gebhart/patrepeval huggingface dataset:
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism (2020)

Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be combined to enable accurate genotype-to-phenotype predictions. We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning algorithms. From a single data-generation cycle, this enables successful forward engineering of complex aromatic amino acid metabolism in yeast, with the best machine learning-guided design recommendations improving tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. Thus, this study highlights the power of combining mechanistic and machine learning models to effectively direct metabolic engineering efforts.
Atom Transfer Radical Polymerization of Isobornyl Acrylate: A Kinetic Modeling Study (2010)

A detailed kinetic modeling study of the atom transfer radical polymerization (ATRP) of isobornyl acrylate (iBoA) is presented. This study combines a detailed reaction scheme with a systematic approach to account for diffusional limitations. Calculated values for diffusion coefficients and the Williams−Landel−Ferry parameters for poly(iBoA) are based on rheological measurements. A good agreement with experimental data is obtained for the polymerization rate, average chain length, and polydispersity index in conditions ranging from 323 to 348 K for targeted chain lengths varying from 50 to 100 and initial activator/deactivator concentrations between 10−50/0−2.5 mol m−3. In these conditions, βC-scission reactions are insignificant and backbiting reactions result in a slight decrease of the polymerization rate and level of control at high conversions only. Termination is subject to diffusional limitations during the whole ATRP, while diffusional limitations on deactivation cannot be neglected at higher conversion. Diffusional limitations are shown to be codetermined by the evolution of the chain length distribution of both the end-chain and mid-chain macromolecular species.
Heat flux reconstruction in the grinding process from temperature data (2009)

The problem considered in this paper deals with reconstruction of heat flux from temperature measurements, where due to lack of data, numerical integration is impossible. The problem is reduced to the determination of unknown complex coefficients of a linear piecewise holomorphic function representing heat flux properties and a quadratic holomorphic function representing complex temperature distribution. This leads to an over-determined system of linear algebraic equations, which are subjected to experimental errors. The reconstruction of heat flux is unique; however, reconstruction of flux directions is non-unique. It contains one free additive parameter. The method is useful in situations where limited data on temperature are provided.
ITGAV and ITGA5 diversely regulate proliferation and adipogenic differentiation of human adipose derived stem cells (2016)

The fate of human adipose tissue stem cells (ASCs) is largely determined by biochemical and mechanical cues from the extracellular matrix (ECM), which are sensed and transmitted by integrins. It is well known that specific ECM constituents influence ASC proliferation and differentiation. Nevertheless, knowledge on how individual integrins regulate distinct processes is still limited. We performed gene profiling of 18 alpha integrins in sorted ASCs and adipocytes, identifying downregulations of RGD-motif binding integrins integrin-alpha-V (ITGAV) and integrin-alpha-5 (ITGA5), upregulation of laminin binding and leukocyte-specific integrins and individual regulations of collagen and LDV-receptors in differentiated adipocytes in-vivo. Gene function analyses in in-vitro cultured ASCs unraveled differential functions of ITGA5 and ITGAV. Knockdown of ITGAV, but not ITGA5 reduced proliferation, caused p21(Cip1) induction, repression of survivin and specific regulation of Hippo pathway mediator TAZ. Gene knockdown of both integrins promoted adipogenic differentiation, while transgenic expression impaired adipogenesis. Inhibition of ITGAV using cilengitide resulted in a similar phenotype, mimicking loss of pan-ITGAV expression using RNAi. Herein we show ASC specific integrin expression patterns and demonstrate distinct regulating roles of both integrins in human ASCs and adipocyte physiology suggesting a negative impact of RDG-motif signaling on adipogenic differentiation of ASCs via ITGA5 and ITGAV.
3D Channel Model Emulation in a MIMO OTA Setup (2013)

