gebhart/patrepeval huggingface dataset:
Conservative Repair of a Chromosomal Double-Strand Break by Single-Strand DNA through Two Steps of Annealing (2006)

The repair of chromosomal double-strand breaks (DSBs) is essential to normal cell growth, and homologous recombination is a universal process for DSB repair. We explored DSB repair mechanisms in the yeast Saccharomyces cerevisiae using single-strand oligonucleotides with homology to both sides of a DSB. Oligonucleotide-directed repair occurred exclusively via Rad52- and Rad59-mediated single-strand annealing (SSA). Even the SSA domain of human Rad52 provided partial complementation for a null rad52 mutation. The repair did not involve Rad51-driven strand invasion, and moreover the suppression of strand invasion increased repair with oligonucleotides. A DSB was shown to activate targeting by oligonucleotides homologous to only one side of the break at large distances (at least 20 kb) from the break in a strand-biased manner, suggesting extensive 5' to 3' resection, followed by the restoration of resected DNA to the double-strand state. We conclude that long resected chromosomal DSB ends are repaired by a single-strand DNA oligonucleotide through two rounds of annealing. The repair by single-strand DNA can be conservative and may allow for accurate restoration of chromosomal DNAs with closely spaced DSBs.
Early detection of driver drowsiness by WPT and FLFNN models (2016)

This paper presents a method that can detect driver's drowsiness by using the wavelet packet transform (WPT) and functional link-based fuzzy neural network (FLFNN) models. Drowsy drivers have been reported to be vulnerable to car accidents. Early detection of drowsiness can help alert drivers or passengers to provide a safety drive on the road. For those old models or cars without equipped with advanced high technologies, there is a dire need to install sensor devices that can effectively detect drowsy status of drivers at an early stage. Photoplethysmography (PPG) is a non-invasive optical technique that measures relative blood volume changes in the blood vessels and has been universally used for research and physiological study. We develop such PPG sensor devices to be installed on the steering wheel to detect the physiological conditions (such as normal to drowsy) by using parameters extracted from the heart rate variability (HRV) obtained from PPG signal calculation. Experimental results revealed that the proposed model is effective in assessing the drowsy levels of drivers.
Comparison of allergy rates in glaucoma patients receiving brimonidine 0.2% monotherapy versus fixed-combination brimonidine 0.2%–timolol 0.5% therapy (2008)

The brimonidine-timolol fixed combination was associated with a 50% lower incidence in ocular allergy compared with 0.2% brimonidine monotherapy. This difference between treatments was not statistically significant (p=0.097) but is likely to be clinically important. Additional studies are needed to evaluate the incidence of ocular allergy associated with brimonidine-timolol fixed combination treatment.
Mesoporous Silica Molecular Sieves Prepared by Ionic and Neutral Surfactant Templating:  A Comparison of Physical Properties (1996)

A series of mesoporous MCM-41 and HMS silica molecular sieves have been prepared by electrostatic and neutral assembly pathways, respectively, and their properties have been compared by a variety of physical techniques. Direct S+I- charge matching between cationic quaternary ammonium ion surfactants (S+) and the anionic silicate precursors (I-) affords long-range hexagonal structures under hydrothermal synthesis conditions (100 °C), but the long-range order is greatly reduced when the synthesis is conducted at ambient temperature. Conversely, owing to weaker assembly forces, counterion-mediated S+X-I+ and neutral S0I0 pathways (where X- is halide and S0 is a primary amine) provide calcined products with the best long-range order when the syntheses are conducted at ambient temperature. In general, MCM-41 silicas formed by electrostatic S+I- or S+X-I+ assembly exhibit greater long-range order than the HMS analogues prepared by the S0I0 assembly. However, the framework-confined pore structures, though dependent on the size of the surfactant, remain uniform, regardless of the fidelity of the long-range hexagonal order. As-synthesized neutral HMS silicas are much more extensively cross-linked than the as-synthesized charged frameworks of MCM-41 analogues, as judged by the 29Si MAS NMR Q4/Q3 Si(O−Si)4-x connectivity ratios. The neutral and extensively cross-linked character of HMS frameworks allows for the efficient and environmentally benign recovery of the template by solvent extraction. In contrast, electrostatically templated MCM-41 derivatives require proton ion exchange or calcination for the complete removal of template from the framework pores. Also, relative to the S+I- and S+X-I+ templated derivatives, HMS mesostructures generally possess thicker framework walls, superior thermal stability upon calcination in air, and a smaller crystallite size, which affords complementary textural mesoporosity for improved access to the framework-confined mesopores.
Structure and organization of the human antimicrobial peptide LL-37 in phospholipid membranes: relevance to the molecular basis for its non-cell-selective activity (1999)

