gebhart/patrepeval huggingface dataset:
Outwitting EF-Tu and the ribosome: translation with d-amino acids (2015)

Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ribosomal synthesis. We introduce an in vitro translation system that enables single incorporation of 17 out of 18 tested d-aa into a polypeptide; incorporation of two or three successive d-aa was also observed in several cases. The system consists of wild-type components and d-aa are introduced via artificially charged, unmodified tRNA(Gly) that was selected according to the rules of 'thermodynamic compensation'. The results reveal an unexpected plasticity of the ribosomal peptidyltransferase center and thus shed new light on the mechanism of chiral discrimination during translation. Furthermore, ribosomal incorporation of d-aa into polypeptides may greatly expand the armamentarium of in vitro translation towards the identification of peptides and proteins with new properties and functions.
The Place of Metaphysics in Wyclif’s Theology (1987)

Wyclif’s theological doctrines are reasonably familiar and I do not intend to dwell upon them unduly here. They had their focus in his concepts of the Church, the Bible and the eucharisr, and they were the outcome of a singular combination of a metaphysics of realism—the belief in the reality of universal essences or natures, such as genera and species, and including being itself as the most universal essence of all—and an apostolic or evangelical view of Christian life, modeled on the life of Christ and his disciples, as one of purely spiritual mission and temporal renunciation. It was that combination which made Wyclif’s religious beliefs distinctive, and it is that which I wish to consider here.
Host-Pathogen Interactions (1976)

The structures of the four wall-released elicitor fractions isolated from the Phytophthora megasperma var. sojae mycelial walls have been examined. The results demonstrate that fraction I is primarily composed of a branched beta-1,3-glucan, similar in structure to the extracellular elicitors described previously (Ayers, A., J. Ebel, F. Finelli, N. Burger, and P. Albersheim. 1976. Plant Physiol. 57: 751-759). Fractions II and IV are primarily composed of a highly branched mannan-containing glycoprotein, with fraction IV richer in protein than fraction II. Fraction III contains, attached to protein, a mixture of the two polysaccharide types found in fraction I and in fractions II and IV. The structural data presented here, in concert with the biological data presented in the previous two papers (Ayers et al. 1976. Plant Physiol. 57: 751-759; 760-765), demonstrate that the only compound produced by P. megasperma var. sojae which contains elicitor activity is the glucan. Evidence is presented that the terminal glycosyl residues of the glucan are required for elicitor activity. In addition, it is demonstrated that 90% of the glucan can be removed enzymically without any loss of biological activity. The active residue of the enzymic digestion is a highly branched 3- and 3,6-linked glucan containing about 4% mannosyl residues. The results presented suggest that the mannosyl residues of the glucan, which represent only about 1% of the undegraded glucan, are likely to participate in the active site of this molecule. The role of elicitors and phytoalexins in host-pathogen interactions is discussed. Evidence for the existence of and possible identity of another factor, which determines race specificity of host-pathogen interactions, is summarized.
A highly integrated dual-band SiGe power amplifier that enables 256 QAM 802.11ac WLAN radio front-end designs (2012)

A highly integrated SiGe BiCMOS PA is presented that enables the emerging high throughput 802.11ac WLAN applications. The PA has two stages for the g-band and three stages for the a-band PA, and integrates matching circuitry, out of band rejection filters, power detectors, and bias controls in a 1.5 ×1.6 mm chip. The g-band PA achieves 28 dB gain with 2% EVM at 18 dBm and 3% at 19.5 dBm output power. The a-band PA achieves 32 dB gain with 2% EVM at 18 dBm and 3% EVM at 19 dBm output power. The design is verified meeting not only the regulatory out-of-band emission requirements but also the linearity requirement of the emerging 256 QAM 802.11ac standard.
Design and Selection Parameters to Accelerate the Discovery of Novel Central Nervous System Positron Emission Tomography (PET) Ligands and Their Application in the Development of a Novel Phosphodiesterase 2A PET Ligand (2013)

