gebhart/patrepeval huggingface dataset:
3-D MRI cardiac segmentation using graph cuts (2014)

We consider the use of graph cuts technique to efficiently segment the full tissue volume of the entire heart or important parts of it such as ventricles in Magnetic Resonance Imaging (MRI) scans for different species. With the segmented 3-D volume of the heart, simulations of electrical waves propagating through the tissue can be done. The modeled wave results can then be compared directly to the experimental data. We use the graph cuts technique to achieve segmentation while letting the user initiate some of the energy cost function parameters. A Mumford-Shah type energy cost function is used. In addition to the data and smoothness terms, two spatial distance terms are incorporated to improve segmentation results. The user has the option of eliminating these terms in case the input data does not contain any useful spatial distance content.
Stabilization of Cytokinin Levels Enhances Arabidopsis Resistance Against Verticillium longisporum (2013)

Verticillium longisporum is a vascular pathogen that infects the Brassicaceae host plants Arabidopsis thaliana and Brassica napus. The soilborne fungus enters the plant via the roots and colonizes the xylem of roots, stems, and leaves. During late stages of infections, Verticillium spp. spread into senescing tissue and switch from biotrophic to a necrotrophic life style. Typical symptoms of V. longisporum-induced disease are stunted growth and leaf chlorosis. Expression analyses of the senescence marker genes SENESCENCE-ASSOCIATED GENE12, SENESCENCE-ASSOCIATED GENE13, and WRKY53 revealed that the observed chlorosis is a consequence of premature senescence triggered by Verticillium infection. Our analyses show that, concomitant with the development of chlorosis, levels of trans-zeatin decrease in infected plants. Potentially, induction of cytokinin oxidase/dehydrogenase expression by Verticillium infection contributes to the observed decreases in cytokinin levels. Stabilization of Arabidopsis cytokinin levels by both pharmacological and genetic approaches inhibits Verticillium proliferation and coincides with reduced disease symptom development. In summary, our results indicate that V. longisporum triggers premature plant senescence for efficient host plant colonization.
Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems (2017)

Analysis of the "AHR-core" genes demonstrates a continued need for studies surrounding the impact of AHR-activity on the transcriptome; genes believed to be consistently regulated by ligand-activated AHR show surprisingly little overlap across species and tissues. Until now, a comprehensive assessment of the transcriptome across these studies was challenging due to differences in array platforms, processing methods and annotation versions. We believe that this package, which is freely available for download ( http://labs.oicr.on.ca/boutros-lab/tcdd-transcriptomics ) will prove to be a highly beneficial resource to the scientific community evaluating the effects of TCDD exposure as well as the variety of functions of the AHR.
Relationship Between Chronic Conditions and Patient Satisfaction with Managed Care (2001)

The objective of this study was to compare the level of satisfaction among members with and without chronic health conditions (asthma, diabetes, hypertension, and elevated plasma lipoprotein) in a large California managed care organization. One year's worth of member satisfaction survey data was analyzed. Results showed that a high percentage of members were satisfied with the health plan and with their access to care. Members with chronic conditions were significantly more satisfied with their access to care than were members without such conditions.
Two-pitch estimation for co-channel speakers separation (2002)

This paper deals with the estimation of fundamental frequency for two speakers recorded on the same channel. We estimate a set of speech models based upon sinusoidal plus autoregressive noise representations. We then detect the best model from this set using Rissanen criterion. Equivalent to a penalized log-likelihood, the criterion is also used to carry out a voicing detection. The detector compares the likelihood of a sinusoid plus noise model with the likelihood of a simple autoregressive model. Several simulations are presented to illustrate this estimation method.
Calculation of Relative Binding Free Energy Differences for Fructose 1,6-Bisphosphatase Inhibitors Using the Thermodynamic Cycle Perturbation Approach (2001)

An iterative, computer-assisted, drug design strategy that combines molecular design, molecular mechanics, molecular dynamics (MD), and free energy perturbation (FEP) calculations with compound synthesis, biochemical testing of inhibitors, and crystallographic structure determination of protein-inhibitor complexes was successfully used to predict the rank order of a series of nucleoside monophosphate analogues as fructose 1,6-bisphosphatase (FBPase) inhibitors. The X-ray structure of FBPase complexed with 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (ZMP) provided structural information used for subsequent analogue design and free energy calculations. The FEP protocol was validated by calculating the free energy differences for the mutation of ZMP (1) to AMP (2). The calculated results showed a net gain of 1.7 kcal/mol, which agreed with the experimental result of 1.3 kcal/mol. FEP calculations were performed for 18 other AMP analogues. Inhibition constants were determined for over half of these analogues, usually after completion of the calculation, and were consistent with the predictions. Solvation free energy differences between AMP and various AMP analogues proved to be an important factor in binding free energies, suggesting that increased desolvation costs associated with the addition of polar groups to an inhibitor must be overcome by stronger ligand-protein interactions if the structural modification is to enhance inhibitor potency. The results indicate that FEP calculations predict relative binding affinities with high accuracy and provide valuable insight into the factors that influence inhibitor binding and therefore should greatly aid efforts to optimize initial lead compounds and reduce the time required for the discovery of new drug candidates.
High-repetition-rate femtosecond optical parametric oscillator based on periodically poled lithium niobate (1997)

