gebhart/patrepeval huggingface dataset:
Regioselectivity Influences in Platinum-Catalyzed Intramolecular Alkyne O–H and N–H Additions (2019)

The steric and electronic drivers of regioselectivity in platinum-catalyzed intramolecular hydroalkoxylation are elucidated. A branch point is found that divides the process between 5-exo and 6-endo selective processes, and enol ethers can be accessed in good yields for both oxygen heterocycles. The main influence arises from an electronic effect, where the alkyne substituent induces a polarization of the alkyne that leads to preferential heteroatom attack at the more electron-deficient carbon. The electronic effects are studied in other contexts, including hydroacyloxylation and hydroamination, and similar trends in directionality are predominant although not uniformly observed.
Exploratory biomarker analysis of the phase 3 KEYNOTE-604 study of pembrolizumab plus etoposide for extensive-stage SCLC. (2023)

8503 Background: In the phase 3 KEYNOTE-604 study of extensive-stage small-cell lung cancer (ES-SCLC; NCT03066778), first-line pembrolizumab (pembro) plus etoposide and platinum (EP) significantly improved PFS vs placebo (pbo) plus EP (HR, 0.75; P = 0.0023), with favorable OS (significance threshold not met; HR, 0.80; P = 0.0164). PFS/OS were similar regardless of PD-L1 CPS. In this exploratory analysis, tumor mutational burden (TMB), 18-gene T cell–inflamed gene expression profile (Tcell inf GEP) and SCLC transcriptional subtypes were assessed as correlates of survival. Methods: Patients (pts) eligible for this analysis of KEYNOTE-604 had previously untreated ES-SCLC with evaluable pretreatment tumor samples. TMB was assessed by whole-exome sequencing (WES) of tumor and matched normal DNA. RNA-seq was used to determine Tcell inf GEP and SCLC transcriptional subtypes (ASCL1, POU2F3, NEUROD1, YAP1, or inflamed). Associations of TMB, Tcell inf GEP, and SCLC subtype with OS were analyzed using an adjusted Cox proportional hazards model. 1-sided (pembro + EP) and 2-sided (pbo + EP) P values were calculated for TMB and Tcell inf GEP (prespecified α = 0.05); 2-sided P values were calculated for SCLC subtype (multiplicity-adjusted, α = 0.10). Clinical utility was assessed using prespecified cutoffs of ≥175 mut/exome for TMB and the first tertile for Tcell inf GEP. Clinical data cutoff date was Dec 2, 2019. Results: Of 453 pts randomized in KEYNOTE-604 (ITT), 318 had WES data (pembro + EP, n = 167; pbo + EP, n = 151), and 316 had RNA-seq data (pembro + EP, n = 159; pbo + EP, n = 157). High TMB was positively associated with OS in the pbo + EP group ( P = 0.005) but not the pembro + EP group ( P = 0.450). There was a positive association between higher Tcell inf GEP and OS in the pembro + EP ( P = 0.003) and pbo + EP ( P &lt; 0.005) groups. SCLC subtypes were not associated with OS in either group (pembro + EP, P = 0.960; pbo + EP, P = 0.999). Clinical benefit of pembro + EP over pbo + EP was demonstrated for TMB &lt;175 mut/exome, but not for TMB ≥175 mut/exome. Pembro + EP benefit over pbo + EP was consistent across Tcell inf GEP subgroups. Conclusions: In this exploratory analysis of biomarker subgroups of KEYNOTE-604, TMB and SCLC subtypes were not associated with OS in the pembro + EP group in pts with ES-SCLC. While Tcell inf GEP was positively associated with OS in both treatment groups, no additional OS benefit was observed with pembro + EP. Further research is warranted to better identify predictive biomarkers to immunotherapy. Clinical trial information: NCT03066778 . [Table: see text]
Fourier Plane-Wave Series Expansion for Holographic MIMO Communications (2022)

