gebhart/patrepeval huggingface dataset:
Apolipoprotein(a) size heterogeneity is related to variable number of repeat sequences in its mRNA (1990)

Plasma apolipoprotein(a) [apo(a)] shows considerable size heterogeneity, existing as discrete glycoprotein isoform variants that range in apparent molecular mass from approximately 400 to 800 kDa. To study the molecular basis of protein size variability, we have isolated liver RNA from individuals with different apo(a) isoforms, and identified apo(a)-specific transcripts using Northern blot analysis. Transcript sizes were shown to be variable (8.0-12 kb) and in all cases were closely correlated with protein masses (590-850 kDa) as determined from immunoblots. Thus, it is almost certain that apo(a) isoform size variation is due to allelic differences in the number of its tandemly repeated sequences of 114 amino acids that resemble kringle four of plasminogen. The high carbohydrate content of apo(a) makes true molecular weight estimations in SDS-PAGE gels difficult. However, a recombinant form of apo(a) containing 17 kringle repeats (calculated molecular mass of 250 kDa) migrates on SDS-PAGE gels only slightly below apoB-100, with an apparent molecular mass of approximately 500 kDa. Since smaller protein isoforms have been observed in the population, this suggests that plasma apo(a) isoforms contain from less than 17 to greater than 30 tandemly repeated kringle units.
Bioavailability of Magnesium Salts – A Review (2014)

Background: Magnesium supplementation is of value in several different medical disorders. Several kinds of Mg-salts are commercially available.Purpose: This review evaluates their bioavailability criteria such as solubility, urinary excretion, and plasma levels of magnesium from studies of different Mg-salts.Conclusion: Although methodology differences were large, the results consistently demonstrate a better bioavailability for Mg-citrate.
Regulation of Neuroprotective Activity of Myocyte-enhancer Factor 2 by cAMP-Protein Kinase A Signaling Pathway in Neuronal Survival (2005)

The transcription factor myocyte-enhancer factor 2 (MEF2) has been shown to be required for the survival of different types of neurons. However, the death- or survival-inducing second messenger pathways that regulate MEF2 activity remain to be fully elucidated. Membrane depolarization by KCl induces neuronal survival that is dependent upon MEF2-mediated gene transactivation. Here we report that membrane depolarizationinduced activation of MEF2 requires the cAMP-protein kinase A (PKA) pathway. Inhibition of the activity of cAMP-PKA pathway attenuates membrane depolarization-induced activation of MEF2 activity and neuronal survival, whereas enhancing the activity of this pathway prevents KCl withdrawal-induced inhibition of MEF2 and neuronal apoptosis. Moreover, PKA directly phosphorylates MEF2 at Thr-20 in vitro to increase MEF2 DNA binding activity. A mutation of Thr-20 to Ala renders MEF2 resistant to PKA phosphorylation in vitro and reduces its DNA binding activity. Transfection of this T20A mutant blocks survival and induces apoptosis in cultured cortical and cerebellar granule neurons. This study identifies the transcription factor MEF2 as a target of cAMP-PKA pathway and demonstrates that PKA phosphorylation of MEF2 is a key step in modulating its DNA binding activity and ability to promote neuronal survival.
Aberrant methylation of the Cyclooxygenase 2 CpG island in colorectal tumors. (2000)

Cyclooxygenases (COXs) are key enzymes that convert arachidonic acid to prostaglandins. Overexpression of one of the COX isozymes, COX2, has been shown to play an important role in colorectal cancer progression. Recently, however, low expression of COX2 has been reported in a subset of colorectal and gastric cancers. Aberrant CpG island methylation and associated transcriptional silencing are common in colorectal cancer, and we therefore investigated the potential role of methylation in the transcriptional silencing of COX2. We examined the methylation status of the COX2 5' CpG island in a series of tumor cell lines. Among the 33 cell lines examined, dense methylation (>70%) of COX2 was detected in 5 cell lines, and partial methylation was detected in 10 cell lines. Detailed methylation mapping using bisulfite genomic sequencing revealed that loss of expression of COX2 mRNA was closely correlated with methylation of a region upstream of exon 1, and expression could be restored by demethylation using the DNA methyltransferase inhibitor 5-aza-deoxycytidine. Aberrant methylation of COX2 was also detected in 12 of 92 (13%) unselected sporadic primary colorectal cancers and 7 of 50 (14%) colorectal adenomas. COX2 methylation was strongly associated with the presence of the CpG island methylator phenotype (P<0.01), inversely related to p53 gene mutation (P<0.01), and unrelated to microsatellite instability status. We propose that COX2 expression in colorectal tumors is modulated by functional factors that favor high expression and by the CpG island methylator phenotype that favors silencing in a subset of cases. These results raise the possibility that tumors with COX2 methylation may be less sensitive to treatment using specific COX2 inhibitors.
Construction of limited diffraction beams with Bessel bases (2002)

