gebhart/patrepeval huggingface dataset:
RAGE Enhances TLR Responses through Binding and Internalization of RNA (2016)

Nucleic acid recognition is an important mechanism that enables the innate immune system to detect microbial infection and tissue damage. To minimize the recognition of self-derived nucleic acids, all nucleic acid-sensing signaling receptors are sequestered away from the cell surface and are activated in the cytoplasm or in endosomes. Nucleic acid sensing in endosomes relies on members of the TLR family. The receptor for advanced glycation end-products (RAGE) was recently shown to bind DNA at the cell surface, facilitating DNA internalization and subsequent recognition by TLR9. In this article, we show that RAGE binds RNA molecules in a sequence-independent manner and enhances cellular RNA uptake into endosomes. Gain- and loss-of-function studies demonstrate that RAGE increases the sensitivity of all ssRNA-sensing TLRs (TLR7, TLR8, TLR13), suggesting that RAGE is an integral part of the endosomal nucleic acid-sensing system.
NSF Center for Chemical Innovation Solar Fuels program (2013)

The NSF Center for Chem. Innovation in Solar Fuels (CCI Solar) focuses on one of the holy&#13;\ngrails of 21st century chem. - the efficient and economical conversion of solar energy into&#13;\nstored chem. fuel. CCI Solar activities directly impact thousands of students, postdoctoral&#13;\nscholars, working scientists, and members of the public at large. Our outreach program&#13;\ndelivers Juice-from-Juice solar science activity kits to elementary, middle, and high school&#13;\nstudents. Solar Energy Activity Lab kits introduce high school and undergraduate students&#13;\nto research involving a combinatorial search for new solar materials. CCI Solar graduate&#13;\nstudents and postdoctoral scholars acquire invaluable experience by serving as mentors in&#13;\nthese outreach programs. CCI Solar researchers are delivering the message of clean&#13;\nrenewable solar fuels in television, radio, and online programs, as well as in public&#13;\nlectures, scientific research conferences, and consultations with local, state, and federal&#13;\ngovernment officials. The technol., environmental, economic, and social benefits of&#13;\nrenewable solar fuels cannot be overstated, as every human being on Earth would be&#13;\nimpacted by the development of sustainable energy resources.
[Computer-assisted knee arthroplasty: comparison with a conventional procedure. Results of 50 cases in a prospective randomized study]. (2001)

Computer-assisted surgery for total knee arthroplasty was found to provide remarkably reliable results. Once the "growing pains" of this new material have been mastered, all surgeons should be able to expect an improvement in the positioning of prosthetic implantations.
Content of intrinsic disorder influences the outcome of cell-free protein synthesis (2015)

Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yields with the contents of intrinsic disorder bioinformatically predicted in the expressed sequences. This analysis revealed strong relationships between intrinsic disorder and protein amenability to heterologous cell-free expression. On the one hand, elevated disorder content was associated with the increased ratio of soluble expression. On the other hand, overall propensity for detectable protein expression decreased with disorder content. We further demonstrated that these tendencies are rooted in some distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation, including sites of ubiquitination and PEST sequences. Our findings suggest that identification of intrinsically disordered regions in the expressed amino acid sequences can be of practical use for predicting expression success and optimizing cell-free protein synthesis.
Incipient plasticity and fully plastic contact behavior of copper coated with a graphene layer (2019)

Cu coated with a graphene layer increases the elastic modulus from 163.4 GPa to 176.7 GPa, as analyzed for the initial elastic loading during nanoindentation by the Hertzian contact theory. This is attributed to stiffening, due to the ultra-high elastic modulus of the graphene layer, and the compressive in-plane residual stresses in the Cu surface volume introduced by the lattice mismatch between graphene and Cu. The graphene layer induces incipient plasticity, manifested by pop-in events during nanoindentation loading, at shallower indentation depths. This could be due to the compressive in-plane residual stress in the Cu surface volume; however, this compressive stress does not significantly change the critical resolved shear stress for the incipient plasticity. Even in the fully plastic contact region, at an indentation depth of 100 nm, the graphene layer affects the stress distribution underneath the indenter, resulting in a lower pile-up height. When considering this reduced pile-up height, the graphene layer is found to enhance elastic modulus by 5%, whereas it has no effect on hardness.
Local orientation-dependent noise propagation for anisotropic denoising of CT-images (2009)

