gebhart/patrepeval huggingface dataset:
Utilising the left-helical conformation of L-DNA for analysing different marker types on a single universal microarray platform (2006)

L-DNA is the perfect mirror-image form of the naturally occurring d-conformation of DNA. Therefore, L-DNA duplexes have the same physical characteristics in terms of solubility, duplex stability and selectivity as D-DNA but form a left-helical double-helix. Because of its chiral difference, L-DNA does not bind to its naturally occurring D-DNA counterpart, however. We analysed some of the properties that are typical for L-DNA. For all the differences, L-DNA is chemically compatible with the D-form of DNA, so that chimeric molecules can be synthesized. We take advantage of the characteristics of L-DNA toward the establishment of a universal microarray that permits the analysis of different kinds of molecular diagnostic information in a single experiment on a single platform, in various combinations. Typical results for the measurement of transcript level variations, genotypic differences and DNA-protein interactions are presented. However, on the basis of the characteristic features of L-DNA, also other applications of this molecule type are discussed.
Progressive multifocal leucoencephalopathy in the era of natalizumab: a review and discussion of the implications. (2006)

Progressive multifocal leucoencephalopathy (PML) is an opportunistic demyelinating infection of immunocompromised patients, caused by the human polyomavirus, JC virus. Prior to 2005, PML had not been described in patients with MS. In early 2005, however, two cases of PML were reported in patients with MS treated with the alpha-antegrin inhibitor, natalizumab. A third case was subsequently described in a patient with Crohn's disease who had also received the agent. These three cases resulted in withdrawal of natalizumab from the market and have had major implications for its reintroduction into clinical use. In this review, we discuss current knowledge concerning PML and its causative agent, the possible role of natalizumab in initiating PML in patients with MS, and the challenges posed by the risk of this infection as the drug returns to clinical use.
Elevated glucose 6-phosphate levels are associated with plasmid mutations in vivo. (1987)

The incubation in vitro of plasmid pBR322 DNA with glucose 6-phosphate (Glc-6-P) has been shown to have a mutagenic effect when the plasmid was transformed into wild-type Escherichia coli. To further investigate the modifications of DNA by the reducing sugar Glc-6-P, we have developed an in vivo model to monitor plasmid DNA mutations. E. coli strains that are defective for phosphoglucose isomerase (strain DF40) alone or phosphoglucose isomerase and glucose-6-phosphate dehydrogenase (strain DF2000) accumulate Glc-6-P when grown in gluconate minimal medium in the presence of glucose. These strains and the control strain K10 were transformed with pAM006, a plasmid that carries the genes for ampicillin resistance and beta-galactosidase production, and grown for 24 hr under conditions that prompted the accumulation of Glc-6-P. An increase in plasmid mutations was observed (7- and 13-fold) that was associated with the increased intracellular levels of Glc-6-P (20- and 30-fold) present in the DF40 and DF2000 E. coli strains, respectively. Growth of the mutant bacteria in gluconate minimal medium does not increase the intracellular levels of Glc-6-P or the rate of plasmid mutations over background. Further characterization of the mutated plasmid DNA showed that insertions, deletions, and point mutations were responsible for the loss of beta-galactosidase production. The increase in plasmid mutations as a function of increased intracellular Glc-6-P levels suggests that the accumulation of adducts formed by Glc-6-P and other reducing sugars may contribute to DNA damage.
Molecular Basis for Tissue Expansion: Clinical Implications for the Surgeon (1998)

A wide variety of tissue expansion techniques have been used for breast reconstruction, craniofacial surgery, and burn care in plastic reconstructive surgery. However, the basic mechanism by which skin and surrounding tissue respond to mechanical expansion remains unclear. Recent studies have revealed the biomechanical aspects of cells subjected to strain and various factors involved in the stretch-induced signal transduction pathway. In this regard, we have reported previously that mechanical force increases keratinocyte growth and protein synthesis and alters cell morphology. The mechanism by which strain causes an enhancement of cellular growth appears to be a network of several integrated cascades, implicating growth factors, cytoskeleton, and the protein kinase family. Recently, additional evidence has accumulated that mechanical strain stimulates signal transduction pathways that could trigger a series of cascades eventually leading to a new skin production. For example, we have evidence suggesting a key role for protein kinase C (PKC) in mechanosignaling as PKC is activated and translocated in keratinocytes subjected to strain in an isoform-specific manner. In this report, molecular mechanisms leading to enhancement of skin surface area are reviewed, and possible future applications are discussed.
The design of uniformly and nonuniformly spaced pseudoquadrature mirror filters (1986)

