gebhart/patrepeval huggingface dataset:
Energy Loss of Hydrogen Atom due to Charge Exchange in Neutral Particle Energy Analyzer (1998)

A neutral particle energy analyzer, which has the carbon stripping foil and the cylindrical electrostatic deflection plate, was designed and constructed for measuring of ion temperature in plasma. The energy calibration and energy resolution were studied in detail for a hydrogen ion at the energy using a duoplasmatron ion source. An energy of hydrogen ion to the deflection plate voltage at the peak ion count rate could be fitted by the expression =3.83V(kV). The measured energy resolution, which was about 2 % at the energy of 3.0 keV and 9 % at the energy of 0.5keV, was better for the increased hydrogen ion energy. For the charge exchanged hydrogen atom due to the carbon stripping foil, the energy calibration, energy loss and resolution were measured to the thickness of the carbon stripping foil. An energy of the charge exchanged hydrogen atom as a function of the deflection plate voltage and carbon foil thickness could be fitted by the expression . The energy loss was to the carbon foil thickness and the energy of the incident neutral hydrogen atom, it could be fitted by the expression . The measured energy resolution for the neutral hydrogen atom, which was between 7 % and 35 % in this experiment region, was increased for the increasing neutral hydrogen atom energy and the decreasing carbon stripping foil thickness.
Effectiveness of Interventions to Reduce Tobacco Smoke Pollution in Homes: A Systematic Review and Meta-Analysis (2015)

Interventions designed to protect children from tobacco smoke are effective in reducing tobacco smoke pollution (as assessed by air nicotine or PM) in homes, but contamination remains. The persistence of significant pollution levels in homes after individual level intervention may signal the need for other population and regulatory measures to help reduce and eliminate childhood tobacco smoke exposure.
Aptamers and aptamer targeted delivery (2009)

When aptamers first emerged almost two decades ago, most were RNA species that bound and tagged or inhibited simple target ligands. Very soon after, the 'selectionologists' developing aptamer technology quickly realized more potential for the aptamer. In recent years, advances in aptamer techniques have enabled the use of aptamers as small molecule inhibitors, diagnostic tools and even therapeutics. Aptamers are now being employed in novel applications. We review, herein, some of the recent and exciting applications of aptamers in cell-specific recognition and delivery.
Phosphate buffer-stabilized 0.1% chlorine dioxide-containing mouth wash facilitated sequestration of Bishphosphonate Related Osteonecrosis of jaw (BRONJ) lesion from a patient who presented with Osteonecrosis of the jaw and a history of intravenous bispho (2010)

Background: Inconclusive protocol and consensus exist at present time regarding treatment of patients who have developed Osteonecrosis of the Jaw (ONJ) following administration of intravenous Bisphosphonates. Most clinicians areÂ avoiding treatment for patients presenting with Â BRONJ due to lack of predictable treatment outcome.
Findings: In this case report, patient was suffering from a non healing lesion on anterior mandible, which was not responsive to any conventional treatment. Patient was recommended to rinse with the PBSCD for treatment of BRONJÂ (Bisphosphonate Related Osteonecrosis of the Jaw) lesion seen on some patients who were on intravenous Bisphosphonate medications for multiple myeloma. Â Patient was recommended to rinse three times a day with PBSCD. After 4Â month use of the solution patient presented with soft tissue healing on previously exposed necrotic bone on mandibular anterior region.
Conclusion: The benefit of Phosphate buffer-stabilized 0.1% chlorine dioxide-containing mouth wash (PBSCD) is discussed. This is a non invasive protocol that has proved to be effective in closing of an open wound.
Hydrolysis of TiCl4: Initial Steps in the Production of TiO2 (2010)

