gebhart/patrepeval huggingface dataset:
Guar Seed ß-Mannan Synthase Is a Member of the Cellulose Synthase Super Gene Family (2004)

Genes for the enzymes that make plant cell wall hemicellulosic polysaccharides remain to be identified. We report here the isolation of a complementary DNA (cDNA) clone encoding one such enzyme, mannan synthase (ManS), that makes the beta-1, 4-mannan backbone of galactomannan, a hemicellulosic storage polysaccharide in guar seed endosperm walls. The soybean somatic embryos expressing ManS cDNA contained high levels of ManS activities that localized to Golgi. Phylogenetically, ManS is closest to group A of the cellulose synthase-like (Csl) sequences from Arabidopsis and rice. Our results provide the biochemical proof for the involvement of the Csl genes in beta-glycan formation in plants.
ChemInform Abstract: A Mild and Efficient Dethioacetalization Employing FeCl3×6H2O: Synthesis of DNA‐Binding Pyrrolo[2,1‐c][1,4]benzodiazepine Ring System and Its Dimers. (2001)

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.
High resolution crystal structure of dengue‐3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition (2013)

Dengue viruses are classified into four serotypes. Here, we report a 1.7 Å crystal structure of a recombinant dengue-3 envelope protein domain III (ED3), which contains most of the putative epitopes. Although the fold was well conserved, we found that a local backbone deformation in the first β-strand, which contains the putative epitope-1, occurred upon domain isolation. Furthermore, a comparison with dengue-2 ED3 indicated a large structural change by as much as 4.0 Å at Asp(662), located in epitope-2. These minute structural and surface properties changes observed in the high resolution ED3 structure represent potential determinants for serospecificity and epitope recognition by antibodies.
Etude de la micro-explosion de biocarburants émulsionnés sous différents schémas de chauffage radiatifs (2022)

La micro-explosion, où seconde atomisation, se produit au sein d'une goutte d'émulsion d'eau dans l'huile, lorsque la phase dispersée atteint la température de saturation. S'en suit alors un changement d'état soudain de la phase aqueuse au sein de la couche huileuse environnante, toujours à l'état liquide, résultant en une fragmentation de cette dernière en un nuage de fines gouttes appelées « gouttes filles ». Ce phénomène, appelé micro-explosion, permet d'obtenir une combustion de meilleure qualité de part une surface totale de combustible en contact avec l'air plus grande dans le cas d'un nuage de fines gouttes par rapport à celui d'une goutte simple. Il a été observé expérimentalement, que le comportement des gouttes d'eau dispersées durant le chauffage précédent la micro-explosion avait un impact significatif sur la qualité de celle-ci. En effet, lorsque sujettes à des mouvements de convection interne (de par l'hétérogénéité du champ de température au sein de l'émulsion), les gouttes d'eau ont tendance à se regrouper en partie basse de la goutte d'émulsion, puis à fusionner (phénomène de coalescence), en des gouttes de taille plus grande. Ce phénomène est accentué par la perte du pouvoir stabilisant du surfactant avec la température. Cette coalescence de petites gouttes en des gouttes de tailles plus grandes semble permettre d'obtenir une micro-explosion plus forte, de par l'énergie plus grande libérée lors du changement de phase. L'étude présentée se propose de mesurer l'influence du chauffage radiatif sur le phénomène de micro-explosion, ainsi que l'importance de la convection interne au sein de la goutte d'émulsion pouvant résulter en la coalescence de la phase dispersée. Pour se faire, la goutte d'émulsion est chauffée à l'aide de deux panneaux radiatifs dont la température de surface est contrôlée et peut-être variée entre 300 et 700°C. L'expérience est filmée à l'aide d'une caméra rapide permettant d'étudier le comportement de l'émulsion durant sa phase de montée en température ainsi que les mouvements des gouttelettes d'eau. L'influence de la distance des panneaux à la goutte ainsi que de la puissance de chauffe est étudiée (délai avant la micro-explosion, puissance radiative reçue...). Différents positionnements des panneaux sont utilisés, afin d'accentuer où de bloquer les mouvements de convection naturelle, et ainsi de mesurer la prépondérance (ou non) de la coalescence de la phase dispersée sur la micro-explosion. Cette étude a pour but de mieux comprendre le comportement des systèmes diphasiques que représentent les émulsions afin d'optimiser les différents paramètres permettant de maximiser la probabilité d'occurrence de la micro-explosion et sa qualité.
Microwave promoted novel synthesis of indenols catalyzed by SiO2 in dry media (2006)

