gebhart/patrepeval huggingface dataset:
Comparing linear and nonlinear mixed model approaches to cosinor analysis (2003)

The cosinor model, used for variables governed by circadian and other biological rhythms, is a nonlinear model in the amplitude and acrophase parameters that has a linear representation upon transformation. With linear cosinor analysis, amplitude and acrophase for each harmonic can be computed as nonlinear functions of the estimated linear regression coefficients. Here a flexible mixed model approach to cosinor analysis is considered, where the fixed effect parameters may enter nonlinearly as acrophase and amplitude for each harmonic or linearly after transformation to regression coefficients. In addition, the random effects may enter nonlinearly as subject-specific deviations from the acrophases and amplitudes or linearly as subject-specific deviations from the regression coefficients. It is also possible for the fixed effects to enter nonlinearly while the random effects enter linearly. Additionally, we evaluate whether including higher order linear harmonic terms as random effects, that is, Rao-Khatri 'covariance adjustment', improves precision. Applying the delta method to nonlinear functions of the parameters from linear mixed cosinor models to obtain approximate variances produces results that are often identical to results from nonlinear mixed models. Consequently, traditional linear cosinor analysis can often be used to estimate and compare the nonlinear parameters of interest, that is, amplitudes and acrophases, via the delta method. This is advantageous since the nonlinear mixed model may have convergence difficulties for more complex models. However, for some multiple-group analyses, the linear cosinor transformation should not be used and we clarify when the two methods are equivalent and when they differ.
The Taxonomy of Developmental Control in Caenorhabditis elegans (1998)

The Caenorhabditis elegans genome sequence was surveyed for transcription factor and signaling gene families that have been shown to regulate development in a variety of species. About 10 to 25 percent of the genes in most of the gene families already have been genetically analyzed in C. elegans, about half of the genes detect probable orthologs in other species, and about 10 to 25 percent of the genes are, at present, unique to C. elegans. Caenorhabditis elegans is also missing genes that are found in vertebrates and other invertebrates. Thus the genome sequence reveals universals in developmental control that are the legacy of metazoan complexity before the Cambrian explosion, as well as genes that have been more recently invented or lost in particular phylogenetic lineages.
Behavioral risk factor surveillance, 1986-1990. (1991)

Since 1984, an increasing number of states (including the District of Columbia) have participated in the Behavioral Risk Factor Surveillance System (BRFSS). This report provides state-specific estimates of the prevalence of selected health-risk behaviors for the years 1986 through 1990. Apparent trends and progress toward several of the year 2000 national health objectives are discussed, both for the entire adult population (persons ages greater than or equal to 18 years) and selected high-risk demographic subgroups. Now that BRFSS includes 45 states and covers over 90% of the nation's adult population, it can be used both as a measure of state-specific risk factor prevalence and an indicator of national trends.
Apoptotic and Antiapoptotic Mechanisms after Traumatic Brain Injury (2001)

Caspase and inhibitor of apoptosis (IAP) expression was examined in rats subjected to moderate traumatic brain injury (TBI) using a parasagittal fluid-percussion brain insult (1.7 to 2.2 atm). Within 1 hour after injury, caspase-8 and -9, two initiators of apoptosis, were predominantly expressed in superficial cortical areas adjacent to the impact site and in the thalamus. Caspase-3, an effector caspase, was evident at 6 hours throughout the traumatized cerebral cortex and hippocampus. Moreover, the authors observed that XIAP, cIAP-1, and cIAP-2, members of the IAP family, were constitutively expressed in the brain. Colocalization of XIAP-immunolabled cells with cell-specific markers indicated that XIAP is expressed within neurons and a subpopulation of oligodendrocytes. Immunoblots of brain extracts revealed that the processed forms of caspase-8, -9, and -3 are present as early as 1 hour after trauma. The appearance of activated caspases corresponded with the detection of cleavage of XIAP into fragments after injury and a concomitant increase in the levels of cIAP-1 and cIAP-2 in the traumatized hemispheres. The current data are consistent with the hypotheses that caspases in both the extrinsic and intrinsic apoptotic pathways are activated after moderate TBI and that IAPs may have a protective role within the brain with alterations in levels and cleavage of IAPs that contribute to cell death in this setting.
Single liquid source plasma-enhanced metalorganic chemical vapor deposition of high-quality YBa2Cu3O7−x thin films (1992)