In X-ray Computed Tomography (CT) the measured projections and consequently the reconstructed CT images are subject to quantum and electronics noise. While noise in the projections can be well described and estimated with a corresponding physics model, the distribution of noise in the reconstructed CT images is not directly evident. Due to attenuation variations along different directions, the nature of noise in CT images is non-stationary and non-isotropic. This complicates the direct application of standard post-processing methods like bilateral filtering. In this article we describe a possibility to compute precise orientation dependent noise estimates for every pixel position. This is done by analytic propagation of projection noise estimates through indirect fan-beam filtered backprojection reconstruction. The resulting orientation dependent image noise estimates are subsequently used in adaptive bilateral filters. Taking into account the non-stationary and non-isotropic nature of noise in CT images, a reduction in image noise of about 55% compared to 39% of the standard approach is achieved with much less variability over different image regions.
Application of Directed Self-Assembly Lithography to Semiconductor Device Manufacturing Process (2013)

Directed self-assembly (DSA) lithography are recently getting in the spotlight as one of the most promising new generation lithography (NGL) candidates, which have a potential to fabricate semiconductor device patterns down to sub-30nm. In this report, latest experimental and simulation results of contact hole shrink process using the DSA are demonstrated.
Damping in 1 GHz laterally-vibrating composite piezoelectric resonators (2015)

This paper focuses on experimentally verifying the physics of damping in 1 GHz laterally-vibrating composite piezoelectric resonators. This work confutes a previously developed theory of interfacial dissipation, a slip phenomenon occurring at the interface between dissimilar materials, which associated damping to a stress jump (or difference in Young's moduli (ΔE)) of the materials forming the interface. This work finds that damping in 1 GHz laterally-vibrating AlN resonators could be attributed to either interfacial dissipation due to an acoustic velocity jump (Δv) or thermoelastic dissipation (TED) in the electrodes.
Electron wave optics in semiconductors (1989)

Starting from fundamental principles, quantitative analogies between quantum mechanical electron waves in semiconductor materials and electromagnetic optical waves in dielectrics are presented. This, in turn, suggests many new classes of electron wave optical devices such as narrow-band superlattice interference filters. Phase effects associated with an electron wave are incorporated using an ‘‘electron wave phase refractive index’’ that is proportional to the square root of the product of the electron effective mass and the electron kinetic energy. It is shown that the amplitude of an electron wave is analogous to the electric field of a TE polarized electromagnetic wave (or to the magnetic field of a TM polarized electromagnetic wave) in a dielectric. Amplitude effects associated with an electron wave are incorporated using an ‘‘electron wave amplitude refractive index’’ that is proportional to the square root of the ratio of the kinetic energy to the effective mass. A simple expression for the critical angle for total internal reflection of an electron wave is developed. By analogy to the electromagnetic optical case, the total electron transmissivity and reflectivity of a semiconductor superlattice is presented. For illustration, an electron wave interference filter that is the counterpart of a multilayer quarter-wave stack thin-film optical interference filter is designed as a variable band gap and variable thickness semiconductor superlattice. Numerous new electron optical devices are suggested.
Apertureless near-field optical microscopy: Tip–sample coupling in elastic light scattering (2003)

For linear light scattering in apertureless scanning near-field optical microscopy, we have studied the correlations between the tip radius of the probe, signal strength, spatial resolution, and sample material. Pronounced variations of the near-field distance dependence on tip shape and dielectric function of the sample are observed. For very sharp metal tips, the scattered near-field signal decays on a 5 nm length scale. Despite this highly localized tip–sample coupling, the contrast is found to depend sensitively on the vertical composition of the sample on a length scale given by the penetration depth of the incident light. The resulting implications on the use of the technique as an analytic probe method are discussed.
Potential antitumor agents. 53. Synthesis, DNA binding properties, and biological activity of perimidines designed as minimal DNA-intercalating agents (1987)

