gebhart/patrepeval huggingface dataset:
Selective UBC 13 Inhibitors (2014)

This probe report describes the identification and development of a potent, sub-micromolar (IC50 = 781 nM), first-in-class, small molecule inhibitor of Ubc13 enzyme activity, ML307. The activity of the probe compound was assessed by its ability to suppress Ubc13-mediated formation of heteropolymeric poly-ubquitination chains comprised of a mix of terbium-labeled and fluorescein-labeled ubiquitin molecules, as monitored by a reduction of the time-resolved fluorescent resonance energy transfer (TR-FRET) signal arising from this chains when synthesized in vitro in collaboration with the Ubc13 cofactor UEV1a. ML307 has excellent solubility and stability in buffer and is not a general cysteine protease inhibitor as it is >128-fold selective against Caspase-3, nor a TR-FRET artifact as it is not inhibitory a TR-FRET assay for Bfl-1, an out of class target. ML307 resulted from an extensive elucidation of the structure-activity relationship (SAR) through the purchase and synthesis of over 90 compounds representing 5 related scaffolds. The level of in vitro potency achieved is unprecedented in the current state of art, thus representing a significant advance and providing a chemical tool for assessing the biological roles and biochemical mechanisms of Ubc13.
Domino Transformation of d-Glucal to Racemic α-Substituted α-Hydroxymethyl Furfuryl Derivatives (2013)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionDomino Transformation of d-Glucal to Racemic α-Substituted α-Hydroxymethyl Furfuryl DerivativesDebaraj Mukherjee, Syed Khalid Yousuf, and Subhash Chandra Taneja*Cite this: Org. Lett. 2013, 15, 12, 3180Publication Date (Web):June 12, 2013Publication History Received29 May 2013Published online12 June 2013Published inissue 21 June 2013https://pubs.acs.org/doi/10.1021/ol400406vhttps://doi.org/10.1021/ol400406vcorrectionACS PublicationsCopyright © 2013 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1153Altmetric-Citations-LEARN 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 PDF (37 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Reaction products Get e-Alerts
Deuterium NMR study of methyl group dynamics in L-alanine (1987)

Deuterium quadrupole echo spectroscopy is used to study the dynamics of the CD3 group in polycrystalline L-alanine-d3. Temperature-dependent quadrupole echo line shapes, their spectral intensities and τ dependence, and the anisotropy of the 2H spin-lattice relaxation were employed to determine the rate and mechanism of the –CD3 group motion. The rigid lattice Pake pattern observed at low temperature (T&amp;lt;−120 °C) transforms to a triplet spectrum characteristic of threefold jumps in the intermediate exchange regime (−120 to −70 °C) and this in turn to a Pake pattern of reduced breadth at higher temperatures (T&amp;gt;−70 °C). The quadrupole echo line shapes and their τ dependence, which are especially sensitive to the rate and mechanism of the motion, can be simulated quantitatively with the threefold jump model. We find Ea=20.0 kJ/mol for this process which is higher than is observed for most methyl groups, probably because of steric crowding in the L-Ala molecule. Finally, we observe a line shape due to the presence of multiple crystallographic forms which suggests that this technique can be extended to studies of the dynamics of more complex systems.
Efficient broadband marine acquisition and processing for improved resolution and deep imaging (2010)

One of the main goals of marine seismic acquisition is to deliver broadband data, rich in both low and high frequencies. The low frequencies are required for deep imaging, for inversion stability and for improved processing such as velocity analyses. The high frequencies are required, in addition to the low-frequencies, for better resolution. The problem of increasing the low-frequency content while maintaining the high-frequency content is caused by the well understood free-surface ghost effect. Towing streamers shallow favors the higher frequencies at the expense of attenuating the low frequencies, while towing streamers deep favors the lower frequencies, at the expense of attenuating frequencies within the seismic bandwidth.
Tubulin GTP hydrolysis influences the structure, mechanical properties, and kinesin-driven transport of microtubules. (1994)

