gebhart/patrepeval huggingface dataset:
Artificial gene amplification reveals an abundance of promiscuous resistance determinants in <i>Escherichia coli</i> (2010)

Duplicated genes provide an important raw material for adaptive evolution. However, the relationship between gene duplication and the emergence of new biochemical functions is complicated, and it has been difficult to quantify the likelihood of evolving novelty in any systematic manner. Here, we describe a comprehensive search for artificially amplified genes that are able to impart new phenotypes on Escherichia coli, provided their expression is up-regulated. We used a high-throughput, library-on-library strategy to screen for resistance to antibiotics and toxins. Cells containing a complete E. coli ORF library were exposed to 237 toxin-containing environments. From 86 of these environments, we identified a total of 115 cases where overexpressed ORFs imparted improved growth. Of the overexpressed ORFs that we tested, most conferred small but reproducible increases in minimum inhibitory concentration (≤16-fold) for their corresponding antibiotics. In many cases, proteins were acting promiscuously to impart resistance. In the absence of toxins, most strains bore no fitness cost associated with ORF overexpression. Our results show that even the genome of a nonpathogenic bacterium harbors a substantial reservoir of resistance genes, which can be readily accessed through overexpression mutations. During the growth of a population under selection, these mutations are most likely to be gene amplifications. Therefore, our work provides validation and biochemical insight into the innovation, amplification, and divergence model of gene evolution under continuous selection [Bergthorsson U, Andersson DI, Roth JR (2007) Proc Natl Acad Sci USA 104:17004-17009], and also illustrates the high frequency at which novel traits can evolve in bacterial populations.
Representing procedural knowledge in expert systems: an application to process control (1985)

The paper presents a novel expert system architecture which supports explicit representation and effective use of both declarative and procedural knowledge. These two types of expert knowledge are represented by means of production rules and event-graphs respectively, and they are processed by a unified inference engine. Communication between the rule level and the event-graph level is based on a full visibility of each level on the internal state of the other, and it is structured in such a way as to allow each level to exert control on the other. This structure offers several advantages over more traditional architectures. Knowledge representation is more natural and transparent; knowledge acquisition turns out to be easier as pieces of knowledge can be immediately represented without the need of complex transformation and restructuring; inference is more effective due to reduced non-determinism resulting from explicit representation of fragments of procedural knowledge in eventgraphs; finally, explanations are more natural and understandable. The proposed architecture has been adopted for the design of PROP, an expert system for on-line monitoring of the cycle water pollution in a thermal power plant. PROP is running on a SUN-2 workstation and has been tested on a sample of real cases.
Excimer Laser-Induced Ti Silicidation to Eliminate the Fine-Line Effect for Integrated Circuit Device Fabrication (2002)

10.1149/1.1510843
Correlation between Live and Post Mortem Skull Conductivity Measurements (2006)

The skull is a tissue with a widely controversial range of conductivity values. This article correlates live skull conductivity measurements with post mortem conductivity measurements with a scaling factor ranging between 2.5 and 4. The scaling factor is validated by a mathematical model that determines the skull conductivity using saline and cerebrospinal fluid (CSF) conductivities and correlated with published physical live and post mortem skull conductivity measurements which show support for this live-to-post mortem scale factor.
Expression and Characterisation of Plasmepsin I from <i>Plasmodium falciparum</i> (1997)

