gebhart/patrepeval huggingface dataset:
The TREK2 Channel Is Involved in the Proliferation of 253J Cell, a Human Bladder Carcinoma Cell (2013)

Bladder cancer is the seventh most common cancer in men that smoke, and the incidence of disease increases with age. The mechanism of occurrence has not yet been established. Potassium channels have been linked with cell proliferation. Some two-pore domain K(+) channels (K2P), such as TASK3 and TREK1, have recently been shown to be overexpressed in cancer cells. Here we focused on the relationship between cell growth and the mechanosensitive K2P channel, TREK2, in the human bladder cancer cell line, 253J. We confirmed that TREK2 was expressed in bladder cancer cell lines by Western blot and quantitative real-time PCR. Using the patch-clamp technique, the mechanosensitive TREK2 channel was recorded in the presence of symmetrical 150 mM KCl solutions. In 253J cells, the TREK2 channel was activated by polyunsaturated fatty acids, intracellular acidosis at -60 mV and mechanical stretch at -40 mV or 40 mV. Furthermore, small interfering RNA (siRNA)-mediated TREK2 knockdown resulted in a slight depolarization from -19.9 mV±0.8 (n=116) to -8.5 mV±1.4 (n=74) and decreased proliferation of 253J cells, compared to negative control siRNA. 253J cells treated with TREK2 siRNA showed a significant increase in the expression of cell cycle boundary proteins p21 and p53 and also a remarkable decrease in protein expression of cyclins D1 and D3. Taken together, the TREK2 channel is present in bladder cancer cell lines and may, at least in part, contribute to cell cycle-dependent growth.
Steady-State Mean-Square Performance of the Hyper H&infin; Filter (2013)

The Hyper H&infin; Filter is an adaptive filtering algorithm, where a forgetting factor &rho; is built into the H&infin; optimization framework as a function of the robustness parameter &gamma;f and determined through the process of &gamma;-iteration. This paper examines how the choice of &gamma;f affects the resultant steady-state mean-square error of this algorithm. For moderately large &gamma;f, a theoretical expression of the excess mean-square error is derived, which turns out to coincide with that of RLS. Based on this expression and numerical simulations, it is shown that there is a trade-off between the robustness and the mean-square performance at steady-state. For balancing this trade-off, preferable values of &gamma;f are also considered.
Myelin and axon pathology in multiple sclerosis assessed by myelin water and multi-shell diffusion imaging (2021)

Damage to the myelin sheath and the neuroaxonal unit is a cardinal feature of multiple sclerosis; however, a detailed characterization of the interaction between myelin and axon damage in vivo remains challenging. We applied myelin water and multi-shell diffusion imaging to quantify the relative damage to myelin and axons (i) among different lesion types; (ii) in normal-appearing tissue; and (iii) across multiple sclerosis clinical subtypes and healthy controls. We also assessed the relation of focal myelin/axon damage with disability and serum neurofilament light chain as a global biological measure of neuroaxonal damage. Ninety-one multiple sclerosis patients (62 relapsing-remitting, 29 progressive) and 72 healthy controls were enrolled in the study. Differences in myelin water fraction and neurite density index were substantial when lesions were compared to healthy control subjects and normal-appearing multiple sclerosis tissue: both white matter and cortical lesions exhibited a decreased myelin water fraction and neurite density index compared with healthy (P < 0.0001) and peri-plaque white matter (P < 0.0001). Periventricular lesions showed decreased myelin water fraction and neurite density index compared with lesions in the juxtacortical region (P < 0.0001 and P < 0.05). Similarly, lesions with paramagnetic rims showed decreased myelin water fraction and neurite density index relative to lesions without a rim (P < 0.0001). Also, in 75% of white matter lesions, the reduction in neurite density index was higher than the reduction in the myelin water fraction. Besides, normal-appearing white and grey matter revealed diffuse reduction of myelin water fraction and neurite density index in multiple sclerosis compared to healthy controls (P < 0.01). Further, a more extensive reduction in myelin water fraction and neurite density index in normal-appearing cortex was observed in progressive versus relapsing-remitting participants. Neurite density index in white matter lesions correlated with disability in patients with clinical deficits (P < 0.01, beta = -10.00); and neurite density index and myelin water fraction in white matter lesions were associated to serum neurofilament light chain in the entire patient cohort (P < 0.01, beta = -3.60 and P < 0.01, beta = 0.13, respectively). These findings suggest that (i) myelin and axon pathology in multiple sclerosis is extensive in both lesions and normal-appearing tissue; (ii) particular types of lesions exhibit more damage to myelin and axons than others; (iii) progressive patients differ from relapsing-remitting patients because of more extensive axon/myelin damage in the cortex; and (iv) myelin and axon pathology in lesions is related to disability in patients with clinical deficits and global measures of neuroaxonal damage.
Application of chiral GC-MS analysis in the detection of natural products adulteration – The example of Chios mastic gum essential oil (2008)

