gebhart/patrepeval huggingface dataset:
Closed-form expressions for interconnection delay, coupling, and crosstalk in VLSIs (1993)

A closed-form formula for a waveform of the RC interconnection line with practical boundary conditions is derived. Expressions are also derived for the voltage slope and transition time of the RC interconnection and for coupling capacitance and crosstalk voltage height, which can be used in VLSI designs. Using the expressions, the optimum linewidth that minimizes RC delay and the trend of RC delay in the scaled-down VLSIs are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Prostacyclin Analogue Treprostinil Blocks NFκB Nuclear Translocation in Human Alveolar Macrophages (2002)

Primary pulmonary hypertension (PPH) is characterized by increased pulmonary arterial pressure and vascular resistance. We and others have observed that inflammatory cytokines and infiltrates are present in the lung tissue, but the significance is uncertain. Treprostinil (TRE), a prostacyclin analogue with extended half-life and chemical stability, has shown promise in the treatment of PPH. We hypothesize that TRE might exert beneficial effects in PPH by antagonizing inflammatory cytokine production in the lung. Here we show that TRE dose-dependently inhibits inflammatory cytokine (tumor necrosis factor-alpha, interleukin-1beta, interleukin-6, and granulocyte macrophage colony-stimulating factor) secretion and gene expression by human alveolar macrophages. TRE blocks NFkappaB activation, but IkappaB-alpha phosphorylation and degradation are unaffected. Moreover, TRE does not affect the formation of the NFkappaB.DNA complex but blocks nuclear translocation of p65. These results are the first to illustrate the anti-cytokine actions of TRE in down-regulating NFkappaB, not through its inhibitory component or by direct binding but by blocking nuclear translocation. These data indicate that inflammatory mechanisms may be important in the pathogenesis of PPH and cytokine antagonism by blocking NFkappaB may contribute to the efficacy of TRE therapy in PPH.
Urinary Pharmacokinetics of 11-Nor-9-carboxy- 9-tetrahydrocannabinol after Controlled Oral 9-Tetrahydrocannabinol Administration (2004)

Understanding the pharmacokinetics of orally administered cannabinoids is vitally important for optimizing therapeutic usage and to determine the impact of positive tests on drug detection programs. In this study, gas chromatography-mass spectrometry (limit of quantitation = 2.5 ng/mL) was used to monitor the excretion of total 11-nor-9-carboxy-Delta(9)-tetrahydrocannabinol (THCCOOH) in 4381 urine voids collected from seven participants throughout a controlled clinical study of multiple oral doses of THC. The National Institute on Drug Abuse Institutional Review Board approved the study and each participant provided informed consent. Seven participants received 0, 0.39, 0.47, 7.5, and 14.8 mg THC/day for five days in this double blind, placebo-controlled, randomized protocol conducted on a closed research ward. No significant differences (P </= 0.05) were observed in mean time of maximum excretion rate, mean maximum excretion rate, and mean terminal elimination half-life (t(1/2)) between the four THC doses, with ranges of 67.4 to 94.9 h, 0.9 to 16.3 micro g/h, and 44.2 to 64.0 h, respectively. Mean apparent elimination t(1/2) of 24.1 +/- 7.8 and 21.1 +/- 4.3 h for the 7.5 and 14.8 mg/day doses, respectively, were calculated from the excretion rate curve prior to the last urine sample with a THCCOOH concentration >/= 15 ng/mL. An average of only 2.9 +/- 1.6%, 2.5 +/- 2.7%, 1.5 +/- 1.4%, and 0.6 +/- 0.5% of the THC in the 0.39, 0.47, 7.5, and 14.8 mg/day doses, respectively, was excreted as THCCOOH in the urine over each 14-day dosing session. This study demonstrated that the terminal urinary elimination t(1/2) of THCCOOH following oral administration was approximately two to three days for doses ranging from 0.39 to 14.8 mg/d. These data also demonstrate that the apparent urinary elimination t(1/2) of THCCOOH prior to reaching a 15 ng/mL concentration is significantly shorter than the terminal urinary elimination t(1/2). These controlled drug administration data should assist in the interpretation of urine cannabinoid results and provide clinicians with valuable information for future pharmacological studies.
A versatile system for detecting transposition in Arabidopsis (1993)

