gebhart/patrepeval huggingface dataset:
Triangular Regulation of Cucurbit[8]uril 1:1 Complexes (2019)

Triangular shapes have inspired scientists over time and are common in nature, such as the flower petals of oxalis triangularis, the triangular faces of tetrahedrite crystals, and the icosahedron faces of virus capsids. Supramolecular chemistry has enabled the construction of triangular assemblies, many of which possess functional features. Among these structures, cucurbiturils have been used to build supramolecular triangles, and we recently reported paramagnetic cucurbit[8]uril (CB[8]) triangles, but the reasons for their formation remain unclear. Several parameters have now been identified to explain their formation. At first sight, the radical nature of the guest was of prime importance in obtaining the triangles, and we focused on extending this concept to biradicals to get supramolecular hexaradicals. Two sodium ions were systematically observed by ESI-MS in trimer structures, and the presence of Na<sup>+</sup> triggered or strengthened the triangulation of CB[8]/guest 1:1 complexes in solution. X-ray crystallography and molecular modeling have allowed the proposal of two plausible sites of residence for the two sodium cations. We then found that a diamagnetic guest with an H-bond acceptor function is equally good at forming CB[8] triangles. Hence, a guest molecule containing a ketone function has been precisely triangulated thanks to CB[8] and sodium cations as determined by DOSY-NMR and DLS. A binding constant for the triangulation of 1:1 to 3:3 complexes is proposed. This concept has finally been extended to the triangulation of ditopic guests toward network formation by the reticulation of CB[8] triangles using dinitroxide biradicals.
A platform for GaAs opto-electronic integrated circuits based on GaAs/AlGaAs regrowth upon patterned InGaP (2009)

We demonstrate how GaAs/AlGaAs regrowth upon patterned InGaP can be utilised to realise self-aligned lasers, window structured superluminescent diodes and distributed feedback lasers. Such realisation demonstrates the promise of this methodology for GaAs-based opto-electronic integrated circuits through new capability for buried waveguides, low reflectivity facets and gratings structures.
Relationship Between Trehalose and Sterol Accumulation During Oxygenation of Cropped Yeast (1993)

An anaerobic brewers' yeast was oxygenated to improve its physiological condition. During this treatment, glycogen, sterol, and trehalose contents were measured at regular intervals. Besides the dissimilation of glycogen and the synthesis of sterols, an unexpected accumulation of trehalose was observed. Moreover, the trehalose and sterol concentrations were correlated. These results are discussed with respect to their biochemical relevance.
A robust hierarchical video shot detection method (2011)

We propose an hierarchical video shot detection method to detect both abrupt and gradual transitions (dissolves and fade-groups). The philosophy of the method is to use a fast algorithm to pre-process the video by removing those frames which strictly does not comprising a normal scene. The remaining frames may contribute to fade-in fade-out or dissolve areas. These frames are processed by a complex and robust shot detection method. We used object(contour) matching as pre-processing algorithm and SURF on top of it for robustness.
Optical Imaging Fiber-Based Single Live Cell Arrays:  A High-Density Cell Assay Platform (2002)

A high-density, ordered array containing thousands of microwells is fabricated on an optical imaging fiber. Each individually addressable microwell is used to accommodate a single living cell. A charged coupled device (CCD) detector is employed to monitor and spatially resolve the fluorescence signals obtained from each individual cell, allowing simultaneous monitoring of cellular responses of all the cells in the array using reporter genes (lacZ, EGFP, ECFP, DsRed) or fluorescent indicators. Yeast and bacteria cell arrays were fabricated and used to perform multiplexed cell assays with resolution at the single-cell level. Monitoring gene expression in single yeast cells carrying a two-hybrid system was used to detect in vivo protein-protein interactions. The single-cell array technology provides a new platform for monitoring the unique multiple responses of large populations of individual cells from different strains or cell lines. The rich data acquired by the cell array has the potential to be employed as a new tool for cell biology research as well as to improve cell-based high-throughput screening (HTS) applications, such as the validation of new disease-associated cellular targets and the early-stage evaluation of potential drug candidates.
Reading on-the-go (2006)