Two aspartic proteinases, plasmepsins I and II, are present in the digestive vacuole of the human malarial parasite Plasmodium falciparum and are believed to be essential for parasite degradation of haemoglobin. Here we report the expression and kinetic characterisation of functional recombinant plasmepsin I. In order to generate active plasmepsin I from its precursor, an autocatalytic cleavage site was introduced into the propart of the zymogen by mutation of Lys110P to Val (P indicates a propart residue). Appropriate refolding of the mutated zymogen then permitted pH-dependent autocatalytic processing of the zymogen to the active mature proteinase. A purification scheme was devised that removed aggregated and misfolded protein to yield pure, fully processable, proplasmepsin I. Kinetic constants for two synthetic peptide substrates and four inhibitors were determined for both recombinant plasmepsin I and recombinant plasmepsin II. Plasmepsin I had 5-10-fold lower k(cat)/Km values than plasmepsin II for the peptide substrates, while the aspartic proteinase inhibitors, selected for their ability to inhibit P. falciparum growth, were found to have up to 80-fold lower inhibition constants for plasmepsin I compared to plasmepsin II. The most active plasmepsin I inhibitors were antagonistic to the antimalarial action of chloroquine on cultured parasites. Northern blot analysis of RNA, isolated from specific stages of the erythrocytic cycle of P. falciparum, showed that the proplasmepsin I gene is expressed in the ring stages whereas the proplasmepsin II gene is not transcribed until the later trophozoite stage of parasite growth. The differences in kinetic properties and temporal expression of the two plasmepsins suggest they are not functionally redundant but play distinct roles in the parasite.
Effects of DDA, CpG-ODN, and plasmid-encoded chicken IFN-γ on protective immunity by a DNA vaccine against IBDV in chickens (2006)

This study examined the adjuvant effects of dimethyl dioctadecyl ammonium bromide (DDA), CpG oligodeoxynucleotides (CpG-ODN), and chicken interferon-gamma (ChIFN-gamma) on a DNA vaccine (pcDNA-VP243) against the infectious bursal disease virus (IBDV). A plasmid encoding chicken IFN-ã was constructed. Twice at 2-week intervals, two-week-old chickens were injected intramuscularly and intraperitoneally with either a DNA vaccine alone or a DNA vaccine together with the respective adjuvants. On week 2 after the second immunization, the chickens were orally challenged with the highly virulent IBDV. The groups that received the DNA vaccines plus either DDA or CpG-ODN showed significantly lower survival rates than the group that received the DNA vaccine alone. However, the survival rates for the DNA vaccine alone and for the DNA vaccine plus ChIFN-gamma were similar. The chickens had no detectable antibodies to the IBDV before the challenge but all the surviving chickens in all groups except for the normal control group showed the induction of antibodies to the IBDV at day 10 after the challenge. As judged by the lymphocyte proliferation assays using the a WST-8 solution performed on the peripheral blood and splenic lymphocytes, the stimulation indices (SI) of the peripheral blood lymphocytes in all groups except for the normal control group were similar immediately before the challenge. At 10 days post-challenge, the SI for DNA vaccine plus either CpG-ODN or ChIFN-gamma was similar to that of the DNA vaccine control group. For splenic lymphocytes, the SI in the DNA vaccine plus CpG-ODN and DNA vaccine plus ChIFN-gamma groups were higher than for the DNA vaccine control. These results suggest that DDA actually compromises the protection against the IBDV by DNA vaccine, and CpG-ODN and IFN-gamma had no significant effect.
Psoralens and Their Application to the Study of Some Molecular Biological Processes (1993)

Psoralens. Recent progress in the preparation of psoralen-DNA photoadducts New approach to the large-scale synthesis of furan-side monoadduct New approach to the large-scale synthesis of diadduct Rationale behind the preparative procedures Studies on the elongation of T7 RNA polymerase on a DNA template containing a site-specifically placed Psoralen cross-link Cross-linking of proteins to DNA via a psoralen Future directions Progress towards structure determination of psoralenated oligonucleotides by NMR and X-ray cyrstallography Synthesis and application of spin-labeled psoralens to the study of DNA dynamics
Video Annotation and Retrieval Using Ontologies and Rule Learning (2010)

An approach for automatic annotation and retrieval of video content uses semantic concept classifiers and ontologies to permit expanded queries to synonyms and concept specializations.
Synthesis of 2-Alkylbenzofurans via Acid-catalyzed Cyclization of 1,1-Dimethoxy-2-phenoxyalkanes (2004)

