gebhart/patrepeval huggingface dataset:
Quality Control and Robust Estimation for cDNA Microarrays With Replicates (2006)

AbstractWe consider robust estimation of gene intensities from cDNA microarray data with replicates. Several statistical methods for estimating gene intensities from microarrays have been proposed, but little work has been done on robust estimation. This is particularly relevant for experiments with replicates, because even one outlying replicate can have a disastrous effect on the estimated intensity for the gene concerned. Because of the many steps involved in the experimental process from hybridization to image analysis, cDNA microarray data often contain outliers. For example, an outlying data value could occur because of scratches or dust on the surface, imperfections in the glass, or imperfections in the array production. We develop a Bayesian hierarchical model for robust estimation of cDNA microarray intensities. Outliers are modeled explicitly using a t-distribution, and our model also addresses such classical issues as design effects, normalization, transformation, and nonconstant variance. Parameter estimation is carried out using Markov chain Monte Carlo. By identifying potential outliers, the method provides automatic quality control of replicate, array, and gene measurements. The method is applied to three publicly available gene expression datasets and compared with three other methods: ANOVA-normalized log ratios, the median log ratio, and estimation after the removal of outliers based on Dixon's test. We find that the between-replicate variability of the intensity estimates is lower for our method than for any of the others. We also address the issue of whether the background should be subtracted when estimating intensities. It has been argued that this should not be done because it increases variability, whereas the arguments for doing so are that there is a physical basis for the image background, and that not doing so will bias downward the estimated log ratios of differentially expressed genes. We show that the arguments on both sides of this debate are correct for our data, but that by using our model one can have the best of both worlds: One can subtract the background without increasing variability by much.KEY WORDS: Bayesian hierarchical modelGene filteringHeteroscedasticityMarkov chain Monte CarloOutlierQuality controlt distribution
Simulation-based Weather Normalization Approach To Study The Impact Of Weather On Energy Use Of Buildings In The U.s. (2013)

Weather normalization is a crucial step in building energy rating and retrofit measurements. Accounting for the impacts of weather on energy use of commercial buildings is a rigorous challenge because of the complexity and diversity in the operation, the mechanical systems, and the use-types available. This paper documents preliminary results of an effort to determine a set of weather adjustment coefficients that can be used to isolate the impacts of weather on energy use of buildings in 1020 weather location sites available in the U.S. The U.S. Department of Energy (DOE) commercial reference building models are adopted as hypothetical models with standard operations to deliver consistency in modeling. The correlation between building envelope design, heating, ventilation and air conditioning (HVAC) system design and properties for different building types and the change in heating and cooling energy consumption caused by variations in weather is examined.
Uptake and Metabolism of Hydroxymatairesinol in Relation to Its Anticarcinogenicity in DMBA-Induced Rat Mammary Carcinoma Model (2001)

The chemopreventive effects of hydroxymatairesinol (HMR), a lignan extracted from Norway spruce (Picea abies), on the development of mammary carcinoma induced by 7,12-dimethylbenz[a]anthracene (DMBA) was studied in rats. HMR administered via diet in an average daily dose of 4.7 mg/kg body wt starting before DMBA induction reduced tumor volume and tumor growth, but no significant reduction in tumor multiplicity (number of tumors/rat) was observed. The predominant histological type in the control group was type B (well-differentiated adenocarcinoma, 78%). The proportion of type B tumors decreased to 35% in the HMR group, while the type A (poorly differentiated) and type C (atrophic) tumor proportions increased. Anticarcinogenic effects of dietary HMR (4.7 mg/kg) were also evident when the administration started after DMBA induction and was seen as growth inhibition of established tumors. Dietary HMR supplementation significantly increased serum and urinary enterolactone and HMR concentrations but had no significant effect on the uterine weight, suggesting that HMR or its major metabolite enterolactone did not have an antiestrogenic effect. Further studies are warranted to further clarify and verify HMR action and the associated mechanisms in mammary tumorigenesis.
Implementation of Formation Shear Slowness Evaluation from Dipole Sonic Waveforms with Tool Presence Effects (2011)

