gebhart/patrepeval huggingface dataset:
A Novel Murine Knock‐in Model for Progranulin‐deficient Frontotemporal Dementia with Nonsense‐mediated mRNA Decay (2018)

Frontotemporal dementia (FTD) is the most common neurodegenerative disorder in individuals under age 60 and has no treatment or cure. Since many cases of FTD result from GRN nonsense mutations, an animal model for this type of mutation is highly desirable for understanding pathogenesis and testing therapies. Here, we generated and characterized Grn R493X knock‐in mice, which model the most common human GRN mutation, a premature stop codon at arginine 493 (R493X). Homozygous Grn R493X mice have markedly reduced Grn mRNA levels, lack detectable progranulin protein, and phenocopy Grn knockout mice, with CNS microgliosis, reduced synaptic density, lipofuscinosis, hyper‐inflammatory macrophages, excessive grooming behavior, and reduced survival. Inhibition of nonsense‐mediated mRNA decay (NMD) by genetic, pharmacological, or antisense oligonucleotide‐based approaches showed that NMD contributes to the reduced mRNA levels in Grn R493X mice and cell lines and in fibroblasts from patients containing the GRN R493X mutation. The expressed truncated R493X mutant protein was functional in several assays in progranulin‐deficient cells, suggesting that NMD inhibition could be an effective as a therapeutic approach for treating progranulin deficiency caused by the R493X mutation. The Grn R493X mice and associated cell lines provide novel model systems to identify therapies for treating FTD resulting from GRN nonsense mutations. Support or Funding Information This work is supported by National Institutes of Health Grants AG023501 (to R.V.F.) and AG047339 (to A.D.N.), VA Merit Award BX002978 (to E.J.H.), the Consortium for Frontotemporal Dementia Research (to R.V.F., T.C.W., E.J.H., S.M.F., and B.L.M.), and the Gladstone Institutes. T.C.W. is an investigator of the Howard Hughes Medical Institute. The Gladstone Institutes received support from a National Center for Research Resources grant RR18928. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Multichannel Two-Stage Beamforming with Unconstrained Beamformer and Distortion Reduction (2013)

This paper proposes a novel multichannel speech enhancement technique for reverberant rooms that is effective when noise sources are spatially stationary, such as a projector fan noise, an air-conditioner noise, and unwanted speech sources at the back of microphones. Speech enhancement performance of the conventional multichannel Wiener filter (MWF) degrades when the Signal-to-Noise Ratio (SNR) of the current microphone input signal changes from the noise-only period. Furthermore, the MWF structure is computationally inefficient, because the MWF updates the whole spatial beamformer periodically to track switching of the speakers (e.g. turn-taking). In contrast to the MWF, the proposed method reduces noise independently of the SNR. The proposed method has a novel two-stage structure, which reduces noise and distortion of the desired source signal in a cascade manner by using two different beamformers. The first beamformer focuses on noise reduction without any constraint on the desired source, which is insensitive to SNR variation. However, the output signal after the first beamformer is distorted. The second beamformer focuses on distortion reduction of the desired source signal. Theoretically, complete elimination of distortion is assured. Additionally, the proposed method has a computationally efficient structure optimized for spatially stationary noise reduction problems. The first beamformer is updated only when the speech enhancement system is initialized. Only the second beamformer is updated periodically to track switching of the active speaker. The experimental results indicate that the proposed method can reduce spatially stationary noise source signals effectively with less distortion of the desired source signal even in a reverberant conference room.
Submergence Tolerant Rice: SUB1’s Journey from Landrace to Modern Cultivar (2010)

Rice landraces tolerant of up to 2 weeks of complete submergence were collected from farmers’ fields in the 1950s. Success in fine mapping of SUBMERGENCE 1 (SUB1), a robust quantitative trait locus from the submergence tolerant FR13A landrace, has enabled marker-assisted breeding of high-yielding rice capable of enduring transient complete submergence. At the molecular level, SUB1 is a variable polygenic locus encoding two or three ethylene responsive factor (ERF) DNA binding proteins. All Oryza sativa accessions encode SUB1B and SUB1C at this locus. An additional ERF, SUB1A, is present at SUB1 in FR13A and other tolerant accessions. The induction of SUB1A expression by ethylene during submergence disrupts the elongation escape strategy typical of lowland and deepwater rice, by limiting ethylene-induced gibberellic acid-promoted elongation. Microarray and metabolite studies confirm that SUB1A orchestrates its effects on metabolism and growth in a submergence-dependent manner. Due to the conditional activity of SUB1A, new “Sub1” mega-varieties effectively provide submergence tolerance without apparent ill effect on development, productivity, or grain quality.
Discovery of new 3-methylquinoxalines as potential anti-cancer agents and apoptosis inducers targeting VEGFR-2: design, synthesis, and <i>in silico</i> studies (2021)