The hydrolysis of titanium tetrachloride (TiCl(4)) to produce titanium dioxide (TiO(2)) nanoparticles has been studied to provide insight into the mechanism for forming these nanoparticles. We provide calculations of the potential energy surfaces, the thermochemistry of the intermediates, and the reaction paths for the initial steps in the hydrolysis of TiCl(4). We assess the role of the titanium oxychlorides (Ti(x)O(y)Cl(z); x = 2-4, y = 1, 3-6, and z = 2, 4, 6) and their viable reaction paths. Using transition-state theory and RRKM theory, we predicted rate constants including the effect of tunneling. Heats of formation at 0 and 298 K are predicted for TiCl(4), TiCl(3)OH, TiOCl(2), TiOClOH, TiCl(2)(OH)(2), TiCl(OH)(3), Ti(OH)(4), and TiO(2) using the CCSD(T) method with correlation consistent basis sets extrapolated to the complete basis set limit and compared with the available experimental data. Clustering energies and heats of formation are calculated for neutral clusters. The calculated heats of formation were used to study condensation reactions that eliminate HCl or H(2)O. The reaction energy is substantially endothermic if more than two HCl molecules are eliminated. The results show that the mechanisms leading to formation of TiO(2) nanoparticles and larger ones are complicated and will have a strong dependence on the experimental conditions.
PDK1 and SGK3 Contribute to the Growth of BRAF-Mutant Melanomas and Are Potential Therapeutic Targets (2015)

Melanoma development involves members of the AGC kinase family, including AKT, PKC, and, most recently, PDK1, as elucidated recently in studies of Braf::Pten mutant melanomas. Here, we report that PDK1 contributes functionally to skin pigmentation and to the development of melanomas harboring a wild-type PTEN genotype, which occurs in about 70% of human melanomas. The PDK1 substrate SGK3 was determined to be an important mediator of PDK1 activities in melanoma cells. Genetic or pharmacologic inhibition of PDK1 and SGK3 attenuated melanoma growth by inducing G1 phase cell-cycle arrest. In a synthetic lethal screen, pan-PI3K inhibition synergized with PDK1 inhibition to suppress melanoma growth, suggesting that focused blockade of PDK1/PI3K signaling might offer a new therapeutic modality for wild-type PTEN tumors. We also noted that responsiveness to PDK1 inhibition associated with decreased expression of pigmentation genes and increased expression of cytokines and inflammatory genes, suggesting a method to stratify patients with melanoma for PDK1-based therapies. Overall, our work highlights the potential significance of PDK1 as a therapeutic target to improve melanoma treatment.
Simple model of spiking neurons (2003)

A model is presented that reproduces spiking and bursting behavior of known types of cortical neurons. The model combines the biologically plausibility of Hodgkin-Huxley-type dynamics and the computational efficiency of integrate-and-fire neurons. Using this model, one can simulate tens of thousands of spiking cortical neurons in real time (1 ms resolution) using a desktop PC.
New design strategy for improving hardware Trojan detection and reducing Trojan activation time (2009)

Hardware Trojans in integrated circuits and systems have become serious concern to fabless semiconductor industry and government agencies in recent years. Most of the previously proposed Trojan detection methods rely on Trojan activation to either observe a faulty output or measure side-channel signals such as transient current or charge. From the authentication stand point, time to trigger a hardware Trojan circuit is a a major concern. This paper analyzes time to (i) generate a transition in functional Trojans and (ii) fully activate them. An efficient dummy flip-flop insertion procedure is proposed to increase Trojan activity. Depending on authentication time and circuit topology, a transition probability threshold is selected so that inserted dummy flip-flops would moderately impact area overhead. The simulation results on s38417 benchmark circuit demonstrate that, with a negligible area overhead, our proposed method can significantly increase Trojan activity and reduce Trojan activation time.
Characterization of an antisense Inr element in the eIF-2 alpha gene. (1994)

We recently discovered an opposing initiator promoter (Inr) downstream of the sense promoter region of the eIF-2 alpha gene (Silverman, T., Noguchi, M., and Safer, B. (1992) J. Biol. Chem. 267, 9738-9742). By reverse transcriptase/polymerase chain reaction analysis of G0 and activated (G1) T-lymphocyte RNAs, overlapping sense and antisense transcripts are now identified. Sense transcription of the eIF-2 alpha gene proceeds from left to right to generate alpha-mRNA; antisense transcription proceeds from right to left to generate RNA, having a sequence complementary to eIF-2 alpha mRNA. Upstream indicates a position 5' relative to the transcription start site. Using DNase I footprint analysis and EMSA, we have found a potential cis-regulatory sequence immediately upstream of the Inr which binds a 43-kDa protein. In addition to conferring protection against DNase I (+457 to +474), the factor also generates hypersensitive sites directly over the Inr (+447 to +457). Insertion of the Inr footprint region into a luciferase reporter gene construct increases expression 150-fold. While mutation of the Inr conserved sequence decreases luciferase activity by 50%, mutation of the 43-kDa factor binding site inhibits luciferase activity by 20%. Sense orientation of the Inr footprint region decreases activity by 80%. The 43-kDa Inr-associated binding protein may be involved in allowing access of RNA polymerase II transcription complexes ot the initiation site of this TATA-less gene. A model for the regulation of eIF-2 alpha expression involving the rapid degradation of dsRNA generated by the relative activities of the two overlapping and opposing promoters is proposed.
Cloning and characterization of a human type II receptor for bone morphogenetic proteins. (1995)

