gebhart/patrepeval huggingface dataset:
Physical parameters affecting the rate and completing of RNA driven hybridization of DNA: new measurements relevant to quantitation based on kinetics (1982)

Differences in the RNA-driven hybridization kinetics of genomic DNA and cDNA probes led us to examine physical parameters affecting these reactions. Cloned cDNA complementary to serum albumin (SA) mRNA hybridized in accordance with single component kinetics, whereas cloned SA genomic DNA hybridized more slowly and with multiple component kinetics. This difference is largely attributable to the relatively short and variable lengths of the mRNA complementary regions in the cloned genomic DNA. The rate of mRNA driven hybridization is affected to about half the extent observed for DNA renaturation as Na+ is increased or decreased from 0.18M. In the annealing of nucleic acids of high sequence complexity, after approximately 70% of reaction has been reached, the rate of the reaction is slowed and completion is not reached under "static" conditions. In practical terms, this is not the case for systems of low sequence complexity. This problem can be largely overcome by continuous or frequent mixing of the reactants, so that complex cDNA probes are hybridized essentially to completion, and kinetics can therefore be more readily compared to simple complexity standards.
A phase II evaluation of nab-paclitaxel in the treatment of recurrent or persistent platinum-resistant ovarian, fallopian tube, or primary peritoneal cancer: A Gynecologic Oncology Group (GOG) study. (2010)

5010 Background: Nab-paclitaxel (Abraxane, ABX) is a novel cremophor-free nanoparticle of albumin-stabilized paclitaxel, which has favorable efficacy and toxicity characteristics relative to other solvent-based taxanes, such as paclitaxel and docetaxel, and is currently approved for recurrent breast cancer. This is the first report of weekly abraxane in patients with recurrent ovarian, fallopian tube or peritoneal cancer (OC). Methods: Eligible patients had OC, that was persistent (n = 5) or progressed within 6 months of completion (n = 42) of primary platinum and taxane-based chemotherapy. All patients were required to have measurable disease, no prior therapy for recurrent disease and GOG performance status of ≤ 2. Treatment was ABX 100 mg/m2 days 1,8,15 on a 28-day schedule. The primary endpoint was RECIST response rate (RR), evaluated in a 2-stage design (with power of 0.90 for a RR of 25% and with alpha of 0.05 for RR of 10%). Results: 51 patients were enrolled, of which 47 are evaluable; median time from frontline therapy completion to registration was just 21 days. Patient demographics include median age: 59 (34-78) years, primary site ovary: 87%, serous histology: 72%, and high-grade: 81%. All patients had measurable disease, one prior chemotherapy regimen and prior surgery. Efficacy: partial response was confirmed in 11 patients (23%); 17 patients (36%) had stable disease. The median progression-free survival (PFS) was 4.5 months (95%CI: 2.1-6.7); overall survival was 17.4 months (95%CI: 12.5, not estimable). 17 patients (36%) had PFS > 6 months. Toxicity: there were no grade 4 events; grade 3 events were neutropenia (6), anemia (3), GI (2), metabolic (2), pain (2), and leukopenia (1); neurosensory toxicity was observed as grade 2: 5; and grade 3: 1. Conclusions: ABX appears to have substantial single-agent activity and to be tolerable in this cohort of highly refractory ovarian cancer patients previously treated with paclitaxel, and further investigation is warranted. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Abraxis BioScience Abraxis BioScience
Silicon on quartz by solid-state diffusion bonding (SSDB) technology (1988)

Silicon wafer and quartz have been successfully bonded together by a two-step thermal treatment process. SIMS measurements shows that after molecular surface activated solvent treatment, the amount of OH on the silicon or quartz surface, which is essential to the first step (low-temperature) bonding strength, is one order of magnitude higher than that on the original silicon or quartz surface. After a high-temperature (850–1250°C) solid-state diffusion process, the bonding strength between silicon and quartz is greatly increased to 150–185 kg/cm2. The material and electrical properties of the silicon on quartz substrate compares favourably with those of the bulk silicon wafer.
Phospholipid vesicle formation and transmembrane protein incorporation using octyl glucoside (1981)