This paper presents a new channel reconstruction technique for 3D geometry-based channels in a multi- probe based MIMO OTA setup. The proposed method provides a general channel reconstruction framework for any spherical power spectrum. The channel reconstruction is formed as convex optimization problems, which give global optimal reconstruction accuracy and allow for a relatively low computational complexity.
Corrosion Resistant Polypyrrole Coated Lead-Alloy Positive Grids for Advanced Lead-Acid Batteries (2019)

We herein report a method for reducing lead-alloy positive grid corrosion in lead acid batteries by developing a polypyrrole (ppy) coating on to the surface of lead-alloy grids through potentiostatic polymerization technique. The experimental results demonstrate that the presence of ppy coating significantly enhances the corrosion resistance and inhibits the oxygen evolution rate as compare to bare grids. C-rate studies of 2 V/2.6 Ah lead-acid cells show ∼15–20% improvement in capacity at low charge-discharge rates (C/20- C/5) and ∼10% at high C rates (C/2 and 3C) for the cells with ppy coating grids in relation to conventional lead-acid cells.
Experimental investigation of melting and solidification processes of phase change material heat exchanger. (2021)

Rapid development and validation of PCM embedded heat exchangers (PCM-HX) concepts warrant a purpose-built test bench. This paper describes a test facility built for testing various PCM-HX configurations and phase change temperatures that will serve to validate the performance of novel PCM-HX designs. The entire test rig is placed in a temperature-controlled environmental chamber. Inside the PCM-HX containers, up to 48 T-type thermocouples can be spatially distributed on and around the tubes depending on the HX type to capture the phase change process over time. In this paper, a straight tube embedded in PCM having a phase change temperature of 37°C in cylindrical containers is tested. The PCM-HX uses water as an in-tube working fluid. Based on the measured data, the energy balance is analyzed, and its temperature distribution is presented. The maximum deviation between the predicted stored energy and the energy stored calculated from experimental measurements is less than 5%.
A high-resolution view of the filament of gas between Abell 399 and Abell 401 from the Atacama Cosmology Telescope and MUSTANG-2 (2021)

ABSTRACT We report a significant detection of the hot intergalactic medium in the filamentary bridge connecting the galaxy clusters Abell 399 and Abell 401. This result is enabled by a low-noise, high-resolution map of the thermal Sunyaev–Zeldovich signal from the Atacama Cosmology Telescope (ACT) and Planck satellite. The ACT data provide the 1.65 arcmin resolution that allows us to clearly separate the profiles of the clusters, whose centres are separated by 37 arcmin, from the gas associated with the filament. A model that fits for only the two clusters is ruled out compared to one that includes a bridge component at &amp;gt;5σ. Using a gas temperature determined from Suzaku X-ray data, we infer a total mass of $(3.3\pm 0.7)\times 10^{14}\, \mathrm{M}_{\odot }$ associated with the filament, comprising about 8 per cent of the entire Abell 399–Abell 401 system. We fit two phenomenological models to the filamentary structure; the favoured model has a width transverse to the axis joining the clusters of ${\sim }1.9\, \mathrm{Mpc}$. When combined with the Suzaku data, we find a gas density of $(0.88\pm 0.24)\times 10^{-4}\, \mathrm{cm}^{-3}$, considerably lower than previously reported. We show that this can be fully explained by a geometry in which the axis joining Abell 399 and Abell 401 has a large component along the line of sight, such that the distance between the clusters is significantly greater than the $3.2\, \mathrm{Mpc}$ projected separation on the plane of the sky. Finally, we present initial results from higher resolution (12.7 arcsec effective) imaging of the bridge with the MUSTANG-2 receiver on the Green Bank Telescope.
Trees Weighting Random Forest Method for Classifying High-Dimensional Noisy Data (2010)