Imagine a MIMO communication system that fully exploits the propagation characteristics offered by an electromagnetic channel and ultimately approaches the limits imposed by wireless communications. This is the concept of Holographic MIMO communications. Accurate and tractable channel modeling is critical to understanding its full potential. Classical stochastic models used by communications theorists are derived under the electromagnetic far-field assumption, i.e. planar wave approximation over the array. However, such assumption breaks down when electromagnetically large (compared to the wavelength) antenna arrays are considered. In this paper, we start from the first principles of wave propagation and provide a Fourier plane-wave series expansion of the channel response, which fully captures the essence of electromagnetic propagation in arbitrary scattering and is also valid in the (radiative) near-field. The expansion is based on the Fourier spectral representation and has an intuitive physical interpretation, as it statistically describes the angular coupling between source and receiver. When discretized uniformly, it leads to a low-rank semi-unitarily equivalent approximation of the electromagnetic channel in the angular domain. The developed channel model is used to compute the ergodic capacity of a point-to-point Holographic MIMO system with different degrees of channel state information.
Dielectric Barrier Discharge Flow Control at Very Low Flight Reynolds Numbers (2008)

Experiments were performed on a flat-plate airfoil and an Eppler E338 airfoil at very low flight Reynolds numbers (3000 ≤ Re ≤ 50,000), in which dielectric barrier discharge plasma actuators were employed at the airfoil leading edges to effect flow control. The actuators were driven in a high-frequency (kilohertz) steady mode and a pulsed mode in which pulse frequency and duty cycle were varied in a systematic fashion. Optimum reduced frequencies for generating poststall lift were approximately between 0.4 and 1, and this was broadly consistent with zero-mass-flux slot-blowing data acquired at Reynolds numbers that were approximately 200 times higher. Nevertheless, profound differences in the response to reduced frequency and duty cycle were observed between the flat-plate and E338 airfoils. In general, actuation produced considerable performance improvements, including an increase in maximum lift coefficient of 0.4 to 0.8 and maintained elevated endurance at significantly higher lift coefficients. Actuation in the steady mode resulted in circulation control at Re = 3000. Pulsed actuation also exerted a significant effect on the wake at prestall angles of attack, in which control of the upper-surface flat-plate bubble shedding produced significant differences in wake spreading and vortex shedding. The flat plate was also tested in a semispan-wing configuration (AR = 6), and the effect of control was comparable with that observed on the airfoil.
Surgical Treatment of Main Thoracic Scoliosis with Thoracoscopic Anterior Instrumentation (2008)

Therapeutic Level IV. See Instructions to Authors for a complete description of levels of evidence.
Comparison of the transient stress–strain response of rubber to its linear dynamic behavior (2011)

Abstract Master curves of the small strain and dynamic shear modulus are compared with the transient mechanical response of rubbers stretched at ambient temperature over a seven‐decade range of strain rates (10 −4 to 10 3 s −1 ). The experiments were carried out on 1,4‐ and 1,2‐polybutadienes and a styrene–butadiene copolymer. These rubbers have respective glass transition temperatures, T g , equal to −93.0, 0.5, and 4.1 °C, so that the room temperature measurements probed the rubbery plateau, the glass transition zone, and the onset of the glassy state. For the 1,4‐polybutadiene, in accord with previous results, strain and strain rate effects were decoupled (additive). For the other two materials, encroachment of the segmental dynamics precluded separation of the effects of strain and rate. These results show that for rubbery polymers near T g the use of linear dynamic data to predict stresses, strain energies, and other mechanical properties at higher strain rates entails large error. For example, the strain rate associated with an upturn in the modulus due to onset of the glass transition was three orders of magnitude higher for large tensile strains than for linear oscillatory shear strains. © 2011 Wiley Periodicals, Inc.* J Polym Sci Part B: Polym Phys, 2011
Biochemical Reaction Networks (2015)

Studies at higher system levels are likely to inform those at the simpler level of the cell and vice versa– Sir Paul Nurse
Polarization diversity optical interface assembly (2023)

Examples herein relate to polarization diversity optical interface assemblies including a single mode optical fiber and first and second grating couplers disposed on a substrate. The first and second grating couplers are coupled to first and second waveguides, respectively. The assemblies further includes an optical connector to couple light between the single mode optical fiber and each of the first and second grating couplers. The optical connector includes a ferrule and a walk-off crystal. The ferrule is coupled to a portion of the single mode optical fiber. The walk-off crystal is configured to spatially separate the light into first and second orthogonal polarization modes prior to passing through the respective first and second grating couplers and/or combine the first and second polarization modes of the light prior to passing through the single mode optical fiber.
An open-label phase 1/2a trial of a genetically modified rodent malaria parasite for immunization against Plasmodium falciparum malaria (2020)