To accelerate the discovery of novel small molecule central nervous system (CNS) positron emission tomography (PET) ligands, we aimed to define a property space that would facilitate ligand design and prioritization, thereby providing a higher probability of success for novel PET ligand development. Toward this end, we built a database consisting of 62 PET ligands that have successfully reached the clinic and 15 radioligands that failed in late-stage development as negative controls. A systematic analysis of these ligands identified a set of preferred parameters for physicochemical properties, brain permeability, and nonspecific binding (NSB). These preferred parameters have subsequently been applied to several programs and have led to the successful development of novel PET ligands with reduced resources and timelines. This strategy is illustrated here by the discovery of the novel phosphodiesterase 2A (PDE2A) PET ligand 4-(3-[(18)F]fluoroazetidin-1-yl)-7-methyl-5-{1-methyl-5-[4-(trifluoromethyl)phenyl]-1H-pyrazol-4-yl}imidazo[5,1-f][1,2,4]triazine, [(18)F]PF-05270430 (5).
In-Process Detection of Tool Failure in Milling Using Cutting Force Models (1989)

The authors show that first and second differencing of a time averaged resultant force is extremely effective in the recognition of tool breakage in milling. In order to be useful in production, however, such a system needs to have a knowledge of allowable levels of the first difference. It is shown that these levels, (thresholds), are extremely dependent on the ratio of cutter radius to width of cut, (immersion ratio). A method of on-line identification of the immersion ratio and threshold tuning is presented with experimental verification.
Comparative Analysis of Hepatic CD14 Expression between Two Different Endotoxin Shock Model Mice: Relation between Hepatic Injury and CD14 Expression (2013)

CD14 is a glycoprotein that recognizes gram-negative bacterial lipopolysaccharide (LPS) and exists in both membrane-bound and soluble forms. Infectious and/or inflammatory diseases induce CD14 expression, which may be involved in the pathology of endotoxin shock. We previously found that the expression of CD14 protein differs among the endotoxin shock models used, although the reasons for these differences are unclear. We hypothesized that the differences in CD14 expression might be due to liver injury, because the hepatic tissue produces CD14 protein. We investigated CD14 expression in the plasma and liver in the carrageenan (CAR)-primed and D-galN-primed mouse models of endotoxin shock. Our results showed that severe liver injury was not induced in CAR-primed endotoxin shock model mice. In this CAR-primed model, the higher mRNA and protein expression of CD14 was observed in the liver, especially in the interlobular bile duct in contrast to D-galN-primed-endotoxin shock model mice. Our findings indicated that the molecular mechanism(s) underlying septic shock in CAR-primed and D-galN-primed endotoxin shock models are quite different. Because CD14 expression is correlated with clinical observations, the CAR-primed endotoxin shock model might be useful for studying the functions of CD14 during septic shock in vivo.
Interactive ray tracing (1999)

this paper, we present interactive volume visualization schemes that use ray tracing as their basic computation method
A Prediction of Radiation Power for the Planar Array Acoustic Transducer Considering Mutual Coupling Effects (1996)

Planar array of acoustic transducer is normally used in a sonar system. Acoustic radiation makes beam pattern in underwater uses. The main source of the beam pattern is due to the transducer array. Therefore, estimation of the acoustic radiated power is necessary to predict the performance and efficiency of the transducer. As an example of the acoustic radiation power, nine acoustic transducers mounted to a rigid infinite baffle are considered in a theoretical model. Each piston's acoustic radiation consists of self- and mutual-radiation impedances. Total radiation impedances and acoustic radiation power of the transducers are extracted using on the theory of an equivalent electric circuit. The theoretical results reveal that acoustic radiation power of the transducer depends on the mutual coupling effects
Identification of passive intermodulation product generation on microwave reflecting surfaces (1992)

New developments in the adaptation of microwave holographic imaging to assess the intermodulation product (IMP) performance of microwave reflectors are described. In particular, a method of assessment of reflecting materials such as wire meshes and carbon fibres that have the potential to generate IMP signals across large areas is given. Identification and location of the apparent IMP sources are provided.
DiPALS: Diaphragm Pacing in patients with Amyotrophic Lateral Sclerosis – a randomised controlled trial (2016)

This project was funded by the National Institute for Health Research Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 20, No. 45. See the HTA programme website for further project information. Additional funding was provided by the Motor Neurone Disease Association of England, Wales and Northern Ireland.
Fabrication and surface chemistry of nanoscale bioarrays designed for the study of cytoskeletal protein binding interactions and their effect on cell motility (2005)

