gebhart/patrepeval huggingface dataset:
Localization of the Putative Sialic Acid-binding Site on the Immunoglobulin Superfamily Cell-surface Molecule CD22 (1996)

B-lymphocyte antigen CD22 is a member of the recently described sialoadhesin family of immunoglobulin-like cell-surface glycoproteins that bind glycoconjugates terminating in sialic acid. One prominent ligand for CD22 is the highly glycosylated leukocyte surface protein CD45. Using surface plasmon resonance spectroscopy, we characterized the interaction of recombinant mouse CD22 with native CD45 purified from rat thymus (CD45-thy). By in situ desialylation and resialylation of immobilized CD45-thy, we show that mouse CD22 binds to the sialoglycoconjugate NeuGc2-6Gal1-4GlcNAc carried on CD45-thy N-glycans. Previous studies have shown that the sialic acid-binding site lies within the two membrane-distal domains of CD22 (domains 1 and 2), which are V-set and C2-set immunoglobulin superfamily domains, respectively. To further localize the binding site, we have made 42 single amino acid substitutions throughout both domains. All 12 mutations that abrogated binding to CD45-thy without disrupting antibody binding were of residues within the GFCCC -sheet of domain 1. These residues are predicted to form a contiguous binding site centered around an arginine residue in the F strand that is conserved in all members of the sialoadhesin family. Our results provide further evidence that immunoglobulin superfamily cell adhesion molecules use the GFCCC -sheet of membrane-distal V-set domains to bind structurally diverse ligands, suggesting that this surface is favored for cell-cell recognition.
I. An Improved Procedure for Alkene Ozonolysis. II. Exploring a New Structural Paradigm for Peroxide Antimalarials. (2011)

The use of ozone for the transformation of alkenes to carbonyls has been well established. The reaction of ozone with alkenes in this fashion generates either a 1,2,4-trioxolane (ozonide) or a hydroperoxyacetal, either of which must undergo a separate reduction step to provide the desired carbonyl compound. There is considerable interest in being able to perform a reductive ozonolysis to directly provide the carbonyl. Previous reports from the Dussault lab have shown that amine N-oxides are able to perform a reductive ozonolysis. In the course of efforts to expand this reaction to other oxyanions it was realized that water was also able to efficiently perform a net reductive ozonolysis via nucleophilic capture of the carbonyl oxide. This transformation was investigated for a variety of substrates and was shown to offer a useful alternative to conventional ozonolysis conditions. Malaria is a global health epidemic that affects between 300-500 million people annually, with the most deadly strain being P. falciparum. The current treatment for malaria is artemisinin combination therapy, but the development of artemisinin-resistant strains of malaria has spurred the need for the development of new treatments. 1,2,4-Trioxolanes exhibit high efficacy against malaria, but concerns remain about their thermal and serum stability. Our analysis of the likely mechanism of action of ozonides guided our development of structurally related 3-alkoxy-1,2-dioxolanes as a potential treatment for malaria. This class of compounds has shown to possess high levels of activity against P. falciparum in vitro. The synthesis of these dioxolanes required the development of new synthetic routes, which will be discussed in detail, as will efforts to optimize the activity of 3-alkoxy-1,2-dioxolanes. In addition, the synthesis and evaluation of 1,2,4-trioxepanes as potential antimalarials was explored. In the course of our investigation into the synthesis of 3-alkoxy-1,2-dioxolanes, we found Re (VII) oxide to be an effective catalyst for the transetherification of 3-alkoxy-1,2-dioxolanes. Re (VII) oxide was briefly explored as a catalyst for allylation or etherification reactions that involve stabilized carbocations as intermediates.
FloWaveNet : A Generative Flow for Raw Audio (2018)

