gebhart/patrepeval huggingface dataset:
Autologous vascular smooth muscle cell-based myocardial gene therapy to induce coronary collateral growth (2004)

For therapeutic angiogenesis to achieve clinical relevance, it must be effective, with minimal side effects to other end organ systems. We developed a cardiac-specific gene delivery mechanism by transfecting autologous vascular smooth muscle cells (VSMC) with VEGF and administering these cells via intracoronary injection. We evaluated the efficacy of this protocol by its ability to stimulate angiogenesis in the presence of a subthreshold stimulus for collateralization. A modified canine repetitive coronary occlusion model was utilized in these experiments with left anterior descending coronary artery occlusions for 2 min every 2 h four times per day for 21 days. An intramyocardial catheter in the perfusion territory of the left anterior descending coronary artery measured proteins in the myocardial interstitial fluid. VSMC from jugular vein explants were isolated, amplified in culture for 3 wk, and transfected with a plasmid expressing VEGF-165 and/or enhanced green fluorescent protein. Cells were injected before commencement of occlusions. VEGF levels in myocardial interstitial fluid were significantly higher in VEGF-transfected animals than in sham (repetitive occlusions without cell transplantation) and control (repetitive occlusions with enhanced green fluorescent protein-transfected cells) animals at the onset of occlusions (P < 0.05). In the VEGF group, collateral flow was increased at day 7 and remained higher than in sham and control groups thereafter. We found that intracoronary administration of VEGF-transfected autologous VSMC effectively promotes collateral development. This approach may provide a way to confine delivery of a gene to a specified organ, thus minimizing complications related to gene transfection in nontargeted organ systems.
Identification and mRNA developmental profiles of two ultraspiracle isoforms in the epidermis and wings of Manduca sexta (1997)

cDNAs were isolated from Manduca sexta that encode two isoforms of an ultraspiracle (USP) homologue MsUSP-1 and MsUSP-2 with different N-terminal A/B regions. The MsUSP-1 cDNA predicts a protein with 97% and 45% amino acid identities in the DNA- and ligand-binding domains respectively to the Drosophila USP and 89% overall identity with Bombyx mori CF1 (an USP homologue). Northern blot hybridizations with probes specific to MsUSP-1 and MsUSP-2 showed transcripts of an approximately equal size (4.5 kb), but with diverse developmental profiles in Manduca epidermis during the two final larval instars and the onset of the adult moult. The MsUSP-1 mRNA was expressed during the intermoult periods, with higher levels around the time of the larval ecdyses and at the onset of wandering behaviour. In contrast, the MsUSP-2 mRNA was up-regulated at times of high ecdysteroid titre during the larval moults, when the MsUSP-1 mRNA disappeared. Together, these conversely regulated isoform mRNAs contribute to the constitutive expression profile of total MsUSP mRNA.
The eukaryotic genome: a system regulated at different hierarchical levels (2003)

Eukaryotic gene expression can be viewed within a conceptual framework in which regulatory mechanisms are integrated at three hierarchical levels. The first is the sequence level, i.e. the linear organization of transcription units and regulatory sequences. Here, developmentally co-regulated genes seem to be organized in clusters in the genome, which constitute individual functional units. The second is the chromatin level, which allows switching between different functional states. Switching between a state that suppresses transcription and one that is permissive for gene activity probably occurs at the level of the gene cluster, involving changes in chromatin structure that are controlled by the interplay between histone modification, DNA methylation, and a variety of repressive and activating mechanisms. This regulatory level is combined with control mechanisms that switch individual genes in the cluster on and off, depending on the properties of the promoter. The third level is the nuclear level, which includes the dynamic 3D spatial organization of the genome inside the cell nucleus. The nucleus is structurally and functionally compartmentalized and epigenetic regulation of gene expression may involve repositioning of loci in the nucleus through changes in large-scale chromatin structure.
Mobile Agent Trajectory Prediction using Bayesian Nonparametric Reachability Trees (2011)

