gebhart/patrepeval huggingface dataset:
Evaluation of Current and New Biomarkers in Severe Preeclampsia: A Microarray Approach Reveals the VSIG4 Gene as a Potential Blood Biomarker (2013)

Preeclampsia is a placental disease characterized by hypertension and proteinuria in pregnant women, and it is associated with a high maternal and neonatal morbidity. However, circulating biomarkers that are able to predict the prognosis of preeclampsia are lacking. Thirty-eight women were included in the current study. They consisted of 19 patients with preeclampsia (13 with severe preeclampsia and 6 with non-severe preeclampsia) and 19 gestational age-matched women with normal pregnancies as controls. We measured circulating factors that are associated with the coagulation pathway (including fibrinogen, fibronectin, factor VIII, antithrombin, protein S and protein C), endothelial activation (such as soluble endoglin and CD146), and the release of total and platelet-derived microparticles. These markers enabled us to discriminate the preeclampsia condition from a normal pregnancy but were not sufficient to distinguish severe from non-severe preeclampsia. We then used a microarray to study the transcriptional signature of blood samples. Preeclampsia patients exhibited a specific transcriptional program distinct from that of the control group of women. Interestingly, we also identified a severity-related transcriptional signature. Functional annotation of the upmodulated signature in severe preeclampsia highlighted two main functions related to "ribosome" and "complement". Finally, we identified 8 genes that were specifically upmodulated in severe preeclampsia compared with non-severe preeclampsia and the normotensive controls. Among these genes, we identified VSIG4 as a potential diagnostic marker of severe preeclampsia. The determination of this gene may improve the prognostic assessment of severe preeclampsia.
Reliability and availability study on substation automation system based on IEC 61850 (2008)

The introduction of IEC61850 standards for substation automation requires the specification of the reliability and availability performance parameter. Presently, the methodology to calculate and verify the parameters is not readily available. This paper proposed a methodology to calculate the parameters at device level, bay level and substation level. The paper will propose suitable monitoring and evaluation of those parameters for future improvement.
Gait Analysis and Muscle Strength in Children with Surgically Treated Clubfeet (1997)

Twenty-three children who had unilateral surgery for idiopathic clubfeet underwent gait analysis and isokinetic muscle-strength testing at an average of 10 years after surgical release. Ankle sagittal-plane kinematics were disturbed in 20 clubfeet. Fifteen children had an internal foot-progression angle. Genu valgum and knee hyperextension were common. Plantarflexion power was decreased by 23% on the side of surgery (p = 0.00005). Quadriceps weakness (defined as a decrease in strength > 10% of the nonoperated-on limb's strength) was seen in nine of 22 operated-on limbs and hamstring weakness in eight of 22. Gastrocsoleus weakness exceeded 10% in 16 of 21 clubfeet. Average weakness of the gastrocsoleus was 27% (p< 0.05). Ten-year analysis of children treated with clubfoot releases revealed disturbances in ankle motion and strength. Loss of plantarflexion power and gastrocsoleus strength can be predicted by Achilles tendon lengthening. Knee kinematic abnormalities and weakness also were seen. These abnormalities produce functional difficulties in gait and may lead to degenerative changes later.
Mutational inactivation of the proapoptotic gene <i>BAX</i> confers selective advantage during tumor clonal evolution (2000)

A remarkable instability at simple repeated sequences characterizes gastrointestinal cancer of the microsatellite mutator phenotype (MMP). Mutations in the DNA mismatch repair gene family underlie the MMP, a landmark for hereditary nonpolyposis colorectal cancer. These tumors define a distinctive pathway for carcinogenesis because they display a particular spectrum of mutated cancer genes containing target repeats for mismatch repair deficiency. One such gene is BAX, a proapoptotic member of the Bcl-2 family of proteins, which plays a key role in programmed cell death. More than half of colon and gastric cancers of the MMP contain BAX frameshifts in a (G)(8) mononucleotide tract. However, the functional significance of these mutations in tumor progression has not been established. Here we show that inactivation of the wild-type BAX allele by de novo frameshift mutations confers a strong advantage during tumor clonal evolution. Tumor subclones with only mutant alleles frequently appeared after inoculation into nude mice of single-cell clones of colon tumor cell lines with normal alleles. In contrast, no clones of BAX-expressing cells were found after inoculation of homozygous cell clones without wild-type BAX. These results support the interpretation that BAX inactivation contributes to tumor progression by providing a survival advantage. In this context, survival analyses show that BAX mutations are indicators of poor prognosis for both colon and gastric cancer of the MMP.
Use of 5-Bromo-4-Chloro-3-Indolyl-α- <scp>d</scp> - <i>N</i> -Acetylneuraminic Acid in a Novel Spot Test To Identify Sialidase Activity in Vaginal Swabs from Women with Bacterial Vaginosis (2000)