Limited diffraction beams have a large depth of field. They could have applications in medical imaging, tissue characterization, Doppler velocity estimation, nondestructive evaluation (NDE) of materials, as well as other physics related areas such as electromagnetics and optics. In this paper, a method is developed that uses limited diffraction beams discovered previously, such as, Bessel beams and X waves, as basis functions to construct new limited diffraction beams that may have practical usefulness. The method is implemented with linear matrix operations. Results show that the method is powerful and can obtain limited diffraction beams that are not intuitive to get directly from solving the wave equation.
Techniques for placement of grid and strip electrodes for intracranial epilepsy surgery monitoring: Pearls and pitfalls (2013)

Intracranial epilepsy monitoring with grid and strip electrodes is a useful tool for the planning of resective epilepsy surgery. Techniques to advance the safety and minimize complications will lead to improved outcomes.
A Review of Diagnostics Methodologies for Metal Additive Manufacturing Processes and Products (2021)

Additive manufacturing technologies based on metal are evolving into an essential advanced manufacturing tool for constructing prototypes and parts that can lead to complex structures, dissimilar metal-based structures that cannot be constructed using conventional metallurgical techniques. Unlike traditional manufacturing processes, the metal AM processes are unreliable due to variable process parameters and a lack of conventionally acceptable evaluation methods. A thorough understanding of various diagnostic techniques is essential to improve the quality of additively manufactured products and provide reliable feedback on the manufacturing processes for improving the quality of the products. This review summarizes and discusses various ex-situ inspections and in-situ monitoring methods, including electron-based methods, thermal methods, acoustic methods, laser breakdown, and mechanical methods, for metal additive manufacturing.
A Maximum Efficiency Point Tracking Control Scheme for Wireless Power Transfer Systems Using Magnetic Resonant Coupling (2014)

With a good balance between power transfer distance and efficiency, wireless power transfer (WPT) using magnetic resonant coupling is preferred in many applications. Generally, WPT systems are desired to provide constant output voltage with the highest possible efficiency as power supplies. However, the highest efficiency is not achieved by the reported closed-loop WPT systems that maintain constant output voltage against coupling and load variations. In this paper, an efficiency evaluation method is put forward to evaluate the closed-loop control schemes. Furthermore, a maximum efficiency point tracking control scheme is proposed to maximize the system efficiency while regulating the output voltage. This control scheme is unique and prominent in that it fixes the operating frequency at the receiving-side resonant frequency and converts both the input voltage and the load resistance at the same time. Thus, the maximum efficiency point on the constant output voltage trajectory can be tracked dynamically. Therefore the system's output voltage can be maintained constant and its efficiency is always the highest. The experimental results show that the maximum efficiency point is tracked and a very high overall efficiency is achieved over wide ranges of coupling coefficient and load resistance.
Dopaquinone redox exchange with dihydroxyindole and dihydroxyindole carboxylic acid (2006)

