gebhart/patrepeval huggingface dataset:
Cyber-Physical Programmable Logic Controller (2013)

Flexible Fertigung, intelligentes Energiemanagement und Mobilitat entwickeln sich zu einer komplexen und geografisch verteilten Topologie von physikalischen (zum Beispiel elektro-mechanisch, chemisch) und informationstechnischen Prozessen (beispielsweise Steuerungen und Software). In diesem Beitrag stellen die Autoren eine zusatzliche Funktionalitat fur speicherprogrammierbare Steuerungen (SPS beziehungsweise PLC, programmable logic controller) vor, um die Interaktion mit ihrer Umwelt zu verbessern. Die Architektur cyber-physical systems programmable logic controller (CPS-PLC) ermoglicht die Kommunikation mit externen und geografisch verteilten Geraten und physikalischen Prozessen zusatzlich zur ublichen Automatisierungspyramide von lokalen, vernetzten Geraten. So ist es dem CPS-PLC moglich, mit komplexer Information von entfernten Quellen umzugehen und auf unerwartete Ereignisse intelligent zu reagieren. Im Artikel wird auch eine modellbasierte Entwurfsmethode beschrieben, um CPS-PLC-Anwendungen zu projektieren, wobei das physikalische Verhalten des kontrollierten Systems ebenso wichtig ist wie Hardware und Software der eingebetteten Steuerung. Die Machbarkeit des Verfahrens wird durch eine Smart-Grid-CPS-Anwendung demonstriert.
Space Curve Approach for IVUS Image Segmentation (2018)

Intravascular ultrasound imaging (IVUS) is an interventional cardiology technique for assessing atherosclerosis lesions in artery. This technique generates images showing the different layers of the artery and allows quantitative measurements reflecting its condition. However due to the acquisition process these images are affected by artifacts like ring-down, guide wire and shadows generated by tissue calcification. In this paper we develop a 3D algorithm based on a helical snake (active contour) for the lumen segmentation in intravascular ultrasound images. The helix snake evolves based on the analysis of the statistical properties computed on windows inside and outside the contour until it reaches the luminal border. In addition we show the influence of the ring-down artifact for the luminal border detection by adding a pre-processing step for reducing its adverse effect. The algorithm was executed on 2190 images from two clinical IVUS sequences of femoral arteries presenting the ringdown artifact. The performance of the algorithm was evaluated with respect to expert manual plots and gave a mean Hausdorff distance of 0.31 mm with overlap of 89.50 % and 94.38 % for respectively Jaccard and Dice indexes improving the result by 0.29 mm, 8.79 % and 5.36 % compared to the result without artifact removal.
Supplemental Figure 4 from Novel Methylated DNA Markers in the Surveillance of Colorectal Cancer Recurrence (2023)

&lt;p&gt;Supplemental Figure 4: Carcinoembryonic antigen (CEA) levels in nanograms per milliliter assayed from 10 microliters serum in the Early Detection experiment are 1.5 times higher than values assayed from 10 microliters of plasma in the Surveillance experiment. Blue reference line marks median values in serum for normal control patients and orange line marks median serum value for stage IV colorectal cancer cases. CEA values in the surveillance samples were re-scaled to allow application of the model derived in the Early Detection analysis to the Surveillance data set.&lt;/p&gt;
Route to Renewable PET: Reaction Pathways and Energetics of Diels–Alder and Dehydrative Aromatization Reactions Between Ethylene and Biomass-Derived Furans Catalyzed by Lewis Acid Molecular Sieves (2015)

