gebhart/patrepeval huggingface dataset:
Data-driven analysis approach for biomarker discovery using molecular-profiling technologies (2005)

High-throughput molecular-profiling technologies provide rapid, efficient and systematic approaches to search for biomarkers. Supervised learning algorithms are naturally suited to analyse a large amount of data generated using these technologies in biomarker discovery efforts. The study demonstrates with two examples a data-driven analysis approach to analysis of large complicated datasets collected in high-throughput technologies in the context of biomarker discovery. The approach consists of two analytic steps: an initial unsupervised analysis to obtain accurate knowledge about sample clustering, followed by a second supervised analysis to identify a small set of putative biomarkers for further experimental characterization. By comparing the most widely applied clustering algorithms using a leukaemia DNA microarray dataset, it was established that principal component analysis-assisted projections of samples from a high-dimensional molecular feature space into a few low dimensional subspaces provides a more effective and accurate way to explore visually and identify data structures that confirm intended experimental effects based on expected group membership. A supervised analysis method, shrunken centroid algorithm, was chosen to take knowledge of sample clustering gained or confirmed by the first step of the analysis to identify a small set of molecules as candidate biomarkers for further experimentation. The approach was applied to two molecular-profiling studies. In the first study, PCA-assisted analysis of DNA microarray data revealed that discrete data structures exist in rat liver gene expression and correlated with blood clinical chemistry and liver pathological damage in response to a chemical toxicant diethylhexylphthalate, a peroxisome-proliferator-activator receptor agonist. Sixteen genes were then identified by shrunken centroid algorithm as the best candidate biomarkers for liver damage. Functional annotations of these genes revealed roles in acute phase response, lipid and fatty acid metabolism and they are functionally relevant to the observed toxicities. In the second study, 26 urine ions identified from a GC/MS spectrum, two of which were glucose fragment ions included as positive controls, showed robust changes with the development of diabetes in Zucker diabetic fatty rats. Further experiments are needed to define their chemical identities and establish functional relevancy to disease development.
Design and Technology of Microwave and Millimeterwave LTCC Circuits and Systems (2007)

LTCC technology has large benefits in microwave and millimeterwave applications. In this presentation an overview is given on the design rules and the technological realization of components, circuits and systems for microwave and millimeter wave applications. The advantages and possible problems of the technology are described.
Impact of TP53 mutations in acute myeloid leukemia patients treated with azacitidine (2020)

Hypomethylating agents are a classical frontline low-intensity therapy for older patients with acute myeloid leukemia. Recently, TP53 gene mutations have been described as a potential predictive biomarker of better outcome in patients treated with a ten-day decitabine regimen., However, functional characteristics of TP53 mutant are heterogeneous, as reflected in multiple functional TP53 classifications and their impact in patients treated with azacitidine is less clear. We analyzed the therapeutic course and outcome of 279 patients treated with azacitidine between 2007 and 2016, prospectively enrolled in our regional healthcare network. By screening 224 of them, we detected TP53 mutations in 55 patients (24.6%), including 53 patients (96.4%) harboring high-risk cytogenetics. The identification of any TP53 mutation was associated with worse overall survival but not with response to azacitidine in the whole cohort and in the subgroup of patients with adverse karyotype. Stratification of patients according to three recent validated functional classifications did not allow the identification of TP53 mutated patients who could benefit from azacitidine. Systematic TP53 mutant classification will deserve further exploration in the setting of patients treated with conventional therapy and in the emerging field of therapies targeting TP53 pathway.
Three-Dimensional Stratification of Bacterial Biofilm Populations in a Moving Bed Biofilm Reactor for Nitritation-Anammox (2014)

