three distributed algorithms and evaluate their applicability for different user mobility assumptions. In particular, it turns out that larger gains can be achieved by imposing average power constraints and allowing opportunistic scheduling instantaneously, rather than controlling the power in a strict way. Furthermore, we introduce a centralized algorithm, which directly solves the underlying optimization and shows fast convergence, as a performance benchmark for the distributed solutions. Moreover, we investigate the deviation from global optimality by comparing to a branch-and-bound-based solution.
Tenet: An Architecture for Tiered Sensor Networks - eScholarship (2007)

Most sensor network research and software design has been guided by an architectural principle that permits multi-node data fusion on small-form-factor, resource-poor nodes, or motes. We argue that this principle leads to fragile and unmanageable systems and explore an alternative. The Tenet architecture is motivated by the observation that future large-scale sensor network deployments will be tiered, consisting of motes in the lower tier and masters, relatively unconstrained 32-bit platform nodes, in the upper tier. Masters provide increased network capacity. Tenet constrains multinode fusion to the master tier while allowing motes to process locally-generated sensor data. This simplifies application development and allows mote-tier software to be reused. Applications running on masters task motes by composing task descriptions from a novel tasking library. We have demonstrated Tenet's effectiveness by implementing and deploying three applications. Our ambient vibration monitoring application collected 3-channel acceleration data at 20 Hz over a 570 ft span of a suspension bridge for 24 hours. In the Pursuit-evasion game, a Pioneer robot used a 56-node sensor network deployed in a hallway of a building to quickly and accurately estimate the location of an evader and successfully captured the mobile evader. In a wildlife counting application, Cyclops nodes used local image processing techniques, configured and expressed as Tenet tasks, to detect the presence of animals and stream the images to a database.
Effects of implant temperature on process characteristics of low energy boron implanted silicon (2012)

The effects of self-amorphization thickness on boron (B) dopant depth profile in silicon (Si) were investigated by cold temperature implant, down to −100°C. Significant B junction depth (Xj) reduction can be achieved for as-implant and post anneal, when the self-amorphization thickness is comparable or deeper than the B implant projected range (implant peak position) and the implant is completed at sufficiently low temperature. There is a transition temperature regime before the appropriate temperature is reached. The Xj reduction is stagnated due to the thickness limitation and the degree of self-amorphization. Temperature dependent surface damage, self-amorphization thickness, diffusion, and activation were also studied. Improvement in carrier mobility is more significant in certain dose regimes at low temperatures. The findings of this study provide important insight in to the control of the junction profile for smaller atomic mass unit (AMU) species, like B, by using the self-amorphization effect at cold temperatures.
Judging a site by its content (2011)

The physical world is rife with cues that allow us to distinguish between safe and unsafe situations. By contrast, the Internet offers a much more ambiguous environment; hence many users are unable to distinguish a scam from a legitimate Web page. To help address this problem, we explore how to train classifiers that can automatically identify malicious Web pages based on clues from their textual content, structural tags, page links, visual appearance, and URLs. Using a contemporary labeled data feed from a large Web mail provider, we extract such features and demonstrate how they can be used to improve classification accuracy over previous, more constrained approaches. In particular, by analyzing the full content of individual Web pages, we more than halve the error rate obtained by a comparably trained classifier that only extracts features from URLs. By training classifiers on different sets of features, we are further able to assess the strength of clues provided by these different sources of information.
From MFM Capacitors Toward Ferroelectric Transistors: Endurance and Disturb Characteristics of ${\rm HfO}_{2}$-Based FeFET Devices (2013)

Ferroelectric Si:HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> has been investigated starting from metal-ferroelectric-metal (MFM) capacitors over metal-ferroelectric-insulator-semiconductor (MFIS) and finally ferroelectric field-effect-transistor (FeFET) devices. Endurance characteristics and field cycling effects recognized for the material itself are shown to also translate to highly scaled 30-nm FeFET devices. Positive-up negative-down as well as pulsed I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> measurements illustrate how ferroelectric material characteristics of MFM capacitors can also be identified in more complex MFIS and FeFET structures. Antiferroelectric-like characteristics observed for relatively high Si dopant concentration reveal significant trapping superimposed onto the ferroelectric memory window limiting the general program/erase endurance of the devices to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> cycles. In addition, worst case disturb scenarios for a VDD/2 and VDD/3 scheme are evaluated to prove the viability of one-transistor memory cell concepts. The ability to tailor the ferroelectric properties by appropriate dopant concentration reveals disturb resilience up to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> disturb cycles while maintaining an I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> to I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> ratio of more than four orders of magnitude.
Reaction mechanism of trypsin-catalysed semisynthesis of human insulin studied by fast atom bombardment mass spectrometry (1991)

