gebhart/patrepeval huggingface dataset:
A 2-step comprehensive high-dose chemoradiotherapy second-line program for relapsed and refractory Hodgkin disease: analysis by intent to treat and development of a prognostic model (2001)

Salvage of patients with relapsed and refractory Hodgkin disease (HD) with high-dose chemoradiotherapy (HDT) and autologous stem cell transplantation (ASCT) results in event-free survival (EFS) rates from 30% to 50%. Unfortunately, the reduction in toxicity associated with modern supportive care has improved EFS by only 5% to 10% and has not reduced the relapse rate. Results of a comprehensive 2-step protocol encompassing dose-dense and dose-intense second-line chemotherapy, followed by HDT and ASCT, are reported. Sixty-five consecutive patients, 22 with primary refractory HD and 43 with relapsed HD, were treated with 2 biweekly cycles of ifosfamide, carboplatin, and etoposide (ICE). Peripheral blood progenitor cells from responding patients were collected, and the patients were given accelerated fractionation involved field radiotherapy (IFRT) followed by cyclophosphamide-etoposide and either intensive accelerated fractionation total lymphoid irradiation or carmustine and ASCT. The EFS rate at a median follow-up of 43 months, as analyzed by intent to treat, was 58%. The response rate to ICE was 88%, and the EFS rate for patients who underwent transplantation was 68%. Cox regression analysis identified 3 factors before the initiation of ICE that predicted for outcome: B symptoms, extranodal disease, and complete remission duration of less than 1 year. EFS rates were 83% for patients with 0 to 1 adverse factors, 27% for patients with 2 factors, and 10% for patients with 3 factors (P <.001). These results compare favorably with other series and document the feasibility and efficacy of giving uniform dose-dense and dose-intense cytoreductive chemotherapy and integrating accelerated fractionation radiotherapy into an ASCT treatment program. This prognostic model provides a basis for risk-adapted HDT.
Development of a pharmacokinetic/pharmacodynamic/disease progression model in NC/Nga mice for development of novel anti-atopic dermatitis drugs (2014)

1. JHL45, a novel immune modulator against atopic dermatitis (AD), was synthesized from decursin isolated from Angelica gigas. The goal is to evaluate the lead compound using quantitative modeling approaches to novel anti-AD drug development. 2. We tested the anti-inflammatory effect of JHL45 by in vitro screening, characterized its in vitro pharmacokinetic (PK) properties. The dose-dependent efficacy of JHL45 was developed using a pharmacokinetics/pharmacodynamics/disease progression (PK/PD/DIS) model in NC/Nga mice. 3. JHL45 has drug-like properties and pharmacological effects when administered orally to treat atopic dermatitis. The developed PK/PD/DIS model described well the rapid metabolism of JHL45, double-peak phenomenon in the PK of decursinol and inhibition of IgE generation by compounds in NC/Nga mice. Also, a quantitative model was developed and used to elucidate the complex interactions between serum IgE concentration and atopic dermatitis symptoms. 4. Our findings indicate that JHL45 has good physicochemical properties and powerful pharmacological effects when administered orally for treatment of AD in rodents.
P2‐472: PHOSPHATIDYLCHOLINE‐DHA: WHERE MODIFIABLE LIFESTYLE FACTORS AND AD PATHOLOGY CONVERGE (2018)