Most modern text-to-speech architectures use a WaveNet vocoder for synthesizing high-fidelity waveform audio, but there have been limitations, such as high inference time, in its practical application due to its ancestral sampling scheme. The recently suggested Parallel WaveNet and ClariNet have achieved real-time audio synthesis capability by incorporating inverse autoregressive flow for parallel sampling. However, these approaches require a two-stage training pipeline with a well-trained teacher network and can only produce natural sound by using probability distillation along with auxiliary loss terms. We propose FloWaveNet, a flow-based generative model for raw audio synthesis. FloWaveNet requires only a single-stage training procedure and a single maximum likelihood loss, without any additional auxiliary terms, and it is inherently parallel due to the characteristics of generative flow. The model can efficiently sample raw audio in real-time, with clarity comparable to previous two-stage parallel models. The code and samples for all models, including our FloWaveNet, are publicly available.
Networked neural spheroid by neuro-bundle mimicking nervous system created by topology effect (2015)

In most animals, the nervous system consists of the central nervous system (CNS) and the peripheral nervous system (PNS), the latter of which connects the CNS to all parts of the body. Damage and/or malfunction of the nervous system causes serious pathologies, including neurodegenerative disorders, spinal cord injury, and Alzheimer's disease. Thus, not surprising, considerable research effort, both in vivo and in vitro, has been devoted to studying the nervous system and signal transmission through it. However, conventional in vitro cell culture systems do not enable control over diverse aspects of the neural microenvironment. Moreover, formation of certain nervous system growth patterns in vitro remains a challenge. In this study, we developed a deep hemispherical, microchannel-networked, concave array system and applied it to generate three-dimensional nerve-like neural bundles. The deep hemicylindrical channel network was easily fabricated by exploiting the meniscus induced by the surface tension of a liquid poly(dimethylsiloxane) (PDMS) prepolymer. Neurospheroids spontaneously aggregated in each deep concave microwell and were networked to neighboring spheroids through the deep hemicylindrical channel. Notably, two types of satellite spheroids also formed in deep hemispherical microchannels through self-aggregation and acted as an anchoring point to enhance formation of nerve-like networks with neighboring spheroids. During neural-network formation, neural progenitor cells successfully differentiated into glial and neuronal cells. These cells secreted laminin, forming an extracellular matrix around the host and satellite spheroids. Electrical stimuli were transmitted between networked neurospheroids in the resulting nerve-like neural bundle, as detected by imaging Ca(2+) signals in responding cells.
Complete assignment of the aromatic proton magnetic resonance spectrum of the kringle 1 domain from human plasminogen: the structure of the ligand-binding site (1987)

The kringle 1 domain of human plasminogen has been investigated by 1H NMR spectroscopy at 300 and 600 MHz on the basis of a fragment obtained via controlled proteolysis of the zymogen with Staphylococcus aureus V8 protease. The aromatic spectrum has been fully analyzed and all resonances assigned. The Tyr ring signals were identified by reference to the recently reported spectra of the plasminogen kringle 4 homologues from human, bovine, and porcine origin [Ramesh, V., Gyenes, M., Patthy, L., & Llinás, M. (1986) Eur. J. Biochem. 159, 581-595]. In particular, Tyr74 was assigned on the basis of a proton Overhauser experiment showing cross-relaxation with the Trp-II (Trp62) indole ring, a connectivity previously observed in all the kringle 4 variants and that clearly represents a conserved feature of the kringle structure. Ligand binding was investigated by monitoring the effects of the antifibrinolytic drugs epsilon-aminohexanoic acid and p-benzylaminesulfonic acid (BASA) on the 1H NMR spectrum of kringle 1. It is observed that although most aromatic resonances are perturbed by ligand presence, the chemical shift response is significantly more marked for Phe36, Trp62, and Tyr72. Proton Overhauser experiments centered on aromatic transitions from these residues reveal efficient cross-relaxation with BASA, which indicates direct contacts between the hydrophobic side chain rings and the ligand hydrocarbon moiety at the binding site. A close interaction is also found between Tyr64 and Try72 which indicates that the residue 64 ring is positioned close to the binding site. Excellent overall agreement is found between the NMR data and the molecular folding of the prothrombin kringle 1 determined crystallographically [Park, C. H., & Tulinsky, A. (1986) Biochemistry 25, 3977-3982]. A structure is proposed here for the kringle 1 lysine-binding site which is based upon the NMR results, the X-ray structure, and computer graphics modeling. It is concluded that although features of the lysine-binding site are common to plasminogen kringles 1 and 4, in kringle 1 the binding site extends beyond the kringle inner loop as it encompasses residues Arg34 and Phe36 as well. Furthermore, it appears that in kringle 1 Arg34 and Asp55 are likely to play a direct role in the ligand-kringle 1 interaction by reinforcing the polarity of the cationic and anionic centers of the side chains of Arg71 and Asp57, which have been implicated to provide the electrostatic charges in kringle 4 that balance those of the ligand dipole at the binding site.
Taxonomy of space–time processingforwireless networks (1998)

