gebhart/patrepeval huggingface dataset:
Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions (2013)

The ERK1/2 MAP kinase pathway is an evolutionarily conserved signaling module that controls many fundamental physiological processes. Deregulated activity of ERK1/2 MAP kinases is associated with developmental syndromes and several human diseases. Despite the importance of this pathway, a comprehensive picture of the natural substrate repertoire and biochemical mechanisms regulated by ERK1/2 is still lacking. In this study, we used large-scale quantitative phosphoproteomics and bioinformatics analyses to identify novel candidate ERK1/2 substrates based on their phosphorylation signature and kinetic profiles in epithelial cells. We identified a total of 7936 phosphorylation sites within 1861 proteins, of which 155 classify as candidate ERK1/2 substrates, including 128 new targets. Candidate ERK1/2 substrates are involved in diverse cellular processes including transcriptional regulation, chromatin remodeling, RNA splicing, cytoskeleton dynamics, cellular junctions and cell signaling. Detailed characterization of one newly identified substrate, the transcriptional regulator JunB, revealed that ERK1/2 phosphorylate JunB on a serine adjacent to the DNA-binding domain, resulting in increased DNA-binding affinity and transcriptional activity. Our study expands the spectrum of cellular functions controlled by ERK1/2 kinases.
Global and local congestion optimization in technology mapping (2003)

In this era of deep submicrometer technologies, interconnects are becoming increasingly important as their effects strongly impact the integrated circuit (IC) functionality and performance. Moreover, logic block size is no longer determined exclusively by total cell area and is often limited by wiring area. However, synthesis optimization objectives are focused on minimizing the number and size of library cells. Methodologies that incorporate congestion within the logic synthesis objective function have been proposed in the past. Nevertheless, we will demonstrate that predicting the true congestion prior to layout is not possible, and the effectiveness of any congestion minimization approach can only be evaluated after routing is completed within the fixed die size. In this paper, we propose a practical, complete methodology which first performs congestion-aware technology mapping using a global weighting factor for the technology-dependent synthesis cost function and then applies incremental localized unmapping and remapping on layout congested areas. This complete approach addresses the problem that one global factor is not suited for all layout regions of the design, which might have very different routing demands. Most importantly, through the application of this methodology to industrial examples, we will show that any attempt at a purely top-down single-pass congestion-aware technology mapping is merely wishful thinking.
Pattern recognition of normal, lightly and heavily calcified bioprosthetic valves implanted in the mitral position (2003)

The performances of two pattern recognition methods for detecting and quantifying valvular degeneration by spectral analysis of the first heart sound were evaluated in 48 patients with a porcine valve in the mitral position. Twenty patients had normal valves, 13 had lightly calcified valves, and 15 had heavily calcified valves. The pattern recognition methods were designed to classify the valve status into three subclasses: normal, degenerated with light calcification (scale 0-2), and degenerated with heavy calcification (scale 3-8). One method was based on a three-class supervised learning approach, while the other was based on a two-node decision rule using a two-class supervised learning approach at each node. The performance of the classifiers based on the Bayes rule and the nearest-neighbor algorithm was expressed in percentage of correct classifications (%CC). Results show that the two-node decision rule provides higher performance (85%CC) than the direct three-class classifiers (75%CC).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prediction of Activity Cliffs Using FEP+ and Gromacs FEP (2019)

Presentation at Alchemical Free Energy workshop in Goettingen on May 27-28, 2019
Long-term survival in thymic carcinoma with postoperative pleural dissemination (2021)

Local control of pleural dissemination may be beneficial in the treatment of postoperative recurrence of thymic carcinoma in limited cases of indolent disease.
Engineering Novel Cell Surface Receptors for Virus-mediated Gene Transfer (1999)