Moving bed biofilm reactors (MBBRs) are increasingly used for nitrogen removal with nitritation-anaerobic ammonium oxidation (anammox) processes in wastewater treatment. Carriers provide protected surfaces where ammonia oxidizing bacteria (AOB) and anammox bacteria form complex biofilms. However, the knowledge about the organization of microbial communities in MBBR biofilms is sparse. We used new cryosectioning and imaging methods for fluorescence in situ hybridization (FISH) to study the structure of biofilms retrieved from carriers in a nitritation-anammox MBBR. The dimensions of the carrier compartments and the biofilm cryosections after FISH showed good correlation, indicating little disturbance of biofilm samples by the treatment. FISH showed that Nitrosomonas europaea/eutropha-related cells dominated the AOB and Candidatus Brocadia fulgida-related cells dominated the anammox guild. New carriers were initially colonized by AOB, followed by anammox bacteria proliferating in the deeper biofilm layers, probably in anaerobic microhabitats created by AOB activity. Mature biofilms showed a pronounced three-dimensional stratification where AOB dominated closer to the biofilm-water interface, whereas anammox were dominant deeper into the carrier space and towards the walls. Our results suggest that current mathematical models may be oversimplifying these three-dimensional systems and unless the multidimensionality of these systems is considered, models may result in suboptimal design of MBBR carriers.
Reproductive response of rats fed turmeric (Curcuma longa L.) and its alcoholic extract (1987)

Reproductive response of rats fed turmeric (500 mg/kg body wt.) and its alcoholic extract (60 mg/kg body wt.) was examined for 3 generations. The data obtained suggested that turmeric and its alcoholic extract were safe at the stated levels with respect to reproductive efficiency.
Noise sources in imaging static Fourier transform spectrometers (2012)

Imaging static Fourier transform spectrometers are well-adapted instruments for remote sensing. However, the path from the raw images to the spectral images is quite long, thus multiplying the potential noise sources. In this article, we propose to review these perturbation sources. We first recall how detector or photon noise on the interferogram affects the estimated spectrum. Then, we focus on inhomogeneities of the focal plane array. Although these inhomogeneities are deterministic, they generate noise when they are ill-corrected. Finally, we describe defects due to errors that may occur during the image processing step. We also give some avenues to limit the impact of these noises.
Screencasts for Enhancing Chemical Engineering Education (2020)

Abstract Screencasts for Enhancing Chemical Engineering EducationChemical & biological engineering faculty have developed over 950 screencasts covering topicsin chemical engineering courses. Screencasts are short videos (typically less than 10 minutes)with narration and are made by digital capture of a tablet PC screen. Screencasts can introduce atopic, solve an example problem, explain a concept, explain a diagram and process, demonstratesoftware use, review for an exam, or present a mini-lecture. They can be used in combinationwith textbooks, online reading quizzes, homework assignments, and office hours. They can alsobe used to create flipped classrooms, where students work under the supervision of the instructorduring class and information delivery is outside of class. Their brevity is an important attributethat distinguishes them from video lectures, and they have significant advantages thatsupplement textbooks and written materials, such as step by step visual explanations of adiagram or series of plots. This personalized method of learning empowers students by givingthem control over the rate of information delivery and when they receive information. As ofOctober 2013, these videos had been watched/downloaded over 2.7 million times and have anoverwhelmingly positive response from students in our classes and through YouTube comments.Building off of this success, our second phase goals include creating 800 more screencasts todevelop over 12 comprehensive chemical engineering courses. Each library of screencasts willbe validated by chemical engineering faculty around the country. We also will be assessing theireffectiveness on improving student learning gains and attitudes. Previous research shows thatscreencasts help minimize cognitive overload, increase student confidence, and allow students totake control of their learning. This allows faculty to use class time for active-learningapproaches, which are more effective than lectures. Thus, the overall effect will be to improveundergraduate chemical engineering education, provide a model for other engineeringdisciplines, and better prepare engineering students for the future.We will provide information on accessing these resources as well as share our insight and bestpractices for other faculty interested in developing their own screencasts. Assessment datacollected from multiple courses and institutions will focus on qualitative student and facultyfeedback. Initial findings related to quantitative learning gains and student attitudes will also bepresented.
Isolation and complete covalent structure of liver microsomal paraoxonase (1999)

