gebhart/patrepeval huggingface dataset:
Automatic and Reproducible Positioning of Phase-Contrast MRI for the Quantification of Global Cerebral Blood Flow (2014)

Phase-Contrast MRI (PC-MRI) is a noninvasive technique to measure blood flow. In particular, global but highly quantitative cerebral blood flow (CBF) measurement using PC-MRI complements several other CBF mapping methods such as arterial spin labeling and dynamic susceptibility contrast MRI by providing a calibration factor. The ability to estimate blood supply in physiological units also lays a foundation for assessment of brain metabolic rate. However, a major obstacle before wider applications of this method is that the slice positioning of the scan, ideally placed perpendicular to the feeding arteries, requires considerable expertise and can present a burden to the operator. In the present work, we proposed that the majority of PC-MRI scans can be positioned using an automatic algorithm, leaving only a small fraction of arteries requiring manual positioning. We implemented and evaluated an algorithm for this purpose based on feature extraction of a survey angiogram, which is of minimal operator dependence. In a comparative test-retest study with 7 subjects, the blood flow measurement using this algorithm showed an inter-session coefficient of variation (CoV) of 4.07 ± 3.03%. The Bland-Altman method showed that the automatic method differs from the manual method by between -8% and 11%, for 95% of the CBF measurements. This is comparable to the variance in CBF measurement using manually-positioned PC MRI alone. In a further application of this algorithm to 157 consecutive subjects from typical clinical cohorts, the algorithm provided successful positioning in 89.7% of the arteries. In 79.6% of the subjects, all four arteries could be planned using the algorithm. Chi-square tests of independence showed that the success rate was not dependent on the age or gender, but the patients showed a trend of lower success rate (p = 0.14) compared to healthy controls. In conclusion, this automatic positioning algorithm could improve the application of PC-MRI in CBF quantification.
A Practical, Precise Method for Frequency Tracking and Phasor Estimation (2004)

Comprehensive analysis of discrete Fourier transform (DFT) error is given in this paper, including why it is accurate when used in the case of synchronous sampling and how error rises when sampling frequency does not synchronized to signal frequency. Simple but precise expressions of phase angle error and amplitude error are given. Practical formulas to calculate the true phase angle and amplitude are presented. The formulas are very simple and precise. Based on the formula to calculate true phase angle, a new frequency tracking method is developed. The proposed method can be calculated recursively. And, with notable accuracy improvement, the calculation burden is little more than the traditional DFT method. Also, an adaptive method to suppress the effect of harmonics is presented, which adds very little calculation burden with satisfying performance. The most distinguished feature of the proposed method is that it is not only precise, but also simple. Some examples are given to demonstrate the feasibility, precision, simpleness and robustness of the proposed method.
New Chemical Processing Technique Deposits Good Quality TiN Thin Films for Microelectronic Applications (1992)

"New Chemical Processing Technique Deposits Good Quality TiN Thin Films for Microelectronic Applications." Materials and Processing Report, 7(5), pp. 5–6
A fast method for large‐scale <i>De Novo</i> peptide and miniprotein structure prediction (2009)

Although peptides have many biological and biomedical implications, an accurate method predicting their equilibrium structural ensembles from amino acid sequences and suitable for large-scale experiments is still missing. We introduce a new approach-PEP-FOLD-to the de novo prediction of peptides and miniproteins. It first predicts, in the terms of a Hidden Markov Model-derived structural alphabet, a limited number of local conformations at each position of the structure. It then performs their assembly using a greedy procedure driven by a coarse-grained energy score. On a benchmark of 52 peptides with 9-23 amino acids, PEP-FOLD generates lowest-energy conformations within 2.8 and 2.3 A Calpha root-mean-square deviation from the full nuclear magnetic resonance structures (NMR) and the NMR rigid cores, respectively, outperforming previous approaches. For 13 miniproteins with 27-49 amino acids, PEP-FOLD reaches an accuracy of 3.6 and 4.6 A Calpha root-mean-square deviation for the most-native and lowest-energy conformations, using the nonflexible regions identified by NMR. PEP-FOLD simulations are fast-a few minutes only-opening therefore, the door to in silico large-scale rational design of new bioactive peptides and miniproteins.
Si CMOS platform for quantum information processing (2016)