There is an urgent need to design new anticancer agents that can prevent cancer cell proliferation even with minimal side effects. Accordingly, two new series of 3-methylquinoxalin-2(1<i>H</i>)-one and 3-methylquinoxaline-2-thiol derivatives were designed to act as VEGFR-2 inhibitors. The designed derivatives were synthesised and evaluated <i>in vitro</i> as cytotoxic agents against two human cancer cell lines namely, HepG-2 and MCF-7. Also, the synthesised derivatives were assessed for their VEGFR-2inhibitory effect. The most promising member <b>11e</b> were further investigated to reach a valuable insight about its apoptotic effect through cell cycle and apoptosis analyses. Moreover, deep investigations were carried out for compound <b>11e</b> using western-plot analyses to detect its effect against some apoptotic and apoptotic parameters including caspase-9, caspase-3, BAX, and Bcl-2. Many <i>in silico</i> investigations including docking, ADMET, toxicity studies were performed to predict binding affinity, pharmacokinetic, drug likeness, and toxicity of the synthesised compounds. The results revealed that compounds <b>11e, 11g, 12e, 12g,</b> and <b>12k</b> exhibited promising cytotoxic activities (IC<sub>50</sub> range is 2.1 - 9.8 µM), comparing to sorafenib (IC<sub>50</sub> = 3.4 and 2.2 µM against MCF-7 and HepG2, respectively). Moreover, <b>11b, 11f, 11g, 12e, 12f, 12g,</b> and <b>12k</b> showed the highest VEGFR-2 inhibitory activities (IC<sub>50</sub> range is 2.9 - 5.4 µM), comparing to sorafenib (IC<sub>50</sub> = 3.07 nM). Additionally, compound <b>11e</b> had good potential to arrest the HepG2 cell growth at G2/M phase and to induce apoptosis by 49.14% compared to the control cells (9.71%). As well, such compound showed a significant increase in the level of caspase-3 (2.34-fold), caspase-9 (2.34-fold), and BAX (3.14-fold), and a significant decrease in Bcl-2 level (3.13-fold). For <i>in silico</i> studies, the synthesised compounds showed binding mode similar to that of the reference compound (sorafenib).
SiO<sub>2</sub>coating of silver nanoparticles by photoinduced chemical vapor deposition (2009)

Gas-phase silver nanoparticles were coated with silicon dioxide (SiO2) by photoinduced chemical vapor deposition (photo-CVD). Silver nanoparticles, produced by inert gas condensation, and a SiO2 precursor, tetraethylorthosilicate (TEOS), were exposed to vacuum ultraviolet (VUV) radiation at atmospheric pressure and varying temperatures. The VUV photons dissociate the TEOS precursor, initiating a chemical reaction that forms SiO2 coatings on the particle surfaces. Coating thicknesses were measured for a variety of operation parameters using tandem differential mobility analysis and transmission electron microscopy. The chemical composition of the particle coatings was analyzed using energy dispersive x-ray spectrometry and Fourier transform infrared spectroscopy. The highest purity films were produced at 300-400 degrees C with low flow rates of additional oxygen. The photo-CVD coating technique was shown to effectively coat nanoparticles and limit core particle agglomeration at concentrations up to 10(7) particles cm(-3).
Acoustic stone localization during lithotripsy. (2010)

It is desirable to mitigate damage to kidney tissue induced by shock waves administered during lithotripsy. Stone movement due to patient respiration causes a fraction of the shock waves to miss the stone. The goal here is to ensure that shock waves are delivered to the kidney only when the kidney stone is in the focal region of the lithotripter. We present the design of a collar with an array of ultrasound transducers that can be retrofitted to a clinical lithotripter. The transducers are used in a pulse-echo mode and a hybrid technique combining numeric time-reversal and MUSIC (MUltiple-SIgnal-Classification) is employed to determine the location of a kidney stone relative to the focus of the lithotripter. A model of the acoustic collar was used to select system parameters including the transducer count, center frequency, and transducer placement. The performance of the collar was assessed by translating artificial kidney stones in water and using porcine body wall as an aberrating layer. Performance will be reported of the system including resolution limit, ability to target multiple stone fragments, and the effect of an aberrating layer. [Work supported by NIH.]
Automatic Recognition of Corneal Nerve Structures in Images from Confocal Microscopy (2008)

Automatic and manual length estimations on the same image were very well correlated, indicating that the automatic procedure is capable of correctly reproducing the differences in nerve length between different subjects.
Long‐term follow‐up of peginterferon and lamivudine combination treatment in HBeAg‐positive chronic hepatitis B† (2005)