Tubulin is a GTPase that hydrolyzes its bound nucleotide triphosphate after it becomes incorporated into a microtubule. The only known consequence of nucleotide hydrolysis is that it increases the dissociation rate of tubulin from the end of the microtubule by 2 orders of magnitude. In this study, we investigated whether microtubules composed of tubulin-GMPCPP (guanylyl alpha,beta-methylenediphosphate) (a very slowly hydrolyzed GTP analog) or tubulin-GDP exhibit additional structural or functional differences. We show that tubulin-GMPCPP microtubules are significantly stiffer than tubulin-GDP microtubules and have a 21% shallower protofilament twist angle. We also find that kinesin, a microtubule-based motor protein, transports tubulin-GMPCPP microtubules at approximately 30% faster rates than tubulin-GDP microtubules. These findings suggest that growing microtubule ends, which are thought to be composed of tubulin-GTP, may have different structural and mechanical properties from the remainder of the microtubule polymer.
A Direct Neurokinin B Projection from the Arcuate Nucleus Regulates Magnocellular Vasopressin Cells of the Supraoptic Nucleus (2015)

Central administration of neurokinin B (NKB) agonists stimulates immediate early gene expression in the hypothalamus and increases the secretion of vasopressin from the posterior pituitary through a mechanism that depends on the activation of neurokinin receptor 3 receptors (NK3R). The present study reports that, in the rat, immunoreactivity for NK3R is expressed in magnocellular vasopressin and oxytocin neurones in the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus, and that NKB immunoreactivity is expressed in fibres in close juxtaposition with vasopressin neurones at both of these sites. Retrograde tracing in the rat shows that some NKB-expressing neurones in the arcuate nucleus project to the SON and, in mice, using an anterograde tracing approach, it is found that kisspeptin-expressing neurones of the arcuate nucleus, which are known to co-express NKB, project to the SON and PVN. Finally, i.c.v. injection of the NK3R agonist senktide is shown to potently increase the electrical activity of vasopressin neurones in the SON in vivo with no significant effect detected on oxytocin neurones. The results suggest that NKB-containing neurones in the arcuate nucleus regulate the secretion of vasopressin from magnocellular neurones in rodents, and the possible significance of this is discussed.
Ionisation and fragmentation of complex glycans with a quadrupole time‐of‐flight mass spectrometer fitted with a matrix‐assisted laser desorption/ionisation ion source (2000)

This paper reports the use of an experimental matrix-assisted laser desorption/ionisation (MALDI) ion source fitted to a quadrupole time-of-flight (Q-Tof) mass spectrometer for the analysis of carbohydrates, particularly the N-linked glycans from glycoproteins. Earlier work on the Q-Tof instrument, using electrospray ionisation, gave excellent MS/MS spectra, particularly from the [M + Na]+ ions, but suffered from the major disadvantages that the signal was often split between singly and multiply charged ions and that sensitivity fell dramatically as the molecular weight of the carbohydrate rose. The MALDI ion source did not suffer from these problems and the instrument produced excellent MS and MS/MS spectra from small amounts of complex, underivatised glycans as well as those derivatised at the reducing terminus. Positive ion MS spectra of sialylated glycans recorded on the new instrument were much less complex than those recorded with a conventional MALDI-TOF instrument because of the absence of ions resulting from metastable (post-source decay, (PSD)) fragmentations occurring in the flight tube. However, considerable fragmentation by loss of sialic acid still occurred. MS/MS spectra of the [M + Na]+ ions from all compounds were almost identical to those recorded earlier with the electrospray-Q-Tof combination and far superior to MALDI-PSD spectra recorded with reflectron-TOF instruments. Spectra are shown for neutral and sialylated N-linked glycans from chicken ovalbumin, riboflavin binding protein, alpha1-acid glycoprotein, bovine fetuin and ribonuclease B, both as free glycans and as those derivatised at their reducing termini. The technique was applied to the structural determination of N-linked glycans from human secretory IgA and Apo-B 100 from human low-density lipoprotein.
High Efficiency White OLEDs for Lighting (2012)