A pulse radiolytic investigation has been conducted to establish whether a redox reaction takes place between dopaquinone and 5,6-dihydroxyindole (DHI) and its 2-carboxylic acid (DHICA) and to measure the rate constants of the interactions. To obviate possible confounding reactions, such as nucleophilic addition, the method employed to generate dopaquinone used the dibromide radical anion acting on dopa to form the semiquinone which rapidly disproportionates to dopaquinone. In the presence of DHI the corresponding indole-5,6-quinone (and/or tautomers) was also formed directly but, by judicious selection of suitable relative concentrations of initial reactants, we were able to detect the formation of additional indolequinone from the redox exchange reaction of DHI with dopaquinone which exhibited a linear dependency on the concentration of DHI. Computer simulation of the experimental time profiles of the absorption changes showed that, under the conditions chosen, redox exchange does proceed but not quite to completion, a forward rate constant of 1.4 x 10(6)/M/s being obtained. This is in the same range as the rate constants previously established for reactions of dopaquinone with cyclodopa and cysteinyldopa. In similar experiments carried out with DHICA, the reaction more obviously does not go to completion and is much slower, k (forward) =1.6 x 10(5)/M/s. We conclude that, in the eumelanogenic pathway, DHI oxidation may take place by redox exchange with dopaquinone, although such a reaction is likely to be less efficient for DHICA.
Serum‐autoantibodies for discovery of prostate cancer specific biomarkers (2011)

A variety of autoantibodies were identified in sera of prostate cancer patients and provide a first step towards autoantibody diagnostics. Serum autoantibodies reflect the disease and represent valuable tools not only for prostate cancer, but also for other diseases affecting the immune response.
An approach to evaluate the efficiency of γ-ray detectors to determine the radioactivity in environmental samples (2014)

This work provides an approach to determine the efficiency of γ-ray detectors with a good accuracy in order to determine the concentrations of either naturally occurring or artificially prepared radionuclides. This approach is based on the efficiency transfer formula (ET), the effective solid angles, the self- absorptions of the source matrix, the attenuation by the source container and the detector housing materials on the detector efficiency. The experimental calibration process was done using radioactive (Cylindrical & Marinelli) sources, in different dimensions, that contain aqueous 152Eu radionuclide. The comparison point to a fine agreement between the experimental measured and calculated efficiencies for the (NaI & HPGe) detectors using volumetric radioactive sources.
Hypermethylation of the human proton-coupled folate transporter (SLC46A1) minimal trancriptional regulatory region in an antifolate-resistant HeLa cell line (2009)

This laboratory recently identified a novel proton-coupled folate transporter (PCFT) that mediates intestinal folate absorption and transport of folates into the central nervous system. The present study focuses on the definition of the minimum transcriptional regulatory region of this gene in HeLa cells and the mechanism(s) underlying the loss of PCFT expression in the methotrexate-resistant HeLa R1-11 cell line. The PCFT transcriptional regulatory controls were localized between -42 and +96 bases from the transcriptional start site using a luciferase-reporter gene system. The promoter is a G + C rich region of 139 nucleotides contained in a CpG island. HeLa R1-11 cells have no mutations in the PCFT open reading frame and its promoter; the transcription/translation machinery is intact because transient transfections in HeLa R1-11 and wild-type HeLa cells produced similar luciferase activities. Hypermethylation at CpG sites within the minimal transcriptional regulatory region was shown in HeLa R1-11 cells as compared with the parental PCFT-competent HeLa cells, using bisulfite conversion and sequence analysis. Treatment with 5-aza-2'-deoxycytidine resulted in a substantial restoration of transport and PCFT mRNA expression and small but significant decreases in methylation in the promoter region. In vitro methylation of the transfected reporter plasmid inhibited luciferase gene expression. Cytogenetics/fluorescence in situ hybridization indicated a loss of half the PCFT gene copies in HeLa R1-11 as compared with PCFT-competent HeLa cells. Taken together, promoter silencing through methylation and gene copy loss accounted for the loss of PCFT activity in antifolate-resistant HeLa R1-11 cells.
[The effect of mini-implant lengths on stress distributions in peri-implant surface]. (2011)

The change of the mini-implant length within 6-12 mm don't show much influence on the stress distribution. The loading type is an important factor influencing stress and displacement of peri-implant bone.
Berberine suppresses proinflammatory responses through AMPK activation in macrophages (2009)

