gebhart/patrepeval huggingface dataset:
Tabu Search—Part II (1990)

This is the second half of a two part series devoted to the tabu search metastrategy for optimization problems. Part I introduced the fundamental ideas of tabu search as an approach for guiding other heuristics to overcome the limitations of local optimality, both in a deterministic and a probabilistic framework. Part I also reported successful applications from a wide range of settings, in which tabu search frequently made it possible to obtain higher quality solutions than previously obtained with competing strategies, generally with less computational effort. Part II, in this issue, examines refinements and more advanced aspects of tabu search. Following a brief review of notation, Part II introduces new dynamic strategies for managing tabu lists, allowing fuller exploitation of underlying evaluation functions. In turn, the elements of staged search and structured move sets are characterized, which bear on the issue of finiteness. Three ways of applying tabu search to the solution of integer programming problems are then described, providing connections also to certain nonlinear programming applications. Finally, the paper concludes with a brief survey of new applications of tabu search that have occurred since the developments reported in Part I. Together with additional comparisons with other methods on a wide body of problems, these include results of parallel processing implementations and the use of tabu search in settings ranging from telecommunications to neural networks. INFORMS Journal on Computing, ISSN 1091-9856, was published as ORSA Journal on Computing from 1989 to 1995 under ISSN 0899-1499.
Atmospheric oxygen plasma activation of silicon (100) surfaces (2010)

Silicon (100) surfaces were converted to a hydrophilic state with a water contact angle of &amp;lt;5° by treatment with a radio frequency, atmospheric pressure helium, and oxygen plasma. A 2 in. wide plasma beam, operating at 250 W, 1.0 l/min O2, 30 l/min He, and a source-to-sample distance of 3±0.1 mm, was scanned over the sample at 100±2 mm/s. Plasma oxidation of HF-etched silicon caused the dispersive component of the surface energy to decrease from 55.1 to 25.8 dyn/cm, whereas the polar component of the surface energy increased from 0.3 to 42.1 dyn/cm. X-ray photoelectron spectroscopy revealed that the treatment generated a monolayer of covalently bonded oxygen on the Si(100) surface 0.15±0.10 nm thick. The surface oxidation kinetics have been measured by monitoring the change in water contact angle with treatment time, and are consistent with a process that is limited by the mass transfer of ground-state oxygen atoms to the silicon surface.
Electronic nose for monitoring the flavour of beers (1993)

The flavour of a beer is determined mainly by its taste and smell, which is generated by about 700 key volatile and non-volatile compounds. Beer flavour is traditionally measured through the use of a combination of conventional analytical tools (e.g., gas chromatography) and organoleptic profiling panels. These methods are not only expensive and time-consuming but also inexact due to a lack of either sensitivity or quantitative information. In this paper an electronic instrument is described that has been designed to measure the odour of beers and supplement or even replace existing analytical methods. The instrument consists of an array of up to 12 conducting polymers, each of which has an electrical resistance that has partial sensitivity to the headspace of beer. The signals from the sensor array are then conditioned by suitable interface circuitry and processed using a chemometric or neural classifier. The results of the application of multivariate statistical techniques are given. The instrument, or electronic nose, is capable of discriminating between various commercial beers and, more significantly, between standard and artificially-tainted beers. An industrial version of this instrument is now undergoing trials in a brewery.
A circuit representation technique for automated circuit design (1999)

We present a method of automatically generating circuit designs using evolutionary search and a set of circuit constructing primitives arranged in a linear sequence. This representation has the desirable property that virtually all sets of circuit-constructing primitives result in valid circuit graphs. While this representation excludes certain circuit topologies, it is capable of generating a rich set of them including many of the useful topologies seen in hand-designed circuits. Our system allows circuit size (number of devices), circuit topology, and device values to he evolved. Using a parallel genetic algorithm and circuit simulation software, we present experimental results as applied to three analog filter and two amplifier design tasks. In all tasks, our system is able to generate circuits that achieve the target specifications. Although the evolved circuits exist as software models, detailed examinations of each suggest that they are electrically well behaved and thus suitable for physical implementation. The modest computational requirements suggest that the ability to evolve complex analog circuit representations in software is becoming more approachable on a single engineering workstation.
Semi-distributed load balancing for massively parallel multicomputer systems (1991)