Indenols are produced in high yields when electron-rich α,β-unsaturated aldehydes adsorbed on silicon dioxide were subjected to microwave irradiation in dry media.
Dietary Supplementation with Fructooligosaccharides Increase Survival Time in a Hamster Model of Clostridium difficile-Colitis (1997)

Fructooligosaccharides (FOS) are an indigestible, highly fermentable carbohydrate with a chain length of 3 to 5. They are known bifidogenic factors which may provide physiological benefits when fed. Two studies investigating the effect of FOS on survival in a hamster model of Clostridium difficile-colitis were conducted. Female golden Syrian hamsters were treated with ciprofloxacin prior to C. difficile (strain VPI 10463) challenge. In experiment one, 41 hamsters were randomized among 1 of 6 treatments arranged in a 2×3 factorial (0 or 30 g FOS/L of drinking water; 0, 0.5×109 colony forming units, or 2.0×109 colony forming units C. difficile challenge). In experiment two, 63 hamsters were randomized among 1 of 8 treatments arranged in a 2×2×2 factorial (0 or 30 g FOS/L of drinking water; 0 or 2.0×109 colony forming units C. difficile challenge; 0 or 50 mg/kg body weight/day vancomycin treatment). In the first experiment, FOS increased (p<0.01) median survival time (MST) of hamsters challenged with C. difficile. In the second experiment, the overall effect of FOS was to improve (p<0.05) MST. These data suggest that dietary supplementation with FOS increases median survival time in a hamster model of Clostridium difficile-colitis. Supplementation with fructooligosaccharides may be beneficial for patients at risk of C. difficile infection in long-term care institutions and hospital wards.
Preparing Precollege Students for the Second Quantum Revolution with Core Concepts in Quantum Information Science (2022)

After the passage of the U.S. National Quantum Initiative Act in December 2018, the National Science Foundation (NSF) and the Office of Science and Technology Policy (OSTP) recently assembled an interagency working group and conducted a workshop titled “Key Concepts for Future Quantum Information Science Learners” that focused on identifying core concepts for future curricular and educator activities to help precollege students engage with quantum information science (QIS). Helping precollege students learn these key concepts in QIS is an effective approach to introducing them to the second quantum revolution and inspiring them to become future contributors in the growing field of quantum information science and technology as leaders in areas related to quantum computing, communication, and sensing. This paper is a call to precollege educators to contemplate including QIS concepts into their existing courses at appropriate levels and get involved in the development of curricular materials suitable for their students. Also, research shows that compare-and-contrast activities can provide an effective approach to helping students learn. Therefore, we illustrate a pedagogical approach that contrasts the classical and quantum concepts so that educators can adapt them for their students in their lesson plans to help them learn the differences between key concepts in quantum and classical contexts.
Contribution of human smooth muscle cells to amyloid angiopathy in AL (light-chain) amyloidosis (2017)

The interaction of amyloidogenic LCs with VSMCs is necessary for the formation of amyloid fibrils that are deposited in peripheral vessels. VSMCs participate in the formation of amyloid by the intracellular processing of AL-LCs, which is possible due to their transformation from a smooth muscle to a macrophage phenotype. The formation of amyloid fibrils occurs in the mature lysosomal compartment of transformed cells. The amyloid that is formed is then extruded into the extracellular matrix.
A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. (1994)