We have previously demonstrated that combination peginterferon and lamivudine treatment has superior antiviral efficacy to lamivudine monotherapy in chronic hepatitis B. In this study, we investigated the long-term posttreatment virological response to this combination treatment. Sustained virological response of patients who completed 32-week peginterferon and 52-week lamivudine combination treatment was compared to patients who completed 52-week lamivudine monotherapy. Sustained response was defined as sustained hepatitis B e antigen (HBeAg) loss and HBV DNA < 100,000 copies/mL from treatment cessation until the end of follow-up. Forty-eight patients receiving combination treatment and 47 patients receiving lamivudine monotherapy were studied. The posttreatment follow-up of patients who received combination treatment was 117 +/- 34 weeks and that of patients receiving lamivudine monotherapy was 124 +/- 29 weeks. At the end of treatment, HBeAg loss occurred in 63% of patients in the combination group and 28% of patients in the lamivudine group (P = .001). The probabilities of sustained response for combination treatment and lamivudine monotherapy were 33% and 13% at week 24, 31% and 11% at week 52, and 29% and 9% at week 76, respectively (log-rank test, P = .0015). No patients developed virological relapse after week 76 until the last visit in either treatment group. All sustained responders had no biochemical relapse (alanine aminotransferase [ALT] > 2 times upper limit of normal) during follow-up. Among the non-sustained responders, biochemical relapse occurred in 32 patients (94%) in the combination group and 38 patients (88%) in the lamivudine group, respectively. In conclusion, combination treatment of peginterferon and lamivudine has a higher sustained virological response than lamivudine monotherapy up to 3 years after treatment.
Magnetic Carbon Nanotubes: Functionalized Fe‐Filled Multiwalled Carbon Nanotubes as Multifunctional Scaffolds for Magnetization of Cancer Cells (Adv. Funct. Mater. 25/2013) (2013)

Epidermoid carcinoma model cell lines overexpressing epidermal growth factor receptor (EGFR+) can be sorted off and selectively killed from a population of a “healthy” (EGFR-) cell line. On page 3173, Davide Bonifazi and co-workers report that this is due to the combined action of the conjugated targeting antibody and the Fe-filled carbon nanotubes, with the latter exerting a magnetic fluid hyperthermia.
Subsurface microbiological heterogeneity: current knowledge, descriptive approaches and applications (1997)

Improved understanding of the spatial and temporal distribution of microbiological properties and processes is critical due to the relative difficulty and high cost of obtaining large numbers of subsurface samples. Quantification of spatial patterns in subsurface environments is important because it is well known that geologic, hydrologic and geochemical properties are not constant in space; rather, they are spatially autocorrelated, or related over certain length scales. Preliminary research indicates that subsurface microbiological properties have similar length scales, and the microbiological properties appear to be spatially correlated to geologic, hydrologic and/or geochemical properties. Temporal variability can also be important in subsurface systems that receive seasonal recharge. In order to better understand heterogeneous subsurface systems, it is critical to sample such that the spatial and temporal patterns are adequately captured, and understand what is causing the variability and spatial patterns. Improved understanding in these two areas will yield more efficient sampling schemes, assist in defining factors that control the distribution of microbiological properties at the field scale, and increase the ability to predict and ultimately model the distribution of microbiological properties and the responses of microbial communities to environmental perturbations such as subsurface contaminant transport and bioremediation.
A Unified Wide-Speed Range Sensorless Control Method for Switched Reluctance Machines Based on Unsaturated Reluctance (2022)

A unified unsaturated-reluctance-based wide speed range sensorless control method for switched reluctance machines (SRMs) is proposed in this article. First, the sensitivity analysis of the estimated position to the possible reluctance calculation error is analyzed. This analysis reveals the feasible regions with low sensitivity and low risk of entering saturation. Then, the unsaturated reluctance in these feasible regions is obtained and modeled. A simple second-order rational expression is proposed to fit the highly nonlinear unsaturated reluctance curve. With this simple model, the rotor position can be analytically calculated only by solving a simple quadratic problem. Based on the abovepresented analysis, a wide-speed range sensorless control is developed. The rotor position is universally estimated from the real-time reluctance value and the proposed analytical model. The high-frequency voltage injection and normal conduction phase are combined to calculate the phase reluctance over the wide-speed range. The concerns of calculating reluctance at the low-speed range are also discussed. A 5.1 kW four-phase 8/6 SRM is used to verify the proposed method. Various steady state and transient state experimental results prove the effectiveness of the proposed sensorless control method.
Remarkable stability in patterns of blood-stage gene expression during episodes of non-lethal Plasmodium yoelii malaria (2012)

