gebhart/patrepeval huggingface dataset:
Synthesis, Characterization, and Dynamic Studies of 12-Vertex η5-Ruthenium(II)closo-Phosphine Complexes with Monoanionic [10-L-nido-7-R-7,8-C2B9H9]-Ligands (2004)

Ruthenacarborane complexes of formula [3-H-3,3-(PPh3)2-8-L-closo-3,1,2-RuC2B9H10)] (L = SMe2 (2a), SEt2 (2b), S(CH2)4 (2c), SEtPh (2d)) and [1-Me-3-H-3,3-(PPh3)2-8-L-closo-3,1,2-RuC2B9H9)] (L = SMe2 (2e), SEt2 (2f)) were prepared by reaction of the respective monoanionic charge-compensated ligands [10-L-nido-7,8-C2B9H10]- and [7-Me-10-L-nido-7,8-C2B9H9]- with [RuCl2(PPh3)3]. Similary, complexes [3-H-3,3,8-(PPh3)3-closo-3,1,2-RuC2B9H10)] (4a) and [3-H-3,3-(PPh3)2-8-PPh2Me-closo-3,1,2-RuC2B9H10)] (4b) were prepared from the corresponding phosphonium ligands. The reaction is done in one pot by reacting the ligand with the Ru(II) complex in a 1.5:1 ratio. All compounds have been fully characterized by multinuclear NMR spectroscopy, and the molecular structures for 2a and 4a have been elucidated by single-crystal X-ray diffraction analysis. The Ru(II) atom in this complex is on the open face of the monoanionic charge-compensated ligand adopting a pseudooctahedral coordination. Formally, three positions are supplied by the C2B3 open face, two PPh3 groups occupy two other positions, and a hydride fulfills the remaining one. The hydride complexes were generated with no special reagent. They result from a dehalogenation in the presence of ethanol.
Macaque prefrontal activity associated with extensive tool use (2002)

Macaques can utilize tools sequentially on a single object or they can modify functions effectively in a relevant context. Two Japanese macaques were scanned by positron emission tomography with H215O during a tool combination task and two control tasks (single tool task and simple stick-waving task). In the tool combination task, monkeys were required to use two identical tools properly in different functions. We found increased activity in the bilateral prefrontal cortex (area 9/46), bilateral intraparietal sulcus regions, right cerebellum, and bilateral early visual cortices during the tool combination task with the right hand, compared with the single tool task. These results suggest that interactions between the fronto-cerebellar and the fronto-parietal circuit are responsible for appropriate and effective modifications of tools in their functions.
Observation of transient phase separation process of liquid crystal/ polymer composites obtained by photo-polymerization induced-phase separation and their electro-optical properties (2013)

A transient phase separated structure during the photo-polymerization induced-phase separation process of liquid crystal/polymer composites consisting of a continuous phase of nematic liquid crystal and a three-dimensional polymer network was successfully observed by interrupting UV light irradiation for photo-polymerization. Those transient composites were characterized by a difference in temperature for nematic-isotropic transition point (Tn-i) of the liquid crystal phase, a comparison of morphology for polymer phase between an initial stage and the last stage of phase separation, and an electro-optical performance at each period of phase separation process. It was found that the composite even at an initial stage of phase separation showed a transparent-turbid (light scattering) operation with an electric field and the UV irradiation period required to attain the final voltage-transmittance curve accorded well with that to give a saturation of Tn-i of the liquid crystal phase. A schematic diagram for photo-polymerization induced-phase separation process was proposed according to investigation into characteristics of the liquid crystal/polymer composites having a transient phase separated structure.
Correction to “Hyper inflammatory syndrome following COVID-19 mRNA vaccine in children: A national post-authorization pharmacovigilance study” (2022)

[This corrects the article DOI: 10.1016/j.lanepe.2022.100393.].
In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus (1999)