In this paper we present a 20-participant controlled experiment to evaluate and compare a head-down visual display and a synthesized speech audio display for comprehending text while mobile. Participants completed reading comprehension trials while walking a path and sitting. We examine overall performance and perceived workload for four conditions: audio-walking, audio-sitting, visual-walking, and visual-sitting. Results suggest audio is an acceptable modality for mobile comprehension of text. Participants' comprehension scores for the audio-walking condition were comparable to the scores for the visual-walking condition. More importantly, participants saw improvements in their ability to navigate the environment when using the audio display.
[Dimensions of the lateral condyle in non-arthritic valgus knees. A cadaver study]. (2002)

Using a population of non arthritic knees, our data demonstrated that the lateral femoral condyle is thicker in valgus knees compared to neutral knees, thus in contradiction with the most common view. We suggest that in fixed valgus knees, beside arthritic wear, there is no deficiency of the posterior lateral condyle of the femur.
Selective absorption enhancement in organic solar cells using light incoupling layers (2010)

We show that capping layers of tris-(8-hydroxy-quinolinato)-aluminum Alq3 enable increased absorption and photocurrent in organic solar cells (OSCs) when using transparent metal films as top electrodes. Furthermore, by varying the capping layer thickness, the optical field in the OSC is tuned for selective wavelengths, opening a possibility of influencing the external quantum efficiency for specific absorber materials. It is described how a second maximum of the optical field intensity can be utilized, which is a concept significant for tandem solar cells. Indium tin oxide (ITO)-free OSCs are presented which show the influence of capping layer on efficiency, saturation, fill factor, and open-circuit voltage, with numerical calculations supporting the experimental evidence of layer-selective enhancement.
Inertial Sensor Based Detection of Freezing of Gait for On-Demand Cueing in Parkinson’s Disease (2020)

Freezing of Gait (FoG) is one of the cardinal symptoms of Parkinson’s disease, which arises in the late stages of the disease. It affects the gait cycle and increases the risk of falling. FoG leads to heterogeneous gait cycles, which makes the detection of gait phases and events difficult. In this article, we introduce a new inertial measurement unit-based approach for detecting Parkinsonian gait phases based on the acceleration, velocity, rate of turn and orientation of the foot. Furthermore, we introduce a new gait evaluation measurement, the so-called GaitScore, for distinguishing between normal and FoG-affected motion phases and thus for detecting FoG episodes. Preliminary results show that the extreme values of the pitch angle during a motion phase provide valuable information for the detection of FoG. The proposed method can detect FoG episodes with a sensitivity of 97% and specificity of 87%. The reference data were generated by clinical experts who annotated FoG episodes in video data synchronized with the measurements of the inertial sensors. The detection of FoG in real-time enables on-demand cueing.
Digital particle image velocimetry (DPIV) robust phase correlation (2009)

A novel correlation technique, the robust phase correlation (RPC), is introduced which amplifies the signal-to-noise ratio of the DPIV cross-correlation to produce velocity estimations that are accurate and robust to a variety of image conditions. Specifically, this estimator shows substantial resilience against additive background noise non-uniform illumination and thermal noise effects. In addition, the RPC is able to substantially reduce bias errors and peak locking in the presence of high shear and rotational motion in comparison with standard cross-correlation algorithms. The success of this technique relies upon an analytical decomposition of the DPIV signal-to-noise ratio, which is then applied as a spectral filter in a novel implementation of the generalized cross-correlation (GCC). The RPC also utilizes advanced windowing techniques to attenuate Fourier-based errors. Because of the GCC filtering, the application of windowing in the RPC is not susceptible to the effects of additive background noise that commonly causes errors for windowed cross-correlation estimation. The RPC estimator is validated using both artificial images and experimental data to demonstrate its enhanced measurement capabilities.
A hierarchical Model Predictive Control framework for autonomous ground vehicles (2008)