The maize transposable element Activator (Ac) has been shown to be active in a number of dicots, including Arabidopsis thaliana, whose small genome and short generation time have favored its wide adoption as a model organism for molecular genetic approaches to plant physiology and development. Using the Ac element and several bacterial and plant marker genes, we have devised a versatile system for identifying plants in which a transposon has excised and reinserted elsewhere in the genome. The transposons have been designed to facilitate the identification of insertions downstream of promoters and in the vicinity of enhancers by the inclusion of a beta-glucuronidase (GUS) gene either lacking a promoter or having a minimal promoter sequence. The system permits the transposon and the source of transposase to be maintained either stably in separate plants or in the same plant. Plants in which transposition is occurring can be identified by the frequent somatic activation of the GUS gene. The herbicide chlorsulfuron is used as a selective agent to identify progeny plants in which the transposon has excised from its original insertion site within a chlorsulfuron-resistant acetolactate synthase gene. Additional selectable markers permit the identification of plants containing a transposed element, but lacking transposase. Here we describe our initial characterization of the system and demonstrate its reliability and efficiency in identifying plants with transposed elements.
Characterization and use of laser-based lysis for cell analysis on-chip (2008)

We demonstrate the use of a pulsed laser microbeam for cell lysis followed by electrophoretic separation of cellular analytes in a microfluidic device. The influence of pulse energy and laser focal point within the microchannel on the threshold for plasma formation was measured. The thickness of the poly(dimethylsiloxane) (PDMS) layer through which the beam travelled was a critical determinant of the threshold energy. An effective optical path length, Leff, for the laser beam can be used to predict the threshold for optical breakdown at different microchannel locations. A key benefit of laser-based cell lysis is the very limited zone (less than 5 microm) of lysis. A second asset is the rapid cell lysis times (approx. microseconds). These features enable two analytes, fluorescein and Oregon Green, from a cell to be electrophoretically separated in the channel in which cell lysis occurred. The resolution and efficiency of the separation of the cellular analytes are similar to those of standards demonstrating the feasibility of using a pulsed laser microbeam in single-cell analysis.
Crystal structures of the vitamin D-binding protein and its complex with actin: Structural basis of the actin-scavenger system (2002)

Actin is the most abundant protein in eukaryotic cells, but its release from cells into blood vessels can be lethal, being associated with clinical situations including hepatic necrosis and septic shock. A homeostatic mechanism, termed the actin-scavenger system, is responsible for the depolymerization and removal of actin from the circulation. During the first phase of this mechanism, gelsolin severs the actin filaments. In the second phase, the vitamin D-binding protein (DBP) traps the actin monomers, which accelerates their clearance. We have determined the crystal structures of DBP by itself and complexed with actin to 2.1 A resolution. Similar to its homologue serum albumin, DBP consists of three related domains. Yet, in DBP a strikingly different organization of the domains gives rise to a large actin-binding cavity. After complex formation the three domains of DBP move slightly to "clamp" onto actin subdomain 3 and to a lesser extent subdomain 1. Contacts between actin and DBP throughout their extensive 3,454-A(2) intermolecular interface involve a mixture of hydrophobic, electrostatic, and solvent-mediated interactions. The area of actin covered by DBP within the complex approximately equals the sum of those covered by gelsolin and profilin. Moreover, certain interactions of DBP with actin mirror those observed in the actin-gelsolin complex, which may explain how DBP can compete effectively with gelsolin for actin binding. Formation of the strong actin-DBP complex proceeds with limited conformational changes to both proteins, demonstrating how DBP has evolved to become an effective actin-scavenger protein.
Protection of synapses against Alzheimer's-linked toxins: Insulin signaling prevents the pathogenic binding of Aβ oligomers (2009)

