gebhart/patrepeval huggingface dataset:
A Prediction Model of Pretreatment HIV RNA Levels in Naïve Thai HIV-infected Patients: An Application for Resource-limited Settings (2017)

Abstract Background The use of abacavir (ABC) and rilpivirine (RPV) in the first-line regimen for naïve HIV-infected patients with pretreatment HIV RNA &amp;gt;100,000 copies/mL is not recommended due to a high rate of treatment failure. If a model could accurately predict pretreatment HIV RNA levels, it would be a useful tool for the selection ABC or RPV in the first-line regimen. Methods Thai HIV-infected adults enrolled in the TREAT Asia HIV Observational Database (TAHOD) and additional patients of Ramathibodi Hospital were eligible if they had an HIV RNA result at the time of antiretroviral therapy initiation. Factors associated with pretreatment HIV RNA &amp;lt;100,000 copies/mL were determined by logistic regression. Based on the results of the final model, a prediction model was created. Results A total of 1,223 patients were included in the analysis. Among those in the derivation data set, median [interquartile range (IQR)] age was 36.3 (30.5–42.9) years, median (IQR) CD4 count was 122 (39–216) cells/mm3, and pretreatment HIV RNA was 100,000 (32,449–229,777) copies/mL. Factors associated with pretreatment HIV RNA &amp;lt;100,000 copies/mL were anemia [odds ratio (OR) 2.05 vs. no anemia; 95% confidence interval (CI) 1.28–3.27], CD4 count &amp;gt;200 cells/mm3 (OR 3.00 vs. CD4 count &amp;lt;200 cells/mm3; 95% CI 2.08–4.33), and non-heterosexual HIV exposure (OR 1.61 vs. heterosexual HIV exposure; 95% CI 1.07–2.43). No AIDS-defining illness (11.5), no anemia (18.5), age &amp;lt;35 years (11), CD4 count &amp;gt;200 cells/mm3 (27), duration of HIV infection &amp;gt;1 year (9), and weight &amp;gt;50 years (11) were included in the clinical prediction tool scores. A score ≥45 yielded a sensitivity of 45.3%, specificity of 76.7%, positive predictive value of 68.1%, and negative predictive value of 56.1% among patients in the derivation. The area under the receiver-operator characteristic curve was 0.655 (95% CI 0.614- 0.696) and 0.600 (95% CI 0.533–0.667) in the derivation and validation patients, respectively. Conclusion Our final prediction model had poor sensitivity and specificity for predicting HIV RNA &amp;lt;100,000 copies/mL. Further study on a larger population with a greater diversity of data variables available is necessary to improve the model. Pretreatment HIV RNA remains necessary before ABC or RPV initiation for naïve Thai HIV-infected patients. Disclosures All authors: No reported disclosures.
Aneurysm of Thoracoabdominal Aorta Involving the Celiac, Superior Mesenteric, and Renal Arteries, Report of Four Cases Treated by Resection and Homograft Replacement (1956)

DeBakey, Michael E. M.D.; Creech, Oscar Jr. M.D.; Morris, George C. Jr. M.D. Author Information
The effect of additional oxidation on the memory characteristics of metal-oxide-semiconductor capacitors with Si nanocrystals (2003)

Metal-oxide-semiconductor (MOS) capacitors with Si nanocrystals (Si-nc) obtained by ion implantation in SiO2 have been studied for nonvolatile memory applications. The use of a thermal oxide and the accurate tuning of the postimplantation processing conditions allow good integrity, reliability, and high retention times. We propose an additional thermal oxidation step after the formation of the Si-nc. This process has enabled growing a thin tunnel oxide at the Si/SiO2 interface completely free of Si-nc and Si excess, leading to a formidable increase of the retention time. In addition the additional oxidation makes it possible to control the size and density of Si-nc. Finally, we show its impact on the memory characteristics of the nanocrystal device (writing speed and programming window).
Rheology of polymer carbon nanotubes composites (2013)

