gebhart/patrepeval huggingface dataset:
Deacetylation of mycothiol-derived ‘waste product’ triggers the last biosynthetic steps of lincosamide antibiotics (2015)

The immediate post-condensation steps in lincomycin biosynthesis are reminiscent of the mycothiol-dependent detoxification system of actinomycetes. This machinery provides the last proven lincomycin intermediate, a mercapturic acid derivative, which formally represents the 'waste product' of the detoxification process. We identified and purified new lincomycin intermediates from the culture broth of deletion mutant strains of <i>Streptomyces lincolnensis</i> and tested these compounds as substrates for proteins putatively involved in lincomycin biosynthesis. The results, based on LC-MS, in-source collision-induced dissociation mass spectrometry and NMR analysis, revealed the final steps of lincomycin biosynthesis, <i>i.e.</i> conversion of the mercapturic acid derivative to lincomycin. Most importantly, we show that deacetylation of the <i>N</i>'-acetyl-<i>S</i>-cysteine residue of the mercapturic acid derivative is required to 'escape' the detoxification-like system and proceed towards completion of the biosynthetic pathway. Additionally, our results, supported by l-cysteine-<sup>13</sup>C<sub>3</sub>, <sup>15</sup>N incorporation experiments, give evidence that a different type of reaction catalysed by the homologous pair of pyridoxal-5'-phosphate-dependent enzymes, LmbF and CcbF, forms the branch point in the biosynthesis of lincomycin and celesticetin, two related lincosamides.
Mast cell proteinases activate precursor forms of collagenase and stromelysin, but not of gelatinases A and B (1994)

Mast cell activation in vivo is often associated with areas of oedema and connective-tissue degradation. Tryptase and chymase are the major serine proteinases released by mast cells, but they appear to have little activity on most components of the extracellular matrix. The matrix metalloproteinases (MMP) are purported to degrade almost all connective tissue elements and are secreted by cells in the form of inactive precursors. Since the mechanisms of MMP activation in vivo are poorly understood we have examined the potential of mast cell proteinases to activate the precursor forms of human collagenase (MMP-1), stromelysin (MMP-3), gelatinase A (MMP-2) and gelatinase B (MMP-9). Mast cell proteinases prepared from purified dog mastocytoma cells were shown to process and activate purified precursor forms of both MMP-1 and MMP-3. Using antipain and chymostatin, inhibitors for tryptase and chymase, respectively, it was demonstrated that both pMMP-1 and pMMP-3 were effectively processed and activated by the chymase component. By contrast, tryptase activated only pMMP-3. The mast cell proteinases were unable to process or activate purified precursor forms of MMP-2 and MMP-9. However, MMP-3 previously activated by mast cell proteinases was shown to activate pMMP-9, but not pMMP-2. Since we have no evidence that mast cells express these four metalloenzymes, the release of mast cell serine proteinases following activation/degranulation could contribute to local metalloproteinase activation and subsequent matrix degradation.
Active memory (1997)

article Free Access Share on Active memory: a new abstraction for memory system simulation Authors: Alvin R. Lebeck Duke Univ. Duke Univ.View Profile , David A. Wood Univ. of Wisconsin, Madison Univ. of Wisconsin, MadisonView Profile Authors Info & Claims ACM Transactions on Modeling and Computer SimulationVolume 7Issue 1Jan. 1997 pp 42–77https://doi.org/10.1145/244804.244806Published:01 January 1997Publication History 21citation470DownloadsMetricsTotal Citations21Total Downloads470Last 12 Months8Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Micromoulding of three-dimensional photonic crystals on silicon crystals (2003)

Society of Manufacturing Engineers (SME) Technical Paper 2003
Modeling antenna close to the human body (2002)

Evaluation of antenna performance needs to be addressed in complex environments rather than in free space. There are many situations when such a need arises. We give examples of evaluation when a human body is in the close proximity of an antenna. In this case, it is also important to evaluate the power absorption in the body in terms of the specific absorption rate (SAR). Two antennas, which show robust performance either on a cellular telephone or on a laptop computer are evaluated. They both operate in two frequency bands allocated for wireless communication. The antenna impedance matching, radiation patterns, and SAR in the user's head are computed using the FDTD method. Work currently in progress is aimed at evaluation of the SAR when the whole human body is in the near radiation field of a directional antenna. In this case, the exposure cannot be effectively be approximated by a limited number of plane waves, and modeling of the antenna together with the human body leads to a very large computational problem, The solution that is being investigated is modification to the FDTD that allows for exclusion of the antenna from the computational space and representation of its radiation characteristic on the Huygens space in FDTD.
<i>TOM1</i> , an <i>Arabidopsis</i> gene required for efficient multiplication of a tobamovirus, encodes a putative transmembrane protein (2000)