We report the first quantum bit (qubit) device implemented on a foundry-compatible Si CMOS platform. The device, fabricated using SOI NanoWire MOSFET technology, is in essence a compact two-gate pFET. The qubit is encoded in the spin degree of freedom of a hole Quantum Dot (QD) defined by one of the Gates. Coherent spin manipulation is performed by means of an RF E-Field signal applied to the Gate itself. By demonstrating qubit functionality in a conventional transistor-like layout and process flow, this result bears relevance for the future up-scaling of qubit architectures, including the opportunity of their co-integration with “classical” Si CMOS control circuitry.
Activity monitoring from real-time triaxial accelerometer data using sensor network (2007)

With the advancement in the wireless sensor network technologies, it is possible to use them for health monitoring from remote location. The monitoring of human movement can provide valuable information about individual’s daily activities. Wireless sensor Node with 3-axes accelerometer were used to monitor daily activities i.e. walking, running, resting and dangerous activities such as falling. Three axes MEMS accelerometer measure body’s acceleration and transmit acceleration data to the base station attached to PC. On the PC the real time accelerometer data is processed and various inferences like walking, running and falling, are taken accordingly. This paper presents the methodologies and parameters used for chest case worn sensor as well as for wrist worn sensor and compare them. The paper also presents various design aspects of real time data acquistion from accelerometer sensor attached to sensor node. Firmware for sensor unit is developed in nesC which use tinyos as a platform. Results shows chest is better position to activity monitoring and fall detection. In total 16 experiments for chest, fall is detected in 13 with an accuracy of 81%.
Principles of Polymerization Engineering (1983)

Fundamentals. Reaction Phenomena. Mixing Effects. Thermal Effects. Flow Phenomena. Polymer Devolatilization. Appendixes. Index.
Abstract 76: MicroRNA-144 Regulates Hepatic ABCA1 and Plasma HDL Following Activation of the Nuclear Receptor FXR (2013)

Rationale The bile acid receptor Farnesoid-X-Receptor (FXR) regulates many aspects of lipid metabolism by various complex and not fully understood molecular mechanisms. We set out to investigate the molecular mechanisms for FXR-dependent regulation of lipid and lipoprotein metabolism. Objective To identify FXR-regulated microRNAs that were subsequently involved in regulating lipid metabolism. Methods and Results ATP binding cassette transporter A1 (ABCA1) is a major determinant of plasma High Density Lipoprotein (HDL)-cholesterol levels. Here we show that activation of the nuclear receptor FXR in vivo increases hepatic levels of miR-144, which in turn lower hepatic ABCA1 and plasma HDL levels. We identified two complementary sequences to miR-144 in the 3’ untranslated region (UTR) of ABCA1 mRNA that are necessary for miR-144-dependent regulation. Overexpression of miR-144 in vitro decreased both cellular ABCA1 protein and cholesterol efflux to lipid-poor apolipoprotein A-I (ApoA-I) protein, whilst overexpression in vivo reduced hepatic ABCA1 protein and plasma HDL- cholesterol. Conversely, silencing miR-144 in mice increased hepatic ABCA1 protein and HDL- cholesterol. In addition, we utilized tissue-specific FXR deficient mice to show that induction of miR-144 and FXR-dependent hypolipidemia requires hepatic, but not intestinal FXR. Finally, we identified functional FXR response elements (FXREs) upstream of the miR-144 locus, consistent with direct FXR regulation. Conclusion In conclusion, we have identified a pathway involving FXR, miR-144 and ABCA1 that together regulate plasma HDL cholesterol. This pathway may be therapeutically targeted in the future in order to increase HDL levels.
Diagnosing Medium Voltage GIS Circuit Breaker by Observing Trip Coil Current with Simulation and Actual Tests (2008)