A high-repetition-rate, femtosecond optical parametric oscillator based on bulk periodically poled lithium niobate is described. This optical parametric oscillator is continuously tunable from 1.12 to 1.50 μm in the signal branch, and signal pulses as short as 60 fs have been observed. The corresponding turning range for the idler branch is from 1.68 to 2.72 μm. Modifications which should result in a femtosecond optical parametric oscillator with a pumping threshold of less than 50 mW are discussed.
Facile biosynthesis of phosphate capped gold nanoparticles by a bacterial isolate Stenotrophomonas maltophilia (2009)

We report intracellular biosynthesis of gold nanoparticles (GNPs) by a strain Stenotrophomonas maltophilia (AuRed02) isolated from the soil samples of Singhbhum gold mines, India. An aqueous solution of gold chloride was reduced to metallic gold in a suspension of disrupted cell mass of AuRed02, which progressively turns into cherry red within 8 h of incubation at 25 °C. The optical spectrum showed the plasmon resonance at 530 nm and analysis by transmission electron microscopy and dynamic light scattering confirmed the formation of around 40 nm GNPs. Zeta potential and Fourier transform infrared measurements confirmed GNPs are capped by negatively charged phosphate groups of NADP.
Hybrid Silicon Devices for Energy-Efficient Optical Transmitters (2012)

Decreasing energy limits for data transport have resulted in efforts to reduce energy consumption in optical interconnects. The authors introduce three possible integration techniques for realizing a hybrid silicon transmitter on a single chip with distributed feedback (DFB) lasers and electro-absorption modulators. They review the current bottlenecks and techniques for further reducing threshold current and increasing the wall-plug efficiency of these lasers.
Deletion and Insertion Mutants of the Multidrug Transporter (1989)

The multidrug transporter is a 170,000-dalton membrane glycoprotein which confers multidrug resistance through its activity as an ATP-dependent efflux pump for hydrophobic, cytotoxic drugs. To determine the essential structural components of this complex membrane transporter we have altered an MDR1 cDNA in an expression vector by deletion and insertion mutations. The structure of the transporter deduced from its amino acid sequence suggests that it consists of two homologous, perhaps functionally autonomous, halves each with six transmembrane segments and a cytoplasmic ATP-binding domain. However, several carboxyl-terminal deletions, one involving 53 amino acids, the second removing 253 amino acids, and an internal deletion within the carboxyl-terminal half of the molecule, totally eliminate the ability of the mutant transporter to confer drug resistance. An internal deletion of the amino-terminal half, which removed residues 140-229, is also nonfunctional. Small carboxylterminal deletions of up to 23 amino acids leave a functional transporter, although the removal of 23 COOH-terminal amino acids reduces its ability to confer colchicine resistance. Insertions of 4 amino acids in a transmembrane domain, and in one of the two ATP-binding regions, have no effect on activity. These studies define some of the limits of allowable deletions and insertions in the MDR1 gene, and demonstrate the requirement for two intact halves of the molecule for a functional multidrug transporter.
ChemInform Abstract: A General Method for Imine Formation Using B(OCH2CF3)3. (2015)

Abstract The approach to various imines bearing different types of N‐substituents is possible under conditions A) or B).
Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins (2009)

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit(DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium, Desulfovibrio desulfuricans G20, also showed similar +42 Da modifications in the same pathway. Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway.
Supplementary Table 1 from Polycomb CBX7 Promotes Initiation of Heritable Repression of Genes Frequently Silenced with Cancer-Specific DNA Hypermethylation (2023)

Supplementary Table 1 from Polycomb CBX7 Promotes Initiation of Heritable Repression of Genes Frequently Silenced with Cancer-Specific DNA Hypermethylation
Table S2 from Lentiviral-Driven Discovery of Cancer Drug Resistance Mutations (2023)

&lt;p&gt;Results of LentiMutate on PCR mutagenized RUVBL1 cDNA and compound B in the H1993 cell line. Values shown are the averages of three biological replicates. The fold enrichment of "All nucleotides" is the sum of substitution rates for all nucleotides in the with doxycycline replicates divided by the sum of substitution rates for all nucleotides without doxycycline (parental) at one nucleotide position. Nucleotide w/ max error refers to the highest substitution rate for a single nucleotide at one nucleotide position.&lt;/p&gt;
A Noise Constrained Least Mean Fourth Adaptive Algorithm (2007)

