gebhart/patrepeval huggingface dataset:
Alignment of DNA sequences (2004)

Sequence alignment is one of the most important operations in computational\nbiology. Alignment of two sequences shows how similar the two sequences are, where there are differences between them, and the correspondence between similar subsequences. All of these represent important information for biologists. For this reason, seeking an effective method for aligning genomic DNA is the major goal of this dissertation.
150 mA LDO with self-adjusting frequency compensation scheme (2011)

A low-drop-out regulator with dynamic biased buffers for self-adjusting frequency compensation is presented. The proposed buffer, based on gm-boost elements, keeps the second pole beyond the unity-gain frequency of the loop by dynamically changing its bias current according to the load condition. The LDO has a quiescent current of 23 µA and is able to deliver 150 mA load current. With wide loop bandwidth and adequate phase margin, improved transient response with 38 mV output variation is achieved under a 0–100 mA load current switching test.
Overexpression of the pseudoautosomal gene MIC2 in Ewing's sarcoma and peripheral primitive neuroectodermal tumor. (1990)

Ewing's Sarcoma (ES), the second most frequent bone tumor in childhood and adolescence, and the probably closely related peripheral primitive neuroectodermal tumor (pPNET) share a unique cytogenetic translocation between chromosomes 11 and 22. Both of them expose high amounts of a glycoprotein on their cell surface, which can be specifically detected by the mAb HBA-71. The cDNA coding for the HBA-71 antigen was isolated by screening a cDNA expression library constructed from a pPNET-derived cell line. Nucleotide sequencing revealed the HBA-71 antigen to be the product of the pseudoautosomal gene MIC2 previously identified by the mAb 12E7 in haematopoietic cells. This antigen is a glycoprotein with a molecular weight of about 29,000 and is expressed in low amounts in most human cell lines and probably normal tissues and tumors with only a few exceptions. In T-cells the antigen is involved in cell adhesion processes. In ES- and pPNET-derived cell lines MIC2 expression is significantly enhanced. No gross changes in posttranslational modification could be observed. The high expression results in easy and specific detection of the antigen in immunocytochemical analysis of paraffin embedded tissue sections making HBA-71 a useful tool in tumor diagnosis.
Realization of efficient quantum gates with a superconducting qubit-qutrit circuit (2019)

Building a quantum computer is a daunting challenge since it requires good control but also good isolation from the environment to minimize decoherence. It is therefore important to realize quantum gates efficiently, using as few operations as possible, to reduce the amount of required control and operation time and thus improve the quantum state coherence. Here we propose a superconducting circuit for implementing a tunable system consisting of a qutrit coupled to two qubits. This system can efficiently accomplish various quantum information tasks, including generation of entanglement of the two qubits and conditional three-qubit quantum gates, such as the Toffoli and Fredkin gates. Furthermore, the system realizes a conditional geometric gate which may be used for holonomic (non-adiabatic) quantum computing. The efficiency, robustness and universality of the presented circuit makes it a promising candidate to serve as a building block for larger networks capable of performing involved quantum computational tasks.
THE ALLERGIC LOAD (1953)

INSPIRED by the reports and teachings of Hansel and others in recent years, an ever-increasing number of otolaryngologists have incorporated into their practices the treatment of allergic diseases of the ears, nose, and throat. Many of these men have retained their original enthusiasm, but some have become dissatisfied with their results and have abandoned allergic therapy entirely. Undoubtedly, one important reason for this unfortunate development was a failure to realize that good allergic management demands a consideration of the patient as a whole. Another major reason may be that, in their preoccupation with the antigen-antibody relationship, they failed to take into consideration some of the other factors which may greatly influence or modify the allergic reaction. Therefore, it seemed to us that a discussion of the concept of the "allergic load" might be of value at this time. While this concept may not satisfy all scientific requirements, it will provide
Trauma score (1981)

The Trauma Score (TS), a simple physiological measure of injury severity, is presented as a modification of the previously reported Triage Index by consensus physician peer review. Performance of the Trauma Score is presented as an index of injury severity both alone and in combination with an anatomic index of injury severity, the Injury Severity Score (ISS) and patient age. The application of these tools for field triage and evaluation of care of the trauma victim is proposed.
Error-Correcting Codes and Invariant Theory: New Applications of a Nineteenth-Century Technique (1977)

An unfashionable nineteenth century technique, invariant theory, has recently been used to study error-correcting codes. This technique is potentially of much wider application, is very powerful, often produces startling results, and (not least) is fun to use.
Photoelectrochemical Water Splitting (2013)