The SelB protein of Escherichia coli is a special elongation factor required for the cotranslational incorporation of the uncommon amino acid selenocysteine into proteins such as formiate dehydrogenases. To do this, SelB binds simultaneously to selenocysteyl-tRNA(Sec) and to an RNA hairpin structure in the mRNA of formiate dehydrogenases located directly 3' of the selenocysteine opal (UGA) codon. The protein is also thought to contain binding sites allowing its interaction with ribosomal proteins and/or rRNA. SelB thus includes specific binding sites for a variety of different RNA molecules. We used an in vitro selection approach with a pool completely randomized at 40 nt to isolate new high-affinity SelB-binding RNA motifs. Our main objective was to investigate which of the various RNA-binding domains in SelB would turn out to be prime targets for aptamer interaction. The resulting sequences were compared with those from a previous SELEX experiment using a degenerate pool of the wild-type formiate dehydrogenase H (fdhF) hairpin sequence (Klug SJ et al., 1997, Proc. Natl. Acad. Sci. USA 94:6676-6681). In four selection cycles an enriched pool of tight SelB-binding aptamers was obtained; sequencing revealed that all aptamers were different in their primary sequence and most bore no recognizable consensus to known RNA motifs. Domain mapping for SelB-binding aptamers showed that despite the different RNA-binding sites in the protein, the vast majority of aptamers bound to the ultimate C-terminus of SelB, the domain responsible for mRNA hairpin binding.
Quadruplex Genotyping of F5, F2, and MTHFR Variants in a Single Closed Tube by High-Resolution Amplicon Melting (2007)

Rapid-cycle PCR with high-resolution melting analysis allows simple and accurate multiplex genotyping to at least a factor of 4.
Abstract 376: Amino Terminal C0-C1f Region of Cardiac Myosin Binding Protein-C is Essential for Normal Cardiac Function (2015)

Rationale: Cardiac myosin binding protein-C (cMyBP-C) is a trans-filament protein that has been shown to regulate cardiac function via its amino terminal (N’) regions. However, it is unknown whether the first 271 residues (C0-C1f region) are necessary to regulate contractile function in vivo. Hypothesis: The N’-region of cMyBP-C is critical for proper cardiac function in vivo. Methods and Results: Transgenic mice with approximately 80% expression of mutant truncated cMyBP-C missing C0-C1f (cMyBP-C 110kDa ), compared to endogenous cMyBP-C, were generated and characterized at 3-months of age. cMyBP-C 110kDa hearts had significantly elevated heart weight/body weight ratio, fibrosis, nuclear area and collagen content compared to hearts from non-transgenic (NTG) littermates. Electron microscopic analysis revealed normal sarcomere structure in cMyBP-C 110kDa hearts but with apparently weaker cMyBP-C stripes. Furthermore, the ability of cMyBP-C to slow actin-filament sliding within the C-zone of native thick filaments isolated from NTG hearts was lost on thick filaments from cMyBP-C 110kDa hearts. Short axis M-mode echocardiography revealed a significant increase in left ventricular (LV) internal diameter during diastole in cMyBP-C 110kDa hearts. Importantly, cMyBP-C 110kDa hearts displayed a significant reduction in fractional shortening compared to hearts from NTG littermates. We further observed a decrease in the thickness of the LV interventricular septum and free wall during systole in cMyBP-C 110kDa hearts. Strain analysis using images acquired from ECG-Gated Kilohertz Visualization identified a significant deficit in global longitudinal strain in cMyBP-C 110kDa hearts compared to NTG hearts. Conclusion: The N’-region of cMyBP-C is indispensable for maintaining normal cardiac morphology and function and loss of this region promotes contractile dysfunction both at the molecular and tissue levels.
On Not Believing What You Read (2018)

