gebhart/patrepeval huggingface dataset:
Rolling circle amplification-mediated hairpin RNA (RMHR) library construction in plants (2008)

Long hairpin RNA (lhRNA) construct-induced gene silencing facilitates the study of gene function in plants and animals, but constructing multiple lhRNA vectors using traditional approaches is both time-consuming and costly. Also, most of the existing approaches are based on sequence-specific cloning of individual sequences, and are therefore not suitable for preparing hpRNA libraries from a pool of mixed target sequences. Here we describe a rolling-circle amplification (RCA)-mediated hpRNA (RMHR) construction system suitable for generating libraries of lhRNA constructs from any gene of interest or pool of genes. Using RMHR we successfully generated a lhRNA library from a Arabidopsis cDNA population containing known and unknown genes, with an average size of 500-800 bp for the inverted-repeat inserts. To validate the RMHR system, lhRNA constructs targeting the beta-glucuronidase (GUS) gene were tested using Agrobacterium infiltration and shown to be effective at inducing GUS silencing in tobacco leaves. Our results indicate that the RMHR technique permits rapid, efficient and low-cost preparation of genome-wide lhRNA expression libraries.
Technologies for augmented reality systems (1996)

We present a real-time stereoscopic video-see-through augmented reality (AR) system applied to the medical procedure known as ultrasound-guided needle biopsy of the breast. The AR system was used by a physician during procedures on breast models and during non-invasive examinations of human subjects. The system merges rendered live ultrasound data and geometric elements with stereo images of the patient acquired through head-mounted video cameras and presents these merged images to the physician in a head-mounted display. The physician sees a volume visualization of the ultrasound data directly under the ultrasound probe, properly registered within the patient and with the biopsy needle. Using this system, a physician successfully guided a needle into an artificial tumor within a training phantom of a human breast.
The clinical significance of early histological rejection with or without biochemical abnormality in adult living donor liver transplantation for hepatitis B virus related end stage liver disease (2006)

There is no agreement regarding the treatment of early allograft rejection (EAR) in adult living donor liver transplantation (LDLT). A protocol biopsy was performed in 62 adult LDLT recipients. Twenty-one patients (33.9%) had histological evidence of EAR. Of these, 14 patients had biochemical abnormalities and seven patients had no associated biochemical abnormalities. None of the seven patients with subclinical EAR (11.3% of the entire study population) were treated, and no subsequent rejection was observed. Gender mismatch (female-to-male) was the single independent risk factor for histological EAR [odds ratio (OR) = 13.458; 95% confidence interval (CI), 1.836-98.649] and the cumulative probability for a subsequent rejection was higher in patients with EAR (OR = 11.085; 95% CI, 1.221-100.654). However, the actuarial 1 year patient and graft survival rate in patients with EAR (81.0% and 85.5%) were similar to those without EAR (92.7% and 97.25%; P = 0.127 and 0.302, respectively). The presence of an initial biochemical abnormality was an independent risk factor for both a decreased patient survival (OR = 5.827; 95% CI, 1.095-31.017; P = 0.039) and graft loss (OR = 20.646; 95% CI, 2.044-208.524; P = 0.010). Subsequent rejection developed more frequently in patients with EAR. However, the survival is not determined by the presence of EAR but by the presence of a biochemical abnormality.
Validation of the obesity paradox by body mass index and waist circumference in patients undergoing percutaneous coronary intervention (2022)