Treatment of 2-phenoxyalkanals 1a-e with methanol at room temperature under homo-or heterogeneous acid-catalysis conditions leads to formation of diacetal as well as some quantities of appropriate 2-alkylbenzofurans. 2-Alkylbenzofurans 3a-e were obtained in high yields via cyclization of the 1,1-dimethoxy-2-phenoxyalkanes 2a-e under mild conditions over Amberlyst 15.
Una mujer para olvidar a Pinochet. (2013)

Chile celebra elecciones presidenciales intentando superar su pasado reciente y afrontar el futuro sin la pesada sombra del dictador.
Frequency upconversion of tunable femtosecond pulses by parametric amplification and sum-frequency generation in a single nonlinear crystal (1995)

Nearly transform-limited femtosecond pulses have been generated between 585 and 620 nm by simultaneous narrow-band seeding at 1.053 μm of an optical parametric amplifier pumped by a tunable high-power Ti:sapphire laser system at 1 kHz and sum-frequency mixing between the resulting idler and the pump pulses in the same nonlinear crystal.
Turbine Startup and Shutdown in Wind Farms Featuring Partial Power Processing Converters (2020)

The wind turbine startup and shutdown procedures for electrical subsystems are straightforward for wind turbines featuring full-scale power electronic converters and have not required significant attentions from the research community. However, for offshore wind farms featuring series-connected dc collection systems and differential power processing capabilities, the controllable wind turbine power converters might not be rated in such a way that a full-scale output power difference can be handled within a series string. As startup and shutdown procedures can require a transition from zero to full power, a more elaborate design is required to ensure that wind turbines can still start and stop reliably under all conditions, without compromising advantages in reduced wind turbine converter ratings with differential power processing capabilities. In this paper, the startup and shutdown procedures for a series-dc wind farm featuring diode-bridge rectifiers and partial power processing converters as wind turbine converters, are investigated and constraints on converter ratings are evaluated.
Efficient flexible polymer light emitting diodes with conducting polymer anodes (2007)

We report polymer light emitting diodes fabricated on flexible poly(ethyleneterephthalate) substrates coated with a layer of poly(3,4-ethylene-dioxythiophene) : poly(styrenesulfonate) that was lithographically patterned to define the anode structure. A blend of poly(9,9-dioctylfluorene-co-benzothiadiazole) and poly(9,9-dioctylfluorene-co-N-(4-butylphenyl)diphenylamine) was then spin-coated on top as the emissive layer and the device was completed by vacuum deposition of a LiF/Al bilayer cathode. The resulting yellow light emitting diodes had typical peak power and current efficiencies of 13.7 lm W−1 and 8.8 cd A−1 respectively, which compare well with values for similar devices fabricated on ITO-coated rigid glass substrates. A maximum luminance in excess of 7300 cd m−2 was achieved.
A high-efficiency traveling-wave power amplifier topology using improved power-combining techniques (1998)

Traditional distributed amplification techniques have allowed for high gain and bandwidth at the expense of low efficiency. The decreased efficiency is primarily due to the existence of an actively loaded artificial transmission line as the output, resulting in backward wave propagation. Using the same traditional input line distributed techniques to achieve high bandwidth, this research has explored a delay line and corporate combining output topology which improves the travelling-wave amplifier's (TWAs) efficiency at large signal by elimination of the backward waves. The broad-band output combiner transforms the amplifier load impedance to that of an optimum load for each device, thus realizing a traveling-wave power amplifier. The results for a 1-9-GHz hybrid circuit are presented.
<title>Development of monolithic Cd<formula><inf><roman>1-x</roman></inf></formula>Zn<formula><inf><roman>x</roman></inf></formula>Te arrays with improved energy and spatial resolution</title> (1994)