The production of semisynthetic human insulin for therapeutic purposes is of considerable importance. During trypsin-catalysed transformation of pig insulin into an ester of insulin of human sequence, the alanyl residue at position B30 is removed and replaced with an esterified residue of threonine. We have carried out this transformation in a medium enriched in 18OH2 and studied the product by MS. In contrast to a previous report, we find that incorporation of label into the B29 - B30 peptide bond occurs during the transformation with threonine methyl ester in aqueous N,N-dimethylacetamide. Quantitative data are presented and the implications of these findings are discussed.
Growth patterns and body composition of transgenic mice expressing mutated bovine somatotropin genes1 (1994)

The objectives of this study were to determine growth rates, feed intakes, feed efficiencies, and chemical composition of mice from three transgenic lines in 10-d periods from weaning to near maturity. Lines M4, M11, and G119K express bovine somatotropin (bST) mutations E117L, L121P-E126G, and G119K and display phenotypes of large, near normal, and small body size, respectively. M4 mice were 28% larger at 28 d and 84% larger at 68 d than non-transgenic control (NTC) mice. M11 mice were the same size at 28 d as NTC but were 25% larger at 68 d. G119K mice were 34% and 25% smaller than NTC at 28 and 68 d, respectively. Growth rates of G119K mice and NTC were similar, whereas growth rates of M11 and M4 mice were increased (P < .05). Feed intakes of M4 and M11 mice were greater than those of NTC mice (P < .05), whereas feed intakes of G119K mice were lower than those of NTC mice (P < .05). Feed efficiency (gain/feed) was improved in M4 and M11 mice (P < .05) and not altered in G119K mice compared to that of NTC mice (P > .05). Chemical composition was also altered by expression of bST analogs in transgenic mice. G119K and M4 mice had increased body fat percentages and decreased body protein percentages in comparison to M11 and NTC mice (P < .05).(ABSTRACT TRUNCATED AT 250 WORDS)
Dynamic sheath formation and sub-THz radiation from laser–metal interactions (2020)

The generation of low-frequency radiation from a short pulse (∼100 fs) laser with mJ energy incident on a metal surface is investigated. The electrons within the metal surface absorb energy from the laser pulse, increasing in temperature to a few electron volts and resulting in some at the high-energy tail of the distribution to overcome the work function barrier. Emission of these electrons from the surface contributes to a surface current which sources secondary radiation emission. The Richardson–Dushman emission picture breaks down due to Coulombic effects and a modified emission model is presented. Previous precedence exists for modified thermionic emission models for laser–metal interactions of a similar nature, such as the one presented by Riffe et al. [J. Opt. Soc. Am. B 10, 1424–1435 (1993)] upon which we elaborate. Surface currents generated by such a mechanism are modeled with a particle-in-cell (PIC) simulation together with a Monte Carlo treatment of electron–neutral collisions with air molecules. The modified emission model, together with the PIC model, provides a numerical basis from which the radiated spectra are estimated due to the time-varying currents emitted from the surface of the metal. Experiments and numerical simulations for air pressure between 0.1 and 1 atm show qualitative agreement as to the pressure dependence of the measured signal energy from the secondary radiation, with Emeasured∝Pair−α for some α near but less than 1. Quantitative agreement between experiments and simulations is improved by including the effect of an additional contribution to secondary emission energy arising from inverse-bremsstrahlung collisions within a nm-scale vapor layer.
VOICE-IF: A MIXED-INITIATIVE SPOKEN DIALOGUE SYSTEM FOR AT&T CONFERENCE SERVICES (2001)