Ribonuclease E has a central role in Escherichia coli mRNA decay and is dependent on a functional product of the rne (also called ams or hmp1) gene. We investigated the requirements for RNase E cleavage by introducing random mutations into the decanucleotide region at the 5' end of pACYC184 RNA I and studying the effects of these mutations on the position of rne-dependent cleavage in vivo and RNase E-mediated cutting in vitro. We find that the precise point of RNase E cleavage can be altered specifically and reproducibly by sequence changes in the region cleaved and, therefore, is not determined by a distance measured in nucleotides from any other sequence or region of secondary structure in RNA I. Although cleavage by RNase E occurs within sequences rich in A and/or U nucleotides and is affected by the extent of continuity of A and U nucleotides in the regions cleaved, there is no simple relationship between the order of nucleotides and the phosphodiester bond cleaved. Thus, our results are not consistent with either the notion that RNase E cleavages are determined by a simple consensus sequence or the contrary view that RNase E has few primary structural constraints other than a preference for cleaving 5' to an AU dinucleotide.
Data from Epigenetic Therapies in Ovarian Cancer Alter Repetitive Element Expression in a <i>TP53</i>-Dependent Manner (2023)

&lt;div&gt;Abstract&lt;p&gt;Epithelial ovarian carcinomas are particularly deadly due to intratumoral heterogeneity, resistance to standard-of-care therapies, and poor response to alternative treatments such as immunotherapy. Targeting the ovarian carcinoma epigenome with DNA methyltransferase inhibitors (DNMTi) or histone deacetylase inhibitors (HDACi) increases immune signaling and recruits CD8&lt;sup&gt;+&lt;/sup&gt; T cells and natural killer cells to fight ovarian carcinoma in murine models. This increased immune activity is caused by increased transcription of repetitive elements (RE) that form double-stranded RNA (dsRNA) and trigger an IFN response. To understand which REs are affected by epigenetic therapies in ovarian carcinoma, we assessed the effect of DNMTi and HDACi on ovarian carcinoma cell lines and patient samples. Subfamily-level (TEtranscripts) and individual locus-level (Telescope) analysis of REs showed that DNMTi treatment upregulated more REs than HDACi treatment. Upregulated REs were predominantly LTR and SINE subfamilies, and SINEs exhibited the greatest loss of DNA methylation upon DNMTi treatment. Cell lines with &lt;i&gt;TP53&lt;/i&gt; mutations exhibited significantly fewer upregulated REs with epigenetic therapy than wild-type &lt;i&gt;TP53&lt;/i&gt; cell lines. This observation was validated using isogenic cell lines; the &lt;i&gt;TP53&lt;/i&gt;-mutant cell line had significantly higher baseline expression of REs but upregulated fewer upon epigenetic treatment. In addition, p53 activation increased expression of REs in wild-type but not mutant cell lines. These data give a comprehensive, genome-wide picture of RE chromatin and transcription-related changes in ovarian carcinoma after epigenetic treatment and implicate p53 in RE transcriptional regulation.&lt;/p&gt;Significance:&lt;p&gt;This study identifies the repetitive element targets of epigenetic therapies in ovarian carcinoma and indicates a role for p53 in this process.&lt;/p&gt;&lt;p&gt;See interview with Katherine B. Chiappinelli, PhD, recipient of the 2022 Cancer Research Early Career Award: &lt;a href="https://vimeo.com/720726570" target="_blank"&gt;https://vimeo.com/720726570&lt;/a&gt;&lt;/p&gt;&lt;/div&gt;
Enol Tosylates as Viable Partners in Pd‐Catalyzed Cross‐Coupling Reactions. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
ChemInform Abstract: Ligand‐Free Copper‐Catalyzed C—S Coupling of Aryl Iodides and Thiols. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Closed Form Sum Rate of Random Beamforming (2012)

In this letter, we carry out analysis to derive the closed form sum rate for a general multi-antenna random beamforming system with an arbitrary but finite number of users. A simple and analytical useful expansion with general utility is first developed to decompose and interpret the probability density function of the selected user's signal-to-interference-plus-noise ratio. By using this decomposition, along with standard integration techniques, the closed form result for the sum rate is obtained. The established result explains the interplay between the system parameters for arbitrary but finite number of users.
Reductive conjugate addition nitro-Mannich route for the stereoselective synthesis of 1,2,3,4-tetrahydroquinoxalines (2016)

