gebhart/patrepeval huggingface dataset:
Using Hoechst 33342 to Target Radioactivity to the Cell Nucleus (2007)

We have explored the use of Hoechst 33342 (H33342) to carry radioactivity to the cell nucleus. H33342 enters cells and targets DNA at adenine-thymine-rich regions of the minor groove. Considerable membrane blebbing and ruffling occur in CHO cells within minutes after its addition to the culture medium in micromolar quantities. Blue vesicles are apparent in the cell cytoplasm, and by 30 min the nuclei are stained dark blue. Upon its binding to DNA, a visible emission shift of the dye can be observed with fluorescence microscopy. We have radioiodinated (125I) H33342 and specifically irradiated nuclear DNA by incubating CHO cells with 125I-H33342 at 37 degrees C and accumulating 125I decays at -90 degrees C. At various times, the cells are thawed and assayed for survival (clonogenicity) and DSB (gamma-H2AX) formation. 125I-H33342 decay leads to a monoexponential decrease in cell survival with a D0 of 122 125I decays per cell and a linear increase in DNA DSB induction (equivalent to 15 gamma-H2AX foci/cell). Cell death is not modified by the radioprotective effects of H33342 because we use considerably lower concentrations than those that provide a slight protection against gamma radiation. We conclude that cell killing by 125I-H33342 and the induction of gamma-H2AX foci are highly correlated.
Efficient Encoding of Quasi-Cyclic Low-Density Parity-Check Codes (2005)

Efficient Encoding of Quasi-Cyclic Low-Density Parity-Check Codes Quasi-cyclic (QC) low-density parity-check (LDPC) codes form an important subclass of LDPC codes. These codes have encoding advantage over other types of LDPC codes. This paper addresses the issue of efficient encoding of QC-LDPC codes. Two methods are presented to find the generator matrices of QC-LDPC codes in systematic-circulant form from their parity-check matrices given in circulant form. Based on the systematic-circulation form of the generator matrix of a QC-LDPC code, various types of encoding circuits using simple shift registers are devised. It is shown that the encoding complexity of a QC-LDPC code is linearly proportional to the number of parity bits of the code for serial encoding, and to the length of the code for high-speed parallel encoding.
Cloning of the RHO1 gene from Candida albicans and its regulation of beta-1,3-glucan synthesis (1997)

The Saccharomyces cerevisiae RHO1 gene encodes a low-molecular-weight GTPase. One of its recently identified functions is the regulation of beta-1,3-glucan synthase, which synthesizes the main component of the fungal cell wall (J. Drgonova et al., Science 272:277-279, 1996; T. Mazur and W. Baginsky, J. Biol. Chem. 271:14604-14609, 1996; and H. Qadota et al., Science 272:279-281, 1996). From the opportunistic pathogenic fungus Candida albicans, we cloned the RHO1 gene by the PCR and cross-hybridization methods. Sequence analysis revealed that the Candida RHO1 gene has a 597-nucleotide region which encodes a putative 22.0-kDa peptide. The deduced amino acid sequence predicts that Candida albicans Rho1p is 82.9% identical to Saccharomyces Rho1p and contains all the domains conserved among Rho-type GTPases from other organisms. The Candida albicans RHO1 gene could rescue a S. cerevisiae strain containing a rho1 deletion. Furthermore, recombinant Candida albicans Rho1p could reactivate the beta-1,3-glucan synthesis activities of both C. albicans and S. cerevisiae membranes in which endogenous Rho1p had been depleted by Tergitol NP-40-NaCl treatment. Candida albicans Rho1p was copurified with the beta-1,3-glucan synthase putative catalytic subunit, Candida albicans Gsc1p, by product entrapment. Candida albicans Rho1p was shown to interact directly with Candida albicans Gsc1p in a ligand overlay assay and a cross-linking study. These results indicate that Candida albicans Rho1p acts in the same manner as Saccharomyces cerevisiae Rho1p to regulate beta-1,3-glucan synthesis.
Data from NOTCH3 Signaling Pathway Plays Crucial Roles in the Proliferation of ErbB2-Negative Human Breast Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;ErbB2-negative breast tumors represent a significant therapeutic hurdle because of a lack of effective molecular targets. Although NOTCH proteins are known to be involved in mammary tumorigenesis, the functional significance of these proteins in ErbB2-negative breast tumors is not clear. In the present study, we examined the expression of activated NOTCH receptors in human breast cancer cell lines, including ErbB2-negative and ErbB2-positive cell lines. Activated NOTCH1 and NOTCH3 proteins generated by γ-secretase were detected in most of the cell lines tested, and both proteins activated CSL-mediated transcription. Down-regulation of NOTCH1 by RNA interference had little or no suppressive effect on the proliferation of either ErbB2-positive or ErbB2-negative cell lines. In contrast, down-regulation of NOTCH3 significantly suppressed proliferation and promoted apoptosis of the ErbB2-negative tumor cell lines. Down-regulation of NOTCH3 did not have a significant effect on the ErbB2-positive tumor cell lines. Down-regulation of CSL also suppressed the proliferation of ErbB2-negative breast tumor cell lines, indicating that the NOTCH-CSL signaling axis is involved in cell proliferation. Finally, &lt;i&gt;NOTCH3&lt;/i&gt; gene amplification was detected in a breast tumor cell line and one breast cancer tissue specimen even though the frequency of &lt;i&gt;NOTCH3&lt;/i&gt; gene amplification was low (&lt;1%). Taken together, these findings indicate that NOTCH3-mediated signaling rather than NOTCH1-mediated signaling plays an important role in the proliferation of ErbB2-negative breast tumor cells and that targeted suppression of this signaling pathway may be a promising strategy for the treatment of ErbB2-negative breast cancers. [Cancer Res 2008;68(6):1881–8]&lt;/p&gt;&lt;/div&gt;
Unknown input estimation for nonlinear descriptor systems via LMIs and Takagi-Sugeno models (2015)