The enantiomeric ratio of volatile compounds is characteristic in each essential oil, but it cannot be determined by usual capillary GCMS analysis. The essential oil of Pistacia lentiscus var. chia L. (Anacardiaceae), mastic oil, is a valuable product. The case of dietary and cosmetic products containing mastic oil is of great importance, due to the well-established biological activities of mastic and mastic oil [1,2], the significance of mastic gum for greek economy and the increasing international interest for such products. Numerous commercial items with a claim of mastic oil content but without certification are found in the market. In order to detect possible adulteration of this type, a method based on the separation of chiral constituents and the determination of their ratio by chiral GCMS analysis has been developed. Samples of cosmetic products (shampoos, showers gels, hand and body creams, toothpastes, soaps) and dietary products (chewing gums) from different companies were extracted with n-hexane for the retrieval of the volatile compounds and the extracts were analyzed by chiral GCMS. The results were compared with those of the analysis of 30 original mastic oil samples supplied by the Chios Mastic Gum Growers Association, as well as commercial mastic oils marketed by other companies. The main discriminating factor was found to be the (+)/(-) α-pinene ratio, which should be less than 99:1, as determined by original mastic oil analysis. Several commercial samples were found to contain much higher proportions of (-) α-pinene, an indication that commercial racemic α-pinene was used for the adulteration of the product. The use of this method to determine such type of adulterations can be helpful in establishing quality and originality in natural product commercial use.
New Insight into the Mechanism of Accumulation and Intraerythrocytic Compartmentation of Albitiazolium, a New Type of Antimalarial (2014)

Bis-thiazolium salts constitute a new class of antihematozoan drugs that inhibit parasite phosphatidylcholine biosynthesis. They specifically accumulate in Plasmodium- and Babesia-infected red blood cells (IRBC). Here, we provide new insight into the choline analogue albitiazolium, which is currently being clinically tested against severe malaria. Concentration-dependent accumulation in P. falciparum-infected erythrocytes reached steady state after 90 to 120 min and was massive throughout the blood cycle, with cellular accumulation ratios of up to 1,000. This could not occur through a lysosomotropic effect, and the extent did not depend on the food vacuole pH, which was the case for the weak base chloroquine. Analysis of albitiazolium accumulation in P. falciparum IRBC revealed a high-affinity component that was restricted to mature stages and suppressed by pepstatin A treatment, and thus likely related to drug accumulation in the parasite food vacuole. Albitiazolium also accumulated in a second high-capacity component present throughout the blood cycle that was likely not related to the food vacuole and also observed with Babesia divergens-infected erythrocytes. Accumulation was strictly glucose dependent, drastically inhibited by H+/K+ and Na+ ionophores upon collapse of ionic gradients, and appeared to be energized by the proton-motive force across the erythrocyte plasma membrane, indicating the importance of transport steps for this permanently charged new type of antimalarial agent. This specific, massive, and irreversible accumulation allows albitiazolium to restrict its toxicity to hematozoa-infected erythrocytes. The intraparasitic compartmentation of albitiazolium corroborates a dual mechanism of action, which could make this new type of antimalarial agent resistant to parasite resistance.
Synthesis of Ethyl (1S,2R,3S,4S,5S)-2,3-O-(Isopropylidene)-4-Hydroxy-Bicyclo[3.1.0]Hexane-Carboxylate from L-Ribose: A Versatile Chiral Synthon for Preparation of Adenosine and P2 Receptor Ligands (2008)

