gebhart/patrepeval huggingface dataset:
Figure S6 from Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure 6 | mTORC1, mTORC1/2 and PI3K-mTORC1/2 inhibitor sensitivities. (A) IC50 of the mTORC1 inhibitor temsirolimus from COSMICs drug screening database in all cancer cell lines vs. ovarian cancer cell lines, horizontal lines indicate geometric mean. (B) MTT assay curves from AZD8055 (left) or everolimus (right) treatment on the aforementioned cell line panel. (C) Expression of p-AKT308, p-AKT473 and p-S6 after 24 (up) and 72h (down) exposure to 100 nM everolimus, AZD8055 or MLN0128 in the OCCC cell lines KOC7C or JHOC5 determined by Western blot. ÃŽÂ²-Actin was used as loading control. Results are representative from n=2 experiments. (D) Expression of p-AKT308, p-AKT473, p-S6 and (cleaved) PARP after 48h exposure to increasing concentrations of everolimus, AZD8055 and dactolisib in the OCCC cell lines KOC7C (up) and JHOC5 (down) determined by Western blot. ÃŽÂ²-Actin was used as loading control. Results are representative from n=2 experiments. (E) Everolimus, AZD8055, GDC0941 and selumetinib IC50 determined for 14 OCCC cell lines (ES2, KOC7C, SMOV2, JHOC5, RMG1, OVMANA, HAC2, OV207, OVTOKO, TOV21G, OVAS, OVCA429, TUOC1 and RMG2) and dactolisib IC50 determined for 7 OCCC cell lines (ES2, KOC7C, SMOV2, JHOC5, RMG1, OVMANA and HAC2) by MTT assay. Selumetinib IC50 of KOC7C was not reached at maximum used concentration of 25 uM. Horizontal lines indicate geometric mean. Data is derived from n{greater than or equal to}2 experiments. (F) Long-term proliferation assay after exposure to increasing concentrations of AZD8055 and dactolisib. Results are representative from n=3 experiments.&lt;/p&gt;
Flavothionato metal complexes: implications for the use of hydroxyflavothiones as green pesticides (2005)

Transition-metal complexes of 3-hydroxyflavothiones have been prepared and structurally characterized; the photochemical properties of these complexes have been examined and are discussed in the context of the use of these compounds as photodegradable pesticides.
Use of Feature Engineering to Predict COVID-19 Mortality (2021)

Rationale: Defining a reliable prognostication method in patients with COVID-19 has remained a challenge. Various combinations of inflammatory markers, including CRP, LDH, and D-dimer, have been predictive of increased severity in this group of patients. None of the markers mentioned, however, have had a significant association with increased mortality. Machine learning has been utilized for predictions related to COVID-19. Prior COVID-19 machine learning models used the original features as the input, but we hypothesize that the model can be improved via synthesis of new features by utilizing feature engineering. We aim to explore the predictive capacities of generated features and evaluate for improvements in COVID-19 mortality prediction. Methods: With the approval of the hospital Institutional Review Board, medical records of two hundred sixty-nine patients with a positive COVID-19 PCR study in two 350-bed medical centers were analyzed retrospectively from March 22nd through May 10th, 2020. One hundred sixty-six variables, including laboratory studies, vital signs, demographics, and comorbidities, were collected in total. Features with greater than 50 percent missing values were dropped. Missing data was imputed with SKlearn Multiple Imputation. Feature selection was performed using sequential feature selection via the machine learning extensions library (MLxtend), which led to a final feature space of seven. Feature engineering was performed using the seven features and four additional features generated. LightGBM was chosen as our classification model. The results were compared between the feature engineering and base datasets. Feature ranking was performed using SHapley Additive exPlanations (SHAP). Partial dependence plots were generated to determine feature value cutoffs that predict increased mortality. Results: LightGBM demonstrated good classification performance with an Area Under the Curve (AUC) of .9 in the base model. The feature engineering group had an increase in AUC to .94. The feature most predictive of COVID-19 mortality based upon the SHAP plot was the product of Maximum Blood Urea Nitrogen and Maximum Respiratory Rate (MaxBUN∗MaxRR). The partial dependence plot demonstrates that at a MaxBUN∗MaxRR value > 1000 there is a rise in SHAP values which denotes a rise in predicted mortality. Conclusion: The use of feature engineering improved predictive performance for mortality related to COVID-19. The strongest feature for the prediction of mortality was MaxBUN∗MaxRR. A sharp rise in predicted mortality was observed when the product of these values exceeded 1000. Feature engineering can be used to improve existing mortality prediction models.
A comprehensive solution for BEOL variation characterization and modeling (2016)