A semidistributed approach is given for load balancing in large parallel and distributed systems which is different from the conventional centralized and fully distributed approaches. The proposed strategy uses a two-level hierarchical control by partitioning the interconnection structure of a distributed or multiprocessor system into independent symmetric regions (spheres) centered at some control points. The central points, called schedulers, optimally schedule tasks within their spheres and maintain state information with low overhead. The authors consider interconnection structures belonging to a number of families of distance transitive graphs for evaluation, and, using their algebraic characteristics, show that identification of spheres and their scheduling points is in general an NP-complete problem. An efficient solution for this problem is presented by making exclusive use of a combinatorial structure known as the Hadamard matrix. The performance of the proposed strategy has been evaluated and compared with an efficient fully distributed strategy through an extensive simulation study. The proposed strategy yielded much better results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases (1993)

We present in Table In addition, new information is included on restriction endonuclease cleavage at sites modified with 5-hydroxymethyluracil (h'5U).
Aziridine Analogs of [[trans-(Epoxysuccinyl)-L-leucyl]amino]-4-guanidinobutane (E-64) as Inhibitors of Cysteine Proteases (1995)

Aziridine derivatives of E-64 have been synthesized, and their characterization against the cysteine proteases cathepsin B, cathepsin L, and papain is reported. The inhibition was found to be strongly pH-dependent, with maximum activity observed at pH 4, indicating that the protonated aziridinium ion form of the inhibitor is the more reactive form. At low pH, the peptide aziridine HO-(L)Az-Leu-NH-iAm inactivated papain with a second-order rate constant, kinac/Ki, of 7.0 x 10(4) M-1 s-1, a value very close to that observed with E-64 or with the corresponding epoxysuccinyl analog HO-(L)Eps-Leu-NH-iAm. This demonstrates that with the correct peptide sequence, aziridine analogs of E-64 can be good irreversible inhibitors of cysteine proteases. Substitution of the epoxysuccinyl moiety by an aziridine does not affect the specificity of inhibition against the three proteases used in this study. The D-diastereomer is the preferred (by 10-fold) diastereomer for the inhibition of cysteine proteases. The reactivity of both diastereomers of iBuNH-Az-LeuPro-OH against cathepsin B was also found to be much lower than that of iBuNH-(L)Eps-LeuPro-OH, which is a potent selective inhibitor of cathepsin B. These differences are attributed mainly to the presence of the protonated aziridine ring, which can modify the binding mode of aziridine analogs at the active site of cysteine proteases.
Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome (2009)

The proteasome is an intricate molecular machine, which serves to degrade proteins following their conjugation to ubiquitin. Substrates dock onto the proteasome at its 19-subunit regulatory particle via a diverse set of ubiquitin receptors and are then translocated into an internal chamber within the 28-subunit proteolytic core particle (CP), where they are hydrolyzed. Substrate is threaded into the CP through a narrow gated channel, and thus translocation requires unfolding of the substrate. Six distinct ATPases in the regulatory particle appear to form a ring complex and to drive unfolding as well as translocation. ATP-dependent, degradation-coupled deubiquitination of the substrate is required both for efficient substrate degradation and for preventing the degradation of the ubiquitin tag. However, the proteasome also contains deubiquitinating enzymes (DUBs) that can remove ubiquitin before substrate degradation initiates, thus allowing some substrates to dissociate from the proteasome and escape degradation. Here we examine the key elements of this molecular machine and how they cooperate in the processing of proteolytic substrates.
Effect of treating periodontitis on C-reactive protein levels: a pilot study (2002)

Periodontitis seems to increase C-reactive protein only in some individuals, presumably the ones reacting to it with a systemic inflammatory reaction. Periodontal treatment decreases C-reactive protein levels in these individuals and it may thus decrease their risk of coronary heart disease.
Applications of Surface Plasmon Resonance (SPR) for the Characterization of Nanoparticles Developed for Biomedical Purposes (2012)

