gebhart/patrepeval huggingface dataset:
Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast (2022)

Abstract Here we report the design, construction and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae . Intending to address one of the central design principles of the Sc2.0 project, the ∼190 kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporated orthogonal genetic elements from non- S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up new opportunities to directly test hypotheses surrounding these essential non-coding RNAs. Highlights De novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae . Increasing the copy number of the 275 highly expressed tRNA genes causes cellular burden, which the host cell likely buffers either by selecting for partial tRNA neochromosome deletions or by increasing its ploidy. The tRNA neochromosome can be chemically extracted and transformed into new strain backgrounds, enabling its transplantation into multi-synthetic chromosome strains to finalize the Sc2.0 strain. Comprehensive functional characterization does not pinpoint a singular cause for the cellular burden caused by the tRNA neochromosome, but does reveal novel insights into its tRNA and structural chromosome biology.
Static and Dynamical Phyllotaxis in a Magnetic Cactus (2009)

While the statics of many simple physical systems reproduce the striking number-theoretical patterns found in the phyllotaxis of living beings, their dynamics reveal unusual excitations: multiple classical rotons and a large family of interconverting topological solitons. As we introduce those, we also demonstrate experimentally for the first time Levitov's celebrated model for phyllotaxis. Applications at different scales and in different areas of physics are proposed and discussed.
Linear phase demodulation using an integrated coherent receiver with an ultra-compact grating beam splitter (2009)

In this paper, for the first time, we demonstrate the closed-loop operation of an integrated coherent receiver with the grating-based beam splitter. The drive voltage to the modulator pair is obtained through the integration of the detector current across the capacitance of the detector and the modulator, and hence, the level of this drive voltage is proportional to the detected photocurrent level. When the photocurrent is sufficiently high to provide adequate loop gain, the integrated receiver can closely track signal phase. Consequently, the demodulated signal is very linear.
Digital Dynamic 3D Monitoring of Lower Incisors Intrusion in Lingual Orthodontics (2018)

This method has proved to be an accurate and reliable approach to dynamically visualize the 3-dimensional positions of the teeth, including their roots, with no additional radiation for in-progress treatment monitoring. The 3-dimensional evaluation showed that the employed lingual appliance allowed to obtain significant lower incisors intrusion with negligible undesired extrusion of premolars employed as anchorage teeth.
Synthesis of 2(3H)-Benzoxazolone Derivatives as Potential Melatonin Receptor Ligands (2003)

International audience
α-Oxyiminophosphonates: chemical and physical properties. Reactions, theoretical calculations, and X-ray crystal structures of (E) and (Z)-dimethyl α-hydroxyiminobenzylphosphonates (1988)

Dialkyl α-oxyiminoalkylphosphonates, obtained by treatment of dialkyl acylphosphonates with hydroxylamine or methoxylamine, are mostly mixtures of E and Z isomers. Structural assignments of the oximes were based on X-ray crystallographic analysis of representative compounds: (E)- and (Z)-dimethyl α-hydroxyiminobenzylphosphonates [(E)- and (Z)-(1a)]. The 31P n.m.r. chemical shifts of the E isomers always appear at lower field than those of the corresponding Z isomers. Thermal fragmentation of (1a) affords benzonitrile and dimethyl hydrogen phosphate, with (Z)-(1a) reacting faster than the E isomer. α-Oxyiminophosphonates undergo E⇌Z isomerization catalysed either by acid or by base under certain conditions, the E isomer being the thermodynamically more stable one. An E+Z mixture of dialkyl α-oxyiminophosphonates can be mono-de-alkylated by non-basic nucleophiles (e.g. NaI) to afford monoalkyl oxyiminophosphonates of unchanged isomeric composition. The geometrical isomers of α-hydroxyiminophosphonates differ in their behaviour under basic conditions. While treatment of (E)-(1a) with NaOH in boiling methanol leads, by mono-de-alkylation, to sodium methyl α-hydroxyiminobenzylphosphonate [(E)-(2a)], under the same conditions (Z)-(1a) undergoes fragmentation, by C–P bond cleavage, to benzonitrile and dimethyl hydrogen phosphate. Control experiments established that the fragmentation of (Z)-α-hydroxyiminophosphonates involves an intramolecular attack on the phosphorus atom by the ionized Z oriented oxime oxygen. Similar differences in behaviour are noted between the isomers of the monoanions of α-hydroxyiminophosphonates. MNDO/H Calculations demonstrate the feasibility of forming internal hydrogen bonds in Z isomers, and their possible contribution to conformational preferences. Single-crystal X-ray diffraction studies of (E)- and (Z)-(1a), and (E)-(2b), clearly identified the geometric isomers and correlated them with the 1H and 31P n.m.r. resonances.
Performance analysis for computer-aided lung nodule detection on LIDC data (2007)

