gebhart/patrepeval huggingface dataset:
Irisflorentin improves α-synuclein accumulation and attenuates 6-OHDA-induced dopaminergic neuron degeneration, implication for Parkinson’s disease therapy (2015)

Parkinson's disease (PD) is a degenerative disorder of the central nervous system that is characterized by progressive loss of dopaminergic neurons in the substantia nigra pars compacta as well as motor impairment. Aggregation of α-synuclein in neuronal cells plays a key role in this disease. At present, therapeutics for PD provides moderate symptomatic benefits, but it is not able to delay the development of the disease. Current efforts toward the treatment of PD are to identify new drugs that slow or arrest the progressive course of PD by interfering with a disease-specific pathogenetic process in PD patients. Irisflorentin derived from the roots of Belamcanda chinensis (L.) DC. is an herb which has been used for the treatment of inflammatory disorders in traditional Chinese medicine. The purpose of the present study was to assess the potential for irisflorentin to ameliorate PD in Caenorhabditis elegans models. Our data reveal that irisflorentin prevents α-synuclein accumulation in the transgenic Caenorhabditis elegans model and also improves dopaminergic neuron degeneration, food-sensing behavior, and life-span in a 6-hydroxydopamine-induced Caenorhabditis elegans model, thus indicating its potential as a anti-parkinsonian drug candidate. Irisflorentin may exert its effects by promoting rpn-3 expression to enhance the activity of proteasomes and down-regulating egl-1 expression to block apoptosis pathways. These findings encourage further investigation on irisflorentin as a possible potent agent for PD treatment.
Figure S7 from Pharmacologic Properties and Preclinical Activity of Sasanlimab, A High-affinity Engineered Anti-Human PD-1 Antibody (2023)

&lt;p&gt;Supplementary Figure 7 shows the binding of sasanlimab to PD-1 by ELISA&lt;/p&gt;
Optical characterization technique for MEMS comb-drive resonators (2009)

A novel optical technique is proposed for the characterization of MEMS resonators. The proposed technique is based on measuring the response of the resonator (resonance frequency and quality factor) optically, which eliminates the electrical parasitic effects. The proposed technique was applied to a comb-drive resonator and the obtained results show good agreement with the standard electrical technique with 2-5% deviation in the resonance frequency and 2-10% in the quality factor.
Demonstration of heterogeneous III–V/Si integration with a compact optical vertical interconnect access (2013)

Heterogeneous III-V/Si integration with a compact optical vertical interconnect access is fabricated and the light coupling efficiency between the III-V/Si waveguide and the silicon nanophotonic waveguide is characterized. The III-V semiconductor material is directly bonded to the silicon-on-insulator (SOI) substrate and etched to form the III-V/Si waveguide for a higher light confinement in the active region. The compact optical vertical interconnect access is formed through tapering a III-V and an SOI layer in the same direction. The measured III-V/Si waveguide has a light coupling efficiency above ~90% to the silicon photonic layer with the tapering structure. This heterogeneous and light coupling structure can provide an efficient platform for photonic systems on chip, including passive and active devices.
Induced polarization applied to biogeophysics: recent advances and future prospects (2019)

ABSTRACT This paper provides an update on the fast‐evolving field of the induced polarization method applied to biogeophysics. It emphasizes recent advances in the understanding of the induced polarization signals stemming from biological materials and their activity, points out new developments and applications, and identifies existing knowledge gaps. The focus of this review is on the application of induced polarization to study living organisms: soil microorganisms and plants (both roots and stems). We first discuss observed links between the induced polarization signal and microbial cell structure, activity and biofilm formation. We provide an up‐to‐date conceptual model of the electrical behaviour of the microbial cells and biofilms under the influence of an external electrical field. We also review the latest biogeophysical studies, including work on hydrocarbon biodegradation, contaminant sequestration, soil strengthening and peatland characterization. We then elaborate on the induced polarization signature of the plant‐root zone, relying on a conceptual model for the generation of biogeophysical signals from a plant‐root cell. First laboratory experiments show that single roots and root system are highly polarizable. They also present encouraging results for imaging root systems embedded in a medium, and gaining information on the mass density distribution, the structure or the physiological characteristics of root systems. In addition, we highlight the application of induced polarization to characterize wood and tree structures through tomography of the stem. Finally, we discuss up‐ and down‐scaling between laboratory and field studies, as well as joint interpretation of induced polarization and other environmental data. We emphasize the need for intermediate‐scale studies and the benefits of using induced polarization as a time‐lapse monitoring method. We conclude with the promising integration of induced polarization in interdisciplinary mechanistic models to better understand and quantify subsurface biogeochemical processes.
Hybrid Scene Compression for Visual Localization (2019)