Random forest is an excellent ensemble learning method, which is composed of multiple decision trees grown on random input samples and splitting nodes on a random subset of features. Due to its good classification and generalization ability, random forest has achieved success in various domains. However, random forest will generate many noisy trees when it learns from the data set that has high dimension with many noise features. These noisy trees will affect the classification accuracy, and even make a wrong decision for new instances. In this paper, we present a new approach to solve this problem through weighting the trees according to their classification ability, which is named Trees Weighting Random Forest (TWRF). Here, Out-Of-Bag, which is the training data subset generated by Bagging and not involved in building decision tree, is used to evaluate the tree. For simplicity, we choose the accuracy as the index that notes tree's classification ability and set it as the tree's weight. Experiments show that TWRF has better performance than the original random forest and other traditional methods, such as C45, Naïve Bayes and so on.
Enamel Mineral Composition of Normal and Cystic Fibrosis Transgenic Mice (1996)

The ability of ameloblasts and the enamel organ to control the influx of ions into the developing enamel is of considerable interest. The development of transgenic mice lacking a cAMP-regulated chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR), provides a model that may prove valuable for the study of ion regulation in developing teeth. The purpose of this investigation was to characterize the mineral content of normal and CF mice. Five homozygous and five heterozygous adult mice having the CFTR knockout transgene were evaluated. The mice were killed with CO2 and their mandibular incisors removed, embedded in methacrylate, and sectioned, and enamel particles from the incisal region were then dissected for analysis. Each particle was analyzed for its calcium, phosphorus, and magnesium content. The normal mice had a mean mineral content of 80.5%, in contrast to the CF mice, that had markedly hypomineralized enamel (mean = 51.5%). The calcium/phosphorus ratios were similar for both groups of mice and were compatible with the enamel consisting primarily of hydroxyapatite mineral. The enamel magnesium content was significantly elevated in the CF mice (mean = 3560 ppm) compared with the normal mice (mean = 2280 ppm). Normal mouse enamel was highly mineralized, while the CF mouse enamel mineral content was significantly reduced and had an elevated level of magnesium. The altered mineral content of CF mouse enamel indicates that CFTR could play an important role in ion regulation and consequently mineralization of mouse enamel.
Residual Stresses in Polycrystalline Diamond Compacts (1994)

The effects of residual stress on the integrity of polycrystalline diamond compact (PDC) cutters was investigated. When the compact cooled from the sintering temperature to room temperature, very high radial compressive stresses were induced in the diamond table, and (generally) much lower radial tensile stresses were induced in the cemented tungsten carbide backing. The magnitudes of these residual stresses were not affected very much by the diameter of the compact. However, the residual stresses were affected significantly by the thickness ratio of the carbide layer to the diamond layer. The higher this ratio the greater was the radial compressive stress in the diamond and the lower was the radial tensile stress in the carbide. This same effect was obtained by sintering a relatively thin layer of tungsten carbide on top of the diamond table.
Optical fiber sensors (1987)

Optical fiber sensor development has led to a new class of sensing device which has demonstrated performance that is competitive with existing technologies. Over 100 fiber sensor types have been fabricated, and the incorporation of many of these devices into engine and flight control, shipboard machinery and damage controls, medical probing, and industrial process controls demonstrations is planned. These demonstrations are aimed at illustrating and quantifying the advantages of fiber sensors in nonlaboratory environments and are the next required step before widespread commercialization of this technology is realized. Despite the significant technological progress realized in optical fiber sensor development, to date only a relatively small number of optical fiber sensors have entered the marketplace.
Factors affecting internal standard selection for quantitative elemental bio-imaging of soft tissues by LA-ICP-MS (2011)

