gebhart/patrepeval huggingface dataset:
Unusually High Thermal Conductivity of Carbon Nanotubes (2000)

Combining equilibrium and nonequilibrium molecular dynamics simulations with accurate carbon potentials, we determine the thermal conductivity lambda of carbon nanotubes and its dependence on temperature. Our results suggest an unusually high value, lambda approximately 6600 W/m K, for an isolated (10,10) nanotube at room temperature, comparable to the thermal conductivity of a hypothetical isolated graphene monolayer or diamond. Our results suggest that these high values of lambda are associated with the large phonon mean free paths in these systems; substantially lower values are predicted and observed for the basal plane of bulk graphite.
Self-assembly for microscale and nanoscale packaging: steps toward self-packaging (2005)

The packaging of microelectromechanical systems (MEMS) and nanoscale devices constitutes an important area of research and development that is vital to the commercialization of such devices. Packaging needs of these devices include interfaces to nonelectronic domains; integration of structures, devices, and subsystems made with incompatible fabrication processes into a single platform; and the ability to handle a very large numbers of parts. Although serial, robotic assembly methods such as pick-and-place have allowed significant manufacturing feats, self-assembly is an attractive option to tackle packaging issues as the size of individual parts decreases below 300 /spl mu/m. In this paper, we review advances made in the usage of self-assembly for packaging and potential directions that growth in this area can assume. In the micrometer scale, we review the use of capillary forces, gravity, shape recognition, and electric fields to guide two- and three-dimensional self-assembly processes. In the nanoscale, we survey the usage of self-assembled molecular monolayers to solve current packaging issues, DNA hybridization for guiding self-assembly processes of nanoscale devices, and methods used to package nanowires or nanotubes into electronic circuits. We conclude with an example of a nanoscale biosensor which directly incorporates the concept of its package into its fabrication process. Even though the idea of a fully self-packaging system has not been demonstrated to date, the body of work reviewed and discussed here presents a solid foundation for the pursuit of this goal.
B3(Fab)-PE38M: a recombinant immunotoxin in which a mutant form of Pseudomonas exotoxin is fused to the Fab fragment of monoclonal antibody B3. (1994)

Recombinant immunotoxins were made by fusing the Fab domain of monoclonal antibody (MAb) B3 to PE38M, a truncated mutant form of Pseudomonas exotoxin (PE). The recombinant toxins were made in Escherichia coli by fusing genes encoding the antibody domains to a gene encoding the mutant form of PE. MAb B3 binds to a carbohydrate antigen found on many kinds of carcinomas. Immunotoxins in which MAb B3 has been chemically coupled to recombinant forms of PE have been shown to be very active cytotoxic agents. PE has also been targeted to tumor cells by replacing the cell-binding domain of PE (domain I) with a single-chain antibody to make a single-chain immunotoxin. In the current study, PE38M, a mutant form of PE, with a deletion of the cell-binding domain (amino acids 1-252) as well as mutations in domain III and some nonessential sequences in domain Ib (amino acids 365-380), was fused to the light chain of MAb B3. This protein was renatured in the presence of the Fd fragment of MAb B3 to produce a Fab-toxin fusion protein. Alternatively, the Fd fragment of MAb B3 was fused to PE38M and combined with the light chain. Both types of B3(Fab)-PE38M were just as active on target cells as previously described single-chain immunotoxins. Furthermore, the B3(Fab)-PE38M produced complete remissions of human tumor xenografts growing in nude mice. B3(Fab)-PE38M has two advantages over single-chain immunotoxins. One is that the yield of recombinant Fab-toxin is very high, with 10-22% of the starting protein recovered as cytotoxically active immunotoxin after chromatographic purification. The second is that the B3(Fab)-PE38M has a much longer survival in the circulation of mice with a t1/2 beta of approximately 5 h.
Use of Sorbent Columns and Haemofiltration in Fulminant Hepatic Failure (1993)