In this review paper the rheology of polymer nanocomposites with dispersed carbon nanotubes is presented. The major factors controlling the rheology of these nanocomposites are the overall concentration of the nanotubes and their state of dispersion. Percolation of anisotropic nanotubes and the transition from isotropic to nematic structures bound the range of concentrations over which the rheological properties of these nanocomposites is dominated by the meso-scale structure and dispersion and are of significance to the processing of nanotube based polymer nanocomposites. The percolation threshold and the concentration for the isotropic to nematic transition are strong functions of the inverse of the effective aspect ratio of the dispersed nanotubes and therefore restrict the range of concentrations over which such nanocomposites can be deployed. In this review we briefly describe the rheology in the dilute regime, where especially for the case of polymer nanocomposites the rheology is dominated by that of the polymer. Subsequently, the percolation phenomenon and rheological significances are presented. Finally, both linear and non-linear rheologies of semi-dilute dispersions with random orientation of nanotubes are discussed in detail. Where possible, the rheological responses are contextualized through the underlying structure of the nanocomposites and interplay of different forces.
Palaeoclimate sensitivity to CO2 and insolation (1997)

The current Quaternary Ice Age is characterized by multiple switches of the global climate between glacials and interglacials. The Louvain-la-Neuve two-dimensional (altitude-latitude) climate model (LLN 2-D model) has been used to simulate the long-term variations of the Northern Hemisphere climate. The model is forced by both the CO2 and the insolation for each day and latitude. The period analyzed here is from 200 ka BP to 200 ka AP. The model provides a total continental ice volume, which compares relatively well with the SPECMAP oxygen-isotope record, the size and extent of the individual Northern Hemisphere ice sheets being in fair agreement with their geological reconstructions. Seven simulations were done to quantify the relative contribution of the insolation and CO2 forcings and of the albedo and water-vapor temperature feedbacks to the last glacial maximum (LGM) cooling. This LGM cooling of 4.5 degrees C would be due to CO2 alone for 20.8%, to insolation and the albedo temperature feedback for 40%, and to the water vapor feedback for 38.6%. If we consider the low CO2 concentration as the only forcing, but allow water vapor to change, 33% of the cooling are explained.
Large enhancement of second order non-linear effects in ionic self-assembled multilayer films (2006)

Ionic self-assembled multilayer (ISAM) films have been combined with plasmonic nanoparticles to yield composite films with second harmonic conversion efficiencies several hundred times larger than the unmodified ISAM films
Segmenting Mechanomyography Measures of Muscle Activity Phases Using Inertial Data (2019)

Electromyography (EMG) is the standard technology for monitoring muscle activity in laboratory environments, either using surface electrodes or fine wire electrodes inserted into the muscle. Due to limitations such as cost, complexity, and technical factors, including skin impedance with surface EMG and the invasive nature of fine wire electrodes, EMG is impractical for use outside of a laboratory environment. Mechanomyography (MMG) is an alternative to EMG, which shows promise in pervasive applications. The present study used an exerting squat-based task to induce muscle fatigue. MMG and EMG amplitude and frequency were compared before, during, and after the squatting task. Combining MMG with inertial measurement unit (IMU) data enabled segmentation of muscle activity at specific points: entering, holding, and exiting the squat. Results show MMG measures of muscle activity were similar to EMG in timing, duration, and magnitude during the fatigue task. The size, cost, unobtrusive nature, and usability of the MMG/IMU technology used, paired with the similar results compared to EMG, suggest that such a system could be suitable in uncontrolled natural environments such as within the home.
A Study of Solder Ball Joint Reliability of Electroless Ni/Pd/Au Plating － Influence of Electroless Pd Plating Film Thickness－ (2016)

We investigated the influences of Pd film thickness of electroless Ni/Pd/Au plating on the solder ball joint reliability during reflow cycles and thermal aging, using high-speed solder ball shear test. As the solder ball, Sn-3.0Ag-0.5Cu solder ball was studied. After multiple reflow cycles and thermal aging, we found that the optimum thickness of Pd film with Sn-3.0Ag-0.5Cu solder ball was 0.05-0.2 μm.
The Role of Polymorphisms in DNA Repair Genes and HPV 18 Integration Status in Cervical Dysplasia (2012)