A light outcoupling substrate and high performance white OLEDs were investigated. The light outcoupilng substrate achieved high light coupling efficiency of 42.8 % in a white OLED. A fluorescent / phosphorescent hybrid two-unit device achieved high luminous efficacy of 56 lm/W, high CRI of 91 and long lifetime of 150,000 h at 1,000 cd/m2. An optically and electrically optimized two-unit of all phosphorescent white OLED realized quite high luminous efficacy of 83 lm/W and was estimated to be half decay lifetime of over 100,000 h.
Investigation of the polymer systems for ArF resists (2003)

Various resists, which consisted of polymer systems, such as methacrylate, acrylate and cycloolefin/maleic anhydride (COMA), were investigated in the viewpoint of etching resistance, lithographic performance and shelf life. The oxide etching rate was in order of acrylate < methacrylate << COMA. The surface roughness of the acrylate type resist after oxide etching was the smallest among all samples. The methacrylate type resist showed high resolution capability as a line and space resist. On the other hand, pattern collapse was observed in the acrylate type resist, and low resolution was shown in the COMA type resist because of the large resist thickness loss. In the case of contacts, the acrylate type resist showed better linearity. The sensitivity of the acrylate and methacrylate type resists kept at room temperature did not changed in 20 days, while the sensitivity of the COMA type resist changed. It was found that the methacrylate type resist was the most suitable as a line and space resist and the acrylate type resist was the most promising as a contact hole resist.
Explicitly Parallel Regular Expressions (2006)

The equivalence of non-deterministic finite automata (NFA ), deterministic finite automata (DFA), regular expressions (RE), and parallel finite automata (PFA) with augmented regular expressions (PRE) is used to relate parallel finite automata to the shuffle operation on regular languages. Our goal is to capitalize on the equivalence of regular expressions and augmented regular expressions to increase parallelization efficiency. We use the existing automated transformation algorithms for the various finite automata listed above, as well as one of our own, to inform a transformation from augmented regular expressions to minimized deterministic finite automata (DFAmin). We then discuss the serialization of augmented regular expressions, and present a brief summary of potential applications, related research, and future directions
Carboxy terminally truncated forms of ribophorin I are degraded in pre-Golgi compartments by a calcium-dependent process. (1992)

Two COOH terminally truncated variants of ribophorin I (RI), a type I transmembrane glycoprotein of 583 amino acids that is segregated to the rough portions of the ER and is associated with the protein-translocating apparatus of this organelle, were expressed in permanent HeLa cell transformants. Both variants, one membrane anchored but lacking part of the cytoplasmic domain (RL467) and the other consisting of the luminal 332 NH2-terminal amino acids (RI332), were retained intracellularly but, in contrast to the endogenous long lived, full length ribophorin I (t 1/2 = 25 h), were rapidly degraded (t 1/2 less than 50 min) by a nonlysosomal mechanism. The absence of a measurable lag phase in the degradation of both truncated ribophorins indicates that their turnover begins in the ER itself. The degradation of RI467 was monophasic (t 1/2 = 50 min) but the rate of degradation of RI332 molecules increased about threefold approximately 50 min after their synthesis. Several pieces of evidence suggest that the increase in degradative rate is the consequence of the transport of RI332 molecules that are not degraded during the first phase to a second degradative compartment. Thus, when added immediately after labeling, ionophores that inhibit vesicular flow out of the ER, such as carbonyl cyanide m-chlorophenylhydrazone (CCCP) and monensin, suppressed the second phase of degradation of RI332. On the other hand, when CCCP was added after the second phase of degradation of RI332 was initiated, the degradation was unaffected. Moreover, in cells treated with brefeldin A the degradation of RI332 became monophasic, and took place with a half-life intermediate between those of the two normal phases. These results point to the existence of two subcellular compartments where abnormal ER proteins can be degraded. One is the ER itself and the second is a non-lysosomal pre-Golgi compartment to which ER proteins are transported by vesicular flow. A survey of the effects of a variety of other ionophores and protease inhibitors on the turnover of RI332 revealed that metalloproteases are involved in both phases of the turnover and that the maintenance of a high Ca2+ concentration is necessary for the degradation of the luminally truncated ribophorin.
Maintenance Olaparib in Patients with Newly Diagnosed Advanced Ovarian Cancer (2018)