Removal of detergent from mixed micelles of egg yolk phosphatidylcholine and octyl glucoside leads to formation of unilamellar phospholipid vesicles with a diameter of about 230 nm. The same procedure applied to mixed micelles containing the transmembrane protein glycophorin A, in addition to lipid and detergent, produces vesicles of the same size with glycophorin incorporated into the bilayer. The pure lipid vesicles are highly impermeable to both anions and cations, and incorporation of up to 220 molecules of glycophorin per vesicle has little effect on permeability.
Purification of chondroitin 6-sulfotransferase secreted from cultured chick embryo chondrocytes. (1993)

Chondroitin 6-sulfotransferase, which transfers sulfate from 3'-phosphoadenylyl sulfate to position 6 of N-acetylgalactosamine in chondroitin, was purified 1,430-fold to apparent homogeneity with a 22% yield from the serum-free culture medium of chick embryo chondrocytes by affinity chromatography on heparin-Sepharose CL-6B, wheat germ agglutinin-agarose, and 3',5'-ADP-agarose. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme showed a single broad protein band with an apparent molecular weight of 75,000. Since the purified enzyme has an apparent molecular weight of 160,000 as judged by gel chromatography on Superose 12, the active form of chondroitin 6-sulfotransferase may be a dimer. The purified enzyme transferred sulfate to chondroitin, chondroitin sulfate, and corneal keratan sulfate. Chondroitin sulfate E from squid cartilage, dermatan, sulfate, and heparan sulfate hardly served as acceptors of the sulfotransferase. The sulfated product derived from keratan sulfate was degraded by keratanase but not by chondroitinase ABC.
A novel wavelength-division-demultiplexer with optical in-plane to surface-normal conversion (1995)

We present a novel surface normal optical wavelength-division-demultiplexer (WDDM), working at 750, 770, 790, 810, 830, and 850 nm wavelengths. The device is based on the integration of a polymer-based planar waveguide, a substrate waveguiding plate, and waveguide holograms. The unique optical in-plane to surface-normal conversion converts the difficult three spatial and three angular edge coupling problem into a planar surface one, resulting in a reliable miniaturized optoelectronic packaging containing a photodetector array and the WDDM. A six-channel wavelength-division-demultiplexer with equally spaced collinear surface-normal outputs are designed and demonstrated in a polymer-based planar waveguide in conjunction with holograms on a glass substrate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Measurement of Total Starch in Cereal Products by Amyloglucosidase-α-Amylase Method: Collaborative Study (1997)

Abstract American Association of Cereal Chem- ists/AOAC collaborative study was conducted to evaluate the accuracy and reliability of an enzyme assay kit procedure for measurement of total starch in a range of cereal grains and products. The flour sample is incubated at 95°C with thermostable α-amylase to catalyze the hydrolysis of starch to maltodextrins, the pH of the slurry is adjusted, and the slurry is treated with a highly purified amyloglucosidase to quantitatively hydrolyze the dextrins to glucose. Glucose is measured with glucose oxidase-peroxidase reagent. Thirty-two collaborators were sent 16 homogeneous test samples as 8 blind duplicates. These samples included chicken feed pellets, white bread, green peas, high- amylose maize starch, white wheat flour, wheat starch, oat bran, and spaghetti. All samples were analyzed by the standard procedure as detailed above; 4 samples (high-amylose maize starch and wheat starch) were also analyzed by a method that requires the samples to be cooked first in dimethyl sulfoxide (DMSO). Relative standard deviations for repeatability (RSDr) ranged from 2.1 to 3.9%, and relative standard deviations for reproducibility (RSDr) ranged from 2.9 to 5.7%. The RSDr value for high amylose maize starch analyzed by the standard (non-DMSO) procedure was 5.7%; the value
Revised amino acid sequence of Qbeta coat protein between positions 1 and 60. (1977)

A reinvestigation of the primary structure of Qbeta coat protein between positions 1 and 60 was undertaken to resolve two discrepancies between the published amino acid seuqence (Maita, T., and Konigsberg, W. (1971) J. Biol. Chem. 246, 5003-5024) and the cognate nucleotide sequence recently determined in our laboratory (C. Escarmis and M. A. Billeter, unpublished results). The 22nd amino acid was asparagine rather than aspartic acid, and an additional amino acid, serine, was present between proline in position 55 and arginine in position 56. The revised structure agrees with the nucleotide sequence determined so far.
MBP-Specific Experimental Autoimmune Encephalomyelitis in C57BL/6 Mice (2004)