Every student should, before graduating, see the 2006 teen-comedy movie Accepted. It’s a broad satire built around some high-school misfits whom no college admissions officer in his right mind would accept, not even in this economy. So they commandeer an abandoned mental asylum and construct their own college based on Marxism (Groucho), and they do to higher education what A Night at the Opera did to Il Trovatore. To a flabbergasted visitor, the teenage president of the college recommends the school newspaper, The Rag. “There’s a great op-ed piece in there about not believing everything you read,” he explains. Like all absurdist comedy, Accepted poses that subversive question, “Who’s absurd here?” It stands upside-down all the pretenses of university life, including its most fundamental pretense, that if we spend years here reading, we will get closer to the truth. Is there, though, any necessary relation between reality and what we find on the printed page? It’s a question that has become particularly acute today, when it seems that every man is his own deconstructionist. When Paul Ricoeur coined the phrase “hermeneutic of suspicion,” he was only recommending this reading strategy to literary theorists, but his students took it quite seriously and in 1968 turned the University of Nanterre into, well, something like the campus in Accepted. And today that skepticism is thoroughly mainstream. According to the Gallup Poll, only 32 percent of Americans in 2016 have confidence in the media, down from a high of 72 percent in 1976, post-Woodward and Bernstein. Among millennials (18-to-29-year-olds), just 11 percent trust the media. In Britain, back in 1975, only about a third of tabloid readers and just 3 percent of readers of “quality” broadsheets felt that their paper “often gets its facts wrong.” But by 2012 no British daily was trusted by a majority of the public “to report fairly and accurately.” In something of a contradiction, the Sun enjoyed both the largest circulation and the lowest level of trust (just 9 percent).
Pulsed voltage electrospray ion source and method for preventing analyte electrolysis (2023)

An electrospray ion source and method of operation includes the application of pulsed voltage to prevent electrolysis of analytes with a low electrochemical potential. The electrospray ion source can include an emitter, a counter electrode, and a power supply. The emitter can include a liquid conduit, a primary working electrode having a liquid contacting surface, and a spray tip, where the liquid conduit and the working electrode are in liquid communication. The counter electrode can be proximate to, but separated from, the spray tip. The power system can supply voltage to the working electrode in the form of a pulse wave, where the pulse wave oscillates between at least an energized voltage and a relaxation voltage. The relaxation duration of the relaxation voltage can range from 1 millisecond to 35 milliseconds. The pulse duration of the energized voltage can be less than 1 millisecond and the frequency of the pulse wave can range from 30 to 800 Hz.
Reactions of solvated metal atoms with organometallic complexes in solution. A metal atom microsolution spectroscopic and synthetic study of the reaction pathways available to singly metal-metal bonded organometallic complexes and their organometallic anions (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of solvated metal atoms with organometallic complexes in solution. A metal atom microsolution spectroscopic and synthetic study of the reaction pathways available to singly metal-metal bonded organometallic complexes and their organometallic anionsGeoffrey A. Ozin, Kraig M. Coleson, and Helmut X. HuberCite this: Organometallics 1983, 2, 3, 415–420Publication Date (Print):March 1, 1983Publication History Published online1 May 2002Published inissue 1 March 1983https://doi.org/10.1021/om00075a011RIGHTS & PERMISSIONSArticle Views95Altmetric-Citations7LEARN 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 InReddit PDF (682 KB) Get e-Alerts Get e-Alerts
Phase‐contrast velocimetry with hyperpolarized 3He for in vitro and in vivo characterization of airflow (2006)

This paper describes a technique that combines radial MRI and phase contrast (PC) to map the velocities of hyperpolarized gases ((3)He) in respiratory airways. The method was evaluated on well known geometries (straight and U-shaped pipes) before it was applied in vivo. Dynamic 2D maps of the three velocity components were obtained from a 10-mm slice with an in-plane spatial resolution of 1.6 mm within 1 s. Integration of the in vitro through-plane velocity over the slice matched the input flow within a relative precision of 6.4%. As expected for the given Reynolds number, a parabolic velocity profile was obtained in the straight pipe. In the U-shaped pipe the three velocity components were measured and compared to a fluid-dynamics simulation so the precision was evaluated as fine as 0.025 m s(-1). The technique also demonstrated its ability to visualize vortices and localize characteristic points, such as the maximum velocity and vortex-center positions. Finally, in vivo feasibility was demonstrated in the human trachea during inhalation.
A Practical Stereoselective Synthesis and Novel Cocrystallizations of an Amphiphatic SGLT-2 Inhibitor (2012)