A hierarchical framework based on Model Predictive Control (MPC) for autonomous vehicles is presented. We formulate a predictive control problem in order to best follow a given path by controlling the front steering angle while fulfilling various physical and design constraints. We start from the low-level active steering-controller presented in [3], [9] and integrate it with a high level trajectory planner. At both levels MPC design is used. At the high-level, a trajectory is computed on-line, in a receding horizon fashion, based on a simplified point-mass vehicle model. At the low- level a MPC controller computes the vehicle inputs in order to best follow the desired trajectory based on detailed nonlinear vehicle model. This article presents the approach, the method for implementing it, and successful preliminary simulative results on slippery roads at high entry speed.
Winged Helix Transcription Factor CPCR1 Is Involved in Regulation of β-Lactam Biosynthesis in the Fungus Acremonium chrysogenum (2004)

Winged helix transcription factors, including members of the forkhead and the RFX subclasses, are characteristic for the eukaryotic domains in animals and fungi but seem to be missing in plants. In this study, in vitro and in vivo approaches were used to determine the functional role of the RFX transcription factor CPCR1 from the filamentous fungus Acremonium chrysogenum in cephalosporin C biosynthesis. Gel retardation analyses were applied to identify new binding sites of the transcription factor in an intergenic promoter region of cephalosporin C biosynthesis genes. Here, we illustrate that CPCR1 recognizes and binds at least two sequences in the intergenic region between the pcbAB and pcbC genes. The in vivo relevance of the two sequences for gene activation was demonstrated by using pcbC promoter-lacZ fusions in A. chrysogenum. The deletion of both CPCR1 binding sites resulted in an extensive reduction of reporter gene activity in transgenic strains (to 12% of the activity level of the control). Furthermore, Acremonium transformants with multiple copies of the cpcR1 gene and knockout strains support the idea of CPCR1 being a regulator of cephalosporin C biosynthesis gene expression. Significant differences in pcbC gene transcript levels were obtained with the knockout transformants. More-than-twofold increases in the pcbC transcript level at 24 and 36 h of cultivation were followed by a reduction to approximately 80% from 48 to 96 h in the knockout strain. The overall levels of the production of cephalosporin C were identical in transformed and nontransformed strains; however, the knockout strains showed a striking reduction in the level of the biosynthesis of intermediate penicillin N to less than 20% of that of the recipient strain. We were able to show that the complementation of the cpcR1 gene in the knockout strains reverses pcbC transcript and penicillin N amounts to levels comparable to those in the control. These results clearly indicate the involvement of CPCR1 in the regulation of cephalosporin C biosynthesis. However, the complexity of the data points to a well-controlled or even functional redundant network of transcription factors, with CPCR1 being only one player within this process.
Improvement of junction leakage of nickel silicided junction by a Ti-capping layer (1999)

A novel NiSi process with a thin Ti-cap layer is proposed, for the first time, to improve the leakage problem of Ni-silicided junction. The Ti-cap samples exhibit a very low leakage current density about 1/spl times/10/sup -9/ A/cm/sup 2/ after 600/spl deg/C annealing, which is one order of magnitude reduction comparing with uncapped samples. From Auger analyzes, it is found that this significant improvement results from suppression of the oxidation of the Ni-silicide during the thermal annealing process.
Synthesis of 1,3-disubstituted-pyrrolo[2,1-a]isoquinoline-2-carboxylic acids, esters and amides (1993)

A number of 1,3-disubstituted pyrrolo [2,1-a] isoquinoline-2-carboxylic esters have been prepared using a variety of independent routes. The corresponding acids and a range of amides were subsequently synthesised. The primary amides were found to differ significantly from those reported to arise from the reaction between the anion of an isoquinoline Reissert compound and an α,β-unsaturated nitrile. Re-investigation has established that the latter reaction does not produce primary amides. The true nature of the products as 2-acyl-3-aminopyrrolo[2,1-a]isoquinolines was established using X-ray crystallography.
NATURAL LANGUAGE QUESTION ANSWERING SYSTEM OVER LINKED DATA (2019)

