gebhart/patrepeval huggingface dataset:
Smad3-mediated Myocardin Silencing (2011)

Both TGF-β and myocardin (MYOCD) are important for smooth muscle cell (SMC) differentiation, but their precise role in regulating the initiation of SMC development is less clear. In TGF-β-induced SMC differentiation of pluripotent C3H10T1/2 progenitors, we found that TGF-β did not significantly induce Myocd mRNA expression until 18 h of stimulation. On the other hand, early SMC markers such as SM α-actin, SM22α, and SM calponin were detectable beginning 2 or 4 h after TGF-β treatment. These results suggest that Myocd expression is blocked during the initiation of TGF-β-induced SMC differentiation. Consistent with its endogenous expression, Myocd promoter activity was not elevated until 18 h following TGF-β stimulation. Surprisingly, Smad signaling was inhibitory to Myocd expression because blockade of Smad signaling enhanced Myocd promoter activity. Overexpression of Smad3, but not Smad2, inhibited Myocd promoter activity. Conversely, shRNA knockdown of Smad3 allowed TGF-β to activate the Myocd promoter in the initial phase of induction. Myocd was activated by PI3 kinase signaling and its downstream target Nkx2.5. Interestingly, Smad3 did not affect PI3 kinase activity. However, Smad3 physically interacted with Nkx2.5. This interaction blocked Nkx2.5 binding to the Myocd promoter in the early stage of TGF-β induction, leading to inhibition of Myocd mRNA expression. Moreover, Smad3 inhibited Nkx2.5-activated Myocd promoter activity in a dose-dependent manner. Taken together, our results reveal a novel mechanism for Smad3-mediated inhibition of Myocd in the initiation phase of SMC differentiation.
The Cleavage of Ethers with Boron Bromide. I. Some Common Ethers (1942)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Cleavage of Ethers with Boron Bromide. I. Some Common EthersF. L. Benton and T. E. DillonCite this: J. Am. Chem. Soc. 1942, 64, 5, 1128–1129Publication Date (Print):May 1, 1942Publication History Published online1 May 2002Published inissue 1 May 1942https://doi.org/10.1021/ja01257a035RIGHTS & PERMISSIONSArticle Views1909Altmetric-Citations80LEARN 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 (206 KB) Get e-Alerts Get e-Alerts
Clad Nd:YAG fibers for laser applications (1987)

We report the implementation of an extrusion method to clad Nd:YAG single crystal fibers with index-matched glasses ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Deltan = 0.048</tex> ). A propagation loss coefficient of 0.08 dB/cm was measured for the fundamental mode of a 41-μm-diameter glass-clad fiber laser, an improvement of about one order of magnitude over unclad fibers. Guided clad fiber lasers operated at 1.064 μm with thresholds as low as 0.3-0.5 mW and up to 65-mW CW output power are also reported. The origins of and means of reducing the residual loss are discussed.
The prebiotic effects of biscuits containing partially hydrolysed guar gum and fructo-oligosaccharides – a human volunteer study (2001)

Prebiotics are non-digestible food ingredients that target selected groups of the human colonic microflora, thus having the ability to alter the composition towards a more 'beneficial' community, i.e. selectively increasing populations of bifidobacteria and/or lactobacilli. In the present study the prebiotic potential of partially hydrolysed guar gum (PHGG) and fructo-oligosaccharides (FOS) in a biscuit was assessed in human volunteers. Fluorescent in situ hybridization using oligonucleotide probes targeting Bacteroides spp., Bifidobacterium spp., Clostridium spp. and Lactobacillus-Enterococcus spp. were used for the bacteriology and total bacteria were enumerated using the fluorescent stain 4',6-diamidino-2-phenylindole. Thirty-one volunteers consumed daily either three experimental biscuits (providing a total (g/d) of 6.6 FOS and 3.4 PHGG) or three placebo biscuits for two 21-d crossover periods. Bifidobacteria significantly increased in number on ingestion of the experimental biscuits compared with pre-treatment and placebo population levels. Bifidobacterial numbers returned to pretreatment levels within 7 d of the cessation of intake of experimental biscuits. A correlation was observed between the initial faecal bifidobacterial numbers and the magnitude of bifidogenesis, with volunteers who possessed low initial population levels of bifidobacteria experiencing the greatest increase in bifidogenesis. No changes were observed in the other bacterial groups monitored during the trial. Thus, the prebiotic nature of FOS and PHGG was maintained in a final food product as evidenced from the selective increase in bifidobacterial numbers.
Immunization with infective larvae of Strongyloides ratti (Nematoda) exposed to microwave radiation. (1983)

Microwaves have not been tested previously for possible application in producing immunogenic preparations of parasites. This study examines the immunizing capacity of microwave-irradiated, infective larvae of Strongyloides ratti in rats. Rats were inoculated subcutaneously with untreated, microwaved, or microwaved and homogenized larvae, or distilled water, and challenged with untreated larvae. Data were collected on egg production and worm number/rat during primary infections and on egg production, worm number/rat, worm size, and eggs in utero/worm following challenge. Our results demonstrated that microwaved, infective larvae (intact or homogenized) of S. ratti were immunogenic for rats, even though they were incapable of reaching the intestine and maturing to adult worms. The immunity elicited by exposure to microwaved larvae was characterized on challenge by a significant reduction in the number of eggs produced/worm, by the formation of perioral plugs, and by reductions in worm numbers and size. These results suggest that microwave radiation may provide a valuable new tool for parasitic vaccine production. In addition, we have demonstrated the occurrence of a feature of the immune response of rats to S. ratti that may have been overlooked previously; i.e., a gut-level response that was elicited by larvae, but manifested against adult worms in the intestine.
Determination of the structural basis for selective binding of Epstein-Barr virus to human complement receptor type 2. (1991)