Flexural waves measured in dipole sonic logging are borehole dispersive modes in which the phase slowness varies with the frequency. The low-frequency asymptote corresponds to the formation shear slowness. Flexural wave propagation is affected by the formation parameters and also the sonic tool presence. This effect is visible in the frequency-slowness domain as well as in the mode excitation function. These effects cannot be ignored to obtain an accurate formation shear slowness. This paper presents the implementation of formation slowness evaluation from sonic waveforms based on the semblance technique. This technique, called Slowness-Time Coherence (STC), is a standard processing technique widely used in sonic processing. It was originally limited to nondispersive waveforms, but has been extended to dispersive waves such as dipole flexural waves. In Dispersive STC (DSTC) processing, the semblance computation is performed in the frequency domain using dispersion modeling. Accurate dispersion modeling requires including tool presence effects to properly estimate shear slowness of the formation. To model these effects linked to a given sonic tool, the tool response is characterized through computational modeling and experiments. The modeled tool effects are included in mode-search processing assuming homogeneous isotropic (HI) formations. Using modeled dispersions that account for the tool presence effects, the resulting shear slowness will be correct. For computational efficiency, the slowness step of the semblance computation is optimized with an efficient sampling scheme, which considers the signal bandwidth and the receiver array aperture. The dispersion modeling with a tool model is performed using a precomputed look-up table instead of running the usual mode-search computation. With this method, the processing includes accurate dispersion modeling, while remaining practical without a loss of accuracy. Processing results are verified with synthetic and field data.
SEARCH FOR NEW PHYSICS IN THE DIPHOTON CHANNEL AT THE ATLAS EXPERIMENT AT THE LHC (2017)

The topic of this thesis is the search for resonances in the di-photon invariant mass spectrum. These resonances are predicted by several models beyond the Standard Model. The analysis of data provided by the ATLAS detector during the Run-2 (years 2015-2016) of LHC will be presented. The di-photon decay channel is used both for precision measurement, for example for the measurement of the Higgs boson mass, and for discovery of BSM physics, like search for Gravitons in the extra dimension context and Higgs bosons in the Two Higgs doublet model context. In the ATLAS detector photons are reconstructed combining the information from the tracker and the electromagnetic calorimeter: the energy of the photons is measured in the calorimeter while the inner detector is used to reconstruct conversions. Their signature is quite simple and they are reconstructed and measured with a good energy resolution, purity and selection efficiency. The main background in photon-related analyses is coming from jets mis-identified as photons, therefore rectangular selection cuts are applied on the shower shapes of the photons. Furthermore an additional selection based on the isolation of the candidates is applied. The di-photon channel was proven to be a very interesting channel and it led to the discovery of the Higgs boson. It has a number of good features like the clean experimental signature, the excellent di-photon mass resolution, and modest jet background. Only particles with integer spin (but different than 1) can decay in a couple of photons. An excess in the di-photon spectrum at high-energy, together with a spin analysis, could be interpreted as the decay of a Graviton (spin-2) or an exotic Higgs boson (spin-0).
Cardiac Protection by Preconditioning Is Generated via an Iron-Signal Created by Proteasomal Degradation of Iron Proteins (2012)