Artificial liver support systems were developed to remove potential toxins from the circulation of patients with liver failure. A wide range of substances have been implicated in the toxic manifestations of liver failure, but no substance(s) has been identified as being of key importance. Charcoal haemoperfusion appeared to be beneficial in early studies, but when clinical trials were performed in 137 patients at King's College Hospital there was no significant improvement in survival over intensive care alone. There have been many studies using haemodialysis/filtration systems, where an improvement in conscious level of the patient was reported, but the effect on survival was less clear. Recently in Japan, continuous high volume haemofiltration with the addition of plasma exchange has been used to support liver failure patients. In liver failure, endotoxaemia and increased cytokine production are important in the pathogenesis of circulatory failure. Experiments on adsorbents to remove cytokines have shown that Amberlite XAD-7 resin can remove significant amounts of tumour necrosis factor and interleukin-6 from liver failure plasma. The development of hepatocyte bioreactors with synthetic and metabolic function for clinical use will be a major advance in liver support.
ClassiPl: an architecture for fast and flexible packet classification (2001)

Packet classification is a fundamental and critical operation to be performed in networking equipment such as switches and routers. The types of classification to be performed encompass a wide range, from well-understood operations such as route table lookups to complex packet identification involving multiple fields in the packet. Furthermore, the advent of application-aware network devices demand the use of flexible packet classifiers that can handle operations such as pattern searches and regular expression matching. Traditionally, depending on the classification types to be implemented, solutions based on CAMs/TCAMs, special function ASICs, and software-based algorithms have been used. These solutions, while adequate, target specific classification applications. This article describes ClassiPl/sup TM/, a programmable hardware architecture that performs packet classification at OC48c line rates. Illustrations and examples show how this architecture can be used in conjunction with software algorithmic techniques to support the classification needs of a variety of applications from packet switching, forwarding, and filtering to layer 7 applications such as server load balancing. We believe that the ClassiPl architecture is scalable and flexible to meet the needs of a broad class of network applications.
Antitumor Activity and Pharmacology of a Selective Focal Adhesion Kinase Inhibitor, PF-562,271 (2008)

Cancer cells are characterized by the ability to grow in an anchorage-independent manner. The activity of the nonreceptor tyrosine kinase, focal adhesion kinase (FAK), is thought to contribute to this phenotype. FAK localizes in focal adhesion plaques and has a role as a scaffolding and signaling protein for other adhesion molecules. Recent studies show a strong correlation between increased FAK expression and phosphorylation status and the invasive phenotype of aggressive human tumors. PF-562,271 is a potent, ATP-competitive, reversible inhibitor of FAK and Pyk2 catalytic activity with a IC(50) of 1.5 and 14 nmol/L, respectively. Additionally, PF-562,271 displayed robust inhibition in an inducible cell-based assay measuring phospho-FAK with an IC(50) of 5 nmol/L. PF-562,271 was evaluated against multiple kinases and displays >100x selectivity against a long list of nontarget kinases. PF-562,271 inhibits FAK phosphorylation in vivo in a dose-dependent fashion (calculated EC(50) of 93 ng/mL, total) after p.o. administration to tumor-bearing mice. In vivo inhibition of FAK phosphorylation (>50%) was sustained for >4 hours with a single p.o. dose of 33 mg/kg. Antitumor efficacy and regressions were observed in multiple human s.c. xenograft models. No weight loss, morbidity, or mortality were observed in any in vivo experiment. Tumor growth inhibition was dose and drug exposure dependent. Taken together, these data show that kinase inhibition with an ATP-competitive small molecule inhibitor of FAK decreases the phospho-status in vivo, resulting in robust antitumor activity.
A Blue-Emitting CdS/Dendrimer Nanocomposite (1998)