1 The Potential Contribution of Photoelectrochemistry in the Global Energy Future 2 Kinetics and Mechanisms of Light-Driven Reactions at Semiconductor Electrodes: Principles and Techniques 3: Structured Materuals for Photoelectrochemical Water Splitting 4: Tandem Photoelectrochemical Cells for Water Splitting 5: Particulate Oxynitrides for Photocatalytic Water Splitting under Visible Light 6: Rapid Screening Methods in the Discovery and Investigation of New Photocatalyst Compositions 7: Oxygen Evolution and Reduction Catalysts: Structural and Electronic Aspects of Transition Metal Based Compounds and Composites 8: The Group II-Nitride Materials Class: from Preparation to Perspectives in Photoelectrocatalysis 9: Epitaxial III-V Thin Film Absorbers: Preparation, Efficient InP Photocathodes and Routes to High Efficiency Tandem Structures 10: Photoelectrochemical Water Splitting: A First Principles Approach 11: Electro- and Photocatalytic Reduction of CO2: The Homogeneous and Hetereogeneous Worlds Collide? 12: Key Intermediates in the Hydrogenation and Electrochemical Reduction of CO2 13: Novel Approaches to Water Splitting by Solar Photons 14: Light Harvesting Strategies Inspired by Nature 15: Electronic Structure and Bonding of Water at Surfaces 16: New Perspectives and a Review of Progress
Interleukin 12 and Th1 responses in inflammatory bowel disease (1998)

Immune phenomena are believed to play a key role in the pathogenesis of tissue damage in Crohn’s disease and ulcerative colitis.1 2 Although some of the immunological perturbations seem to be shared by Crohn’s disease and ulcerative colitis, there are important distinguishing features, possibly reflecting different pathways of immune mediated intestinal inflammation. Evidence indicates that macrophage and T cell derived cytokines play a key role in the amplification and perpetuation of the inflammatory response in both disorders.3 No aberrant cytokine secretion has been documented in inflammatory bowel disease (IBD) and no convincing evidence has as yet been provided that cytokine changes occur as a result of disease specific immune activation. However, a number of quantitative changes in the secretion and/or activity of both proinflammatory and regulatory cytokines have been reported in Crohn’s disease and ulcerative colitis. Based on variation in the magnitude of these changes there seem to be different cytokine profiles into which the inflammatory process may fall during the course of the disease. Studies from murine models indicate that two T lymphocyte subsets may be defined depending on their cytokine secretion profiles: Th1 lymphocytes producing interleukin (IL) 2 and interferon γ (IFN-γ), and Th2 lymphocytes producing IL-4, IL-5 and IL-10. When taken together all available data from both …
Infrared and Raman study of interlayer anions CO<sub>3</sub><sup>2−</sup>, NO<sub>3</sub><sup>−</sup>, SO<sub>4</sub><sup>2−</sup>and ClO<sub>4</sub><sup>−</sup>in Mg/Al-hydrotalcite (2002)

The difference in the local environment of CO32-, NO3-, SO42-, and ClO4- in Mg/Al-hydrotalcite compared to the free anions was studied by infrared and Raman spectroscopy. In comparison to free CO32- a shift toward lower wavenumbers was observed. A band around 3000-3200 cm-1 has been attributed to the bridging mode H2O-CO32-. The IR spectrum of CO3- hydrotalcite clearly shows the split ν3 band around 1365 and 1400 cm-1 together with weak ν2 and ν4 modes around 870 and 667 cm-1. The ν1 mode is activated and observed as a weak band around 1012 cm-1. The Raman spectrum shows a strong ν1 band at 1053 cm-1 plus weak ν3 and ν4 modes around 1403 and 695 cm-1. The symmetry of the carbonate anions is lowered from D3h to C2s resulting in activation of the IR inactive ν1 mode around 1050-1060 cm-1. In addition, the ν3 shows a splitting of 30-60 cm-1. Although NO0 hydrotalcite has incorporated some CO32- the IR shows a strong ν3 mode at 1360 cm-1 with a weak band at 827 cm-1, and the ν4 band is observed at 667 cm-1, although it is largely obscured by the hydrotalcite lattice modes. The Raman spectrum shows a strong ν1 mode at 1044 cm-1 with a weaker ν4 band at 712 cm-1. The ν3 mode at 1355 cm-1 is obscured by a broad band due to the presence of CO32-. The symmetry of NO3- did not change when incorporated in hydrotalcite. The IR spectrum of SO4-hydrotalcite shows a strong ν3 at 1126, ν4 at 614 and a weak v1 mode at 981 cm-1. The Raman spectrum is characterized by a strong ν1 mode at 982 cm-1 plus medium ν2 and ν4 bands at 453 and 611 cm-1; ν3 cannot be identified as a separate band, although a broad band can be seen around 1134 cm-1. The site symmetry of SO42- is lowered from Td to C2ν. The distortion of ClO4- in the interlayer of hydrotalcite is reflected in the IR spectrum with both ν3 and ν4 bands split around 1096 and 1145 cm-1 and 626 and 635 cm-1, respectively. A weak ν1 band is observed at 935 cm-1. The Raman spectrum shows a strong ν1 mode at 936 cm-1 plus ν2 and ν4 bands at 461 and 626 cm-1, respectively. A ν3 mode cannot be clearly recognized, but a broad band is visible around 1110 cm-1. These data indicative a lowering of symmetry from Td to Cs.
Targeting Intracellular Oncoproteins with Antibody Therapy or Vaccination (2011)