In this work, a noise-constrained least mean fourth (NCLMF) adaptive algorithm is proposed. Based on the fact that in many practical applications an accurate estimate of the measurement noise variance is available, or can be easily estimated, the learning speed of the LMF algorithm can be then increased considerably by adding a constraint to it. This noise constrained LMF algorithm can be seen as a variable step-size LMF algorithm. The main aim of this paper is to derive the NCLMF adaptive algorithm, analyze its convergence behaviour, and assess its performance in different noise environments. Moreover, the concept of energy conservation is used to carry out the rigorous steady-state analysis. Finally, a number of simulation results are carried out to corroborate the theoretical findings, and as expected, improved performance is obtained through the use of this technique over the traditional LMF algorithm.
AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques (2018)

Abstract In biological assays, automated cell/colony segmentation and counting is imperative owing to huge image sets. Problems occurring due to drifting image acquisition conditions, background noise and high variation in colony features in experiments demand a user-friendly, adaptive and robust image processing/analysis method. We present AutoCellSeg (based on MATLAB) that implements a supervised automatic and robust image segmentation method. AutoCellSeg utilizes multi-thresholding aided by a feedback-based watershed algorithm taking segmentation plausibility criteria into account. It is usable in different operation modes and intuitively enables the user to select object features interactively for supervised image segmentation method. It allows the user to correct results with a graphical interface. This publicly available tool outperforms tools like OpenCFU and CellProfiler in terms of accuracy and provides many additional useful features for end-users.
Aromatic Polyimides With Low Dielectric Constants (1994)

Linear aromatic polyimides developed containing dimethylsilane linkages in dianhydride portions of molecules and at least one trifluoromethyl group in each of diamine portions. Polyimides offer advantages of thermal stability, low density, resistance to ionizing radiation, toughness, flexibility, and exhibit lower dielectric constants. Also polyimides nearly transparent and colorless; an advantage in protective coating of solar photovoltaic cells, optical components, and antennas.
An integrated process planning system using feature reasoning and space search-based optimization (1999)

Abstract In this paper we describe the architecture of a new integrated process planning system, called 31-PP, which is comprised of three modules: feature completion, process selection, and process sequencing. We have applied a knowledge-based approach to feature completion and process selection, and the space search algorithm for process sequencing. The resulting process planning system provides for both upstream and downstream integration of CAPP with CAD and scheduling systems, rej.pectively. Description of the methodologies and procedures is provided and some experimental results that demonstrate the system performance are presented.
Monolithically-integrated long verticle cavity surface emitting laser incorporating a concave micromirror on a glass substrate (2004)

We present a fully monolithically integrated vertical laser using an InGaAs/GaAs/AlGaAs gain medium directly bonded to a glass substrate with a concave micromirror. The lasing wavelength is 980 nm with maximum output power of 39 mW.
Retraction: Iterative Transmit/Receive Antenna Selection in MIMO Systems Based on Channel Capacity Analysis (2011)

Notification from Editors “Iterative Transmit/Receive Antenna Selection in MIMO Systems Based on Channel Capacity Analysis” by Peng LAN, Ju LIU, Fenggang SUN and Peng XUE, IEICE Transactions on Communications, vol.E94-B, no.3, pp.844-847, March 2011. This manuscript was canceled on August 6, 2013 because it was found to be a duplicate submission.
Inhibition of protein kinase CK2 prevents the progression of glomerulonephritis (2005)

Glomerulonephritis (GN) is a progressive inflammation that may be caused by a variety of underlying disorders. It is the primary cause of chronic renal failure and end-stage renal disease, which require dialysis and transplantation worldwide. Immunosuppressive therapy has been used to treat GN clinically, but this treatment has had insufficient therapeutic effects. Here, we show that protein kinase CK2 is a key molecule in the progression of GN. cDNA microarray analysis identified CK2alpha, the catalytic subunit of CK2, as a GN-related, differentially expressed gene. Overexpression of CK2alpha was noted in the proliferative glomerular lesions in rat GN models and in renal biopsy specimens from lupus nephritis or IgA nephropathy patients. Administration of either antisense oligodeoxynucleotide against CK2alpha or low molecular weight CK2-specific inhibitors effectively prevented the progression of renal pathology in the rat GN models. The resolution of GN by CK2 inhibition may result from its suppression of extracellular signal-regulated kinase-mediated cell proliferation, and its suppression of inflammatory and fibrotic processes that are enhanced in GN. Our results show that CK2 plays a critical role in the progression of immunogenic renal injury, and therefore, CK2 is a potential target for GN therapy.
The commercialization of nanotechnology: the five critical success factors to a nanotech-enabled whole product (2013)