Ischemia associated injury of the myocardium is caused by oxidative damage during reperfusion. Myocardial protection by ischemic preconditioning (IPC) was shown to be mediated by a transient 'iron-signal' that leads to the accumulation of apoferritin and sequestration of reactive iron released during the ischemia. Here we identified the source of this 'iron signal' and evaluated its role in the mechanisms of cardiac protection by hypoxic preconditioning. Rat hearts were retrogradely perfused and the effect of proteasomal and lysosomal protease inhibitors on ferritin levels were measured. The iron-signal was abolished, ferritin levels were not increased and cardiac protection was diminished by inhibition of the proteasome prior to IPC. Similarly, double amounts of ferritin and better recovery after ex vivo ischemia-and-reperfusion (I/R) were found in hearts from in vivo hypoxia pre-conditioned animals. IPC followed by normoxic perfusion for 30 min ('delay') prior to I/R caused a reduced ferritin accumulation at the end of the ischemia phase and reduced protection. Full restoration of the IPC-mediated cardiac protection was achieved by employing lysosomal inhibitors during the 'delay'. In conclusion, proteasomal protein degradation of iron-proteins causes the generation of the 'iron-signal' by IPC, ensuing de-novo apoferritin synthesis and thus, sequestering reactive iron. Lysosomal proteases are involved in subsequent ferritin breakdown as revealed by the use of specific pathway inhibitors during the 'delay'. We suggest that proteasomal iron-protein degradation is a stress response causing an expeditious cytosolic iron release thus, altering iron homeostasis to protect the myocardium during I/R, while lysosomal ferritin degradation is part of housekeeping iron homeostasis.
High Affinity of Thallium Ions to Copper Hexacyanoferrate Films (2001)

High affinity of thallium(I) ions with respect to a copper hexacyanoferrate (CuHCF) film was found. Interaction between the CuHCF film and thallium(I) ions was investigated using the electrochemical quartz crystal microbalance and cyclic voltammetric techniques. In 0.5 M solution, at submillimolar concentrations of Tl(I) ions, the CuHCF film reversibly transforms, during electrochemical experiments, from the potassium into the thallium form. For slightly higher (several millimoles) Tl(I) concentrations, the electrochemical and gravimetric responses prove that the CuHCF film behaves as the thallium form only. Its formal potential calculated from the dependence of the on [Tl(I)], is for 0.28 V more positive than that found for the potassium form. Experimental results obtained suggest that in both cases, potassium(I) and thallium(I) ions, exchange in interstitial positions takes place. Since the ionic radii and the hydration parameters of both ions are similar, we concluded that this high affinity of thallium(I) ions with respect to the CuHCF film, 250-100 times higher than that of potassium(I) ion, results from chemical interactions. In consequence, the solubility product of a thallium analogue of copper hexacyanoferrate is much smaller than that of the potassium form. For different forms they are equal to values): 37.8 46.3 and 17.2 © 2001 The Electrochemical Society. All rights reserved.
The mRNA coding for the nucleosomal protein H2A ofLeishmaniais polyadenylated and has stem-loops at the 3′ end (1991)

Journal Article The mRNA coding for the nucleosomal protein H2A of Leishmania is polyadenylated and has stem-loops at the 3′ end Get access Manuel Soto, Manuel Soto Centro de Biologia Molecular, Facultad de Ciencias, Universidad Autónoma de MadridCanto Blanco 28049, Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar José Maria Requena, José Maria Requena Centro de Biologia Molecular, Facultad de Ciencias, Universidad Autónoma de MadridCanto Blanco 28049, Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar Antonio Jimenez-Ruiz, Antonio Jimenez-Ruiz Centro de Biologia Molecular, Facultad de Ciencias, Universidad Autónoma de MadridCanto Blanco 28049, Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar Carlos Alonso Carlos Alonso Centro de Biologia Molecular, Facultad de Ciencias, Universidad Autónoma de MadridCanto Blanco 28049, Madrid, Spain Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 16, 25 August 1991, Page 4554, https://doi.org/10.1093/nar/19.16.4554 Published: 25 August 1991 Article history Accepted: 20 June 1991 Published: 25 August 1991
Nutrition, Santé Animale, Qualité : Comment les mesurer dans mon steak ? (2015)

National audience
Effects of dipotassium-trioxohydroxytetrafluorotriborate, K2[B3O3F4OH], on cell viability and gene expression of common human cancer drug targets in a melanoma cell line (2015)