A series of compounds based on perimidine have been synthesized and evaluated for their DNA-binding properties and antitumor activity. The fused tricyclic permidine chromophore appears to be the minimal structural requirement for intercalative binding to DNA since the mode of binding could be dictated by the position of attachment of the side chain. The intercalating compounds have DNA association constants (log K = 5.8-6.5) and cytotoxic potencies (IC50 = 500-1500 nM) comparable to those shown by other classes of linear, tricyclic DNA-intercalating antitumor agents (acridinecarboxamides, phenazinecarboxamides), but none of the compounds showed in vivo activity.
Multi-resolution optical 3D sensor (2007)

A new multi resolution self calibrating optical 3D measurement system using fringe projection technique named "kolibri FLEX multi" will be presented. It can be utilised to acquire the all around shape of small to medium objects, simultaneously. The basic measurement principle is the phasogrammetric approach /1,2,3/ in combination with the method of virtual landmarks for the merging of the 3D single views. The system consists in minimum of two fringe projection sensors. The sensors are mounted on a rotation stage illuminating the object from different directions. The measurement fields of the sensors can be chosen different, here as an example 40mm and 180mm in diameter. In the measurement the object can be scanned at the same time with these two resolutions. Using the method of virtual landmarks both point clouds are calculated within the same world coordinate system resulting in a common 3D-point cloud. The final point cloud includes the overview of the object with low point density (wide field) and a region with high point density (focussed view) at the same time. The advantage of the new method is the possibility to measure with different resolutions at the same object region without any mechanical changes in the system or data post processing. Typical parameters of the system are: the measurement time is 2min for 12 images and the measurement accuracy is below 3&mgr;m up to 10 &mgr;m. The flexibility makes the measurement system useful for a wide range of applications such as quality control, rapid prototyping, design and CAD/CAM which will be shown in the paper.
Modulation of protease nexin-1 activity by polysaccharides (2006)

Protease nexin-1 (PN-1) is a non-circulating pericellular serpin expressed by vascular cells. PN-1 inhibits different proteases but when associated with glycosaminoglycans, its activity is mainly directed towards thrombin. Fucoidans are sulphated polysaccharides which can interact with several serpins and have antithrombotic and anticoagulant properties in vivo with a lower hemorrhagic risk than heparin. The purpose of this study was to compare the effects of low (LMW) or high molecular weight (HMW) fucoidans to those of standard heparin and LMW heparin on PN-1 properties. Using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) and affinity coelectrophoresis, we observed that polysaccharides bound to thrombin, PN-1 and the thrombin/PN-1 complex. Progress curve kinetics showed that LMW and HMW fucoidans accelerate thrombin inhibition by PN-1 (111 and 402 fold, respectively) whereas the acceleration by LMW heparin and standard heparin was only of 36- and of 307-fold, respectively. Moreover, the formation of PN-1/(125)I-thrombin complex was increased in the presence of heparin, HMW and LMW fucoidans, but barely by LMW heparin. The dose response followed a bell shape curve, again suggesting the formation of ternary complexes between thrombin, PN-1 and polysaccharides. We also investigated the ability of polysaccharides to remove PN-1 bound to the cell membrane of smooth muscle cells in culture. PN-1 was detached by fucoidans and heparins and was still able to inhibit thrombin. In conclusion, fucoidans reduce cell-associated PN-1 and thrombin/PN-1 complexes and increase the antithrombin activity of PN-1. The capacity of PN-1 to regulate the pericellular activity of thrombin amongst other proteases reinforces the therapeutical interest of fucoidans.
Chemistry of Phenylurea Cytokinins (2019)