Host-encoded factors play an important role in virus multiplication, acting in concert with virus-encoded factors. However, information regarding the host factors involved in this process is limited. Here we report the map-based cloning of an Arabidopsis thaliana gene, TOM1, which is necessary for the efficient multiplication of tobamoviruses, positive-strand RNA viruses infecting a wide variety of plants. The TOM1 mRNA is suggested to encode a 291-aa polypeptide that is predicted to be a multipass transmembrane protein. The Sos recruitment assay supported the hypothesis that TOM1 is associated with membranes, and in addition, that TOM1 interacts with the helicase domain of tobamovirus-encoded replication proteins. Taken into account that the tobamovirus replication complex is associated with membranes, we propose that TOM1 participates in the in vivo formation of the replication complex by serving as a membrane anchor.
Solid-Phase Synthesis of 1,2,5-Trisubstituted 4-Imidazolidinones (2002)

An efficient method for the preparation of 1,2,5-trisubstituted 4-imidazolidinones is presented. The synthetic approach is based on the formation of an N-[1-(benzotriazol-1-yl)alkyl] moiety on the amino group of a MBHA resin-bound amino acid. The nucleophilic substitution of the benzotriazole group with an amidic nitrogen results in the formation of a five-membered imidazolidinone ring. The reaction is nonstereospecific and produces diastereomers in ratios that vary depending on the substituents on the ring. A variety of N-alpha-alkylated amino acids were cyclized with aromatic, aliphatic, and heterocyclic aldehydes to determine optimal reaction conditions and to select building blocks for the future preparation of a large, diverse range of individual trisubstituted imidazolidinones as well as a mixture-based combinatorial library.
Modelling a neural network using an algebraic method (2014)

In this paper, a framework based on algebraic structures to formalize various types of neural networks is presented. The working strategy is to break down neural networks into building blocks, relationships between each building block, and their operations. Building blocks are collections of primary components or neurons. In turn, neurons are collections of properties functioning as single entities, transforming an input into an output. We perceive a neuron as a function. Thus the flow of information in a neural network is a composition between functions. Moreover, we also define an abstract data structure called a layer which is a collection of entities which exist in the same time step. This layer concept allows the parallel computation of our model. There are two types of operation in our model; recalling operators and training operators. The recalling operators are operators that challenge the neural network with data. The training operators are operators that change parameters of neurons to fit with the data. This point of view means that all neural networks can be constructed or modelled using the same structures with different parameters.
An Integrated I-Q Mixer for Software-Defined Radio Applications (2004)

The software defined This design case history radio takes advan-provides a lesson in prodtage of digital siguct development, describnal processing to move ing a new microwave I-Q channel filtering, interfer-mixer that addresses many ence suppression, auto-of the shortcomings found matic gain control, modu-in earlier designs. lation and demodulation from hardware into software. As shown in Figure 1, the block diagram for a software defined radio includes RF functions and analog and digital baseband signal processing. For simple, high volume, low performance applications, all of these functions might be implemented on a single chip. For
Accelerated Visual Context Classification on a Low-Power Smartwatch (2016)

Data produced by wearable sensors is key in contexts such as performance enhancement and training help for sports and fitness, continuous monitoring for aging people and for chronic disease management, and in gaming and entertainment. Unfortunately, wearable devices currently in the market are either incapable of complex functionality or severely impaired by short battery lifetime. In this work, we present a smart watch platform based on an ultralow-power (ULP) heterogeneous system composed of a TI MSP430 microcontroller, the PULP programmable parallel accelerator, and a set of ULP sensors, including a camera. The embedded PULP accelerator enables state-of-the-art context classification based on convolutional neural networks to be applied within a sub-10-mW system power envelope. Our methodology enables to reach high accuracy in context classification over five classes (up to 84%, with three classes over five reaching more than 90% accuracy), while consuming 2.2 mJ per classification, or an ultralow energy consumption of less than 91 μJ per classification with an accuracy of 64%-3.2× better than chance. Our results suggest that the proposed heterogeneous platform can provide up to 500× speedup with respect to the MSP430 within a similar power envelope, which would enable complex computer vision algorithms to be executed in highly power-constrained scenarios.
A New TV Video/Sound Detector IC (1974)