Substitution of the ribose moiety of various nucleosides and nucleotides with the (N)-methanocarba ring system increases the potency and selectivity as ligands at certain subtypes of adenosine and P2 receptors. We have prepared a key intermediate in the synthesis of these derivatives, ethyl (1S,2R,3S,4S,5S)-2,3-O-(isopropylidene)-4-hydroxybicyclo[3.1.0]hexane-carboxylate (15), starting from L-ribose (8) as a readily available, enantiopure building block. L-ribose was converted to the corresponding 5'-iodo derivative (9), which was cleaved reductively with Zn. Improvements were made in subsequent steps corresponding to a published route to biologically important (N)-methanocarba 5'-uronamido nucleosides, and new steps were added to prepare related 5'-nucleotides.
Supplementary Figure 3B from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus (2023)

Supplementary Figure 3B from Aberrant Silencing of Cancer-Related Genes by CpG Hypermethylation Occurs Independently of Their Spatial Organization in the Nucleus
Demonstration of subpopulations of Dane particles (1976)

Two populations of Dane particles were isolated from the plasma of individuals carrying hepatitis B surface antigen. These populations had densities in CsCl of 1.22 and 1.20 g/ml. Endogenous DNA polymerase activity was found to be associated only with the heavier of these two populations. Using a positive stain, electron microscopic examination of these particles suggested that the heavier the particle contained nucleic acid in its core whereas the lighter particle appeared empty. Cores isolated from Dane particles with densities of 1.22 and 1.20 g/ml banded in CsCl at densities of 1.36 and 1.30 g/ml, respectively. Endogenous DNA polymerase activity was associated only with the higher density core particles.
Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2 (1995)

An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The structure has been solved by X-ray diffraction analysis and has been refined to an R-factor of 19.7% at a resolution of 2.0 A. The ligand is found to bind in the minor groove, at the central four AATT base pairs of the B-DNA double helix, with the involvement of a number of van der Waals contacts and hydrogen bonds. There are significant differences in minor groove width for the two compounds, along much of the AATT region. In particular this structure shows a narrower groove at the 3' end of the binding site consistent with the narrower cross-section of the imidazole group compared with the piperazine ring of Hoechst 33258 and therefore a smaller perturbation in groove width. The higher binding affinity to DNA shown by this analogue compared with Hoechst 33258 itself, has been rationalised in terms of these differences.
Low-Cost Light-Weight Quick-Manufacturable Blades for Human-Scale Wind Turbines (2011)

A novel blade design for small wind turbines intended for residential use in rural locations and/or developing nations has been developed. Traditionally, blades for these turbines are carved from weather resistant woods which may be costly and difficult to manufacture. This work seeks to reduce cost and construction time by developing blades from readily available PVC drainage pipe. The blade design underwent airfoil optimization regarding the blade twist along its length and drop, via computational fluid dynamic (CFD) simulations with open source software. Blades were built of PVC using the new CFD design and tested on field operation, the manufacturing process as well as their performance was monitored and recorded in terms of comparison with classical wood-based design.
Fine Tuning Consumer Feedback Based Recommender Systems Using Deep Learning Models on Word Vector Space Representations (2019)