This paper presents an unknown inputs observer for nonlinear descriptor systems. The approach uses the Takagi-Sugeno representation of the nonlinear model. In order to obtain strict linear matrix inequalities a novel observer structure is given. Thus the conditions can be efficiently solved via convex optimization techniques. A numerical example is provided to illustrate the performance of the proposed approach.
House Money Effects in Public Good Experiments (2002)

Abstract Are decisions in economics experiments distorted because the money subjects risk comes from the experimenter rather than their own pockets? There is some evidence that people receiving small, one time “windfall gains” have a higher marginal propensity to consume them, and when doing so, exhibit greater risk-seeking behaviour. This has been found in individual decision making experiments when anticipated wealth effects have been controlled, and labelled the “house money effect.” In public good experiments, house money effects could be driving the high levels of voluntary contributions commonly observed. This possibility is tested by comparing VCM contribution rates when subjects supply their own endowments with those when endowments are provided, while holding constant the distribution of promised earnings. No evidence of house money effects is found, suggesting that use of “free” initial money endowments does not distort subsequent contributions in VCM environments.
Global Expression Profiling and Physiological Characterization ofCorynebacterium glutamicumGrown in the Presence ofl-Valine (2003)

Addition of L-valine (50 to 200 mM) to glucose minimal medium had no effect on the growth of wild-type Corynebacterium glutamicum ATCC 13032 but inhibited the growth of the derived valine production strain VAL1 [13032 DeltailvA DeltapanBC(pJC1ilvBNCD)] in a concentration-dependent manner. In order to explore this strain-specific valine effect, genomewide expression profiling was performed using DNA microarrays, which showed that valine caused an increased ilvBN mRNA level in VAL1 but not in the wild type. This unexpected result was confirmed by an increased cellular level of the ilvB protein product, i.e., the large subunit of acetohydroxyacid synthase (AHAS), and by an increased AHAS activity of valine-treated VAL1 cells. The conclusion that valine caused the limitation of another branched-chain amino acid was confirmed by showing that high concentrations of L-isoleucine could relieve the valine effect on VAL1 whereas L-leucine had the same effect as valine. The valine-caused isoleucine limitation was supported by the finding that the inhibitory valine effect was linked to the ilvA deletion that results in isoleucine auxotrophy. Taken together, these results implied that the valine effect is caused by competition for uptake of isoleucine by the carrier BrnQ, which transports all branched-chained amino acids. Indeed, valine inhibition could also be relieved by supplementing VAL1 with the dipeptide isoleucyl-isoleucine, which is taken up by a dipeptide transport system rather than by BrnQ. Interestingly, addition of external valine stimulated valine production by VAL1. This effect is most probably due to a reduced carbon usage for biomass production and to the increased expression of ilvBN, indicating that AHAS activity may still be a limiting factor for valine production in the VAL1 strain.
ChemInform Abstract: Amino Acids. Part 14. Diastereoselective Addition of Benzenesulfenyl Chloride to 1‐Acryloylproline Esters. (1989)