The absence of viral receptors is a major barrier to efficient gene transfer in many cells. To overcome this barrier, we developed an artificial receptor based on expression of a novel sugar. We fed cells an unnatural monosaccharide, a modified mannosamine that replaced the acetyl group with a levulinate group (ManLev). ManLev was metabolized and incorporated into cell-surface glycoconjugates. The synthetic sugar decorated the cell surface with a unique ketone group that served as a foundation on which we built an adenovirus receptor by covalently binding biotin hydrazide to the ketone. The artificial receptor enhanced adenoviral vector binding and gene transfer to cells that are relatively resistant to adenovirus infection. These data are the first to suggest the feasibility of a strategy that improves the efficiency of gene transfer by using the biosynthetic machinery of the cell to engineer novel sugars on the cell surface.
Sustainable Societal Infrastructures: A Resilient Approach to Prevent Conflicting Claims of Drinking Water and Other Infrastructures (2020)

Societal infrastructures are the lifeblood of societies, and the sustainability of infrastructures is very important. Societal infrastructures can experience conflicting spatial claims with other societal infrastructures, disturbing the sustainable situation. The objective of this paper is to design large infrastructures, with a focus on the Drinking Water Infrastructure (DWI), in a more sustainable way by using the resilience concept. To study this, a case study was done in the Netherlands, where an overlap is present between the DWI and the protection zones, and a new railroad and water safety measures in the river IJssel. The case showed that conflicting infrastructures are inflexible and unable to adapt to change due to several reasons in the governance and in the infrastructure system itself. The case was useful for identifying eight design principles to prevent conflicting claims between large infrastructures.
Electrical and structural properties of rapid thermally annealed boron-doped silicon films deposited by plasma-enhanced chemical-vapor deposition (1994)

The structural, electrical, and piezoresistive properties of in situ boron-doped thin silicon layers deposited by plasma-enhanced chemical-vapor deposition at 320 °C on oxidized silicon substrates and subjected to a rapid thermal anneal (1100 °C for 20 s) have been investigated. Macroscopic electrical parameters derived from resistivity and Hall-effect measurements were compared to microscopic characteristics deduced from optical data to explain the low-temperature coefficients of resistance measured on this polycrystalline material. Finally, the piezoresistivity gauge factors of these heavily doped layers are discussed in view of their internal stress state and of other structural characteristics.
Working fluid parametric analysis for regenerative supercritical organic Rankine cycles for medium geothermal reservoir temperatures (2017)

The conversion efficiency of geothermal energy is very low. For low-temperature resources, such as geothermal energy, a supercritical organic Rankine cycle (ORC) has been shown to be more efficient than an ORC. Regenerative supercritical ORCs have been proven to yield even higher efficiencies for cases where the heat source is limited above the ambient temperature. Most studies on these cycles have focused on turbine inlet temperatures between 80 and 130˚C. Only a few studies have explored other working fluids between 180 and 350˚C but did not analyze optimum turbine inlet pressures. Turbine inlet temperatures ranging from 170 to 240˚C were tested with the heat source provided by a medium temperature geothermal reservoir. A parametric analysis was performed for various turbine inlet pressures and temperatures. The fluids tested included cis-butene, pentane, isopentane, butane, isobutane, carbon dioxide, neopentane, propylene, and propane. Temperatures and pressures were selected for each tested fluid to achieve maximum first law efficiency, second law efficiency, cycle effectiveness, and net work.
Feasibility of smartphone-based hearing-aid apps for patients with mild hearing loss: an exploratory pilot study (Preprint) (2020)

