gebhart/patrepeval huggingface dataset:
Multivariate Least-Squares Methods Applied to the Quantitative Spectral Analysis of Multicomponent Samples (1985)

In an extension of earlier work, weighted multivariate least-squares methods of quantitative FT-IR analysis have been developed. A linear least-squares approximation to nonlinearities in the Beer-Lambert law is made by allowing the reference spectra to be a set of known mixtures. The incorporation of nonzero intercepts in the relation between absorbance and concentration further improves the approximation of nonlinearities while simultaneously accounting for nonzero spectral baselines. Pathlength variations are also accommodated in the analysis, and under certain conditions, unknown sample pathlengths can be determined. All spectral data are used to improve the precision and accuracy of the estimated concentrations. During the calibration phase of the analysis, pure component spectra are estimated from the standard mixture spectra. These can be compared with the measured pure component spectra to determine which vibrations experience nonlinear behavior. In the predictive phase of the analysis, the calculated spectra are used in our previous least-squares analysis to estimate sample component concentrations. These methods were applied to the analysis of the IR spectra of binary mixtures of esters. Even with severely overlapping spectral bands and nonlinearities in the Beer-Lambert law, the average relative error in the estimated concentrations was &lt;1%.
Comparative Analysis of Histophilus somni Immunoglobulin-binding Protein A (IbpA) with Other Fic Domain-containing Enzymes Reveals Differences in Substrate and Nucleotide Specificities (2011)

A new family of adenylyltransferases, defined by the presence of a Fic domain, was recently discovered to catalyze the addition of adenosine monophosphate (AMP) to Rho GTPases (Yarbrough, M. L., Li, Y., Kinch, L. N., Grishin, N. V., Ball, H. L., and Orth, K. (2009) Science 323, 269-272; Worby, C. A., Mattoo, S., Kruger, R. P., Corbeil, L. B., Koller, A., Mendez, J. C., Zekarias, B., Lazar, C., and Dixon, J. E. (2009) Mol. Cell 34, 93-103). This adenylylation event inactivates Rho GTPases by preventing them from binding to their downstream effectors. We reported that the Fic domain(s) of the immunoglobulin-binding protein A (IbpA) from the pathogenic bacterium Histophilus somni adenylylates mammalian Rho GTPases, RhoA, Rac1, and Cdc42, thereby inducing host cytoskeletal collapse, which allows H. somni to breach alveolar barriers and cause septicemia. The IbpA-mediated adenylylation occurs on a functionally critical tyrosine in the switch 1 region of these GTPases. Here, we conduct a detailed characterization of the IbpA Fic2 domain and compare its activity with other known Fic adenylyltransferases, VopS (Vibrio outer protein S) from the bacterial pathogen Vibrio parahaemolyticus and the human protein HYPE (huntingtin yeast interacting protein E; also called FicD). We also included the Fic domains of the secreted protein, PfhB2, from the opportunistic pathogen Pasteurella multocida, in our analysis. PfhB2 shares a common domain architecture with IbpA and contains two Fic domains. We demonstrate that the PfhB2 Fic domains also possess adenylyltransferase activity that targets the switch 1 tyrosine of Rho GTPases. Comparative kinetic and phylogenetic analyses of IbpA-Fic2 with the Fic domains of PfhB2, VopS, and HYPE reveal important aspects of their specificities for Rho GTPases and nucleotide usage and offer mechanistic insights for determining nucleotide and substrate specificities for these enzymes. Finally, we compare the evolutionary lineages of Fic proteins with those of other known adenylyltransferases.
Casimir force and the quantum theory of lossy optical cavities (2003)

We present a derivation of the Casimir force between two parallel plane mirrors at zero temperature. The two mirrors and the cavity they enclose are treated as quantum optical networks. They are, in general, lossy and characterized by frequency-dependent reflection amplitudes. The additional fluctuations accompanying losses are deduced from expressions of the optical theorem. A general proof is given for the theorem relating the spectral density inside the cavity to the reflection amplitudes seen by the inner fields. This density determines the vacuum radiation pressure and, therefore, the Casimir force. The force is obtained as an integral over the real frequencies, including the contribution of evanescent waves besides that of ordinary waves, and then as an integral over imaginary frequencies. The demonstration relies only on general properties obeyed by real mirrors which also enforce general constraints for the variation of the Casimir force.
Monoclonal Antibodies to Human Cell Surface Antigens (2003)