High-quality YBa2Cu3O7−x films were grown in situ on LaAlO3 (100) by a novel single liquid source plasma-enhanced metalorganic chemical vapor deposition (CVD) process. The metalorganic complexes M (thd)n, (thd=2,2,6,6-tetramethyl-3-5-heptanedionate; M=Y, Ba, Cu) were dissolved in an organic solution and injected into a vaporizer immediately upstream of the reactor inlet. The single liquid source technique dramatically simplifies current CVD processing and can significantly improve the process reproducibility. X-ray diffraction measurements indicated that single phase, highly c-axis oriented YBa2Cu3O7−x was formed in situ at a substrate temperature 680 °C. The as-deposited films exhibited a mirrorlike surface, had transition temperature Tc0≂89 K, ΔTc&amp;lt;1 K, and Jc (77 K)=106 A/cm2.
Headaches and Women: Treatment of the Pregnant and Lactating Migraineur (1993)

Migraine is a hormonally sensitive episodic headache disorder which may worsen during the first trimester, but usually improves during later pregnancy. Its treatment can be difficult because of the risks of injury to the fetus and newborn. These risks include teratogenicity, embryo mortality, fetal growth abnormalities, and perinatal effect. This paper reviews the effects of drugs on the fetus and newborn, their FDA classification, and their use during both pregnancy and lactation. Specific recommendations are given.
Diversity of Domain V of 23S rRNA Gene Sequence in Different Enterococcus Species (2000)

The highly conserved central loop of domain V of 23S RNA (nucleotides 2042 to 2628; Escherichia coli numbering) is implicated in peptidyltransferase activity and represents one of the target sites for macrolide, lincosamide, and streptogramin B antibiotics. DNA encoding domain V (590 bp) of several species of Enterococcus was amplified by PCR. Twenty enterococcal isolates were tested, including Enterococcus faecium (six isolates), Enterococcus faecalis, Enterococcus avium, Enterococcus durans, Enterococcus gallinarum, Enterococcus casseliflavus (two isolates of each), and Enterococcus raffinosus, Enterococcus mundtii, Enterococcus malodoratus, and Enterococcus hirae (one isolate of each). For all isolates, species identification by biochemical testing was corroborated by 16S rRNA gene sequencing. The sequence of domain V of the 23S rRNA gene from E. faecium and E. faecalis differed from those of all other enterococci. The domain V sequences of E. durans and E. hirae were identical. This was also true for E. gallinarum and E. casseliflavus. E. avium differed from E. casseliflavus by 23 bases, from E. durans by 16 bases, and from E. malodoratus by 2 bases. E. avium differed from E. raffinosus by one base. Despite the fact that domain V is considered to be highly conserved, substantial differences were identified between several enterococcal species.
An Introduction To Compressive Sampling (2008)

Conventional approaches to sampling signals or images follow Shannon's theorem: the sampling rate must be at least twice the maximum frequency present in the signal (Nyquist rate). In the field of data conversion, standard analog-to-digital converter (ADC) technology implements the usual quantized Shannon representation - the signal is uniformly sampled at or above the Nyquist rate. This article surveys the theory of compressive sampling, also known as compressed sensing or CS, a novel sensing/sampling paradigm that goes against the common wisdom in data acquisition. CS theory asserts that one can recover certain signals and images from far fewer samples or measurements than traditional methods use.
Electrochemical and physicochemical properties of small phosphonium cation ionic liquid electrolytes with high lithium salt content (2015)

Electrolytes of a room temperature ionic liquid (RTIL), trimethyl(isobutyl)phosphonium (P111i4) bis(fluorosulfonyl)imide (FSI) with a wide range of lithium bis(fluorosulfonyl)imide (LiFSI) salt concentrations (up to 3.8 mol kg(-1) of salt in the RTIL) were characterised using a combination of techniques including viscosity, conductivity, differential scanning calorimetry (DSC), electrochemical impedance spectroscopy (EIS), nuclear magnetic resonance (NMR) and cyclic voltammetry (CV). We show that the FSI-based electrolyte containing a high salt concentration (e.g. 1 : 1 salt to IL molar ratio, equivalent to 3.2 mol kg(-1) of LiFSI) displays unusual transport behavior with respect to lithium ion mobility and promising electrochemical behavior, despite an increase in viscosity. These electrolytes could compete with the more traditionally studied nitrogen-based ionic liquids (ILs) in lithium battery applications.
The Infection of Clover Root Hairs by Nodule Bacteria Studied by a Simple Glass Slide Technique (1957)