Abstract Despite the fact that cervical cancer is one of the leading causes of death in women worldwide, research has yet to elucidate why some HPV-infected women develop cancerous lesions while others are able to clear the infection. Previous studies have shown that HPV integration status may be associated with cervical cancer development, and yet, host genetic factors that may be involved in the viral integration process have not yet been identified. The purpose of this study was to examine the association between both HPV 18 viral integration status and single nucleotide polymorphisms (SNPs) in non-homologous end-joining (NHEJ) DNA repair pathway genes on cervical dysplasia. Specifically, we sought to compare women with no dysplasia to those with low-grade or high-grade squamous intraepithelial lesions. Methods: A total of 765 women were selected from two large trials designed to evaluate optical technologies for cervical cancer. Genotyping was performed using the Illumina Golden Gate platform. HPV 18 integration status was determined using a previously established protocol. Chi-square tests were conducted to determine which SNPs were associated with normal cytology, low-grade, or high-grade lesions. Among participants with cervical dysplasia, polytomous logistic regression models were used to evaluate the effect of each polymorphism on viral integration status. An additive genetic model was used for all tests. P-values were adjusted using the false discovery rate method. Results: Women with high-grade lesions were significantly younger than women with low-grade or no lesions. Tag-SNPs in 13 DNA repair genes, including MRE11A, ATM, and XRCC4, were significantly associated with cervical dysplasia. Most participants had a mix of both episomal and integrated HPV 18. Tag-SNPs in the XRCC4, PRKCH, and MRE11A genes were found to be significantly associated with HPV 18 integration status. Conclusion: Our study indicates that host genetic variation in NHEJ DNA repair pathway genes, including MRE11A and XRCC4, are significantly associated with HPV 18 integration, and that these genes may play a key role in determining cervical cancer development and progression. This is the first study to examine host genetic variation in association with the viral integration event.
A new method for developing optical CDMA address code sequences using the genetic algorithm (2002)

A new method for developing optical CDMA address code sequences is presented. The method is based on the genetic algorithm, which has already shown success in developing two-dimensional correlation functions for pattern recognition applications. The algorithm is very flexible in terms of optimization criteria, thus adequate for various optical CDMA applications, including coherent and non-coherent systems. Preliminary computer experimental results are presented, indicating very good discrimination ratios, and very fast convergence of the search process. Important implications include synchronization-independent CDMA system design, optical beat noise reduction, optical power budget improvement, and enhanced security.
Cloning and Characterization of Haploid Germ Cell-Specific Genes (2004)

In most multicellular organisms, fertilized eggs differentiate into somatic and germ cells. They become separated during the early developmental stages and have quite different roles. Germ cells maintain species continuity, whereas somatic cells ensure the constitution and activity of the individual. In other words, somatic cells help the germ cells to ensure survival and continuity of the species. Thus, germ cells play a fundamental role in multi-cellular organisms.To understand the unique mechanism of germ cell differentiation, the most straightforward strategy is to identify and characterize differentiation-specific molecules and their associated genes in germ cells. We have cloned haploid germ-cell-specific cDNAs from a subtracted cDNA library that was generated by subtracting the mRNA of 17-day-old mouse testes (before haploid germ cells develop) from the cDNA of 35-day-old mouse testes. Detailed mRNA expression analysis revealed that the genes corresponding to the cloned cDNAs were exclusively expressed in germ cells at all steps of differentiation, at specific steps of differentiation, or at specific steps in the development of haploid germ cells. The expression of all of these genes was developmentally controlled. The products of germ-cell-specific genes included various proteins having roles in spermatogenesis. Some germ-cell-specific isozymes of previously known enzymes for energy metabolism are interesting examples.We also isolated the genomic DNA of haploid-specific genes and identified a number of regulatory motifs in the gene-promoter regions that were essential for transcription. One of these motifs, the cyclic AMP response element, was present in the promoter regions of several testis-specific genes, and was deemed to be functionally important. However, the haspin gene-promoter region did not contain a CRE motif. Similarly, the promoter regions of the MMP-28 (Illman et al. 2001), Hormone-sensitive lipase (Blaise et al. 2001), ldhc (Jethanandani and Goldberg 2001), SP-10 (Reddi et al. 1999) genes, which were specifically expressed in haploid germ cells, did not have CRE motifs. These findings suggest the existence of haploid germ-cell-specific regulatory proteins specifically regulate the expression of haploid germ-cell-specific genes. Here, we describe our recent findings of germ-cell-specific genes and gene products, and discuss the relevance of our approaches to the study of germ cell differentiation mechanisms.
Cascaded five-fold mode-order switching device (2004)