Abstract This appendix lists the cluster of differentiation (CD) designations for the nearly 300 different leukocyte surface molecules that have been assigned and approved by the nomenclature committee of the International Union of Immunological societies (IUIS).
Notes on the nesting of wedge-tailed shearwaters on Heron Island (1992)

Wedge -tailed Shearwaters Puffinus pacificus are numerous on Heron Island in the Capricorn-Bunker Group (23 degrees26'S, 151 degrees54'E), where they maybe found nesting in close proximity to the Heron Island Research Station. Egg-laying begins in early December and the last birds are fledged towards the end of April (Ogden 1979).
Comparison of the selective cytotoxic effects of immunotoxins containing ricin A chain or pokeweed antiviral protein and anti-Thy 1.1 monoclonal antibodies. (1984)

Ricin A chain and pokeweed antiviral protein (PAP), two enzymes that inhibit the action of eukaryotic ribosomes, were coupled by cleavable, N-succinimidyl-3-(2-pyridyldithio)propionate, and noncleavable m-maleimidobenzoyl-N-hydroxysuccinimide ester, cross-linking reagents to monoclonal antibodies directed against Thy 1.1 antigen. Leukemia cells that contained Thy 1.1 antigen were selectively killed compared to Thy 1.2-containing cells. The composition of the conjugates was determined by radioimmunoassay, and most of the immunotoxins contained about equal molar quantities of antibody and ribosomal inhibitor. Ricin A chain linked to antibody by a noncleavable m-maleimidobenzoyl-N-hydroxysuccinimide ester cross-link was not cytotoxic, but PAP coupled to the same antibody was. Both immunotoxins linked by a cleavable disulfide bond were cytotoxic. Disulfide-linked F(ab')2-PAP was cytotoxic, but it was about 45 times less efficient than disulfide-linked IgG-PAP. There was only a 3.2-fold difference in their ability to inhibit ribosomes in vitro. The relative difference between in vitro action and cytotoxicity could be accounted for by differences in the affinity of the immunotoxins to the cell surface. Neither PAP or ricin A chain disulfide linked to a monoclonal antibody against Mr 15,000 envelope protein, a murine leukemia virus coat protein, were not cytotoxic, although both conjugates bound to the cell surface. Because of its stability, ease of purification, and lack of an analogue of ricin B chain, PAP may be more useful than ricin A for immunotoxin synthesis.
Histone deacetylase inhibitors in clinical development (2004)

In addition to a variety of other novel agents, interest in histone deacetylase inhibitors (HDACIs) as antineoplastic drugs has recently accelerated and increasing numbers of these compounds have entered clinical trials in humans. HDACIs represent a prototype of molecularly targeted agents that perturb signal transduction, cell cycle-regulatory and survival-related pathways. Newer generation HDACIs have been introduced into the clinical arena that are considerably more potent on a molar basis than their predecessors and are beginning to show early evidence of activity, particularly in hematopoietic malignancies. In addition, there is an increasing appreciation of the fact that HDACIs may act through mechanisms other than induction of histone acetylation and, as in the case of other molecularly-targeted agents, it is conceivable that the ultimate role of HDACIs in cancer therapy will be as modulators of apoptosis induced by other cytotoxic agents. One particularly promising strategy involves attempts to combine HDACIs with other novel agents to promote tumour cell differentiation or apoptosis. The present review focuses on recent insights into the mechanisms by which HDACIs exert their anticancer effects, either alone or in combination with other compounds, as well as attempts to translate these findings into the clinic.
Pentostatin for the Treatment of Chronic Graft-Versus-Host Disease in Children (2003)