A comprehensive variation model is critical to achieve both competitive design and manufacturing yield in advanced technologies. Conventionally, as long as FEOL (front end of line) statistical model is appropriate, BEOL (back end of line) variations given by lumping multiple variation sources into few corners is enough to achieve reliable simulation results. However, as BEOL contribution is becoming more important with device scaling, simulation results with conventional corner model may not always produce optimal design margin. We thus propose a more comprehensive solution for BEOL variations characterization and modeling associated with statistical Monte Carlo simulation.
Hotspot management and its applications in ultralow <inline-formula><math display="inline" overflow="scroll"><msub><mi mathvariant="normal">k</mi><mn>1</mn></msub></math></inline-formula> lithography (2009)

We have constructed a hotspot management flow and applied the flow to large-scale integration (LSI) manufacturing in the ultralow k1 lithography era. This flow involves three main management steps: hotspot reduction, hotspot extraction, and hotspot monitoring. Hotspot reduction works with lithography-friendly restricted design rule (RDR) and manufacturability check (MC). Hotspot extraction is carried out with a view to realizing short operation time and accurate extraction. Hotspot monitoring is achieved with tolerance-based verification in the mask fabrication process and wafer process (lithography and etching). These technology elements could be integrated into the LSI fabrication flow for reduction of total cost, quick turnaround time (TAT), and ramp-up to volume production. In addition to discussion of the technology elements in hotspot management, we also provide typical applications for important decisions in LSI fabrication: photomask availability for any exposure tools ("exposure tool yokoten") and process condition updates in LSI fabrication.
Spiro-β-lactam BSS-730A Displays Potent Activity against HIV and Plasmodium (2021)

The high burden of malaria and HIV/AIDS prevents economic and social progress in developing countries. A continuing need exists for development of novel drugs and treatment regimens for both diseases in order to address the tolerability and long-term safety concerns associated with current treatment options and the emergence of drug resistance. We describe new spiro-β-lactam derivatives with potent (nM) activity against HIV and <i>Plasmodium</i> and no activity against bacteria and yeast. The best performing molecule of the series, BSS-730A, inhibited both HIV-1 and HIV-2 replication with an IC<sub>50</sub> of 13 ± 9.59 nM and <i>P. berghei</i> hepatic infection with an IC<sub>50</sub> of 0.55 ± 0.14 μM with a clear impact on parasite development. BSS-730A was also active against the erythrocytic stages of <i>P. falciparum</i>, with an estimated IC<sub>50</sub> of 0.43 ± 0.04 μM. Time-of-addition studies showed that BSS-730A potentially affects all stages of the HIV replicative cycle, suggesting a complex mechanism of action. BSS-730A was active against multidrug-resistant HIV isolates, with a median 2.4-fold higher IC<sub>50</sub> relative to control isolates. BSS-730A was equally active against R5 and X4 HIV isolates and displayed strong synergism with the entry inhibitor AMD3100. BSS-730A is a promising candidate for development as a potential therapeutic and/or prophylactic agent against HIV and <i>Plasmodium</i>.
Type II transmembrane serine proteases (2003)

The recent availability of human and mouse genome sequences and expressed sequence tag databases facilitated the identification of a large new family of membrane anchored serine proteases, the type II transmembrane serine proteases or TTSPs. Analyses of human inherited disorders and gene targeting studies in mice have revealed that several members of this new protease family have critical functions in development and health. Preliminary studies also suggest that aberrant expression of type II transmembrane serine proteases may be linked to disease progression. The knowledge gathered thus far of the genetics, physiology, and pathology of this interesting new serine protease family will be reviewed here in brief.
Oxygen-Activated Growth and Bandgap Tunability of Large Single-Crystal Bilayer Graphene (2016)