Localizing an image w.r.t. a 3D scene model represents a core task for many computer vision applications. An increasing number of real-world applications of visual localization on mobile devices, e.g., Augmented Reality or autonomous robots such as drones or self-driving cars, demand localization approaches to minimize storage and bandwidth requirements. Compressing the 3D models used for localization thus becomes a practical necessity. In this work, we introduce a new hybrid compression algorithm that uses a given memory limit in a more effective way. Rather than treating all 3D points equally, it represents a small set of points with full appearance information and an additional, larger set of points with compressed information. This enables our approach to obtain a more complete scene representation without increasing the memory requirements, leading to a superior performance compared to previous compression schemes. As part of our contribution, we show how to handle ambiguous matches arising from point compression during RANSAC. Besides outperforming previous compression techniques in terms of pose accuracy under the same memory constraints, our compression scheme itself is also more efficient. Furthermore, the localization rates and accuracy obtained with our approach are comparable to state-of-the-art feature-based methods, while using a small fraction of the memory.
Application of triazoles as bioisosteres and linkers in the development of microtubule targeting agents (2020)

The triazole ring system has emerged as an exciting prospect in the optimization studies of promising lead molecules in the quest for new drugs for clinical usage. Several marketed drugs possess these versatile moieties that are used in a wide range of medical indications. This stems from the unique intrinsic properties of triazoles, which impart stability to the basic pharmacophoric unit with an added advantage of being a bioisostere of different chemical functionalities. In the last decade, the use of triazoles as bioisosteres and linkers in the development of microtubule targeting agents has been extensively investigated. The present review highlights the advances in this promising area of drug discovery and development.
A Comprehensive Review on the Therapeutic Versatility of Imidazo [2,1-b]thiazoles (2019)

The present review, covering a number of aspects, is expected to provide useful insights in the design of imidazo[2,1-b]thiazole-based compounds and would inspire the medicinal chemists for a comprehensive and target-oriented information to achieve a major breakthrough in the development of clinically viable candidates.
Magnetic resonance elastography (MRE) detects medullary renal fibrosis (2012)

MRE is a noninvasive novel MRI modality that detects changes in tissue viscoelastic properties by imaging shear wave propagation. Renal artery stenosis (RAS) induces kidney fibrosis, yet we have previously shown that concomitant reductions in renal perfusion pressure mask an increase in cortical stiffness. We hypothesized that due to its lower vascular volume and turgor, change es in medullary elasticity in RAS would be detectable by MRE. MRE 3D elastograms were obtained in pigs after 10 weeks of RAS or matched controls (n=6 per group), and contrast‐enhanced computed tomography images obtained in the same pigs guided selection of MRE medullary regions of interest (Fig 1). Trichrome staining was used for computer‐aided quantification of medullary fibrosis ex‐vivo. The renal medulla was significantly more fibrotic (5.96±0.19 vs. 1.82±0.49%, p&lt;0.001) and stiffer (10.9±0.84 vs. 7.88±0.26 kPa, p&lt;0.05) in RAS compared to controls (Fig 1 and 2). The histological degree of medullary fibrosis directly correlated with MRE‐derived stiffness (R 2 =0.55, p&lt;0.05, Fig 3). This study therefore suggests that renal medullary MRE may be useful for detection of chronic kidney fibrosis in RAS. Grant Funding Source: NIH DK73608, HL77131 , HL085307 , and EB001981
Surface Enrichment and Depletion Effects of Ions Dissolved in an Ionic Liquid: An X‐ray Photoelectron Spectroscopy Study (2006)