The antimicrobial peptide LL-37 belongs to the cathelicidin family and is the first amphipathic alpha-helical peptide isolated from human. LL-37 is considered to play an important role in the first line of defence against local infection and systemic invasion of pathogens at sites of inflammation and wounds. Understanding its mode of action may assist in the development of antimicrobial agents mimicking those of the human immune system. In vitro studies revealed that LL-37 is cytotoxic to both bacterial and normal eukaryotic cells. To gain insight into the mechanism of its non-cell-selective cytotoxicity, we synthesized and structurally and functionally characterized LL-37, its N-terminal truncated form FF-33, and their fluorescent derivatives (which retained structure and activity). The results showed several differences, between LL-37 and other native antimicrobial peptides, that may shed light on its in vivo activities. Most interestingly, LL-37 exists in equilibrium between monomers and oligomers in solution at very low concentrations. Also, it is significantly resistant to proteolytic degradation in solution, and when bound to both zwitterionic (mimicking mammalian membranes) and negatively charged membranes (mimicking bacterial membranes). The results also showed a role for the N-terminus in proteolytic resistance and haemolytic activity, but not in antimicrobial activity. The LL-37 mode of action with negatively charged membranes suggests a detergent-like effect via a 'carpet-like' mechanism. However, the ability of LL-37 to oligomerize in zwitterionic membranes might suggest the formation of a transmembrane pore in normal eukaryotic cells. To examine this possibility we used polarized attenuated total reflectance Fourier-transform infrared spectroscopy and found that the peptide is predominantly alpha-helical and oriented nearly parallel with the surface of zwitterionic-lipid membranes. This result does not support the channel-forming hypothesis, but rather it supports the detergent-like effect.
Muscular Subaortic Stenosis (1982)

A quarter of a century has passed since Brock's original report1 of the condition characterized by asymmetric septal hypertrophy and a subaortic pressure gradient (muscular subaortic stenosis).2 The pressure gradient may be affected by changes in myocardial contractility, systemic vascular resistance, and ventricular volume.3 Propranolol has little effect on the pressure gradient at rest, but it may diminish the increment that occurs with exercise.4 Verapamil has a greater effect than propranolol in reducing the gradient at rest, although substantial gradients (>50 mm Hg) have persisted even after high doses of intravenous verapamil, and in one patient the gradient markedly increased. . . .
Low-Temperature Solution Processing of Graphene−Carbon Nanotube Hybrid Materials for High-Performance Transparent Conductors (2009)

We report the formation of a nanocomposite comprised of chemically converted graphene and carbon nanotubes. Our solution-based method does not require surfactants, thus preserving the intrinsic electronic and mechanical properties of both components, delivering 240 ohms/square at 86% transmittance. This low-temperature process is completely compatible with flexible substrates and does not require a sophisticated transfer process. We believe that this technology is inexpensive, is massively scalable, and does not suffer from several shortcomings of indium tin oxide. A proof-of-concept application in a polymer solar cell with power conversion efficiency of 0.85% is demonstrated. Preliminary experiments in chemical doping are presented and show that optimization of this material is not limited to improvements in layer morphology.
A broad-angle polarization beam splitter based on a simple dielectric periodic structure (2007)

We propose a novel broad-angle polarization beam splitter utilizing the spatial dispersion of a special multi-layered dielectric periodic structure. The equal-frequency contours of this structure are flat lines for TE polarization but curved lines for TM polarization at a designed frequency. This special multi-layered structure has a fixed optical thickness for TE polarization for all incident angles. A polarization beam splitter working over a broad range of angle (from 0 degrees to 70 degrees ) is achieved by stacking two such multi-layered structures of finite length (in the normal direction) with a half-period shift in the transverse direction.
New Metabolites with Nematicidal and Antimicrobial Activities from the Ascomycete Lachnum papyraceum (Karst.) Karst. VIII. Isolation, Structure Determination and Biological Activities of Minor Metabolites Structurally Related to Mycorrhizin A. (1996)

Five new minor metabolites, papyracon D (6), 6-O-methylpapyracon B (9), 6-O-methylpapyracon C (10), lachnumfuran A (11) and lachnumlactone A (12a), together with the known chloromycorrhizinol A (4), have been isolated from extracts of the culture fluids of the ascomycete Lachnum papyraceum. The compounds, which structures were determined by spectroscopic methods, are structurally related to the nematicidal and antibiotic mycorrhizin A (1), which also is produced by the fungus. The nematicidal, antibiotic and cytotoxic activities of the new compounds are weaker compared to those of mycorrhizin A (1). Papyracon D (6) possesses the highest antibiotic activities while lachnumlactone A (12a) is the most nematicidal and cytotoxic.
Direct Cultivation of the Causative Agent of Human Granulocytic Ehrlichiosis (1996)