This paper presents an efficient trajectory prediction algorithm that has been developed to improve the performance of future collision avoidance and detection systems. The main idea is to embed the inferred intention information of surrounding agents into their estimated reachability sets to obtain a probabilistic description of their future paths. More specifically, the proposed approach combines the recently developed RRT-Reach algorithm and mixtures of Gaussian Processes. RRT-Reach was introduced by the authors as an extension of the closed-loop rapidly-exploring random tree (CL-RRT) algorithm to compute reachable sets of moving objects in real-time. A mixture of Gaussian processes (GP) is a flexible nonparametric Bayesian model used to represent a distribution over trajectories and have been previously demonstrated by the authors in a UAV interception and tracking of ground vehicles planning scheme. The mixture is trained using typical maneuvers learned from statistical data, and RRT-Reach utilizes samples from the GP to grow probabilistically weighted feasible paths of the surrounding vehicles. The resulting approach, denoted as RR-GP, has RRTReach’s benefits of computing trajectories that are dynamically feasible by construction, therefore efficiently approximating the reachability set of surrounding vehicles following typical patterns. RRT-GP also features the GP mixture’s benefits of providing a probabilistic weighting on the feasible trajectories produced by RRTReach, allowing our system to systematically weight trajectories by their likelihood. A demonstrative example on a car-like vehicle illustrates the advantages of the RR-GP approach by comparing it to two other GP-based algorithms.
Cloning, Expression, Characterization and Application of Bst DNA Polymerase Large Fragment. (1999)

DNA sequencing using thermostable DNA polymerase is very valuable in molecular biology. From a specific strain of Bacillus stearothermophilus, the gene of the Bst DNA polymerase large fragment which had no 5'-3' exonuclease activity was cloned and recombined into an expression vector pYZ23,and the constructed plasmid was introduced into Escherichia coli JF1125,then the expressed protein was isolated and purified. The genetic engineered product shows characteristics similar with the purified natural Bst DNA polymerase large fragment. It will benefit the wide application of Bst DNA polymerase and the study of the relationship between the structure and function of Bst DNA polymerase.
In Vivo 7.0-Tesla Magnetic Resonance Imaging of the Wrist and Hand: Technical Aspects and Applications (2009)

Magnetic resonance imaging (MRI) at 7.0 T has the potential for higher signal-to-noise ratio (SNR), improved spectral resolution, and faster imaging compared with 1.5-T and 3.0-T MR systems. This is especially interesting for challenging imaging regions like the wrist and the hand because of the small size of the visualized anatomical structures; the increase in SNR could then be directly converted into higher spatial resolution of the images. Practically, imaging at 7.0 T poses a variety of technical challenges such as static (B (0)) and radiofrequency (B (1)) homogeneities, shimming, chemical shift artifacts, susceptibility artifacts, alterations in tissue contrast, specific absorption rate limitations, coil construction, and pulse sequence tuning. Despite these limitations, this first experience in anatomical imaging of the wrist and the hand at 7.0 T is very promising. Functional imaging techniques will gain importance at ultra-high-field MRI and need to be assessed in detail in the future.
False FHL: A Normal Variant Posing Risks in Posterior Hindfoot Endoscopy (2010)

Posterior hindfoot endoscopy has been more commonly used in the treatment of various pathologies by surgeons with different arthroscopic experience. The flexor hallucis longus is usually the initial and most important landmark serving as a medial boundary for the arthroscope and instruments to avoid inadvertent injury to the tibial nerve and vessels. We report 2 cases in which the presence of the peroneocalcaneus internus muscle, "false FHL," imitated the flexor hallucis longus, risking imminent neurovascular injury during the initial endoscopic exposure. Awareness of this rare anatomic variation, preoperative magnetic resonance imaging studies, and intraoperative differentiation techniques were found helpful to avoid devastating complications.
A probabilistic approach for cross-spectral matrix denoising: Benchmarking with some recent methods (2020)