For more than one decade computer aided detection (CAD) for pulmonary nodules has been an active research area. There are numerous publications dedicated to this topic. Most authors have created their own database with their own ground truth for validation. This makes it hard to compare the performance of different systems with each other. It is a known fact that the performance of a CAD system can differ significantly depending on which data it is tested and on the underlying ground truth. The lung image data base consortium (LIDC) has recently released 93 publicly available lung images with ground truth lists from 4 different radiologists. This data base will make it possible to compare the performance of different CAD algorithms. In this paper we do the first step to use the LIDC data as a benchmark test. We present a CAD algorithm with a validation study on these data sets. The CAD performance was analyzed by virtue of multiple Free Response Receiver Operator Characteristic (FROC) curves for different lower thresholds of the nodule diameter. There are different ways to merge the ground truth lists of the 4 radiologists and we discuss the performance of our CAD algorithm for several of these possibilities. For nodules with a volume-equivalent diameter &#8805;4mm which have been simultaneously confirmed by all four radiologists our CAD system shows a detection rate of 89 % at a median false positive rate of 2 findings per patient.
PINK1 Is a Negative Regulator of Growth and the Warburg Effect in Glioblastoma (2016)

Proliferating cancer cells are characterized by high rates of glycolysis, lactate production, and altered mitochondrial metabolism. This metabolic reprogramming provides important metabolites for proliferation of tumor cells, including glioblastoma. These biological processes, however, generate oxidative stress that must be balanced through detoxification of reactive oxygen species (ROS). Using an unbiased retroviral loss-of-function screen in nontransformed human astrocytes, we demonstrate that mitochondrial PTEN-induced kinase 1 (PINK1) is a regulator of the Warburg effect and negative regulator of glioblastoma growth. We report that loss of PINK1 contributes to the Warburg effect through ROS-dependent stabilization of hypoxia-inducible factor-1A and reduced pyruvate kinase muscle isozyme 2 activity, both key regulators of aerobic glycolysis. Mechanistically, PINK1 suppresses ROS and tumor growth through FOXO3a, a master regulator of oxidative stress and superoxide dismutase 2. These findings highlight the importance of PINK1 and ROS balance in normal and tumor cells. PINK1 loss was observed in a significant number of human brain tumors including glioblastoma (n > 900) and correlated with poor patient survival. PINK1 overexpression attenuates in vivo glioblastoma growth in orthotopic mouse xenograft models and a transgenic glioblastoma model in Drosophila Cancer Res; 76(16); 4708-19. ©2016 AACR.
Isotopic decay of urinary or plasma 3‐methylhistidine as a potential biomarker of pathologic skeletal muscle loss (2013)

The findings from this study suggest that an index of 3MH production can be obtained from an easily administered test involving oral administration of a stable isotope tracer of 3MH followed by three plasma or urine samples collected over 5-6 h the next day.
A “Slide Rule” to Adjust Insulin Dose Using Trend Arrows in Adults with Type 1 Diabetes: Test in Silico and in Real Life (2021)

The proposed slide rule performed well both in silico and in real life, suggesting that it could be safely adopted by individuals with T1D to improve glucose control.
Synthesis and Characterization of Se35Te65−xGex Nanoparticle Films and Their Optical Properties (2012)

Thin films of Se 35 Te 65− x Ge x ( x = 0, 3, 6, 9, 12) nanoparticles were synthesized using thermal evaporation method. They were characterized by X‐ray diffraction (XRD), scanning electron microscope (SEM), and absorption and transmission spectra. XRD results show that these films are of amorphous nature, while SEM images show nanoparticles with average particle size around 30 nm. No significant changes are observed in morphology of the deposited films by changing concentrations of Te and Ge. The optical behaviors of these films have been studied using the absorption and transmission spectra in the spectral region 400–1100 nm. The absorption, extinction coefficients and refractive index were obtained and investigated in more detail. The optical band gap ( E g ) values were also determined and are found to decrease from 0.83 to 0.69 eV by increasing the concentration of Ge from 0 to 12. The transmission spectra for the thin films of Se 35 Te 65− x Ge x nanoparticles show strong absorption at wavelength less than 500 nm and become highly transparent at wavelength above 800 nm. No significant changes in the transmission spectra are observed by increasing concentration of Ge. These results might be useful for development of optical disks and other semiconducting devices based on these nanochalcogenides.
Interferometric SOA-based cascaded wavelength conversion (2002)

SOA-based wavelength conversion is obtained in an interferometric device exploiting two synchronous cascaded conversion processes in a SLALOM followed by a nonlinear filter. An accurate analysis and experimental eye-diagrams demonstrate significant signal quality improvement.
Global Coordinate Method for Determining Sensitivity in Assembly Tolerance Analysis (1998)