Chronic graft-versus-host disease (cGVHD) is a major barrier to successful allogeneic stem cell transplantation. Pentostatin has been used to treat cGVHD in a small series of pediatric patients. The authors report the results of the first five pediatric patients receiving pentostatin for refractory cGVHD at Johns Hopkins Hospital. In this early experience, the authors saw considerable symptom response in their patients. Every patient in this series demonstrated a significant improvement in skin and oral symptoms. An increased incidence of infection secondary to pentostatin was not observed. No patient was permanently discontinued from pentostatin subsequent to side effects. If these promising results continue, a trial of pentostatin as a first-line therapy for cGVHD should be considered to potentially reduce our dependence on high-dose steroids for its treatment.
Human dendritic cell subsets in NOD/SCID mice engrafted with CD34+ hematopoietic progenitors (2003)

Distinct human dendritic cell (DC) subsets differentially control immunity. Thus, insights into their in vivo functions are important to understand the launching and modulation of immune responses. We show that nonobese diabetic/LtSz-scid/scid (NOD/SCID) mice engrafted with human CD34+ hematopoietic progenitors develop human myeloid and plasmacytoid DCs. The skin displays immature DCs expressing Langerin, while other tissues display interstitial DCs. Myeloid DCs from these mice induce proliferation of allogeneic CD4 T cells in vitro, and bone marrow human cells containing plasmacytoid DCs release interferon-alpha (IFN-alpha) upon influenza virus exposure. Injection of influenza virus into reconstituted mice triggers IFN-alpha release and maturation of mDCs. Thus, these mice may provide a model to study the pathophysiology of human DC subsets.
Writing current reduction for high-density phase-change RAM (2004)

By developing a chalcogenide memory element that can be operated at low writing current, we have demonstrated the possibility of high-density phase-change random access memory. We have investigated the phase transition behaviors as a function of various process factors including contact size, cell size and thickness, doping concentration in chalcogenide material and cell structure. As a result, we have observed that the writing current is reduced down to 0.7 mA.
Fine Tuning and Efficient T Cell Activation with Stimulatory aCD3 Nanoarrays (2013)

Anti-CD3 (aCD3) nanoarrays fabricated by self-assembled nanopatterning combined with site-directed protein immobilization techniques represent a novel T cell stimulatory platform that allows tight control over ligand orientation and surface density. Here, we show that activation of primary human CD4+ T cells, defined by CD69 upregulation, IL-2 production and cell proliferation, correlates with aCD3 density on nanoarrays. Immobilization of aCD3 through nanopatterning had two effects: cell activation was significantly higher on these surfaces than on aCD3-coated plastics and allowed unprecedented fine-tuning of T cell response.
Solid-State Nanopore Technologies for Nanopore-Based DNA Analysis (2007)

Nanopore-based DNA analysis is a new single-molecule technique that involves monitoring the flow of ions through a narrow pore, and detecting changes in this flow as DNA molecules also pass through the pore. It has the potential to carry out a range of laboratory and medical DNA analyses, orders of magnitude faster than current methods. Initial experiments used a protein channel for its pre-defined, precise structure, but since then several approaches for the fabrication of solid-state pores have been developed. These aim to match the capabilities of biochannels, while also providing increased durability, control over pore geometry and compatibility with semiconductor and microfluidics fabrication techniques. This review summarizes each solid-state nanopore fabrication technique reported to date, and compares their advantages and disadvantages. Methods and applications for nanopore surface modification are also presented, followed by a discussion of approaches used to measure pore size, geometry and surface properties. The review concludes with an outlook on the future of solid-state nanopores.
Cloning of the cDNA and gene for a human D2 dopamine receptor. (1989)

A clone encoding a human D2 dopamine receptor was isolated from a pituitary cDNA library and sequenced. The deduced protein sequence is 96% identical with that of the cloned rat receptor with one major difference: the human receptor contains an additional 29 amino acids in its putative third cytoplasmic loop. Southern blotting demonstrated the presence of only one human D2 receptor gene. Two overlapping phage containing the gene were isolated and characterized. DNA sequence analysis of these clones showed that the coding sequence is interrupted by six introns and that the additional amino acids present in the human pituitary receptor are encoded by a single exon of 87 base pairs. The involvement of this sequence in alternative splicing and its biological significance are discussed.
Effects of Stent Design and Atherosclerotic Plaque Composition on Arterial Wall Biomechanics (2008)