Great interest is currently being devoted to the development of nanoparticles (NPs) for biomedical purposes, designed to improve the pharmacokinetic profile of their cargos (either imaging probes or drugs) and to enhance the specific targeting at the disease site. Recent works suggest that Surface Plasmon Resonance (SPR), widely used for the analysis of biomolecular interactions, represents a technique of choice for rapid and quantitative analyses of the interaction between NPs--functionalized with specific ligands--and their putative biological targets. Moreover, SPR can provide important details on the formation and the role of the protein "corona", i.e., the protein layer which coats NPs once they come into contact with biological fluids. These novel applications of SPR sensors may be very useful to characterize, screen and develop nanodevices for biomedical purposes.
P4 Peptide Therapy Rescues Aged Mice from Fatal Pneumococcal Sepsis (2010)

FIG.2. P4 with serotype-specific IgG confers protection to 11-month-old BALB/c mice against intranasal S. pneumoniae serotype 3 (WU2) challenge.Intravenous injection of P4 (100 g/mouse) with gamma globulin (100 l/mouse) at 48 and 72 h after challenge provided highly significant protection (95%; P ϭ 0.02) from S. pneumoniae WU2 infection.
Strategies for migraine management (1991)

According to widely accepted theory, migraine is a self-limited neurogenic sterile inflammation characterized by initial cerebral vasoconstriction, subsequent extracranial and intracranial vasodilation, sterile inflammation, and secondary muscle contraction. It is characterized by recurrent attacks of headache, usually unilateral and accompanied by nausea, vomiting, and, often, other symptoms. Frequency, duration, and intensity of attacks are widely variable. Migraine affects more women than men, and is often related to menses. Patients with classic migraine experience visual or neurologic prodromes, but vague "premonitions" occur in both classic and common migraine. Precipitating factors include foods, alcohol, medications, visual stimuli, changes in routine, and stress. The first-line agent for abortive therapy is ergotamine; corticosteroids are indicated for prolonged headache. Propranolol is recommended for daily prophylactic therapy, and alternatives include calcium channel blockers, nonsteroidal anti-inflammatory agents, and tricyclic antidepressants.
Cisplatin-DNA adducts are molecular decoys for the ribosomal RNA transcription factor hUBF (human upstream binding factor). (1994)

The toxicity of DNA-damaging agents is widely believed to result from the formation of lesions that block polymerases or disrupt the integrity of the genome. A mechanism heretofore not addressed is that DNA damage may titrate essential DNA-binding proteins away from their natural sites of action. This report shows that the ribosomal RNA (rRNA) transcription factor hUBF (human upstream binding factor) binds with striking affinity (Kd(app) approximately 60 pM) to the intrastrand cis-[Pt(NH3)2](2+-d(GpG) crosslink formed by the anticancer drug cis-diamminedichloroplatinum(II) (cisplatin). When protein blots of human cell extracts are probed with cisplatin-modified DNA, 97- and 94-kDa proteins are detected, consistent with the known sites of hUBF species. A similar analysis of blots containing in vitro translated hUBF confirmed that the protein binds cisplatin adducts with high specificity. By contrast, DNA adducts of the clinically ineffective trans isomer of cisplatin, trans-diamminedichloroplatinum(II), are not recognized by hUBF. DNase I inhibition patterns of hUBF bound to a 100-base-pair DNA fragment containing a centrally located cis-[Pt(NH3)2](2+)-d(GpG) crosslink reveal specific protein-DNA interactions in a 14-base-pair region flanking the adduct. The affinity of hUBF for the rRNA promoter is similar (Kd(app) approximately 18 pM) to that measured for the cisplatin adduct. In addition, we observe that the hUBF-promoter interaction is highly sensitive to the antagonistic effects of cisplatin-DNA adducts. These results suggest that a cisplatin-mediated transcription-factor-hijacking mechanisms could disrupt rRNA synthesis, which is stimulated in proliferating cells.
Effects of Adenosine on Intraocular Pressure, Optic Nerve Head Blood Flow, and Choroidal Blood Flow in Healthy Humans (2003)

These data are consistent with adenosine inducing choroidal and optic nerve head vasodilatation and reducing IOP in healthy humans. Considering the neuroprotective properties of adenosine described in previous animal experiments the adenosine system is an attractive target system for therapeutic approaches in glaucoma.
Tantalum nitride metal gate FD-SOI CMOS FETs using low resistivity self-grown bcc-tantalum layer (2001)