Element response variations under different laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) operating conditions were investigated to identify important factors for selecting an internal standard (IS) for quantitative elemental bio-imaging. Analytes covering a range of atomic masses and first ionisation potentials (FIP) were selected to investigate the signal response variation with changes in laser spot diameter, mass bias and cell sampling position. In all cases, an IS improved experimental precision regardless of a close match in element mass or FIP but optimal analyte/IS combinations depended on the difference in masses of the analyte and IS. Particular attention was paid to 13C as this isotope is typically used as an IS in elemental bio-imaging applications. Despite its non-ideal IS characteristics (often different mass and FIP to many analytes), possibility of abundance sensitivity effects and poor signal-to-background ratio, 13C was a suitable IS candidate exhibiting a linear response with respect to the mass ablated, apparent independence from the high abundance of the adjacent 14N mass peak and effective analyte normalisation after background subtraction as long as the 13C signal from the sample was at least 6% of the gross signal.
Effect of Pregabalin on Radiotherapy-Related Neuropathic Pain in Patients With Head and Neck Cancer: A Randomized Controlled Trial (2018)

Patients treated with pregabalin with radiotherapy-related neuropathic pain had greater pain alleviation, better mood states, and higher quality of life compared with patients in the placebo group, with a good tolerability.
ChemInform Abstract: α‐BROMO KETONES OF THE BICYCLO(3.3.1)NONANE SERIES. 4. SYNTHESIS OF NORADAMANTANE STRUCTURE (1976)

Abstract Beim Erhitzen der Verbindungen (I) oder (III) in konz. Schwefelsäure entsteht überraschend 3,7‐Dibrom‐noradamantan‐2,6‐dion (II).
Fractionation of Linear Polyethylene with Gel Permeation Chromatography. (1973)

The number and weight average molecular weights were determined for two samples of linear polyethylenes distributed by the Macromolecular Division of IUPAC. The methods used were GPC, osmotic pressure, infrared analysis, melt viscosity and intrinsic viscosity. Data interpretations are discussed for each method. By comparing the results the average molecular weights were obtained; for one sample, MN = 10,500 to 11,000 and MW = 150,000 to 165,000: for another sample, MN = 13,600 to 18,500, and MW = 40,000 to 48,000.
Ubiquitin fusion expression and tissue-dependent targeting of hG-CSF in transgenic tobacco (2011)

In this study, the expression of bioactive hG-CSF in transgenic plants was improved through ubiquitin fusion strategy, demonstrating that protein expression can be enhanced in both plant leaves and seeds through fusion with ubiquitin and providing a typical case of tissue-dependent expression of recombinant protein in transgenic plants.
THE DUALIZED STANDARD MODEL AND ITS APPLICATIONS — AN INTERIM REPORT (1999)

Based on a non-Abelian generalization of electric–magnetic duality, the Dualized Standard Model (DSM) suggests a natural explanation for exactly three generations of fermions as the "dual colour" [Formula: see text] symmetry broken in a particular manner. The resulting scheme then offers on the one hand a fermion mass hierarchy and a perturbative method for calculating the mass and mixing parameters of the Standard Model fermions, and on the other hand testable predictions for new phenomena ranging from rare meson decays to ultra-high energy cosmic rays. Calculations to one-loop order gives, at the cost of adjusting only three real parameters, values for the following quantities all (except one) in very good agreement with experiment: the quark CKM matrix elements ‖V rs ‖, the lepton CKM matrix elements ‖U rs ‖, and the second generation masses m c , m s , m μ . This means, in particular, that it gives near maximal mixing U μ3 between ν μ and ν τ as observed by SuperKamiokande, Kamiokande and Soudan, while keeping small the corresponding quark angles V cb , V ts . In addition, the scheme gives (i) rough order-of-magnitude estimates for the masses of the lowest generation, (ii) predictions for low energy FCNC effects such as K L → eμ, and (iii) a possible explanation for the long-standing puzzle of air showers beyond the GZK cut-off. All these together, however, still represent but a portion of the possible physical consequences derivable from the DSM scheme, the majority of which are yet to be explored.
Pilot-based channel estimation for FBMC/OQAM systems under strong frequency selectivity (2016)