The paradoxical association of obesity with mortality, named the “obesity paradox”, has been inconsistent, possibly due to a difference between body mass index (BMI) and central obesity, estimated by waist circumference (WC) as patterns of adiposity. We enrolled 8513 participants from the Kumamoto Intervention Conference Study, a multicenter registry that included consecutive patients undergoing percutaneous coronary intervention (PCI) at 18 centers between 2008 and 2017 in Japan. Patients were divided into quartiles in ascending order of the BMI or WC. The primary endpoints were all-cause mortality and cardiovascular death within a year. There were 186 deaths (case fatality rate, 22.1/1000 person-years) during the follow-up period. The lowest group (1st quartile) of BMI or WC had the worst prognosis among the quartiles (1st quartile, 4.2%; 2nd quartile, 1.9%; 3rd quartile, 1.5%; 4th quartile, 1.1%; P < 0.001 (χ2) and 1st quartile, 4.1%; 2nd quartile, 2.3%; 3rd quartile, 1.2%; 4th quartile, 1.5%; P < 0.001 (χ2), respectively). Similar results were obtained for cardiovascular death. In a multivariable analysis adjusted by nine conventional factors, the lowest group (1st quartile) of BMI (hazards ratio, 2.748; 95% confidence interval [CI], 1.712–4.411) and WC (hazards ratio, 2.340; 95% CI, 1.525–3.589) were independent prognostic factors for all-cause mortality. By dividing the participants into two groups according to either the BMI or WC based on the National Cholesterol Education Program Adult Treatment Panel III and World Health Organization classification, the highest mortality was observed in the lower group. However, the C-statistic after adding BMI (quartile) to conventional factors was found to be slightly higher than BMI (two categories) and WC (two categories) (0.735 vs. 0.734). The obesity paradox was observed in patients after PCI, and single-use of BMI (or WC) was sufficient to predict the prognosis of patients after PCI.
The performance analysis of MIMO-beamforming technologies for underwater channel environments (2012)

In this paper, we have analyzed the performance of MIMO combined with beamforming technologies as a way to reduce the distance between sensors while achieving the MIMO gain and beamforming gain simultaneously in underwater channel environments. After analyzing the simulation results, we found out that the average SINR increases 6.5dB when adapting the MIMO-beamforming technologies with four receiving sensors.
New algorithms for recovering highly corrupted images with impulse noise (2012)

In this work, we present a new method of noise removal which is applied on images corrupted by impulse noise. This new algorithm has a good trade-off between quantitative and qualitative properties of the recovered image and the computation time. In this new method, the corrupted pixels are replaced by using a median filter or, they are estimated by their neighbors’ values. Our proposed method shows better results especially in very high density noisy images than Standard Median Filter (SMF), Adaptive Median Filter (AMF) and some other well-known filters for removing impulse noise. Experimental results show the superiority of the proposed algorithm in measures of PSNR and SSIM, specifically when the image is corrupted with more than 90% impulse noise.
Performance Evaluation of Topology based Routing Protocols in a VANET Highway Scenario (2016)

Vehicular Ad-Hoc Network (VANET) has been derived from the well-established Mobile Ad-hoc Network (MANET). It facilitates wireless communication among vehicles to roadside equipment. Such kind of communication is utilized for different purposes such as safety, comfort, or even entertainment. The performance of VANET applications are highly determined by its underlying routing protocols. In this paper, the authors investigate the performance of topology based MANET routing protocols (AODV, DSDV and DSR) in a VANET highway design using NCTUNS 6.0 simulator. Different parameters are varied including speed, node density, propagation loss model, fading effects, data rate and payload. The selected routing protocols are then evaluated in terms of performance metrics throughput, packet drop and packet collision. Results shows that the performance of routing protocols depends on the application requirements in terms of throughput, delay and percentage of packet drops.
Hereditary Haemochromatosis in Two Cousins with Cluster Headache (2002)

A 60-year-old woman with secondary chronic cluster headache had increased serum ferritin and serum transferrin saturation and was homozygous for the C282Y mutation in the HFE gene, which is indicative of hereditary haemochromatosis. Treatment with venesection that normalized her iron stores led to a radical improvement of her headache complaints that had been daily for several years. Later, the headache returned to some degree in spite of normal serum ferritin levels. Her cousin, a 33-year-old man who had had episodic cluster headache for several years, also had increased transferrin saturation and was compound heterozygous for two mutations, a genotype known to be associated with a slightly increased frequency of haemochromatosis. This is the first report of a headache disorder in a patient with hereditary haemochromatosis. The coexistence of the two disorders may be a mere coincidence, but the temporary improvement of headache from depletion of iron stores may indicate a causal relation, possibly mediated by iron deposits in pain-modulating centres in the brainstem.
Clock Synchronization Mechanisms for a Distributed Autonomous System (1996)

A self-organizing mechanical system is currently developed at the Mechanical Engineering Laboratory. The system is composed of many mechanical units and in order to generate cooperative motion, it is required to establish common clock timing. In this paper, two algorithms are proposed to establish the common clock without being trapped in a deadlock condition. The algorithms work in the situation that all units follow the same procedure and neighbor-neighbor communication is possible. The operation of the units is analyzed with a physical spring damper model and it is concluded that with these algorithms the common clock timing can be established if parameters are chosen correctly in each unit.
Pattern Separation and Completion in Olfaction (2009)