Berberine (BBR) has been shown to improve several metabolic disorders, such as obesity, type 2 diabetes, and dyslipidemia, by stimulating AMP-activated protein kinase (AMPK). However, the effects of BBR on proinflammatory responses in macrophages are poorly understood. Here we show that BBR represses proinflammatory responses through AMPK activation in macrophages. In adipose tissue of obese db/db mice, BBR treatment significantly downregulated the expression of proinflammatory genes such as TNF-alpha, IL-1beta, IL-6, monocyte chemoattractant protein-1 (MCP-1), inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2). Consistently, BBR inhibited LPS-induced expression of proinflammatory genes including IL-1beta, IL-6, iNOS, MCP-1, COX-2, and matrix metalloprotease-9 in peritoneal macrophages and RAW 264.7 cells. Upon various proinflammatory signals including LPS, free fatty acids, and hydrogen peroxide, BBR suppressed the phosphorylation of MAPKs, such as p38, ERK, and JNK, and the level of reactive oxygen species in macrophages. Moreover, these inhibitory effects of BBR on proinflammatory responses were abolished by AMPK inhibition via either compound C, an AMPK inhibitor, or dominant-negative AMPK, implying that BBR would downregulate proinflammatory responses in macrophages via AMPK stimulation.
Graphic StoryWriter (1992)

The Graphic StoryWriter (GSW) is an interactive system that enables its users to create structurally complete stories through the manipulation of graphic objects in a simulated storybook. A rule-based story engine manages character and prop interaction, guides story development, and generates text. Through the simple interface and story writing engine, the Graphic StoryWriter provides an environment for early readers to learn about story structures, to experience the relationship between pictures and text, and to experiment with causal effects. This paper describes the motivation for and design of the Graphic StoryWriter, and reports on an empirical comparison of childrens' stories generated orally and using the GSW.
Changes in Gut and Plasma Microbiome following Exercise Challenge in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) (2015)

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disease characterized by intense and debilitating fatigue not due to physical activity that has persisted for at least 6 months, post-exertional malaise, unrefreshing sleep, and accompanied by a number of secondary symptoms, including sore throat, memory and concentration impairment, headache, and muscle/joint pain. In patients with post-exertional malaise, significant worsening of symptoms occurs following physical exertion and exercise challenge serves as a useful method for identifying biomarkers for exertion intolerance. Evidence suggests that intestinal dysbiosis and systemic responses to gut microorganisms may play a role in the symptomology of ME/CFS. As such, we hypothesized that post-exertion worsening of ME/CFS symptoms could be due to increased bacterial translocation from the intestine into the systemic circulation. To test this hypothesis, we collected symptom reports and blood and stool samples from ten clinically characterized ME/CFS patients and ten matched healthy controls before and 15 minutes, 48 hours, and 72 hours after a maximal exercise challenge. Microbiomes of blood and stool samples were examined. Stool sample microbiomes differed between ME/CFS patients and healthy controls in the abundance of several major bacterial phyla. Following maximal exercise challenge, there was an increase in relative abundance of 6 of the 9 major bacterial phyla/genera in ME/CFS patients from baseline to 72 hours post-exercise compared to only 2 of the 9 phyla/genera in controls (p = 0.005). There was also a significant difference in clearance of specific bacterial phyla from blood following exercise with high levels of bacterial sequences maintained at 72 hours post-exercise in ME/CFS patients versus clearance in the controls. These results provide evidence for a systemic effect of an altered gut microbiome in ME/CFS patients compared to controls. Upon exercise challenge, there were significant changes in the abundance of major bacterial phyla in the gut in ME/CFS patients not observed in healthy controls. In addition, compared to controls clearance of bacteria from the blood was delayed in ME/CFS patients following exercise. These findings suggest a role for an altered gut microbiome and increased bacterial translocation following exercise in ME/CFS patients that may account for the profound post-exertional malaise experienced by ME/CFS patients.
Swing-up control problem for a self-erecting double inverted pendulum (2002)