Synapse deterioration underlying severe memory loss in early Alzheimer's disease (AD) is thought to be caused by soluble amyloid beta (Abeta) oligomers. Mechanistically, soluble Abeta oligomers, also referred to as Abeta-derived diffusible ligands (ADDLs), act as highly specific pathogenic ligands, binding to sites localized at particular synapses. This binding triggers oxidative stress, loss of synaptic spines, and ectopic redistribution of receptors critical to plasticity and memory. We report here the existence of a protective mechanism that naturally shields synapses against ADDL-induced deterioration. Synapse pathology was investigated in mature cultures of hippocampal neurons. Before spine loss, ADDLs caused major downregulation of plasma membrane insulin receptors (IRs), via a mechanism sensitive to calcium calmodulin-dependent kinase II (CaMKII) and casein kinase II (CK2) inhibition. Most significantly, this loss of surface IRs, and ADDL-induced oxidative stress and synaptic spine deterioration, could be completely prevented by insulin. At submaximal insulin doses, protection was potentiated by rosiglitazone, an insulin-sensitizing drug used to treat type 2 diabetes. The mechanism of insulin protection entailed a marked reduction in pathogenic ADDL binding. Surprisingly, insulin failed to block ADDL binding when IR tyrosine kinase activity was inhibited; in fact, a significant increase in binding was caused by IR inhibition. The protective role of insulin thus derives from IR signaling-dependent downregulation of ADDL binding sites rather than ligand competition. The finding that synapse vulnerability to ADDLs can be mitigated by insulin suggests that bolstering brain insulin signaling, which can decline with aging and diabetes, could have significant potential to slow or deter AD pathogenesis.
Specific Chromosome Defect Associated with Human Small-Cell Lung Cancer: Deletion 3p(14-23) (1982)

A specific, acquired chromosomal abnormality (deletion 3p) has been found in at least one chromosome 3 in 100 percent of the metaphases in 12 of 12 cell lines cultured from human small-cell lung cancer tissue and in 2-day tumor culture specimens from three patients. Analysis of the shortest region of overlap shows the deletion to be 3p(14-23). This specific change was not seen in five of five lung cancer cell lines other than small-cell lung cancer or in two lymphoblastoid lines cultured from cells of small-cell lung cancer patients whose tumors had the 3p deletion.
The AWK Programming Language (1988)

Preface. 1. An AWK Tutorial. Getting Started. Simple Output. Fancier Output. Selection. Computing with AWK. Control-Flow Statements. Arrays. A Handful of Useful One-liners. What Next? 2. The AWK Lanaguage. Patterns. Actions. User-Defined Functions. Output. Input. Interaction with Other Programs. Summary. 3. Data Processing. Data Transformation and Reduction. Data Validation. Bundle and Unbundle. Multiline Records. Summary. 4. Reports and Databases. Generating Reports. Packaged Queries. A Relational Database System. Summary. 5. Processing Words. Random Text Generation. Interactive Text-Manipulation. Text Processing. Summary. 6. Little Languages. An Assembler and Interpreter. A Language for Drawing Graphs. A Sort Generator. A Reverse-Polish Calculator. An Infix Calculator. Recursive-Descent Parsing. Summary. 7. Experiments with Algorithms. Sorting. Profiling. Topological Sorting. Make: A File Updating Program. Summary. 8. Epilog. AWK as a Language. Performance. Conclusion. Appendix A: AWK Summary. Appendix B: Answers to Selected Exercises. Index.
Solving Multi-Objective Multi-Constrained Optimization Problems Using Hybrid Ants System and Tabu Search (2003)

In this paper, we study the effectiveness of the classical divide-and-conquer paradigm where sub-problems are divided along objective functions and constraints, and conquered via a hybridized meta-heuristic. The “Divide” technique involves breaking the problems into several sub-problems such that each sub-problem now contains only a single objective subject to a partial set of constraints. In addition, each sub-problem is related to another through one or more common constraints. The “Conquer” technique on the other hand, refers to a single generic scheme that is able to self-adapt through various Derived Models to solve different sub-problems. Each derived model represents a different degree of collaboration between two (or more) core meta-heuristics. The advantage of the derived models lies in the ability to exploit the strength and cover the weakness of the meta-heuristics under the scheme.
Serum deoxythymidine kinase gives prognostic information in chronic lymphocytic leukemia (1984)