This paper presents the Voice-IF system; a mixedinitiative spoken dialogue system for AT&T conference services. One objective for creating Voice-IF is to provide a vehicle for evaluating our technologies in speech synthesis, recognition, understanding, dialogue and user interfaces on a real application with relatively novice users. Another objective is to design, build and test a set of tools that allow us to rapidly prototype spoken dialogue applications. In this paper, we describe the performance of Voice-IF during its 6-week deployment period. In particular, we report a) results of perceptual evaluations of the synthesized speech, b) system performance and user satisfaction ratings, c) PARADISE analysis of the data, and d) comparisons with other systems, including the W99 conference registration system used at the ASRU’99 workshop and the Travel Communicator system.
Abstract 5065: Harnessing epigenetic reprogramming by histone deacetylase inhibitor MS275 for pancreatic cancer therapy (2017)

Abstract Pancreatic ductal adenocarcinoma (PDAC) accounts for more than 85% of pancreatic cancer and is one of the most lethal malignancies with limited therapeutic options. Chromatin-modulating small molecules, or epigenetic drugs, have the ability to reprogram cell fate and alter disease phenotypes. The potential of these drugs for PDAC therapy remains to be fully investigated. Screening a panel of epigenetic drugs identified MS275 (MS, also called entinostat), a histone deacetylase inhibitor, as capable of suppressing PDAC cell proliferation and inhibiting stromal fibrosis. Genome-wide expression analysis revealed that MS extensively reprograms the transcriptomes of tumor cells and cancer-associated fibroblasts (CAFs). In tumor cells, MS downregulates genes important for cell cycle progression inducing cytostasis. In CAFs, MS specifically represses the profibrotic transcription program responsive to TGF-beta, effectively inhibiting the fibrotic response. Consistent with this, MS blocks the activation of pancreatic stellate cells, the primary source for CAFs in PDAC, to repress the fibroblast-like phenotypes in these cells. Using an orthotopic transplantation model, we confirmed that MS treatment reduces tumor cell proliferation and decreases intratumoral fibrotic content. Importantly, we showed that MS substantially enhances chemocytotoxicity, synergizing with gemcitabine to reduce tumor burden in PDAC mouse models. Our study establishes a novel therapeutic strategy for PDAC based on epigenetic reprogramming induced by HDAC inhibition. Citation Format: Gaoyang Liang, Ruth Yu, Christopher Liddle, Morgan Truitt, Corina Antal, Annette Atkins, Ester Banayo, Michael Downes, Ronald Evans. Harnessing epigenetic reprogramming by histone deacetylase inhibitor MS275 for pancreatic cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5065. doi:10.1158/1538-7445.AM2017-5065
Conjugation of cis -OPDA with amino acids is a conserved pathway affecting cis -OPDA homeostasis upon stress responses (2023)

Abstract Jasmonates (JAs) are a family of oxylipin phytohormones regulating plant development and growth and mediating ‘defense versus growth’ responses. The upstream JA biosynthetic precursor cis -(+)-12-oxo-phytodienoic acid ( cis -OPDA) has been reported to act independently of the COI1-mediated JA signaling in several stress-induced and developmental processes. However, its means of perception and metabolism are only partially understood. Furthermore, cis -OPDA, but not JA, occurs in non-vascular plant species, such as bryophytes, exhibiting specific functions in defense and development. A few years ago, a low abundant isoleucine analog of the biologically active JA-Ile, OPDA-Ile, was detected in wounded leaves of flowering plants, opening up to the possibility that conjugation of cis -OPDA to amino acids might be a relevant mechanism for cis -OPDA regulation. Here, we extended the analysis of amino acid conjugates of cis -OPDA and identified naturally occurring OPDA-Val, OPDA-Phe, OPDA-Ala, OPDA-Glu, and OPDA-Asp in response to biotic and abiotic stress in Arabidopsis. The newly identified OPDA-amino acid conjugates show cis -OPDA-related plant responses in a JAR1-dependent manner. We also discovered that the synthesis and hydrolysis of cis -OPDA amino acid conjugates are regulated by members of the amidosynthetase GH3 and the amidohydrolase ILR1/ILL families. Finally, we found that the cis -OPDA conjugative pathway already functions in non-vascular plants and gymnosperms. Thus, one level of regulation by which plants modulate cis -OPDA homeostasis is the synthesis and hydrolysis of OPDA-amino acid conjugates, which temporarily store cis -OPDA in stress responses.
Liposomes Act as Effective Biolubricants for Friction Reduction in Human Synovial Joints (2009)