Scattered pilot-aided channel estimation in offset QAM-based filter bank multicarrier (FBMC/OQAM) systems has so far been only considered for channels of mild frequency selectivity. In more demanding scenarios, the classical auxiliary pilot (AP) idea has been shown to result in severe error floors. In this paper, a novel pilot-aided channel estimation method is developed which for the first time extends the applicability of the AP idea to highly frequency selective channels. The development relies on a Taylor series approximation of the signal model, which is able to accurately and concisely describe such scenarios. The obtained channel estimate can be viewed as a linear combination of the outputs of multiple parallel analysis filter banks each employing a derivative of the original prototype filter. The reported simulation results corroborate the analysis, demonstrating the effectiveness of the proposed method in estimating channels of strong frequency selectivity.
Fundamental limits and achievable strategies for low energy compressed sensing with applications in wireless communication (2016)

We consider energy-efficient decoding for multiuser detection in a wireless channel with n potential users, each of which participates with probability p. We model this problem as that of energy-efficient decoding for support recovery in a compressed sensing setup where the decoder is required to identify the support of the compressed signal vector. We use a communication complexity measure of “bit-meters” in our calculations because of its close connection to energy consumption. The measure focuses on energy required to move information on a computational substrate, which while a dominant cost in modern circuits, is not captured by the Turing machine model. In this model of energy consumption, we provide both upper bounds and lower bounds on required energy consumption in recovering the sensed signal. By comparing a lower bound on “fixed-schedule” decoding with an upper bound on “flexible-schedule,” we establish that allowing for flexibility in the schedule of message-passing at the decoder can reduce energy in order sense. This establishes the utility of adaptivity and asynchronicity in VLSI implementations of compressed sensing decoders and presents a contrast to prior works that show that both fixed schedule and flexible schedule architectures perform similarly in decoders for channel coding. Moreover, our decoder consumes (in an order-sense) fewer bit-meters than previous computationally efficient algorithms implemented directly on any flexible-scheduled decoders when the probability p is small enough.
Liner malseating is rare with two modular dual-mobility designs (2022)

The incidence of DM liner malseating after primary THA was low, with no known clinical consequences at mid-term follow-up. Malseating is not exclusive of design, and these findings emphasize the importance of careful evaluation of the liner after impaction to avoid this complication. Cite this article: <i>Bone Joint J</i> 2022;104-B(5):598-603.
Supplementary Figure and Table Legends from Genome-Wide DNA Methylation Profiling of CpG Islands in Breast Cancer Identifies Novel Genes Associated with Tumorigenicity (2023)

Supplementary Figure and Table Legends from Genome-Wide DNA Methylation Profiling of CpG Islands in Breast Cancer Identifies Novel Genes Associated with Tumorigenicity
Appropriate Intravenous Doses of L-Thyroxine and Magnesium in a Thyroidectomized Patient with Thyroid and Parathyroid Carcinomas Receiving Total Parenteral Nutrition During Acute Necrotizing Pancreatitis. (1995)

A totally thyroidectomized patient with thyroid and parathyroid carcinomas, which had developed after neck irradiation in childhood, became hypercalcemic due to pulmonary metastases. The hypercalcemia was ameliorated by intermittent iv administration of bisphosphonate for 3.5 years, but this gradually became refractory to the bisphosphonate treatment. After right thoracotomy for resection of pulmonary metastases, acute necrotizing pancreatitis developed. The patient was therefore placed on total parenteral nutrition supplemented with T4 and a restricted dose of magnesium. Thyroxine(T4) (30 μg/day, iv) was not sufficient to maintain euthyroidism, but a higher dose (60 μg/day) elicited mild hyperthyroidism to the same extent as that elicited by an oral dose of 100 μg/day. The present case showed that the appropriate iv dose of T4 in this thyroidectomized patient with acute pancreatitis was about 60% of the oral dose. Furthermore, bisphosphonates (pamidronate and alendronate) and magnesium depletion were very effective in controlling the hypercalcemia.(Internal Medicine 34:176-182, 1995)