&#x0D; &#x0D; Linked Data project is aimed to give&#x0D; more details on any subject through the big knowledge bases defined on the web.&#x0D; In this context, knowledge bases offer endpoint service user interfaces to&#x0D; query their data. Because of the SPARQL query language limitation of these&#x0D; knowledge bases, a significant number of web users are unable to benefit from&#x0D; these services. In this paper, an English natural language question answering&#x0D; system over Linked Data is proposed in order to eliminate this limitation. The proposed&#x0D; system's main processes can be listed as follows: (1) Extracting Part-Of-Speech&#x0D; (POS) tags, (2) pattern extraction &amp;amp; preparing appropriate SPARQL queries,&#x0D; (3) executing user queries &amp;amp; displaying the results. The features which are&#x0D; not provided by the endpoint services of knowledge bases such as dynamic&#x0D; paging, voice search and answer vocalization which make the usage of the proposed system to be possible by the visually-impaired&#x0D; web users, question-answer caching, social media integration, and live spell&#x0D; checking are proposed. According to experimental results, the proposed system’s&#x0D; question answering performance is improved between 2 and 12 times through the&#x0D; type of natural language question thanks to the question-answer caching&#x0D; mechanism.
The inverse-electron demand Diels–Alder reaction of tetrazines with cyclic enol ethers (2022)

Abstract Inverse electron-demand Diels–Alder additions (iEDDA) between 1,2,4,5-tetrazines and suitable unsaturated dienophiles such as olefins, alkynes, or enol ethers provide facile access to pyridazines. Herein the use of cyclic enol ether derivatives for preparing pyridazines bearing 2-hydroxyethyl, 3-hyproxypropyl, and 3-oxopropyl substituents at the 4-position is disclosed and second order rate constants for the reactions with 2,3-dihydrofuran, 3,4-dihydro-2 H -pyran, and 2-methoxy-3,4-dihydro-2 H -pyran are presented. Graphical abstract
Sensitivity of magnetic resonance imaging of dendritic cells for in vivo tracking of cellular cancer vaccines (2006)

Success of immunotherapy with dendritic cells (DC) to treat cancer is highly dependent on their interaction with and activation of antigen specific T cells. To maximize DC-T cell contact accurate delivery of the therapeutic cells into the lymph node, or efficient trafficking of DC to the lymph nodes of the patient is essential. Since responses are seen in some patients but not in others, monitoring of the injected cells may be of major importance. Tracking of cells with magnetic resonance (MR) imaging is a non-invasive method that provides detailed anatomical information and is therefore more informative for the evaluation of the localization of therapeutic cells after injection than e.g. scintigraphic imaging. To challenge the sensitivity of this novel technique, we investigated the minimum amount of label and the number of cells required for MR imaging and the effect of labeling on DC function. DC were labeled with different concentrations of a clinically approved MR contrast agent consisting of superparamagnetic iron oxide particles and were imaged at both 3 and 7 T. Our results demonstrate the following: (i) When loaded with 30 (+/-4) pg Fe/cell, cell numbers as low as 1,000 cells/mm3 at 3 T and 500 cells/mm3 at 7 T could be readily imaged; (ii) Labeling does not affect cell viability and function; (iii) Because of its high spatial resolution and sensitivity, MRI is ideally suited to track therapeutic cells in vivo.
Vaccine visualization using a zwitterionic near-infrared fluorophore (Conference Presentation) (2020)

There remains a paucity of methodological tools to determine the biodistribution of vaccine antigens. In response to this, we established a near-infrared (NIR) imaging method using a NIR fluorophore, ZW800-1C, conjugated with different sizes of vaccine antigens that allows for real-time monitoring of the fate of delivered vaccines in vivo. The fluorescent signal observed using the system after a model vaccine injection in mice recapitulated the size-dependent transport of the vaccine into the secondary lymphoid tissue. This methodology can be broadly applied for optimization of formulations and safety evaluation of clinical vaccines.
ChemInform Abstract: Total Synthesis of Rutaecarpine and Analogues by Tandem Azido Reductive Cyclization Assisted by Microwave Irradiation. (2011)