We have designed a system engineered to mimic biological spatial order. The system consists of nanoscale dots organized into hierarchical arrays in which structural parameters, such as spacing and orientation, are systematically varied. These arrays are used to probe the spatial distributions of binding sites in biomolecules. In this paper, we describe the fabrication process, including lithography and biofunctionalization, and we discuss issues related to surface chemistry that are critical to creating robust, biologically active nanoarrays.
Withaferin A Regulates LRRK2 Levels by Interfering with the Hsp90- Cdc37 Chaperone Complex (2015)

Leucine-Rich Repeat Kinase 2 (LRRK2) is a large, multi-domain protein that has been found to be mutated in patients with familial and sporadic Parkinson's disease, Alzheimer's disease and Crohn's disease. While the functions of LRRK2 are still largely unclear and mutations in LRRK2 are associated with adverse gain-of-function activities such as increased kinase activity, increased levels of LRRK2 alone are associated with toxicity in neurons. Consequently, exploring mechanisms to decrease levels of LRRK2 using pharmacological inhibitors would be highly advantageous. Previous work has shown that the chaperone heat shock protein 90 (Hsp90) and its co-chaperone Cdc37 interact with and stabilize LRRK2. In the current study, we explore the regulation of LRRK2 by withaferin A (WA), a potent inhibitor of the interaction between Hsp90 and Cdc37. We report that treatment of the microglial cell line N9 with WA causes a decrease in cellular levels of LRRK2 in a dose- and time-dependent manner. We also find that treatment with WA disrupts the interaction between Hsp90, its co-chaperone Cdc37 and LRRK2, which leads to the destabilization and decreased levels of LRRK2. Additionally, treatment with celastrol, which is also an inhibitor of the Hsp90-Cdc37 complex, decreased LRRK2 levels. Interestingly, treatment with WA in the presence of celastrol enhanced the clearance of LRRK2. Overall, our data suggest that LRRK2 levels can be regulated by targeting the Hsp90-Cdc37 complex, which may have implications in the search for therapeutic strategies for Alzheimer's disease, Parkinson's disease and other LRRK2 proteinopathies.
Stimulation of glioma-cell migration by laminin and inhibition by anti-α3 and anti-β1 integrin antibodies (1996)

An induction of laminin in the confrontation zone between tumor cells and normal brain tissue has been observed in our model systems in vivo and in vitro. In order to study the effects of ECM components on glioma-cell migration and invasion, we have used 2 lacZ-transfected glioma cell lines, AN1/lacZ and U-251 /lacZ. Cell migration from multicellular spheroids was studied using different types of media: DMEM with 10% serum, Ultra Culture medium, and filtrated DMEM with serum in which the protein fraction > 100 kDa had been removed by ultrafiltration. Laminin, fibronectin and collagen type-IV were individually added to the different media, and cell migration from the spheroids was studied. The results show that cell migration in both cell lines, was stimulated by laminin and fibronectin. Collagen type-IV stimulated only cell migration of U-251/lacZ cells. Scanning electron microscopy revealed an extensive change in cell shape as a result of laminin stimulation. Flowcytometric studies showed that both AN1/lacZ and U-251/lacZ strongly express the alpha3 beta1 integrin receptor, which can bind to several ECM components (laminin, fibronectin, collagen). Immunofluorescence microscopy demonstrated that the same integrin sub-units were expressed in multicellular spheroids. When monoclonal antibodies to alpha3 and beta1 were added to the laminin-stimulated cultures, cell migration was significantly reduced. This indicates that the alpha3 beta1 integrin receptor plays an important role during glioma-cell migration.
COVID-19 y Embarazo (2020)

Una infección por el virus SARS-CoV-2 ha afectado a una gran parte de la población mundial desde el mes de diciembre del 2019. Las manifestaciones clínicas en pacientes embarazadas con COVID-19 son parecidas a la población general. El gold standard en el diagnóstico de esta enfermedad es la reacción en cadena de la polimerasa con transcriptasa reversa en tiempo real (RT-PCR). Se recomiendan imágenes diagnósticas de tórax como radiografías y TACs para la evaluación completa en pacientes embarazadas sospechosas de COVID-19.El manejo de la paciente embarazada con COVID-19 se basa en la estratificación y el cuidado de soporte, con toma de decisiones en equipos multidisciplinarios. El tratamiento todavía es experimental y parece no haber contraindicación para el parto vaginal. El ministerio de salud de Costa Rica ha emitido algunos lineamientos sobre COVID-19 que conciernen a la mujer embarazada y la lactancia materna.
Co-ordination in Disaster Recovery Management:The Roles of CSV and Municipalities (1992)