Bernal (AB)-stacked bilayer graphene (BLG) is a semiconductor whose bandgap can be tuned by a transverse electric field, making it a unique material for a number of electronic and photonic devices. A scalable approach to synthesize high-quality BLG is therefore critical, which requires minimal crystalline defects in both graphene layers and maximal area of Bernal stacking, which is necessary for bandgap tunability. Here we demonstrate that in an oxygen-activated chemical vapour deposition (CVD) process, half-millimetre size, Bernal-stacked BLG single crystals can be synthesized on Cu. Besides the traditional surface-limited growth mechanism for SLG (1st layer), we discovered new microscopic steps governing the growth of the 2nd graphene layer below the 1st layer as the diffusion of carbon atoms through the Cu bulk after complete dehydrogenation of hydrocarbon molecules on the Cu surface, which does not occur in the absence of oxygen. Moreover, we found that the efficient diffusion of the carbon atoms present at the interface between Cu and the 1st graphene layer further facilitates growth of large domains of the 2nd layer. The CVD BLG has superior electrical quality, with a device on/off ratio greater than 10 4, and a tunable bandgap up to ∼100meV at a displacement field of 0.9Vnm-1.
Effect of Dapagliflozin on Health Status and Quality of Life Across the Spectrum of Ejection Fraction: Participant-Level Pooled Analysis from the DAPA-HF and DELIVER Trials (2023)

NCT03036124 and NCT03619213.
A 7 μW Offset- and Temperature-Compensated pH-to-Digital Converter (2017)

This paper demonstrates a micropower offset- and temperature-compensated smart pH sensor, intended for use in battery-powered RFID systems that monitor the quality of perishable products. Low operation power is essential in such systems to enable autonomous logging of environmental parameters, such as the pH level, over extended periods of time using only a small, low-cost battery. The pH-sensing element in this work is an ion-sensitive extended-gate field-effect transistor (EGFET), which is incorporated in a low-power sensor front-end. The front-end outputs a pH-dependent voltage, which is then digitized by means of a co-integrated incremental delta-sigma ADC. To compensate for the offset and temperature cross-sensitivity of the EGFET, a compensation scheme using a calibration process and a temperature sensor has been devised. A prototype chip has been realized in a 0.16 μ m CMOS process. It occupies 0.35 × 3.9 mm 2 of die area and draws only 4 μ A from a 1.8 V supply. Two different types of custom packaging have been used for measurement purposes. The pH sensor achieves a linearity of better than ±0.1 for pH values ranging from 4 to 10. The calibration and compensation scheme reduces errors due to temperature cross-sensitivity to less than ±0.1 in the temperature range of 6°C to 25°C.
Friction and Heat at the Head Disk Interface caused by Thermal Protrusion Touchdown (2006)

The head disk interface spacing in current disk drives is controlled by thermal protrusion of a small heater coil near the read write element of the slider body. By adjusting the power to the heater coil, the clearance can be very accurately adjusted. In addition to controlling clearance, the amount of interference can be adjusted when going into contact. In this paper, we investigate the slider dynamics during the transition from flying to contact. In particular, the touchdown/takeoff hysteresis is analyzed by monitoring the friction, MR resistance, tribo-current, acoustic emission and laser Doppler signal from the slider. A novel disk texture was developed that significantly improved the contact dynamics and hysteresis. When comparing disk roughness, we observe increased clearance on smoother disks, however, when going into contact, increased friction, heat, slider bouncing vibrations, and increased hysteresis is observed.
Fatigue effect in ferroelectric PbZr1−xTixO3 thin films (2006)