For some diseases, successful vaccines have been developed using a nonpathogenic counterpart of the causative microorganism of choice. The nonpathogenicity of the rodent <i>Plasmodium berghei</i> (<i>Pb</i>) parasite in humans prompted us to evaluate its potential as a platform for vaccination against human infection by <i>Plasmodium falciparum</i> (<i>Pf</i>), a causative agent of malaria. We hypothesized that the genetic insertion of a leading protein target for clinical development of a malaria vaccine, <i>Pf</i> circumsporozoite protein (CSP), in its natural pre-erythrocytic environment, would enhance <i>Pb</i>'s capacity to induce protective immunity against <i>Pf</i> infection. Hence, we recently generated a transgenic <i>Pb</i> sporozoite immunization platform expressing <i>Pf</i>CSP (<i>Pb</i>Vac), and we now report the clinical evaluation of its biological activity against controlled human malaria infection (CHMI). This first-in-human trial shows that <i>Pb</i>Vac is safe and well tolerated, when administered by a total of ~300 <i>Pb</i>Vac-infected mosquitoes per volunteer. Although protective efficacy evaluated by CHMI showed no sterile protection at the tested dose, significant delays in patency (2.2 days, <i>P</i> = 0.03) and decreased parasite density were observed after immunization, corresponding to an estimated 95% reduction in <i>Pf</i> liver parasite burden (confidence interval, 56 to 99%; <i>P</i> = 0.010). <i>Pb</i>Vac elicits dose-dependent cross-species cellular immune responses and functional <i>Pf</i>CSP-dependent antibody responses that efficiently block <i>Pf</i> sporozoite invasion of liver cells in vitro. This study demonstrates that <i>Pb</i>Vac immunization elicits a marked biological effect, inhibiting a subsequent infection by the human <i>Pf</i> parasite, and establishes the clinical validation of a new paradigm in malaria vaccination.
In-Situ TEM Characterization of Nucleation and Growth of Nanopatterned Oxides (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
Magnetically Stimulated Drug Release Using Nanoparticles Capped by Self-Assembling Peptides (2019)

A novel self-assembling peptide-functionalized core-shell mesoporous silica nanoparticle was developed as a drug carrier. Superparamagnetic manganese- and cobalt-doped iron oxide nanoparticles formed the core for the mesoporous silica shell coating. On the silica outer shell, the peptide Boc-Phe-Phe-Gly-Gly-COOH was covalently conjugated by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride and <i>N</i>-hydroxysulfosuccinimide sodium salt coupling. The self-assembling property of the peptide at physiological temperature was utilized to block the pore openings, while the disassembly at elevated local particle temperature released cargo molecules without bulk heating that would cause cell damage. Both conventional heating and heating in an alternating magnetic field were tested for the release of fluorescein and daunorubicin. In vitro experiments showed high cytotoxicity on pancreatic carcinoma cells (PANC-1) when this delivery system was activated by an alternating magnetic field, while control particles without drugs showed no obvious cytotoxicity.
Tetra-N-propylammonium Perruthenate (TPAP) (2007)

The crystalline, non-volatile and air-stable material tetra-N-propylammonium perruthenate (TPAP) is an important commercial catalytic oxidant, mostly used in natural products synthesis due to its ease of use, excellent performance and versatility. [1] In 1987, Ley and co-workers first introduced TPAP as a readily soluble, nonvolatile, air-stable oxidant for alcohols. [1] [2] It behaves as an overall three-electron oxidant for a wide range of multifunctional species. The full potential of TPAP was revealed when its catalytic behavior with N-methylmorpholine N-oxide (NMO) as terminal oxidant was uncovered. [3] It is stable at room temperature and may be stored for long periods under low-temperature condition. The TPAP-O2 oxidizing system meets several principles of Green Chemistry [4] and raises the prospect for industrial oxidations because of (i) its applicability in oxidation of a wide range of alcohols, (ii) its potential as terminal oxidant with air, (iii) the simple separation of the catalyst from the products, and (iv) its chemoselectivity and tolerance against many functional groups. The catalyst is inert towards double bonds, polyenes, enones, halides, cyclopropanes, epoxides, acetals, esters, amides, lactones, amines, peroxides, and catechols. Clean oxidation of alcohols occurs with TPAP in systems where competitive β-elimination poses a problem with other oxidants. [5] In addition to that, oxidation with TPAP can be achieved without racemization of the adjacent stereogenic α-centers and without double-bond migration. [4]
Using Resonance Energy Transfer to Improve Exciton Harvesting in Organic–Inorganic Hybrid Photovoltaic Cells (2005)