Community Services Victoria (CSV) is identified as the principal recovery agency. It has a role in facilitating and coordinating the range of disaster recovery activities undertaken by other agencies and municipalities. The CSV has to address the key areas of planning, coordination arrangements, service delivery and resource availability, within each municipality to manage an effective disaster recovery plan.
In Silico Prediction of Compounds Binding to Human Plasma Proteins by QSAR Models (2017)

Plasma protein binding (PPB) is a significant pharmacokinetic property of compounds in drug discovery and design. Due to the high cost and time-consuming nature of experimental assays, in silico approaches have been developed to assess the binding profiles of chemicals. However, because of unambiguity and the lack of uniform experimental data, most available predictive models are far from satisfactory. In this study, an elaborately curated training set containing 967 diverse pharmaceuticals with plasma-protein-bound fractions (f<sub>b</sub> ) was used to construct quantitative structure-activity relationship (QSAR) models by six machine learning algorithms with 26 molecular descriptors. Furthermore, we combined all of the individual learners to yield consensus prediction, marginally improving the accuracy of the consensus model. The model performance was estimated by tenfold cross validation and three external validation sets comprising 242 pharmaceutical, 397 industrial, and 231 newly designed chemicals, respectively. The models showed excellent performance for the entire test set, with mean absolute error (MAE) ranging from 0.126 to 0.178, demonstrating that our models could be used by a chemist when drawing a molecular structure from scratch. Meanwhile, structural descriptors contributing significantly to the predictive power of the models were related to the binding mechanisms, and the trend in terms of their effects on PPB can serve as guidance for the structural modification of chemicals. The applicability domain was also defined to distinguish favorable predictions from unfavorable predictions.
Yes, we GAN: Applying adversarial techniques for autonomous driving (2019)

Generative Adversarial Networks (GAN) have gained a lot of popularity from their introduction in 2014 till present. Research on GAN is rapidly growing and there are many variants of the original GAN focusing on various aspects of deep learning. GAN are perceived as the most impactful direction of machine learning in the last decade. This paper focuses on the application of GAN in autonomous driving including topics such as advanced data augmentation, loss function learning, semi-supervised learning, etc. We formalize and review key applications of adversarial techniques and discuss challenges and open problems to be addressed.
Measurements of Soil Carbon by Neutron-Gamma Analysis in Static and Scanning Modes (2017)

The herein described application of the inelastic neutron scattering (INS) method for soil carbon analysis is based on the registration and analysis of gamma rays created when neutrons interact with soil elements. The main parts of the INS system are a pulsed neutron generator, NaI(Tl) gamma detectors, split electronics to separate gamma spectra due to INS and thermo-neutron capture (TNC) processes, and software for gamma spectra acquisition and data processing. This method has several advantages over other methods in that it is a non-destructive in situ method that measures the average carbon content in large soil volumes, is negligibly impacted by local sharp changes in soil carbon, and can be used in stationary or scanning modes. The result of the INS method is the carbon content from a site with a footprint of ~2.5 - 3 m<sup>2</sup> in the stationary regime, or the average carbon content of the traversed area in the scanning regime. The measurement range of the current INS system is >1.5 carbon weight % (standard deviation ± 0.3 w%) in the upper 10 cm soil layer for a 1 hmeasurement.
Imaging of high‐intensity focused ultrasound‐induced lesions in soft biological tissue using thermoacoustic tomography (2004)