Recently it was found that dipotassium-trioxohydroxytetrafluorotriborate, K2(B3O3F4OH), is a potent and highly specific inhibitor of precancerous cell processes. We conducted gene expression profiling of human melanoma cells before and after treatment with two concentrations (0.1 and 1 mM) of this boron inorganic derivative in order to assess its effects on deregulation of genes associated with tumor pathways. Parallel trypan blue exclusion assay was performed to assess the cytotoxicity effects of this chemical. Treatment with K2(B3O3F4OH) induced a significant decrease of cell viability in melanoma cellline at both tested concentrations. Furthermore, these treatments caused deregulation of more than 30 genes known as common anti-tumor drug targets. IGF-1 and hTERT were found to be significantly downregulated and this result may imply potential use of K2(B3O3F4OH) as an inhibitor or human telomerase and insulin-like growth factor 1, both of which are associated with various tumor pathways.
Model-Based Biosignal Interpretation (1994)

Two relatively new approaches to model-based biosignal interpretation, qualitative simulation and modelling by causal probabilistic networks, are compared to modelling by differential equations. A major problem in applying a model to an individual patient is the estimation of the parameters. The available observations are unlikely to allow a proper estimation of the parameters, and even if they do, the task appears to have exponential computational complexity if the model is non-linear. Causal probabilistic networks have both differential equation models and qualitative simulation as special cases, and they can provide both Bayesian and maximum-likelihood parameter estimates, in most cases in much less than exponential time. In addition, they can calculate the probabilities required for a decision-theoretical approach to medical decision support. The practical applicability of causal probabilistic networks to real medical problems is illustrated by a model of glucose metabolism which is used to adjust insulin therapy in type I diabetic patients.
A wearable 3D motion sensing system integrated with a Bluetooth smart phone application: A system level overview (2017)

An era of ubiquitous motion sensing has just begun. All electronic gadgets ranging from game consoles to mobile phones have some sort of motion sensors in them. In contrast to rigid motion sensing systems, this paper presents a system level description of a wearable 3D motion sensor. The sensing mechanism is based upon well-established magnetic and inertial measurement unit (MIMU), which integrates accelerometer, gyroscope and magnetometer data. Two sensor boards have been integrated within a wearable arm sleeve to capture 3D orientation of the human arm. The sensors have been interfaced with a Bluetooth transceiver chip, which transmits data to a mobile phone app using standard Bluetooth protocol. An android mobile phone app has been developed to display the human arm motion in real time.
Sarcoidosis (2020)

Sarcoidosis is a systemic disease characterized by the presence of noncaseating granulomas, which accumulate in affected organs. The incidence, organ involvement, and disease severity depend on environmental exposures and host factors. The cause of sarcoidosis remains unknown. Any organ can be affected; however, involvement of the lung, heart, and nervous system contributes most to morbidity and mortality. This review discusses the epidemiology, etiology, genetics, pathogenesis, diagnosis (including clinical manifestations), differential diagnosis, management, complications, and prognosis of sarcoidosis. Figures depict the pathogenesis of sarcoidosis, radiographic stages of sarcoidosis, contrast-enhanced magnetic resonance imaging of a patient with neurosarcoidosis, noncaseating granuloma from a tissue biopsy of a patient with sarcoidosis, various manifestations of sarcoidosis, approach to the use of anti-inflammatory therapy for sarcoidosis, and an algorithm for symptomatic disease. This review contains 7 highly rendered figures, 3 tables, and 126 references Keywords: cardiac sarcoidosis, hilar lymphadenopathy, Löfgren syndrome, neurosarcoidosis, noncaseating granuloma, sarcoidosis, uveitis
Role of the Stat4 N Domain in Receptor Proximal Tyrosine Phosphorylation (2000)