Bone morphogenetic proteins (BMPs) are members of the transforming growth factor beta superfamily. Several members of this family have been shown to transduce their signals through binding to type I and type II serine-(threonine) kinase receptors. Here we report the cDNA cloning and characterization of a human type II receptor for BMPs (BMPR-II), which is distantly related to DAF-4, a BMP type II receptor from Caenorhabditis elegans. In transfected COS-1 cells, osteogenic protein (OP)-1/BMP-7, and less efficiently BMP-4, bound to BMPR-II. BMPR-II bound ligands only weakly alone, but the binding was facilitated by the presence of previously identified type I receptors for BMPs. Binding of OP-1/BMP-7 to BMPR-II was also observed in nontransfected cell lines. Moreover, a transcriptional activation signal was transduced by BMPR-II in the presence of type I receptors after stimulation by OP-1/BMP-7.
Techniques for Rearing Laboratory Colonies of Tobacco Hornworms and Pink Bollworms1 (1976)

Larval tobacco hornworms, Manduca sexta (L.), were individually reared in polystyrene containers on an artificial diet. The developmental period (egg to adult) was completed in ca. 40 days at 26° C, which allowed production of 9 generations/year. Weights of the 5th stage larvae and pupae ranged from 7.5-9 g and 4.0-5.5 g, respectively. Survival of the immature stages ranged from 94-97%. Cage populations of 50-70 pairs of adults yielded 5000+ eggs/day when night temperatures were maintained at 26-28°C. From 1000-5000 hornworms were produced each week at an estimated cost (excluding labor and overhead) of ca. 30/1000. Colonies of the pink bollworm, Pectinophora gossypiella (Saunders), were also reared on the tobacco hornworm diet. The larvae were reared individually in polystyrene vials covered with polyethylene caps which prevented excessive drying of the larval diet even at low room humidities of 20-30%. Performance of the colony was as good as that of pink bollworms reared on other diets, and microbiol contamination was rarely encountered.
Colorimetric Nucleic Acid Testing Assay for RNA Virus Detection Based on Circle-to-Circle Amplification of Padlock Probes (2011)

We developed a molecular diagnostic method for detection of RNA virus based on padlock probes and colorimetric readout. The feasibility of our approach was demonstrated by using detection of Crimean-Congo hemorrhagic fever (CCHF) virus as a model. Compared with conventional PCR-based methods, our approach does not require advanced equipment, involves easier assay design, and has a sensitivity of 10(3) viral copies/ml. By using a cocktail of padlock probes, synthetic templates representing different viral strain variants could be detected. We analyzed 34 CCHF patient samples, and all patients were correctly diagnosed when the results were compared to those of the current real-time PCR method. This is the first time that highly specific padlock probes have been applied to detection of a highly variable target sequence typical of RNA viruses.
Telomere Length Trajectory and Its Determinants in Persons with Coronary Artery Disease: Longitudinal Findings from the Heart and Soul Study (2010)

Leukocyte telomere length may increase as well as decrease in persons with coronary artery disease. Telomere length trajectory is powerfully influenced by baseline telomere length, possibly suggesting negative feedback regulation. Age, male sex, and abdominal obesity independently predict telomere shortening. The mechanisms and reversibility of telomeric aging in cardiovascular disease deserve further study.
‘Camelising’ human antibody fragments: NMR studies on VH domains (1994)