A numerical cascaded five-fold mode-order switching device has been simulated for selective mode-order conversion in cases where an arbitrary type of mode-order conversion is desired without the need of reconfiguring the connections within the device.
Power SAWs (1996)

Applications employing digital signal processing (DSP) has mushroomed over the past fifteen years. DSP techniques are now employed in television and radio receivers, in telephones, in automobile engines, in medical diagnostics, in robotics, in military systems, to just name a few. Its popularity stems from its flexibility. DSP also parallels the advances made in low cost computers and specialized integrated circuits (ICs). In a few applications, however, these digital techniques are either too slow or consume too much power to be practical. Examples include ultra-high frequency (UHF) filters and convolvers. In such applications, analog techniques can often perform the same tasks much more efficiently. Of the analog techniques, those employing surface acoustic waves (SAWs) offer unique capabilities for processing signals in the 30 MHz to 2 GHz frequency range. We examine this technology and review some of its applications.
A quenched fluorescent substrate for thimet peptidase containing a new fluorescent amino acid, DL-2-amino-3-(7-methoxy-4-coumaryl)propionic acid (1991)

DL-2-Amino-3-(7-methoxy-4-coumaryl)propionic acid, a new fluorescent amino acid (abbreviated to Amp), has been synthesized to provide an alternative to tryptophan in quenched fluorescent peptide substrates for peptidases. The model compound Ac-DL-Amp-NH2 was intensely fluorescent with an excitation maximum at 328 nm and an emission maximum at 392 nm. Fmoc (fluoren-9-ylmethoxycarbonyl)-DL-Amp was made to allow the solid-phase synthesis of Amp-containing peptides by the Fmoc-polyamide method. The peptide derivative Dnp (2,4-dinitrophenyl)-Pro-Leu-Gly-Pro-DL-Amp-D-Lys was cleaved by thimet peptidase at the Leu-Gly bond, with a 20-fold enhancement of fluorescence. The value of kcat./Km for thimet peptidase was 6.7 x 10(5) M-1.s-1, compared with the value of 2.4 x 10(5) M-1.s-1 for the tryptophan-containing analogue, Dnp-Pro-Leu-Gly-Pro-Trp-D-Lys.
Nitrogen fixation by native Bradyrhizobia in symbiosis with Lupinus mariae-josephae requires a T3SS encoding a NopE-like effector (2013)

Several bradyrhizobial isolates from L. mariae-josephae root nodules [1] contain a type III secretion system (T3SS) within a cluster of about 30 genes. Among those genes, ttsI codes for the transcriptional activator of the system. Mutation of ttsI resulted in the formation of white, non-fixing nodules with the natural legume host, L. mariae-josephae. The T3SS cluster also contains a gene coding for a NopE-like protein. NopE proteins have been demonstrated to be effectors in the Bradyrhizobium-soybean symbiosis [2] and belong to a small group of poorly characterized proteins from plant-associated bacteria that contain one or two autocleavage motifs known as DUF1521 (Schirrmeister et al. 2011). The amino acid sequence of a NopE-like protein in the L. mariae-josephae strain LmjC contains just one autocatalytic motif. This is unlike NopE1 and NopE2 proteins secreted by the T3SS of B. japonicum, that contain two motifs [3]. The autocleavage of LmjC NopE protein was analyzed after expression in E. coli and purification. Two protein fragments of the predicted sizes appeared in the presence of Ca2+, Cu2+, Cd2+, Zn2+ and Mn2+ cations. In contrast, autocleavage did not take place in the presence of Ni2+, Co2+ or Mg2+. Site-directed mutagenesis of the DUF1521 motif in LmjC NopE abolished self-cleavage in vitro. Symbiotic competence of a NopE- mutant with the L. mariae-josephae host was not affected. Possible roles of NopE are discussed.
Percutaneous nephrostomy experience in pediatric patients: comparison of fine and thick needle techniques (2022)