SUMMARY: A simple glass slide technique has been devised for the continuous microscopical observation of growth and infection of root hairs of clover seedlings. The method involves an aseptic cultivation of seedlings on microscope slides which are partly immersed in a mineral salts medium. The roots are protected by a cover-slip. By this procedure, the root hairs of white clover inoculated with nodule bacteria were studied. The earliest infection was observed to take place within 48 hr. of inoculation, on 4-day-old seedlings. In branched hairs the growth of the thread from a lateral branch towards the hair tip is tentatively explained as an effect of the position of the hair nucleus relative to the site of infection.
Oncogenes-antioncogenes and virus therapy of cancer. (1990)

Viruses can render services to mankind. 1. Retroviruses pinpoint and transduce cellular oncogenes. 2. Retroviral vectors can introduce antioncogenes (the RB gene) into malignant cells thus rendering the recipient cells nonmalignant. 3. Oncolytic viruses lyse tumor cells. 4. Parvoviruses replicate only in dividing cells and exert lysis and antioncogene effect in tumor cells without affecting resting normal cells. 5. Myxo- and paramyxoviruses (and other viruses) upgrade the immunogenicity of cell surface antigens thus eliciting rejection type host immunity against these cells which is operational against not virus-infected cells of the same type (post-oncolytic antitumor immunity). 6. Viruses or virally infected cells (including tumor cells) induce the production of lymphokines and cytokines (interferons, interleukins and tumor necrosis factor) and activate NK cells and specific immune T cells cytotoxic to virus-infected cells (including tumor cells). 7. Measles virus may activate suppressor cells and both directly (by infecting lymphoma cells) and indirectly (by inducing molecular mediators of suppressor mononuclear cells inhibitory to the growth of neoplastic lymphoid and hematopoietic cells) induce remissions of lympho- and hematopoietic malignancies. 8. Retroviral vectors deliver genes into tumor cells for encoding new surface antigens that render the tumor cells highly antigenic and more vulnerable to rejection type immune reactions of the host. Examples illustrate each statement. Immunotherapy of tumors with active tumor-specific immunization after the induction of suppressor cells by fetal antigens and the elimination of the proliferating suppressor clones by cyclophosphamide will again be proposed.
Components of Eukaryotic-like Protein Signaling Pathways in Mycobacterium tuberculosis (1997)

Eukaryotic-like protein kinases have been identified recently in several prokaryotes by comparative studies of DNA sequences and Western blotting techniques using antiphosphoprotein antibodies. Examination of the Mycobacterium tuberculosis genome by means of PCR amplification with consensus primers, Southern hybridization, and comparative analysis of DNA sequences with genomic databases revealed the existence of at least seven eukaryotic-like protein kinases in this pathogen. In addition, we report the biochemical identification of phosphorylated proteins in M. tuberculosis. Taken together, these findings show that M. tuberculosis possesses elements of cell signaling similar to those observed in eukaryotic organisms. We suggest that some of these processes may play roles in the pathogenesis of M. tuberculosis.
Antibody-Pseudomonas exotoxin A conjugates cytotoxic to human breast cancer cells in vitro. (1986)

Breast tumor selective antibodies (MAB) conjugated to Pseudomonas exotoxin A (PE) formed immunotoxins with potent cytotoxicities for human breast tumor cell lines. The most effective of the MAB-PE conjugates were about 500-fold more toxic to the breast tumor target cell lines than to the nontarget human fibroblast cell line. Specificity of cytotoxicity by MAB-PE conjugates was demonstrated by protection of target cells in the presence of excess unconjugated homologous antibody. A MAB-PE conjugate inhibited protein synthesis more rapidly than the corresponding MAB-ricin toxin A chain (RTA) conjugate. Generally, there was a direct correlation between the cytotoxicity of RTA and PE when conjugated to the same MAB: MABs that made highly cytotoxic RTA conjugates made effective PE conjugates and MABs that made poorly cytotoxic RTA conjugates made PE conjugates of low cytotoxicity; however, one MAB-PE immunotoxin was cytotoxic to the human breast tumor cell lines, whereas the corresponding MAB-RTA immunotoxin was noncytotoxic at the highest dose tested. In contrast to MAB-RTA conjugates, which require a cleavable (disulfide) linkage for maximal in vitro cytotoxicity, MAB-PE conjugates were about equally cytotoxic when linked by either a cleavable or noncleavable (thioether) bond.
Possible dissociation of the heparin-binding and mitogenic activities of heparin-binding (acidic fibroblast) growth factor-1 from its receptor-binding activities by site-directed mutagenesis of a single lysine residue. (1990)