The nervous system must provide a mechanism for very precise discrimination of differing patterns of activity, yet at the same time, there must be a mechanism for generalization to prevent all experiences from being independent and novel. Pattern separation and completion by cortical circuits contribute to these processes, respectively. Based on theoretical and computational models of the piriform cortex and experimental designs developed for hippocampal spatial memory, we provide evidence for pattern separation and completion in the olfactory system and demonstrate the predictive power of these two processes for behavioral odor perception.
Seed dispersal pattern of a composite weed Tridax procumbens L. (2005)

The dispersal pattern of a weed Tridax procumbens wasinvestigated in an agricultural field. Two seed traps were designed,one to examine the dispersal pattern of isolated individuals andanother to study the dispersal distances from a cluster of T.procumbens plants. The dispersal curves of both isolated individualsand cluster of plants followed an exponential model. Seeds dispersedin all directions but the movement was primarily in the direction ofwind (westerly direction) while the movement was least in theleeward direction. The factors influencing anemochorous dispersal ofcomposite seeds are discussed.
Monitoring the Crystal Structure and the Electrochemical Properties of Na3(VO)2(PO4)2F through Fe3+ Substitution (2019)

We here present the synthesis of a new material, Na<sub>3</sub>(VO)Fe(PO<sub>4</sub>)<sub>2</sub>F<sub>2</sub>, by the sol-gel method. Its atomic and electronic structural descriptions are determined by a combination of several diffraction and spectroscopy techniques such as synchrotron X-ray powder diffraction and synchrotron X-ray absorption spectroscopy at V and Fe K edges, <sup>57</sup>Fe Mössbauer, and <sup>31</sup>P solid-state nuclear magnetic resonance spectroscopy. The crystal structure of this newly obtained phase is similar to that of Na<sub>3</sub>(VO)<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>F, with a random distribution of Fe<sup>3+</sup> ions over vanadium sites. Even though Fe<sup>3+</sup> and V<sup>4+</sup> ions situate on the same crystallographic position, their local environment can be studied separately using <sup>57</sup>Fe Mössbauer and X-ray absorption spectroscopy at Fe and V K edges, respectively. The Fe<sup>3+</sup> ion resides in a symmetric octahedral environment, while the octahedral site of V<sup>4+</sup> is greatly distorted due to the presence of the vanadyl bond. No electrochemical activity of the Fe<sup>4+</sup>/Fe<sup>3+</sup> redox couple is detected, at least up to 5 V, whereas the reduction of Fe<sup>3+</sup> to Fe<sup>2+</sup> has been observed at ∼1.5 V versus Na<sup>+</sup>/Na through the insertion of 0.5 Na<sup>+</sup> into Na<sub>3</sub>(VO)Fe(PO<sub>4</sub>)<sub>2</sub>F<sub>2</sub>. Comparing to Na<sub>3</sub>(VO)<sub>2</sub>(PO<sub>4</sub>)<sub>2</sub>F, the electrochemical profile of Na<sub>3</sub>(VO)Fe(PO<sub>4</sub>)<sub>2</sub>F<sub>2</sub> in the same cycling condition shows a smaller polarization which could be due to a slight improvement in Na<sup>+</sup> diffusion process thanks to the presence of Fe<sup>3+</sup> in the framework. Furthermore, the desodiation mechanism occurring upon charging is investigated by operando synchrotron X-ray diffraction and operando synchrotron X-ray absorption at V K edge.
ChemInform Abstract: Synthesis of N3‐Fumaramoyl‐L‐2,3‐diaminopropanoic Acid Analogues, the Irreversible Inhibitors of Glucosamine Synthetase. (1986)

Abstract Ausgehend von NZ‐tert.‐Butoxycarbonyl‐2,3‐diaminopropionsäure bzw. NZ‐tert.‐Butoxycarbonyl‐L‐2,4‐diaminobuttersäure werden die im Titel genannten Verbindungen (I) hergestellt und auf die Fä; higkeit zur Inhibierung von Glucosamin‐6‐phosphat‐Synthetase untersucht.
In Vivo Pharmacodynamic Evaluation of an FtsZ Inhibitor, TXA-709, and Its Active Metabolite, TXA-707, in a Murine Neutropenic Thigh Infection Model (2015)