A human heavy chain variable domain (VH) was expressed in bacteria for structural analysis by NMR spectroscopy. NMR analysis was initially impossible due to the short transverse proton relaxation time of the VH, probably caused by aggregation through the exposed interface naturally in contact with the light chain. The relaxation time was improved to normal values when this interface was mutated to mimic heavy chains of camel antibodies naturally devoid of light chains and through the use of the detergent CHAPS. Assignment of NMR signals will now be possible after isotopic labeling. Implications for the design of VH domains as minimum size immunoreagents are outlined.
Complex Coacervate Microcapsules for Mammalian Cell Culture and Artificial Organ Development (1993)

A number of combinations of anionic and cationic polymers, the majority being polysaccharides, were screened to determine their suitability for the development of alternative microcapsule formulations capable of supporting cells. The capsules were taken through a limited optimization and then evaluated on the bases of rupture strength, permeability to albumin, and ability of their components to promote the attachment, aggregation, and function of encapsulated rabbit hepatocytes. The widely used alginate-polylysine capsules were employed as a comparative standard in all tests. A number of the new formulations compared favorably with the standard, and some exhibited superior performance in specific areas. Hepatocyte function, as evaluated by the rate of urea synthesis, showed no significant differences between formulations over a 24-h test period. One formulation, composed of the polysaccharides (carboxymethyl)cellulose, chondroitin sulfate A, chitosan, and polygalacturonate, was found to be superior to alginate-polylysine capsules in the areas investigated and supported the long-term survival and growth of liver endothelial cells.
Imaging Cell Surface Glycosylation in Vivo Using “Double Click” Chemistry (2013)

Dynamic alterations in cell surface glycosylation occur in numerous biological processes that involve cell-cell communication and cell migration. We report here imaging of cell surface glycosylation in live mice using double click chemistry. Cell surface glycans were metabolically labeled using peracetylated azido-labeled N-acetylgalactosamine and then reacted, in the first click reaction, with either a cyclooctyne, in a Huisgen [3 + 2] cycloaddition, or with a Staudinger phosphine, via Staudinger ligation. The second click reaction was a [4 + 2] inverse electron demand Diels-Alder reaction between a trans-cyclooctene and a tetrazine, where the latter reagent had been fluorescently labeled with a far-red fluorophore. After administration of the fluorescent tetrazine, the bifunctional cyclooctyne-cyclooctene produced significant azido sugar-dependent fluorescence labeling of tumor, kidney, liver, spleen, and small intestine in vivo, where the kidney and tumor could be imaged noninvasively in the live mouse.
Gpr54 −/− mice show more pronounced defects in spermatogenesis than Kiss1 −/− mice and improved spermatogenesis with age when exposed to dietary phytoestrogens (2010)

Mice with mutations in the kisspeptin signaling pathway (Kiss1(-/-) or Gpr54(-/-)) have low gonadotrophic hormone levels, small testes, and impaired spermatogenesis. Between 2 and 7 months of age, however, the testes of the mutant mice increase in weight and in Gpr54(-/-) mice, the number of seminiferous tubules containing spermatids/spermatozoa increases from 17 to 78%. In contrast, the Kiss1(-/-) mice have a less severe defect in spermatogenesis and larger testes than Gpr54(-/-) mice at both 2 and 7 months of age. The reason for the improved spermatogenesis was investigated. Plasma testosterone and FSH levels did not increase with age in the mutant mice and remained much lower than in wild-type (WT) mice. In contrast, intratesticular testosterone levels were similar between mutant and WT mice. These data indicate that age-related spermatogenesis can be completed under conditions of low plasma testosterone and FSH and that intratesticular testosterone may contribute to this process. In addition, however, when the Gpr54(-/-) mice were fed a phytoestrogen-free diet, they showed no age-related increase in testes weight or improved spermatogenesis. Thus, both genetic and environmental factors are involved in the improved spermatogenesis in the mutant mice as they age although the mice still remain infertile. These data show that the possible impact of dietary phytoestrogens should be taken into account when studying the phenotype of mutant mice with defects in the reproductive axis.
A Polycistronic MicroRNA Cluster, miR-17-92 , Is Overexpressed in Human Lung Cancers and Enhances Cell Proliferation (2005)