Abstract A few metal clad switchgear (MCSG) trip failures were found in the past two decades and the main causes were found related to the characteristics of operation mechanism. Meanwhile, the characteristics of circuit breaker operation mechanism are related to its trip coil current. Mechanical model and electrical model for trip mechanism of circuit breaker of 23-kV GIS are proposed in this article. Trip coil current with different resist force and shaft gap are simulated with MATLAB. One medium voltage GIS trip coil current under different conditions are measured to make a comparison with computer simulation results. Finally, current patterns are proposed as quick reference data for diagnosing operation mechanism failure.
High-Throughput Screen for Inhibitors of Transglycosylase and/or Transpeptidase Activities of <i>Escherichia coli</i> Penicillin Binding Protein 1b (2003)

Penicillin binding protein (PBP) 1b of Escherichia coli has both transglycosylase and transpeptidase activities, which are attractive targets for the discovery of new antibacterial agents. A high-throughput assay that detects inhibitors of the PBPs was described previously, but it cannot distinguish them from inhibitors of the MraY, MurG, and lipid pyrophosphorylase. We report on a method that distinguishes inhibitors of both activities of the PBPs from those of the other three enzymes. Radioactive peptidoglycan was synthesized by using E. coli membranes. Following termination of the reaction the products were analyzed in three ways. Wheat germ agglutinin (WGA)-coated scintillation proximity assay (SPA) beads were added to one set, and the same beads together with a detergent were added to a second set. Type A polyethylenimine-coated WGA-coated SPA beads were added to a third set. By comparison of the results of assays run in parallel under the first two conditions, inhibitors of the transpeptidase and transglycosylase could be distinguished from inhibitors of the other enzymes, as the inhibitors of the other enzymes showed similar inhibitory concentrations (IC(50)s) under both conditions but the inhibitors of the PBPs showed insignificant inhibition in the absence of detergent. Furthermore, comparison of the results of assays run under conditions two and three enabled the distinction of transpeptidase inhibitors. Penicillin and other beta-lactams showed insignificant inhibition with type A beads compared with that shown with WGA-coated SPA beads plus detergent. However, inhibitors of the other four enzymes (tunicamycin, nisin, bacitracin, and moenomycin) showed similar IC(50)s under both conditions. We show that the main PBP being measured under these conditions is PBP 1b. This screen can be used to find novel transglycosylase or transpeptidase inhibitors.
Urokinase binding and receptor identification in cultured endothelial cells. (1991)

Recombinant human single-chain urokinase (rscu-PA), two-chain urokinase (tcu-PA), and diisopropyl-fluorophosphate-treated tcu-PA (DFP-tcu-PA) bound to cultured human and porcine endothelial cells in a rapid, saturable, dose-dependent and reversible manner. Analysis of specific binding results in cultured human umbilical vein endothelial cells (HUVECs) gave the following estimated values for Kd and Bmax: 0.57 +/- 0.08 nM (mean +/- S.E.) and 188,000 +/- 18,000 sites/cell for 125I-labeled rscu-PA; 0.54 +/- 0.10 nM and 132,000 +/- 23,900 sites/cells for 125I-labeled tcu-PA; 0.89 +/- 0.14 nM and 143,000 +/- 30,300 sites/cell for 125I-labeled DFP-tcu-PA, respectively. Values for Kd were similar for primary and subcultured (six passages) HUVECs, but Bmax values were lower in subcultured HUVECs. Similar Kd values were found in cultured porcine endothelial cells; however, Bmax values varied depending on the endothelial cell type. All 125I-labeled urokinase forms yielded similar cross-linked approximately 110-kDa ligand-receptor complexes with cultured HUVECs, and 125I-labeled DFP-tcu-PA bound to a single major approximately 55-kDa protein in whole-cell lysates (ligand blotting/autoradiography), suggesting the presence of a single major approximately 55-kDa urokinase receptor in cultured HUVECs. The approximately 55-kDa urokinase receptor, isolated from several separate batches of cultured HUVECs (3-5 micrograms of protein, approximately 1 x 10(9) cells), by ligand affinity chromatography, exhibited the following properties: retained biologic activity as evidenced by its ability to bind 125I-labeled rscu-PA by ligand blotting/autoradiography and formation of a cross-linked 125I-labeled approximately 110-kDa rscu-PA-receptor complex; single-chain approximately 55-kDa protein, following reduction; complete conversion to and formation of a single major deglycosylated approximately 35-kDa protein, following treatment with N-glycanase.
Synthesis of regiospecifically substituted 2-hydroxybenzocyclobutenones (1997)