A taxonomy of space–time signal processing is addressed in terms of architectural and algorithmic classification, and the influence of the propagation channel on the space–time processing. The architecture is classified according to link structure, channel reuse and multiple access scheme. Algorithms are classified into channel estimation methods, TDMA and CDMA receive algorithms and space–time transmit algorithms. Finally, the effects of Doppler spread, delay spread and angle spread on space–time processing are discussed.
Acetone-Butanol Fermentation of Sugars (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcetone-Butanol Fermentation of SugarsSamuel C. BeeschCite this: Ind. Eng. Chem. 1952, 44, 7, 1677–1682Publication Date (Print):July 1, 1952Publication History Published online1 May 2002Published inissue 1 July 1952https://pubs.acs.org/doi/10.1021/ie50511a054https://doi.org/10.1021/ie50511a054research-articleACS PublicationsRequest reuse permissionsArticle Views793Altmetric-Citations57LEARN 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 options Get e-Alerts
Changing Perspectives of Stress Gastritis Prophylaxis (1994)

Controversies still exist regarding the need to provide prophylaxis, the choice of an agent, and the relative importance of previously identified risk factors. Further well-designed studies are needed before consensus can be reached.
Efficient transient expression system based on square pulse electroporation and in vivo luciferase assay of fertilized fish eggs (1993)

Electroporation mediated DNA transfer into fish eggs has been improved by using a train of square pulses. Fertilized eggs of African catfish (Clarias gariepinus), zebrafish (Brachydanio rerio) and rosy barb (Barbus conchonius) were dechorionated enzymatically followed by application of pulses. Efficiency of plasmid DNA delivery was significantly increased by applying multiple pulses on dechorionated eggs. Optimization of physical parameters such as field strength, pulse width and pulse numbers resulted in reproducible transient expression in 25-50% of embryos and larvae by using the firefly luciferase and the E. coli beta-galactosidase (lacZ) genes both driven by CMV IE1 promoter. Temporal luciferase expression was assayed using both qualitative (sheet film) and quantitative (scintillation counting) methods in developing embryos and fry in vivo. Spatial expression of lacZ was assayed by histochemical staining. A number of embryos revealed foreign gene product also localised in the vegetal pole of the embryo.
Impact of surface topography and laser pulse duration for laser ablation of solar cell front side passivating SiNx layers (2010)