The validity of measuring vaginal sialidase activity to identify bacterial vaginosis (BV) was determined by using 5-bromo-4-chloro-3-indolyl-alpha-D-N-acetylneuraminic acid in a near-patient test. The sensitivity and specificity of the test for prediction of BV were 95.6 and 96.3%, respectively. Positive and negative predictive values were 95.6 and 96.3%, respectively. This test may be an alternative to Gram staining.
Membrane‐bound melatonin receptor MT1 down‐regulates estrogen responsive genes in breast cancer cells (2009)

Melatonin possesses anti-estrogenic effects on estrogen receptor expressing (ER+) breast cancer cells in culture by reducing cell cycle progression and cell proliferation. There is increasing agreement that on a cellular level the effects of melatonin are primarily induced by the membrane-bound receptor MT1. The participation of a second, nuclear receptor of the group of ligand-dependent transcription factors, called RZRalpha, is under debate. In this study we used a number of breast cancer cell lines differing in their expression of the estrogen receptor and the two known melatonin receptors. In MCF-7 breast cancer cells transfected with a vector carrying the MT1 gene (MCF-7Mel1a) binding of CREB-protein to the cAMP-responsive element of the breast cancer suppressing gene BRCA-1 was more strongly reduced by treatment with melatonin than in the parental cells. Expression of estrogen responsive genes was determined in serum-starved cells, cells stimulated for 16 hr with estradiol and cells subsequently treated with melatonin. Expression of BRCA-1, p53, p21(WAF) and c-myc were up-regulated by estradiol. Treatment of the stimulated cells with melatonin counteracted the increase induced by estradiol almost completely. The more MT1 a cell line expressed, the stronger was the reduction of the expression of the estradiol-induced genes. There was no correlation between the expression of the nuclear receptor RZRalpha and the effects of melatonin on these genes.
ANTIETHANOL EFFECTS OF INDOL-3-YLPYRUVIC ACID IN MICE (1994)

Indol-3-ylpyruvic acid (IPA, 10-100 mg/kg), an endogenous metabolite of tryptophan, shortened ethanol anaesthesia in C57Bl/6 male mice and diminished the post-ethanol (23 hr) inhibition of locomotion. In an elevated plus-maze, IPA had an anxiolytic effect in short-sleep, but not in long-sleep, mice. IPA did not modify ethanol-induced or caffeine-induced stimulation of spontaneous locomotion or the anxiogenic effect of pentylenetetrazole in an elevated plus-maze. The probable involvement of IPA in the defence mechanisms in alcoholism is suggested.
Note: Mechanical study of micromachined polydimethylsiloxane elastic microposts (2010)

This paper reports the detailed statistical measurement of Young's modulus (E) and spring constant of micromachined three-dimensional polydimethylsiloxane microposts with various sizes using atomic force microscope. The paper also describes the design and fabrication of these microposts. The micropost array was fabricated with a height to diameter aspect ratio of up to 10. We have found that posts with different sizes have different E values, and posts that are cured at room temperature have smaller Young's modulus than the ones that are cured at 65 °C for the same duration.
Restless Legs Syndrome and Periodic Movements in Sleep (1986)

Seven patients suffering from restless legs syndrome (RLS) and periodic movements in sleep (PMS) were investigated before and after treatment with L-Dopa. The effect of treatment was evaluated by polysomnography, structured interviews, and daily questionnaires. Sleep organization and subjective complaints improved during treatment with 100 to 200 mg of L-Dopa. Polysomnographic recordings also revealed a significant decrease of periodic leg movements during the first third of the night and a rebound during the last third. These results and previous biochemical findings raise the hypothesis that RLS and PMS may both result from reduced dopaminergic activity in the CNS, perhaps resulting from decreased sensibility of postsynaptic receptors.
HANDLING DATA SKEW IN MAPREDUCE (2011)