Evidence suggests that a judicious choice of stent design can minimize stress while maintaining a patent lumen in stenotic arteries. If confronted with a rigid, calcified plaque, stent design is more important, as design differences can impose dramatically different stress fields, while still providing arterial patency. Alternatively, stent design is not as much of an issue when treating a soft, lipid-laden plaque, as stress fields do not vary significantly among stent designs.
LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids (1999)

Mammalian imprinted genes are frequently arranged in clusters on particular chromosomes. The imprinting cluster on human chromosome 11p15 is associated with Beckwith-Wiedemann syndrome (BWS) and a variety of human cancers. To clarify the genomic organization of the imprinted cluster, an extensive screen for differentially expressed transcripts in the 11p15 region was performed using monochromosomal hybrids with a paternal or maternal human chromosome 11. Here we describe an imprinted antisense transcript identified within the KvLQT1 locus, which is associated with multiple balanced chromosomal rearrangements in BWS and an additional breakpoint in embryonal rhabdoid tumors. The transcript, called LIT1 (long QT intronic transcript 1), was expressed preferentially from the paternal allele and produced in most human tissues. Methylation analysis revealed that an intronic CpG island was specifically methylated on the silent maternal allele and that four of 13 BWS patients showed complete loss of maternal methylation at the CpG island, suggesting that antisense regulation is involved in the development of human disease. In addition, we found that eight of eight Wilms' tumors exhibited normal imprinting of LIT1 and five of five tumors displayed normal differential methylation at the intronic CpG island. This contrasts with five of six tumors showing loss of imprinting of IGF2. We conclude that the imprinted gene domain at the KvLQT1 locus is discordantly regulated in cancer from the imprinted domain at the IGF2 locus. Thus, this positional approach using human monochromosomal hybrids could contribute to the efficient identification of imprinted loci in humans.
Immunoglobulin E Production in the Absence of Interleukin-4-Secreting CD1-Dependent Cells (1997)

A lymphocyte population that expresses surface markers found on T cells and natural killer (NK) cells secretes large amounts of interleukin-4 (IL-4) immediately after T cell receptor ligation. These NK-like T cells are thus thought to be important for the initiation of type 2 T helper cell (TH2) responses. CD1-deficient mice were found to lack this lymphocyte subset, but they could nevertheless mount a protypical TH2 response; after immunization with antibody to immunoglobulin D (IgD), CD1-deficient mice produced IgE. Thus, although dependent on CD1 for their development, IL-4-secreting NK-like T cells are not required for TH2 responses.
Wafer Bonding and Layer Transfer Processes for High Efficiency Solar Cells (2003)

A wafer-bonded four-junction cell design consisting of InGaAs, InGaAsP, GaAs, and Ga0.5In0.5P subcells that could reach one-sun AM0 efficiencies of 35.4% is described. The design relies on wafer-bonding and layer transfer for integration of non-lattice-matched subcells. Wafer bonding and layer transfer processes have shown promise in the fabrication of InP/Si epitaxial templates for growth of the bottom InGaAs and InGaAsP subcells on a Si support substrate. Subsequent wafer bonding and layer transfer of a thin Ge layer onto the lower subcell stack can serve as an epitaxial template for GaAs and Ga0.5In0.5P subcells. Additionally, wafer bonded Ge/Si substrates offer the possibility to improve the mechanical performance of existing triple-junction solar cell designs, while simultaneously reducing their cost. Present results indicate that optically active III/V compound semiconductors can be grown on both Ge/Si and InP/Si heterostructures. Current-voltage electrical characterization of the interfaces of these structures indicates that both InP/Si and Ge/Si interfaces have specific resistances lower than 0.1 W?cm2 for heavily doped wafer bonded interfaces, enabling back surface power extraction from the finished cell structure.
<title>Fabrication of fine metal microstructures packaged in the bonded glass substrates</title> (1999)