Paraoxonase (PON1) is a serum esterase exclusively associated with high-density lipoproteins; it might confer protection against coronary artery disease by destroying pro-inflammatory oxidized lipids in oxidized low-density lipoproteins. Here I show that rabbit liver microsomes contain a PON analogue (MsPON) and report the isolation and complete covalent structure of MsPON. In detergent-solubilized microsomes, MsPON co-purifies with the microsomal triacylglycerol transfer protein (MTP) complex. MsPON was separated from the complex and purified to homogeneity under non-denaturing conditions. Automated sequence analysis of intact MsPON and peptides obtained from enzymic and chemical cleavages led to the elucidation of the complete covalent structure of MsPON. The protein is a single polypeptide consisting of 350 residues. The sequence of rabbit liver microsomal MsPON is 60% identical with that of rabbit serum PON1, and 84% identical with the sequence predicted by a human cDNA of unknown function, designated PON3. MsPON has a hydrophobic segment at the N-terminus that might serve to anchor the protein to the microsomal membrane or to the MTP complex. Unlike in the serum enzyme, two potential N-glycan acceptor sites in MsPON are not glycosylated. An absence of N-glycans was also indicated in the rabbit liver MTP. MsPON has a single free cysteine residue at position 38 and a disulphide bond between Cys-279 and Cys-348. The microsomal enzyme lacks three residues at the N-terminus that are present in the serum protein. MsPON lacks four residues at the C-terminus that are present in the rabbit serum protein but absent from human serum PON1. On the basis of the observation that MsPON displays a high degree of similarity with serum PON1, it is proposed that MsPON might have a function related to that of PON1 in serum high-density lipoprotein complexes.
The Relationship between the Distribution of Common Carp and Their Environmental DNA in a Small Lake (2014)

Although environmental DNA (eDNA) has been used to infer the presence of rare aquatic species, many facets of this technique remain unresolved. In particular, the relationship between eDNA and fish distribution is not known. We examined the relationship between the distribution of fish and their eDNA (detection rate and concentration) in a lake. A quantitative PCR (qPCR) assay for a region within the cytochrome b gene of the common carp (Cyprinus carpio or 'carp'), an ubiquitous invasive fish, was developed and used to measure eDNA in Lake Staring (MN, USA), in which both the density of carp and their distribution have been closely monitored for several years. Surface water, sub-surface water, and sediment were sampled from 22 locations in the lake, including areas frequently used by carp. In water, areas of high carp use had a higher rate of detection and concentration of eDNA, but there was no effect of fish use on sediment eDNA. The detection rate and concentration of eDNA in surface and sub-surface water were not significantly different (p≥0.5), indicating that eDNA did not accumulate in surface water. The detection rate followed the trend: high-use water > low-use water > sediment. The concentration of eDNA in sediment samples that were above the limit of detection were several orders of magnitude greater than water on a per mass basis, but a poor limit of detection led to low detection rates. The patchy distribution of eDNA in the water of our study lake suggests that the mechanisms that remove eDNA from the water column, such as decay and sedimentation, are rapid. Taken together, these results indicate that effective eDNA sampling methods should be informed by fish distribution, as eDNA concentration was shown to vary dramatically between samples taken less than 100 m apart.
Analysis of GaN power MOSFET exporsure to pulsed overcurrents (2015)

The advancement of wide bandgap semiconductor materials has led to the development of Gallium Nitride (GaN) power semiconductor devices, specifically GaN Power MOSFETs. GaN devices have improved characteristics in carrier mobility and on-state resistance compared to Silicon solid state switches. With the development of these new power semiconductor devices a need was established to understand the behavior of the devices switching performance under stress, with regards to situations in pulsing circuits. Through the examination of the switching characteristics of GaN devices, the results can be used for the improvement of advanced pulsing circuit design with GaN solid state switches. In this paper the authors develop a test bed to expose the GaN Power MOSFETs to single and repetitive pulsed overcurrents. The test bed was developed using a Pulse Ring Down board in a radially symmetric configuration to minimize the total equivalent inductance and resistance. The test bed switches the GaN MOSFET with low impedance between the DC bus and ground to induce the stress the MOSFET experiences during pulsed overcurrents. The DC characteristics were measured between switching sets to reveal characteristic signs of potential degradation and failure modes due to pulsed overcurrents. The single and repetitive pulse switching characteristics are captured, analyzed, and shown.
Phenomenology-informed techniques for machine learning with measured and synthetic SAR imagery (2021)