<sec> <title>BACKGROUND</title> Underuse of hearing aids is caused by several factors, including the stigma associated with hearing disability, affordability, and lack of awareness of rising hearing impairment associated with the growing population. Thus, there is a significant opportunity for the development of direct-to-consumer devices. For the past few years, smartphone-based hearing-aid apps have become more numerous and diverse, but few studies have investigated them. </sec> <sec> <title>OBJECTIVE</title> This study aimed to elucidate the electroacoustic characteristics and potential user benefits of a selection of currently available hearing-aid apps. </sec> <sec> <title>METHODS</title> We investigated the apps based on hearing-aid control standards (American National Standards Institute) using measurement procedures from previous studies. We categorized the apps and excluded those we considered inefficient. We investigated a selection of user-friendly, low-end apps, EarMachine and Sound Amplifier, with warble-tone audiometry, word recognition testing in unaided and aided conditions, and hearing-in-noise test in quiet and noise-front conditions in a group of users with mild hearing impairment (n = 7) as a pilot for a future long-term investigation. Results from the apps were compared with those of a conventional hearing aid. </sec> <sec> <title>RESULTS</title> Five of 14 apps were considered unusable based on low scores in several metrics, while the others varied across the range of electroacoustic measurements. The apps that we considered “high end” that provided lower processing latencies and audiogram-based fitting algorithms were superior overall. The clinical performance of the listeners tended to be better when using hearing aid, while the low end hearing-aid apps had limited benefits on the users. </sec> <sec> <title>CONCLUSIONS</title> Some apps showed the potential to benefit users with limited cases of minimal or mild hearing loss if the inconvenience of relatively poor electroacoustic performance did not outweigh the benefits of amplification. </sec>
Replicode: A Constructivist Programming Paradigm and Language (2013)

Replicode is a language designed to encode short parallel programs and executable models, and is centered on the notions of extensive pattern-matching and dynamic code production.\nThe language is domain independent and has been designed to build systems that are modelbased and model-driven, as production systems that can modify their own code. More over, Replicode supports the distribution of knowledge and computation across clusters of computing nodes.\nThis document describes Replicode and its executive, i.e. the system that executes Replicode constructions. The Replicode executive is meant to run on Linux 64 bits and Windows 7 32/64 bits platforms and interoperate with custom C++ code.\nThe motivations for the Replicode language, the constructivist paradigm it rests on, and the higher-level AI goals targeted by its construction, are described by Thórisson (2012), Nivel and Thórisson (2009), and Thórisson and Nivel (2009a, 2009b).\nAn overview presents the main concepts of the language. Section 3 describes the general structure of Replicode objects and describes pattern matching. Section 4 describes the execution model of Replicode and section 5 describes how computation and knowledge are structured and controlled. Section 6 describes the high-level reasoning facilities offered by the system. Finally, section 7 describes how the computation is distributed over a cluster of computing nodes.\nConsult Annex 1 for a formal definition of Replicode, Annex 2 for a specification of the executive, Annex 3 for the specification of the executable code format (r-code) and its C++ API, and Annex 4 for the definition of the Replicode Extension C++ API.
Colloidal Quantum Dot Light-Emitting Diodes Employing Phosphorescent Small Organic Molecules as Efficient Exciton Harvesters (2014)

Nonradiative energy transfer (NRET) is an alternative excitation mechanism in colloidal quantum dot (QD) based electroluminescent devices (QLEDs). Here, we develop hybrid highly spectrally pure QLEDs that facilitate energy transfer pumping via NRET from a phosphorescent small organic molecule-codoped charge transport layer to the adjacent QDs. A partially codoped exciton funnelling electron transport layer is proposed and optimized for enhanced QLED performance while exhibiting very high color purity of 99%. These energy transfer pumped hybrid QLEDs demonstrate a 6-fold enhancement factor in the external quantum efficiency over the conventional QLED structure, in which energy transfer pumping is intrinsically weak.
Edge-ray design of compact etendue-limited folded-optic collimators (2004)