Pb Zr 1 − x Ti x O 3 (PZT) is one preferred ferroelectric material being used in nonvolatile ferroelectric random access memory devices. The use of oxide electrodes like IrO2 or SrRuO3 (SRO) is necessary to suppress the serious loss of polarization due to bipolar voltage cycling. Although, there are a number of models under discussion, the origin of the fatigue phenomenon is still not completely understood. In this paper, the fatigue effect of ferroelectric Pb(Zr0.40,Ti0.60)O3 thin films has been studied in detail. To achieve a deeper understanding of the effect, several PZT samples with different electrode materials were investigated. After determining the dependence of the single fatigue parameters, a simulation approach was made to analyze the fatigue effect qualitatively. A sample with SRO electrodes was measured up to 1013cycles and no fatigue of the switchable polarization was observed.
The unique hypusine modification of eIF5A promotes islet β cell inflammation and dysfunction in mice (2010)

In both type 1 and type 2 diabetes, pancreatic islet dysfunction results in part from cytokine-mediated inflammation. The ubiquitous eukaryotic translation initiation factor 5A (eIF5A), which is the only protein to contain the amino acid hypusine, contributes to the production of proinflammatory cytokines. We therefore investigated whether eIF5A participates in the inflammatory cascade leading to islet dysfunction during the development of diabetes. As described herein, we found that eIF5A regulates iNOS levels and that eIF5A depletion as well as the inhibition of hypusination protects against glucose intolerance in inflammatory mouse models of diabetes. We observed that following knockdown of eIF5A expression, mice were resistant to beta cell loss and the development of hyperglycemia in the low-dose streptozotocin model of diabetes. The depletion of eIF5A led to impaired translation of iNOS-encoding mRNA within the islet. A role for the hypusine residue of eIF5A in islet inflammatory responses was suggested by the observation that inhibition of hypusine synthesis reduced translation of iNOS-encoding mRNA in rodent beta cells and human islets and protected mice against the development of glucose intolerance the low-dose streptozotocin model of diabetes. Further analysis revealed that hypusine is required in part for nuclear export of iNOS-encoding mRNA, a process that involved the export protein exportin1. These observations identify the hypusine modification of eIF5A as a potential therapeutic target for preserving islet function under inflammatory conditions.
Label-free isolation of prostate circulating tumor cells using Vortex microfluidic technology (2017)

There has been increased interest in utilizing non-invasive "liquid biopsies" to identify biomarkers for cancer prognosis and monitoring, and to isolate genetic material that can predict response to targeted therapies. Circulating tumor cells (CTCs) have emerged as such a biomarker providing both genetic and phenotypic information about tumor evolution, potentially from both primary and metastatic sites. Currently, available CTC isolation approaches, including immunoaffinity and size-based filtration, have focused on high capture efficiency but with lower purity and often long and manual sample preparation, which limits the use of captured CTCs for downstream analyses. Here, we describe the use of the microfluidic Vortex Chip for size-based isolation of CTCs from 22 patients with advanced prostate cancer and, from an enumeration study on 18 of these patients, find that we can capture CTCs with high purity (from 1.74 to 37.59%) and efficiency (from 1.88 to 93.75 CTCs/7.5 mL) in less than 1 h. Interestingly, more atypical large circulating cells were identified in five age-matched healthy donors (46-77 years old; 1.25-2.50 CTCs/7.5 mL) than in five healthy donors <30 years old (21-27 years old; 0.00 CTC/7.5 mL). Using a threshold calculated from the five age-matched healthy donors (3.37 CTCs/mL), we identified CTCs in 80% of the prostate cancer patients. We also found that a fraction of the cells collected (11.5%) did not express epithelial prostate markers (cytokeratin and/or prostate-specific antigen) and that some instead expressed markers of epithelial-mesenchymal transition, i.e., vimentin and N-cadherin. We also show that the purity and DNA yield of isolated cells is amenable to targeted amplification and next-generation sequencing, without whole genome amplification, identifying unique mutations in 10 of 15 samples and 0 of 4 healthy samples.
Programmable-output PFC rectifier with dynamic efficiency and transient response optimization (2012)

This paper introduces a digitally-controlled 2-stage single-phase rectifier with power factor correction (PFC) that is well suited for emerging low-power applications requiring programmable supply voltage. The rectifier is a modification of a flyback-buck cascaded configuration where the intermediate energy storage capacitor is replaced by a non-symmetric capacitive divider with independent control of tap voltages. The voltages are dynamically controlled through a single secondary winding, such that the optimized efficiency and reduced size of the downstream stage are achieved without sacrificing dynamic response. Results obtained with a 30W universal-input experimental prototype confirm fast transient response during efficiency optimization, operation with a near unity power factor, and about a 50% reduction in the flyback capacitor value, as compared to single-stage solutions.
Pre-flashover luminosity along an alumina/vacuum interface (1994)