The effective exciton diffusion length of poly(3-hexylthiophene) (P3HT) can be improved with resonance-energy transfer from P3HT to poly(N-dodecyl-2,5-bis(2'-thienyl)pyrrole-2,1,3-benzothiadiazole) (PTPTB), a low-bandgap polymer, which results in a threefold increase of the photocurrent. Directional resonance energy transfer to the exciton-splitting interface has the potential to overcome a number of limitations associated with exciton transport in polymer photovoltaic cells.
Object-based coding for long-term archive of surveillance video (2003)

This paper describes video coding and segmentation techniques that can be used to achieve significant increase in storage capacity. Specifically, we examine the possibility to use object- based coding for efficient long-term archiving of surveillance video. We consider surveillance systems with many camera sources in which we are required to store several months of video data for each source, thus storage capacity is a major concern. The paper considers several automatic segmentation algorithms. With each algorithm, we analyze the shape coding overhead and implication on overall storage requirements, as well as the effect each algorithm has on the reconstructed quality of frames. Additionally, this paper reviews techniques to dynamically control the temporal rate of objects in the scene and perform bit allocation. Experimental results show that up to 90% savings in storage can be achieved with the proposed method compared to frame-based video coding techniques. The cost for this savings is that the accuracy of the background is compromised; however, we feel that this is satisfactory for the application under consideration.
Binding Properties of Adenosine Deaminase Interacted with Theophylline (2004)

Thermodynamic studies were carried out to evaluate the binding of theophylline on adenosine deaminase (ADA) in 50 mM sodium phosphate buffer pH 7.5, at 300 K, using isothermal titration calorimetry (ITC). A simple method for determination of binding isotherm in the drug--ADA interaction was applied using ITC data. ADA has two binding sites for theophylline, which show positive cooperativity in its sites. The intrinsic association equilibrium constants are 6 and 52 mM(-1) in the first and second binding sites, respectively. Hence, occupation of the first site has produced an appreciable enhancement by 8.7 of the binding affinity of the second site. The molar enthalpies of binding are -12.2 and -14.9 kJ/mol in the first and second binding sites, respectively.
Power of protein/tRNA functional assembly against aberrant aggregation (2017)

Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis. Here, we show that TrmFO carries an unstable protein structure that can partially mis-unfold leading to either formation of irregular and nonfunctional soluble oligomers endowed with hyper-thermal stability or large amorphous aggregates in the presence of salts. Mutagenesis confirmed that this peculiarity is an intrinsic property of a polypeptide and it is independent of the flavin coenzyme. Structural characterization and kinetic studies identified several regions of the protein that enjoy conformational changes and more particularly pinpointed the N-terminal subdomain as being a key element in the mechanisms of oligomerization and aggregation. Only stabilization of this region via tRNA suppresses these aberrant protein states. Although protein chaperones emerged as major actors against aggregation, our study emphasizes that other powerful mechanisms exist such as the stabilizing effect of functional assemblies that provide an additional layer of protection against the instability of the proteome.
delta psi-mediated signalling in the bacteriorhodopsin-dependent photoresponse (1996)