The operation of multiplier and video amplifier circuits used in present TV IF detector ICs is explained. A new detector is described which uses a separate sound detector to allow conventional trapping before the video detector. The sound carrier output is buffered and the video detector features differential inputs and special circuitry to handle input overloads. An NPN video amplifier uses differential to single-ended conversion to improve linearity and dc stability. The 14 lead device also includes an auxiliary video output, a carrier source for AFT, and a sync separator device.
Glucocorticoid (dexamethasone)-induced metabolome changes in healthy males suggest prediction of response and side effects (2015)

Glucocorticoids are indispensable anti-inflammatory and decongestant drugs with high prevalence of use at (~)0.9% of the adult population. Better holistic insights into glucocorticoid-induced changes are crucial for effective use as concurrent medication and management of adverse effects. The profiles of 214 metabolites from plasma of 20 male healthy volunteers were recorded prior to and after ingestion of a single dose of 4 mg dexamethasone (+20 mg pantoprazole). Samples were drawn at three predefined time points per day: seven untreated (day 1 midday - day 3 midday) and four treated (day 3 evening - day 4 evening) per volunteer. Statistical analysis revealed tremendous impact of dexamethasone on the metabolome with 150 of 214 metabolites being significantly deregulated on at least one time point after treatment (ANOVA, Benjamini-Hochberg corrected, q < 0.05). Inter-person variability was high and remained uninfluenced by treatment. The clearly visible circadian rhythm prior to treatment was almost completely suppressed and deregulated by dexamethasone. The results draw a holistic picture of the severe metabolic deregulation induced by single-dose, short-term glucocorticoid application. The observed metabolic changes suggest a potential for early detection of severe side effects, raising hope for personalized early countermeasures increasing quality of life and reducing health care costs.
Cancellation of show-through in duplex scanning (2000)

When scanning a page with printing on both sides, the printing on the back-side often shows through in the scan of the front-side because the page is not completely opaque. This phenomenon of show-through is analyzed and an image processing method for removal of this commonly encountered degradation is developed. A simplified mathematical model is obtained from first physical principles. The model is linearized using suitable transformations and simplifying approximations. Based on the linearized model, an adaptive linear-filtering scheme is developed for the electronic removal of show-through using scans of both sides of the document. Experimental results demonstrating the effectiveness of the method developed are presented.
Diminazene Aceturate Improves Autonomic Modulation in Pulmonary Hypertension (2011)

Our studies have demonstrated that diminazene aceturate (DIZE) protects rats from monocrotaline (MCT)-induced pulmonary hypertension (PH). The present study was conducted to determine if these effects of DIZE are associated with improvements in autonomic nervous system (ANS) modulation. A single dose of MCT (50mg/kg) was subcutaneously injected to induce PH. A subset of MCT rats were treated with DIZE (15mg/kg/day) for 21 days. ANS control was evaluated by spectral and symbolic analysis of heart rate variability (HRV). MCT induced a significant (p<0.001) increase in right ventricular systolic pressure (62±14mmHg) when compared to all other groups (Control: 26±6; DIZE alone: 29±5; MCT+DIZE: 31±7). MCT treatment was associated with a significant decrease in HRV versus control (s2; Control: 93±32; DIZE: 64±58; MCT+DIZE: 41±15 and MCT: 14±11) and with an increase in the cardiac sympathetic modulation, observed by 0V pattern of symbolic analysis (Control: 4±1; DIZE: 8.8±6.1; MCT+DIZE: 2.9±2.4 and MCT: 11±6.3). This observation was confirmed by the LF/HF index of spectral analysis (Control: 0.4±0.09; DIZE: 0.06±0.007; MCT+DIZE: 0.14±0.1and MCT: 1.0±0.7) which showed that DIZE was able to recover the ANS balance. Thus, our results demonstrate that MCT-induced PH is associated with a significant increase in sympathetic modulation and a decrease in HRV. Furthermore, DIZE was able to reestablish the ANS balance.
Automotive engine idle speed control optimization using least squares support vector machine and genetic algorithm (2008)