Abstract (S)‐Proline esters such as (I) react with acryloyl chloride (II) to give the acryloylproline esters (III), the conformer ratios of which are determined by NMR and shown to diminish with the bulkiness of the ester group.
Characterization of leakage behaviors of high-k gate stacks by electron-beam-induced current (2008)

Microscopical investigation of leakage behaviors of Hf-based high-k gate stacks was achieved by means of electron-beam-induced current (EBIC) method. Carrier separated EBIC measurement has found that in non-stressed samples, hole conduction in pMOS is significantly enhanced by trap-assisted tunneling, while electron conduction in nMOS is independent of traps. The transport mechanisms of electron and holes in non-stressed high-k MOS capacitors were clarified. After stressing, positive charged traps are induced in nMOS and enhance electron conduction.
The role of cross‐reactive carbohydrate determinants in the diagnosis of occupational allergy (2010)

Cite this as: S. Quirce and G. Salcedo, Clinical &amp; Experimental Allergy, 2010 (40) 962–964.
Thermotropic Biaxial Nematic Liquid Crystals (2004)

We have synthesized liquid crystal (LC) mesogens based on a nonlinear oxadiazole unit that exhibit nematic phases near $200\text{ }\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$. Polarized microscopy and conoscopy indicate that these LCs are biaxial nematics. Unambiguous and quantitative evidence for biaxiality is achieved using $^{2}\mathrm{H}$ NMR spectroscopy. ``2D powder'' spectra, obtained by rotating $^{2}\mathrm{H}$-labeled samples about an axis perpendicular to the magnetic field at $\ensuremath{\sim}200\text{ }\text{ }\mathrm{Hz}$, yield phase biaxiality parameters of $\ensuremath{\sim}0.1$ when coupled with rigorous and proven simulations.
PROPOSAL FOR ROAD DAMAGE DATA SHARING SYSTEM USING THREE-DIMENSIONAL POINT CLOUD DATA (2023)

我が国の社会インフラ施設の多くは高度経済成長期に集中的に整備されたため，老朽化に伴う維持管理の需要増大が喫緊の課題であり，より効率的かつ戦略的な維持管理が求められている．従来の道路維持管理では，2次元データを用いた管理が主流である．しかし，橋梁や法面の詳細構造，点検箇所を把握しづらいことや，点検者と補修担当者が異なる場合や経験の浅い技術者の場合に現場の状況を正しく理解できないという課題がある．本研究では，維持管理業務の効率化およびデータの蓄積を目的として，道路の損傷を視覚表現に優れ情報共有が容易な3次元点群データとして計測して可視化し，これを損傷の概要とともに2次元地図上に可視化する情報システムを提案した．そして，実務者によるシステム評価を行い，その有用性と課題を示した．
Ambulatory Position and Orientation Tracking Fusing Magnetic and Inertial Sensing (2007)

This paper presents the design and testing of a portable magnetic system combined with miniature inertial sensors for ambulatory 6 degrees of freedom (DOF) human motion tracking. The magnetic system consists of three orthogonal coils, the source, fixed to the body and 3-D magnetic sensors, fixed to remote body segments, which measure the fields generated by the source. Based on the measured signals, a processor calculates the relative positions and orientations between source and sensor. Magnetic actuation requires a substantial amount of energy which limits the update rate with a set of batteries. Moreover, the magnetic field can easily be disturbed by ferromagnetic materials or other sources. Inertial sensors can be sampled at high rates, require only little energy and do not suffer from magnetic interferences. However, accelerometers and gyroscopes can only measure changes in position and orientation and suffer from integration drift. By combing measurements from both systems in a complementary Kalman filter structure, an optimal solution for position and orientation estimates is obtained. The magnetic system provides 6 DOF measurements at a relatively low update rate while the inertial sensors track the changes position and orientation in between the magnetic updates. The implemented system is tested against a lab-bound camera tracking system for several functional body movements. The accuracy was about 5 mm for position and 3 degrees for orientation measurements. Errors were higher during movements with high velocities due to relative movement between source and sensor within one cycle of magnetic actuation.
Nuclear karyopherin alpha-2 (KPNA2) expression predicts poor survival in patients with advanced breast cancer. (2008)