Oberflächen ionischer Flüssigkeiten: Laut winkelabhängiger Röntgenphotoelektronenspektroskopie (XPS) weicht die Zusammensetzung einer Lösung von [Pt(NH3)4]Cl2 in der ionischen Flüssigkeit 1-Ethyl-3-methylimidazolium(EMIM)ethylsulfat an der Oberfläche deutlich von der im Volumen ab. [Pt(NH3)4]2+ wird an der Oberfläche auf Kosten des EMIM-Kations angereichert, während die Cl−-Konzentration bis auf Werte unterhalb der XPS-Detektionsgrenze abnimmt.
Noninvasive Imaging of Endogenous Neural Stem Cell MobilizationIn VivoUsing Positron Emission Tomography (2010)

Neural stem cells reside in two major niches in the adult brain [i.e., the subventricular zone (SVZ) and the dentate gyrus of the hippocampus]. Insults to the brain such as cerebral ischemia result in a physiological mobilization of endogenous neural stem cells. Since recent studies showed that pharmacological stimulation can be used to expand the endogenous neural stem cell niche, hope has been raised to enhance the brain's own regenerative capacity. For the evaluation of such novel therapeutic approaches, longitudinal and intraindividual monitoring of the endogenous neural stem cell niche would be required. However, to date no conclusive imaging technique has been established. We used positron emission tomography (PET) and the radiotracer 3'-deoxy-3'-[(18)F]fluoro-l-thymidine ([(18)F]FLT) that enables imaging and measuring of proliferation to noninvasively detect endogenous neural stem cells in the normal and diseased adult rat brain in vivo. This method indeed visualized neural stem cell niches in the living rat brain, identified as increased [(18)F]FLT-binding in the SVZ and the hippocampus. Focal cerebral ischemia and subsequent damage of the blood-brain barrier did not interfere with the capability of [(18)F]FLT-PET to visualize neural stem cell mobilization. Moreover, [(18)F]FLT-PET allowed for an in vivo quantification of increased neural stem cell mobilization caused by pharmacological stimulation or by focal cerebral ischemia. The data suggest that noninvasive longitudinal monitoring and quantification of endogenous neural stem cell activation in the brain is feasible and that [(18)F]FLT-PET could be used to monitor the effects of drugs aimed at expanding the neural stem cell niche.
Generation of highly mutually coherent hard-x-ray pulse pairs with an amplitude-splitting delay line (2021)

Beam splitters and delay lines are among the key building blocks of modern-day optical laser technology. Progress in x-ray free electron laser source development and applications over the past decade is calling for their counterpart operating at the Angstrom wavelength regime. Recent efforts in x-ray optics development demonstrate relatively stable delay lines that most often adopt the division-of-wavefront approach for the beam splitting and recombination. However, the two exit beams in such configurations struggle to achieve sufficient mutual coherence to enable applications such as interferometry, correlation spectroscopy, and nonlinear spectroscopy. We present an experimental realization of the generation of highly mutually coherent pulse pairs using an amplitude-split delay line design based on transmission grating beam splitters and channel-cut crystals. The performance of the prototype system was analyzed in the context of x-ray coherent scattering and correlation spectroscopy, where nearly identical high-contrast speckle patterns from both branches were observed. We show in addition the high level of dynamical stability during continuous delay scans, a capability essential for high sensitivity ultrafast measurements.
LSTMs for Inferring Planetary Boundary Layer Height (PBLH) (2021)