Antibiotics with novel mechanisms of action are urgently needed. Processes of cellular division are attractive targets for new drug development. FtsZ, an integral protein involved in cell cytokinesis, is a representative example. In the present study, the pharmacodynamic (PD) activity of an FtsZ inhibitor, TXA-709, and its active metabolite, TXA-707, was evaluated in the neutropenic murine thigh infection model against 5 Staphylococcus aureus isolates, including both methicillin-susceptible and methicillin-resistant isolates. The pharmacokinetics (PK) of the TXA-707 active metabolite were examined after oral administration of the TXA-709 prodrug at 10, 40, and 160 mg/kg of body weight. The half-life ranged from 3.2 to 4.4 h, and the area under the concentration-time curve (AUC) and maximum concentration of drug in serum (Cmax) were relatively linear over the doses studied. All organisms exhibited an MIC of 1 mg/liter. Dose fractionation demonstrated the area under the concentration-time curve over 24 h in the steady state divided by the MIC (AUC/MIC ratio) to be the PD index most closely linked to efficacy (R(2) = 0.72). Dose-dependent activity was demonstrated against all 5 isolates, and the methicillin-resistance phenotype did not alter the pharmacokinetic/pharmacodynamic (PK/PD) targets. Net stasis was achieved against all isolates and a 1-log10 kill level against 4 isolates. PD targets included total drug 24-h AUC/MIC values of 122 for net stasis and 243 for 1-log10 killing. TXA-709 and TXA-707 are a promising novel antibacterial class and compound for S. aureus infections. These results should prove useful for design of clinical dosing regimen trials.
Fiber‐Optic High‐Resolution Genetic Screening Using Gold‐Labeled Gene Probes (2012)

A new, ultra-sensitive genetic screening tool based on a fiber-optic (FO) surface plasmon biosensor and gold-labeled gene probes is presented. The assay allows for the detection and location of single-point mutations (SNP) at significantly reduced cost and high speed. The assay is evaluated for SNP detection of 3 different DNA targets, including a GC-rich cancer gene fragment and a long bacterial sequence. The data proves that the accuracy of the FO-SNP test is as good or, in some applications, better than classical high-resolution melting (HRM). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Network-based approach for targeting human kinases commonly associated with amyotrophic lateral sclerosis and cancer (2022)

This network-based study presented hereby contributes to a better knowledge of the molecular underpinning of comorbidities associated with the kinases associated with the ALS disease and provides the potential therapeutic targets to disrupt the highly complex disease-causing network.
Editorial: Alternative Splicing Regulation in Plants (2020)

EDITORIAL article Front. Plant Sci., 09 July 2020 | https://doi.org/10.3389/fpls.2020.00913
Indole-3-carbinol and its N-alkoxy derivatives preferentially target ER α -positive breast cancer cells (2014)

Indole-3-carbinol (I3C) is a natural anti-carcinogenic compound found at high concentrations in Brassica vegetables. I3C was recently reported to inhibit neutrophil elastase (NE) activity, while consequently limiting the proteolytic processing of full length cyclin E into pro-tumorigenic low molecular weight cyclin E (LMW-E). In this study, we hypothesized that inhibition of NE activity and resultant LMW-E generation is critical to the anti-tumor effects of I3C. LMW-E was predominately expressed by ERα-negative breast cancer cell lines. However, ERα-positive cell lines demonstrated the greatest sensitivity to the anti-tumor effects of I3C and its more potent N-alkoxy derivatives. We found that I3C was incapable of inhibiting NE activity or the generation of LMW-E. Therefore, this pathway did not contribute to the anti-tumor activity of I3C. Gene expression analyzes identified ligand-activated aryl hydrocarbon receptor (AhR), which mediated sensitivity to the anti-tumor effects of I3C in ERα-positive MCF-7 cells. In this model system, the reactive oxygen species (ROS)-induced upregulation of ATF-3 and pro-apoptotic BH3-only proteins (e.g. NOXA) contributed to the sensitivity of ERα-positive breast cancer cells to the anti-tumor effects of I3C. Overexpression of ERα in MDA-MB-231 cells, which normally lack ERα expression, increased sensitivity to the anti-tumor effects of I3C, demonstrating a direct role for ERα in mediating the sensitivity of breast cancer cell lines to I3C. Our results suggest that ERα signaling amplified the pro-apoptotic effect of I3C-induced AhR signaling in luminal breast cancer cell lines, which was mediated in part through oxidative stress induced upregulation of ATF-3 and downstream BH3-only proteins.
Real‐time update of calibration model for better monitoring of batch processes using spectroscopy (2004)