The use of maintenance therapy with olaparib provided a substantial benefit with regard to progression-free survival among women with newly diagnosed advanced ovarian cancer and a BRCA1/2 mutation, with a 70% lower risk of disease progression or death with olaparib than with placebo. (Funded by AstraZeneca and Merck; SOLO1 ClinicalTrials.gov number, NCT01844986 .).
Optical sheet memory system (1992)

Abstract This paper proposes a system for information storage and delivery. It is based on the new concept where the information corresponding to 10 still pictures and approximately 3 min of sound are encoded digitally and printed on a postcard as a dot pattern to be read and restored. The system is called an optical postcard system. In this study, after the basic technologies for the realization of this system are investigated, the printed optical postcard and the reproducing system are constructed experimentally. As a result of there production experiment, the information recorded on the postcard is read and the original picture and sound signal are played back. This indicates that the information can be delivered by optical postcard. The proposed idea of an information storage/delivery system can be applied not only to postcard‐sized sheet, but also to sheets of various sizes. Also, there can be various applications which differ from the use of the traditional information media, e.g., the the use of the traditional information media, e.g., the zine.
Forschung 2019 (2020)

Bericht mit Forschungsprojekten aus verschiedenen Bereichen der OTH Regensburg mit dem Schwerpunktthema "Künstliche Intelligenz" und einem Gespräch zur "Medizin der Zukunft"
Making a Computational Attorney (2023)

This “blue sky idea” paper outlines the opportunities and challenges in data mining and machine learning involving making a computational attorney — an intelligent software agent capable of helping human lawyers with a wide range of complex high-level legal tasks such as drafting legal briefs for the prosecution or defense in court. In particular, we discuss what a ChatGPT-like Large Legal Language Model (L3M) can and cannot do today, which will inspire researchers with promising short-term and long-term research objectives.
Sympathetic nerve activity in normal and cystic follicles from isolated bovine ovary: local effect of beta-adrenergic stimulation on steroid secretion (2011)

Cystic ovarian disease (COD) is an important cause of abnormal estrous behavior and infertility in dairy cows. COD is mainly observed in high-yielding dairy cows during the first months post-partum, a period of high stress. We have previously reported that, in lower mammals, stress induces a cystic condition similar to the polycystic ovary syndrome in humans and that stress is a definitive component in the human pathology. To know if COD in cows is also associated with high sympathetic activity, we studied isolated small antral (5 mm), preovulatory (10 mm) and cystic follicles (25 mm). Cystic follicles which present an area 600 fold greater compared with preovulatory follicles has only 10 times less concentration of NE as compared with small antral and preovulatory follicles but they had 10 times more NE in follicular fluid, suggesting a high efflux of neurotransmitter from the cyst wall. This suggestion was reinforced by the high basal release of recently taken-up 3H-NE found in cystic follicles. While lower levels of beta-adrenergic receptor were found in cystic follicles, there was a heightened response to the beta-adrenergic agonist isoproterenol and to hCG, as measured by testosterone secretion. There was however an unexpected capacity of the ovary in vitro to produce cortisol and to secrete it in response to hCG but not to isoproterenol. These data suggest that, during COD, the bovine ovary is under high sympathetic nerve activity that in addition to an increased response to hCG in cortisol secretion could participate in COD development.
Disorders of Thiamine Metabolism (2016)