MapReduce systems have become popular for processing large data sets and are increasingly being used in e-science applications. In contrast to simple application scenarios like word count, e-science applications involve complex computations which pose new challenges to MapReduce systems. In particular, (a) the runtime complexity of the reducer task is typically high, and (b) scientific data is often skewed. This leads to highly varying execution times for the reducers. Varying execution times result in low resource utilisation and high overall execution time since the next MapReduce cycle can only start after all reducers are done. In this paper we address the problem of efficiently processing MapReduce jobs with complex reducer tasks over skewed data. We define a new cost model that takes into account non-linear reducer tasks and we provide an algorithm to estimate the cost in a distributed environment. We propose two load balancing approaches, fine partitioning and dynamic fragmentation, that are based on our cost model and can deal with both skewed data and complex reduce tasks. Fine partitioning produces a fixed number of data partitions, dynamic fragmentation dynamically splits large partitions into smaller portions and replicates data if necessary. Our approaches can be seamlessly integrated into existing MapReduce systems like Hadoop. We empirically evaluate our solution on both synthetic data and real data from an e-science application.
Sorcin Associates with the Pore-forming Subunit of Voltage-dependent L-type Ca2+ Channels (1998)

Intracellular Ca2+ release in muscle is governed by functional communication between the voltage-dependent L-type Ca2+ channel and the intracellular Ca2+ release channel by processes that are incompletely understood. We previously showed that sorcin binds to cardiac Ca2+ release channel/ryanodine receptors and decreases channel open probability in planar lipid bilayers. In addition, we showed that sorcin antibody immunoprecipitates ryanodine receptors from metabolically labeled cardiac myocytes along with a second protein having a molecular weight similar to that of the alpha1 subunit of cardiac L-type Ca2+ channels. We now demonstrate that sorcin biochemically associates with cardiac and skeletal muscle L-type Ca2+ channels specifically within the cytoplasmically oriented C-terminal region of the alpha1 subunits, providing evidence that the second protein recovered by sorcin antibody from cardiac myocytes was the 240-kDa L-type Ca2+ channel alpha1 subunit. Anti-sorcin antibody immunoprecipitated full-length alpha1 subunits from cardiac myocytes, C2C12 myotubes, and transfected non-muscle cells expressing alpha1 subunits. In contrast, the anti-sorcin antibody did not immunoprecipitate C-terminal truncated forms of alpha1 subunits that were detected in myotubes. Recombinant sorcin bound to cardiac and skeletal HIS6-tagged alpha1 C termini immobilized on Ni2+ resin. Additionally, anti-sorcin antibody immunoprecipitated C-terminal fragments of the cardiac alpha1 subunit exogenously expressed in mammalian cells. The results identified a putative sorcin binding domain within the C terminus of the alpha1 subunit. These observations, along with the demonstration that sorcin accumulated substantially during physiological maturation of the excitation-contraction coupling apparatus in developing postnatal rat heart and differentiating C2C12 muscle cells, suggest that sorcin may mediate interchannel communication during excitation-contraction coupling in heart and skeletal muscle.
Cumulative Renal Damage in Oogs by Repeated Treatment with Extracorporeal Shock Waves (1996)

Minimal doses of shock waves cause renal damage and repeated ESWL sessions may result in an accumulation of damage. Considering that the damage is dose-dependent, divided ESWL treatments at a low frequency rate are advisable in a clinical setting.
Toxins and bioactive compounds from cyanobacteria and their implications on human health. (2002)