Purpose Nowadays, automotive engines are controlled by electronic control units (ECUs), and the engine idle speed performance is significantly affected by the setup of control parameters in the ECU. The engine ECU tune‐up is done empirically through tests on a dynamometer (dyno). In this way, a lot of time, fuel and human resources are consumed, while the optimal control parameters may not be obtained. The purpose of this paper is to propose a novel ECU setup optimization approach for engine idle speed control. Design/methodology/approach In the first phase of the approach, Latin hypercube sampling (LHS) and a multi‐input/output least squares support vector machine (LS‐SVM) is proposed to build up an engine idle speed model based on dyno test data, and then a genetic algorithm (GA) is applied to obtain optimal ECU setting automatically subject to various user‐defined constraints. Findings The study shows that the predicted results using the estimated model from LS‐SVM are in good agreement with the actual test results. Moreover, the optimization results show a significant improvement on idle speed performance in a test engine. Practical implications As the methodology is generic it can be applied to different vehicle control optimization problems. Originality/value The research is the first attempt to integrate a couple of paradigms (LHS, multi‐input/output LS‐SVM and GA) into a general framework for constrained multivariable optimization problems under insufficient system information. The proposed multi‐input/output LS‐SVM for modelling of multi‐input/output systems is original, because the traditional LS‐SVM modelling approach is suitable for multi‐input, but single output systems. Finally, this is the first use of the novel integrated framework for automotive engine idle‐speed control optimization.
Item Generation for Test Development (2013)

Contents: H. Braun, Foreword. S.H. Irvine, Item Generation for Test Development: An Introduction. Prologue and Epilogue: Remembering Samuel J. Messick. Part I:Psychometric and Cognitive Theory of Item Generation. S.H. Irvine, The Foundations of Item Generation for Mass Testing. S. Newstead, P. Bradon, S. Handley, J. Evans, I. Dennis, Using the Psychology of Reasoning to Predict the Difficulty of Analytical Reasoning Problems. I. Dennis, S. Handley, P. Bradon, J. Evans, S. Newstead, Approaches to Modeling Item-Generative Tests. L. Swanson, Discussant Remarks. Discussion. Part II:Construct-Oriented Approaches to Item Generation. R.J. Mislevy, L.S. Steinberg, R.G. Almond, On the Roles of Task Model Variables in Assessment Design. M.K. Enright, K.M. Sheehan, Modeling the Difficulty of Quantitative Reasoning Items: Implications for Item Generation. L.F. Hornke, Item-Generation Models for Higher Order Cognitive Functions. C. Lewis, Discussant Remarks. Discussion. Part III:From Theory to Implementation. I.I. Bejar, Generative Testing: From Conception to Implementation. S.E. Embretson, Generating Abstract Reasoning Items With Cognitive Theory. P.C. Kyllonen, Item Generation for Repeated Testing of Human Performance. D. Wright, Scoring Tests When Items Have Been Generated. H. Wainer, On the Automatic Generation of Test Items: Some Whens, Whys, and Hows. Part IV:Applications of Item-Generative Principles. D. Bartram, The MICROPAT Pilot Selection Battery: Applications of Generative Techniques for Item-Based and Task-Based Tests. K-M. Goeters, B. Lorenz, On the Implementation of Item Generation Principles for the Design of Aptitude Testing in Aviation. M.K. Singley, R.E. Bennett, Item Generation and Beyond: Applications of Schema Theory to Mathematics Assessment. R. Morgan, Discussant Remarks. Discussion.
Disuse deterioration of human skeletal muscle challenged by resistive exercise superimposed with vibration: evidence from structural and proteomic analysis (2014)