Phospholipids (PL) form the matrix of biological membranes and of the lipoprotein envelope monolayer, and are responsible for many of the unique physicochemical, biochemical, and biological properties of these supermolecular bioassemblies. It was suggested that phospholipids present in the synovial fluid (SF) and on the surface of articular cartilage have major involvement in the low friction of cartilage, which is essential for proper mobility of synovial joints. In pathologies, such as impaired biolubrication (leading to common joint disorders such as osteoarthritis), the level of phospholipids in the SF is reduced. Using a human-sourced cartilage-on-cartilage setup, we studied to what extent and how phospholipids act as highly effective cartilage biolubricants. We found that large multilamellar vesicles (MLV), >800 nm in diameter, composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) or of a mixture of DMPC and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) are superior lubricants in comparison to MLV composed of other phosphatidylcholines. Introducing cholesterol into liposomes resulted in less effective lubricants. DMPC-MLV was also superior to small unilamellar vesicles (SUV), <100 nm in diameter, composed of DMPC. MLV are superior to SUV due to MLV retention at and near (<200 microm below) the cartilage surface, while SUV penetrate deeper into the cartilage (450-730 microm). Superiority of specific PL compositions is explained by the thermotropic behavior (including compressibility) of the lipid bilayer. Correlating physicochemical properties of the MLV with the friction results suggests that MLV having lipid bilayers in the liquid-disordered phase and having a solid-ordered to liquid-disordered phase transition temperature slightly below physiological temperature are optimal for lubrication. High phospholipid headgroup hydration, high compressibility, and softness are the common denominators of all efficient PL compositions. The high efficiency of DMPC-MLV and DMPC/DPPC-MLV as cartilage lubricants combined with their resistance to degradation at 37 degrees C supports further evaluation of these MLV for treatment of joint impairments related to poor lubrication. This work also demonstrates the relevance of basic physicochemical properties of phospholipids to their activities in biological systems.
Instantaneous degrees of freedom of downlink interference channels with multiuser diversity (2011)

Independent channel fading across different users in a wireless network enables the system to exploit multiuser diversity. In this paper, we investigate the impact of user scheduling on the instantaneous degrees of freedom of multiple interfering cellular networks. Particularly, we consider a homogeneous multiple cellular downlink scenario with multiple users per cell. We show that if the number of users in a cell scales faster than linearly with SNR, the instantaneous degrees of freedom with multiuser diversity increases and converges to L in both mean-square (m.s.) sense and almost sure (a.s.) sense for an L-cell downlink interference channel, even though very limited channel feedback is needed. Each user is equipped with L-1 antennas to capture the multidimensional out-of-cell interference from other base stations, while the base station has a single antenna. The user scheduling strategy that achieves L instantaneous degrees of freedom is to poll users experiencing only a small amount of out-of-cell interference. The instantaneous degrees of freedom with multiuser diversity and its convergence mode are compared to those of conventional interference alignment. Furthermore, the user scaling law is relaxed when ergodic throughout is analyzed.
Optical horn antennas for efficiently transferring photons from a quantum emitter to a single-mode optical fiber (2013)

We theoretically demonstrate highly efficient optical coupling between a single quantum emitter and a monomode optical fiber over remarkably broad spectral ranges by extending the concept of horn antenna to optics. The optical horn antenna directs the radiation from the emitter toward the optical fiber and efficiently phase-matches the photon emission with the fiber mode. Numerical results show that an optical horn antenna can funnel up to 85% of the radiation from a dipolar source within an emission cone semi-angle as small as 7 degrees (antenna directivity of 300). It is also shown that 50% of the emitted power from the dipolar source can be collected and coupled to an SMF-28 fiber mode over spectral ranges larger than 1000 nm, with a maximum energy transfer reaching 70 %. This approach may open new perspectives in quantum optics and sensing.