977 Purpose: Intensive lymph node involvement indicates poor prognosis in breast cancer patients. The significance of other molecular prognostic factors in this subgroup is unclear. Karyopherin alpha-2 (KPNA2) has been reported as an important factor of tumorgenesis and progression of breast cancer. The aim of the present study was to evaluate the impact of KPNA2 expression on prognosis of patients with high risk breast cancer (HRBC) and response to intensive chemotherapy within the randomized WSG-AM-01 trial.  Methods: KPNA2 nuclear expression (> 10% vs. 9 positive lymph nodes) randomized to tandem high dose vs. conventional dose-dense chemotherapy. Results were correlated with clinical outcome (median follow-up 63.3 months) by Kaplan-Meier and multivariate Cox regression analysis including molecular subtypes, determined by k-clustering (k=5).  Results: KPNA2 overexpression (n=74, 39%) significantly correlated with shorter event-free (EFS) and overall survival (OS) in both therapy arms by univariate analysis. Multivariate analysis showed that the overexpression of KPNA2 was an independent negative prognostic factor for overall survival (hazard ratio=1.89, 95% CI=1.06-3.35, p=0.03). This predictive value was independent of basal-like and HER2 subtypes, and was significantly associated with KPNA2 immunoreactivity.  Conclusion: Our data suggest the use of nuclear KPNA2 expression as novel prognostic marker in node-positive patients. KPNA2 expression may be also considered as a marker of global chemoresistance, which can not be overcome by conventional dose-modification of chemotherapy in HRBC patients.
Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation (2007)

The amphibian Xenopus provides a model organism for investigating microRNA expression during vertebrate embryogenesis and development. Searching available Xenopus genome databases using known human pre-miRNAs as query sequences, more than 300 genes encoding 142 Xenopus tropicalis miRNAs were identified. Analysis of Xenopus tropicalis miRNA genes revealed a predominate positioning within introns of protein-coding and nonprotein-coding RNA Pol II-transcribed genes. MiRNA genes were also located in pre-mRNA exons and positioned intergenically between known protein-coding genes. Many miRNA species were found in multiple locations and in more than one genomic context. MiRNA genes were also clustered throughout the genome, indicating the potential for the cotranscription and coordinate expression of miRNAs located in a given cluster. Northern blot analysis confirmed the expression of many identified miRNAs in both X. tropicalis and X. laevis. Comparison of X. tropicalis and X. laevis blots revealed comparable expression profiles, although several miRNAs exhibited species-specific expression in different tissues. More detailed analysis revealed that for some miRNAs, the tissue-specific expression profile of the pri-miRNA precursor was distinctly different from that of the mature miRNA profile. Differential miRNA precursor processing in both the nucleus and cytoplasm was implicated in the observed tissue-specific differences. These observations indicated that post-transcriptional processing plays an important role in regulating miRNA expression in the amphibian Xenopus.
Colloids engineering and filtration to enhance the sensitivity of paper-based biosensors B Biointerfaces (2011)