Array measurements can be contaminated by strong noise, especially when dealing with microphones located near or in a flow. The denoising of these measurements is crucial to allow efficient data analysis or source imaging. In this paper, a denoising approach based on a Probabilistic Factor Analysis is proposed. It relies on a decomposition of the measured cross-spectral matrix (CSM) using the inherent correlation structure of the acoustical field and of the flow-induced noise. This method is compared with three existing approaches, aiming at denoising the CSM, without any reference or background noise measurements and without any information about the sources of interest. All these methods make the assumption that the noise is statistically uncorrelated over the microphones, and only one of them significantly impairs the off-diagonal terms of the CSM. The main features of each method are first reviewed, and the performances of the methods are then evaluated by way of numerical simulations along with measurements in a closed-section wind tunnel.
Impact of Biomimetic Diamond-like Carbon coated Titanium on Osteoblast and Osteoclast Differentiation in vitro (2014)

To examine the effects of hydrogen amount-altered biomimetic DLC film, osteoblastic MC3T3-E1 cells and osteoclastic RAW264.7 cells were cultured on titanium (Ti) disks coated with or without DLC including various amount of hydrogen. The amount of hydrogen in DLC film is reduced from 20.9% to 0.8%. Real-time quantitative reverse transcriptase-polymerase chain reaction analysis showed that typeⅠcollagen mRNA in MC3T3-E1 cells cultured on specific hydrogen-containing DLC coated Ti disks was significantly higher than those of control Ti disks. In addition, specific hydrogen-containing DLC coated Ti disks significantly inhibited the expression of TRAP mRNA in RANKL-treated RAW264.7 cells. These results, taken together, suggested that biomimetic DLC altered osteoblast and osteoclast differentiation, which could promise long-term success of implant therapy.
Efficacy of Current Drugs Against Soil-Transmitted Helminth Infections (2008)

Single-dose oral albendazole, mebendazole, and pyrantel pamoate show high cure rates against A lumbricoides. For hookworm infection, albendazole was more efficacious than mebendazole and pyrantel pamoate. Treatment of T trichiura with single oral doses of current anthelminthics is unsatisfactory. New anthelminthics are urgently needed.
Carbon doped GaN layers grown by Pseudo‐Halide Vapour Phase Epitaxy (2017)

Pseudo‐Halide Vapour Phase Epitaxy (PHVPE) was utilized to grow thick carbon doped GaN layers to study their suitability as semi‐insulating (SI) substrates. With in‐situ waste gas analysis by FTIR spectroscopy, the carbon doping from the HCN precursor gas was indirectly controlled in a wide range up to 5 × 10 19 cm –3 . The grown layers were characterized by Scanning Electron Microscopy (SEM), Secondary Ion Mass Spectroscopy (SIMS), Photoluminescence (PL), Micro‐Raman‐Spectroscopy, Hall effect measurement, and High Resolution X‐Ray Diffractometry (HRXRD). Similar to the impurity incorporation (O, Si, Mg and Zn), carbon distribution proved to be inhomogeneous, due to its increased incorporation on facets of so‐called V‐pits.
Gold Nanoparticles as Spectroscopic Enhancers for in Vitro Studies on Single Viruses (2003)

Gold particles with diameters between 2.5 and 4.5 nm have been introduced in the inner cavity of an icosahedral brome mosaic virus. The optical properties of single gold-marked virions have been tested in-vitro with respect to the characteristic plasmon polariton resonance. The shift in the plasmon polariton resonance of a single Au particle encapsulated in a virus with respect to a free particle in solution indicates a close interaction between the basic residues on the inner wall of the capsid and the negative surface charge of the particle. Incorporation of a pair of Au particles, approximately 4 nm diameter, is shown to be a frequent event. In this case, the dependence of the two-particle surface plasmon spectrum on the interparticle distance and the strong particle/capsid wall interaction suggest that, in the future, it will be possible to use encapsulated Au particles to track changes in the viral capsid volume in real-time and in a physiological environment.
Psoralenamines. 3. Synthesis, pharmacological behavior, and DNA binding of 5-(aminomethyl)-8-methoxy-, 5-[[(3-aminopropyl)oxy]methyl]- and 8-[(3-aminopropyl)oxy]psoralen derivatives (1985)