In this paper, we describe new work which is part of a larger study to understand how machine learning could be used to augment existing methods for calculating and estimating the Planetary Boundary Layer Height (PBLH). We describe how a Long Short-Term Memory (LSTM) Network could be used to learn PBLH changes over time for different geographical locations across the United States, used in conjunction with the WRF-Chem model. If the machine learning method could achieve accuracy levels similar to the model-based calculations, then it is feasible for the deep learning model to be used as an embedded method for the WRF-Chem model. The paper shows promising results that warrant more exploration. We describe results for two experiments in particular. The first experiment used 20 geographical locations for a two-month period of hourly WRF-Chem calculated PBLH. In this experiment, we evaluated how well the LSTM could learn PBLH by using limited data across a set of nearby locations. This model achieved RMSE of .11 on predicted PBLH. The second experiment used one year of hourly PBLH calculations from the WRF-Chem model to evaluate the LSTM prediction for a selection of three locations with separate LSTM models, achieving RMSE scores of 0.04, 0.01 and 0.05, respectively. We describe these results and the future plans for this work.
Micromagnetics of Magnetization Reversal in Patterned Magnetic Recording Medium (2006)

Selected aspects of the recording physics of data storage systems based on patterned magnetic recording medium are discussed. The micromagnetic study of the magnetization reversal in patterned magnetic recording medium is presented. The effects of bit size, head/medium misregistration, bit-to-bit spacing, soft underlayer (SUL) patterning, and side wall roughness on magnetization reversal are explored. The results offer the guidelines for the design and optimization of patterned magnetic recording medium.
Nonpolar AlGaN-Cladding-Free Blue Laser Diodes with InGaN Waveguiding (2009)

We have demonstrated AlGaN-cladding-free m-plane InGaN-based blue laser diodes (LDs) using a novel structure that employs 50-nm-thick n- and p-type InxGa1-xN (x = 5–10%) as waveguiding layers. The thick, high In content InGaN waveguiding layers provided significant refractive index contrast to the GaN cladding layers, thereby eliminating the need for AlGaN cladding. Under pulsed operation, lasing was achieved at 442 nm with a threshold current density of 10 kA/cm2.
Towards effective clustering techniques for the analysis of electric power grids (2013)

Clustering is an important data analysis technique with numerous applications in the analysis of electric power grids. Standard clustering techniques are oblivious to the rich structural and dynamic information available for power grids. Therefore, by exploiting the inherent topological and electrical structure in the power grid data, we propose new methods for clustering with applications to model reduction, locational marginal pricing, phasor measurement unit (PMU or synchrophasor) placement, and power system protection. We focus our attention on model reduction for analysis based on time-series information from synchrophasor measurement devices, and spectral techniques for clustering. By comparing different clustering techniques on two instances of realistic power grids we show that the solutions are related and therefore one could leverage that relationship for a computational advantage. Thus, by contrasting different clustering techniques we make a case for exploiting structure inherent in the data with implications for several domains including power systems.
Exploring and Understanding the Role of Workshop Environments in Personal Fabrication Processes (2019)

Growing interest in personal fabrication has resulted in many ways to ideate, design, and prototype, in addition to studies of who a maker is and the challenges they face. Less attention, however, has focused on the role of the environment in fabrication processes. By understanding how interactions with tools, fixtures, materials, and spaces shape workflows, we can better determine how to design the next generation of workshops, design tools, and fabrication equipment to support personal fabrication activities. To build this understanding, site visits and interviews at local makerspaces, fabrication studios, and workshops were conducted. These visits uncovered the rich practices and roadblocks generated by workshops today. The observations identified the importance of spatial layouts, territoriality and occupant agency, distributed knowledge, and organizational flux, among others, to design and fabrication processes. These observations were further synthesized into one possible direction for such spaces: hybrid workshops (i.e., environments that can leverage computation and responsive architecture to enhance a maker's ability to design and fabricate). This work identifies how such spaces could harness the rich practices and eliminate the challenges found with workshops today and discusses the technical innovations and philosophical questions that hybrid workshops will pose to the future of personal fabrication.
Removing bias from discrete time models based on finite interval response data (1996)

Modern off-line system identification methods necessarily form a system realization using a finite amount of data. The models constructed are usually of an order smaller than the actual order of the physical system because it is not practical to model the relatively unimportant states. A method is presented to improve the selection of the important states and the model order in system identification methods based on generalized Hankel matrices. When forming a reduced-order model, it is critical to be able to accurately identify the important states and to select the appropriate model order. Some currently popular methods implicitly contain a frequency weighting that comes from the use of a finite tune interval of data in the identification. A method is presented to remove this implicit bias, and excellent results are obtained, even when the response data used span only a fraction of a cycle of the dominant frequency.
Liquid crystal trimers showing stable anticlinic structures in smectic C and I phases (2003)