In the past, quadrature mirror filters (QMF's) have been used to derive both uniformly and nonuniformly spaced filterbanks. A pair of QMF's divides a signal into two equal bands which can be decimated at 2:1 and subsequently combined to reconstruct the original signal. In order to derive filterbanks with more than two bands, QMF's are combined in a binary tree structure. Pseudoquadrature mirror filters are similar to QMF's but can be designed to split a signal directly into any number of equally spaced bands, thus generalizing the QMF concept. In this paper, the theory of pseudoquadrature mirror filters is reviewed. These filters retain the desirable property that the channel signals from a uniformly spaced bank of M filters can be decimated by M:1, then interpolated and reassembled to reproduce the original signal. An extension is made to the theory to allow a set of nonuniformly spaced filters to be derived from a uniformly spaced set and still retain all the desirable characteristics. Another extension to the theory is the derivation of a family of different sized filterbanks, all derived from the same original prototype. Potential applications for the new filterbanks include improvements in subband coding of speech and music, and analog scrambling of speech.
Curcumin inhibits endometriosis endometrial cells by reducing estradiol production. (2013)

In summary, in this study we found that E2 is important in ectopic endometrium, and epithelial cell is in dominant position with E2 secretion. Curcumin was able to suppress the proliferation of endometrial cells by reducing the E2 value.
Doping reaction of PH3 and B2H6 with Si(100) (1986)

The reaction of phosphine PH3 and diborane B2H6 on Si(100) surfaces was studied by surface analytical techniques in relation to the in situ doping process in the chemical vapor deposition of silicon. Phosphine chemisorbs readily either nondissociatively at room temperature or dissociatively with the formation of silicon–hydrogen bonds at higher temperatures. Hydrogen can be desorbed at temperatures above 400 °C to generate a phosphorus layer. Phosphorus is not effective in shifting the Fermi level until the coverage reaches 2×1014/cm2. A maximum shift of 0.45 eV toward the conduction band was observed. In contrast, diborane has a very small sticking coefficient and the way to deposit boron is to decompose diborane directly on the silicon surface at temperatures above 600 °C. Boron at coverages less than 2×1014/cm2 is very effective in shifting the Fermi level toward the valence band and a maximum change of 0.4 eV was observed.
Reflexive collision avoidance: a generalized approach (2002)

A generalized approach to reflexive obstacle avoidance is proposed. Reflex control is a method that guarantees collision avoidance with minimum nonessential influence on higher-level controls. The reflex controller described consists of two sub-modules: the C-space inspector and the active reflex controller. The C-space inspector inspects and approves prisms in C-space that are free from obstacles. The active reflex controller acts like a filter with respect to collision avoidance, which approves or replaces higher-level commands based on the free-space prisms returned from the C-space inspector. The reflex controller serves well as a building block in obstacle avoidance and path planning algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
EXAFS Investigations of the Mechanism of Facilitated Ion Transfer into a Room-Temperature Ionic Liquid (2002)

The Sr(II)-crown ether complexes formed in a room-temperature ionic liquid (RTIL), 1-methyl-3-pentylimidazolium bis[(trifluoromethyl)sulfonyl]amide, have been studied by X-ray absorption fine structure measurements at the Sr K-edge. When a Sr(NO(3))(2)-crown ether complex is directly dissolved in a water-saturated RTIL, both nitrate ligands and the crown ether coordinate the Sr, as observed in a conventional two-phase water-octanol system. When the cationic Sr-crown ether complex is created in a two-phase water-RTIL system, however, only cationic Sr-crown ether complexes are observed in the RTIL phase. This difference in the coordination complexes arises from differences in the mechanism of cation extraction between the RTIL and conventional molecular organic solvents, a finding with important implications for synthesis, catalysis, and ion separations using two-phase water-RTIL systems.
Phase I Safety, Pharmacokinetics, and Clinical Activity Study of Lapatinib (GW572016), a Reversible Dual Inhibitor of Epidermal Growth Factor Receptor Tyrosine Kinases, in Heavily Pretreated Patients With Metastatic Carcinomas (2005)