Regiospecifically substituted 2-hydroxybenzocyclobutenones were synthesized from the corresponding TBS protected 2-bromo-mandelate esters via halogen–metal exchange, cyclization, and subsequent deprotection. Keywords: 2-hydroxybenzocyclobutenones, halogen–metal exchange, benzocyclobutenediones, 2-bromomandelate esters.
The Developments and Challenges in OLED,Flexible and See-through Display Technologies,and Organic Luminescent Materials (2009)

OLED has attracting increasing attentions and regards for its potential advantages in future display.Future displays are supposed to be flexible and see-through.In this paper,developments in above-mentioned display technologies were briefly summarized.Also,the current level and challenges were analyzed.Organic luminescent materials play fundamental role in the developments of these technologies.Organic luminescent materials still suffer from low carrier mobility and low operational stability,which hamper their application in display technology.
The TGF- β Family Member Growth Differentiation Factor 15 (GDF15) Regulates the Self-Renewal of Multiple Myeloma Cancer Stem Cells (2011)

Abstract Abstract 2954 Multiple myeloma (MM) cancer stem cells (CSCs) possess both enhanced tumorigenic potential and relative drug resistance suggesting they play a major role in disease relapse and progression. Therefore, a better understanding of the processes regulating MM CSCs may lead to the development of novel therapies that prevent tumor regrowth and improve long-term outcomes. Normal stem cells are tightly regulated by factors within the local microenvironment that include both soluble factors and direct contact with accessory cells. However, external factors regulating MM CSCs have not been identified. Recent studies have demonstrated that stromal cells in the MM bone marrow microenvironment secrete growth differentiation factor 15 (GDF15), a member of the TGF-b family. We initially studied the role of this cytokine in the pathogenesis of MM by examining circulating GDF15 levels in MM patients. Compared to healthy volunteers, we found that median GDF15 levels were significantly increased in MM patients (821 vs. 390 pg/ml; n=16; p<0.05) and increased with disease stage (Stage II=585 pg/ml, Stage III=1, 004 pg/ml). To examine the functional effects of GDF15 on MM cells, we cultured human MM cell lines (NCI-H929, RPMI 8226) with recombinant GDF15 and found that it induced the expansion of isolated CD138neg MM CSCs in a dose-dependent manner but had little impact on the growth of CD138+ plasma cells (Fig). Furthermore, GDF15 enhanced clonogenic myeloma growth as evidenced by increased colony formation that was maintained during serial replating, a surrogate for self-renewal. This effect appeared to be GDF15 specific since it could be blocked using anti-GDF15 antibody. Similarly, GDF15 treatment increased the in vitro clonogenic growth of MM CSCs from primary clinical bone marrow specimens. We also investigated the down-stream cellular pathways potentially mediating the effects of GDF15 and found that it activates the AKT signaling pathway known to improve the self-renewal of embryonic (ES) and normal hematopoietic stem cells. GDF15 also induced expression of the SOX2 transcription factor known to be upregulated in CD138neg MM CSCs. Since SOX2 is required for the self-renewal of ES cells and the generation of induced pluripotent stem (iPS) cells, its induction by GDF15 may also increase the self-renewal of MM CSCs. GDF15 is the first soluble factor identified that regulates MM CSCs, and its effects are mediated by the activation of highly conserved self-renewal programs. Disclosures: No relevant conflicts of interest to declare.
Monoclonal Antibody Against the Lupus Antigen Sm Cross-Reacts with RNA Polymerase I (1989)