Experimental autoimmune encephalomyelitis-resistant mice have highly encephalitogenic myelin basic protein (MBP)speci c T cell clones that recognize a MBP peptide with high a nity for MHC class II.
Hybrid hepatitis B virus core-pre-S proteins synthesized in avirulent Salmonella typhimurium and Salmonella typhi for oral vaccination (1994)

Avirulent salmonellae expressing foreign genes are attractive for use as oral vaccine carriers. To facilitate the stable expression of heterologous genes without conferring antibiotic resistance, a deletion of the asdA1 gene was introduced into Salmonella typhimurium and S. typhi delta cya delta crp mutant vaccine strains. An asd-complementing plasmid expressing hybrid hepatitis B virus nucleocapsid-pre-S (HBcAg-pre-S) particles was constructed. These hybrid HBcAg-pre-S particle genes were stably expressed in S. typhimurium and S. typhi delta cya delta crp mutant vaccine strains in this balanced, lethal host-vector combination. A single oral immunization of BALB/c mice with a recombinant S. typhimurium delta cya delta crp mutant synthesizing hybrid HBcAg-pre-S elicited potentially virus-neutralizing anti-pre-S serum immunoglobulin G antibodies. In addition, serum immunoglobulin G recognizing S. typhimurium lipopolysaccharide was induced. Distribution in tissue after oral immunization was analyzed in one plasmid-strain combination. The recombinant S. typhimurium colonized the gut-associated lymphoid tissue and the spleen and persisted for over 4 weeks, retaining the HBcAg-pre-S expression plasmid. An isogenic virulence plasmid-cured S. typhimurium delta cya delta crp strain expressing the same HBcAg-pre-S gene had reduced immunogenicity for the carried antigen after oral immunization.
GeoLANMAR: Geo Assisted Landmark Routing for Scalable, Group Motion Wireless Ad Hoc Networks (2005)

Network scalability becomes a critical issue when it is associated to the routing protocols for ad hoc networks. It is important to design protocols able to manage the state information stored in the mobile nodes and the control protocol overhead so that they scale to the increasing number of nodes in the network. Our proposed approach is to use a hybrid routing protocol, with local scope table-driven routing and long distance geo-forwarding. This approach permits to overcome possible location inaccuracies that affect flat geo-routing (e.g. inaccurate GPS) and most important to reduce the routing update overhead of flat link-state protocol. In this framework, the integration between geo-coordinate and table-driven IP addressing is introduced. The proposed protocol, called geo assisted landmark routing (GeoLANMAR), integrates group management with geo-forwarding and IP group management performance evaluation shows the scalability improvement of the GeoLANMAR protocol in terms of control overhead as compared with the standard landmark routing protocol
Topical Application of Ketoconazole Stimulates Hair Growth in C3H/HeN Mice (2005)

Ketoconazole (KCZ) is an imidazole anti-fungal agent that is also effective in topical applications for treating seborrheic dermatitis and dandruff. Recently, topical use of 2% KCZ shampoo has been reported to have had a clinically therapeutic effect on androgenetic alopecia. The present study was conducted with the purpose of quantitatively examining the stimulatory effect of KCZ on hair growth in a mouse model. Coat hairs on the dorsal skin of seven week-old male C3H/HeN mice were gently clipped, and either 2% KCZ solution in 95% ethanol or a vehicle solution was topically applied once daily for three weeks. The clipped area was photographed, and the ratio of re-grown coat area was then calculated. The results demonstrated that 2% KCZ had a macroscopically significant stimulatory effect compared with the vehicle group (p<0.01, n=10). Repeated experiments showed similar effects, confirming the efficacy of KCZ as a hair growth stimulant. Although the therapeutic mechanism of topical KCZ for hair growth is unclear, our results suggest that topical applications of the substance are useful for treating seborrheic dermatitis accompanied by hair regression or male pattern hair loss.
Effects of Diethyl Spermine Analogues in Human Bladder Cancer Cell Lines in Culture (1993)