Taken together, these results indicate that 1) P. yoelii gene expression remains stable in the presence of a changing host environment, and 2) concurrent expression of a large number of the polymorphic yir and pyst-a genes, rather than differential expression in response to specific host factors, may in itself limit the effectiveness of host immune responses.
Elementary Classroom Vocabulary Experiences (2021)

This study aimed to examine language at the teacher/classroom level among second-grade classrooms that differ in socioeconomic backgrounds. Measures of teachers’ vocabulary input across the school day throughout the school year were examined. There was a significant difference in the proportion of academic word use between classes that differed in the percentage of students on free or reduced-price lunch. Teachers in classes of students from higher socioeconomic backgrounds used more academic words. Class vocabulary level significantly predicted the proportion of academic word use and the proportion of grade-level vocabulary use. Once class vocabulary level was accounted for, the percentage of students on free or reduced-price lunch was no longer predictive. However, some classes of students may be at a disadvantage in their exposure to academic and grade-level vocabulary words given that school is the most likely place for many students to be exposed to these curriculum words.
Model-based characterization of permanent magnets with a 3D Hall-Sensor array (2016)

Demagnetization and defects of permanent magnets used in electric drives can occur during their production or due to operating stresses and lead to reduced reliability and performance. In this paper a novel technique for magnet quality monitoring is proposed. It uses an array of 3D Hall-Sensors to measure the magnetic flux density in the proximity of the magnet. The measurement system and the expected defects are modeled analytically. Based on this model an optimal estimation method for nonlinear systems is used to determine the critical parameters of the magnet. For these parameters pass/fail limits can be applied for production tests and quality monitoring. During our research simulations and measurements were carried out to validate the proposed method.
The association of the <i>HLA‐A*24:02, B*39:01</i> and <i>B*39:06</i> alleles with type 1 diabetes is restricted to specific <i>HLA‐DR/DQ</i> haplotypes in Finns (2017)

The independent predisposing effect of the HLA-B*39:06 allele with type 1 diabetes was confirmed in the Finnish population but the association of the A*24:02 and B*39:01 alleles remained inconclusive whilst both A*24:02 and B*39:01 affected the progression rate from seroconversion to autoantibody positivity to overt type 1 diabetes.
Empirical Modeling of the Effect of Incidents on Congestion and Travel Time Prediction: Case Study of Attica Tollway in Athens, Greece (2008)

An empirical model is presented which relates incidents with congestion and travel time prediction. Incident and travel time data from the Attica Tollway (AT) in Athens, Greece have been studied according to the framework and the following conclusions are drawn: 1) There is significant time-of-day variability in the effect of incidents on delay; 2) There is significant route-to-route variability in the effect of incidents on delay. Delay characteristics, especially maximum delay observed for the route, is strongly correlated (with correlation coefficient of 0.68) with the incident-delay correlation; 3) Breakdowns and accidents have largest impact on delay and thus need to be managed with high priority, while other incidents have small impact; and 4) The real-time travel time prediction, such as what is displayed on a CMS, could be improved by bias-reduction using the knowledge of an accident that has just happened. These results imply that it is critical for incident management plan and real-time travel time prediction to be based on empirical study using site-specific data on incidents and congestion. The proposed empirical modeling framework can facilitate development of such incident management plan and improve real-time travel time prediction reflecting incident information.
Distributed precoding for MISO interference channels with channel mean feedback: Algorithms and analysis (2013)

This work focuses on the design and analysis of distributed stochastic precoding algorithms for multiple-input single-output (MISO) interference channels, where each transmitter is provided with mean information of its intended channel and that of interfering channels. Unlike in cases where exact channel gains are known as in most existing works, here generalrank precoding is required for optimality instead of the rank-one beamforming. An efficient algorithm for the distributed implementation of the Nash equilibrium precoding is first proposed. A sufficient condition for this algorithm to converge to the unique equilibrium is derived for the two-user case based on stochastic ordering, and is valid for a wide range of system parameters. To improve the sum-rate performance under medium to strong interference, a pricing-based algorithm is also provided and its convergence analyzed. The two algorithms are compared in terms of sum-rate and system overhead.
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics (2017)

Abstract Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy towards accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics dataset against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and variants identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin, and release iPtgxDBs for B. henselae , Bradyrhozibium diazoefficiens and Escherichia coli as well as the software to generate such proteogenomics search databases for any prokaryote.
Treatment efficacy of a probiotic preparation for non‐alcoholic steatohepatitis: A pilot trial (2017)

Short-term treatment with the probiotic cocktail caused significant improvement of liver inflammation without adverse events and, thus, may represent a promising candidate therapeutic approach for NASH.
<scp>ALPS</scp>‐<scp>N</scp>eo pain and stress assessment scale for neonates—A measure for procedural pain (2023)

ALPS-Neo may be used as a measure for procedural pain.