This chapter describes the structure-activity relationships and some biological aspects of the urea cytokinins. In any attempt at molecular superposition of different types of cytokinins, the trans structure should be used for the active conformation of the urea cytokinins. N. P. Kefford et al. reported that the substitution of a benzyl group for the phenyl group of N,N'-diphenylureas converts them from active cytokinins to antagonists in the chlorophyll retention bio-assay. The similar structure-relationships between the adenine cytokinins and the urea cytokinins, the similar biological activity characteristic to cytokinins, and the occurrence of a common, highly specific binding protein indicate that the pheny lurea compounds described possess intrinsic cytokinin properties. The research on phenylurea cytokinins originated from the work of Dr. Torigoe supervised by Professor Okamoto and Professor Isogai. Since the early study, the most extensive work was performed by Dr. Takahashi.
The Clinical Impact of Flow Titration on Epoprostenol Delivery via High Flow Nasal Cannula for ICU Patients with Pulmonary Hypertension or Right Ventricular Dysfunction: A Retrospective Cohort Comparison Study (2020)

(1) Background: inhaled epoprostenol (iEPO) delivered via high-flow nasal cannula (HFNC) has been reported to be effective for pulmonary hypertension and right ventricular dysfunction. In vitro studies have identified HFNC gas flow as a key factor in trans-nasal aerosol delivery efficiency; however, little evidence is available on the clinical impact of flow titration on trans-nasal aerosol delivery. At our institution, iEPO via HFNC was initiated in 2015 and the concept of flow titration during iEPO via HFNC has been gradually accepted and carried out by clinicians in the recent years. (2) Methods: a retrospective review of the electronic medical records for all adult patients who received iEPO via HFNC in a tertiary teaching hospital. Pre- and post- iEPO responses were reported for patients whose HFNC flow was titrated or maintained constant during iEPO delivery. Positive response to iEPO was defined as the reduction of mean pulmonary arterial pressure (mPAP) > 10% for pulmonary hypertension patients or the improvement of oxygenation [pulse oximetry (SpO<sub>2</sub>)/fraction of inhaled oxygen (F<sub>I</sub>O<sub>2</sub>)] > 20%. The number of responders to iEPO was compared between groups with titrated vs constant flow. (3) Results: 51 patients who used iEPO to treat pulmonary hypertension and/or right ventricular dysfunction were reviewed. Following iEPO administration via HFNC, mPAP decreased (43.6 ± 11.7 vs. 36.3 ± 9.7 mmHg, <i>p</i> < 0.001). Among the 51 patients, 24 had concomitant refractory hypoxemia, their oxygenation (SpO<sub>2</sub>/F<sub>I</sub>O<sub>2</sub>) improved after iEPO delivery (127.8 ± 45.7 vs. 157.6 ± 62.2, <i>p</i> < 0.001). During iEPO initiation, gas flow was titrated in 25 patients and the remaining 26 patients used constant flow. The percentage of patients in the flow titration group who met the criteria for a positive response was higher compared to the group with constant flow (85.7% vs. 50%, <i>p</i> = 0.035). Pre- vs post-iEPO responses were significant in the flow titration group included improvement in cardiac output (<i>p</i> = 0.050), cardiac index (<i>p</i> = 0.021) and F<sub>I</sub>O<sub>2</sub> reduction (<i>p</i> = 0.016). These improvements in hemodynamics and F<sub>I</sub>O<sub>2</sub> were not observed in the constant flow group. (4) Conclusion: in patients with pulmonary hypertension and/or right ventricular dysfunction, trans-nasal iEPO decreased pulmonary arterial pressure. It also improved oxygenation in patients with combined refractory hypoxemia. These improvements were more evident in patients whose gas flow was titrated during iEPO initiation than those patients using constant flow.
MR-guided adaptive focusing of ultrasound (2010)