The fibroblast or heparin-binding growth factors (HBGFs) are thought to be modulators of cell growth and migration, angiogenesis, wound repair, neurite extension, and mesoderm induction. A better understanding of the structural basis for the different activities of these proteins should facilitate the development of agonists and antagonists of specific HBGF activities and identification of the signal transduction pathways involved in the mechanisms of action of these growth factors. Chemical modification studies of Harper and Lobb (Harper, J. W., and R. R. Lobb. 1988. Biochemistry. 27:671-678) implicated lysine 132 in HBGF-1 (acidic fibroblast growth factor) as being important to the heparin-binding, receptor-binding, and mitogenic activities of the protein. We changed lysine 132 to a glutamic acid residue by site-directed mutagenesis of the human cDNA and expressed the mutant protein in Escherichia coli to obtain sufficient quantities for functional studies. Replacement of this lysine with glutamic acid reduces the apparent affinity of HBGF-1 for immobilized heparin (elutes at 0.45 M NaCl vs. 1.1 M NaCl for wild-type). Mitogenic assays established two points: (a) human recombinant HBGF-1 is highly dependent on the presence of heparin for optimal mitogenic activity, and (b) the change of lysine 132 to glutamic acid drastically reduces the specific mitogenic activity of HBGF-1. The poor mitogenic activity of the mutant protein does not appear to be due to a reduced affinity for the HBGF receptor. Similarly, the mutant HBGF-1 can stimulate tyrosine kinase activity and induce protooncogene expression. Differences in the biological properties of the wild-type and mutant proteins were observed in transfection studies. Mutant HBGF-1 expression in transfected NIH 3T3 cells did not induce the same transformed phenotype characteristic of cells expressing wild-type HBGF-1. Together these data indicate that different functional properties of HBGF-1 may be dissociated at the structural level.
Mutation detection using nucleotide analogs that alter electrophoretic mobility (1989)

A simple primer extension assay has been developed to distinguish homologous DNA segments differing by as little as a single nucleotide. DNA strands are synthesized with one of the four natural nucleotides replaced with an analog that affects electrophoretic mobility. DNAs that are the same length but differ in the number of analog molecules per strand exhibit different mobilities on a sequencing gel. In combination with the polymerase chain reaction (PCR; 1, 2), this method has been used to distinguish mutant and normal alleles of the human insulin receptor gene that differ by a single-base substitution. The method appears to be generally applicable to the detection of any nucleotide polymorphism in any segment of DNA.
Preliminary evaluation of intratumoral injection of a streptococcus pyrogenes preparation in patients with malignant brain tumors (1980)

Thirteen patients with malignant brain tumors, 12 anaplastic gliomas and one metastatic tumor, received repeated intratumoral injections of an immunopotentiator, Picibanil, prepared from streptococcus pyogenes. All patients tolerated this therapy; morbidity rates were acceptable. Significant tumor regression was noted on computerized tomography scanning for 6 of 12 patients for whom scanning was performed. Histologic examination of the post-therapy specimens obtained from 8 patients revealed that inflammatory reactions were evoked in all of the tumors, although the extent of inflammatory changes varied from patient to patient and mostly was localized to an area surrounding the intratumoral tubes.
Induction of neuropilin-1 and vascular endothelial growth factor by epidermal growth factor in human gastric cancer cells (2003)

The epidermal growth factor receptor (EGF-R) pathway plays a pivotal role in the progression of human gastric cancer. The angiogenic factor vascular endothelial growth factor (VEGF) has been shown to be induced by EGF in various cancer cell lines. Neuropilin-1 (NRP-1) acts as a coreceptor for VEGF-165 and increases its affinity for VEGF receptor 2 (VEGFR-2) in endothelial cells. Furthermore, NRP-1 has been found to be expressed by tumour cells and has been shown to enhance tumour angiogenesis and growth in preclinical models. We examined the expression of NRP-1 mRNA and EGF-R protein in seven human gastric cancer cell lines. NRP-1 expression was expressed in five of seven cell lines, and EGF-R expression closely mirrored NRP-1 expression. Moreover, in EGF-R-positive NCI-N87 and ST-2 cells, EGF induced both NRP-1 and VEGF mRNA expression. C225, a monoclonal antibody to EGF-R, blocked EGF-induced NRP-1 and VEGF expression in NCI-N87 cells in a dose-dependent manner. The treatment of NCI-N87 cells with EGF resulted in increases in phosphorylation of Erk1/2, Akt, and P38. Blockade of the Erk, phosphatidylinositol-3 kinase/Akt, or P38 pathways in this cell line prevented EGF induction of NRP-1 and VEGF. These results suggest that regulation of NRP-1 expression in human gastric cancer is intimately associated with the EGF/EGF-R system. Activation of EGF-R might contribute to gastric cancer angiogenesis by a mechanism that involves upregulation of VEGF and NRP-1 expression via multiple signalling pathways.
Phase and transmission errors aware OPC solution for PSM: feasability demonstration (2001)