Antibody-based therapies have better specificity and thus improved efficacy over standard chemotherapy regimens, which result in extended survival and improved quality of life for cancer patients. Because antibodies are viewed as too large to access intracellular locations, antibody therapy has traditionally targeted extracellular or secreted proteins expressed by cancer cells. However, many oncogenic proteins are found within the cell (such as intracellular phosphatases/kinases and transcription factors) and have therefore not been pursued for antibody therapies. Here, we explored the possibility of antibody therapy or vaccination against intracellular proteins. As proofs of concept, we selected three representative intracellular proteins as immunogens for tumor vaccine studies: PRL-3 (phosphatase of regenerating liver 3), a cancer-associated phosphatase; EGFP (enhanced green fluorescent protein), a general reporter; and mT (polyomavirus middle T), the polyomavirus middle T oncoprotein. A variety of tumors that expressed these intracellular proteins were clearly inhibited by their respective exogenous antibodies or by antigen-induced host antibodies (vaccination). These anticancer activities were reproducibly observed in hundreds of C57BL/6 tumor-bearing mice and MMTV-PymT transgenic breast tumor mice. Our in vivo data suggest that immunotherapies can target not only extracellular but also intracellular oncoproteins.
Safety and efficacy of intravitreal anti-VEGF injections for age-related macular degeneration (2009)

Review of current literature suggests that intravitreal antivascular endothelial growth factor agents are generally a safe and effective treatment for neovascular AMD for up to 2-3 years. Presently, there is level I evidence to substantiate this conclusion for pegaptanib and ranibizumab, but not bevacizumab.
Modulation of Schottky barrier height for NiSi/Si(110) diodes using an antimony interlayer (2011)

The barrier height modulation of Ni-silicided Schottky contacts fabricated on n-Si(100), n-Si(110), p-Si(100) and p-Si(110) substrate using an antimony (Sb) interlayer was investigated. The Sb layer was directly sputter-deposited on Si substrate followed by the regular Ni deposition and rapid thermal annealing. It is revealed that NiSi can still form even with the Sb interlayer and the effective Schottky barrier height can be significantly modulated on all kinds of Si substrates.
Depth-dependency of bulb implosions as a low-frequency sound source (2013)

Measurements of a depth-dependent characteristic of light bulb implosion in shallow water are presented. Incandescent bulb 500W was used as a sound source and its height and width are 12, 11 cm, respectively. A number of time series, which were imploded at less than depth of 100 m, were obtained by a hydrophone and high resolution analog-to-digital converter. Subsequent negative and positive pressure pulses in a time domain were well defined. As imploding depths are deeper, bubble pulse periods are decreasing in time. This phenomenon gave a significant impact on the primary resonant frequency caused by bubble oscillations. The main energy is concentrated in the frequency range of 100 to 500 Hz. The energy spectral densities in this band show the value of 170 to 185 dB (re 1μPa2sec/Hz @ 1m). Semiempirical relationships were derived from the time and frequency domain data and compared to the result reported in previous studies. Some differences are found in accordance with imploding depth. Possible causes for this are presented. This paper provides useful criteria to researchers who are going to use imploding light bulbs as an acoustic source.
Realtime Rigid Body Simulation Using Impulses (2006)