The air-gap RXI lens efficiently produces a very narrow beam from high-powered LEDs. This design has an aspect ratio of 5, with both front surface and reflecting back surface designed simultaneously from periphery inwards, as profiles of circular symmetry, via applying the edge-ray principle to the chip geometry. The light source is a Lambertian-glowing cube 1.2 mm square and 0.15 mm high, as viewed through its clear (n=1.54) package dome, with emission down to 95&deg; from the symmetry axis. A given exit-aperture diameter defines a minimum, etendue-limited collimation angle, &#945;=arcsin(chip-width/diameter). At the center of the back surface is a tailored quasi-hemispheric cavity surrounding the source and serving to uniformly distribute the source flux over the front surface. The front surface reflects that source flux to the back surface, which reflects it back forward again, accomplishing the optical folding thereby. The back surface is shaped so that the light it reflects forward will be refracted out the front surface to become the collimated output beam.
Microfluidic hubs, systems, and methods for interface fluidic modules (2023)

Embodiments of microfluidic hubs and systems are described that may be used to connect fluidic modules. A space between surfaces may be set by fixtures described herein. In some examples a fixture may set substrate-to-substrate spacing based on a distance between registration surfaces on which the respective substrates rest. Fluidic interfaces are described, including examples where fluid conduits (e.g. capillaries) extend into the fixture to the space between surfaces. Droplets of fluid may be introduced to and/or removed from microfluidic hubs described herein, and fluid actuators may be used to move droplets within the space between surfaces. Continuous flow modules may be integrated with the hubs in some examples.
ChemInform Abstract: Synthetic Studies on Arene‐Olefin Cycloadditions. Part 10. A Concise, Stereocontrolled Total Synthesis of (.+‐.)‐Laurenene. (1988)

Abstract Diels‐Alder of the diene (II) with toluyne affords the adduct (III) which alternatively can be prepared starting from benzoquinone and (II) via a six‐step procedure (37% overall yield).
Altered DNA Polymerase ι Expression in Breast Cancer Cells Leads to a Reduction in DNA Replication Fidelity and a Higher Rate of Mutagenesis (2004)

The recently discovered human enzyme DNA polymerase iota (pol iota) has been shown to have an exceptionally high error rate on artificial DNA templates. Although there is a considerable body of in vitro evidence for a role for pol iota in DNA lesion bypass, there is no in vivo evidence to confirm this action. We report here that pol iota expression is elevated in breast cancer cells and correlates with a significant decrease in DNA replication fidelity. We also demonstrate that UV treatment of breast cancer cells additionally increases pol iota expression with a peak occurring between 30 min and 2 h after cellular insult. This implies that the change in pol iota expression is an early event after UV-mediated DNA damage. That pol iota may play a role in the higher mutation frequencies observed in breast cancer cells was suggested when a reduction in mutation frequency was found after pol iota was immunodepleted from nuclear extracts of the cells. Analysis of the UV-induced mutation spectra revealed that > 90% were point mutations. The analysis also demonstrated a decreased C --> T nucleotide transition and an increased C --> A transversion rate. Overall, our data strongly suggest that pol iota may be involved in the generation of both increased spontaneous and translesion mutations during DNA replication in breast cancer cells, thereby contributing to the accumulation of genetic damage.
Comparing between estimation approaches: admissible and dominating linear estimators (2006)

We treat the problem of evaluating the performance of linear estimators for estimating a deterministic parameter vector x in a linear regression model, with the mean-squared error (MSE) as the performance measure. Since the MSE depends on the unknown vector x, a direct comparison between estimators is a difficult problem. Here, we consider a framework for examining the MSE of different linear estimation approaches based on the concepts of admissible and dominating estimators. We develop a general procedure for determining whether or not a linear estimator is MSE admissible, and for constructing an estimator strictly dominating a given inadmissible method so that its MSE is smaller for all x. In particular, we show that both problems can be addressed in a unified manner for arbitrary constraint sets on x by considering a certain convex optimization problem. We then demonstrate the details of our method for the case in which x is constrained to an ellipsoidal set and for unrestricted choices of x. As a by-product of our results, we derive a closed-form solution for the minimax MSE estimator on an ellipsoid, which is valid for arbitrary model parameters, as long as the signal-to-noise-ratio exceeds a certain threshold.
A Reconfigurable Architecture for Wireless Communication Systems (2006)