Phenomenology-Informed (PI) Machine Learning is introduced to address the unique challenges faced when applying modern machine-learning object recognition techniques to the SAR domain. PI-ML includes a collection of data normalization and augmentation techniques inspired by successful SAR ATR algorithms designed to bridge the gap between simulated and real-world SAR data for use in training Convolutional Neural Networks (CNNs) that perform well in the low-noise, feature-dense space of camera-based imagery. The efficacy of PI-ML will be evaluated using ResNet, EfficientNet, and other networks, using both traditional training techniques and all-SAR transfer learning.
The breast cancer resistance protein protects against a major chlorophyll-derived dietary phototoxin and protoporphyria (2002)

The breast cancer resistance protein (BCRPABCG2) is a member of the ATP-binding cassette family of drug transporters and confers resistance to various anticancer drugs. We show here that mice lacking Bcrp1Abcg2 become extremely sensitive to the dietary chlorophyll-breakdown product pheophorbide a, resulting in severe, sometimes lethal phototoxic lesions on light-exposed skin. Pheophorbide a occurs in various plant-derived foods and food supplements. Bcrp1 transports pheophorbide a and is highly efficient in limiting its uptake from ingested food. Bcrp1(-/-) mice also displayed a previously unknown type of protoporphyria. Erythrocyte levels of the heme precursor and phototoxin protoporphyrin IX, which is structurally related to pheophorbide a, were increased 10-fold. Transplantation with wild-type bone marrow cured the protoporphyria and reduced the phototoxin sensitivity of Bcrp1(-/-) mice. These results indicate that humans or animals with low or absent BCRP activity may be at increased risk for developing protoporphyria and diet-dependent phototoxicity and provide a striking illustration of the importance of drug transporters in protection from toxicity of normal food constituents.
Transient Electromagnetic Modeling of the ZR Accelerator Water Convolute and Stack (2005)

The ZR accelerator is a refurbishment of Sandia National Laboratories Z accelerator [1]. The ZR accelerator components were designed using electrostatic and circuit modeling tools. Transient electromagnetic modeling has played a complementary role in the analysis of ZR components [2]. In this paper we describe a 3D transient electromagnetic analysis of the ZR water convolute and stack using edge-based finite element techniques.
Plasma cholesterol lowering action of bile acid binding polymers in experimental animals (1960)

Feeding of bile acid binding polymeric organic bases inhibited cholesterol rise and aortic. plaque formation in cholesterol-fed cockerels, lowered plasma cholesterol concentrations in normocholesterolemic cockerels and dogs, and increased fecal bile acid and sterol output in a dog. In experiments lasting as long as one year these substances have not produced visible toxic effects. They are thought to act by binding the bile acids in the intestinal tract.
Risk Factors for Surgical Site Infection Following Total Joint Arthroplasty (2014)

Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Organizational strategy, managerial decision‐making, and market‐based environmental policies: utility company bidding behavior in the sulfur dioxide allowance trading auctions (1997)