Lapatinib was well tolerated at doses ranging from 500 to 1,600 mg once daily. Clinical activity was observed in heavily pretreated patients with ErbB1-expressing and/or ErbB2-overexpressing metastatic cancers, including four PRs in patients with trastuzumab-resistant breast cancers and prolonged stable disease in 10 patients.
Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase (2001)

Functional consequences of 12 mutations-10 missense, 1 splicing defect, and 1 frameshift mutation-were characterized in the uroporphyrinogen decarboxylase (URO-D) gene found in Utah pedigrees with familial porphyria cutanea tarda (F-PCT). All but one mutation altered a restriction site in the URO-D gene, permitting identification of affected relatives using a combination of polymerase chain reaction and restriction enzyme digestion. In a bacterial expression system, 3 of the missense mutants were found in inclusion bodies, but 7 were expressed as soluble proteins. Enzymatic activity of soluble, recombinant mutant URO-D genes ranged from 29% to 94% of normal. URO-D mRNA levels in Epstein-Barr-virus transformed cells derived from patients were normal (with the exception of the frameshift mutation) even though protein levels were lower than normal, suggesting that missense mutations generally cause unstable URO-Ds in vivo. The crystal structures of 3 mutant URO-Ds were solved, and the structural consequences of the mutations were defined. All missense mutations reported here and by others were mapped to the crystal structure of URO-D, and structural effects were predicted. These studies define structural and functional consequences of URO-D mutations occurring in patients with F-PCT.
Oral fumaric acid esters for the treatment of active multiple sclerosis: an open‐label, baseline‐controlled pilot study (2006)

An exploratory, prospective, open-label study of fumaric acid esters (FAE, Fumaderm(R)) was conducted in patients with relapsing-remitting multiple sclerosis (RRMS). The study consisted of the following four phases: 6-week baseline, 18-week treatment (target dose of 720 mg/day), 4-week washout, and a second 48-week treatment phase (target dose of 360 mg/day). Ten patients with an Expanded Disability Status Scale (EDSS) score of 2.0-6.0 and at least one gadolinium-enhancing (Gd+) lesion on T1-weighted magnetic resonance imaging (MRI) brain scans participated in the study. Safety was assessed by adverse events (AEs), blood chemistry/hematology, electrocardiogram, and urinalysis. The primary efficacy outcomes were number and volume of Gd+ lesions. Other clinical outcomes included EDSS score, ambulation index (AI), and nine-hole peg test (9-HPT). Effects of FAE on intracellular cytokine profiles, T-cell apoptosis, and soluble adhesion molecules were also assessed. Three patients withdrew during the first 3 weeks of the study because of side effects, non-compliance, and follow-up loss. The most common AEs were gastrointestinal symptoms and flushing; all AEs were reported as mild and reversible. FAE produced significant reductions from baseline in number (P < 0.05) and volume (P < 0.01) of Gd+ lesions after 18 weeks of treatment; this effect persisted during the second treatment phase at half the target dose after the 4-week washout period. EDSS scores, AI, and 9-HPT remained stable or slightly improved from baseline in all patients. Measures of T-cell function demonstrated alterations in cytokines and circulating tumor necrosis factor. The results of this exploratory study suggest that further studies of FAE in patients with MS are warranted.
Genomic DNA sequence for human C-reactive protein. (1985)

The gene for the prototype acute phase reactant, C-reactive protein, has been isolated from two lambda phage libraries containing inserted human DNA fragments using synthetic oligonucleotide probes. Nucleotide sequence analysis indicates that after coding for a signal peptide of 18 amino acids and the first two amino acids of the mature protein, there is an intron of 278 base pairs followed by the nucleotide sequence for the remaining 204 amino acids. The intron is unusual in that it contains on the positive strand a poly(A) stretch 16 nucleotides long and a poly(GT) region 30 nucleotides long which could adopt the Z-form of DNA. The nucleotide sequence reported here confirms the amino acid sequence of mature C-reactive protein as originally reported except that it codes for an additional 19 amino acids beginning at position 62. Thus DNA sequence analysis predicts that the mature protein consists of 206 amino acids rather than 187 as originally reported. The mRNA cap site is located 104 nucleotides from the start of the signal peptide and there is a 3' noncoding region 1.2 kilobase pairs in length. The gene has a typical promoter containing the sequences TATAAAT and CAAT 29 and 81 base pairs upstream, respectively, of the cap site.
Beneficial effects of the phosphodiesterase inhibitors BRL 61063, pentoxifylline, and rolipram in a murine model of endotoxin shock. (1994)