The biochemical and antiproliferative effects of two recently developed N-alkylated analogues of naturally-occurring polyamines, N1,N14-diethylhomospermine (DEHSPM) and N1,N11-diethylnorspermine (DENSPM), were investigated in two human transitional cell carcinoma (TCC) lines, T24 and J82. Parallel studies with the ornithine decarboxylase enzyme inhibitor alpha-difluoromethylornithine (DFMO) were included for comparison. DENSPM displayed greater antiproliferative activity than DEHSPM in both TCC cell lines. Both analogues were strikingly more potent than DFMO. DEHSPM and DENSPM suppressed the activity of the major biosynthetic enzymes, ornithine decarboxylase and S-adenosylmethionine decarboxylase. However, differences in the resulting polyamine depletion suggest that the substantial antiproliferative activity of these analogues may result from mechanisms other than polyamine depletion. The greater polyamine depletion seen with DENSPM is thought to result from its striking induction of spermidine/spermine N1-acetyltransferase. DENSPM is an attractive agent for further preclinical and clinical development, possibly as a chemopreventive agent, in TCC of the bladder.
Programming the shape-shifting of flat soft matter: from self-rolling/self-twisting materials to self-folding origami (2016)

Rational programming of the shape-shifting behavior of flat materials (possibly decorated with complex surface features) to create complex three-dimensional structures.
Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP cyclohydrolase II in Escherichia coli (1993)

GTP cyclohydrolase II catalyzes the first committed step in the biosynthesis of riboflavin. The gene coding for this enzyme in Escherichia coli has been cloned by marker rescue. Sequencing indicated an open reading frame of 588 bp coding for a 21.8-kDa peptide of 196 amino acids. The gene was mapped to a position at 28.2 min on the E. coli chromosome and is identical with ribA. GTP cyclohydrolase II was overexpressed in a recombinant strain carrying a plasmid with the cloned gene. The enzyme was purified to homogeneity from the recombinant strain. The N-terminal sequence determined by Edman degradation was identical to the predicted sequence. The sequence is homologous to the 3' part of the central open reading frame in the riboflavin operon of Bacillus subtilis.
Gestalt Theory Rearranged: Back to Wertheimer (2017)

Wertheimer’s seminal paper of 1923 was of gerat influence in psychology and other sciences. Wertheimer also emphasized the weaknesses of the newborn Gestalt theory: too many basic laws, and the ambiguity of definitions. At the same time, the paper contained potential solutions to these problems, in the form of a number of very important ideas, some of which were presented implicitly: perception through imitation, communicative nature of linear drawings and writings, transfer from the visual domain to motor domain, linguistic interpretation of the Gestalt. In this paper it will be shown that based on these ideas the Gestalt theory can be rearranged so that the main notions can be well defined, and the general principle of Gestalt perception, which overarches all known laws and unifies different Gestalt phenomena (the imitation principle) can be introduced. The presented model of Gestalt perception is supported by fundamental neurophysiological data – the mirror neurons phenomenon and simulation theory.
A form of circulating ICAM-1 in human serum (1991)

A circulating form of the usually membrane-bound intercellular adhesion molecule-1 (ICAM-1) was identified and characterized in normal human serum, and in sera from patients with leukocyte adhesion deficiency (LAD). The molecule, designated circulating ICAM-1 (cICAM-1) was detected and quantitated by sandwich ELISA. Levels of cICAM-1 in sera from normal individuals ranged from 100 to 200 ng/ml. Sera from LAD patients had elevated cICAM-1 levels ranging from 200 to 700 ng/ml. The elevated levels of cICAM-1 in LAD sera may be due to an inability to adsorb cICAM-1 to cell-bound LFA-1 or may be an indirect result of the pathology accompanying the syndrome. cICAM-1 bound to mAb specific for four distinct ICAM-1 epitopes localized in domains D1, D2, D4, and D5, and displayed similar molecular size properties as recombinant soluble ICAM-1 on FPLC size-exclusion chromatography. When immobilized via a domain D5-specific mAb, cICAM-1 mediated function (LFA-1)-dependent lymphocyte adhesion equivalent to sICAM-1. These data indicate that cICAM-1 contains most, if not all, of the five extracellular domains of membrane ICAM-1, as well as the ability to bind specifically to LFA-1. The cellular source of cICAM-1 appeared to be from mononuclear cells; only lymphoid cell lines or primary PBMC cultures had detectable levels of cICAM-1 in cell culture supernatants. Because cICAM-1 retains the ability to bind specifically to LFA-1, it may act to regulate cell adhesion by promoting de-adhesion. Alternatively, cICAM-1 may be the indirect consequence of inflammation or tissue damage. As such, the detection of cICAM-1 could be useful as a marker of inflammatory disease.
Two Microphones Speech Enhancement System Based On A Double Fast Recursive Least Squares (Dfrls) Algorithm (1996)