MicroRNAs (miRNAs) are small noncoding RNAs, thought to be involved in physiologic and developmental processes by negatively regulating expression of target genes. We have previously reported frequent down-regulation of the let-7 miRNA family in lung cancers and, in the present study, assessed alteration in a panel of 19 lung cancer cell lines. As a result, we found for the first time that the miR-17-92 cluster, which comprises seven miRNAs and resides in intron 3 of the C13orf25 gene at 13q31.3, is markedly overexpressed in lung cancers, especially with small-cell lung cancer histology. Southern blot analysis revealed the presence of increased gene copy numbers of the miRNA cluster in a fraction of lung cancer cell lines with overexpression. In addition, we were able to show predominant localization of C13orf25 transcripts within the nucleus and introduction of the expression construct of the miR-17-92 cluster, but not the putative open reading frame of C13orf25, enhancing lung cancer cell growth. These findings clearly suggest that marked overexpression of the miR-17-92 cluster with occasional gene amplification may play a role in the development of lung cancers, especially in their most aggressive form, small-cell lung cancer, and that the C13orf25 gene may well be serving as a vehicle in this regard.
Novel avermectins produced by mutational biosynthesis. (1991)

Avermectins with a wide range of novel C-25 substituents have been prepared by feeding carboxylic acids or their biosynthetic precursors to a Streptomyces avermitilis mutant strain ATCC 53568. This organism lacks the ability to form isobutyric and S-2-methylbutyric acids from their 2-oxo acid precursors and thus is unable to produce natural avermectins unless supplied with these acids. The novel avermectins produced by mutational biosynthesis possess broad-spectrum antiparasitic activity.
Interaction of Nanoparticles with Lipid Membrane (2008)

A nanoscale range of surface feature curvatures where lipid membranes lose integrity and form pores has been found experimentally. The pores were experimentally observed in the l-alpha-dimyristoyl phosphatidylcholine membrane around 1.2-22 nm polar nanoparticles deposited on mica surface. Lipid bilayer envelops or closely follows surface features with the curvatures outside of that region. This finding provides essential information for the understanding of nanoparticle-lipid membrane interaction, cytotoxicity, preparation of biomolecular templates and supported lipid membranes on rough and patterned surfaces.
Microvortex for focusing, guiding and sorting of particles (2008)

We report a microvortex manipulator (MVM) that is a passive, scalable system with great potential for the manipulation and separation of particulate samples in microfluidic environments. The movement of particles is determined by a unique combination of helical flow, buoyant, and gravitational forces. Helical flows are induced by topographically patterned microchannel surfaces, which have previously been used for molecular mixing in microfluidic devices. We illustrate the mechanism of MVM and its applications in passive focusing of beads and cells into parallel streams and guiding of particles and cells. We also explore the application of the unique density-selectivity of microvortex focusing and successfully sort a mixture of two bead populations whose density difference is as small as 0.1 g cm(-3).
Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. (1994)

The primate Alu interspersed repeats can be subdivided into classes on the basis of shared nucleotides at a set of diagnostic positions. Each of the classes of Alu sequences is apparently the result of past retrotransposition of transcripts of highly conserved class-specific source genes that differed from each other at the diagnostic positions. The nucleotides at the majority of positions are identical among the source genes and therefore were identical among all of the Alu sequences at the time of their insertion. These CONSBI (conserved before insertion) positions are useful because the changes that have occurred after insertion are recognizable and the divergence resulting from nucleotide substitutions, insertions, and deletions is informative. The divergence of Alu sequences at the CONSBI positions is a measure of the time since a class was inserted. The greatest majority of Alu sequences are in one class (identified as class II), and it is particularly suitable for such examination, since nearly full-length sequences are now known for nearly a thousand members of this class. The average divergence of class II members indicates that the class has an average age of about 40 million years. The distribution in divergence of class II accurately fits a sum of two Poisson distributions. The implication is that class II Alu sequences were derived from two massive past events of insertion of many Alu sequences. In this model the younger subset of class II sequences (corresponding to about 300,000 copies in the genome) has an average divergence of 5% at CONSBI positions. The older set of class II sequences (corresponding to about 150,000 genomic copies) has a 9% average divergence. Based on the drift rate of primate DNA sequences, the events of insertion probably occurred 30-50 million years ago. The goodness of the fit to the Poisson distribution indicates that no significant number of members of class II have been inserted since 30 million years ago.