A series of derivatives of 5-(aminomethyl)-8-methoxypsoralens, 8-[(3-aminopropyl)oxy]psoralens, and 5-[[[3-(tri-methylammonio)propyl]methyl]-8-methoxypsoralen has been synthesized and their potential as PUVA reagents examined. While the DNA association constants of selected psoralens were found to be 10(5)-10(6)L mol-1, corresponding to efficient binding, flow linear dichroism studies indicated that only the 8-substituted psoralens bind to DNA by intercalation. Furthermore, the ability to photoinduce interstrand cross-links in calf thymus DNA, in vitro, was as efficient as that of 8-methoxypsoralen for the 8-substituted psoralens, which were up to 25 times as efficient as the 5-substituted psoralens. Four of the psoralens studied were radiolabeled and used to study photobinding to DNA. Analogously to the cross-binding results, the 8-substituted psoralens were more efficiently photobound than the 5-substituted, while only slight differences were found in the photobinding-cross-linking ratio. The photoreactivity of the aminopsoralens toward cyclohexene and 2'-deoxythymidine was enhanced compared to that of 8-methoxypsoralen, the effect being most pronounced when the amino group is close to the furocoumarin ring system. Most of the new compounds were less photocytotoxic than 8-methoxypsoralen to NHIK 3025 cells, in vitro, and they caused less light-induced DNA interstrand cross-linking, in situ, in these cells. A clear correlation between the photocytotoxicity and the DNA cross-linking ability of the psoralens was observed. Several of the derivatives showed more pronounced effects in the light-dependent skin thickening (inflammatory) test on mice than 8-methoxypsoralen. No correlation between DNA cross-linking capacity, in vitro, and skin phototoxicity was found for this series of psoralens.
[Air pollution and cardiac and respiratory function in three groups of patients]. (2003)

The association between exposure to urban air pollution and cardiac or respiratory impairments in susceptible subjects was evaluated in a panel study including 11 patients with chronic obstructive pulmonary disease (COPD), 7 with ischemic heart disease (IHD), and 11 asthmatics resident in Rome (Italy). Patients underwent repeated 24 h Holter EKG monitoring, 12 h pulse oximetry at night and spirometry examinations during 1999 summer and winter. Multiple linear regression models for repeated individual measures (fixed-effect) were used to analyse the relationship between average daily concentrations of pollutants (PM10-2.5, PM2.5 NO2 and O3) and outcome variables, controlling for meteorological conditions, survey period, and week-ends. In the BPCO panel, increasing ambient PM2.5 levels were associated with increased heart rate and decreased respiratory function. In the asthmatic panel, inverse associations between pulmonary function and both NO2 and PM10-2.5 concentrations were observed, as well as direct association between ambient NO2 concentrations and NO in exhaled breath. In the IHD panel an increase of hearth rate variability associated with increasing concentration of PM2.5 was observed.
Preparation of chlorofluoroacetic acid derivatives for the analysis of chiral alcohols (1994)

(R)- and (S)-Chlorofluoroacetic acid (CFA) esters of several Chiral secondary alcohols have been prepared and compared with the corresponding esters of Mosher's acid. CFA itself is a readily accessible and optically stable acid which gives the expected diastereoisomeric products with Chiral alcohols without epimerization. The resulting diastereoisomers are more volatile than those derived from Mosher's acid, and are well resolved by both GC and HPLC. Both 1H and 19F NMR spectra of CFA esters show characteristic signals in regions rarely overlapped by other signals. Since CFA is a strong organic acid, it reacts with alcohols spontaneously to give esters without any additional catalysis.
Structural effects on the performance of epoxide-based negative-tone molecular resists (2019)

Several 0.26N tetramethylammonium hydroxide (TMAH)-soluble epoxide molecular resists have been synthesized and are reported here. Previously, the patterning performance of 1,1,2,2-tetrakis(p-hydroxyphenyl)ethane-3 epoxide (TPOE-3Ep) was reported and resolved 26 nm lines using extreme ultraviolet lithography. Here, a deeper study is performed to determine the effects of various structural features on the lithographic performance of 0.26N TMAH-soluble molecular resists. Increasing the number of phenols resulted in a notable increase in the glass transition temperature (Tg) of these materials, which required high postexposure bake (PEB) temperatures to achieve normalized remaining thickness (NRT) values of 1 in methyl isobutyl ketone development. Such high PEB temperatures resulted in insoluble material (high NRT values) in unexposed regions in the 248 nm contrast curves. Methyl groups were introduced adjacent to the hydroxyl group of phenol in an attempt to lower the Tg of the resists to allow the use of lower PEB temperatures. The methyl groups only slightly lowered the Tg of the resists, while detrimentally reducing the final NRT. Thus, instead of using the TPOE core or its methylated analog, a smaller core was used, and the resist trihydroxyphenyl ethane (THPE)-2Ep was designed and synthesized to be a low-Tg base-soluble resist. THPE-2Ep has a Tg of 41 °C and showed promising early performance using e-beam lithography and resolves 30 nm lines in 0.26N TMAH developer at a dose of 72 μC/cm2 at a PEB of 50 °C.
Studies on the Biosynthesis of Sterol Side Chain in Higher Plants (2000)