Regulation shapes decision making and human behavior. However its impact - as it has often been argued – can encourage or stifle innovation, especially in relation to emerging technologies such as nanotechnologies. It is therefore not surprising that the regulatory debate in relation to nanotechnologies is highly contested. As an increasing number of products incorporating nanomaterials and nanoparticles make their way onto the market in an environmental of imperfect information, such debates have only intensified. The aim of this chapter is to introduce readers to the notion of regulation and illustrate how regulation in its many guises is currently being employed to the regulation of nanotechnologies.
An Area and Power Efficient Cartesian Phase Shifter + Mixer Circuit Applied to WLAN System (2007)

A two-antenna array receiver is designed for WLAN application to build a maximum ratio combiner (MRC) system. A new signal-path Cartesian phase generation and combination technique is proposed to shift the RF signal by 22.5 phase steps. The 3 dB improvement in received SNR is achieved in comparison to single path receiver. The 0.29 mm^2 RF paths consumes 30 mW in 0.13 mum CMOS process.
Network Architectures for 4G: Cost Considerations (2007)

As 3G wireless networks evolve toward 4G, various wireless network technology organizations are considering a major redesign of the network architecture. We present a perspective on such a redesign motivated primarily by cost considerations. We examine some tenets for the design of 4G wireless network architectures that are aimed at improving costs in various aspects of the network. One tenet is the maximization of economies of scale by partitioning the functionality among network elements in a way that maximizes the potential domain of applicability of the network elements. Another is reduction of the number of distinct types of network elements needed by flattening the levels of hierarchy in the execution of various functions. We explain our reasoning by illustrating a way of redesigning the current 3GPP network architecture based on these tenets.
Removable Rigid Dressings for Postoperative Management of Transtibial Amputations: A Review of Published Evidence (2017)

II.
Evidence that dopamine-2 mechanisms control renal function (1990)

Dopamine is synthesized by the kidney, and dopamine-2 (DA2) receptors are present in the renal glomerulus. However, no role for DA2 receptors in the kidney has been defined. We investigated the possible role of DA2 receptors in control of renal function by intrarenal infusion of a highly specific DA2 antagonist YM-09151 (YM), in conscious uninephrectomized dogs (n = 5) in metabolic balance at Na intake 40 meq/day. YM infused at 0.01 pmol.kg-1.min-1 did not cause any changes in urinary flow rate or Na excretion. Administration of YM (infusions from 0.1 to 10.0 pmol.kg-1.min-1) caused a significant dose-dependent diuresis (F = 20.3; P less than 0.001) and natriuresis (F = 35.2; P less than 0.0001) and an increase in glomerular filtration rate (F = 45.4; P less than 0.0001), renal plasma flow (F = 209.3; P less than 0.0001), and filtration fraction (F = 11.2; P less than 0.0001). No significant changes in plasma renin activity, plasma aldosterone concentration, or mean arterial blood pressure occurred with any of the doses of YM infused into the renal artery. Coinfusion of LY-171555, a specific DA2 agonist, at a dose that itself did not affect renal function, completely abrogated the renal hemodynamic and excretory changes induced by YM. The data suggest that dopamine produced intrarenally may act at renal vascular and/or glomerular DA2 receptors to control renal function.
Synthetic and characterization aspects of dimethylaminoethyl methacrylate reversible addition fragmentation chain transfer (RAFT) polymerization (2005)

Abstract 2‐cyanoprop‐2‐yl dithiobenzoate (CPDB) mediated RAFT polymerization of dimethylaminoethyl methacrylate (DMAEMA) was carried out in dioxane at 90 °C. The influence of several parameters, such as the monomer to CPDB molar ratio (100 to 500), the monomer concentration (2 mol·L −1 to 5.9 mol·L −1 ), and CPDB to initiator molar ratio (1 to 10), was evaluated with regards to conversion and polymerization duration, as well as control of molar mass and molar mass distributions. Number average molar masses from 10,000 to 70,000 g·mol −1 can be targeted. The determination of the molar masses has been carried out by size exclusion chromatography (SEC) with a refractometer detector with poly(methyl methacrylate) (PMMA) standards. The experimental values were lower than the expected ones. Then, SEC in aqueous medium with an online laser light scattering detector was used both to get absolute molar masses and to recalibrate the SEC column in THF. Characterization of well‐controlled PDMAEMA samples has been performed by proton NMR spectroscopy and matrix assisted laser desorption ionization time of flight mass spectrometry. Finally, a chain extension experiment was evaluated with regard to living features. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3551–3565, 2005