gebhart/patrepeval huggingface dataset:
Persistence of Transmitted HIV-1 Drug Resistance Mutations Associated with Fitness Costs and Viral Genetic Backgrounds (2015)

Transmission of drug-resistant pathogens presents an almost-universal challenge for fighting infectious diseases. Transmitted drug resistance mutations (TDRM) can persist in the absence of drugs for considerable time. It is generally believed that differential TDRM-persistence is caused, at least partially, by variations in TDRM-fitness-costs. However, in vivo epidemiological evidence for the impact of fitness costs on TDRM-persistence is rare. Here, we studied the persistence of TDRM in HIV-1 using longitudinally-sampled nucleotide sequences from the Swiss-HIV-Cohort-Study (SHCS). All treatment-naïve individuals with TDRM at baseline were included. Persistence of TDRM was quantified via reversion rates (RR) determined with interval-censored survival models. Fitness costs of TDRM were estimated in the genetic background in which they occurred using a previously published and validated machine-learning algorithm (based on in vitro replicative capacities) and were included in the survival models as explanatory variables. In 857 sequential samples from 168 treatment-naïve patients, 17 TDRM were analyzed. RR varied substantially and ranged from 174.0/100-person-years;CI=[51.4, 588.8] (for 184V) to 2.7/100-person-years;[0.7, 10.9] (for 215D). RR increased significantly with fitness cost (increase by 1.6[1.3,2.0] per standard deviation of fitness costs). When subdividing fitness costs into the average fitness cost of a given mutation and the deviation from the average fitness cost of a mutation in a given genetic background, we found that both components were significantly associated with reversion-rates. Our results show that the substantial variations of TDRM persistence in the absence of drugs are associated with fitness-cost differences both among mutations and among different genetic backgrounds for the same mutation.
Guest Editorial Next-Generation Spectrum-Efficient and Elastic Optical Transport Networks (2013)

The six papers in this special issue are devoted to the topic of next generation spectrum efficient and elastic optical transport systems.
Fluorophosphonate‐Based Degrader Identifies Degradable Serine Hydrolases by Quantitative Proteomics (2020)

Novel chemical biology probes linking a serine hydrolase-directed fluorophosphonate warhead and cereblon-binding pomalidomide were assessed for the degradation of serine hydrolases. A quantitative proteomics approach to detect degraded proteins revealed that, despite the engagement of ∼40 serine hydrolases, degradation was achieved for only a single serine hydrolase, lysophospholipase II (LYPLA2).
An optimal design of the LLC resonant converter based on peak gain estimation (2012)

The LLC resonant converter topology is widely used in DC-DC converter applications for its advantage in achieving high efficiency and high power density. However, due to the complexity in the analysis, the converter lacks a clear design method to help selecting the optimal circuit parameters. In this paper, an optimal design method is developed based on the operation mode analysis and peak gain estimation. With the optimal design, the converter can minimize the conduction loss while maintaining the required gain range. A 400W, 400V output and 25V-38V input LLC converter is built using the proposed method, which achieves above 98% peak efficiency. As a comparison, the conventional searching method is used to reselect the LLC components for the same specifications, and the experiments show that the optimal design has better performance.
Impaired Diurnal Pattern of Meal Tolerance and Insulin Sensitivity in Type 2 Diabetes: Implications for Therapy (2022)