It has been shown previously that the proton-pumping activity of bacteriorhodopsin from Halobacterium salinarium can transmit an attractant signal to the bacterial flagella upon an increase in light intensity over a wide range of wavelengths. Here, we studied the effect of blue light on phototactic responses by the mutant strain Pho8l-B4, which lacks both sensory rhodopsins but has the ability to synthesize bacteriorhodopsin. Under conditions in which bacteriorhodopsin was largely accumulated as the M412 bacteriorhodopsin photocycle intermediate, halobacterial cells responded to blue light as a repellent. This response was pronounced when the membrane electric potential level was high in the presence of arginine, active oxygen consumption, or high-background long-wavelength light intensity but was inhibited by an uncoupler of oxidative phosphorylation (carbonyl cyanide 3-chlorophenylhydrazone) and was inverted in a background of low long-wavelength light intensity. The response to changes in the intensity of blue light under high background light was asymmetric, since removal of blue light did not produce an expected suppression of reversals. Addition of ammonium acetate, which is known to reduce the pH gradient changes across the membrane, did not inhibit the repellent effect of blue light, while the discharge of the membrane electric potential by tetraphenylphosphonium ions inhibited this sensory reaction. We conclude that the primary signal from bacteriorhodopsin to the sensory pathway involves changes in membrane potential.
Reconstruction of Soft Tissue Defect on Distal Leg with Extensor Digitorum Brevis Myo-Cutaneous Flap (2006)

Purpose: To report of a series of successful reconstruction of soft tissue defect on distal leg with extensor digitorum brevis myo-cutaneous flap. Methods: Between April 2002 to December 2004, 7 patients with soft tissue defect on distal leg were operated with Extensor Digiotorum Brevis myocutaneous flap. 6 of these patients had osteomyelitis.Results: Extensor Digiotorum Brevis myocutaneous flap were used in 6 patients and reverse flow flap was used in one patient. Average follow up was 19 months. All flap were survived 100% without any complication and osteomyelitis were controled in all cases. Aesthetic and functional out come were excellent on both recipient and donor sites.Conclusion: The advantages of this flap are effectively control of local wound infection, constant and reliable anatomical structures, adequately thin flap. Technical easiness for raising flap and wide arch of rotation. Extensor Digitorum Brevis myo-cutaneous flap is one of ideal option for the reconstruction of distal leg and foot defects.
Stimulated echo diffusion tensor imaging (STEAM-DTI) with varying diffusion times as a probe of breast tissue (2016)

Purpose To explore the application of diffusion tensor imaging (DTI) for breast tissue and breast pathologies using a stimulated-echo acquisition mode (STEAM) with variable diffusion times. Materials and Methods In this Health Insurance Portability and Accountability Act-compliant study, approved by the local institutional review board, eight patients and six healthy volunteers underwent an MRI examination at 3 Tesla including STEAM-DTI with several diffusion times ranging from 68.5 to 902.5 ms. A DTI model was fitted to the data for each diffusion time, and parametric maps of mean diffusivity, fractional anisotropy, axial diffusivity, and radial diffusivity were computed for healthy fibroglandular tissue (FGT) and lesions. The median value of radial diffusivity for FGT was fitted to a linear decay to obtain an estimation of the surface-to-volume ratio, from which the radial diameter was calculated. Results For healthy FGT, radial diffusivity presented a linear decay with the square root of the diffusion time resulting in a range of estimated radial diameters from 202 to 496 µm, while axial diffusivity presented a nearly time-independent diffusion. Residual fat signal was reduced at longer diffusion times due to the shorter T1 of fat. Residual fat signal to the overall signal in the healthy volunteers' FGT was found to range from 2.39% to 2.55% (shortest mixing time), and from 0.40% to 0.51% (longest mixing time) for the b500 images. Conclusion The use of variable diffusion times may provide an in vivo noninvasive tool to probe diffusion lengths in breast tissue and breast pathology, and might aid by improving fat suppression at longer diffusion times. Level of Evidence: 2 J. Magn. Reson. Imaging 2017;45:84–93.
An Irrelevant Variability Normalization Based Discriminative Training Approach for Online Handwritten Chinese Character Recognition (2013)

This paper presents a discriminative training approach to irrelevant variability normalization (IVN) based joint training of feature transforms and prototype-based classifier for recognition of online handwritten Chinese characters. A sample separation margin based minimum classification error criterion is adopted in IVN-based training, while an Rprop algorithm is used for optimizing the objective function. The IVN-trained recognizer can be made both compact and efficient by using a two-level fast-match tree whose internal nodes coincide with the labels of feature transforms. The effectiveness of the proposed approach is confirmed on an online handwritten character recognition task with a vocabulary of 9,306 characters.