Many species of cyanobacteria (blue-green algae) produce secondary metabolites with potent biotoxic or cytotoxic properties. These metabolites differ from the intermediates and cofactor compounds that are essential for cell structural synthesis and energy transduction. The mass growth of cyanobacteria which develop in fresh, brackish and, marine waters commonly contain potent toxins. Cyanobacterial toxins or cyanotoxins are responsible for or implicated in animal poisoning, human gastroenteritis, dermal contact irritations and primary liver cancer in humans. These toxins (microcystins, nodularins, saxitoxins, anatoxin-a, anatoxin-a(s), cylindrospermopsin) are structurally diverse and their effects range from liver damage, including liver cancer to neurotoxicity. Several incidents of human illness and more recently, the death of 60 haemodialysis patients in Caruaru, Brazil, have been linked to the presence of microcystins in water. In response to the growing concern about the non-lethal acute and chronic effects of microcystins, World Health Organization has recently set a new provisional guideline value for microcystin-LR of 1.0 microg/L in drinking water. Cyanobacteria including microcystin-producing strains produce a large number of peptide compounds, e.g. micropeptins, cyanopeptolins, microviridin, circinamide, aeruginosin, with varying bioactivities and potential pharmacological application. This article discusses briefly cyanobacterial toxins and their implications on human health.
Reproducible Containers (2020)

We describe the design and implementation of DetTrace, a reproducible container abstraction for Linux implemented in user space. All computation that occurs inside a DetTrace container is a pure function of the initial filesystem state of the container. Reproducible containers can be used for a variety of purposes, including replication for fault-tolerance, reproducible software builds and reproducible data analytics. We use DetTrace to achieve, in an automatic fashion, reproducibility for 12,130 Debian package builds, containing over 800 million lines of code, as well as bioinformatics and machine learning workflows. We show that, while software in each of these domains is initially irreproducible, DetTrace brings reproducibility without requiring any hardware, OS or application changes. DetTrace's performance is dictated by the frequency of system calls: IO-intensive software builds have an average overhead of 3.49x, while a compute-bound bioinformatics workflow is under 2%.
Two-Dimensional Gel Electrophoresis of Proteins in Healthy Roots and Clubroots of<i>Brassica oleracea</i> (1994)

Abstract Seedlings of Brassica oleracea were infected by the pathogenic fungus Plasmodiophora brassicae. causing clubroot formation. Proteins from healthy roots and clubroots were extracted by two different methods and analysed by two-dimensional gel electrophoresis. Host-proteins induced during clubroot infection were not analysed, since the fungus was always present in the infected roots. This work showed that several proteins present in non-infected roots were lost or strongly reduced in the infected roots.
High expression of synthetic human interferon-gamma cDNA in E. coli. (1995)

Human interferon-gamma (IFN-gamma) cDNA was synthesized, and it makes the usage of favorable codons in E. coli. The authors got 9 different expression plasmids which contain the synthetic IFN-gamma-cDNA and have different spaces between SD sequence and ATG. The free energies G0f298 in the formation of stable secondary structure in the translation initiation region (TIR) are different in various expression plasmids. One of them, pLY4-gamma 5, can highly yield INF-gamma which will be about 60%-80% of the total bacterial proteins, such a high expression was hardly noted in literature. The reasons of high expression in this work are optimal spaces between SD and ATC, favorable delta G0f298, favourable condons usage for E. coli.
Sliding Mode Observer for Internal Combustion Engine Misfire Detection. (2007)

A nonlinear model representing the chamber internal pressure dynamics gathered by means of the ideal gas behavior is used for misfire detection. This model shows that the misfire phenomena is an actuator fault. The use of the pressure variable is the key to achieve a reliable misfire detection. The pressure dynamics are in terms of the crankshaft angle, which is regarded as the independent variable. A sliding mode observer is used as a residual generator for the detection scheme, and it is shown that misfire detection can be accomplished by such method.
VOLTAGE-MODE DDCC-BASED MULTIFUNCTION FILTERS (2007)

Two new voltage-mode multifunction biquadratic filter configurations were proposed. The first proposed high-input impedance multifunction filter with single input and four outputs, which can simultaneously realize voltage-mode low-pass, band-pass, and high-pass filter responses employing all grounded passive components. The second proposed configuration is a slight modification of the first proposed circuit. It leads two more notch and all-pass transfer functions than the first proposed circuit. Moreover, both the proposed circuits still offer the following advantages: (i) orthogonal control of ω o and Q, (ii) low active and passive sensitivity performances, (iii) simpler configuration due to the use of noninverting type differential difference current conveyors (DDCCs) only.
Effects of dietary fat levels on the absorption and tissue accumulation of probucol in the rat. (1994)