An environmental policy approach gaining increasing acceptance among regulators, industry, and environmental groups is the use of market-based instruments. The growth of such programs results in an important research need to understand how organizations respond to these tools. Our managerial and organizational decision-making study examines the sulfur dioxide allowance trading program, part of the effort to reduce acid rain in the United States. This is one of the most visible and significant environmental market-based approaches as it is being implemented on a nationwide scale and impacts an important corporate sector—the utility industry. Our study seeks to understand why utility company participation in this program, as measured by bidding for allowances in auctions, has been under 10% of utilities able to bid, despite the low price of the allowances relative to alternative sulfur dioxide control measures. We utilize the organizational strategy literature to develop and structure our hypotheses. Our data collection method involves a mail survey to management's of 142 utility companies to assess their attitudes concerning a number of variables which were hypothesized to influence company bidding in the March 1994 allowance auctions. This attitudinal approach was selected since the newness of the sulfur dioxide allowance trading program results in utility decision-making significantly depending on management's perceptions of factors, such as future retaking rulings, state regulations, and public opinion, which are not easily observable or measurable by other methods. The study finds that a range of organizational strategy models—economic, behavioral, stakeholder, and learning—are useful for understanding the observed behavior. A number of variables consistent with each model are shown to influence managerial decision-making to bid in the auctions. These variables include the expected treatment of the carrying costs of the allowances by public utility commissions, the costs of the allowances relative to other compliance strategies, an auction design characteristic, public opinion in the utility's service area, the importance of the allowances to meet demand growth, the competitive environment in which the utility operates, and the innovativeness of the utility. The findings are useful for gaining greater insight into managerial decision-making and organizational strategy as well as for improving both this specific market-based policy tool and the increasing number of market-based policy tools applied to other environmental issues. © 1997 John Wiley & Sons, Ltd.
Preliminary observations on the effects of the Chinese medicinal herbs Astragalus membranaceus and Ligustrum lucidum on lymphocyte blastogenic responses. (1983)

The biological effects of extracts of two Chinese medicinal herbs, Astragalus membranaceus and Ligustrum lucidum, on in vitro lymphocyte blastogenesis were assessed. Aqueous extracts augmented the spontaneous [3H]thymidine incorporation in the mononuclear cells (MNC) of 14 normal subjects from 273.0 to 609.3 counts per minute (cpm) and 252.9 to 656.9 cpm for the two herbs, respectively. The stimulation indices were 2.4 and 3.1, respectively (p less than 0.001). They also augmented the proliferation of normal subjects' lymphocytes induced by suboptimal concentrations of phytohemagglutinin (PHA) from 5084.6 to 23,398.3 and 221.7 to 24,132.8 cpm, of concanavalin A (con A) from 4046.5 to 15,661.5 and 677.6 to 14,644.6 cpm, and of pokeweed mitogen (PWM) from 4377.9 to 24,405.6 and 322.7 to 11,730.0 cpm, respectively (p less than 0.00). Herb extracts augmented the PHA responses of the MNC from 14 cancer patients significantly (p less than 0.01 and p less than 0.05, respectively). Extracts of L. lucidum also augmented the con A response of patients (p less than 0.05). The augmenting effect of the herbs on the PHA, con A, and PWM responses was dose dependent, and proliferation was inhibited at higher concentrations. The optimal concentration for stimulating the MNC of cancer patients was 100 micrograms/ml, compared to 10 micrograms/ml for the MNC of normal donors. MNC of seven patients depressed the mitogen responses of normal cells in a co-culture system. This was partially abrogated in five by preincubating the patients' cells in herb extracts for 45 min or by irradiation of the patients' cells. These results suggest that the herb extracts contain immunomodulatory components which may be useful in the immunotherapy of disease.
An energy balance of high-speed abrasive water jet erosion (1999)

High-speed abrasive water jetting is an alternative tool for machining engineering materials. The energy dissipation processes involved in this erosion process have not been investigated systematically. In this paper, a model is developed to calculate the energy dissipation in workpieces eroded by abrasive water jets. By introducing an energy dissipation function χ(Φ). the model enables the estimation of the energy absorption as a function of the erosion depth. The energy dissipation function can be expressed by a second-order polynomial approximation. Measurements of the reaction forces on the exiting slurry after the erosion process, material removal experiments and fracture tests are conducted to separate the components of the energy dissipation parameter, such as damping, friction and erosion debris generation.