In order to realize fine microstructures with high aspect ratio, tow kind of thick-resist-based metal molding processes were studied. A novel technique obtaining fine line/space and high aspect ratio thick photoresist patterns on a glass substrate by the simple UV lithography was developed. A three-layer resist method using reactive ion etching (RIE) for patterning thick photoresist was also examined. The former method is to use fine thin metal patterns formed on the glass substrate as the exposure mask. A thick negative photoresist is coated on it and UV light is illuminated from the backside. Perfect contact between mask and photoresist is obtained and the influence of light diffraction is also avoided. By using SU-8 as the negative photoresist, minimum line/space of 1 micrometers and high aspect ratio of about 5 was achieved. The metal layer is served as a seed layer for Ni electroplating as well. Metal microstructures were also fabricated by the three-layer resist method using the thick photoresist-thin SiO<SUB>2</SUB>-thin photoresist structure. Even an usual contact UV lithography was applied to pattern the thin photoresist layer and a usual CCP-RIE was used to etch the SiO<SUB>2</SUB> and thick photoresists layer, at least 1 micrometers gap microstructures were obtained by the Ni electroplating. Micro-packaging method using SiO<SUB>2</SUB>-SiO<SUB>2</SUB> bonding with hydrofluoric acid was also studied. HF bonding conditions suitable for micropackaging were examined under different HF concentration, pressure, and temperature. Reasonable bond strength equal to that by the anodic bonding is obtained under high-applied pressure during bonding. Packaging method is posed using combination of the thick-resist-based molding and the HF bonding.
Nosocomial Bloodstream Infections in HIV-Infected Patients: Attributable Mortality and Extension of Hospital Stay (1998)

A 3-year prospective matched case-control study was performed to investigate the potential risk factors, prognostic indicators, extension of hospital stay, and attributable mortality of nosocomial bloodstream infections in HIV-infected patients. Matching variables were: age, gender, number of circulating CD4+ T lymphocytes, cause of hospital admission, hospitalization in the same ward within the 6 weeks of diagnosis of the case, and length of stay before the day of infection in the case. Eighty-four cases and 168 matched controls were studied. Nosocomial bloodstream infections complicated about 3 of 1000 hospital days per patient in the study period. With step-wise logistic regression analysis, the most important predictors for developing nosocomial bloodstream infections were: increasing value of Acute Physiology and Chronic Health Evaluation (APACHE II) score (p = .001) and use of central venous catheter (CVC) (p = .002). The excess of hospital stay attributable to nosocomial bloodstream infections was 17 days. The crude mortality rate was 43%. The attributable mortality rate was estimated to be 27% (95% confidence interval [CI] = 13%-48%). The estimated risk ratio for death was 3.91 (95% CI = 2.06-7.44). Multivariate analysis identified two prognostic indicators that were significantly associated with unfavorable outcome of bloodstream infections: number of circulating CD4+ T cells <100/mm3 (p = .002) and APACHE II score >15 (p = .01). Nosocomial bloodstream infections are more common in patients with advanced HIV disease. Important cofactors are high APACHE II score and use of CVC. These infections can cause an excess mortality and significantly prolong the hospital stay of HIV-infected patients.
Spatio-temporal segmentation based on region merging (1998)

This paper proposes a technique for spatio-temporal segmentation to identify the objects present in the scene represented in a video sequence. This technique processes two consecutive frames at a time. A region-merging approach is used to identify the objects in the scene. Starting from an oversegmentation of the current frame, the objects are formed by iteratively merging regions together. Regions are merged based on their mutual spatio-temporal similarity. We propose a modified Kolmogorov-Smirnov test for estimating the temporal similarity. The region-merging process is based on a weighted, directed graph. Two complementary graph-based clustering rules are proposed, namely, the strong rule and the weak rule. These rules take advantage of the natural structures present in the graph. Experimental results on different types of scenes demonstrate the ability of the proposed technique to automatically partition the scene into its constituent objects.