A homogeneous series of chiral trimeric compounds, possessing three biphenyl mesogenic cores connected by flexible alkyl spacers, were prepared and the liquid-crystalline properties investigated. The trimers were designed to have chiral moieties at both peripheral ends of the molecular structure and the properties were compared with those of the related dimeric and monomeric systems. Some of the optically active trimers showed stable antiferroelectric smectic C and I phases. The racemic mixture of optical isomers also showed anticlinic versions of the smectic C and I phases, however, synclinic structures were not observed. The optical isomers and the racemic mixture showed quite similar transition temperatures, suggesting that the chirality-induced properties have little effect on the stability of the anticlinic structures. The trimers showed a third-order X-ray diffraction peak indicating the formation of a higher order smectic layer structure, which is considered to stabilize the anticlinic molecular ordering.
Assessment of association between BRAF mutation status in melanoma tumors and response to ipilimumab. (2011)

2587 Background: Ipilimumab, a fully-human monoclonal antibody against CTLA-4, has demonstrated significant improvement in overall survival (OS) in previously treated advanced melanoma patients. The BRAF inhibitor, RG7204 (also known as PLX4032) has shown high objective response rates (up to 78%) in melanoma patients harbouring the BRAFV600E mutation but not in patients without the mutation (e.g. wild-type BRAF). As an immune potentiator, it is likely that ipilimumab acts independently of BRAF kinase mutations and similar activity in BRAF mutation positive and negative patients is expected. This retrospective analysis was carried out to assess if BRAF status affects the clinical activity of ipilimumab. Methods: CA184-004 was a randomized, double-blind, multicenter phase 2 trial of 82 previously treated or untreated patients with unresectable stage III or stage IV melanoma. Patients received ipilimumab 3 or 10 mg/kg every 3 weeks for 4 doses followed by maintenance dosing in eligible patients. The BRAFV600E mutation status for 80 patients was determined in tumor biopsies by PCR-based assays. Data on disease control were available for 69 patients with evaluated BRAFV600E mutation status. Analysis of the association of the BRAFV600E mutation status and safety of ipilimumab were not performed. Results: Rates of objective responses and stable disease in patients with BRAFV600E mutation positive tumors (0% CR, 10% PR, 20% SD) were comparable to those in patients with the wild-type gene (3.2% CR, 9.7% PR, 22.6% SD). Eleven patients displayed durable disease control (DDC: Complete response, partial response or stable disease lasting ≥ 24 weeks) of which 6 (55%) had BRAFV600E mutation positive tumors and 5 (45%) did not. In the 48 patients showing no DDC, the mutation frequency was 50%. Conclusions: In this study, no association between BRAFV600E mutation status of melanoma tumors and DDC after treatment with ipilimumab was detected at any dose.
Tunable Prussian blue analogues for the selective synthesis of propargylamines through A3 coupling (2018)

M<sup>1</sup>[Co(CN)<sub>6</sub>]<sub>2/3</sub>-type Prussian blue analogues (M<sup>1</sup>–Co PBAs) were studied as catalysts for the synthesis of propargylamines <italic>via</italic> A<sup>3</sup> coupling of phenylacetylene, benzaldehyde and piperidine.
Comparing a MWIR and LWIR polarimetric imaging for surface swimmer detection (2008)

Previously, we have investigated the use of Long-Wave Infra-Red (LWIR) polarimetric imaging for the detection of surface swimmers in a maritime environment. While better contrast and longer range are expected with Mid-Wave Infra-Red (MWIR) polarimetric imaging, the cost of such a system is higher than a polarimetric imager operating in the LWIR due to the advent of higher-performance micro-bolometer imaging arrays. The actual performance of a MWIR polarimetric imager to detect a person in the water is presented. A comparative analysis of system cost between MWIR and LWIR systems is also discussed.