We describe the cultivation of the agent of human granulocytic ehrlichiosis in cell culture. The ability to isolate this organism should lead to a better understanding of the biology, treatment, and epidemiology of this emerging infection.
Achievement of high cell density and high antibody productivity by a controlled‐fed perfusion bioreactor process (2000)

Controlled feeding of nutrient supplements to a cell culture to enhance monoclonal antibody productivity has been practiced widely in high-yield, fed-batch processes. In this study, a similar feeding concept has been applied to a perfused culture and evaluated for the effects on bioreactor productivity and product quality. Our experimental results show that, by using such a “controlled-fed perfusion” approach, the volumetric antibody productivity (antibody per liter per day) was significantly increased by nearly twofold over the perfusion process, and surpassed fed-batch and batch processes by almost tenfold. The substantial boost in the overall productivity is attributable primarily to the combined effects of increased cell density as well as reduced product dilution. Both were achieved through careful nutrient supplementation in conjunction with metabolite minimization. As the manufacturing process evolved from roller bottles to the controlled-fed perfusion bioreactor system, the immunoreactivity and the cDNA sequences of the antibody were well preserved. However, the product glycosylation distribution patterns did alter. The controlled-feed perfusion process demonstrated a unique encompassment of the advantages of fed-batch and perfusion methods; that is, high product concentration with high volume throughput. Therefore, it may be very suitable for large-scale production of monoclonal antibodies. © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng 69: 74–82, 2000.
T cell and interferon-gamma involvement in the adjuvant action of a detoxified endotoxin. (1989)

The adjuvant activities of a detoxified derivative of endotoxic lipopolysaccharides, isolated from the outer membrane of gram-negative bacteria, were evaluated in aging mice. This monophosphoryl lipid A (MPL) (Ribi) was capable of enhancing antibody production in vitro in splenic cultures from 2-3-month-old male Balb/c mice as well as cultures from 22-24-month-old Balb/c mice. Separation of spleen cells from MPL and phosphate-buffered saline-injected mice into adherent and nonadherent populations and subsequent mixing of populations and culture with antigen implicated an adherent cell as being involved in the enhancement of antibody formation induced by MPL. However, separation of normal spleen cells into purified populations of adherent cells, T-lymphocytes, and B-lymphocytes, followed by in vitro stimulation of the individual populations with MPL and subsequent transfer into cultures of normal spleen cells, revealed only the T cell as capable of transferring the enhancement of antibody formation. In addition, culture filtrates from MPL-stimulated T cells were able to enhance antibody production by spleen cell cultures from aging mice twofold above that of filtrates from unstimulated T cells. The enhancement of antibody formation induced by such filtrates and also by MPL in spleen cell cultures from young and aging mice was inhibited by a monoclonal antibody (MAb) to recombinant interferon-gamma (rIFN-gamma) as well as antiserum against IFN-alpha, -beta, and -gamma, but not by an antiserum to IFN-alpha/beta. Enhancement of antibody formation correlated well with an increase in interleukin-1 (IL-1) but not with an increase in IL-2 production. Addition of anti-asialo-GM1 MAb plus complement to the effective spleen populations did not diminish the adjuvant action.
The Prosody of Backchannels in American English (2007)

We examine prosodic and contextual factors characterizing the backchannel function of single affirmative words. Data is drawn from collaborative task-oriented dialogues between speakers of Standard American English. Despite high lexical variability, backchannels are prosodically well defined: they have higher pitch and intensity and greater pitch slope than affirmative words expressing other pragmatic functions. Additionally, we identify phrase-final rising pitch as a salient trigger for backchanneling.
Individual differences in the peripheral immune system promote resilience versus susceptibility to social stress (2014)

Depression and anxiety disorders are associated with increased release of peripheral cytokines; however, their functional relevance remains unknown. Using a social stress model in mice, we find preexisting individual differences in the sensitivity of the peripheral immune system that predict and promote vulnerability to social stress. Cytokine profiles were obtained 20 min after the first social stress exposure. Of the cytokines regulated by stress, IL-6 was most highly up-regulated only in mice that ultimately developed a susceptible behavioral phenotype following a subsequent chronic stress, and levels remained elevated for at least 1 mo. We confirmed a similar elevation of serum IL-6 in two separate cohorts of patients with treatment-resistant major depressive disorder. Before any physical contact in mice, we observed individual differences in IL-6 levels from ex vivo stimulated leukocytes that predict susceptibility versus resilience to a subsequent stressor. To shift the sensitivity of the peripheral immune system to a pro- or antidepressant state, bone marrow (BM) chimeras were generated by transplanting hematopoietic progenitor cells from stress-susceptible mice releasing high IL-6 or from IL-6 knockout (IL-6(-/-)) mice. Stress-susceptible BM chimeras exhibited increased social avoidance behavior after exposure to either subthreshold repeated social defeat stress (RSDS) or a purely emotional stressor termed witness defeat. IL-6(-/-) BM chimeric and IL-6(-/-) mice, as well as those treated with a systemic IL-6 monoclonal antibody, were resilient to social stress. These data establish that preexisting differences in stress-responsive IL-6 release from BM-derived leukocytes functionally contribute to social stress-induced behavioral abnormalities.
Filling of Sub-µm Through-holes by Self-sputter Deposition (1994)