The development and progression of Alzheimer's Disease (AD) is influenced by multiple risk factors, such as hypertension, diabetes and obesity, and potentially modifiable lifestyle factors like diet and physical activity. However, it is not fully understood how these influences are modifying disease risk and progression. In recent years, numerous publications have employed “omics” techniques to study the effects of various diseases, healthy aging, nutrition and/or physical activity on blood and brain parameters. An important body of evidence from lipidomics points towards peripheral and central disturbances in phospholipid homeostasis in AD. Physical exercise and nutrition also impact phospholipid homeostasis and seem to have the opposite effect, compared to AD. Aim: To determine which aspects in phospholipid homeostasis affected in AD, can also be altered by modifiable factors such as nutrition and physical exercise. Literature published after 1980 in Cochrane Central Register of Controlled Trials, Medline, and Embase electronic databases was systematically analyzed using Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines to detect studies meeting the selection criteria. Search terms used: AD patients, controls, phospholipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, plasmalogen, phosphoethanolamine, phosphocholine, glycerolphosphocholine, glycerophospholipid, cardiolipin, glycerolipid, ganglioside, sphingolipid, ceramide, sulfatide, lipidomics. Random-effects meta-analysis using a linear mixed-model with correction for age differences between AD patients and controls were performed when 4-or-more publications were retrieved. Meta-analyses show significantly lower levels of PC-DHA species both in the circulation (9 studies, approximately 15% lower) as in the brain (9 studies, approximately 10% lower) of patients with AD versus healthy elderly. Additional meta-analyses for other phospholipids in blood and in the brain are currently being finalized and will be presented. Lower peripheral and central PC-DHA appears to be a consistent sign of altered phospholipid metabolism in AD. Previously, lower plasma PC-DHA has been recognized as an AD-risk elevating factor and decline of brain PC-DHA has been linked to postsynaptic disruption. Interestingly, modifiable influences such as exercise or nutrition lead to elevated plasma PC-DHA levels. Thus, PC-DHA can serve as a measurable factor integrating the metabolic alterations associated with AD and the influence of modifiable lifestyle factors.
Supplementary Figure from Transcriptomic Determinants of Response to Pembrolizumab Monotherapy across Solid Tumor Types (2023)

Supplementary Figure from Transcriptomic Determinants of Response to Pembrolizumab Monotherapy across Solid Tumor Types
A Rationally Designed Universal Catalyst for Suzuki–Miyaura Coupling Processes (2004)

Unprecedented scope, reactivity, and stability are displayed by a new catalyst system. This was demonstrated with general and efficient syntheses of sterically hindered (hetero)biaryls (see examples shown), mild coupling reactions of alkyl boron derivatives, and rapid coupling reactions of aryl chlorides at room temperature. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z53615_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Copper‐Catalyzed Oxidative C−H Bond Functionalization of N‐Allylbenzamide for Regioselective C−N and C−O Bond Formation (2019)

Copper-catalyzed oxidative couplings of N-allylbenzamides for C-N and C-O bond formations have been developed through C-H bond functionalization. To demonstrate the utility of this approach, it was applied to the synthesis of β-aminoimides and imides. To the best of our knowledge, these are the first examples in which different classes of N-containing compounds have been directly prepared from the readily available N-allylbenzamides using an inexpensive catalyst/oxidant/base (CuSO<sub>4</sub> /TBHP/Cs<sub>2</sub> CO<sub>3</sub> ) system.
Homolysis of N‐alkoxyamines: A Computational Study (2006)

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (Tc), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.
Supplementary Table 3 from Somatic Mosaic Chromosomal Alterations and Death of Cardiovascular Disease Causes among Cancer Survivors (2023)

&lt;p&gt;Supplementary Table 3: Sensitivity analyses by Cox regression considering additional covariates&lt;/p&gt;
Figure S3 from Intratumoral G100, a TLR4 Agonist, Induces Antitumor Immune Responses and Tumor Regression in Patients with Merkel Cell Carcinoma (2023)

&lt;p&gt;Figure S3 shows quantification of new and induced TCR clones in tumor and blood&lt;/p&gt;
A hybrid one-dimensional/Womersley model of pulsatile blood flow in the entire coronary arterial tree (2007)