The parameters of the polarizable force field used for molecular dynamics simulations of Li diffusion in high-concentration lithium bis(trifluoromethanesulfonyl)amide (Li[TFSA]) sulfone (sulfolane, dimethylsulfone, ethylmethylsulfone, and ethyl-<i>i</i>-propylsulfone) solutions were refined. The densities of the solutions obtained by molecular dynamics simulations reproduced well the experimental values. The calculated concentration, temperature, and solvent dependencies of self-diffusion coefficients of ions and solvents in the mixtures well reproduce the experimentally observed dependencies. <i>Ab initio</i> calculations show that the intermolecular interactions between Li ions and four sulfones are not largely different. Conformational analyses show that sulfolane can change the conformation more easily owing to lower barrier height for pseudorotation compared to the rotational barrier heights of diethylsulfone and ethylmethylsulfone. Molecular dynamics simulations indicate that the easy conformation change of solvent affects the rotational relaxation of the solvent and the diffusion of Li ion in the mixture. The easy conformation change of sulfolane is one of the causes of faster diffusion of Li ion in the mixture of Li[TFSA] and sulfolane compared to the mixtures of smaller dimethylsulfone and ethylmethylsulfone.
A low-cost 4&#x00D7;25Gbps PAM4 module for short-reach optical interconnection (2014)

A low-cost 4×25Gbps PAM4 module for short-reach optical interconnection has been proposed using the commercial low-cost 10Gbps DML TOSA and PIN ROSA. This scheme has been demonstrated over 2km SMF and can also be used for MMF interconnection.
1-(1,2,5-Thiadiazol-4-yl)-4-azatricyclo[2.2.1.0<sup>2,6</sup>]heptanes as New Potent Muscarinic M<sub>1</sub> Agonists:  Structure−Activity Relationship for 3-Aryl-2-propyn-1-yloxy and 3-Aryl-2-propyn-1-ylthio Derivatives (1999)

Two new series of 1-(1,2,5-thiadiazol-4-yl)-4-azatricyclo[2.2.1.0(2, 6)]heptanes were synthesized and evaluated for their in vitro activity in cell lines transfected with either the human M1 or M2 receptor. 3-Phenyl-2-propyn-1-yloxy and -1-ylthio analogues substituted with halogen in the meta position showed high functional potency, efficacy, and selectivity toward the M1 receptor subtype. A quite unique functional M1 receptor selectivity was observed for compounds 8b, 8d, 8f, 9b, 9d, and 9f. Bioavailability studies in rats indicated an oral bioavailability of about 20-30%, with the N-oxide as the only detected metabolite.
<i>Astragalus Membranaceus</i> and <i>Polygonum Multijlorum</i> Protect Rat Heart Mitochondria Against Lipid Peroxidation (1994)

We isolated rat heart mitochondria and induced lipid peroxidation with ADP and FeSO4. Oxygen consumption and MDA formation were measured for quantitating the amount of lipid peroxidation. Using these methods, we screened the water extracts of 14 Chinese medicinal herbs for their effect on lipid peroxidation. It was found that Astragalus membranaceus inhibited 42.1 +/- 3.4% of oxygen consumption and 39.8 +/- 3.2% of MDA production at concentration of 2 mg dried herb/ml mitochondrial suspension. At the same concentration, Polygonum multiflorum inhibited 52.1 +/- 7.3% of oxygen consumption and 50.9 +/- 5.3% of MDA production. Other herbs did not inhibit lipid peroxidation to 50% of control at concentration up to 6 mg dried herb/ml mitochondrial suspension. Purification and identification of the active component(s) in Astragalus membranaceus and Polygonum multiflorum as well as their clinical application await further studies.
Association of FGFR1 with ERα Maintains Ligand-Independent ER Transcription and Mediates Resistance to Estrogen Deprivation in ER+ Breast Cancer (2017)