A concise, high yielding and structurally divergent synthesis of complex 1,2,3,4-tetrahydroquinoxalines with excellent diastereoselectivity is described. A wide array of nitroalkenes and imines derived from commercially available aromatic aldehydes and 2-chloroanalines were subjected to a key reductive conjugate addition nitro-Mannich reaction to give diastereomerically pure β-nitro amines. Sequential reduction of the nitro function followed by Pd-catalyzed intramolecular N-arylation of the resultant primary amine onto the 2-chloroanailine gives highly substituted 1,2,3,4-tetrahydroquinoxalines. Non basic imines were found to participate better in the nitro-Mannich reaction if the stronger acid methanesulfonic acid was used to promote the reaction. The 3 step reaction sequence should be useful for the array synthesis of drug like scaffolds.
Novel availability metrics for network topologies (2008)

This paper presents two novel definitions for availability concerning communication networks. It is shown that currently used network availability metrics cannot fully describe the resiliency of a network. The aim of this paper is to provide metrics that enable network operators to compare different network topology designs assuming a given population distribution. A transport network is considered to be in down state when at least a certain percentage of all subscribers for at least 10 seconds have no connectivity, or have only poor performance. We also present another availability metric named Session Completion Ratio, which is a more user-centric performance indicator since any user with poor performance or no connectivity deteriorates the overall network performance. Simulation results are presented and different transport network topologies are compared based on their availability performance, followed by a case study, where the availability of a network is improved by allocating extra capacity on the links. The results proved that single link failure-tolerant capacity setting leads to high-availability. Finally a tool is presented that helps identifying those parts of the network that have the strongest influence on resiliency.
A laser scanning radar based autonomous lateral vehicle following control scheme for automated highways (2004)

This paper describes the development of an autonomous vehicle following control scheme using a laser scanning radar sensor (LIDAR) for automated highway applications. The LIDAR sensor measures the ego-vehicle's relative position with respect to its preceding vehicle, and the newly developed control scheme uses the LIDAR measurements to control the ego-vehicle to follow the lead vehicle. This research is conducted as part of the efforts on fault management of automated highway systems by California PATH. The new control scheme can be used as a back-up system for the current PATH magnetometer-based road following control scheme in case of magnetometer failure. This paper describes the LIDAR sensor, discusses key issues in the system design, and provides experimental results.
A Water Polishing Process to Improve Ceria Abrasive Removal (2019)

This study details the improved ceria abrasive removal on SiO2 wafer during the post CMP water polishing (buff clean) process. Initially, the zeta potentials of the wafer and ceria abrasive were measured according to pH and compared with the zeta potential and pH change during water polishing. From these measurements, it was determined that the zeta potential difference between the ceria abrasive and the wafer decreased during water polishing. The electrical repulsion between them decreased as well. Additionally, ceria abrasive removal was measured using a surface defect inspection system. The abrasive removal increased when water polishing conditions such as pressure, rotation speed and processing time increased. Chemical enhancement and a pad cleaning process also increased the ceria abrasive removal. Consequently, the total defect counts were reduced by 91.8% with the optimized water polishing condition. These results provide useful data for determining optimal water polishing conditions for more effective post CMP cleaning.
Product Differences in Intra-articular Hyaluronic Acids for Osteoarthritis of the Knee (2015)

Despite similarities, IA-HA products should not be treated as a group, as there are differences in IA-HA products that influence both efficacy and safety. In the available literature, IA-HA products with a molecular weight ≥3000 kDa and those derived from biological fermentation relate to superior efficacy and safety-factors that may influence selection an IA-HA product for OA of the knee.
Using A Genetic A ic for Meta Modeling (1996)

The identification of metabolic systems is a complex task due to the complexity of the system and limited knowledge about the model. Mathematical equations and ODE’s have been used to capture the structure of the model, and the conventional optimization techniques have been used to identify the parameters of the model. In general, however, a pure mathematical formulation of the model is difficult due to parametric uncertainty and incomplete knowledge of mechanisms. In this paper, we propose a modeling approach that (1) uses fuzzy rule-based model to augment algebraic enzyme models that are incomplete, and (2) uses a hybrid genetic algorithm to identify uncertain parameters in the model. The hybrid genetic algorithm (GA) integrates a GA with the simplex method in functional optimization to improve the GA’s convergence rate. We have applied this approach to modeling the rate of three enzyme reactions in E. cola’central metabolism. The proposed modeling strategy allows (1) easy incorporation of qualitative insights into a pure mathematical model and (2) adaptive identification and optimization of key parameters to fit system behaviors observed in biochemical experiments.
Development of a Photoacoustic, Ultrasound and Fluorescence Imaging Catheter for the Study of Atherosclerotic Plaque (2014)