New wireless communication standards are introduced even before the previous standards are fully utilized. The increasing number of wireless communication standards creates new demands for their platform architectures. In addition to high data rate, low cost and low power consumption requirements for these systems, they need to be flexible enough to support multiple standards in a multimode radio system. In this paper, we introduce a new version of MorphoSys, a reconfigurable architecture which is designed for wireless communication systems. Experimental results show that for the wireless systems it provides a performance close to ASICs while is flexible enough to support changes in the current standards
Enhanced Optical Transmission through MacEtch‐Fabricated Buried Metal Gratings (2015)

Metallic films with subwavelength apertures, integrated into a semiconductor by metal-assisted chemical etch (MacEtch), demonstrate enhanced transmission when compared to bare semiconductor surfaces. The resulting "buried" metallic structures are characterized spectroscopically and modeled using rigorous coupled wave analysis. These composite materials offer potential integration with optoelectronic devices, for simultaneous near-uniform electrical contact and strong optical coupling to free space.
Frequency-tuned electromagnetic field therapy improves post-stroke motor function: A pilot randomized controlled trial (2022)

https://clinicaltrials.gov/ct2/show/NCT04039178, identifier: NCT04039178.
Steady-state characteristis of 3-phase cage induction generators in TSCAOI configuration (2015)

This paper investigates the steady-state characteristics of 3-phase cage induction machines that use two series-connected and one isolated (TSCAOI) phase winding configuration to generate single phase electricity. In this configuration, one phase-winding excites the machine while the remaining two in series generate electricity at constant frequency under varying rotor speeds. The steady-state model, which is derived using symmetrical components, provides a clear insight into the behavior of the generator in TSCAOI configuration. Simulated steady state characteristics of a 3 kW, 4-pole generator are presented under various operating conditions to demonstrate the usefulness of the proposed model.
Markägarens förväntningar hos en skogsinspektor (2019)

Sweden, which is a very forest-enriched country where the forest industry is a big part of Sweden's economy. In our report, a timber business is described between two parties a forest owner and a purchaser of a purchasing organization. We will then examine in this study what expectations one has as a forest owner on a buyer. We will primarily focus on how to build trust and long-term business relationships, depending on different forest objectives with their forestry. The result of the survey is based on interviews with purchasers at a forest company, Södra and various forest owners. The buyers were first interviewed and had to rank different alternatives that then laid the foundation for the forest owners' interview number. We had a response rate for forest owners of 83 percent and for purchaser’s 80 percent. Something that we in the result come up with when building this was that the purchaser should primarily act professionally and show interest in the forest owners. In order to build a long-term business relationship, good communication and quality of the services offered are required. The long-term perspective is set high both by forest owners and by buyers when one sees a security in the store, they want to say that one knows what one gets in the future. Peace and security are also something that is addressed and counted in security.
A Random Access Protocol for Pilot Allocation in Crowded Massive MIMO Systems (2017)

The massive multiple-input multiple-output (MIMO) technology has great potential to manage the rapid growth of wireless data traffic. Massive MIMO achieves tremendous spectral efficiency by spatial multiplexing many tens of user equipments (UEs). These gains are only achieved in practice if many more UEs can connect efficiently to the network than today. As the number of UEs increases, while each UE intermittently accesses the network, the random access functionality becomes essential to share the limited number of pilots among the UEs. In this paper, we revisit the random access problem in the Massive MIMO context and develop a reengineered protocol, termed <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">strongest-user collision resolution</i> (SUCRe). An accessing UE asks for a dedicated pilot by sending an uncoordinated random access pilot, with a risk that other UEs send the same pilot. The favorable propagation of massive MIMO channels is utilized to enable distributed collision detection at each UE, thereby determining the strength of the contenders’ signals and deciding to repeat the pilot if the UE judges that its signal at the receiver is the strongest. The SUCRe protocol resolves the vast majority of all pilot collisions in crowded urban scenarios and continues to admit UEs efficiently in overloaded networks.