We have fabricated several monolithic x-ray detector arrays from Cd<SUB>0.9</SUB>Zn<SUB>0.1</SUB>Te material. The principle advantages of this material are its relatively high stopping power and room temperature operation. Recently fabricated linear arrays exhibit improved spatial and energy resolution as compared to our previous versions. Each array is 25.3 mm long with 32 independent detector elements, yielding a center-to-center spacing of 0.8 mm. Gaps of less than 100 micrometers , but with greater than 2 gigaohms of resistance, separate the pixel contacts. Our results indicate that smaller spacings and gap widths are possible with our current fabrication methods. The arrays have been operated in a pulse counting mode with photon energy discrimination. Results for energy resolution and spatial response are presented. Examples of low dose x ray transmission images obtained with a prototype linear scanner utilizing multiple arrays are shown here. By using the energy discrimination capability of the arrays and electronic readout, we have also been able to generate dual-energy images of various samples.
Intermittent antegrade warm myocardial protection compared to intermittent cold blood cardioplegia in elective coronary surgery – do we have to change? (2003)

IAWBC is a safe and simple method in elective on-pump coronary artery bypass surgery. Significantly lower ischemic markers suggest an improved myocardial protection compared to cold blood cardioplegia in these patients.
Trading Accuracy for Energy in Stochastic Circuit Design (2017)

As we approach the limits of traditional Moore’s-Law scaling, alternative computing techniques that consume energy more efficiently become attractive. Stochastic computing (SC), as a re-emerging computing technique, is a low-cost and error-tolerant alternative to conventional binary circuits in several important applications such as image processing and communications. SC allows a natural accuracy-energy tradeoff that has been exploited in the past. This article presents an accuracy-energy tradeoff technique for SC circuits that reduces their energy consumption with virtually no accuracy loss. To this end, we employ voltage or frequency scaling, which normally reduce energy consumption at the cost of timing errors. Then we show that due to their inherent error tolerance, SC circuits operate satisfactorily without significant accuracy loss even with aggressive scaling. This significantly improves their energy efficiency. In contrast, conventional binary circuits quickly fail as the supply voltage decreases. To find the most energy-efficient operating point of an SC circuit, we propose an error estimation method that allows us to quickly explore the circuit’s design space. The error estimation method is based on Markov chain and least-squares regression. Furthermore, we investigate opportunities to optimize SC circuits under such aggressive scaling. We find that logical and physical design techniques can be combined to significantly expand the already-powerful accuracy-energy tradeoff possibilities of SC. In particular, we demonstrate that careful adjustment of path delays can lead to significant error reduction under voltage and frequency scaling. We perform buffer insertion and route detouring to achieve more balanced path delays. These techniques differ from conventional path-balancing techniques whose goal is to minimize power consumption by resizing the non-critical paths. The goal of our path-balancing approach is to increase error cancellation chances in voltage-/frequency-scaled SC circuits. Our circuit optimization comprehends the tradeoff between power overheads due to inserted buffers and wires versus the energy reduction from supply voltage downscaling enabled by more balanced path delays. Simulation results show that our optimized SC circuits can tolerate aggressive voltage scaling with no significant signal-to-noise ratio (SNR) degradation. In one example, a 40% supply voltage reduction (1V to 0.6V) on the SC circuit leads to 66% energy saving (20.7pJ to 6.9pJ) and makes it more efficient than its conventional binary counterpart. In the same example, a 100% frequency boosting (400ps to 200ps) of the optimized circuits leads to no significant SNR degradation. We also show that process variation and temperature variation have limited impact on optimized SC circuits. The error change is less than 5% when temperature changes by 100°C or process condition changes from worst case to best case.
Detection of the effects of ingested caffeine on fertility of cocks by homospermic and heterospermic insemination (1981)

Cocks were fed diets containing 0, 0.025, 0.05, 0.075 or 0.1% caffeine during a 14-day treatment period. The number of spermatozoa produced by cocks fed 0.075 or 0.1% caffeine declined sharply at 12 days after onset of treatment. Hens were inseminated with a constant number of spermatozoa from individual cocks. The fertility of cocks fed 0.05, 0.075 or 0.1% caffeine declined during the 17-day post-treatment period and then returned to pretreatment levels. Cocks whose offspring were distinguishable were paired and relative fertility was assessed in a heterospermic test. One cock in each pair was fed 0.05% caffeine during the treatment period. Hens were inseminated with semen mixed within pairs. The proportion of chicks sired by cocks fed caffeine decreased during treatment and remined at that level until 17 days after treatment, when it increased to pretreatment levels. The percentage of total eggs hatched declined concomitantly with the reduction in the proportions of chicks sired by treated cocks. These results indicate that the effect of low levels of a toxin could be detected by reduced numbers of eggs hatched after heterospermic insemination with semen of normal appearance.
The Effect of Physical Therapy Treatment in Patients with Subjective Tinnitus: A Systematic Review (2016)