A practical synthesis of the SGLT-2 inhibitor β-C-aryl-d-glucoside (1) has been developed. The route employed 2,3,4,6-tetra-O-trimethlysilyl-d-glucano-1,5-lactone as the key chiral building block, prepared efficiently from the commercially available, inexpensive raw materials, d-gluconolactone and trimethylsilyl chloride. The salient step in the synthesis is the Lewis acid-mediated stereoselective reduction of a methyl C-aryl peracetylated glycoside using a silyl hydride to set the stereochemistry of the crucial anomeric chiral center. Several novel cocrystalline complexes of 1 with l-phenylalanine and l-proline were discovered. Single-crystal structures of these complexes and several synthetic intermediates have been determined. The l-phenylalanine complex was developed and used to purify and isolate the API. All steps were implemented at multikilogram scale.
Increasing Persistence through Scattering Environments by using Circularly Polarized Light. (2016)

Abstract not provided.
Angled Vortex Fluidic Mediated Multicomponent Photocatalytic and Transition Metal‐Catalyzed Reactions (2018)

The dynamic thin film formed in an angled rapidly rotating tube in a vortex fluidic device (VFD) is effective in facilitating multicomponent reactions (MCRs) as photocatalytic or metal-mediated processes. Here, we demonstrate the utility of the VFD by using two known MCRs, an Ugi-type three component reaction and an A<sup>3</sup> -coupling reaction. The Ugi-type reaction can be done in either confined or continuous-flow modes of operation of the microfluidic platform whereas the A<sup>3</sup> -coupling reaction was optimized for the confined mode of operation. The examples tested gave excellent yields with short reaction times.
An electrically-stimulate optically-record microsystem based on active CMOS multi-electrode array for dissociated cell cultures (2011)

Calcium fluorescence-based optical recording combined with patch-clamp stimulation has become the standard technique for analyzing neural network behavior. At best, stimulation is limited to only a few channels in this case. Passive multielectrode arrays for two-dimensional electrophysiology only offer electrode densities of 60 electrodes per mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Here, we report an active multielectrode array, constructed with a standard complementary metal-oxide-semiconductor (CMOS) technology, to perform localized extracellular stimulation of dispersed cell cultures. A 256×256 array integrated with in-pixel stimulators on a 4-by-4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> CMOS chip noninvasively stimulate hippocampal cells cultured on chip at cellular resolution. Combined with calcium imaging using high-affinity indicators, we demonstrate the ability to observe spatiotemporal dynamics of neural activity.
Mutagenesis and Functional Characterization of the RNA and Protein Components of the toxIN Abortive Infection and Toxin-Antitoxin Locus of Erwinia (2009)

Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multiple adaptive resistance mechanisms. These mechanisms include the abortive infection systems, which promote "altruistic suicide" of an infected cell, protecting the clonal population. A cryptic plasmid of Erwinia carotovora subsp. atroseptica, pECA1039, has been shown to encode an abortive infection system. This highly effective system is active across multiple genera of gram-negative bacteria and against a spectrum of phages. Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module. ToxIN is the first member of a new type III class of protein-RNA toxin-antitoxin modules, of which there are multiple homologues cross-genera. We characterized in more detail the abortive infection phenotype of ToxIN using a suite of Erwinia phages and performed mutagenesis of the ToxI and ToxN components. We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN. Furthermore, site-directed mutagenesis of ToxN revealed key conserved amino acids in this defining member of the new group of toxic proteins. The mechanism of phage activation of the ToxIN system was investigated and was shown to have no effect on the levels of the ToxN protein. Finally, evidence of negative autoregulation of the toxIN operon, a common feature of toxin-antitoxin systems, is presented. This work on the components of the ToxIN system suggests that there is very tight toxin regulation prior to suicide activation by incoming phage.
Realistic flight conditions on ground: new research facility for cabin ventilation (2022)