Adaptive focusing of ultrasonic waves under the guidance of a magnetic resonance (MR) system is demonstrated for medical applications. This technique is based on the maximization of the ultrasonic wave intensity at one targeted point in space. The wave intensity is indirectly estimated from the local tissue displacement induced at the chosen focus by the acoustic radiation force of ultrasonic beams. Coded ultrasonic waves are transmitted by an ultrasonic array and an MRI scanner is used to measure the resulting local displacements through a motion-sensitive MR sequence. After the transmission of a set of spatially encoded ultrasonic waves, a non-iterative inversion process is employed to accurately estimate the spatial-temporal aberration induced by the propagation medium and to maximize the acoustical intensity at the target.Both programmable and physical aberrating layers introducing strong distortions (up to 2pi radians) were recovered within acceptable errors (<0.8 rad). This noninvasive technique is shown to accurately correct phase aberrations in a phantom gel with negligible heat deposition and limited acquisition time. These refocusing performances demonstrate a major potential in the field of MR-guided ultrasound therapy in particular for transcranial brain high-intensity focused ultrasound.
Cerebral perfusion of the left reading network predicts recovery of reading in subacute to chronic stroke (2019)

Better understanding of cerebral blood flow (CBF) perfusion in stroke recovery can help inform decisions about optimal timing and targets of restorative treatments. In this study, we examined the relationship between cerebral perfusion and recovery from stroke-induced reading deficits. Left stroke patients were tested with a noninvasive CBF measure (arterial spin labeling) <5 weeks post-stroke, and a subset had follow up testing >3 months post-stroke. We measured blood flow perfusion within the left and right sides of the brain, in areas surrounding the lesion, and areas belonging to the reading network. Two hypotheses were tested. The first was that recovery of reading function depends on increased perfusion around the stroke lesion. This hypothesis was not supported by our findings. The second hypothesis was that increased perfusion of intact areas within the reading circuit is tightly coupled with recovery. Our findings are consistent with this hypothesis. Specifically, higher perfusion in the left reading network measured during the subacute stroke period predicted better reading ability and phonology competence in the chronic period. In contrast, higher perfusion of the right homologous regions was associated with decreased reading accuracy and phonology competence in the subacute and chronic periods. These findings suggest that recovery of reading and language competence may rely on improved blood flow in the reading network of the language-dominant hemisphere.
Intracellular imaging of metmyoglobin and oxygen using new dual purpose probe EYFP‐Myoglobin‐mCherry (2021)

The biological relevance of nitric oxide (NO) and reactive oxygen species (ROS) in signaling, metabolic regulation, and disease treatment has become abundantly clear. The dramatic change in NO/ROS processing that accompanies a changing oxygen landscape calls for new imaging tools that can provide cellular details about both [O<sub>2</sub> ] and the production of reactive species. Myoglobin oxidation to the met state by NO/ROS is a known sensor with absorbance changes in the visible range. We previously employed Förster resonance energy transfer to read out the deoxygenation/oxygenation of myoglobin, creating the subcellular [O<sub>2</sub> ] sensor Myoglobin-mCherry. We now add the fluorescent protein EYFP to this sensor to create a novel probe that senses both met formation, a proxy for ROS/NO exposure, and [O<sub>2</sub> ]. Since both proteins are present in the construct, it can also relieve users from the need to measure fluorescence lifetime, making [O<sub>2</sub> ] sensing available to a wider group of laboratories.
Comparison of Fast Scintillators With TOF PET Potential (2009)

The renewed interest in time-of-flight (TOF) positron emission tomography (PET) has been accompanied by new research in the development of fast scintillators, mainly halides and/or lutetium-based compounds doped with Ce or Pr. In this work we measure some intrinsic properties of these materials, such as decay time and light output, which have a direct effect on time resolution, the key performance parameter for a TOF-grade detector. In particular, we report on measurements on LSO:Ce, LuAG:Pr, LuYAP:Ce, LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce and LaCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> :Ce. The scintillators are characterized in terms of absolute light yield, decay time, energy resolution, emission and excitation spectra, and time resolution. A new figure of merit to compare scintillators based on their performance in a TOF PET scanner is introduced. This figure of merit, the TOF effective sensitivity eta , includes both interaction probability and timing characteristics.