Atherosclerotic cardiovascular diseases are a major cause of death in industrialized countries. Molecular imaging modalities are increasingly recognized to be a promising avenue towards improved diagnosis and for the evaluation of new drug therapies. In this work, we present an acquisition system and associated catheter enabling simultaneous photoacoustic, ultrasound and fluorescence imaging of arteries designed for in vivo imaging. The catheter performance is evaluated in tissue-mimicking phantoms. Simultaneous imaging with three modalities is demonstrated at frame rates of 30 images per second for ultrasound and fluorescence and 1 image per 13 seconds for photoacoustic. Acquired radio-frequency ultrasound data could be processed to obtain radial strain elastograms. With motorized pullback, 3D imaging of phantoms was performed using the three modalities.
RNA Sequence Elements Required for High Affinity Binding by the Zinc Finger Domain of Tristetraprolin (2004)

Tristetraprolin (TTP) binds AU-rich elements (AREs) encoded within selected labile mRNAs and targets these transcripts for rapid cytoplasmic decay. RNA binding by TTP is mediated by an approximately 70-amino acid domain containing two tandemly arrayed CCCH zinc fingers. Here we show that a 73-amino acid peptide spanning the TTP zinc finger domain, denoted TTP73, forms a dynamic, equimolar RNA.peptide complex with a 13-nucleotide fragment of the ARE from tumor necrosis factor alpha mRNA, which includes small but significant contributions from ionic interactions. Association of TTP73 with high affinity RNA substrates is accompanied by a large negative change in heat capacity without substantial modification of RNA structure, consistent with conformational changes in the peptide moiety during RNA binding. Analyses using mutant ARE substrates indicate that two adenylate residues located 3-6 bases apart within a uridylate-rich sequence are sufficient for high affinity recognition by TTP73 (K(d) <20 nm), with optimal affinity observed for RNA substrates containing AUUUA or AUUUUA. Linkage of conformational changes and binding affinity to the presence and spacing of these adenylate residues provides a thermodynamic basis for the RNA substrate specificity of TTP.
Nanostructured Photonic Power Splitter Design via Convolutional Neural Networks (2019)

We train a convolutional neural network (CNN) that can predict the optical response of randomly generated nanopatterned photonic power splitters in a 2400 design space with a prediction correlation coefficient of 85 %.
Requirements for ion and solute transport, and pH regulation during enamel maturation (2011)

Transcellular bicarbonate transport is suspected to be an important pathway used by ameloblasts to regulate extracellular pH and support crystal growth during enamel maturation. Proteins that play a role in amelogenesis include members of the ABC transporters (SLC gene family and CFTR). A number of carbonic anhydrases (CAs) have also been identified. The defined functions of these genes are likely interlinked during enamel mineralization. The purpose of this study is to quantify relative mRNA levels of individual SLC, Cftr, and CAs in enamel cells obtained from secretory and maturation stages on rat incisors. We also present novel data on the enamel phenotypes for two animal models, a mutant porcine (CFTR-ΔF508) and the NBCe1-null mouse. Our data show that two SLCs (AE2 and NBCe1), Cftr, and Car2, Car3, Car6, and Car12 are all significantly up-regulated at the onset of the maturation stage of amelogenesis when compared to the secretory stage. The remaining SLCs and CA gene transcripts showed negligible expression or no significant change in expression from secretory to maturation stages. The enamel of CFTR-ΔF508 adult pigs was hypomineralized and showed abnormal crystal growth. NBCe1-null mice enamel was structurally defective and had a marked decrease in mineral content relative to wild-type. These data demonstrate the importance of many non-matrix proteins to amelogenesis and that the expression levels of multiple genes regulating extracellular pH are modulated during enamel maturation in response to an increased need for pH buffering during hydroxyapatite crystal growth.