Silica molecular sieves that have the zeolite beta topology and contain framework Lewis acid centers (e.g., Zr-β, Sn-β) are useful catalysts in the Diels–Alder and dehydrative aromatization reactions between ethylene and various renewable furans for the production of biobased terephthalic acid precursors. Here, the main side products in the synthesis of methyl 4-(methoxymethyl)benzene carboxylate that are obtained by reacting ethylene with methyl 5-(methoxymethyl)-furan-2-carboxylate are identified, and an overall reaction pathway is proposed. Madon–Boudart experiments using Zr-β samples of varying Si/Zr ratios clearly indicate that there are no transport limitations to the rate of reaction for the synthesis of p-xylene from 2,5-dimethylfuran and ethylene and strongly suggest no mass transport limitations in the synthesis of methyl p-toluate from methyl 5-methyl-2-furoate and ethylene. Measured apparent activation energies for these reaction-limited systems are small (&lt;10.5 kcal/mol), suggesting that apparent activation energies are derived from a collection of parameters and are not true activation energies for a single chemical step. In addition, 13C kinetic isotope effects (KIE) in the synthesis of MMBC and MPT measured by gas chromatography/isotope-ratio mass spectrometry in reactant-depletion experiments support the Madon–Boudart result that these systems are not transport-limited and the KIE values agree with those previously reported for Diels–Alder cycloadditions.
Effect of machine perfusion preservation on delayed graft function in non-heart-beating donor kidneys -early results (1997)

Abstract. The functioning of non-heart-beating (NHB) donor kidneys upon transplantation is often delayed. To evaluate the effect of preservation by machine perfusion (MP) on early post-transplant function, 37 NHB donor kidneys were compared to 74 matched heart-beating (HB) donor kidneys preserved by cold storage (CS). The NHB donor kidneys were subject to 49 + 34 min of warm ischemia. Delayed function (DF) and primary nonfunction (PNF) rates were significantly higher for NHB than for HB donor kidneys (49 % and 19 % vs 34 % and 7 %, respectively). Consequently, renal function was impaired but recovered within 6 months. MP could not eliminate the differences in DF rate between NHB and HB donor kidneys. However, NHB donor kidneys preserved by MP showed less DF than that reported in kidneys preserved by CS. This suggests that MP has a beneficial effect on ischemically damaged kidneys. The similar results observed with category 2 and category 3 NHB donors also suggest this effect. The high PNF rate emphasizes the need for viability tests that prevent the transplantation of nonviable organs. We conclude that MP alone is not sufficient to reduce DF and PNF rates in NHB donor kidneys.
Lack of Association between Preoperative Statin Use and Respiratory and Neurologic Complications after Cardiac Surgery (2017)

Preoperative statin use did not reduce pulmonary or neurologic complications after cardiac surgery.
Normal subject breast imaging with a portable near infrared tomographic imaging system (2016)

A portable hybrid frequency domain (FD) - continuous wave (CW) Near-Infrared spectroscopy system has been developed for breast imaging. Physiologically reasonable values of chromophore concentrations were recovered for normal subject measurements.
Parameter Estimation And Order Selection For Linear Regression Problems (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Integrated methods for production of clean char and its combustion properties. Interim final technical report, September 1, 1991--December 31, 1992 (1992)

An integrated method consisting of physical coal cleaning, mild gasification (MG) and low temperature oxidation (LTO) is proposed to produce chars with S0{sub 2} emissions at least 50% lower than those of their parent coals. MG and char desulfurization studies are conducted in both a batch fluidized-bed reactor (FBR) and in a continuous rotary tube kiln (RTK). Combustion properties and ash deposition behaviors of desulfurized chars are determined at the US EPA in a 14 kW pilot-scale combustor and at UNDEERC in a drop tube furnace (DTF). This project is cost-shared with the US EPA and the US DOE through UNDEERC. MG chars were prepared from l00 {times} 200 mesh size fractions of each of six coals selected from the Illinois Basin Coal (IBC) Sample Program in a FBR. under non-optimized conditions, desulfurized chars with S0{sub 2} emissions 60--71% lower than the parent coals were made, depending on the coal. Chars prepared from four of the six coals had SO{sub 2} emissions less than 2.5 lbs S0{sub 2}/MMBtu. Optimization of LTO conditions revealed that the greatest reduction in S0{sub 2} emissions was obtained using smaller particle diameters, steam during both MG and LTO, a higher temperature and higher oxygen partial pressure. Under optimized conditions, S0{sub 2} emissions of one of the coals were reduced nearly 67%, from 4.60 to 1.49 lbs S0{sub 2}/MMBtu. About 40 pounds of low-sulfur char were prepared from IBC-102 in the RTK. The amount of sulfur removed in the RTK was less than in the FBR, and gave a char with S0{sub 2} emissions of about 2.4 lbs S0{sub 2}/MMBtu. The greater sulfur removal in the FBR was attributed to a smaller mean particle diameter, better gas-solid contact and/or decreased partial pressure of S0{sub 2}.
Using Polypyrrole Coating to Improve Cycling Stability of NaTi2(PO4)3as an Aqueous Na-Ion Anode (2015)