CdS/dendrimer nanocomposites that emit blue light are formed by the arrested precipitation of nanometer-scale CdS quantum dots in the presence of Starburst (poly(aminoamine)) dendrimers as the stabilizing host. The authors report a strong photoluminescence with emission maxima at about 450 nm. The optoelectronic properties of the CdS clusters are shown to be sensitive to synthesis conditions, including dendrimer type, solvent type, and the concentration of dendrimer and other solutes. Thin films of these materials prepared by solution casting retain the optoelectronic properties of the parent solutions.
Evaluation of the Dade MicroScan MICroSTREP Antimicrobial Susceptibility Testing Panel with Selected Streptococcus pneumoniae Challenge Strains and Recent Clinical Isolates (1998)

The MicroScan MICroSTREP panel is a recently marketed frozen broth microdilution panel for susceptibility testing of various streptococci, including Streptococcus pneumoniae. The panel contains 10 antimicrobial agents in cation-adjusted Mueller-Hinton broth supplemented with 3% lysed horse blood, similar in concept to the National Committee for Clinical Laboratory Standards (NCCLS) reference broth microdilution method for testing streptococci. A group of 210 isolates of S. pneumoniae were selected to include isolates with previously documented resistance to agents incorporated in the MICroSTREP panel, as well as recent invasive clinical isolates. All isolates were tested simultaneously with the MICroSTREP panel and an NCCLS reference panel whose drug concentrations were prepared to coincide with those of the MICroSTREP panel. Of the 210 isolates, 5 failed to grow in the MICroSTREP panel; 3 of those also did not grow in the reference panel. Essential agreement of MICs determined by the two methods (test MIC +/- one dilution of the reference MIC) was 99.6% overall and ranged from 98.0% with chloramphenicol to 100% with penicillin, ceftriaxone, erythromycin, tetracycline, and vancomycin. There were no very major or major interpretive category errors resulting from the MICroSTREP panel tests. Minor interpretive category errors ranged from 12.2% with cefotaxime and 9.8% with ceftriaxone (due mainly to clustering of MICs for the selected strains near the breakpoints) to 0% with chloramphenicol and vancomycin. These results indicate that the MicroScan MICroSTREP frozen panels provide susceptibility results with pneumococci that are essentially equivalent to results derived by the NCCLS reference broth microdilution procedure.
Development of Indole-3-Acetic Acid-Producing Escherichia coli by Functional Expression of IpdC, AspC, and Iad1 (2013)

Biosynthesis of indole-3-acetic acid (IAA) via the indole-3-pyruvic acid pathway involves three kinds of enzymes; aminotransferase encoded by aspC, indole-3-pyruvic acid decarboxylase encoded by ipdC, and indole-3-acetic acid dehydrogenase encoded by iad1. The ipdC from Enterobacter cloacae ATCC 13047, aspC from Escherichia coli, and iad1 from Ustilago maydis were cloned and expressed under the control of the tac and sod promoters in E. coli. According to SDS-PAGE and enzyme activity, IpdC and Iad1 showed good expression under the control of P(tac), whereas AspC was efficiently expressed by P(sod) originating from Corynebacterium glutamicum. The activities of IpdC, AspC, and Iad1 from the crude extracts of recombinant E. coli Top 10 were 215.6, 5.7, and 272.1 nmol/min/mg-protein, respectively. The recombinant E. coli DH5α expressing IpdC, AspC, and Iad1 produced about 1.1 g/l of IAA and 0.13 g/l of tryptophol (TOL) after 48 h of cultivation in LB medium with 2 g/l tryptophan. To improve IAA production, a tnaA gene mediating indole formation from tryptophan was deleted. As a result, E. coli IAA68 with expression of the three genes produced 1.8 g/l of IAA, which is a 1.6- fold increase compared with wild-type DH5α harboring the same plasmids. Moreover, the complete conversion of tryptophan to IAA was achieved by E. coli IAA68. Finally, E. coli IAA68 produced 3.0 g/l of IAA after 24 h cultivation in LB medium supplemented with 4 g/l of tryptophan.
The Magnetic Properties and Structure of Hemoglobin, Oxyhemoglobin and Carbonmonoxyhemoglobin (1936)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Reduced-state sequence estimation for coded modulation of intersymbol interference channels (1989)