A recently developed deoxythymidine kinase assay, utilizing iodine-125-iodo-deoxyuridine as substrate and capable of detecting enzyme activity in serum from healthy humans, was used in an investigation of sera from 55 untreated patients with chronic lymphocytic leukemia (CLL). When confined to the study, the patients were classified as having progressive or indolent disease and according to Rai stage. The results showed a significant correlation between serum deoxythymidine kinase activity (S-TK) and disease status, i.e., higher values were found in patients with progressive disease, compared to those with indolent disease. S-TK also correlated with Rai stage. S-TK values of more than 40 times the normal value were found in some patients. All patients with S-TK greater than 8.4 units had a disease that was or became progressive during the observation period. Within the patient group with indolent disease two groups that differed with regard to prognosis could be distinguished according to their initial S-TK values. In longitudinal studies of 18 patients with indolent disease, S-TK was found to exceed 8.4 units only on one occasion during an observation period of up to 68 months. In patients with indolent disease, a transition to progressive disease was parallelled by an increase in S-TK. Studies of S-TK levels in 18 patients receiving treatment showed that S-TK decreased during successful therapy. S-TK was also found to increase when the disease was reactivated. From these results it is concluded that S-TK could be used as a prognostic marker for the individual CLL patient. Furthermore, S-TK seems to be useful for longitudinal follow-up studies of disease status, both in indolent disease and in progressive disease during treatment.
Sexual Arousability and the Menstrual Cycle1 (1981)

Using a balanced experimental design, 30 regularly cycling woman not using oral contraceptives, aged 20 to 30 years, were assessed in a laboratory setting during the follicular, ovulatory, and luteal phases. Sexual arousal was measured by self-report and by photoplethysmographic recordings of vaginal vasocongestion. Plasma estradiol, progesterone, and testosterone were determined by radioimmunoassay. There were marked and consistent individual differences among the women in their sexual arousability. Subjective reports of sexual arousal did not differ among menstrual cycle phases, by physiologic arousal did vary with significantly higher mean levels of arousal occurring during the follicular and luteal phases than during the ovulation phase. While hormones fluctuated predictably with menstrual cycle phase, there were wide individual differences in absolute values among women. The correlations between estradiol, progesterone and testosterone and the subjective and objective assessments of arousability were mainly low and insignificant. Some evidence suggestive of a relation between testosterone and sexual arousability was observed with three subgroups of woman were formed on the basis of relative average testosterone concentrations.
Dependence of the Thermal History of Asteroids on Accretion Rate and Duration (1999)

All thermal models of asteroidal bodies to date have assumed accretion to be instantaneous (e.g. [1], [2], [3], [4], [5], [6]) to make computation easier. This simplification ignored two critical questions. First, Al is more potent as a heat source when the body is accreting compared to the period after accretion. Does accounting for the heat released by Al during accretion significantly change the thermal history of the asteroid? Second, accretion models constitute an entire field of study in itself (e.g. [7], [8]) . What effects do various accretionary models have on the thermal history of an asteroid? [9] first incorporated incremental accretion in a finite element heat transfer code with a moving boundary condition. The observation of asteroidal cooling because of accretion of cold material [9] was found to be erroneous [6]. In this work, we compare the thermal output of codes with three endmember growth functions, for models where the time of initiation of accretion (with respect to CAI formation) and the duration of accretion are varied.
고구마 β - 아밀라아제의 안정성에 관한 연구 ( 1 ) (1996)

고구마 β-아밀라아제를 아세톤 분별침전, DEAE Sephadex A-50, Sephadex G-200으로 정제하였다. 정제효소의 열안정성은 효소농도가 높을수록 높았다. pH 5, 65℃에서 1시간반 후, 효소농도 30㎍/ml 이하에서는 실활하였지만, 100㎍/ml에서는 25%의 활성이 남았다. 정제효소는 pH 4∼10 범위에서 안정하였고, 글리세롤은 pH 안정성을 증가시켰다. NaCl은 pH 4.8, 0.5M 농도에서 효소활성을 100% 저해하였다. SDS는 pH 5, 37℃에서 12시간 반응시킨 결과 0.05% 농도에서 효소활성을 완전히 저해하였다. 염산구아니딘은 pH 5, 37℃에서 13시간 반응시킨 결과 1M 농도에서, 우레아는 8M농도에서 효소활성을 완전히 저해하였다.
Mapping whispering-gallery modes in microspheres with a near-field probe (1995)

We demonstrate the use of a near-field probe to map the angular dependence of high-Q whispering-gallery modes in fused-silica microspheres. The mapping is performed by placing a micrometer-sized tip formed on the end of a monomode fiber into the evanescent f ield at the microsphere surface, causing light to be coupled from the microsphere resonance into the fiber guided mode. The light output of the fiber is then measured while the tip is moved to different points on the microsphere surface. We have used this method to investigate the lifting of spherical degeneracy in the system.
Detecting algorithmically generated malicious domain names (2010)