Objectives: The aim of this study is to assess the effect of needle size in pediatric percutaneous nephrostomy (PN) placement in terms of complications and success rates. Methods: Seventy one percutaneous nephrostomies were performed in 51 patients aged 1 month to 18 years (mean 6.03 ± 5.88 years) between May 2012 and March 2020. Demographic data, indication for PN placement, puncture technique (calyceal entry level: upper, middle, lower pole or pelvis) and needle size, anesthesia type (general or local anesthesia), duration of catheter use and complications were retrospectively retrieved from the hospital electronic recording system. Results: Thirty procedures were performed using a 21 gauge needle and 41 procedures using a 18 gauge needle. There was no statistically significant difference between the two groups in terms of age, gender, degree of hydronephrosis, and calyceal entry level. Technical success and complication rates were similar in two groups (p = 0.423). Conclusions: In the pediatric age group, both 18 and 21 gauge needle techniques can be used safely based on the preference of the interventionalist.
Malaria and red cell genetic defects (1989)

The study of inherited RBC resistance to malaria has increased our knowledge of the biochemistry and physiology of the host-parasite interaction and suggested potential sites for therapeutic intervention. Discovery by Jensen and Trager of the in vitro culture system for P falciparum has facilitated research in this area. Known RBC defects may affect invasion, growth, or merozoite liberation (Fig 1). Significant advances made in understanding mechanisms underlying protection against malaria should not obscure the fact that the data are far from complete. More knowledge is needed about the influence of the erythrocyte cytoskeleton on invasion and growth of parasites as well as the potential role of phospholipids, erythrocyte enzymes other than G6PD, or other metabolic products. Application of DNA analysis and recombinant technology may have an increasing impact on study of the interaction of RBC defects with malarial parasites.
Editorial: The Red Cell Life-Cycle From Erythropoiesis to Clearance (2018)

EDITORIAL article Front. Physiol., 08 November 2018Sec. Membrane Physiology and Membrane Biophysics Volume 9 - 2018 | https://doi.org/10.3389/fphys.2018.01537
Proposing New Potential Candidates to Inhibit EGFR via Machine Learning Algorithm (2023)

Abstract One of the main issues in solid tumours is progressive mutation in epidermal growth factor receptors (EGFR) gene, which activates signalling pathways that create new blood vessels. In this study, it was attempted to find new a therapeutic candidate to inhibit EGFR. One of the cost-effective alternative methods to find new inhibitors has been the repositioning approach of existing drugs. The critical point of computational drug repositioning method is saving time and cost to remove the pre-clinical step and accelerate the drug discovery process. Hence, an ensemble computational-experimental approach, consisting of three different steps, a machine learning model, simulation of drug-target interaction and experimental characterization, was developed. The machine learning type used here was different tree classification method, which is one of the best randomize machine learning model to identify potential inhibitors from weak inhibitors. The machine learning step aimed to discover the approved drugs with the highest possible success rate in the experimental step. Finally, out of the nine chosen drugs, seven compounds had been confirmed to inhibit EGFR in the published articles since 2019. Hence, two identified compounds, in addition to gefitinib, as a positive control, and one neutral, were considered via molecular docking study. Finally, eight proposed drugs, including gefitinib, were investigated using MTT assay and In-Cell ELISA to characterise the drugs effect on A431 cell growth and EGFR-signaling. From our experiments, we could conclude that salicylic acid and piperazine could play an EGFR-inhibitor role like gefitinib.
EVALUATION OF THE MAISOTSENKO POWER CYCLE THERMODYNAMIC EFFICIENCY (2011)

Fuel economy and pollution reduction are becoming more and more important issues from year to year. Companies and governments with practically unlimited resources are heavily investing in heat recovery technologies, struggling for every percent of efficiency. The Maisotsenko power cycle (M-power cycle) is one of the most promising heat recovery technologies to solve these problems. This paper includes the concept of M-power cycle for turbine engines through the Idalex humidifying air recuperator and validation of M-power cycle benefits based on the heat and mass exchanger test results and data from the HAT cycle. Provided analysis confirms the M-cycle's unique heat recovery capabilities and indicates that the thermodynamic efficiency of a turbine engine utilizing an M-power cycle could reach 80%, significantly higher than the efficiency of Brayton engines and even combining cycles.