In the present bed rest (BR) study, 23 volunteers were randomized into 3 subgroups: 60 d BR control (Ctr); BR with resistive exercise (RE; lower-limb load); and resistive vibration exercise (RVE; RE with superimposed vibration). The aim was to analyze by confocal and electron microscopy the effects of vibration on myofibril and filament integrity in soleus (Sol) and vastus lateralis (VL) muscle; differential proteomics of contractile, cytoskeletal, and costameric proteins (TN-C, ROCK1, and FAK); and expression of PGC1α and atrophy-related master genes MuRF1 and MuRF2. RVE (but not RE) preserved myofiber size and phenotype in Sol and VL by overexpressing MYBPC1 (42%, P ≤ 0.01), WDR1 (39%, P ≤ 0.01), sarcosin (84%, P ≤ 0.01), and CKM (20%, P ≤ 0.01) and prevented myofibrillar ultrastructural damage as detectable by MuRF1 expression. In Sol, cytoskeletal and contractile proteins were normalized by RVE, and TN-C increased (59%, P ≤ 0.01); the latter also with RE (108%, P ≤ 0.01). In VL, the outcomes of both RVE (acting on sarcosin and desmin) and RE (by way of troponinT-slow and MYL2) were similar. RVE appears to be a highly efficient countermeasure protocol against muscle atrophy and ultrastructural and molecular dysregulation induced by chronic disuse.
Deletion Analysis of Pichia PGK1 Promoter and Construction of an Episomal Vector for Heterologous Protein Expression in P. pastoris (2007)

Approximately 2.0 kb of the promoter region of the Pichia pastoris phosphoglycerate kinase gene (PGK1) was reduced to a 266 bp fragment and this minimized portion was used for construction of a new episomal constitutive expression vector in P. pastoris. As an approach to developing a constitutive expression vector in P. pastoris, the GAP promoter region of the Pichia expression vector pGAPZB was replaced with sequentially deleted PGK1 promoter fragments fused to a beta-galactosidase gene. When a lacZ gene was used as a reporter gene, PGK1 promoter strength was lower than that of the constitutive GAP promoter but it was higher than TEF1. We report here the development of the pPGKZ-E vector as a new episomal expression vector for heterologous gene expression by removing non-essential regions of the PGK1 promoter. This broadens the choice of episomal expression vectors for controlled constitutive expression in P. pastoris.
Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy (2016)

Anti-PD-1 therapy yields objective clinical responses in 30-40% of advanced melanoma patients. Since most patients do not respond, predictive biomarkers to guide treatment selection are needed. We hypothesize that MHC-I/II expression is required for tumour antigen presentation and may predict anti-PD-1 therapy response. In this study, across 60 melanoma cell lines, we find bimodal expression patterns of MHC-II, while MHC-I expression was ubiquitous. A unique subset of melanomas are capable of expressing MHC-II under basal or IFNγ-stimulated conditions. Using pathway analysis, we show that MHC-II(+) cell lines demonstrate signatures of 'PD-1 signalling', 'allograft rejection' and 'T-cell receptor signalling', among others. In two independent cohorts of anti-PD-1-treated melanoma patients, MHC-II positivity on tumour cells is associated with therapeutic response, progression-free and overall survival, as well as CD4(+) and CD8(+) tumour infiltrate. MHC-II(+) tumours can be identified by melanoma-specific immunohistochemistry using commercially available antibodies for HLA-DR to improve anti-PD-1 patient selection.
Connecting the Dots (2016)

From Big Data to Healthy Heart R ising capacity to measure extensive arrays of biological parameters has ushered in an era of biomedical big data. As massive datasets from large cohorts become the norm, the discipline of data science has emerged to tackle data-driven problems at the intersection of biomedical research and patient care. We introduce several sources of cardiovascular big data and discuss the importance of maximizing participation in data-driven knowledge production models.
Low-Profile Three-Arm Folded Dipole Antenna for UHF Band RFID Tags Mountable on Metallic Objects (2010)

A low-profile radio frequency identification (RFID) tag mountable on metallic objects is presented, which employs a multiple-arm folded dipole antenna. The proposed antenna is printed on a single-layer circuit board with an overall thickness of 1.5 mm not requiring any via or shorting plate. The presented configuration allows to match an RFID chip impedance with an imaginary part around - 400 Ω . A slightly modified version of the tag that allows an easy tuning of the frequency response is illustrated as well as a more compact tag obtained by allowing the use of vias. Prototypes for the RFID UHF band allocated in Europe have been fabricated, and measurements of the impedance and read range are provided.