A tantalum nitride (TaNx) metal gate complementary metal oxide semiconductor (CMOS) technology using low-resistivity (/spl sim/15 /spl mu//spl Omega/cm), bcc (body-centered-cubic)-phase tantalum metal layer has been developed, featuring low-temperature processing below 550/spl deg/C except for gate oxide formation. It was found for the first time that TaNx works not only as a buffer layer which prevents tantalum metal film and gate oxide film from reacting with each other, but also as a seed layer which helps self-growth of bcc-phase tantalum films by hetero-epitaxy. Furthermore, we have demonstrated that the work function of TaNx gate is close to midgap of silicon, hence similar to titanium nitride (TiNx) gate. We have also demonstrated that MOS capacitors on bulk and fully-depleted silicon-on-insulator (FD-SOI) CMOS with TaNx/bcc-Ta/TaNx stacked metal gate structure have excellent electrical characteristics and that the ring-oscillator fabricated using the stacked metal gate CMOS can be operated successfully with 3.8 nm-thickness gate oxide.
Oligosaccharides of hyaluronic acid increased epidermal cell stemness by modulation of integrin expression (2012)

These findings suggest that oligosaccharides of HA increase the differentiation of the epidermis. In addition, increased number of p63, a putative stem cell marker of the skin, showed that oligosaccharides of HA promote the survival of basal stem cells by modulating the expression of integrin-α6 and integrin-β1. Finally, it can be said that inflammation-induced small-sized oligosaccharides can have beneficial effects on epidermal regeneration and topically applied oligosaccharide of HA can have healing effects in skin problems.
Identification of the Human c- myc Protein Nuclear Translocation Signal (1988)

We identified and characterized two regions of the human c-myc protein that target proteins into the nucleus. Using mutant c-myc proteins and proteins that fuse portions of c-myc to chicken muscle pyruvate kinase, we found that residues 320 to 328 (PAAKRVKLD; peptide M1) induced complete nuclear localization, and their removal from c-myc resulted in mutant proteins that distributed in both the nucleus and cytoplasm but retained rat embryo cell cotransforming activity. Residues 364 to 374 (RQRRNELKRSP; peptide M2) induced only partial nuclear targeting, and their removal from c-myc resulted in mutant proteins that remained nuclear but were cotransformationally inactive. We conjugated synthetic peptides containing M1 or M2 to human serum albumin and microinjected the conjugate into the cytoplasm of Vero cells. The peptide containing M1 caused rapid and complete nuclear accumulation, whereas that containing M2 caused slower and only partial nuclear localization. Thus, M1 functions as the nuclear localization signal of c-myc, and M2 serves some other and essential function.
Role of Metal Contacts in Designing High-Performance Monolayer n-Type WSe2 Field Effect Transistors (2013)

This work presents a systematic study toward the design and first demonstration of high-performance n-type monolayer tungsten diselenide (WSe2) field effect transistors (FET) by selecting the contact metal based on understanding the physics of contact between metal and monolayer WSe2. Device measurements supported by ab initio density functional theory (DFT) calculations indicate that the d-orbitals of the contact metal play a key role in forming low resistance ohmic contacts with monolayer WSe2. On the basis of this understanding, indium (In) leads to small ohmic contact resistance with WSe2 and consequently, back-gated In-WSe2 FETs attained a record ON-current of 210 μA/μm, which is the highest value achieved in any monolayer transition-metal dichalcogenide- (TMD) based FET to date. An electron mobility of 142 cm(2)/V·s (with an ON/OFF current ratio exceeding 10(6)) is also achieved with In-WSe2 FETs at room temperature. This is the highest electron mobility reported for any back gated monolayer TMD material till date. The performance of n-type monolayer WSe2 FET was further improved by Al2O3 deposition on top of WSe2 to suppress the Coulomb scattering. Under the high-κ dielectric environment, electron mobility of Ag-WSe2 FET reached ~202 cm(2)/V·s with an ON/OFF ratio of over 10(6) and a high ON-current of 205 μA/μm. In tandem with a recent report of p-type monolayer WSe2 FET ( Fang , H . et al. Nano Lett. 2012 , 12 , ( 7 ), 3788 - 3792 ), this demonstration of a high-performance n-type monolayer WSe2 FET corroborates the superb potential of WSe2 for complementary digital logic applications.
Fatty Acid Activation in Cyanobacteria Mediated by Acyl-Acyl Carrier Protein Synthetase Enables Fatty Acid Recycling (2010)