Abstract A convenient three‐step synthesis is presented for rutaecarpine (Va) and analogues such as euxylophoricine A (Vb) and C (Vc) involving a microwave‐assisted nickel boride reduction in the final cyclization step.
Flexible and stretchable nanowire-coated fibers for optoelectronic probing of spinal cord circuits (2017)

Studies of neural pathways that contribute to loss and recovery of function following paralyzing spinal cord injury require devices for modulating and recording electrophysiological activity in specific neurons. These devices must be sufficiently flexible to match the low elastic modulus of neural tissue and to withstand repeated strains experienced by the spinal cord during normal movement. We report flexible, stretchable probes consisting of thermally drawn polymer fibers coated with micrometer-thick conductive meshes of silver nanowires. These hybrid probes maintain low optical transmission losses in the visible range and impedance suitable for extracellular recording under strains exceeding those occurring in mammalian spinal cords. Evaluation in freely moving mice confirms the ability of these probes to record endogenous electrophysiological activity in the spinal cord. Simultaneous stimulation and recording is demonstrated in transgenic mice expressing channelrhodopsin 2, where optical excitation evokes electromyographic activity and hindlimb movement correlated to local field potentials measured in the spinal cord.
Pharmacokinetics of caffeic acid phenethyl ester and its catechol‐ring fluorinated derivative following intravenous administration to rats (2009)

The pharmacokinetic profiles of caffeic acid phenethyl ester (CAPE) and its catechol-ring fluorinated derivative (FCAPE) were determined in rats after intravenous administration of 5, 10 or 20 mg/kg for CAPE and 20 mg/kg for FCAPE, respectively. The plasma concentrations of CAPE and FCAPE were measured using a validated liquid chromatography tandem mass spectrometric method. The pharmacokinetic parameters were estimated using non compartmental analysis (NCA) and biexponential fit. The results showed that the area under the plasma concentration-time curve for CAPE treatment increased in a proportion greater than the increase in dose from 5 to 20 mg/kg of CAPE. Total body clearance values for CAPE ranged from 42.1 to 172 ml/min/kg (NCA) and decreased with the increasing dose of CAPE. Similarly, the volume of distribution values for CAPE ranged from 1555 to 5209 ml/kg, decreasing with increasing dose. The elimination half-life for CAPE ranged from 21.2 to 26.7 min and was independent of dose. That FCAPE was distributed extensively into rat tissues and eliminated rapidly was indicated by a high value of volume of distribution and similar short elimination half-life as that of CAPE.
Sensor Transforms for Invariant Image Enhancement (2002)

The invariant image [1, 2] formed from an RGB image taken under light that can be approximated as Planckian solves the colour constancy problem at a single pixel. The invariant is a very useful tool for possible use in a large number of computer vision problems, such as removal of shadows from images [3]. This image is formed by projecting log-log chromaticity coordinates into a 1D direction determined by a calibration of the imaging camera. The invariant can be formed whether or not gammacorrection is applied to images and thus can work for ordinary webcam images, for example, once a self-calibration is carried out [3]. As such, the invariant image is an important new mechanism for image understanding. Since the resulting greyscale image is approximately independent of illumination, it is impervious to lighting change and hence to the presence of shadows. However, in forming the invariant image, it can sometimes happen that shadows are not completely removed. Here, we consider the problem of simple matrixing of sensor values so that the resulting invariant image is improved. To do so, we consider the calibration images and apply an optimization routine for establishing a 3 &#xD7; 3 matrix to apply to the sensors, prior to forming the invariant, with an eye to improving lighting invariance. We find that an optimization does indeed improve the invariant. The resulting image generally has smaller entropy value because the invariant value is smoothed out across former shadow boundaries; thus the new invariant more smoothly captures the underlying intrinsic reflectance properties in the scene.