gebhart/patrepeval huggingface dataset:
Two Ginseng UDP-Glycosyltransferases Synthesize Ginsenoside Rg3 and Rd (2014)

Ginseng is a medicinal herb that requires cultivation under shade conditions, typically for 4-6 years, before harvesting. The principal components of ginseng are ginsenosides, glycosylated tetracyclic terpenes. Dammarene-type ginsenosides are classified into two groups, protopanaxadiol (PPD) and protopanaxatriol (PPT), based on their hydroxylation patterns, and further diverge to diverse ginsenosides through differential glycosylation. Three early enzymes, dammarenediol-II synthase (DS) and two P450 enzymes, protopanaxadiol synthase (PPDS) and protopanaxatriol synthase (PPTS), have been reported, but glycosyltransferases that are necessary to synthesize specific ginsenosides have not yet been fully identified. To discover glycosyltransferases responsible for ginsenoside biosynthesis, we sequenced and assembled the ginseng transcriptome de novo and characterized two UDP-glycosyltransferases (PgUGTs): PgUGT74AE2 and PgUGT94Q2. PgUGT74AE2 transfers a glucose moiety from UDP-glucose (UDP-Glc) to the C3 hydroxyl groups of PPD and compound K to form Rh2 and F2, respectively, whereas PgUGT94Q2 transfers a glucose moiety from UDP-Glc to Rh2 and F2 to form Rg3 and Rd, respectively. Introduction of the two UGT genes into yeast together with PgDS and PgPPDS resulted in the de novo production of Rg3. Our results indicate that these two UGTs are key enzymes for the synthesis of ginsenosides and provide a method for producing specific ginsenosides through yeast fermentation.
Abnormal Proteins in the Cerebrospinal Fluid of Patients with Creutzfeldt–Jakob Disease (1986)

We studied more than 300 cerebrospinal fluid proteins from 21 patients with Creutzfeldt-Jakob disease. We also examined cerebrospinal fluid from 100 normal controls and more than 400 patients with various neurologic disorders other than Creutzfeldt-Jakob disease. Four abnormal proteins that were identified in the patients with Creutzfeldt-Jakob disease were absent in the normal persons. Two of these proteins (Mr [relative molecular mass], 40,000; pl [isoelectric point], 5.7 and Mr 40,000; pl 5.9) were also present in some patients with multiple sclerosis, herpes simplex encephalitis, schizophrenia, Parkinson's disease, or Guillain-Barré or Behçet's syndrome. Two proteins (Mr 26,000; pl 5.2 and Mr 29,000; pl 5.1) were present in all patients with Creutzfeldt-Jakob disease and in 5 of 10 patients with herpes simplex encephalitis, but in none of the other control groups. A subsequent blinded study of these cerebrospinal fluid proteins from patients with Creutzfeldt-Jakob disease, Alzheimer's disease, Huntington's disease, multi-infarct dementia, parkinsonism dementia of Guam, or the specific dementia of the acquired immunodeficiency syndrome resulted in the ability to distinguish all cases of Creutzfeldt-Jakob disease from the other types of dementia. Although the identity and origin of the abnormal spinal fluid proteins are not yet known, these preliminary results suggest that their presence may help in the diagnosis of Creutzfeldt-Jakob disease.
Runtime Semantic Query Optimization for Event Stream Processing (2008)

Detecting complex patterns in event streams, i.e., complex event processing (CEP), has become increasingly important for modern enterprises to react quickly to critical situations. In many practical cases business events are generated based on pre-defined business logics. Hence constraints, such as occurrence and order constraints, often hold among events. Reasoning using these known constraints enables us to predict the non-occurrences of certain future events, thereby helping us to identify and then terminate the long running query processes that are guaranteed to not lead to successful matches. In this work, we focus on exploiting event constraints to optimize CEP over large volumes of business transaction streams. Since the optimization opportunities arise at runtime, we develop a runtime query unsatisfiability (RunSAT) checking technique that detects optimal points for terminating query evaluation. To assure efficiency of RunSAT checking, we propose mechanisms to precompute the query failure conditions to be checked at runtime. This guarantees a constant-time RunSAT reasoning cost, making our technique highly scalable. We realize our optimal query termination strategies by augmenting the query with Event-Condition-Action rules encoding the pre-computed failure conditions. This results in an event processing solution compatible with state-of-the-art CEP architectures. Extensive experimental results demonstrate that significant performance gains are achieved, while the optimization overhead is small.
Data from CMVpp65 Vaccine Enhances the Antitumor Efficacy of Adoptively Transferred CD19-Redirected CMV-Specific T Cells (2023)