Abstract Tolerance sensitivity indicates the influence of individual component tolerances in an assembly on the variation of a critical assembly feature or dimension. Important applications include assembly tolerance analysis and tolerance allocation. This paper presents a new method for determining tolerance sensitivity using vector loop assembly tolerance models. With a vector loop model, the assembly kinematic constraints or assembly functions can be established automatically as implicit functions. This method evaluates the derivatives of the kinematic constraint equations with respect to both manufactured dimensions and assembly variables. The derivative matrices are then used to calculate the tolerance sensitivity matrix. This is a closed form method which relates the derivatives of the assembly functions to the coordinates of the joints or nodes and the orientations of the vectors and the local joint axes in an assembly. It is accurate, simple and very suitable for design iterations.
Enabling tools for engineering collagenous tissues integrating bioreactors, intravital imaging, and biomechanical modeling (2009)

Many investigators have engineered diverse connective tissues having good mechanical properties, yet few tools enable a global understanding of the associated formation of collagen fibers, the primary determinant of connective tissue stiffness. Toward this end, we developed a biomechanical model for collagenous tissues grown on polymer scaffolds that accounts for the kinetics of polymer degradation as well as the synthesis and degradation of multiple families of collagen fibers in response to cyclic strains imparted in a bioreactor. The model predicted well both overall thickness and stress-stretch relationships for tubular engineered vessels cultured for 8 weeks, and suggested that a steady state had not yet been reached. To facilitate future refinements of the model, we also developed bioreactors that enable intravital nonlinear optical microscopic imaging. Using these tools, we found that collagen fiber alignment was driven strongly by nondegraded polymer fibers at early times during culture, with subsequent mechano-stimulated dispersal of fiber orientations as polymer fibers degraded. In summary, mathematical models of growth and remodeling of engineered tissues cultured on polymeric scaffolds can predict evolving tissue morphology and mechanics after long periods of culture, and related empirical observations promise to further our understanding of collagen matrix development in vitro.
ChemInform Abstract: Macrocyclic Hexapeptide Analogues of the Thrombin Receptor (PAR‐1) Activation Motif SFLLRN. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 3 from αvβ6 Integrin Promotes Castrate-Resistant Prostate Cancer through JNK1-Mediated Activation of Androgen Receptor (2023)

&lt;p&gt;alphavbeta6 integrin, but not alphavbeta3 integrin, promotes tumor growth.&lt;/p&gt;
Effect of temperature on the development and voltinism of the rice stem borer, Chilo suppressalis (Lepidoptera: Pyralidae) in Taiwan (2013)

The effect of temperature on development of populations of the rice stem borer from Hsilo (23.8°N), Tounan (23.7°N) and Pingtong (22.7°N), Taiwan, was investigated. The development rates of these populations increased with increasing temperature from 20 to 30°C. The mean developmental periods of eggs, larvae, and male and female pupae in the Hsilo population were 7.7, 33.0, 7.6 and 7.1 days at 25°C under 14L : 10D photoperiod and the theoretical threshold temperatures for development were 8.9, 9.2, 10.4 and 10.5°C, respectively. Effective temperature sums for development were 124, 521, 111 and 103 day-degrees, respectively. These results suggest in Hsilo population that 4 or 5 generations occur annually in central and southern Taiwan. In the Tounan and Pingtong populations, which require lower effective temperature sums for larval development than the Hsilo population, 5 or 6 generations may occur in a year.
Ancestral differences in the distribution of the Δ2642 glutamic acid polymorphism is associated with varying CAG repeat lengths on normal chromosomes: insights into the genetic evolution of Huntington disease (1995)

This study addresses genetic factors associated with normal variation of the CAG repeat in the Huntington disease (HD) gene. To achieve this, we have studied patterns of variation of three trinucleotide repeats in the HD gene including the CAG and adjacent CCG repeats as well as a GAG polymorphism at residue 2642 (delta 2642). We have previously demonstrated that variation in the CCG repeat is associated with variation of the CAG repeat length on normal chromosomes. Here we show that differences in the GAG trinucleotide polymorphism at residue 2642 is also significantly correlated with CAG size on normal chromosomes. The B allele which is associated with higher CAG repeat lengths on normal chromosomes is markedly enriched on affected chromosomes. Furthermore, this glutamic acid polymorphism shows significant variation in different ancestries and is absent in chromosomes of Japanese, Black and Chinese descent. Haplotype analysis of both the CCG and delta 2642 polymorphisms have indicated that both are independently associated with differences in CAG length on normal chromosomes. These findings lead to a model for the genetic evolution of new mutations for HD preferentially occurring on normal chromosomes with higher CAG repeat lengths and a CCG repeat length of seven and/or a deletion of the glutamic acid residue at delta 2642. This study also provides additional evidence for genetic contributions to demographic differences in prevalence rates for HD.
Metathesis of acetylenes by tungsten(VI)-alkylidyne complexes (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetathesis of acetylenes by tungsten(VI)-alkylidyne complexesJeffrey H. Wengrovius, Jose Sancho, and Richard R. SchrockCite this: J. Am. Chem. Soc. 1981, 103, 13, 3932–3934Publication Date (Print):July 1, 1981Publication History Published online1 May 2002Published inissue 1 July 1981https://pubs.acs.org/doi/10.1021/ja00403a058https://doi.org/10.1021/ja00403a058research-articleACS PublicationsRequest reuse permissionsArticle Views2111Altmetric-Citations244LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Backbone-Anchoring, Solid-Phase Synthesis Strategy To Access a Library of Peptidouridine-Containing Small Molecules (2022)