In cyanobacteria fatty acids destined for lipid synthesis can be synthesized de novo, but also exogenous free fatty acids from the culture medium can be directly incorporated into lipids. Activation of exogenous fatty acids is likely required prior to their utilization. To identify the enzymatic activity responsible for activation we cloned candidate genes from Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 and identified the encoded proteins as acyl-acyl carrier protein synthetases (Aas). The enzymes catalyze the ATP-dependent esterification of fatty acids to the thiol of acyl carrier protein. The two protein sequences are only distantly related to known prokaryotic Aas proteins but they display strong similarity to sequences that can be found in almost all organisms that perform oxygenic photosynthesis. To investigate the biological role of Aas activity in cyanobacteria, aas knockout mutants were generated in the background of Synechocystis sp. PCC 6803 and S. elongatus PCC 7942. The mutant strains showed two phenotypes characterized by the inability to utilize exogenous fatty acids and by the secretion of endogenous fatty acids into the culture medium. The analyses of extracellular and intracellular fatty acid profiles of aas mutant strains as well as labeling experiments indicated that the detected free fatty acids are released from membrane lipids. The data suggest a considerable turnover of lipid molecules and a role for Aas activity in recycling the released fatty acids. In this model, lipid degradation represents a third supply of fatty acids for lipid synthesis in cyanobacteria.
A study on the scalability of non-preferred hand mode manipulation (2007)

In pen-tablet input devices modes allow overloading of the electronic stylus. In the case of two modes, switching modes with the non-preferred hand is most effective [12]. Further, allowing temporal overlap of mode switch and pen action boosts speed [11]. We examine the effect of increasing the number of interface modes accessible via non-preferred hand mode switching on task performance in pen-tablet interfaces. We demonstrate that the temporal benefit of overlapping mode-selection and pen action for the two mode case is preserved as the number of modes increases. This benefit is the result of both concurrent action of the hands, and reduced planning time for the overall task. Finally, while allowing bimanual overlap is still faster it takes longer to switch modes as the number of modes increases. Improved understanding of the temporal costs presented assists in the design of pen-tablet interfaces with larger sets of interface modes.
Molecular Glass Resists for High-Resolution Patterning (2006)

This paper describes a series of photoresists constructed from glass-forming, low-molecular-weight organic compounds, also known as molecular glasses. Compared with traditional polymeric resists, molecular glass resists are composed of smaller and more-uniform molecular building blocks. In this work, both positive-tone and negative-tone molecular glass photoresists with a range of core structures were designed and synthesized for study in advanced lithography. These molecular glass resists have asymmetric, rigid cores, which is important for producing glassy materials with glass transition temperatures substantially above room temperature. For positive-tone molecular glass photoresists, amorphous films could be obtained by partial protection of the core structure. Images were produced using photoacid-generator-catalyzed deprotection chemistry. Amorphous negative-tone resists were obtained by mixing molecular glass core structures with another minor resist component such as a photo cross-linker. It was shown by SEC that the molecular weight of the exposed and cross-linked negative-tone resist was less than 2000 g/mol, thus indicating that the solubility change is largely due to a molecular-weight increase. Both types of materials exhibited high sensitivity and resolution. Several resist characteristics were studied to assess their potential as high-resolution resists. These molecular glasses showed high fluorocarbon etch resistance that is comparable to that of poly(hydroxystyrene). Lower line edge roughness was obtained for the negative-tone molecular glass compared to a negative-tone polymeric e-beam resist. The resulting materials exhibited high sensitivity and resolution close to the tool limit under 248 nm exposures when using a chemical amplification process. A well-resolved pattern as small as 50 nm was obtained for the negative-tone molecular glass by e-beam exposure, indicating the excellent potential of using low molecular molar mass molecular glasses to form high-resolution structures.