Three inhibitors of calcium-dependent cyclic adenosine 3'5'-monophosphate (cAMP) dependent phosphodiesterase IV (PDE IV) were evaluated for their effects on lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF) production in vitro and in vivo and for their ability to protect mice from LPS-induced lethality in D-galactosamine (D-gal) sensitized mice. In vitro, on LPS-stimulated murine peritoneal macrophages (PEM), BRL 61063 (1,3-di(cyclopropylmethyl)-8-aminoxanthine) and rolipram (4-(3-cyclopentyloxy-4-methoxyphenyl)-2-pyrrolidone) had similar TNF inhibitory activity with an IC50 ranging from 0.1 to 0.5 microM. Pentoxifylline (PTX), (3,7-dimethyl-1-(5-oxohexyl)xanthine) was less potent with an IC50 = 100 microM. In vivo, there was a rank order potency on serum TNF levels in LPS challenged D-gal sensitized mice. BRL 61063 inhibited TNF production with an ID50 of 0.1 mg/kg, rolipram at 1 mg/kg, and PTX at 200 mg/kg. Thus, BRL 61063 is 2,000 times more potent than PTX in reducing TNF serum levels in this model. Interestingly, TNF is implicated as having a central pathogenic role in the LPS/D-gal model, since survival of animals correlated directly with reduction of serum TNF levels for all three compounds tested. It is proposed that potent inhibitors of TNF may have therapeutic activity in disease states where TNF appears to play a role in the pathogenesis of the disease.
Detecting and locating cell phone signals from avalanche victims using unmanned aerial vehicles (2015)

Scores of avalanche injuries and fatalities occur annually. This research presents an avalanche search and rescue (SAR) proof-of-concept option that utilizes a small unmanned aerial vehicle (UAV) helicopter with a payload capable of detecting and locating a buried victim's cell phone. Cell phones involved in this research were modern-day fourth generation (4G) Long Term Evolution (LTE) devices with an application specifically designed for potential SAR detection. This study focused primarily on radio frequency (RF) propagation modeling through snow and air. The analysis and associated field trials demonstrate that it is feasible to detect these cell phone devices through avalanche debris up to 7 feet deep. Alpine UAS inclement flight demonstrations were also conducted. Although many studies have been published on detecting the position of mobile cellular devices, this is the first of its kind to quantify the detection of a cell phone that is buried under the snow.
Alpha and β chemokines induce NK cell migration and enhance NK-mediated cytolysis (1995)

Chemokines have been shown to play an important role in both the adhesion and migration of numerous leukocytic cell types, including granulocytes, monocytes, mast cells, and T lymphocytes. However, the biologic effects of chemokines on NK cells remain to be defined. Chemotaxis studies using purified human NK cells and a panel of human recombinant chemokines revealed that macrophage inflammatory protein (MIP)-1 alpha and IFN-inducible protein-10 (IP-10) are potent NK cell chemoattractants in vitro. Modest but significant chemotactic (not chemokinetic) responses were also observed in response to RANTES, MCP-1, MCP-2, MCP-3, and MIP-1 beta. Chemokine receptor expression on human NK cells was determined through displacement and Scatchard analyses, using a panel of radiolabeled chemokines, and revealed the presence of both distinct and shared chemokine receptors with affinities similar to those previously described for other cell types. Functional studies have also revealed that the beta chemokines and IP-10 are capable of augmenting NK- but not LAK- or ADCC-specific cytolytic responses in both a dose- and donor-dependent fashion. Neutralization analysis using Abs specific for various adhesion molecules revealed that NK:tumor cell conjugate formation is required for chemokine-induced NK killing. In addition, NK cells incubated in the presence of beta chemokines and IP-10 for 4 h induced the release of granule-derived serine esterases, suggesting a possible mechanism for chemokine-mediated NK killing. These results suggest that chemokines not only play an important role in the recruitment of NK cells, but also may be important mediators of NK cell degranulation augmenting local tumor cell destruction.
The pKaof the General Acid/Base Carboxyl Group of a Glycosidase Cycles during Catalysis:  A13C-NMR Study ofBacillus circulansXylanase (1996)