Local contact openings in SiNx layers that passivate the front side of solar cells offer an attractive alternative to the current standard “fire-through” screen printing process for front grid fabrication. Additionally, this technology can be used for enabling a selective emitter. In the present paper, we investigate laser ablation of SiNx layers on planar and textured silicon surfaces for various laser wavelengths and pulse durations in the nanosecond (ns) to femtosecond (fs) range. We characterize the dark J-V characteristics of diodes with laser contact openings in the SiNx layer passivating the emitter. Our results show that on alkaline textured surfaces the ablation by a ns laser produces less damage than by an ultrashort pulse laser. The dark currents of alkaline textured diodes treated with picosecond (ps) or fs lasers are one order of magnitude higher than those of ns laser treated diodes. High ideality factors furthermore indicate crystal damage in the ∼500 nm deep space charge region of the diodes. Scanning electron microscope and transmission electron microscope images of textured samples, confirm the presence of extensive and deep crystal damage after ps laser ablation, which are not observed in laser treated samples with planar surfaces. Correspondingly, for planar surfaces we find for both, ns and for ps laser ablated regions, emitter saturation current densities J0e,abl of ∼2 pA/cm2. The recombination in textured samples in contrast differs vastly for ns and ps laser ablation. The ns laser results in an only slightly increased value of 3.7 pA/cm2 while the ps laser treated sample was not evaluable due to severe crystal damage leading to effective lifetimes of &amp;lt;5 μs.
The new laboratory (1989)

It will cost a billion dollars, ten billion volts 'twill give,It will take five thousand scholars seven years to make it live …Take away your billion dollars, take away your tainted gold,You can keep your damn ten billion volts, my soul will not be sold.– © Arthur Roberts, “Take Away Your Billion Dollars” (also known as the Brookhaven National Anthem) (1946)
Triptolide functions as a potent angiogenesis inhibitor (2009)

Triptolide is a key anti-inflammatory compound of the Chinese herbal medicine Tripterygium wilfordii Hook. f. (Celastraceae). It also possesses potent antitumor activity. In this study, we show that triptolide is an angiogenesis inhibitor based on various angiogenesis assays. The IC(50) in in vitro assays was 45 nM, which was much lower than the plasma concentrations of triptolide in the rat or human administered with T. wilfordii extracts for treating inflammation. When dosed in vivo, triptolide potently inhibited angiogenesis at 100 nM in Matrigel plug assay. Triptolide at 0.75 mg/kg/day significantly blocked tumor angiogenesis and tumor progression in murine tumorigenesis assay. The underlying mechanism of triptolide correlated with downregulation of proangiogenic Tie2 and VEGFR-2 expression in human umbilical vein endothelial cell by semiquantitative RT-PCR and western blot analysis. Although Tie2 inhibition appeared to be a later event as compared with VEGFR-2, Tie2 overexpression significantly attenuated the inhibitory effect of triptolide on endothelial proliferation and network formation. By contrast, Tie2 knockdown mimicked the inhibitory effect of triptolide on endothelial network formation. Our findings suggest that antitumor action of triptolide is partly via inhibition of tumor angiogenesis by blocking 2 endothelial receptor-mediated signaling pathways, and triptolide can be a promising antiangiogenic agent.
Physiological Changes at Parturition and Their Relationship to Metabolic Disorders (1997)

Most of the metabolic diseases of dairy cows-milk fever, ketosis, retained placenta, and displacement of the abomasum-occur within the first 2 wk of lactation. The etiology of many of those metabolic diseases that are not clinically apparent during the first 2 wk of lactation, such as laminitis, can be traced back to insults that occurred during early lactation. In addition to metabolic disease, the overwhelming majority of infectious disease, in particular mastitis, becomes clinically apparent during the first 2 wk of lactation. Three basic physiological functions must be maintained during the periparturient period if disease is to be avoided: adaptation of the rumen to lactation diets that are high in energy density, maintenance of normocalcemia, and maintenance of a strong immune system. The incidence of both metabolic and infectious diseases is greatly increased whenever one or more of these physiological functions are impaired. This paper discusses the etiological role of each of these factors in the development of common diseases encountered during the periparturient period.
Real world research (1997)

There is a perception that research is a straightforward process and follows a recipe book approach. It is a myth that has been perpetuated by some who have never undertaken research yet are expected to teach it. In reality, it can be as messy and uncertain as practice itself and it is important for researchers, teachers and practitioners to recognise this. It does not follow the neat prescription that one finds in books, nor should it if it is going to be tailored to individual projects. It's not mysterious, or a talent bestowed on a golden few - it's a skill like any other, to be learned and developed.
Prayer and care (2009)