Filling of sub-µ m holes with a high aspect ratio by self-sputter deposition of copper is investigated. Good bottom coverages of 100% by means of thinner thin-film deposition and 50% by thicker thin-film deposition are attained. It is found that the bottom coverage decreases sharply when the ratio of the distance between the target and the substrate, D st , to the diameter of the erosion center ring is less than 1, and although the bottom coverage by the self-sputter deposition at lower pressures saturates at longer D st , that by the conventional sputter deposition at higher pressures decreases with D st . The bottom coverage also decreases with increases of the pressure, the thin film thickness deposited, and the radial distance of the substrate position from the target center toward the erosion center.
Cognitive Slowing in Parkinson's Disease: A Behavioral Evaluation Independent of Motor Slowing (2002)

Parkinson's disease (PD) is attributable primarily to depletion of dopamine in the basal ganglia, but the full effects of this depletion are unknown. It is well known that PD involves motor slowing, and although it is not easy to distinguish between the motor and cognitive components of behavior, clinical observations suggest that cognitive processing may also be compromised. However, it remains unclear whether such cognitive involvement exists, and if so, to what extent. Previous studies of cognitive slowing in PD have yielded conflicting results. This may be attributable to variations in experimental procedures, because most of the experiments used reaction-time tasks, which are inevitably confounded by motor components. In the present study, we evaluated the speed of cognitive processing in patients with PD without bradykinesia as a variable. We developed a mental-operation task that required serial updating of mental representations in response to a series of visual stimuli. By changing the speed of visual presentation and evaluating performance accuracy, the speed of cognitive processing was assessed independently of motor slowing. Cognitive impairment in PD became evident when higher speeds of cognitive processing (verbal more so than spatial) were required. In addition, cognitive slowing and motor slowing were significantly correlated. The results of the present study suggest that slowing in PD is not restricted to the motor domain but can be generally observed in other domains of behavior, including cognitive mental operations.
Considerations for Internet Group Management Protocol (IGMP) and Multicast Listener Discovery (MLD) Snooping Switches (2006)

This memo describes the recommendations for Internet Group Management Protocol (IGMP) and Multicast Listener Discovery (MLD) snooping switches.These are based on best current practices for IGMPv2, with further considerations for IGMPv3-and MLDv2-snooping.Additional areas of relevance, such as link layer topology changes and Ethernet-specific encapsulation issues, are also considered.This behaviour works well for broadcast packets that are intended to be seen or processed by all connected nodes.In the case of multicast packets, however, this approach could lead to less efficient use of network bandwidth, particularly when the packet is Christensen, et al.
Cathepsin B expression and its correlation with tumor-associated laminin and tumor progression in gastric cancer. (1998)

Increased cathepsin B expression by tumor cells associated with decreased tumor-associated laminin may suggest a mechanism for local tumor progression and metastasis. Staining for cathepsin B and laminin may be of prognostic value in gastric carcinomas.
The relationship between diabetes and pancreatic cancer. (2003)

About 80% of pancreatic cancer patients have glucose intolerance or frank diabetes. This observation has led to the following two hypotheses: i. pancreatic cancer causes the associated diabetes and ii. the conditions associated with diabetes promote the development of pancreatic cancer. Evidence supporting both hypotheses has been accumulated in previous studies. This article reviews these studies, especially those that have been conducted recently.
The Role of Focal Adhesion Kinase Binding in the Regulation of Tyrosine Phosphorylation of Paxillin (1999)

Focal adhesion kinase (FAK) and paxillin are focal adhesion-associated, phosphotyrosine-containing proteins that physically interact. A previous study has demonstrated that paxillin contains two binding sites for FAK. We have further characterized these two binding sites and have demonstrated that the binding affinity of the carboxyl-terminal domain of FAK is the same for each of the two binding sites. The presence of both binding sites increases the affinity for FAK by 5-10-fold. A conserved paxillin sequence called the LD motif has been implicated in FAK binding. We show that mutations in the LD motifs in both FAK-binding sites are required to dramatically impair FAK binding in vitro. A paxillin mutant containing point mutations in both FAK-binding sites was characterized. The mutant exhibited reduced levels of phosphotyrosine relative to wild type paxillin in subconfluent cells growing in culture, following cell adhesion to fibronectin and in src-transformed fibroblasts. These results suggest that paxillin must bind FAK for maximal phosphorylation in response to cell adhesion and that FAK may function to direct tyrosine phosphorylation of paxillin in the process of transformation by the src oncogene.