Publication in the conference proceedings of EUSIPCO, Trieste, Italy, 1996
New approaches in the management of insomnia: weighing the advantages of prolonged-release melatonin and synthetic melatoninergic agonists (2009)

Hypnotic effects of melatonin and melatoninergic drugs are mediated via MT(1) and MT(2) receptors, especially those in the circadian pacemaker, the suprachiasmatic nucleus, which acts on the hypothalamic sleep switch. Therefore, they differ fundamentally from GABAergic hypnotics. Melatoninergic agonists primarily favor sleep initiation and reset the circadian clock to phases allowing persistent sleep, as required in circadian rhythm sleep disorders. A major obstacle for the use of melatonin to support sleep maintenance in primary insomnia results from its short half-life in the circulation. Solutions to this problem have been sought by developing prolonged-release formulations of the natural hormone, or melatoninergic drugs of longer half-life, such as ramelteon, tasimelteon and agomelatine. With all these drugs, improvements of sleep are statistically demonstrable, but remain limited, especially in primary chronic insomnia, so that GABAergic drugs may be indicated. Melatoninergic agonists do not cause next-day hangover and withdrawal effects, or dependence. They do not induce behavioral changes, as sometimes observed with z-drugs. Despite otherwise good tolerability, the use of melatoninergic drugs in children, adolescents, and during pregnancy has been a matter of concern, and should be avoided in autoimmune diseases and Parkinsonism. Problems and limits of melatoninergic hypnotics are compared.
Mechanisms for laser control of chemical reactions (2002)

During the past several years, a new technique for realistic simulations of the interaction of light with matter has been developed and employed. Recent simulations of laser pulses interacting with molecules clearly demonstrate the potential for control of chemical reactions through various mechanisms, which include the following: (i) excitation of electrons to states that have different bonding properties; (ii) control of electron populations through a coherent pump-pulse, control-pulse sequence; and (iii) control of molecular vibrations through a pump-control sequence. Significant chemical insights are gained when one can watch a realistic animation of species interacting and reacting. One can monitor the time evolution of electronic states and their occupancy, as well as the motion of the atoms. One can also observe the evolution from reactants to products through transition states. Finally, one can determine how this evolution is affected by the various properties of the laser pulses, including intensity, duration, phase, and the interval between pulses.
Recruitment of the Sonic hedgehog signalling cascade in electroconvulsive seizure‐mediated regulation of adult rat hippocampal neurogenesis (2005)

Electroconvulsive seizure (ECS) induces structural remodelling in the adult mammalian brain, including an increase in adult hippocampal neurogenesis. The molecular mechanisms that underlie this increase in the proliferation of adult hippocampal progenitors are at present not well understood. We hypothesized that ECS may recruit the Sonic hedgehog (Shh) pathway to mediate its effects on adult hippocampal neurogenesis, as Shh is known to enhance the proliferation of neuronal progenitors and is expressed in the adult basal forebrain, a region that sends robust projections to the hippocampus. Here we demonstrate that the ECS-induced increase in proliferation of adult hippocampal progenitors was completely blocked in animals treated with cyclopamine, a pharmacological inhibitor of Shh signalling. Our results suggest that both acute and chronic ECS enhance Shh signalling in the adult hippocampus, as we observed a robust upregulation of Patched (Ptc) mRNA, a component of the Shh receptor complex and a downstream transcriptional target of Shh signalling. This increase was rapid and restricted to the dentate gyrus, where the adult hippocampal progenitors reside. In addition, both acute and chronic ECS decreased Smoothened (Smo) mRNA, the other component of the Shh receptor complex, selectively within the dentate gyrus. However, ECS did not appear to influence Shh expression within the basal forebrain, the site from which it has been suggested to be anterogradely transported to the hippocampus. Together, our findings demonstrate that ECS regulates the Shh signalling cascade and indicate that the Shh pathway may be an important mechanism through which ECS enhances adult hippocampal neurogenesis.