In order to reduce the large calibration matrix usually required for calibrating multiwavelength optical sensors, a simple algorithm based on the addition in process of new standards is proposed. A small calibration model, based on 14 standards, is periodically updated by spectra collected on-line during fermentation operation. Concentrations related to these spectra are reconciled into best-estimated values, by considering carbon and oxygen balances. Using this method, fructose, acetate, and gluconacetan were monitored during batch fermentations of Gluconacetobacter xylinus 12281 using mid-infrared spectroscopy. It is shown that this algorithm compensates for noncalibrated events such as production or consumption of by-products. The standard error of prediction (SEP) values were 0.99, 0.10, and 0.90 g/L for fructose, acetate, and gluconacetan, respectively. By contrast, without an updating of the calibration model, the SEP values were 2.46, 0.92, and 1.04 g/L for fructose, acetate, and gluconacetan, respectively. Using only 14 standards, it was therefore possible to approach the performance of an 88-standard-based calibration model having SEP values of 1.11, 0.37, and 0.79 g/L for fructose, acetate, and gluconacetan, respectively. Therefore, the proposed algorithm is a valuable approach to reduce the calibration time of multiwavelength optical sensors.
Figure S4 from <i>ZFTA</i> Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors (2023)

&lt;p&gt;ZFTA-RELAFUS1 chromatin binding and remodelling&lt;/p&gt;
Mo(CO)6-Catalyzed Reduction of N,N-Dimethylthioformamide by Silanes, Germanes, and Stannanes (R3EH) To Produce Trimethylamine and Group 14 Thioethers (R3E–S–ER3) (2011)

Treatment of N,N-dimethylthioformamide (DMTF) with a variety of silanes, germanes, and stannanes (R3EH; E = Si, Ge, Sn) in the presence of Mo(CO)6 leads to facile reduction to trimethylamine and the corresponding group 14 thioethers, (R3E)2S. In the reactions we are able to observe the intermediacy of the catalytically active Mo(CO)5(S═CHNMe2) and completely characterize it, including single-crystal X-ray structural analysis. In the case of R3SnH, the reduction occurs without the need for a metal catalyst, presumably via a free radical process.
Contribution of Borehole Digital Imagery in Core-Log-Seismic Integration (2007)

The Integrated Ocean Drilling Program (IODP) and the International Continental Drilling Program (ICDP) use many new technologies to increase the quality of core data. A problem with drilling deep oceanic or continental crust, as well as shallow fractured rock or karstic formations, is that core recovery can be low, and much of the recovered material often consists of small, disrupted core pieces that are frequently biased toward particular types of rocks (lithologies). Even when core recovery is high (in the case of sedimentary formation), recovered cores are not always oriented;as a result, detailed structural and paleomagnetic studies are impaired.
Palladium Complexes of N‐Heterocyclic Carbenes as Catalysts for Cross‐Coupling Reactions—A Synthetic Chemist's Perspective (2007)

Palladium-catalyzed C-C and C-N bond-forming reactions are among the most versatile and powerful synthetic methods. For the last 15 years, N-heterocyclic carbenes (NHCs) have enjoyed increasing popularity as ligands in Pd-mediated cross-coupling and related transformations because of their superior performance compared to the more traditional tertiary phosphanes. The strong sigma-electron-donating ability of NHCs renders oxidative insertion even in challenging substrates facile, while their steric bulk and particular topology is responsible for fast reductive elimination. The strong Pd-NHC bonds contribute to the high stability of the active species, even at low ligand/Pd ratios and high temperatures. With a number of commercially available, stable, user-friendly, and powerful NHC-Pd precatalysts, the goal of a universal cross-coupling catalyst is within reach. This Review discusses the basics of Pd-NHC chemistry to understand the peculiarities of these catalysts and then gives a critical discussion on their application in C-C and C-N cross-coupling as well as carbopalladation reactions.