<div>Abstract<p><b>Purpose:</b> T cells engineered with chimeric antigen receptors (CAR) recognizing CD19 can induce complete remission of B-cell malignancies in clinical trials; however, in some disease settings, CAR therapy confers only modest clinical benefit due to attenuated persistence of CAR T cells. The purpose of this study was to enhance persistence and augment the antitumor activity of adoptively transferred CD19CAR T cells by restimulating CAR<sup>+</sup> T cells through an endogenous cytomegalovirus (CMV)-specific T-cell receptor.</p><p><b>Experimental Design:</b> CMV-specific T cells from CMV seropositive healthy donors were selected after stimulation with pp65 protein and transduced with clinical-grade lentivirus expressing the CD19R:CD28:ζ/EGFRt CAR. The resultant bispecific T cells, targeting CMV and CD19, were expanded via CD19 CAR-mediated signals using CD19-expressing cells.</p><p><b>Results:</b> The bispecific T cells proliferated vigorously after engagement with either endogenous CMVpp65 T-cell receptors or engineered CD19 CARs, exhibiting specific cytolytic activity and IFNγ secretion. Upon adoptive transfer into immunodeficient mice bearing human lymphomas, the bispecific T cells exhibited proliferative response and enhanced antitumor activity following CMVpp65 peptide vaccine administration.</p><p><b>Conclusions:</b> We have redirected CMV-specific T cells to recognize and lyse tumor cells via CD19CARs, while maintaining their ability to proliferate in response to CMV antigen stimulation. These results illustrate the clinical applications of CMV vaccine to augment the antitumor activity of adoptively transferred CD19CAR T cells in patients with B-cell malignancies. <i>Clin Cancer Res; 21(13); 2993–3002. ©2015 AACR</i>.</p></div>
IMRT Treatment Planning on 4D Geometries for the Era of Dynamic MLC Tracking (2013)

The problem addressed here was to obtain optimal and deliverable dynamic multileaf collimator (MLC) leaf sequences from four-dimensional (4D) geometries for dynamic MLC tracking delivery. The envisaged scenario was where respiratory phase and position information of the target was available during treatment, from which the optimal treatment plan could be further adapted in real time. A tool for 4D treatment plan optimization was developed that integrates a commercially available treatment planning system and a general-purpose optimization system. The 4D planning method was applied to the 4D computed tomography planning scans of three lung cancer patients. The optimization variables were MLC leaf positions as a function of monitor units and respiratory phase. The objective function was the deformable dose-summed 4D treatment plan score. MLC leaf motion was constrained by the maximum leaf velocity between control points in terms of monitor units for tumor motion parallel to the leaf travel direction and between phases for tumor motion parallel to the leaf travel direction. For comparison and a starting point for the 4D optimization, three-dimensional (3D) optimization was performed on each of the phases. The output of the 4D IMRT planning process is a leaf sequence which is a function of both monitor unit and phase, which can be delivered to a patient whose breathing may vary between the imaging and treatment sessions. The 4D treatment plan score improved during 4D optimization by 34%, 4%, and 50% for Patients A, B, and C, respectively, indicating 4D optimization generated a better 4D treatment plan than the deformable sum of individually optimized phase plans. The dose-volume histograms for each phase remained similar, indicating robustness of the 4D treatment plan to respiratory variations expected during treatment delivery. In summary, 4D optimization for respiratory phase-dependent treatment planning with dynamic MLC motion tracking improved the 4D treatment plan score by 4-50% compared with 3D optimization. The 4D treatment plans had leaf sequences that varied from phase to phase to account for anatomic motion, but showed similar target dose distributions in each phase. The current method could in principle be generalized for use in offline replanning between fractions or for online 4D treatment planning based on 4D cone-beam CT images. Computation time remains a challenge.
Precision X-Band Linac Technologies for Nuclear Photonics Gamma-Ray Sources (2014)

Abstract Not Provided
The MIRA Method for DNA Methylation Analysis (2008)

DNA methylation patterns are often altered in human cancer and aberrant methylation is considered a hallmark of malignant transformation. Several methods have been developed for the characterization of gene-specific and genome-wide DNA methylation patterns. In this chapter, we describe the methylated-CpG island recovery assay (MIRA), which is based on the high affinity of the MBD2b/MBD3L1 complex for double-stranded CpG-methylated DNA. MIRA has been used in combination with microarray platforms to map DNA methylation patterns across the human genome.
Decomposable Neural Paraphrase Generation (2019)

Paraphrasing exists at different granularity levels, such as lexical level, phrasal level and sentential level. This paper presents Decomposable Neural Paraphrase Generator (DNPG), a Transformer-based model that can learn and generate paraphrases of a sentence at different levels of granularity in a disentangled way. Specifically, the model is composed of multiple encoders and decoders with different structures, each of which corresponds to a specific granularity. The empirical study shows that the decomposition mechanism of DNPG makes paraphrase generation more interpretable and controllable. Based on DNPG, we further develop an unsupervised domain adaptation method for paraphrase generation. Experimental results show that the proposed model achieves competitive in-domain performance compared to the state-of-the-art neural models, and significantly better performance when adapting to a new domain.
Development of New Aqueous Resin Ink for Sign Graphics (2016)