The paper presents a procedure to swing-up a double pendulum mounted on a cart. The aim of this problem is to take the system from its stable position to the inverted position by moving the cart. A technique to design controlled trajectories for nonlinear underactuated mechanisms is developed. The reference trajectory is obtained as a result of the optimisation of an initial trajectory defined through interpolation by splines. This reference is tracked using a gain scheduling linear quadratic optimal controller specifically designed for the reference trajectory. Simulation and the experimental results confirm the validity of this approach.
Dynamic sympathetic regulation of left ventricular contractility studied in the isolated canine heart (1998)

We investigated the dynamic sympathetic regulation of left ventricular end-systolic elastance ( E es ) using an isolated canine ventricular preparation with functioning sympathetic nerves intact. We estimated the transfer function from both stellate ganglion stimulation to E es and ganglion stimulation to heart rate (HR) for both left and right ganglia by means of the white noise approach and transformed those transfer functions into corresponding step responses. The HR response was much larger with right sympathetic stimulation than with left sympathetic stimulation (4.3 ± 1.4 vs. 0.7 ± 0.6 beats ⋅ min −1 ⋅ Hz −1 , P < 0.01). In contrast, the E es responses without pacing were not significantly different between left and right sympathetic stimulation (0.72 ± 0.34 vs. 0.76 ± 0.42 mmHg ⋅ ml −1 ⋅ Hz −1 ). Fixed-rate pacing significantly decreased the E es response to right sympathetic stimulation (0.53 ± 0.43 mmHg ⋅ ml −1 ⋅ Hz −1 , P < 0.01), but not to left sympathetic stimulation (0.67 ± 0.32 mmHg ⋅ ml −1 ⋅ Hz −1 , not significant). Although the mechanism by which the sympathetic nervous system regulates cardiac contractility is different depending on whether the left or right sympathetic nerves are activated, this difference does not affect the apparent response of E es to dynamic sympathetic stimulation.
Analysis of free-space coupling to photonic lanterns in the presence of tilt errors (2017)

Free space coupling to photonic lanterns is more tolerant to tilt errors and F-number mismatch than coupling to single-mode fibers. We analyze the coupling efficiency to single-mode fiber, and 3-mode and 6-mode photonic lanterns in the presence of these errors.
Agr-related sequences in Staphylococcus lugdunensis (1993)

Sequences related to the Staphylococcus aureus accessory gene regulator (agr) were demonstrated in S. lugdunensis by Southern blot analysis of 13 strains and sequencing of the S. lugdunensis agr-like locus (agr-sl). Northern blot analysis of cellular RNA revealed the presence of a transcript having homology with the agr-P3 transcript (RNAIII) for three of the six strains tested. The three strains containing this transcript produce a hemolysin with phenotypic properties similar to that of S. aureusδ-hemolysin. Nevertheless, unlike agr-P3 from S. aureus, agr-sl does not encode any potential peptides homologous to S. aureusδ-hemolysin, suggesting that the hemolytic activity detected in S. lugdunensis is encoded elsewhere and may be controlled by agr-sl.
Improved rejection band in SAW ladder filters using high frequency shunt element (2005)

A novel SAW ladder filter is presented which utilizes a high-frequency shunt resonator to achieve improved attenuation within a relatively wide band of frequencies above the passband. Conventional impedance element resonators provide electrical matching within the passband between the high-frequency shunt element and the input and output ports.
Estrogen or antiprogestin treatment induces complete regression of pulmonary and axillary metastases in an experimental model of breast cancer progression (2005)

In this paper we demonstrate, using the C7-2-HI metastatic transplantable ductal mammary tumor, that endocrine therapy can induce complete regression of spontaneous lymph node and lung metastases in a mouse model of breast cancer progression. This tumor expresses high levels of estrogen and progesterone receptors and shows a high incidence of early axillary lymph nodes and lung metastases; using this model we had previously shown complete tumor regression of subcutaneous implants. Interestingly, although the metastases showed a more differentiated histology as compared with the primary growth, they underwent complete regression when treated with estrogens or antiprogestins. This phenomenon was associated with sustained cytostasis and apoptosis accompanied by increases in p21 and p27 expression and early tissue remodeling. These results highlight the essential role of PR in regulating cell proliferation in this model as well as its possible use as therapeutic target.