Aqueous alkali - ion batteries offer an economical method for large-scale energy storage demanded by current sources of renewable energy. Although NASICON-type NaTi2(PO4)3 is an attractive anode material with high capacity and a low redox potential allowing for high voltage cells, it suffers from considerable capacity fade when cycled slowly and deeply. In this work polypyrrole has been introduced as a coating for NaTi2(PO4)3 through a high-energy ballmilling process. When an excessive coating was applied, no redox reactions from the NaTi2(PO4)3 were visible due to the poor Na+ diffusion through the polypyrrole. However, the as-coated composites containing 5 wt% polypyrrole showed much better capacity retention compared to the uncoated material, retaining 57% of the initial discharge capacity after 50 cycles compared to the uncoated material, which retained only 10% of the initial discharge capacity. It is concluded that coating NaTi2(PO4)3 with conducting polymers can be an effective strategy for promoting battery lifetime.
The effect of oligosaccharides on glycoprotein stability (1995)

A series of experiments aimed at determining the sites of glycosylation of Staphylococcal nuclease (SNase) were conducted.
Expanding Explainability: Towards Social Transparency in AI systems (2021)

As AI-powered systems increasingly mediate consequential decision-making, their explainability is critical for end-users to take informed and accountable actions. Explanations in human-human interactions are socially-situated. AI systems are often socio-organizationally embedded. However, Explainable AI (XAI) approaches have been predominantly algorithm-centered. We take a developmental step towards socially-situated XAI by introducing and exploring Social Transparency (ST), a sociotechnically informed perspective that incorporates the socio-organizational context into explaining AI-mediated decision-making. To explore ST conceptually, we conducted interviews with 29 AI users and practitioners grounded in a speculative design scenario. We suggested constitutive design elements of ST and developed a conceptual framework to unpack ST’s effect and implications at the technical, decision-making, and organizational level. The framework showcases how ST can potentially calibrate trust in AI, improve decision-making, facilitate organizational collective actions, and cultivate holistic explainability. Our work contributes to the discourse of Human-Centered XAI by expanding the design space of XAI.
On the reliability of PCA for complex hyperspectral data (2009)

Principal Component Analysis (PCA) is a popular tool for initial investigation of hyperspectral image data. There are many ways in which the estimated eigenvalues and eigenvectors of the covariance matrix are used. Further steps in the analysis or model building for hyperspectral images are often dependent on those estimated quantities. It is therefore important to know how precisely the eigenvalues and eigenvectors are estimated, and how the precision depends on the sampling scheme, the sample size, and the covariance structure of the data. This issue is especially relevant for applications such as difficult target detection, where the precision of further steps in the algorithm may depend on the reliable knowledge of the estimated eigenvalues and eigenvectors. The sampling properties of eigenvalues and eigenvectors are known to some extent in statistical literature (mostly in the form of asymptotic results for large sample sizes). Unfortunately, those results usually do not apply in the context of hyperspectral images. In this paper, we investigate the sampling properties of eigenvalues and eigenvectors under three scenarios. The first two scenarios consider the type of sampling traditionally used in statistics, and the third scenario considers the variability due to image noise, which is more appropriate for hyperspectral imaging applications. For all three scenarios, we show the precision associated with the estimated eigenvalues and eigenvectors.
Musical note segmentation employing combined time and frequency analyses (2004)

In this paper we describe a musical stream note segmentation method that employs time-domain and frequency-domain analysis methods working in conjunction. The method has two demonstrated benefits: first, it leads to reliable results with very low probability of either missing or of falsely detecting notes, and second, it has temporal resolution on the order of 1 msec. We have applied the method to a variety of monophonic musical instrument recordings, including the clarinet, piano and violin, with results that vary from 95% to 100% accuracy.
Highly reliable STT-MRAM adopting advanced MTJs with controlled domain wall pinning (2022)