An aqueous resin ink was developed which can offer excellent image qualities on non-permeating media such as plastic media with an inkjet printer. The print speed with this aqueous resin ink reaches the level of solvent-inks diffused as inks for non-permeating media for sign graphic, i.e., at least 30m2/h. In order to increase the print speed, it is important that the ink has good compatibility to the coating layer of non-permeating media. It was found that kinds of solvents added to the ink were highly related to the compatibility. Furthermore, such solvents have a particular feature in common. Solvents with specific range of fractional parameter have high coating layer-solving ability. To show validity of this mechanism, a new method for evaluation of ink fixation was developed. With this new method, it was proved that higher concentration of coating-layer-solving solvent gave ink faster fixation onto the non-permeating media. Furthermore, we also discovered that the characteristics of the pigment dispersion element in an ink formula greatly affected the discharging reliability.
Spontaneous Root-Nodule Formation in the Model Legume<i>Lotus japonicus</i>: A Novel Class of Mutants Nodulates in the Absence of Rhizobia (2006)

Root-nodule development in legumes is an inducible developmental process initially triggered by perception of lipochitin-oligosaccharide signals secreted by the bacterial microsymbiont. In nature, rhizobial colonization and invasion of the legume root is therefore a prerequisite for formation of nitrogen-fixing root nodules. Here, we report isolation and characterization of chemically induced spontaneously nodulating mutants in a model legume amenable to molecular genetics. Six mutant lines of Lotus japonicus were identified in a screen for spontaneous nodule development under axenic conditions, i.e., in the absence of rhizobia. Spontaneous nodules do not contain rhizobia, bacteroids, or infection threads. Phenotypically, they resemble ineffective white nodules formed by some bacterial mutants on wild-type plants or certain plant mutants inoculated with wild-type Mesorhizobium loti. Spontaneous nodules formed on mutant lines show the ontogeny and characteristic histological features described for rhizobia-induced nodules on wild-type plants. Physiological responses to nitrate and ethylene are also maintained, as elevated levels inhibit spontaneous nodulation. Activation of the nodule developmental program in spontaneous nodules was shown for the early nodulin genes Enod2 and Nin, which are both upregulated in spontaneous nodules as well as in rhizobial nodules. Both monogenic recessive and dominant spontaneous nodule formation (snf) mutations were isolated in this mutant screen, and map positions were determined for three loci. We suggest that future molecular characterization of these mutants will identify key plant determinants involved in regulating nodulation and provide new insight into plant organ development.
RaPP: Novelty Detection with Reconstruction along Projection Pathway (2020)

We propose RaPP, a new methodology for novelty detection by utilizing hidden space activation values obtained from a deep autoencoder. Precisely, RaPP compares input and its autoencoder reconstruction not only in the input space but also in the hidden spaces. We show that if we feed a reconstructed input to the same autoencoder again, its activated values in a hidden space are equivalent to the corresponding reconstruction in that hidden space given the original input. In order to aggregate the hidden space activation values, we propose two metrics, which enhance the novelty detection performance. Through extensive experiments using diverse datasets, we validate that RaPP improves novelty detection performances of autoencoder-based approaches. Besides, we show that RaPP outperforms recent novelty detection methods evaluated on popular benchmarks.
Ultra-low temperature sensitive deep-well quantum cascade lasers (λ=4.8 µm) via uptapering conduction band edge of injector regions (2009)

A new design feature for deep-well quantum cascade (QC) lasers, in which the conduction band edge of the injector region is uptapered, results in virtual suppression of carrier leakage out of the active regions of 4.8 µm emitting devices. For heatsink temperatures in the 20–90°C range the characteristic temperature coefficients for threshold, T0, and slope efficiency, T1, reach values as high as 278 and 285 K, respectively, which are nearly twice the values for conventional QC lasers. At 20°C, the threshold current density for uncoated, 30 period, 3 mm-long devices is only ∼1.8 kA/cm2.
Software tools for quantum control: improving quantum computer performance through noise and error suppression (2021)