Paper-based biosensors represent a disruptive technology by providing instantaneous and low-cost diagnostics for health and environmental applications. The lack of sensitivity can be an obstacle for this technology to compete with traditional analytical instrumentations. Aiming to improve the sensitivity of a paper-based colorimetric biosensor, we have applied colloids engineering in combination with filtration to lower the paper substrate backgrounds and optimize the immobilization of bio-molecules on paper. A model system consisting of an enzyme, alkaline phosphatase (ALP), and an inorganic colloid, calcium carbonate (CC), flocculated by a cationic dimethylamino-ethyl-methacrylate polyacrylamide (CPAM), demonstrated that the optimized CC flocs are best for enhancing the detecting sensitivity of ALP. The CC floc structure on paper was optimized by modulating its structure in suspension. Subsequently, the filtration process and the wicking ability of paper enabled to freeze the deposited CC structure inherited from the suspension. The incorporation of biomolecules into the CC before immobilizing on paper through filtration provided not only a better microenvironment, but also a higher surface density of immobilized biomolecules. The ALP detection limit of 117fmol per zone (5mm circle) in the current study was fifty times lower than that of the common soaking method for biomolecule immobilization. The minimum amount of biomolecules per unit substrate area required for detection was lowered by over an order of magnitude, compared with spotting methods (i.e. inkjet printing). The improvement was also demonstrated by the steepest slope of standard curve, the lowest background, and the highest activity of the bioactive paper probed with the diluted BCIP/NBT liquid substrates.
CONTROL OF FAMILYWISE ERRORS IN MULTIPLE ENDPOINT ASSESSMENTS VIA STEPWISE PERMUTATION TESTS (1996)

We describe permutation based sequentially rejective multiple comparison procedures useful in multiple endpoint assessments. We used Monte Carlo methods to compare the power of these newly devised tests to that of tests due to Holm and Rom as well as to the classical Bonferroni method. We illustrate applications of the methods with analysis of visual field data collected from optic neuritis patients. We conclude that the new methods are particularly useful when there are many endpoints involved, the data are significantly correlated, and/or the distributional assumptions are questionable.
Quality in the combat: the QFD in support to design of tactics (2012)

Currently, the international public opinion condemns collateral damages incidents related with warlike activities. In this sense, the present work suggests the use of the Quality Function Deployment (QFD) method in the conception and development of tactics, with the intention to improve quality in the combat by minimizing the damages provoked by wars. To this end, initially, general considerations regarding the development of tactics, QFD and morphological matrix are described, followed by the examination of the proposal under the focus of the productivity frontier. In conclusion, the QFD current application is helpful to improve the tactics involved, equipment selection and to put into practice the perceived procedures to minimize collateral damages, offering better quality to combat actions.
AB037. P-05. Evaluation of infrared spectral signature associated with pathology as biomarker for cancer progression in cholangiocarcinoma (2019)

Background: Cholangiocarcinoma (CCA) is a cancer of the bile duct epithelium and remains an important public health problem in Southeast Asia, with a particularly in Northeast Thailand due to its high incidence and high fatality rates. The highest prevalence of Opisthorchis viverrini (OV) related CCA found in northeast Thailand. The disease is difficult to early diagnose and is usually fatal because patients usually come to the physician at the advance stage and the effective non-surgical therapy is not currently available. In this study, we aim to focus on periductal fibrosis and bile duct cells initiated into cancer development, which are characterized by Fourier transform infrared (FTIR) microspectroscopy giving specific spectra corresponding to biomarkers as an early diagnosis of CCA. Methods: Here the liver tissue sections from the OV-infected hamster to induce tumor were performed. FTIR spectral changes were monitored in a time dependent manner during 6 months of tumor induction under the parameters of analysis using 64 co-added scans at 10 µm × 10 µm aperture size with 4 cm−1 spectral resolution. Following spectral preprocessing, infrared spectra were interrogated with principal component analysis (PCA). Moreover, the histochemical staining for fibrosis and bile duct epithelium of hamster tissues were stained by serious red and CK19, respectively. Results: Firstly, the result provided the discrimination of periductal fibrosis and bile duct cells in the circumstance. From PCA, the major infrared (IR) peaks of periductal fibrosis showed signature spectra at amide I (1,648 to 1,645 cm−1: beta-sheet form); CH3 asymmetric methyl deformation (1,454 cm−1) collagen III (1,338 cm−1) and collagen triplet (1,282, 1,235 and 1,201 cm−1). Secondly, the discrimination of pre-cancerous (1 month) and cancer cholangiocytes (over 2 months) after OV-infection had been classified by definite specific vibrational bands of biomolecules. Characteristic spectral changes included increase intensity of a band from phosphate groups (1,080 cm−1) and C=O carboxylic esters (1,735 cm−1) in cancer cells. Conclusions: This information implies that FTIR microspectroscopy is the potential tool to provide a spectral signature of biochemical components acting as a molecular probe of sample composition in the detection and diagnosis of a disease including CCA.