The effects of dietary fat level on the absorption and tissue accumulation of probucol (PB, CAS 23288-49-5) were studied in male Wistar rats. Addition of 1% PB (w/w) to the diets as compared to the diets without an addition (P) resulted in a decrease in the concentration of both serum and high-density lipoprotein (HDL) cholesterol as well as TBA-reactive substances (TBARS), without influencing food intake or growth. When rats were fed with the PB diet, the apparent intestinal absorption of PB was 7.9%, while the serum PB level was 5 micrograms/ml. The tissue distribution of PB, when expressed per g of tissue, was highest in the adrenal glands, followed by the liver, heart, epididymal adipose tissues, kidneys, lung, spleen, and testes. The addition of 10% olive oil (PBO) to the PB diet (w/w) appeared to double the PB diet-induced increase in apparent intestinal absorption and the serum concentration of PB. Furthermore, compared with the PB diet, the PBO diet caused 3- to 4-fold higher accumulation of PB in the liver and its subcellular fractions and 2-fold higher accumulation in the spleen. However, there was no further accumulation of the drug in the heart, kidneys, lungs, and testes. Incorporation of the drugs into adipose tissues was significantly lower with the PBO diet than with the PB diet. These results suggest that dietary manipulation leads to changes in the intestinal absorption and serum level of PB.
A monolithic data acquisition channel (1983)

A monolithic data acquisition channel has been fabricated using a double level polysilicon NMOS process. The channel consists of a switched-capacitor filter, a continuous-time active RC filter, and a successive approximation analog-to-digital converter. The IC is in the form of a parts kit for a data acquisition channel so that each functional component can be characterized independently. Stitch bonds are used to connect the elements together to form the complete monolithic channel. Each element is implemented with a symmetric, fully differential structure. The measured dynamic range of the channel is 86.1 dB when using ± 5 V supplies.
A multistage system to detect epileptiform activity in the EEG (1993)

A PC-based system has been developed to automatically detect epileptiform activity in sixteen-channel bipolar EEG's. The system consists of three stages: data collection, feature extraction, and event detection. The feature extractor employs a mimetic approach to detect candidate epileptiform transients on individual channels, while an expert system is used to detect focal and nonfocal multichannel epileptiform events. Considerable use of spatial and temporal contextual information present in the EEG aids both in the detection of epileptiform events and in the rejection of artifacts and background activity as events. Classification of events as definite or probable overcomes, to some extent, the problem of maintaining high detection rates while eliminating false detections. So far, the system has only been evaluated on development data but, although this does not provide a true measure of performance, the results are nevertheless impressive. Data from 11 patients, totaling 180 minutes of sixteen-channel bipolar EEG's, have been analyzed. A total of 45-71% (average 58%) of epileptiform events reported by the human expert in any EEG were detected as definite with no false detections (i.e., 100% selectivity) and 60-100% (average 80%) as either definite or probable but at the expense of up to nine false detections per hour. Importantly, the highest detection rates were achieved on EEG's containing little epileptiform activity and no false detections were made on normal EEG's.
Simulation of a solid-state cooler with electrocaloric elements (2009)

The dynamics of change in temperature at the edges of a layered structure consisting of one or more electrocaloric and heat-conducting elements in response to pulses of a periodic electric field has been studied with the use of the finite-element method. The possibility of using ceramic materials and (Ba,Sr)TiO3 films as electrocaloric and heat-conducting elements of linear and radial cooling structures is considered. The difference between the temperatures at the center and periphery of the radial film microstructure with two interdigital circular electrode lines is 2.5 K. An increase in the number of lines and the electric field frequency leads to an increase of the thermal effect.
Use of sacrificial spacers for fabricating LDD transistors in a CMOS process (1986)

The use of sacrificial spacers for LDD transistors in a CMOS process is described. LPCVD nitride or PSG is employed as the sidewall-spacer material which is selectively etched off after the LDD's n-/n+ junction formation, thus allowing subsequent shallow p+ implant self-aligning to the polysilicon gate. Deeper n-/n+ junctions with adequate drain/gate overlap for n-channel LDD transistors to minimise hot-electron effects can then be made while simultaneously the shallow p+ junction with high punch-through immunity is preserved for p-channel transistors. The conflicting diffusion requirements in forming n-/n+ and p+ source-drain junction depths are therefore decoupled.