Thiamine is a water-soluble vitamin acting in the mitochondria as a cofactor for energy metabolism and, in the cytoplasm, in the pentose phosphate biosynthetic pathway. Its transport through the plasma membrane requires two transporters with overlapping functions: THTR1 encoded by SLC19A2, and THTR2 encoded by SLC19A3. Thiamine is transformed into its active form, thiamine pyrophosphate (TPP) by a kinase encoded by the <italic>TPK1</italic> gene. Then it may enter the mitochondria through a TPP transporter encoded by SLC25A19. Mutations in SLC19A2 cause thiamine-responsive megaloblastic anemia (TRMA). Mutations in SLC19A3 cause biotin/thiamine–responsive basal ganglia disease. Mutations in SLC25A19 may cause early microcephaly with death in infancy (also called Amish microcephaly) or a later-onset bilateral striatal necrosis with progressive peripheral neuropathy. Recently, mutations in the <italic>TPK1</italic> gene have been associated with recurrent encephalopathy with mild lactic acidosis.
Electro-Conjugate Fluid Jet-Driven Micro Artificial Antagonistic Muscle Actuators and their Integration (2010)

An electro-conjugate fluid (ECF) is a type of dielectric and functional fluid that generates a powerful jet flow when subjected to high DC voltage. Although a high voltage is needed to generate the jet flow, the current is quite low at several microamperes, resulting in a total power consumption of several milliwatts. Using this smart fluid, we can develop micro fluid-driven mechanical components without any bulky pumps. Also, it is clarified that the power density of the ECF jet is higher when the electrode pair is miniaturized; therefore, it is suitable for micro actuators. Here, we propose and fabricate three types of soft actuators with an antagonistic configuration: (i) micro artificial muscle cells, (ii) a McKibben-type micro artificial muscle actuator using the ECF effect and (iii) a micro finger actuator with two chambers to bend. The actuators basically consist of a silicone rubber tube covered with a fiber sleeve and a micro pressure source using the ECF effect. Next, we apply and integrate these actuators into a micro robot hand, driven with ECF jets. The driving characteristics of the micro artificial muscle actuator and the integrated micro ECF hand with ECF fingers were fabricated and experimentally investigated. The experimental results show that this ECF jet actuation is effective for driving soft micro hands.
Flexible, transparent single-walled carbon nanotube transistors with graphene electrodes (2010)

This paper reports a mechanically flexible, transparent thin film transistor that uses graphene as a conducting electrode and single-walled carbon nanotubes (SWNTs) as a semiconducting channel. These SWNTs and graphene films were printed on flexible plastic substrates using a printing method. The resulting devices exhibited a mobility of ∼ 2 cm(2) V(-1) s -1), On/Off ratio of ∼ 10(2), transmittance of ∼ 81% and excellent mechanical bendability.
Optimizing polymerase chain reaction conditions for the human perlecan (HSPG2) promoter (2009)

Perlecan, also called HSPG2, is a heparan sulfate proteoglycan predominantly located in basement membranes and the matrix surrounding endothelial, mesenchymal and stromal cells. The reactive stroma surrounding prostate cancer cell lines produces high levels of the protein which may play a role in delivery of growth and angiogenic factors, aiding survival and growth of metastatic tumors. The overall goal of this project was to study the promoter in order to understand the up‐regulation of perlecan in the tumor reactive stroma which occurs via transcriptional increases in perlecan biosynthesis. The sequence for the human HSPG2 promoter was found using public databases and compared to a published human sequence (Iozzo et al., 1997) and a mouse promoter sequence found in online databases. Several transcription factor binding sites of interest were identified for further study including NFkB, CREB, Smad3, Elk‐1, c‐Jun and TCF/LEF‐1. Currently we are working to build a promoter‐reporter construct by isolating the promoter region using polymerase chain reaction (PCR) amplification. Our current strategy seeks to optimize the PCR conditions with different sets of primers. The next step will be creating a fluorescence protein reporter construct of the full promoter sequence in order to test the effects of the identified pathways. This research was funded by the HHMI program and NIH/NCI P01 CA098912.