Nucleoside diphosphate sugar (NDP-sugar) substrates provide the inspiration for nucleoside analogue inhibitor scaffolds. By employing solid-phase synthesis, we provide a method to access a library of peptidouridine inhibitors with both minimal compound handling and purification steps. Specifically, this strategy is exemplified by generating uridine diphosphate sugar (UDP-sugar) mimics, which allow for compound elaboration by altering the dipeptide composition, the N-terminal linkage, and a pendant aryl group. To exemplify the versatility, 41 unique nucleoside analogues are presented.
Artificial Neural Networks Applied to Survival Prediction in Breast Cancer (1999)

In this study, we evaluated the accuracy of a neural network in predicting 5-, 10- and 15-year breast-cancer-specific survival. A series of 951 breast cancer patients was divided into a training set of 651 and a validation set of 300 patients. Eight variables were entered as input to the network: tumor size, axillary nodal status, histological type, mitotic count, nuclear pleomorphism, tubule formation, tumor necrosis and age. The area under the ROC curve (AUC) was used as a measure of accuracy of the prediction models in generating survival estimates for the patients in the independent validation set. The AUC values of the neural network models for 5-, 10- and 15-year breast-cancer-specific survival were 0.909, 0.886 and 0.883, respectively. The corresponding AUC values for logistic regression were 0.897, 0.862 and 0.858. Axillary lymph node status (N0 vs. N+) predicted 5-year survival with a specificity of 71% and a sensitivity of 77%. The sensitivity of the neural network model was 91% at this specificity level. The rate of false predictions at 5 years was 82/300 for nodal status and 40/300 for the neural network. When nodal status was excluded from the neural network model, the rate of false predictions increased only to 49/300 (AUC 0. 877). An artificial neural network is very accurate in the 5-, 10- and 15-year breast-cancer-specific survival prediction. The consistently high accuracy over time and the good predictive performance of a network trained without information on nodal status demonstrate that neural networks can be important tools for cancer survival prediction.
Mid-infrared high-Q germanium microring resonator (2018)

Germanium is a promising material for mid-infrared (MIR) integrated photonics due to its CMOS compatibility and wide transparency window covering the fingerprint spectral region (2-15 μm). However, due to the limited quality and structural configurations of conventional germanium-based integration platforms, the realization of high-Q on-chip germanium resonators in the MIR spectral range remains challenging to date. Here we experimentally demonstrate an air-cladding MIR germanium microring resonator with, to the best of our knowledge, the highest loaded Q-factor of ∼57,000 across all germanium-based integration platforms to date. A propagation loss of 5.4 dB/cm and a high extinction ratio of 22 dB approaching the critical coupling condition are experimentally realized. These are enabled by our smart-cut methods for developing high-quality germanium-on-insulator wafers and by implementing our suspended-membrane structure. Our high-Q germanium microring resonator is a promising step towards a number of on-chip applications in the MIR spectral range.
High-resolution,in vivoretinal imaging using adaptive optics and its future role in ophthalmology (2005)

Until recently it was impossible to fully realize the optical resolution afforded by the human eye due to the inherent optical aberrations. These aberrations limit the ability to see fine structure in the retinal layers and visual perception of the outside world. A conventional spectacle or contact lens refraction only provides a static amelioration of the lowest order aberrations, namely defocus and astigmatism. In addition, all of these distortions are constantly evolving due to changes in accommodation and head/eye movements. The technique of adaptive optics not only corrects all of the static spatial modes but also measures and corrects any dynamic changes. Such systems have allowed for routine in vivo cellular imaging, the classification of individual photoreceptor cells and have enabled psychophysical testing of human visual function at the neural level. This review introduces the principle of adaptive optics and the key hardware required to implement such a scheme. The integration of adaptive optics into different imaging modalities is presented along with descriptions of current systems in use today and the experimental results obtained to date. Finally, the review concludes by discussing future technology and gives the author's prediction of how the field will evolve over the coming years.