<b>Purpose:</b><i>FGFR1</i> amplification occurs in approximately 15% of estrogen receptor-positive (ER<sup>+</sup>) human breast cancers. We investigated mechanisms by which <i>FGFR1</i> amplification confers antiestrogen resistance to ER<sup>+</sup> breast cancer.<b>Experimental Design:</b> ER<sup>+</sup> tumors from patients treated with letrozole before surgery were subjected to Ki67 IHC, FGFR1 FISH, and RNA sequencing (RNA-seq). ER<sup>+</sup>/<i>FGFR1</i>-amplified breast cancer cells, and patient-derived xenografts (PDX) were treated with FGFR1 siRNA or the FGFR tyrosine kinase inhibitor lucitanib. Endpoints were cell/xenograft growth, FGFR1/ERα association by coimmunoprecipitation and proximity ligation, ER genomic activity by ChIP sequencing, and gene expression by RT-PCR.<b>Results:</b> ER<sup>+</sup>/<i>FGFR1</i>-amplified tumors in patients treated with letrozole maintained cell proliferation (Ki67). Estrogen deprivation increased total and nuclear FGFR1 and FGF ligands expression in ER<sup>+</sup>/<i>FGFR1-</i>amplified primary tumors and breast cancer cells. In estrogen-free conditions, FGFR1 associated with ERα in tumor cell nuclei and regulated the transcription of ER-dependent genes. This association was inhibited by a kinase-dead FGFR1 mutant and by treatment with lucitanib. ChIP-seq analysis of estrogen-deprived ER<sup>+</sup>/<i>FGFR1</i>-amplified cells showed binding of FGFR1 and ERα to DNA. Treatment with fulvestrant and/or lucitanib reduced FGFR1 and ERα binding to DNA. RNA-seq data from <i>FGFR1</i>-amplified patients' tumors treated with letrozole showed enrichment of estrogen response and E2F target genes. Finally, growth of ER<sup>+</sup>/<i>FGFR1-</i>amplified cells and PDXs was more potently inhibited by fulvestrant and lucitanib combined than each drug alone.<b>Conclusion</b>s<b>:</b> These data suggest the ERα pathway remains active in estrogen-deprived ER<sup>+</sup>/<i>FGFR1</i>-amplified breast cancers. Therefore, these tumors are endocrine resistant and should be candidates for treatment with combinations of ER and FGFR antagonists. <i>Clin Cancer Res; 23(20); 6138-50. ©2017 AACR</i>.
Intermembrane cholesterol transfer: Role of sterol carrier proteins and phosphatidylserine (1990)

The effect of phosphatidylserine and sterol carrier proteins on cholesterol exchange was determined using an assay not requiring separation of donor and acceptor membrane vesicles. Sterol carrier protein-2 (SCP2, also called nonspecific lipid transfer protein), but not fatty acid binding protein (FABP, also called sterol carrier protein), enhanced the initial rate of sterol exchange between neutral zwitterionic phosphatidylcholine small unilamellar vesicles (SUV) 2.3-fold. Phosphatidylserine at 10 mol% increased the initial rate of spontaneous and of SCP2-mediated (but not FABP-mediated) sterol exchange by 22% and 44-fold, respectively. The SCP2 potentiation of sterol transfer was dependent on SCP2 concentration and on phosphatidylserine concentration. The SCP2-mediated sterol transfer was inhibited by a variety of cations including KCl, divalent metal ions, and neomycin. The data suggest that SCP2 increase in activity for sterol transfer may be partly ascribed to charge on the phospholipid.
[Cu<sub>12</sub>S<sub>8</sub>]<sup>4⊖</sup>: A Closed Binary Copper(<scp>I</scp>) Sulfide Cage with Cuboctahedral Metal and Cubic Sulfur Arrangements (1984)

As the largest CuS cluster known to date, [Cu12S8]4⊖ occupies a special position. It is the first copper(I) complex containing exclusively sulfidic ligands that has been isolated. The Ph4P salt is formed on reaction of CuCl2·2H2O with EtS⊖ and Li2S in the presence of Ph4PBr.
Couple passive voltage contrast with scanning probe microscope to identify invisible defect out (2005)

As most of us know, PVC (passive voltage contrast) is a popular technique used to determine open or short issue on failure analysis field as presented in T. Sakai et al. (1999). And SPM (scanning probe microscopy) is another powerful technique for measuring characterization of dielectric or judging gate-oxide integrity of device as stated in M. P. Murell et al. (1993). In this paper, a judicious and effective ratiocinating method that coupled PVC with SPM would be discussed for revealing some special invisible defect modes, which were imperceptible to observe and very difficult to identify out by means of traditional PFA skills. And two such examples, whose failure position could not be caught exactly not only for the most sensitive PVC but high-resolution current mapping of SPM, would be presented to certify the benefit and excellence of this ratiocinating method. After our experiment, to apply such ratiocinating method could provide a good thinking in profile and help to reason the fault model. Simultaneously, the specific failure mechanism and defect location could be deduced before the conclusive PFA. Thus failure analysis turn-around time would not be wasted and yield-improving strategy could be proposed as soon as possible. So the application is successful.
Intraoperative parathyroid hormone as an indicator for parathyroid gland preservation in thyroid surgery (2011)

Intraoperative PTH assay may allow intraoperative monitoring of parathyroid function, predicting postoperative outcomes, may identify patients at risk of developing postoperative hypoparathyroidism, guiding surgeons to re-examine removed specimens for inadvertently removed parathyroid tissue with possible auto transplantation, or more practically a guide to early replacement therapy to prevent hypocalcaemia, leading to safe and early hospital discharge. Limitations in our study to be reconsidered in further studies, are relative small sample size, inability for randomisation, and the variable values reported for the cut off value of PTH causing hypocalcaemic symptoms needing intervention.