Campesterol (3) and dihydrobrassicasterol (4), typical C28-sterols in higher plants, are biosynthesized from a steroidal 24-ene precursor (desmosterol 1) via 24-methylenecholesterol (2) and 24-methyldesmosterol (5). A typical plant C29-sterol, sitosterol (6), is produced from 24-methylenecholesterol via isofucosterol (7) and 24-ethyldesmosterol (8). The biosynthetic mechanism, focussing stereochemical features, of these side-chain transformations has been studied in detail by feeding regio- and stereoselectively 13C- or 2H-labeled steroidal substrates to cell cultures of higher plants such as Oryza sativa, Catharanthus roseus and Morus alba. These studies allowed to correlate the metabolic origin of C-26 and C-27 of the intermediate sterols. It has been established that the 1st methylation leading to 24-methylenecholesterol from desmosterol involves a Re-face hydrogen migration from C-24 to C-25 based on unambiguous assignment of the isopropyl pro-R-Me and pro-S-Me of 24-methylenecholesterol. The 2nd methylation leading to isofucosterol was revealed to proceed in a trans-mechanism in which addition of the methyl group and elimination of the C-28 hydrogen occur on opposite faces of the original delta 24(28) plane. The double bond isomerization from delta 24(28) to delta 24(25) was found to proceed in a syn-SE2' mechanism with the pro-S-methyl group of isofucosterol becoming the (E)-methyl of 24-ethyldesmosterol. Finally, feeding studies of [E-Me-13C]- and [Z-Me-13C]-24-methyldesmosterols established that an anti-mode of hydrogen addition is operating in the conversion of 24-methyldesmosterol to campesterol and dihydrobrassicasterol. Similar studies established that 24-ethyldesmosterol is converted to sitosterol in an anti-mode of hydrogen addition. In addition, the mechanism of sterol side-chain formation in hairy roots of Ajuga reptans var. atropurpurea is briefly described.
Orf virus interleukin-10 inhibits cytokine synthesis in activated human THP-1 monocytes, but only partially impairs their proliferation (2007)

The sheep parapoxvirus orf virus (ORFV) induces acute, pustular skin lesions in humans. ORFV encodes an orthologue of interleukin-10 (IL-10) that, whilst it closely resembles ovine IL-10 (91 % amino acid identity), shows only 75 % amino acid identity to human IL-10 (hIL-10). The anti-inflammatory potential of ORFV IL-10 in human ORFV infection was investigated by examining its immunosuppressive effects on THP-1 monocytes. ORFV IL-10 and hIL-10 were shown to have equivalent inhibitory effects on the synthesis of proinflammatory cytokines in lipopolysaccharide-activated monocytes, but differed in their abilities to inhibit monocyte proliferation. Structural modelling of ORFV IL-10 revealed differences from hIL-10 in residues predicted to interact with IL-10 co-receptor 2 (IL-10R2), whereas there were very few differences in the residues predicted to interact with IL-10R1. These findings suggest that the partial ability of ORFV IL-10 to inhibit THP-1 monocyte proliferation may be due to the absence of critical residues that mediate the interaction with human IL-10R2.
Antimicrobial activity of alexidine, chlorhexidine and cetrimide against Streptococcus mutans biofilm (2014)

The present study shows that, when used for one minute, 2% and 1% alexidine, and 0.2% cetrimide, achieve eradication of Streptococcus mutans biofilm in most specimens when applied to a dentin-volumetric model.