In almost every consumer-based service domain today, there exists a feedback system which captures how the consumer felt about the services they received. This feedback system makes or breaks the business of the service provider as a lot of future purchase decisions are driven based on this. Based on the feedbacks received, organizations are trying to drill down on the negative aspects and market the positive aspects with more outreach. Our innovation is focused on extracting maximum value from the underlying feedback system - by automatically deriving semantic context and lexical associations for each document sub-unit of the written feedbacks using word vector representation and word embeddings. Further, basis the information extracted from the analysis unit, a secondary recommendation unit will be set up that automatically analyzes the output from the analysis unit and accordingly performs latent structure identification and polarity analysis to suggest substitute options or viable alternatives based on the consumers' behavior and feedback. The ultimate objective is to produce automated contextualization based feasible recommendations using deep learning models, having minimal supervision and error rate.
High resolution allelotype of nonfunctional pancreatic endocrine tumors: identification of two molecular subgroups with clinical implications. (2001)

A high resolution allelotype for nonfunctional pancreatic endocrine tumors (NF-PETs) has been generated by microsatellite analysis of DNA from 16 frozen cases, each probed with 394 markers. Two subgroups of NF-PETs were found. Seven cases showed frequent, large allelic deletions [loss of heterozygosity (LOH)] with an average fractional allelic loss (FAL) of 0.55, whereas nine cases showed a small number of random losses with a FAL of 0.15. Designated high or low FAL, respectively, these genetic phenotypes showed correlation with the ploidy status: high-FAL tumors were aneuploid, low-FAL were diploid. Chromosomes 6q and 11q showed LOH in >60% of cases. About 50% of cases had losses on 11p, 20q, and 21. Selected LOH analysis on an additional 16 paraffin-embedded NF-PETs confirmed the high frequency of 6q and 11q LOH. The allelotype of NF-PET is markedly different from that of either ductal or acinar tumors of the pancreas as well as from that of functional-PETs. Moreover, whereas deletions involving chromosome 11 also are a feature of functional-PETs, the involvement of chromosome 6q is characteristic of NF-PETs. Survival analysis showed that none of the single chromosomal alterations was associated with outcome, whereas ploidy status is an independent factor adding prognostic information to that furnished by the proliferative index measured by Ki-67 immunohistochemistry.
Redshift of edge emission from AlGaInP light-emitting diodes and correlation with electron-hole recombination lifetime (2008)

The edge emission from AlGaInP light-emitting diodes showed a red-shifted peak in addition to the peak of surface emission. This shift resulted from the quantum-well absorption of the guided wave. Although the shift degrades the color quality and the extraction efficiency of the device, it helps elucidate many important optical properties of the material and the dynamics of carrier recombination, including the electron-hole recombination lifetime, the optical joint density of state, the spontaneous emission spectrum and the absorption spectrum. A simple concept of the bimolecular recombination is established. The corresponding coefficient can be expressed by a simple formula and was therefore determined.
Incremental redundancy (IR) schemes for W-CDMA HS-DSCH (2003)

The paper compares two hybrid automatic repeat request (HARQ) schemes using incremental redundancy (IR) which have been proposed for the UMTS (W-CDMA) high speed downlink shared channel (HS-DSCH). Their relative throughput performance is reported for various channel conditions. It is shown that the two-stage rate-matching scheme has marginally worse performance compared to the alternative block interleaving scheme for certain coding rates and under some channel conditions.
Robust Object Recognition based on Regular Framing and Depth Aspect Image (2002)

A method of model-based object recognition for a cluttered depth scene including multiple objects is proposed. A novel model representation, named depth aspect image, is also defined as an orientation standardized appearance from the original depth data of objects, which is transformed through tuples of three barycenters defined within regularly defined voxels. A robust matching scheme, named least quantile of residuals, can achieve not only object recognition with depth aspect images but also verification with candidate models. The sparsely distributed barycenters and the robust matching make the ICP-based rough registration and the following verification process much faster and more reliable. In this paper, we show recognition experiments on 100 scenes contained multiple objects from a library of 4 models. 1
On Seamless Offloading of Delay Sensitive Vehicular Services over Mobile Edge Computing (2020)