We demonstrate highly reliable STT-MRAM whose array-level write error has been eliminated by lowering the density of domain wall pinning sites in the MTJs. The core part of investigation includes the identification and quantification of domain wall pinning sites, characterization and modeling of the pinning sites, and correlation of the density of pinning sites with array-level write error rate. The experimental results show that domain wall pinning is geometrically localized and reproduced upon the repeated writing cycles. By controlling the domain wall pinning, we obtain high-density MTJ array having superior reliability without notable trailing bits of write fail.
Comparative Aspects of Luteinizing Hormone-Releasing Hormone Structure and Function in Vertebrate Phylogeny* (1980)

Immunoreactive LHRH was detected in hypothalamic and extrahypothalamic brain extracts of the rat, bird (pigeon and chicken), reptile (tortoise and lizard), amphibian (frog and toad), teleost (cichid), and elasmobranch (dogfish) and in the whole brain of the cyclostome (bagfish). The concentration of hypothalamic immunoreactive LHRH was more than 5-fold greater than that of the extrahypothalamic brain. Mammalian and amphibian hypothalamic immunoreactive LHRH yielded displacement curves parallel to those of synthetic LHRH in assays employing four antisera which recognize different regions of the decapeptide, thus suggesting a similarity in the structure of their LHRH. Hypothalamic immunoreactive LHRH from the bird, reptile, teleost, and elasmobranch differed from the mammalian and amphibian peptide in yielding displacement curves nonparallel to those of synthetic LHRH with three different antisera (1076, 743, and 744) which bind between Trp3 and Pro9 of LHRH. The differenece in structure appears to be near Leu7. With antiserum 422 which binds the NH2- and CO2H- termini of LHRH, bird, reptile, and teleost hypothalamic extracts yielded displacement curves parallel to that of synthetic LHRH. Bird, reptile, and teleost hypothalamic extracts showed displacement curves parallel to each other in all assays. In studies on the relative quantitation of LHRH, all four antisera gave similar values of immunoreactive LHRH concentration in mammalian hypothalamic extracts and in amphibian hypothalamic extracts. By contrast, assay of bird, reptile, teleost, and elasmobranch hypothalamic extracts with antiserum 422 gave much higher values than did the other antisera, suggesting that the LHRH peptide is structurally different from mammalian and amphibian LHRH in the region of Leu7 but similar at the NH2- and CO2H-termini. These conclusions are supported by studies on the biological activity of hypothalamic LHRH from the different species using dispersed ovine anterior pituitary cells in culture. The LH release responses to equivalent amounts of immunoreactive LHRH (as measured by antiserum 422 which binds a region of LHRH essential for biological activity) from the various species were similar, indicating that the biologically active region of the molecule has been conserved in evolution. Structural differences in vertebrate hypothalamic immunoreactive LHRH were confirmed by cation exchange and high pressure liquid chromatography. Our findings of differences and similarities in vertebrate LHRH support a contemporary phylogenetic scheme.
New Antiparasitic Bis‐Naphthoquinone Derivatives (2019)

A series of bis-naphthoquinone derivatives prepared by condensation of aryl aldehydes with lawsone were tested for antiparasitic activities against Toxoplasma gondii and Trypanosoma brucei parasites. Monofluorophenyl derivative 1a, 3,4-difluorophenyl analog 1c and furyl compound 1l exhibited significant activity against T. gondii cells and appear to be new promising drug candidates against this parasite. The 3,4,5-trifluorophenyl derivative 1g and the isovanillyl derivative 1j displayed selective activity against Leishmania major amastigotes.
Oxygen Reactions in a Non‐Aqueous Li+ Electrolyte (2011)

Taking the shortcut: Spectroscopic data (see picture) provide direct evidence that in non-aqueous Li+ electrolyte, O2 is reduced to O2−, which then forms LiO2 on the electrode surface which disproportionates to Li2O2. On charging, Li2O2 decomposes directly, in a one-step reaction to evolve O2 and does not pass through LiO2 as an intermediate. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Albertian errors in head-mounted displays: I Choice of eye-point location for a near- or far-field task visualization (2004)