Using a frequency-domain Womersley-type model, we previously simulated pulsatile blood flow throughout the coronary arterial tree. Although this model represents a good approximation for the smaller vessels, it does not take into account the nonlinear convective energy losses in larger vessels. Here, using Womersley's theory, we present a hybrid model that considers the nonlinear effects for the larger epicardial arteries while simulating the distal vessels (down to the 1st capillary segments) with the use of Womersley's Theory. The main trunk and primary branches were discretized and modeled with one-dimensional Navier-Stokes equations, while the smaller-diameter vessels were treated as Womersley-type vessels. Energy losses associated with vessel bifurcations were incorporated in the present analysis. The formulation enables prediction of impedance and pressure and pulsatile flow distribution throughout the entire coronary arterial tree down to the first capillary segments in the arrested, vasodilated state. We found that the nonlinear convective term is negligible and the loss of energy at a bifurcation is small in the larger epicardial vessels of an arrested heart. Furthermore, we found that the flow waves along the trunk or at the primary branches tend to scale (normalized with respect to their mean values) to a single curve, except for a small phase angle difference. Finally, the model predictions for the inlet pressure and flow waves are in excellent agreement with previously published experimental results. This hybrid one-dimensional/Womersley model is an efficient approach that captures the essence of the hemodynamics of a complex large-scale vascular network. The present model has numerous applications to understanding the dynamics of coronary circulation.
Author response: The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells (2015)

Inflammation is used by the immune system to protect and repair tissues after an injury or infection. However, if inflammation is too strong, or goes on for too long, it can damage tissues. This is seen in autoimmune diseases such as inflammatory bowel disease and type 1 diabetes. Therefore, precise regulation of the inflammatory response is essential for maintaining human health. White blood cells known as T cells are central regulators of tissue inflammation. To achieve this goal, they develop into subtypes with specialized roles. For example, some T helper cells release chemical signals that trigger inflammation and other immune responses. Regulatory T (Treg) cells then shut down these immune responses once they are no longer needed. Many autoimmune and other inflammatory diseases are thought to arise—at least partially—because Treg cells fail to stop the inflammatory response. Boosting the number or the activity of Treg cells could therefore help to treat these diseases. However, technical difficulties have made it difficult to investigate the genes and molecular pathways that control how this subtype of white blood cells develops. Khor et al. thought that discovering new chemicals that increase the number of Treg cells without harming them could help to identify the pathways that control their development. Khor et al. screened over 3000 chemicals, many of which are drugs currently approved for use in humans, for their effect on immature T cells that were taken from mice and grown in the laboratory. This ‘unbiased chemical biology’ approach identified several chemicals that both encouraged the T cells to develop into Treg cells and reduced the numbers that became inflammation-promoting T helper cells. Khor et al. then focused on one of these chemicals, called harmine. Tests in mice showed that harmine reduces the extent of experimentally induced inflammatory reactions. Treg cells generated by treating immature T cells with harmine had the same effect. Further experiments showed that harmine exerts these effects, at least in part, by inhibiting the activity of a protein called DYRK1A. When DYRK1A was removed from maturing mouse T cells grown in the laboratory, the T cells tended to develop into anti-inflammatory Treg cells. These findings therefore identify DYRK1A as part of a pathway that suppresses the development of Treg cells. It remains to be discovered how it does this, and whether other DYRK protein family members have similar roles.
Application of solid state NMR for the study of surface bound species and fossil fuels (2014)

In this study, stimulated echo with pulsed field gradients was used to measure the diffusion of two different solvents, water and hexane, in AP-MSN-2.7 and AP-MSN-3.7. The resulting data were then fit using two different methods. Based on these fits, the diffusion of hexane in AP-MSN-2.7 was shown to be slower than in the larger pores. This agrees well with our studies of catalytic activity, which show an increase in the reaction rate with the increase in pore size. Thus, both substrate inhibition and diffusion played a role in the decreased efficiency of the APMSN with small pore sizes.
Array and element design for complementary large-volume power deposition patterns in microwave heating (1994)