To assess the diurnal patterns of postprandial glucose tolerance and insulin sensitivity, 19 subjects with type 2 diabetes (8 women; 60 ± 11 years; BMI 32 ± 5 kg/m2) and 19 anthropometrically matched subjects with no diabetes (ND; 11 women; 53 ± 12 years; BMI 29 ± 5 kg/m2) were studied during breakfast (B), lunch (L), and dinner (D) with identical mixed meals (75 g carbohydrates) on 3 consecutive days in a randomized Latin square design. Three stable isotopes of glucose were ustilized to estimate meal fluxes, and mathematical models were used in estimating indices of insulin action and β-cell function. Postmeal glucose excursions were higher at D versus B and at D versus L in type 2 diabetes (P < 0.05), while in ND they were higher at D versus B (P = 0.025) and at L versus B (P = 0.04). The insulin area under the curve was highest at B compared with L and D in type 2 diabetes, while no differences were observed in ND. Disposition index (DI) was higher at B than at L (P < 0.01) and at D (P < 0.001) in ND subjects, whereas DI was low with unchanging pattern across B-L-D in individuals with type 2 diabetes. Furthermore, between-meal differences in β-cell responsivity to glucose (F) and insulin sensitivity (SI) were concurrent with changes in the DI within groups. Fasting and postmeal glucose, insulin, and C-peptide concentrations, along with estimates of endogenous glucose production (EGP), Rd, SI, F, hepatic extraction of insulin, insulin secretion rate, extracted insulin, and DI, were altered in type 2 diabetes compared with ND (P < 0.011 for all). The data show a diurnal pattern of postprandial glucose tolerance in overweight otherwise glucose-tolerant ND individuals that differs from overweight individuals with type 2 diabetes. The results not only provide valuable insight into management strategies for better glycemic control in people with type 2 diabetes, but also improved understanding of daytime glucose metabolism in overweight individuals without impaired glucose tolerance or overt diabetes.
Interactions of Cavitation Bubbles Observed by High-Speed Imaging in Shock Wave Lithotripsy (2006)

A multi‐frame high‐speed photography was used to investigate the dynamics of cavitation bubbles induced by a passage of a lithotripter shock wave in a water tank. Solitary bubbles in the free field each radiated a shock wave upon collapse, and typically emitted a micro‐jet on the rebound following initial collapse. For bubbles in clouds, emitted jets were directed toward neighboring bubbles and could break the spherical symmetry of the neighboring bubbles before they in turn collapsed. Bubbles at the periphery of a cluster underwent collapse before the bubbles at the center. Observations with high‐speed imaging confirm previous predictions that bubbles in a cavitation cloud do not cycle independently of one another but instead interact as a dynamic bubble cluster.
Mining diverse opinions (2012)

Network operations that support tactical missions are often characterized by evolving information that needs to be delivered over bandwidth constrained communication networks and presented to a social/cognitive network with limited human attention span and high stress. Most past research efforts on data dissemination examined syntactic redundancy between data items (e.g., common bit strings, entropy coding and compression, etc.), but only limited work has examined the problem of reducing semantic redundancy with the goal of providing higher quality information to end users. In this paper we propose to measure semantic redundancy in large volume text streams using online topic models and opinion analysis (e.g., topic = Location X and opinion = possible_hazard <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , safe_zone <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> ). By suppressing semantically redundant content one can better utilize bottleneck resources such as bandwidth on a resource constrained network or attention time of a human user. However, unlike syntactic redundancy (e.g., lossless compression, lossy compression with small reconstruction errors), a semantic redundancy based approach is faced with the challenge of having to deal with larger inaccuracies (e.g., false positive and false negative probabilities in an opinion classifier). This paper seeks to quantify the effectiveness of a semantic redundancy based approach (over its syntactic counterparts) as a function of such inaccuracies and present a detailed experimental evaluation using realistic information flows collected from an enterprise network with about 1500 users <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Analytic design of an achromatic double grating coupler (1991)

A method for designing a double grating for coupling a polychromatic wave out of a waveguide with negligible angular dispersion is presented. It is based on calculating analytically two different grating functions, such that the chromatic dispersion of the first grating function is compensated by the second grating function. It is shown that the usable wavelength range can be increased by more than 2 orders of magnitude relative to conventional grating couplers for typical angular tolerance.
Current status of Nikon's F2 exposure tool development (2001)