The authors investigated the detection of trellis codes designed for channels that are intersymbol interference free when they operate in the presence of intersymbol interference. A well-structured reduced-state sequence estimation (RSSE) algorithm is described which can achieve the performance of maximum-likelihood sequence estimation (MLSE) with drastically reduced complexity. Well-defined reduced-state trellises are first constructed by merging the states of the ML supertrellis using set partitioning principles. Then the Viterbi algorithm is used to search these trellises. A special case of RSSE, called parallel decision-feedback decoding, uses the encoder trellis, yet on channels with large attenuation distortion it can provide a significantly better performance than linear equalization. The performance of RSSE is examined analytically and through simulation, and then compared to that of MLSE and ideal decision-feedback equalization. It is noted that the performance advantage of RSSE can be obtained without significantly increasing the decoding delay or complicating an adaptive implementation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Utility of duplex ultrasound in the diagnosis of asymptomatic catheter-induced subclavian vein thrombosis. (1991)

Asymptomatic thrombosis of the subclavian vein is common after placement of indwelling catheters. The sequelae of these thrombi are not known. Investigation is hampered by the requirement for venography for diagnosis; consequently, a noninvasive method of diagnosis would be welcome in this context. We have studied prospectively 32 subclavian catheters to determine the usefulness of duplex ultrasound in diagnosing asymptomatic thrombosis. Sixteen arm venograms were normal and all gave normal duplex scans. No false-positive scans were obtained. Eleven venograms demonstrated nonocclusive mural thrombi. Only three of these were seen with duplex ultrasound. Five totally occlusive thrombi were seen on venography, of which only two were detected with duplex sonography. The three thrombi not found with duplex ultrasound were short proximal venous occlusions. The insensitivity of this technique to asymptomatic subclavian thrombi limits its usefulness as a screening tool.
The phosphodiesterase-4 inhibitor rolipram reverses Aβ-induced cognitive impairment and neuroinflammatory and apoptotic responses in rats (2011)

β-amyloid (Aβ) peptides play an important role in cognition deficits, neuroinflammation, and apoptosis observed in Alzheimer's disease (AD). Activation of cyclic AMP (cAMP) signalling enhances memory and inhibits inflammatory and apoptotic responses. However, it is not known whether inhibition of phosphodiesterase-4 (PDE4), a critical controller of intracellular cAMP concentrations, affects AD-associated neuroinflammatory and apoptotic responses and whether these responses contribute to deficits of memory mediated by cAMP signalling. We addressed these issues using memory tests and neurochemical measures. Specifically, rats microinfused with aggregated Aβ25-35 (10 μg/side) into bilateral CA1 subregions displayed deficits in learning ability and memory, as evidenced by decreases in escape latency during acquisition trials and exploratory activities in the probe trial in the water-maze task and 24-h retention in the passive avoidance test. These effects were reversed by rolipram (0.1, 0.25 and 0.5 mg/kg.d i.p.), a prototypic PDE4 inhibitor, in a dose-dependent manner. Interestingly, Aβ25-35-treated rats also displayed decreases in expression of phosphorylated cAMP response-element binding protein (pCREB) and Bcl-2, but increases in expression of NF-κB p65 and Bax in the hippocampus; these effects were also reversed by rolipram in a dose-dependent manner. Similar neurochemical results were observed by replacing Aβ25-35 with Aβ1-42, a full-length amyloid peptide that quickly forms toxic oligomers. These results suggest that PDE4 inhibitors such as rolipram may reverse Aβ-induced memory deficits at least in part via the attenuation of neuronal inflammation and apoptosis mediated by cAMP/CREB signalling. PDE4 could be a target for treatment of memory loss associated with AD.
In vitro studies of water activity and bacterial growth inhibition of sucrose-polyethylene glycol 400-hydrogen peroxide and xylose-polyethylene glycol 400-hydrogen peroxide pastes used to treat infected wounds (1991)