Abstract Effectively manipulating quantum computing (QC) hardware in the presence of imperfect devices and control systems is a central challenge in realizing useful quantum computers. Susceptibility to noise critically limits the performance and capabilities of today’s so-called noisy intermediate-scale quantum devices, as well as any future QC technologies. Fortunately, quantum control enables efficient execution of quantum logic operations and quantum algorithms with built-in robustness to errors, and without the need for complex logical encoding. In this manuscript we introduce software tools for the application and integration of quantum control in QC research, serving the needs of hardware R&D teams, algorithm developers, and end users. We provide an overview of a set of Python-based classical software tools for creating and deploying optimized quantum control solutions at various layers of the QC software stack. We describe a software architecture leveraging both high-performance distributed cloud computation and local custom integration into hardware systems, and explain how key functionality is integrable with other software packages and quantum programming languages. Our presentation includes a detailed mathematical overview of key features including a flexible optimization toolkit, engineering-inspired filter functions for analyzing noise susceptibility in high-dimensional Hilbert spaces, and new approaches to noise and hardware characterization. Pseudocode is presented in order to elucidate common programming workflows for these tasks, and performance benchmarking is reported for numerically intensive tasks, highlighting the benefits of the selected cloud-compute architecture. Finally, we present a series of case studies demonstrating the application of quantum control solutions derived from these tools in real experimental settings using both trapped-ion and superconducting quantum computer hardware.
Stereospecific Synthesis of (R)-Aminocarnitine (Emeriamine) Starting from (R)-Carnitine via Double Inversion of Configuration (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific Synthesis of (R)-Aminocarnitine (Emeriamine) Starting from (R)-Carnitine via Double Inversion of ConfigurationRoberto Castagnani, Francesco De Angelis, Enrico De Fusco, Fabio Giannessi, Domenico Misiti, Domenico Meloni, and Maria Ornella TintiCite this: J. Org. Chem. 1995, 60, 25, 8318–8319Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/jo00130a039https://doi.org/10.1021/jo00130a039research-articleACS PublicationsRequest reuse permissionsArticle Views548Altmetric-Citations17LEARN 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
34.4L: <i>Late‐News Paper</i> : Polarization Independent Projection Systems Using Thin Film Polymer Polarization Gratings and Standard Liquid Crystal Microdisplays (2009)

Abstract We report on our progress in using polymer Polarization Gratings (PGs) to enhance the brightness of standard Liquid Crystal (LC) microdisplays. By replacing conventional polarizers with PGs, high transmittance (>85%) and contrast ratios (>300:1) can be achieved with common LC modes and unpolarized input light. Using this approach, we demonstrate a polymer‐PG projection display prototype with double the brightness compared to a polarizer‐based system using the same illumination (input acceptance angles≥±15°).
Petroleum Radiation Processing (2013)

This book presents a summary of the research progress in the field of petroleum radiation processing, which has produced technology that offers effective and economic solutions for some pressing oil refining challenges. It provides a systematic description of the most important experiments on radiation cracking for different types of petroleum feedstock, including crude oils, heavy oil residues, and bitumen. The book provides a detailed introduction to radiation methods based on radiation-thermal and low-temperature cracking of hydrocarbons, emphasizing high-viscous oil feedstocks that are difficult to process by conventional methods.
Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid (2009)

Many cephalopods exhibit remarkable dermal iridescence, a component of their complex, dynamic camouflage and communication. In the species Euprymna scolopes, the light-organ iridescence is static and is due to reflectin protein-based platelets assembled into lamellar thin-film reflectors called iridosomes, contained within iridescent cells called iridocytes. Squid in the family Loliginidae appear to be unique in which the dermis possesses a dynamic iridescent component with reflective, coloured structures that are assembled and disassembled under the control of the muscarinic cholinergic system and the associated neurotransmitter acetylcholine (ACh). Here we present the sequences and characterization of three new members of the reflectin family associated with the dynamically changeable iridescence in Loligo and not found in static Euprymna iridophores. In addition, we show that application of genistein, a protein tyrosine kinase inhibitor, suppresses ACh- and calcium-induced iridescence in Loligo. We further demonstrate that two of these novel reflectins are extensively phosphorylated in concert with the activation of iridescence by exogenous ACh. This phosphorylation and the correlated iridescence can be blocked with genistein. Our results suggest that tyrosine phosphorylation of reflectin proteins is involved in the regulation of dynamic iridescence in Loligo.
Visibility transition planning for dynamic camera control (2009)

We present a real-time camera control system that uses a global planning algorithm to compute large, occlusion free camera paths through complex environments. The algorithm incorporates the visibility of a focus point into the search strategy, so that a path is chosen along which the focus target will be in view. The efficiency of our algorithm comes from a visibility-aware roadmap data structure that permits the precomputation of a coarse representation of all collision-free paths through an environment, together with an estimate of the pair-wise visibility between all portions of the scene. Our runtime system executes a path planning algorithm using the precomputed roadmap values to find a coarse path, and then refines the path using a sequence of occlusion maps computed on-the-fly. An iterative smoothing algorithm, together with a physically-based camera model, ensures that the path followed by the camera is smooth in both space and time. Our global planning strategy on the visibility-aware roadmap enables large-scale camera transitions as well as a local third-person camera module that follows a player and avoids obstructed viewpoints. The data structure itself adapts at run-time to dynamic occluders that move in an environment. We demonstrate these capabilities in several realistic game environments.