Current status of Nikon's F2 tool development is reported. At first, the required otpical performance of F2 tools will be discussed. Image simulation results show that the required NA for 70 nm is 0.8 or more. Then Nikon's approaches to realize the optics and tools are presented. For the F2 tools, the most important elements are the projection optics and gas purging of the light path. As for the projection optics, conventional lens type may not be applicable for F2 wavelength, and new type catadioptric optics may have to be developed. In this paper, designs of some catadioptric types and some all refractive types are shown and compared. AR-coatings are very important to obtain enough illumination power. New data on Nikon's AR-coatings are presented. For the gas purging, Nikon has already achieved oxygen concentration less than 1 ppm and further improvements are now in development. Results of gas purging are also presented.
Applied Quantum X Implant System: Technology Enhancements to Enable Production-Worthy Performance at the 45 nm Node (2006)

Mechanical scanning of the wafer in 2 dimensions is one approach that has been used to achieve single wafer processing for high current ion implantation. This approach simplifies the beamline design, compared to scanned beam or ribbon beam architectures, but has required a number of new technologies and methods in the scanner hardware and in dosimetry control. The Applied® Quantum X Implant system was designed to incorporate these new technologies, and has achieved the process performance and low energy productivity required for advanced junction formation at the 65 nm technology node. Since its introduction, extensive qualification and development work has been carried out, to extend its capability to the next technology generation. A number of further innovations and improvements to the beamline and platform have been developed, extending its throughput and process control capability to be production‐worthy at 45 nm.This paper will review the process control challenges associated with the 2d mechanical scanning approach and the new methods and hardware that have recently been implemented on the Applied Quantum X Implant system. The theory and design of the enhancements will be described and illustrated with process data in the areas of angle control, dosimetry and energy purity.
Advanced FIB mask repair technology for ArF lithography: III (2001)

The design rule of the semiconductor devices is getting dramatically tighter as the progress of lithography technology. Photomask is a key factor to support the lithography technology. Defect repairing technology becomes more important than ever for keeping the photomasks' integrity in the manufacturing processes. When using conventional FIB, however, there are issues of transmission loss due to riverbed and gallium stain for opaque defect repairs as well as the problem raised by halo around repair areas for clear defect repairs. Because of these issues, it is necessary to develop the new FIB mask repairing system for 130nm node. We have been developing the new FIB mask repair system since 1998 and have been testing the repairing performance. The results were published at both PMJ2000 and BACUS2000. This time, we introduce the prototype system's outline, and report preliminary data of imaging damage and repair accuracy for the first time in public.
Methods and systems using encapsulated tracers and chemicals for reservoir interrogation and manipulation (2023)

An apparatus, method, and system of reservoir interrogation. A tracer is encapsulating in a receptacle. The receptacle containing the tracer is injected into the reservoir. The tracer is analyzed for reservoir interrogation.
A Practical Synthesis of Highly Functionalized Fused 1,6-Dihydroimidazo-[1,2-a]imidazole-2,5-diones, Key Intermediates for LFA-1 Inhibitors (2004)

Corrected by: A Practical Synthesis of Highly Functionalized Fused 1,6-Dihydroimidazo-[1,2-a]imidazole-2,5-diones, Key Intermediates for LFA-1 InhibitorsSynlett 2005; 2005(01): 186-186DOI: 10.1055/s-2004-836064
(Invited) Supercritical Drying: A Sustainable Solution to Pattern Collapse of High-Aspect-Ratio and Low-Mechanical-Strength Device Structures (2015)

Collapse of nanostructures with high aspect ratio and/or low mechanical strength during drying step in wet process has become a critical issue in semiconductor industry. Even current workable drying practices are facing steeply rising challenges from rapid device scaling advancements. The objective of this work, following evaluation of multiple advanced drying technique, is to develop a sustainable non-stiction drying solution incorporating supercritical fluids. Leaning-free performance has been consistently demonstrated with our supercritical drying sequence on 2x NAND STI (trench aspect ratio ~20) and low-k trench structures, where pattern collapses were observed under conventional solvent-assisted drying or even with advanced self-assembled monolayer approach. Release of sporadic stiction and complete recovery from global pattern leaning were both achieved with our integrated supercritical drying process. Particle performance &lt; 50 adders @0.09μm in average was attained with background particles subtracted. Metallic contamination analysis with TXRF showed all metal components interested were below detection limit.
Mapping specific resistance genes to Leptosphaeria maculans in rapeseed (Brassica napus L.) (2003)