In interstitial hyperthermia cancer treatment and other invasive microwave heating applications, arrays of implanted coaxial dipoles have been used to provide regional heating of human tissue and a variety of materials. Phase modulation of the array-element excitations has been proposed as a means of obtaining uniform, time-average power densities. In the paper an insulated monopole at its second resonance is described as an alternative to the large-diameter coaxial dipole, and a pair of complementary excitations is proposed as a means of obtaining uniform, time-average power density. The array configuration considered consists of four monopoles inserted into a homogeneous medium having a high, complex permittivity. The cases of bare metal and insulated monopoles are analyzed using the method of moments and the theory of insulated antennas in matter.
Finite width currents, non-uniform magnetic shear and the current driven ion cyclotron instability. Memorandum report (1983)

Our earlier results that non-local effects due to even a small magnetic shear produce a significant reduction of the growth rate of the ion cyclotron instability driven by a uniform current are now generalized to finite width currents. Externally prescribed as well as self-consistent shears are considered. If the current width Lc exceeds the shear length Ls, the previous results are recovered. Shear becomes less effective with reduction of Lc, and for typical parameters, the growth rate attains its (shearless) local value for Lc/Ls approximately less than 10/sup -2/. Non-local effects of the finite current width itself come into play if Lc is further reduced to a few ion Larmor radii and can quench the instability.
Fabrication of 3D silicon photonic crystal structures using conventional micromachining technology (2004)

In this paper, we present a novel method for the fabrication of three-dimensional (3D) photonic crystal structures using conventional planar silicon micromachining technology. It overcomes the disadvantages of the methods hitherto reported in the literature for the fabrication of 3D photonic crystal devices, which include high complexity of multi-step processes, tight alignment tolerances, long turnaround times, and incompatibility with an integrated photonics platform. The method utilizes a single planar etch mask coupled with time multiplexed sidewall passivating deep anisotropic reactive ion etching along with isotropic etch process to create three-dimensional photonic crystal devices. In the process, anisotropic etching is followed by isotropic etching leading to the formation of sphere like voids. This step is followed by sidewall polymer deposition and local removal of the polymer from the bottom of the spheres that allows the etch process to be repeated and produce many layers. For the etch mask initially patterned with a square lattice, the etch sequence methodology explained above yields a 3D structure with simple cubic symmetry. Theoretical calculations predict that this structure should possess a complete photonic band gap. Optimization of the photonic band gap can be achieved by using different lattices (square, triangular, hexagonal) as the etch mask to produce photonic crystals with different crystalline structures. Further, by utilizing this fabrication scheme, photonic crystals over a wide range of the electromagnetic spectrum (<3Thz to >300Thz) can be fabricated by scaling the etch times and the mask dimensions.
Inelastic processes in ion-molecule collisions: Ar$sup +$ and He$sup +$ on N$sub 2$ at low-keV energies (1975)

The Ar$sup +$+N$sub 2$ collision is studied at energies from 1.0 to 3.0 keV and in an angular range between 0 and 4.0 deg. The energy-loss spectra of the scattered ions demonstrate the presence of elastic scattering and inelastic processes arising from vibro-rotational exitation of the ground electronic state of N$sub 2$, electronic excitation of the target with concomitant vibro- rotational excitation, and target ionization. Studies of the angular dependence of these processes suggest that (a) the collisions involve the entire molecule and are thus not adequately described in terms of a binary collision model, (b) electronic and vibrational excitation occur via mechanisms which exhibit negligible coupling, and (c) electronic excitation of N$sub 2$ is due predominatly to the B $sup 3$Pi/subg/$Yields$X $sup 1$$Sigma$/subg/$sup +$ transition as evidenced by observation of the onset of dissociation at larger scattering angles. The probability of charge exchange in Ar$sup +$+N$sub 2$ and N$sup +$+N$sub 2$ collisions is also investigated and shows an angular behavior very similar to that found in He$sup +$+N$sub 2$. Inelastic scattering results for He$sup +$+N$sub 2$ are reported.
Variable sampling rate controller design for brushless DC motor (2003)