Water activity and bacterial growth inhibition have been studied in formulations comprising either sucrose or xylose along with polyethylene glycol 400 and hydrogen peroxide. The pastes are chemically stable for 6 months if stored at 2 to 8 degrees C and have been shown to lower water activity to levels below those essential for bacterial growth and to be bactericidal even when diluted up to 50% with serum. Of the organisms tested, Staphylococcus aureus proved the least susceptible to the bactericidal effects of these pastes, and candida and gram-negative organisms proved the most susceptible. Pastes without hydrogen peroxide were less rapidly bactericidal than pastes with hydrogen peroxide, while polyethylene glycol 400 itself was found to have considerable antimicrobial activity. It is suggested that sucrose paste may be of benefit as a treatment for infected and malodorous wounds.
α-Enones in heterocyclic synthesis of indazole, thiazine, chromene and quinoline derivatives with their antimicrobial activities (2009)

α-Enones 1a,b react additively with hydrazine hydrate, thiourea, diethyl malonate, malononitrile, as well as ethyl cyanoacetate. Simultaneous cyclisation of the resulting 1:1 adducts yields indazole, thiazine, chromene and quinoline derivatives. The structures of all the synthesised compounds were confirmed by micro analytical and spectral data. The antimicrobial activity of some of the synthesised compounds were tested.
ClariNet: Parallel Wave Generation in End-to-End Text-to-Speech (2018)

In this work, we propose a new solution for parallel wave generation by WaveNet. In contrast to parallel WaveNet (van den Oord et al., 2018), we distill a Gaussian inverse autoregressive flow from the autoregressive WaveNet by minimizing a regularized KL divergence between their highly-peaked output distributions. Our method computes the KL divergence in closed-form, which simplifies the training algorithm and provides very efficient distillation. In addition, we introduce the first text-to-wave neural architecture for speech synthesis, which is fully convolutional and enables fast end-to-end training from scratch. It significantly outperforms the previous pipeline that connects a text-to-spectrogram model to a separately trained WaveNet (Ping et al., 2018). We also successfully distill a parallel waveform synthesizer conditioned on the hidden representation in this end-to-end model.
Gut microbiome of the Hadza hunter-gatherers (2014)

Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza's ability to digest and extract valuable nutrition from fibrous plant foods.
Phase I and Pharmacokinetic Study of Farnesyl Protein Transferase Inhibitor R115777 in Advanced Cancer (2000)

R115777 is bioavailable after oral administration and has an acceptable toxicity profile. Based upon pharmacokinetic data, the recommended dose for phase II trials is 500 mg orally bid (total daily dose, 1, 000 mg) for 5 consecutive days followed by 9 days of rest. Studies of continuous dosing and studies of R115777 in combination with chemotherapy are ongoing.
RNA tumor viruses (1982)

This book contains 12 selections. Some of the titles are: Genome Structure;Genetics of Retroviruses;Functions and Origins of Retroviral Transforming Genes;Human T-cell Retroviruses;Replications of Retroviruses;and Endogenous Viruses.
Modeling Users’ Mobile App Privacy Preferences: Restoring Usability in a Sea of Permission Settings (2018)

In this paper, we investigate the feasibility of identifying a small set of privacy profiles as a way of helping users manage their mobile app privacy preferences. Our analysis does not limit itself to looking at permissions people feel comfortable granting to an app. Instead it relies on static code analysis to determine the purpose for which an app requests each of its permissions, distinguishing for instance between apps relying on particular permissions to deliver their core functionality and apps requesting these permissions to share information with advertising networks or social networks. Using privacy preferences that reflect people’s comfort with the purpose for which different apps request their permissions, we use clustering techniques to identify privacy profiles. A major contribution of this work is to show that, while people’s mobile app privacy preferences are diverse, it is possible to identify a small number of privacy profiles that collectively do a good job at capturing these diverse preferences.