Recent Botnets such as Conficker, Kraken and Torpig have used DNS based "domain fluxing" for command-and-control, where each Bot queries for existence of a series of domain names and the owner has to register only one such domain name. In this paper, we develop a methodology to detect such "domain fluxes" in DNS traffic by looking for patterns inherent to domain names that are generated algorithmically, in contrast to those generated by humans. In particular, we look at distribution of alphanumeric characters as well as bigrams in all domains that are mapped to the same set of IP-addresses. We present and compare the performance of several distance metrics, including KL-distance, Edit distance and Jaccard measure. We train by using a good data set of domains obtained via a crawl of domains mapped to all IPv4 address space and modeling bad data sets based on behaviors seen so far and expected. We also apply our methodology to packet traces collected at a Tier-1 ISP and show we can automatically detect domain fluxing as used by Conficker botnet with minimal false positives.
Proteomics analysis of BHK‐21 cells infected with a fixed strain of rabies virus (2009)

Rabies is a neurotropic virus that causes a life threatening acute viral encephalitis. The complex relationship of rabies virus (RV) with the host leads to its replication and spreading toward the neural network, where viral pathogenic effects appeared as neuronal dysfunction. In order to better understand the molecular basis of this relationship, a proteomics study on baby hamster kidney cells infected with challenge virus standard strain of RV was performed. This cell line is an in vitro model for rabies infection and is commonly used for viral seed preparation. The direct effect of the virus on cellular protein machinery was investigated by 2-DE proteome mapping of infected versus control cells followed by LC-MS/MS identification. This analysis revealed significant changes in expression of 14 proteins, seven of these proteins were viral and the remaining were host proteins with different known functions: cytoskeletal (capping protein, vimentin), anti-oxidative stress (superoxide dismutase), regulatory (Stathmin), and protein synthesis (P0). Despite of limited changes appeared upon rabies infection, they present a set of interesting biochemical pathways for further investigation on viral-host interaction.
Estimation of the Potential of an Oil-Viscosity-Reducing Bacteria, Petrotoga sp., Isolated from an Oilfield for MEOR (2009)

One thermophilic anaerobic oil-degrading bacterium was successfully isolated from reservoir brine of Yabase oilfield,&lt;br&gt;INPEX Corp., Akita, Japan. The potential of the isolated bacterium as a candidate for Microbial EOR (MEOR) was estimated&lt;br&gt;in this study.
Cytokine Expanded Myeloid Precursors Function as Regulatory Antigen-Presenting Cells and Promote Tolerance through IL-10-Producing Regulatory T Cells (2005)

The initiation of graft-vs-host disease (GVHD) after stem cell transplantation is dependent on direct Ag presentation by host APCs, whereas the effect of donor APC populations is unclear. We studied the role of indirect Ag presentation in allogenic T cell responses by adding populations of cytokine-expanded donor APC to hemopoietic grafts that would otherwise induce lethal GVHD. Progenipoietin-1 (a synthetic G-CSF/Flt-3 ligand molecule) and G-CSF expanded myeloid dendritic cells (DC), plasmacytoid DC, and a novel granulocyte-monocyte precursor population (GM) that differentiate into class II+,CD80/CD86+,CD40- APC during GVHD. Whereas addition of plasmacytoid and myeloid donor DC augmented GVHD, GM cells promoted transplant tolerance by MHC class II-restricted generation of IL-10-secreting, Ag-specific regulatory T cells. Importantly, although GM cells abrogated GVHD, graft-vs-leukemia effects were preserved. Thus, a population of cytokine-expanded GM precursors function as regulatory APCs, suggesting that G-CSF derivatives may have application in disorders characterized by a loss of self-tolerance.
PD-L1/PD-1 Signal Deficiency Promotes Allogeneic Immune Responses and Accelerates Heart Allograft Rejection (2008)

Absence of PD-L1 input triggers a stimulatory signal to effector T cells and APCs, accelerating heart allograft rejection. Engagement of the PD-L1 signal on T cells or APCs may be necessary to induce transplant tolerance.