Abstract A new full-scale test bench was developed and set up at the German Aerospace Center in Göttingen to experimentally analyze novel ventilation approaches for aircraft under realistic thermodynamic boundary conditions. The new ground-based test rig represents a modern twin-aisle cabin layout characteristic for long-haul airliners. In addition to having a realistic cabin geometry, it also facilitates the experimental simulation of thermodynamic boundary conditions to study the performance of alternative ventilation concepts for different flight phases (e.g., climbing or cruising). The implemented fuselage elements as well as the floor are temperature controllable. Using this kind of mantle heating/cooling system allows dynamic changes of inner surface temperatures in a range covering the operationally relevant temperature and time scales. With this experimental set-up, a complete flight scenario (i.e., taxiing, climbing, cruising and descent) can be simulated thermodynamically. Thermal manikins were used during the studies to simulate the passenger’s heat impact experimentally. Latest measurement techniques comprising the acquisition of flow velocities, fluid temperatures as well as surface temperatures were used. Based on these data, integral quantities like the mean temperature stratification and mean velocity levels near the manikins, the heat removal efficiency as well as the predicted mean vote and the percentage of dissatisfied passengers were calculated to score the ventilation concepts in terms of passenger comfort for two different operational scenarios under steady boundary conditions.
LiST: Lite Prompted Self-training Makes Parameter-Efficient Few-shot Learners (2021)

We present a new method LiST is short for Lite Prompted Self-Training for parameter-efficient fine-tuning of large pre-trained language models (PLMs) for few-shot learning. LiST improves over recent methods that adopt prompt-based fine-tuning (FN) using two key techniques. The first is the use of self-training to leverage large amounts of unlabeled data for prompt-based FN in few-shot settings. We use self-training in conjunction with meta-learning for re-weighting noisy pseudo-prompt labels. Self-training is expensive as it requires updating all the model parameters repetitively. Therefore, we use a second technique for light-weight fine-tuning where we introduce a small number of task-specific parameters that are fine-tuned during self-training while keeping the PLM encoder frozen. Our experiments show that LiST can effectively leverage unlabeled data to improve the model performance for few-shot learning. Additionally, the fine-tuning is efficient as it only updates a small percentage of parameters and the overall model footprint is reduced since several tasks can share a common PLM encoder as backbone. A comprehensive study on six NLU tasks demonstrate LiST to improve by 35% over classic fine-tuning and 6% over prompt-based FN with 96% reduction in number of trainable parameters when fine-tuned with no more than 30 labeled examples from each task. With only 14M tunable parameters, LiST outperforms GPT-3 in-context learning by 33% on few-shot NLU tasks.
Kinetics and Structure during Self-Assembly of Oppositely Charged Proteins in Aqueous Solution (2011)

Self-assembly in aqueous solution of two oppositely charged globular proteins, hen egg white lysozyme (LYS) and bovine calcium-depleted α-lactalbumin (apo α-LA), was investigated at pH 7.5. The aggregation rate of equimolar mixtures of the two proteins was determined using static and dynamic light scattering as a function of the ionic strength (15-70 mM) and protein concentration (0.28-2.8 g/L) at 25 and 45 °C. The morphology of formed supramolecular structures was observed by confocal laser scanning microscopy. When the two proteins are mixed, small aggregates were formed rapidly that subsequently grew by collision and fusion. The aggregation process led on larger length scales to irregularly shaped flocs at 25 °C, but to monodisperse homogeneous spheres at 45 °C. Both the initial rate of aggregation and the fraction of proteins that associated decreased strongly with decreasing protein concentration or increasing ionic strength but was independent of the temperature.