Stat4 is activated by the cytokines interleukin 12 and alpha interferon (IFN-alpha) and plays a significant role in directing development of naïve CD4(+) T cells to the Th1 phenotype. Signal transducers and activators of transcription (STAT) proteins undergo phosphorylation on a conserved tyrosine residue, resulting in homo- and heterodimerization, nuclear translocation, and DNA binding. Stat4 can bind to single IFN-gamma-activated sites (GASs) as a dimer or bind two tandem GASs as a pair of STAT dimers, or tetramer, stabilized through N-terminal domain (N domain) interactions between dimers. We uncovered an unexpected effect of the Stat4 N domain in controlling the proximal activation of Stat4 by tyrosine phosphorylation at activated receptor complexes. Mutation of the N domain at tryptophan residue W37, predicted to interrupt N domain dimer formation, unexpectedly prevented IFN-alpha-induced tyrosine phosphorylation of the Stat4 monomer, blocking dimer formation and nuclear translocation. Furthermore, N domains appear to exert private STAT functions, since interchanging the N domains between Stat1 and Stat4 prevented receptor-mediated tyrosine phosphorylation in one case and interrupted STAT-specific gene activation in another. Finally, replacement of the N domain of Stat1 with that of Stat4 abrogated the normal Stat2 dependence of Stat1 phosphorylation, again suggesting the domains are not equivalent. Thus, in addition to its role in STAT tetramerization, the conserved STAT N domain appears to participate in very proximal steps of receptor-mediated ligand-induced tyrosine phosphorylation.
A software memory partition approach for eliminating bank-level interference in multicore systems (2012)

Main memory system is a shared resource in modern multicore machines, resulting in serious interference, which causes performance degradation in terms of throughput slowdown and unfairness. Numerous new memory scheduling algorithms have been proposed to address the interference problem. However, these algorithms usually employ complex scheduling logic and need hardware modification to memory controllers, as a result, industrial venders seem to have some hesitation in adopting them.
A micromachined, silicon mass-air-flow sensor for automotive applications (2002)

A micromachined, monolithic silicon mass-air-flow sensor has been developed for measuring engine intake air flows in the range of 1-60 m/s. It has a response time of under 1 ms and can be temperature compensated to a deviation of +or-3.5% error or less in indicated flow over a temperature range of -30 degrees C to +40 degrees C. The device can withstand bombardment by particles up to 50- mu m in size in the air stream, or larger ones if elements with reduced accuracy are used. A more rugged design, using larger silicon beams but retaining good temperature compensation capability, can be achieved by modifying the beam ends and their support to increase the thermal isolation between the beams and the rest of the silicon chip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development of an inexpensive guidance system for agricultural purposes (2005)

Robotics is a rapidly growing technology and robots have pervaded into most of the industries. Robotics and automation are designed to remove the human factor from the labor intensive and monotonous work and thereby decrease the associated costs. The application of robotics to agriculture is fairly recent. Robotic applications in agriculture vary from autonomous row-guidance tractors to fruit picking robots. Similarly, soil testing and soil sampling is one area in agriculture where automation of tasks and the employment of an autonomous robot would be of great use to consultants and farmers employing site specific farming techniques. Soil testing is an important part of farming used to determine the average nutrient status in a field and to obtain a measure of nutrient availability in the field. Fertilizers and other nutrients are applied to the fields based on different soil tests. Site specific farming is greatly dependent on soil testing and can result in increased yield, reduced cost and reduced water pollution. Soil testing requires a lot of soil samples and soil sampling is a time consuming, laborious process and expensive process. Most of the consultants employing site specific techniques use ATVs to get around large fields when sampling. The development of an autonomous guidance system for an ATV to perform soil sampling would be greatly beneficial to them. Labor costs would be significantly reduced and the operators would be subjected to fewer environmental elements. The use of ATVs ensures that no extra capital is needed to buy a vehicle. The use of a small vehicle like an ATV also causes less soil compaction. A WAAS enabled Differential GPS with accuracies to within 9.84 feet was used as the position sensor. Pocket PCs are more portable than a laptop computer and are more suitable for farm conditions. Shape files were used to provide the sampling points as input to the guidance program. A guidance program was made to operate on a PDA and provide guidance instructions. A microprocessor was programmed to read the guidance instructions and actuate the different components like throttle and steering. Tests were conducted to test the accuracy and consistency of the system. The offsets of each stop point from the test point were documented and analyzed. The results indicated that the system was as accurate as the GPS used for guidance. They also indicated that a guidance system can be realized with the use of very few components