Résumés des communications du 6.Blackleg Workshop
Memristor (2012)

The memristor (M) is considered to be the fourth two-terminal passive element in electronics, alongside the resistor (R), the capacitor (C), and the inductor (L). Its existence was postulated in 1971 but its first implementation was reported in 2008. Where was it hiding all that time and what can we do with it? Come and learn how the memristor completes the roster of electronic devices much like a missing particle that physicists seek to complete their tableaus.
Association of Chocolate Consumption with Hearing Loss and Tinnitus in Middle-Aged People Based on the Korean National Health and Nutrition Examination Survey 2012–2013 (2019)

Chocolate, which is produced from cocoa, exerts antioxidant and anti-inflammatory effects that ameliorate neurodegenerative diseases. We hypothesized that chocolate consumption would protect against hearing loss and tinnitus. We evaluated the hearing and tinnitus data, as well as the chocolate consumption, of middle-aged participants (40⁻64 years of age) of the 2012⁻2013 Korean National Health and Nutrition Examination Survey. All of the subjects underwent a medical interview, physical examination, audiological evaluation, tinnitus questionnaire, and nutrition examination. A total of 3575 subjects 40⁻64 years of age were enrolled. The rate of any hearing loss (unilateral or bilateral) in the subjects who consumed chocolate (26.78% (338/1262)) was significantly lower than that in those who did not (35.97% (832/2313)) (<i>p</i> < 0.001). Chocolate consumption was independently associated with low odds of any hearing loss (adjusted odds ratio = 0.83, 95% confidence interval = 0.70 to 0.98, <i>p</i> = 0.03). Moreover, the severity of hearing loss was inversely correlated with the frequency of chocolate consumption. In contrast to chocolate, there was no association between hearing loss and the consumption of sweet products without cocoa. Chocolate consumption was also not associated with tinnitus or tinnitus-related annoyance. Our results suggest that a chocolate-based diet may protect middle-aged people from hearing loss.
Confined PFSA–zeolite composite membrane for self-humidifying fuel cell (2011)

Perfluorosulfonic acid (PFSA) polyelectrolyte confined in subnanoliter volume within zeolite cladded walls exhibits higher glass transition temperature and excellent tolerance to high-temperature fuel cell operation under dry conditions, generating an order of magnitude higher power density than standard PEMFC.
Spread spectrum switching: low noise modulation technique for PWM inverter drives (1992)

Electric motors operated on fixed period PWM waveforms emit objectionable, predominantly tonal, acoustic noise in addition to the more usual motor noises. These additional components essentially reflect the harmonic structure of the applied PWM waveform and occur as a series of tonal ‘combs’ centred on multiples of the PWM switching frequency. The tonal nature of the noise significantly increases its perceived annoyance. Spread spectrum switching is presented here as a technique which effectively ‘breaks up’ the characteristically tonal noise of a PWM drive, replacing it with a wideband atonal noise. This is achieved by pseudorandomly varying the instantaneous PWM switching frequency from one cycle to the next, resulting in the generation of broadband (‘whitish’) voltage, and consequently acoustic, spectra. Compared to a fixed period modulator, the emission of a broadband atonal noise from the driven motor is definitely prefeable, from a listener&apos;s perspective, with additional advantages arising from the minimal excitation of natural resonances in the drive system due to the broadband nature of the harmonic energy.
INCLUSION REMOVAL IN A TUNDISH BY GAS BUBBLING (2004)