The brushless DC (BLDC) motor uses a few Hall sensors to determine the position of the rotor and to subsequently drive the motor. Without additional hardware, the velocity measurement depends on the consecutive sensor outputs. Therefore, the speed measurement frequency in a BLDC motor is velocity dependent. Conventional approach for the BLDC motor control uses shunt resistor to allow constant current sampling rate. However, the sampling time for the velocity measurement is still variable. To solve this problem, this paper proposes a variable sampling frequency observer (VSFO) for the velocity estimation. A constant sampling rate model-based controller can then be build around the proposed VSFO. The paper also presents a conservative controller design procedure to guarantee system stability. Experimental results showed that the proposed control is effective. The VSFO provides an access to accurate velocity measurement. It also offers additional freedom in the control design.
Development of Ga-Doped Transparent Conducting Zinc Oxide Films by Joule-Heating Pulsed Laser Deposition (2011)

Ga-doped zinc oxide films were prepared by a novel Joule-heating pulsed laser deposition (PLD)
Spinal Implant Development, Modeling, and Testing to Achieve Customizable and Nonlinear Stiffness (2012)

The spine naturally has a nonlinear force-deflection characteristic which facilitates passive stability, and thus there is a need for spinal implants that duplicate this behavior to provide stabilization when the spine loses stiffness through injury, degeneration, or surgery. Additionally, due to the complexity and variability in the mechanics of spinal dysfunction, implants could potentially benefit from incorporating a customizable stiffness into their design. This paper presents a spinal implant with contact-aided inserts that provide a customizable nonlinear stiffness. An analytical model was utilized to optimize the device design, and the model was then verified using a finite element model. Validation was performed on physical prototypes, first in isolation using a tensile tester and then using cadaveric testing on an in-house spine tester. Testing confirmed the performance of the implant and it was observed that the device increased mechanical stability to the spinal segment in flexion-extension and lateral-bending.
Advances in Robotics: The DLR Experience (1999)

Key items in the development of a new smart robot generation are explained in light of DLR’s recent activities in robotics research. These items are the design of articulated hands, ultra-lightweight links, and joint drive systems with integrated joint torque control, sensory feedback including real-time 3-D vision, learning and skill-transfer, modeling the environment using sensorfusion, and new sensor-based off-line programming techniques based on teaching by showing in a virtual environment.
Removal of Inhibitory Effects in a Serum Cardiac Troponin I Immunoassay (2009)

The measurement of cardiac troponin I (cTnI)1 has become the gold standard for the clinical diagnosis of myocardial infarction (1). Varieties of commercial sandwich-type immunoassays are used for the measurement of cTnI concentration in human serum or plasma. Several of these assays use pairs of monoclonal antihuman cTnI antibodies with high specificities for the invariant part of the cTnI molecule (amino acid residues 30–110), in accordance with the recommended guidelines (2). These assays are often based on magnetic beads or latex particles to take advantage of the ease of bead/particle washing, which can minimize assay interference by matrix proteins. Signal amplification by means of chemiluminescence or electrochemiluminescence allows the detection of serum cTnI at concentrations <0.05 μg/L.

As a part of the recent effort of the IFCC Working Group for Standardization of Troponin I to develop a cTnI reference measurement system (1), we have used various measurement techniques to investigate binding affinities between 6 monoclonal antibodies (mAbs) obtained from HyTest (each serving as either the capture or the detection antibody) and cTnI, in the form of either a reference material (NIST SRM 2921) or a cTnI-positive serum pool (PS). One of the techniques is the multiplexed bead array (3), which resembles the commercial bead- or particle-based immunoassays. The capture mAb molecules are covalently immobilized on different bead populations to capture cTnI. The bound cTnI …
Microwave Assisted Suzuki Reactions for the Preparation of the Antifungal 3-Aryl-5-methyl-2,5-dihydrofuran-2-ones (2005)

The Suzuki cross-coupling reaction of arylboronic acids with a bromo-furanone has been developed to prepare a series of substituted 2,5-dihydrofuran-2-ones related to the fungal metabolite, incrustoporin. A protocol of microwave heating was introduced to improve synthesis throughput.