To follow the SIA roadmap, lithographers must deal everyday with the bad effects of a low-kl lithography transfer process. One of the ways to reduce the pressure associated with such low-kl values is to use Alternating Phase Shift Masks (henceforth “Alt-PSM”). Unfortunately, Alt-PSM also has some drawbacks, such as transmission imbalance between the phase shifted and non-phase shifted areas, and aspect ratio phase etch depth variation resulting from the mask etching process. Moreover, fast two-dimensional simulators that are commonly used in resolution enhancement simulation are unable to directly predict these inherently three-dimensional effects. We demonstrate a general approach to simulate and correct these effects in large circuit designs by combining accurate mask representation with Optical and Process Correction (“OPC”). Using a DRC tool, geometry in the input circuit design is partitioned based on size and shape. Guided by accurate three-dimensional simulations or empirical data, these partitions may be classified and assigned different phases and transmission values to more realistically simulate the mask. By using this more accurate mask representation in our integrated OPC tool, Calibre OPCPro, we are able to correct designs for these three-dimensional mask effects as well as for conventional proximity effects.
PCR-Based Methods for Detecting Single-Locus DNA Methylation Biomarkers in Cancer Diagnostics, Prognostics, and Response to Treatment (2009)

Numerous traditional and new PCR-based methods have been developed for detecting DNA methylation at single loci. All have characteristic advantages and disadvantages, particularly with regard to use in clinical settings.
Pyrene-Assisted Synthesis of Size-Controlled Gold Nanoparticles in Sodium Dodecyl Sulfate Micelles (2005)

Gold nanoparticles prepared by chemical reduction in sodium dodecyl sulfate (SDS) solution are size-controlled with the addition of pyrene. Micellar electrokinetic capillary chromatography (MEKC) is applied to the system to examine the size and polydispersity of gold nanoparticles and to show that pyrene has the extraordinary effect in decreasing the size and narrowing the dispersity of gold nanoparticles. The MEKC electropherograms further suggest that pyrene could be oxidized by the aqueous Au(III) complexes first. All the reduced Au complexes were then solubilized in the pyrene-SDS micelles. The growth of gold nanoparticles beyond the embryonic stage was subsequently inhibited by the encapsulating SDS and electrophilic pyrene.
The role of bactericidal/permeability-increasing protein as a natural inhibitor of bacterial endotoxin (1992)

Systemic release of endotoxin (LPS) after Gram-negative infection initiates a cascade of host cytokines that are thought to be the direct cause of shock, multisystem organ failure, and death. Endogenous LPS-binding proteins may play a role in regulating LPS toxicity in vivo. The human neutrophil granule protein bactericidal/permeability-increasing protein (BPI) shares sequence homology and immunocrossreactivity with an acute phase lipopolysaccharide binding protein (LBP) which has been shown to bind to LPS and accelerate LPS activation of neutrophils and macrophages. Although structurally similar, LBP and BPI are apparently functionally antagonistic. We previously showed that BPI inhibits LPS-mediated neutrophil activation in vitro. Here we demonstrate that BPI binds to LPS near the lipid A domain, and formation of the LPS-BPI complex abrogates detrimental host responses to LPS. For example, BPI blocks LPS-stimulated TNF release in vitro and in vivo, and LPS complexed to BPI is not pyrogenic in rabbits. Results demonstrating that BPI is released by stimulated human neutrophils further support the idea that BPI functions extracellularly in vivo to neutralize endotoxin. Taken together, these data argue that BPI neutralizes the toxic effects of LPS in vivo, and that BPI may represent a new therapeutic approach to the treatment of endotoxic shock.