AbstractThe probabilities of inclusion removal from liquid steel by collision and attachment to rising gas bubbles have been analyzed. A simple mathematical model of inclusion removal by gas bubbling in a tundish has been developed. It was found that maintaining bubble size in the range of 0.5 to 3 mm should enhance inclusion removal efficiency. Increasing the bubbly volume fraction in the tundish and the tundish residence time can be used to improve the inclusion removal efficiency by gas bubbling. However, the formation of small bubbles in a tundish may be problematic as bubble size is affected by the high wetting angles typical of liquid metal contact with bubble orifice materials.On a analysé la probabilité de l'enlèvement d'inclusions de l'acier liquide par collision et attachement à des bulles ascendantes de gaz. On a développé un modèle mathématique simple de l'enlèvement d'inclusions par barbotage de gaz dans un panier de coulée. On a trouvé que le maintien de la taille de bulle dans la plage de 0.5 à 3 mm devrait accroître le rendement de l'enlèvement d'inclusions. On peut utiliser l'augmentation de la fraction volumique de bulles dans le panier de coulée et son temps de résidence pour améliorer le rendement de l'enlèvement d'inclusions par barbotage de gaz. Cependant, la formation de petites bulles dans un panier de coulée peut être un problème car la taille des bulles est affectée par les angles mouillants élevés typiques du contact du métal liquide avec les matériaux d'orifice de bulle.
Partial sequence of rat prothrombin and the activity of two related pentapeptides as substrates for the vitamin K‐dependent carboxylase system (1977)

The data was gathered during fieldwork which took place between February 2014 and August 2016, and involved the collection of 207 in-depth interviews with migrants across both urban and rural locations. In recruiting participants, we focused upon those who had been resident in Scotland for more than one and less than ten years. 59 expert interviews were conducted with a range of stakeholders: representatives of local councils, service providers, migrant associations, English for Speakers of Other Languages (ESOL) practitioners and employers. This project studies perspectives and experiences of 'social security' amongst migrants from Central Eastern Europe and the Former Soviet Union in Scotland. Through its long-term and deep engagement with migrant communities in a number of urban and rural sites, including 2 large cities, a number of smaller towns and remote rural locations, the project delivers significant new and original empirical data, and has generated new academic insight through an innovative synthesis of existing theoretical frameworks. Moreover, the project develops practical and policy outcomes and solutions through the use of participatory action research. A first phase of in-depth qualitative research identified key themes and areas of concern, drawing particularly on migrants’ own experiences and perspectives. This was followed by the phase of participatory action research, during which the project team worked directly with migrants, migrant organisations, policymakers, service providers and employers to develop practical projects addressing particular issues. The process of developing these projects was underpinned by short, medium and long-term goals relating to the determination of 'best practice', and the potential for replication in broader local, regional and national contexts.
Chapter 7 Sensors for Critical Path Monitoring (2008)

Modern processes are becoming more sensitive to noise [25]. In addition to technology parameters having larger variation with each new technology generation [1], [20], timing sensitivity to such environmental conditions as temperature [19], [31], aging [3], workload [19], [13], cross-talk noise in wires [18], NBTI [12], and many other effects is increasing. Noise processes that effect timing are described as random or systematic, and they are measured from die to die and within die [6], [32]. Random noise is less dependent on the integrated circuit’s design than systematic noise and it is characterized by a number of statistics such as its mean and standard deviation. Systematic noise results from characteristics of the manufacturing process or from the physical design and can be predicted once the underlying process causing the variation is understood. For example, the wire thickness in technologies that use copper metallization is dependent on the wire density and wire width [21]. Once the source of systematic variation is identified, designs can be adjusted or processing can be modified to reduce the variation [27], [1]. Die-to-die noise measurements measure the statistical difference between separate integrated circuit die and inter-die noise is measured within a single die [5], [4]. The increasing timing uncertainty due to noise processes as technology scales is creating a need for on-chip timing sensors that can be explained using Figure 7.1. During the early design stages of the integrated circuit, assuming it is a microprocessor, an iterative process is used to develop the architecture to meet the performance targets of the intended application. Once the architecture is defined, the microprocessor passes through logic,