An imaging technology, thermoacoustic tomograpy (TAT), was applied to the visualization of high-intensity focused ultrasound (HIFU)-induced lesions. A single, spherically focused ultrasonic transducer, operating at a central frequency of approximately 4 MHz, was used to generate a HIFU field in fresh porcine muscle. Microwave pulses from a 3-GHz microwave generator were then employed to generate thermoacoustic sources in this tissue sample. The thermoacoustic signals were detected by an unfocused ultrasonic transducer that was scanned around the sample. To emphasize the boundaries between the lesion and its surrounding tissue, a local-tomography-type reconstruction method was applied to reconstruct the TAT images of the lesions. Good contrast was obtained between the lesion and the tissue surrounding it. Gross pathologic photographs of the tissue samples confirmed the TAT images. This work demonstrates that TAT may potentially be used to image HIFU-induced lesions in biological tissues.
Formation of voids in a doped polymethylmethacrylate polymer (2002)

We report on the formation of submicrometer voids within a doped polymethylmethacrylate (PMMA) polymer under multiphoton absorption excited by an infrared laser beam. An ultrashort pulsed laser beam of pulse width 80 fs at a repetition rate of 82 MHz and a wavelength of 800 nm is focused into a PMMA-based photorefractive polymer consisting of 2,5-dimethyl-4(p-nitrophenylazo)anisole, 2,4,7-trinitro-9-fluorenone, and N-ethylcarbazole. The large change in refractive index associated with a void allows confocal reflection microscopy to be used as a detection method. Voids can be arranged in a multilayered structure for read-only high-density optical data storage.
Monitoring Dopamine Release from Single Living Vesicles with Nanoelectrodes (2005)

Carbon fiber nanoelectrodes (tip diameter = ca. 100 nm) have been first used to monitor real-time dopamine release from single living vesicles of single rat pheochromocytoma (PC12) cells. The experiments show that active and inactive release sites exist on the surface of cells, and the spatial distributions have been differentiated even in the same active release zone. It is first demonstrated that multiple vesicles can sequentially release dopamine at the same site of the cell surface, which possibly plays the main role in the dopamine release from PC12 cells.
Low-power CMOS digital design with dual embedded adaptive power supplies (2000)

A low-power CMOS design methodology with dual embedded adaptive power supplies is presented. A variable supply-voltage scheme for dual power supplies, namely, the dual-VS scheme, is presented. It is found that the lower supply voltage should be set at 0.7 of the higher supply voltage to minimize chip power dissipation. This knowledge aids designers in the decision of the optimal supply voltages within a restricted design time. An MEPG-4 video codec chip is designed at 2.5 and 1.75 V for internal circuits that are generated from an external power supply of 3.3 V by the dual-VS circuits. Power dissipation is reduced by 57% without degrading circuit performance compared to a conventional CMOS design.
Protox-resistant common waterhemp (<i>Amaranthus rudis</i>) response to herbicides applied at different growth stages (2006)

Greenhouse and field studies were conducted with a population of common waterhemp resistant to POST protoporphyrinogen oxidase (protox)-inhibiting herbicides to compare its response to PRE and POST applications of selected herbicides. In the greenhouse, a dose–response study of PRE applications of acifluorfen, fomesafen, or lactofen was conducted on protox-susceptible and -resistant common waterhemp. The protox-resistant biotype was approximately 6.3, 2.5, and 2.6 times more resistant than the susceptible biotype to acifluorfen, fomesafen, and lactofen, respectively. In a separate study under field conditions, protox-resistant common waterhemp were treated with PRE and POST applications of acifluorfen, azafenidin, flumioxazin, fomesafen, lactofen, oxyfluorfen, or sulfentrazone. At 14 and 28 d after POST treatment (DAPT) in 2002 and 2004, all PRE applications of herbicides gave greater control than did POST applications. At 14 DAPT, oxyfluorfen had the greatest difference in PRE and POST control, with 85 and 10% control in 2002, respectively. An additional field study was conducted to determine the stage of growth at which resistance to protox-inhibiting herbicides becomes most prevalent. Protox-resistant common waterhemp were treated with herbicides at the 2-leaf, 4- to 6-leaf, and 8- to 10-leaf growth stage. Acifluorfen and fomesafen at 420 g ha −1 gave greater than 90% control at the 2-leaf stage and 4- to 6-leaf stage, except in 2003 when control was 85% with acifluorfen. In 2003 and 2004, common waterhemp control at the 8- to 10-leaf stage ranged between 54 and 75% with acifluorfen or fomesafen. Results indicate that common waterhemp resistance to customary rates of POST protox-inhibiting herbicides becomes prevalent after the 4- to 6-leaf growth stage.