A theoretical investigation of rendered depth and angular errors, or Albertian errors, linked to natural eye movements in binocular head-mounted displays (HMDs) is presented for three possible eye-point locations: the center of the entrance pupil, the nodal point, and the center of rotation of the eye. A numerical quantification was conducted for both the pupil and the center of rotation of the eye under the assumption that the user will operate solely in either the near field under an associated instrumentation setting or the far field under a different setting. Under these conditions, the eyes are taken to gaze in the plane of the stereoscopic images. Across conditions, results show that the center of the entrance pupil minimizes rendered angular errors, while the center of rotation minimizes rendered position errors. Significantly, this investigation quantifies that under proper setting of the HMD and correct choice of the eye points, rendered depth and angular errors can be brought to be either negligible or within specification of even the most stringent applications in performance of tasks in either the near field or the far field.
Predicting the Rock Sonic Logs While Drilling by Random Forest and Decision Tree-Based Algorithms (2021)

Abstract The sonic data provide significant rock properties that are commonly used for designing the operational programs for drilling, rock fracturing, and development operations. The conventional methods for acquiring the rock sonic data in terms of compressional and shear slowness (ΔTc and ΔTs) are considered costly and time-consuming operations. The target of this paper is to propose machine learning models for predicting the sonic logs from the drilling data in real-time. Decision tree (DT) and random forest (RF) were employed as train-based algorithms for building the sonic prediction models for drilling complex lithology rocks that have limestone, sandstone, shale, and carbonate formations. The input data for the models include the surface drilling parameters to predict the shear and compressional slowness. The study employed data set of 2888 data points for building and testing the model, while another collected 2863 data set was utilized for further validation of the sonic models. Sensitivity investigations were performed for DT and RF models to confirm optimal accuracy. The correlation of coefficient (R) and average absolute percentage error (AAPE) were used to check the models’ accuracy between the actual values and models’ outputs, in addition to the sonic log profiles. The results indicated that the developed sonic models have a high capability for the sonic prediction from the drilling data as the DT model recorded R higher than 0.967 and AAPE less than 2.76% for ΔTc and ΔTs models, while RF showed R higher than 0.991 with AAPE less than 1.07%. The further validation process for the developed models indicated the great results for the sonic prediction and the RF model outperformed DT models as RF showed R higher than 0.986 with AAPE less than 1.12% while DT prediction recorded R greater than 0.93 with AAPE less than 1.95%. The sonic prediction through the developed models will save the cost and time for acquiring the sonic data through the conventional methods and will provide real-time estimation from the drilling parameters.
Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity (2016)

Systemic sclerosis (SSc) is a rare autoimmune disease with the highest case-fatality rate of all connective tissue diseases. Current efforts to determine patient response to a given treatment using the modified Rodnan skin score (mRSS) are complicated by interclinician variability, confounding, and the time required between sequential mRSS measurements to observe meaningful change. There is an unmet critical need for an objective metric of SSc disease severity. Here, we performed an integrated, multicohort analysis of SSc transcriptome data across 7 datasets from 6 centers composed of 515 samples. Using 158 skin samples from SSc patients and healthy controls recruited at 2 centers as a discovery cohort, we identified a 415-gene expression signature specific for SSc, and validated its ability to distinguish SSc patients from healthy controls in an additional 357 skin samples from 5 independent cohorts. Next, we defined the SSc skin severity score (4S). In every SSc cohort of skin biopsy samples analyzed in our study, 4S correlated significantly with mRSS, allowing objective quantification of SSc disease severity. Using transcriptome data from the largest longitudinal trial of SSc patients to date, we showed that 4S allowed us to objectively monitor individual SSc patients over time, as (a) the change in 4S of a patient is significantly correlated with change in the mRSS, and (b) the change in 4S at 12 months of treatment could predict the change in mRSS at 24 months. Our results suggest that 4S could be used to distinguish treatment responders from nonresponders prior to mRSS change. Our results demonstrate the potential clinical utility of a novel robust molecular signature and a computational approach to SSc disease severity quantification.