<b>Background:</b> Tinnitus is a very common symptom that often causes distress and decreases the patient's quality of life. Apart from the well-known causes, tinnitus can in some cases be elicited by dysfunctions of the cervical spine or the temporomandibular joint (TMJ). To date however, it is unclear whether alleviation of these dysfunctions, by physical therapy treatment, also decreases the tinnitus complaints. Such physical therapy could be an interesting treatment option for patients that are now often left without treatment. <b>Objectives:</b> The aim of this review was to investigate the current evidence regarding physical therapy treatment in patients with tinnitus. <b>Data sources:</b> The online databases Pubmed, Web of Science, Cochrane, and Embase were searched up to March 2016. Two independent reviewers conducted the data extraction and methodological quality assessment. <b>Study eligibility criteria:</b> Only randomized controlled trials and quasi-experimental trials were included in the review. Studies had to be written in English, French, Dutch, or German. <b>Participants and interventions:</b> The included studies investigated the effect of physical therapy treatment modalities on tinnitus severity in patients suffering from subjective tinnitus. <b>Results:</b> Six studies were included in this review, four investigating cervical spine treatment and two investigating TMJ treatment. These studies show positive effects of cervical spine treatment (manipulations, exercises, triggerpoint treatment) on tinnitus severity. Additionally, decrease in tinnitus severity and intensity was demonstrated after TMJ treatment, following splints, occlusal adjustments as well as jaw exercises. <b>Limitations:</b> The risk of bias in the included studies was high, mainly due to lack of randomization, lack of blinding of subjects, therapists, and/or investigators. Additionally, risk of bias is present due to incomplete presentation of the data and selective reporting. A major issue of the reviewed papers is the heterogeneity of the included study populations, treatments and outcome measures, which inhibit data pooling and meta-analysis. <b>Conclusions:</b> Despite the methodological issues in the included studies and the consequent low quality evidence, it is noteworthy that all included studies show positive treatment effects. Before recommendations can be made, these results need to be confirmed in larger, high quality studies, using unambiguous inclusion criteria, state-of-the-art treatment, and high quality outcome measures.
PeopleNet (2005)

People often seek information by asking other people even when they have access to vast reservoirs of information such as the Internet and libraries. This is because people are great sources of unique information, especially that which is location-specific, community-specific and time-specific. Social networking is effective because this type of information is often not easily available anywhere else. In this paper, we conceive a wireless virtual social network which mimics the way people seek information via social networking. PeopleNet is a simple, scalable and low-cost architecture for efficient information search in a distributed manner. It uses the infrastructure to propagate queries of a given type to users in specific geographic locations, called bazaars. Within each bazaar, the query is further propagated between neighboring nodes via peer-to-peer connectivity until it finds a matching query. The PeopleNet architecture can overlay easily on existing cellular infrastructure and entails minimal software installation. We identify three metrics for system performance: (i) probability of a match, (ii) time to find a match and (iii) number of matches found by a query. We describe two simple models, called the swap and spread models, for query propagation within a bazaar. We qualitatively argue that the swap model is better with respect to the performance metrics identified and demonstrate this via simulations. Next, we compute analytically the probability of match for the swap model. We show that the probability of match can be significantly improved if, prior to swapping queries, the nodes exchange some limited information about their buffer contents. We propose a simple greedy algorithm which uses this limited information to decide which queries to swap. We show via simulation that this algorithm achieves significantly better performance. Overall our results demonstrate that PeopleNet, with its bazaar concept and peer-to-peer query propagation, can provide a simple and efficient mechanism for seeking information.