Mobile-edge computing (MEC) is a promising paradigm to improve the quality of computation experience for vehicles. Thanks to the reduced latency and high computational capability the MEC can offer, the conventional split between on-board (vehicle) vs off-board (server) computation will be revolutionized while allowing a seamless experience even for delay-sensitive services. In this paper, we show the effectiveness of an optimal selection of a sub-set of available MECs for service replication, necessary to satisfy an offloaded request submitted by a vehicle, while ensuring service continuity in a mobility environment. Our algorithm self adapts to meet any given risk target which is a metric introduced to assess service continuity while minimizing the overall power consumption and respecting the hardware constraints of the MEC.
Synthesis of (−)-PNU-286607 by Asymmetric Cyclization of Alkylidene Barbiturates (2009)

PNU-286607 is the first member of a promising, novel class of antibacterial agents that act by inhibiting bacterial DNA gyrase, a target of clinical significance. Importantly, PNU-286607 displays little cross-resistance with marketed antibacterial agents and is active against methicillin-resistant staphylococcus aureus (MRSA) and fluoroquinoline-resistant bacterial strains. Despite the apparent stereochemical complexity of this unique spirocyclic barbituric acid compound, the racemic core is accessible by a two-step route employing a relatively obscure rearrangement of vinyl anilines, known in the literature as the "tert-amino effect." After a full investigation of the stereochemical course of the racemic reaction, starting with the meso cis-dimethylmorpholine, a practical asymmetric variant of this process was developed.
Low axial drift stage and temperature controlled liquid cell for z-scan fluorescence correlation spectroscopy in an inverted confocal geometry (2011)

A recent iteration of fluorescence correlation spectroscopy (FCS), z-scan FCS, has drawn attention for its elegant solution to the problem of quantitative sample positioning when investigating two-dimensional systems while simultaneously providing an excellent method for extracting calibration-free diffusion coefficients. Unfortunately, the measurement of planar systems using (FCS and) z-scan FCS still requires extremely mechanically stable sample positioning, relative to a microscope objective. As axial sample position serves as the inherent length calibration, instabilities in sample position will affect measured diffusion coefficients. Here, we detail the design and function of a highly stable and mechanically simple inverted microscope stage that includes a temperature controlled liquid cell. The stage and sample cell are ideally suited to planar membrane investigations, but generally amenable to any quantitative microscopy that requires low drift and excellent axial and lateral stability. In the present work we evaluate the performance of our custom stage system and compare it with the stock microscope stage and typical sample sealing and holding methods.
A 262-GHz Wireless IFoF Uplink With Remote Down-Conversion Using Optically Generated Sub-THz LO (2022)

We experimentally demonstrate the feasibility of a 262-GHz wireless intermediate frequency (IF)-over-fiber (IFoF) uplink with frequency down-conversion at a remote antenna unit (RAU). To distribute many RAUs for the coverage of terahertz (THz) wireless communications, it is important to simplify the RAU for the THz uplink. The remote down-conversion with a subharmonic mixer and a uni-traveling carrier-photodiode (UTC-PD) is driven by two optical tone signals from the central office (CO). This can reduce the high-frequency and wideband devices of the networks. Instead of coherent detection, the RAU can be simplified with optical transmission and direct detection (DD) by using a conventional optical modulator and a photodiode (PD). We measured the phase noise of the system and compensated for it with blind phase recovery. Then, the error vector magnitudes (EVMs) of the received signals were measured as a function of THz Tx power, optically generated local oscillator (LO) power, and THz wireless link distance. Single-channel 45- and 30-Gb/s data transmission was achieved over a 5-km fiber and 1-m THz wireless link based on soft- ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2\times 10^{-2}$ </tex-math></inline-formula> ) and hard-decision ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$3.8\times 10^{-3}$ </tex-math></inline-formula> ) forward error correction (FEC) thresholds, respectively.
Rearrangement of Homoallylic Alcohols Induced by DAST (2006)

[reaction: see text] Treatment of beta,gamma-unsaturated monoprotected 1,2-diols with diethylaminosulfur trifluoride (DAST) allows the stereoselective formation of beta,gamma-unsaturated aldehydes in good yields and with a good transfer of chirality.