Monoclonal anti-Sm antibody, a specificity directed against a constituent of nuclear ribonucleoprotein and considered to be a marker for systemic lupus erythematosus (SLE), was tested for its ability to react with four other rheumatic disease antigens of known enzymatic activity. No binding of the antibody was observed in radioimmunoassays with immobilized protein kinase NII, poly(A) polymerase, or topoisomerase I. In contrast, anti-Sm antibody did react with RNA polymerase I. Under conditions of antibody excess, anti-Sm was determined to bind RNA polymerase I on an equimolar basis, indicating that the polymerase possesses a single epitope recognized by the anti-Sm antibody. Addition of the anti-Sm antibody to in vitro transcription reactions resulted in inhibition of RNA polymerase I activity but had no effect on the reaction catalyzed by RNA polymerase II. When the subunits of RNA polymerase I were separated by polyacrylamide gel electrophoresis under denaturing conditions and incorporated individually into the radioimmunoassay, anti-Sm antibody bound only to the sixth polymerase polypeptide (Mr, 21,000). These data establish an immunological relationship between two important rheumatic disease antigens and help explain the apparent diversity of the autoimmune response in murine and human SLE.
Effects of salts, solvents, and substituents on the reaction of cellulose with epoxy compounds (1976)

Abstract Effects of salts, solvents, and substituents on the reaction of cellulose with epoxy compounds were re‐investigated and compared with the published data. The salt effect could be described mainly by the electronegativity or the acidity of the cations, and also by the nucleophilicity or the basicity of the anions. The variation of the reaction with solvents for epoxy compounds could be explained by the solubility parameter of the solvents. The substituent effect of the epoxy compounds on this addition reaction was elucidated by the modified Taft's equation, (log k −log k 0 )/σ * =( Q p – Q s E s )/σ * . The mechanism for the reaction was discussed in the light of the reinvestigated phenomena.
Respiratory resistance with histamine challenge by single-breath and forced oscillation methods (1986)

Relaxed expirations were obtained from five anesthetized dogs under control conditions and during various rates of intravenous infusion of histamine. All volume vs. time curves obtained from 20 ms to 2 s after the start of expiration were poorly described by a single exponential function but were fitted very well by a biexponential function. The resistance of the respiratory system as a function of frequency from 2 to 26 Hz was also determined by the forced oscillation method in the same dogs. Three two-compartment models of the respiratory system were identified from the exponentials fitted to the relaxed expiration data, and the one that had the most plausible parameter values under control conditions consisted of a homogeneous lung compartment connected to a viscoelastic compartment. Although a two-compartment model is arguably appropriate for describing relaxed expirations in normal dogs, physiological considerations suggest that there should be more than two interacting components with histamine infusion. We cannot identify all these components from our data, however. The equivalent complex impedance of the respiratory system was also calculated from the biexponential curves and showed significant variation in resistance over the frequency range from 0 to 2 Hz and negligible variation above 2 Hz. The calculated resistances at 2 Hz were consistently higher than those obtained by the forced oscillation method, which may be due to the nonlinear behavior of the respiratory system during relaxed expiration. We conclude that the single-breath and forced oscillation methods should be viewed as providing complimentary information about respiratory resistance.
Frontiers in Glycomics; Bioinformatics and Biomarkers in Disease September 11‐13, 2006 Natcher Conference Center, NIH Campus, Bethesda, MD, USA (2007)

This is a short summary of a meeting entitled "The Frontiers in Glycomics; Bioinformatics and Biomarkers in Disease" which was jointly organized by the NIH Consortium for Functional Glycomics (CFG), Human Disease Glycomics/Proteome Initiative (HGPI), National Cancer Institute, National Institute of General Medical Sciences, Japan Society for the Promotion of Science and National Center for Research Resources held at the NIH Campus, Bethesda, MD, Natcher Conference Center in September 11-13, 2006.
Functional analysis of the<i>Bacillus subtilis cysK</i>and<i>cysJI</i>genes (2001)

The function of the Bacillus subtilis cysK and cysJI (previously designated yvgQR) genes, expected to be involved in the assimilatory sulfate reduction pathway, was investigated. A B. subtilis mutant with a deletion in the cysJI genes was unable to use sulfate or sulfite as sulfur source, which confirmed that these genes encode sulfite reductase. A mutant with a transposon insertion in the cysK gene, whose deduced protein sequence showed similarity to cysteine synthases, grew poorly on sulfate and butanesulfonate. A strain in which cysK and yrhA, a cysK paralog, were inactivated was unable to grow with sulfate. Whereas expression of the cysJI genes was induced by sulfate, expression of cysK was repressed both by sulfate and by cysteine.