The 20 kDa xylanase from Bacillus circulans carries out hydrolysis of xylan via a two-step mechanism involving a covalent glycosyl-enzyme intermediate. In this double-displacement reaction, Glu78 functions as a nucleophile to form the intermediate, while Glu172 acts as a general acid catalyst during glycosylation, protonating the departing aglycone, and then as a general base during deglycosylation, deprotonating the attacking water. The dual role of Glu172 places specific demands upon its ionization states and hence pKa values. 13C-NMR titrations of xylanase, labeled with [delta-13C]glutamic acid, have revealed pKa values of 4.6 and 6.7 for Glu78 and Glu172, respectively. These agree well with the apparent pKa values obtained from a study of the pH dependence of kcat/Km and demonstrate that, at the enzyme's pH optimum of 5.7, the nucleophile Glu78 is deprotonated and the general acid Glu172 initially protonated. Remarkably, the pKa for Glu172 drops to 4.2 in a trapped covalent glycosyl-enzyme intermediate, formed by reaction with 2', 4'-dinitrophenyl 2-deoxy-2-fluoro-beta-xylobioside [Miao et al. (1994) Biochemistry 33, 7027-7032]. A similar pKa is measured for Glu172 when a glutamine is present at position 78. This large decrease in pKa of approximately 2.5 units is consistent with the role of Glu172 as a general base catalyst in the deglycosylation step and appears to be a consequence of both reduced electrostatic repulsion due to neutralization of Glu78 and a conformational change in the protein. Such "pKa cycling" during catalysis is likely to be a common phenomenon in glycosidases.
Excess “read-through” acetylcholinesterase attenuates but the “synaptic” variant intensifies neurodeterioration correlates (2000)

Acute stress increases the risk for neurodegeneration, but the molecular signals regulating the shift from transient stress responses to progressive disease are not yet known. The "read-through" variant of acetylcholinesterase (AChE-R) accumulates in the mammalian brain under acute stress. Therefore, markers of neurodeterioration were examined in transgenic mice overexpressing either AChE-R or the "synaptic" AChE variant, AChE-S. Several observations demonstrate that excess AChE-R attenuates, whereas AChE-S intensifies, neurodeterioration. In the somatosensory cortex, AChE-S transgenics, but not AChE-R or control FVB/N mice, displayed a high density of curled neuronal processes indicative of hyperexcitation. In the hippocampus, AChE-S and control mice, but not AChE-R transgenics, presented progressive accumulation of clustered, heat shock protein 70-immunopositive neuronal fragments and displayed a high incidence of reactive astrocytes. Our findings suggest that AChE-R serves as a modulator that may play a role in preventing the shift from transient, acute stress to progressive neurological disease.
Insect olfaction from model systems to disease control (2011)

Great progress has been made in the field of insect olfaction in recent years. Receptors, neurons, and circuits have been defined in considerable detail, and the mechanisms by which they detect, encode, and process sensory stimuli are being unraveled. We provide a guide to recent progress in the field, with special attention to advances made in the genetic model organism Drosophila. We highlight key questions that merit additional investigation. We then present our view of how recent advances may be applied to the control of disease-carrying insects such as mosquitoes, which transmit disease to hundreds of millions of people each year. We suggest how progress in defining the basic mechanisms of insect olfaction may lead to means of disrupting host-seeking and other olfactory behaviors, thereby reducing the transmission of deadly diseases.
Effect of Film-Forming Compounds on the Development of Leaf Rust on Wheat Seedlings (1991)

The effect of film-forming antitranspirants and glues on the development of leaf rust (caused by Puccinia recondita f. sp. tritici) was assessed on wheat seedlings (Triticum aestivum «Ceeon»). When applied before rust inoculation, the compounds Bio-Film, Folicote, and Vapor Gard markedly reduced the number of pustules per square centimeter. Postinoculation application had a significantly smaller effect on suppression of rust development (.)