There is evidence that praying for a sick person can aid their recovery, says Stephen Wright
Photoinhibition in Mutants of Arabidopsis Deficient in Thylakoid Unsaturation (2002)

Thylakoid lipid composition in higher plants is characterized by a high level of fatty acid unsaturation. We have screened four mutants of Arabidopsis that have reduced levels of fatty acid unsaturation. Three of the mutant lines tested, fad5, fad6, and the fad3-2 fad7-2 fad8 triple mutant, were more susceptible to photoinhibition than wild-type Arabidopsis, whereas one mutant, fab1, was indistinguishable from wild type. The fad3-2 fad7-2 fad8 triple mutant, which contains no trienoic fatty acids in its thylakoid membranes, was most susceptible to photoinhibition. Detailed investigation of photoinhibition in the triple mutant revealed that the rate of photoinactivation of PSII was the same in wild-type and mutant plants. However, the recovery of photoinactivated PSII was slower in fad3-2 fad7-2 fad8, relative to wild type, at all temperatures below 27 degrees C. These results indicate that trienoic fatty acids of thylakoid membrane lipids are required for low-temperature recovery from photoinhibition in Arabidopsis.
The Hippo–YAP pathway in organ size control and tumorigenesis: an updated version (2010)

The Hippo signaling pathway is gaining recognition as an important player in both organ size control and tumorigenesis, which are physiological and pathological processes that share common cellular signaling mechanisms. Upon activation by stimuli such as high cell density in cell culture, the Hippo pathway kinase cascade phosphorylates and inhibits the Yes-associated protein (YAP)/TAZ transcription coactivators representing the major signaling output of the pathway. Altered gene expression resulting from YAP/TAZ inhibition affects cell number by repressing cell proliferation and promoting apoptosis, thereby limiting organ size. Recent studies have provided new insights into the Hippo signaling pathway, elucidating novel phosphorylation-dependent and independent mechanisms of YAP/Yki inhibition by the Hippo pathway, new Hippo pathway components, novel YAP target transcription factors and target genes, and the three-dimensional structure of the YAP-TEAD complex, and providing further evidence for the involvement of YAP and the Hippo pathway in tumorigenesis.
Hydrozirconation-transmetalation. A mild, direct route to higher order vinylic cuprates from monosubstituted acetylenes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrozirconation-transmetalation. A mild, direct route to higher order vinylic cuprates from monosubstituted acetylenesBruce H. Lipshutz and Edmund L. EllsworthCite this: J. Am. Chem. Soc. 1990, 112, 20, 7440–7441Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00176a079https://doi.org/10.1021/ja00176a079research-articleACS PublicationsRequest reuse permissionsArticle Views962Altmetric-Citations98LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase (2012)

MCP-1-induced protein 1 (MCPIP1) plays an important role in the downregulation of the LPS-induced immune response by acting as an RNase targeting IL-6 and IL-12b mRNAs. A conserved domain located in the N-terminal part of MCPIP1 is thought to be responsible for its RNase activity, but its catalytic mechanism is not well understood due to the lack of an atomic resolution structure. We determined the 3D crystal structure of this MCPIP1 N-terminal conserved RNase domain at a resolution of 2.0 Å. The overall structure of MCPIP1 N-terminal conserved domain shares high structural homology with PilT N-terminal domain. We show that the RNase catalytic center is composed of several acidic residues, verifying their importance by site-specific mutagenesis. A positively charged arm close to the catalytic center may act as an RNA substrate-binding site, since exchange of critical positively charged residues on this arm with alanine partially abolish the RNase activity of MCPIP1 in vivo. Our structure of the MCPIP1 N-terminal conserved domain reveals the details of the catalytic center and provides a greater understanding of the RNA degradation mechanism.