Two preflashover luminosity phases, one near the voltage peak (phase I) and the other just prior to the onset of voltage collapse (phase II), are found to be associated with the surface flashover of alumina in vacuum. The light emission is also observed under the no-breakdown condition (phase III). A new ancillary experiment, performed using three high-sensitivity photomultiplier tubes (two viewing the dielectric surface head-on and the other viewing edge-on) indicates that the plasma corresponding to phases I and III does not expand away from the insulator surface; whereas the plasma of phase II expands away from that surface. The observed results suggest qualitatively that the phases I and III may be attributed to a solid state process whilst the phase II may be a mixed response of both solid state and gaseous processes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MEASUREMENT OF ABDOMINAL FAT WITH MAGNETIC RESONANCE IMAGING (1990)

Lancaster, J. L. Ph.D; Ghiatas, A. A. M.D.; Kilcoyne, R. F. M.D.; Alyassin, A. M. B.S.; Bonora, E. M.D.; DeFronzo, R. A. M.D. Author Information
Automatic Identification of the Cardiac Rest Period Using Template Updating for Magnetic Resonance Coronary Angiography (2016)

The purpose of this study was to develop an automated method without user interaction for selecting the optimal data acquisition window in magnetic resonance coronary angiography (MRCA). The major problem in MRCA is the effective suppression of coronary motion resulting from respiration and cardiac contraction. To compensate for cardiac movement, data acquisition is generally limited to the period when the coronary artery is not moving, mainly during end-diastole, and is referred to as the cardiac rest period. Generally, the cardiac rest period is identi ed by the operator. Therefore, it is subjective and requires an experienced operator for accurate identi cation. As for the region of interest, the right coronary artery is known as an appropriate region for determining the cardiac rest period. Previous studies attempted to determine the position of coronary artery using template matching techniques or difference between the pixel intensities along frames of the cine images, but the detection accuracy of the cardiac rest period was not suf ciently high. In this study, we estimated the position of coronary artery using the mitral valve, tricuspid valve and the apex as known coordinates. Then, the position of the coronary artery was estimated with high accuracy using a template matching technique. In addition, we proposed a method to track the position of coronary artery in a cine image by updating the template to determine the cardiac rest period. As a result, automatic determination of the cardiac rest period was possible in 24 subjects.
Transient Polymers for Low-k Dielectrics and Decomposing Electronic Devices (2016)

Presented on September 16, 2016 at 12:00 p.m. in the Marcus Nanotechnology Building, room 1116.
P19-01. Pre-clinical immunogenicity of mosaic Asian AE/B HIV-1 DNA vaccine in mice (2009)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing (2009)

MicroRNAs (miRNA) are short single-stranded RNA molecules that regulate gene expression post-transcriptionally by binding to complementary sequences in the 3' untranslated region (3' UTR) of target mRNAs. MiRNAs participate in the regulation of myogenesis, and identification of the complete set of miRNAs expressed in muscles is likely to significantly increase our understanding of muscle growth and development. To determine the identity and abundance of miRNA in porcine skeletal muscle, we applied a deep sequencing approach. This allowed us to identify the sequences and relative expression levels of 212 annotated miRNA genes, thereby providing a thorough account of the miRNA transcriptome in porcine muscle tissue. The expression levels displayed a very large range, as reflected by the number of sequence reads, which varied from single counts for rare miRNAs to several million reads for the most abundant miRNAs. Moreover, we identified numerous examples of mature miRNAs that were derived from opposite sides of the same predicted precursor stem-loop structures, and also observed length and sequence heterogeneity at the 5' and 3' ends. Furthermore, KEGG pathway analysis suggested that highly expressed miRNAs are involved in skeletal muscle development and regeneration, signal transduction, cell-cell and cell-extracellular matrix communication and neural development and function.