Epstein-Barr virus (EBV) is an oncogenic herpesvirus that selectively infects and immortalizes human B lymphocytes. One determinant of this narrow tropism is human CR2, the only viral receptor within the superfamily of proteins that contain short consensus repeats (SCRs). Human CR2 serves as a receptor for both C3dg and the gp350/220 glycoprotein of EBV, and binds the monoclonal antibody (mAb) OKB7, which blocks binding of both ligands to the receptor. In contrast, although murine CR2 is capable of binding human C3dg and this interaction can be blocked with the mAb 7G6, it does not bind OKB7 or EBV. We have determined the structural basis for absolute specificity of EBV for human CR2 through characterization of a panel of 24 human-murine chimeric receptors, all of which bind human C3dg. The results indicate that preferential binding of EBV to human CR2 is not due to unique amino acids that are capable of binding the virus, but reflects a distinct receptor conformation that can be achieved in murine CR2 with single amino acid substitutions in two discontinuous regions of the primary structure: replacement of proline at position 15 with the corresponding serine from human CR2, and elimination of a potential N-linked glycosylation site between SCR-1 and SCR-2. Furthermore, species-specific binding of EBV, OKB7, and 7G6 can all be manipulated through substitutions among residues 8-15, suggesting that this octapeptide is part of a structural determinant that is critical for binding of both viral and natural ligands to CR2.
Structure of the mouseklothogene and its two transcripts encoding membrane and secreted protein1 (1998)

We previously established a novel mouse model for human aging and identified the genetic foundation responsible for it. A defect in expression of a novel gene, termed klotho (kl), leads to a syndrome resembling human aging in mice. The kl gene encodes a single-pass membrane protein whose extracellular domain carries homology to beta-glucosidases. In this report, we present the entire mouse kl gene organization. The mouse kl gene spans about 50 kilobases and consists of five exons. The promoter region lacks a TATA-box and contains four potential binding sites for SP1. We further show that two kl gene transcripts encoding membrane or secreted protein are generated through alternative transcriptional termination. These findings provide fundamental information for further study of the kl gene which may regulate aging in vivo.
C-20 Stereospecific introduction of a steroid side chain (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTC-20 Stereospecific introduction of a steroid side chainAndrew D. Batcho, Donald E. Berger, Milan R. Uskokovic, and Barry B. SniderCite this: J. Am. Chem. Soc. 1981, 103, 5, 1293–1295Publication Date (Print):March 1, 1981Publication History Published online1 May 2002Published inissue 1 March 1981https://doi.org/10.1021/ja00395a085RIGHTS & PERMISSIONSArticle Views217Altmetric-Citations34LEARN 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 (432 KB) Get e-Alerts Get e-Alerts
Reduced hypothalamic-pituitary-adrenal axis activity in chronic multi-site musculoskeletal pain: partly masked by depressive and anxiety disorders (2014)

Our results suggest hypocortisolemia in chronic multi-site musculoskeletal pain. However, if chronic pain is accompanied by a depressive or anxiety disorder, typically related to hypercortisolemia, the association between cortisol levels and chronic multi-site musculoskeletal pain appears to be partly masked. Future studies should take psychopathology into account when examining HPA-axis function in chronic pain.
Identification of Small Molecule Binding Sites within Proteins Using Phage Display Technology (2001)

Affinity selection of peptides displayed on phage particles was used as the basis for mapping molecular contacts between small molecule ligands and their protein targets. Analysis of the crystal structures of complexes between proteins and small molecule ligands revealed that virtually all ligands of molecular weight 300 Da or greater have a continuous binding epitope of 5 residues or more. This observation led to the development of a technique for binding site identification which involves statistical analysis of an affinity-selected set of peptides obtained by screening of libraries of random, phage-displayed peptides against small molecules attached to solid surfaces. A random sample of the selected peptides is sequenced and used as input for a similarity scanning program which calculates cumulative similarity scores along the length of the putative receptor. Regions of the protein sequence exhibiting the highest similarity with the selected peptides proved to have a high probability of being involved in ligand binding. This technique has been employed successfully to map the contact residues in multiple known targets of the anticancer drugs paclitaxel (Taxol), docetaxel (Taxotere) and 2-methoxyestradiol and the glycosaminoglycan hyaluronan, and to identify a novel paclitaxel receptor [1]. These data corroborate the observation that the binding properties of peptides displayed on the surface of phage particles can mimic the binding properties of peptides in naturally occurring proteins. It follows directly that structural context is relatively unimportant for determining the binding properties of these disordered peptides. This technique represents a novel, rapid, high resolution method for identifying potential ligand binding sites in the absence of three-dimensional information and has the potential to greatly enhance the speed of development of novel small molecule pharmaceuticals.
Majorana zero modes and topological quantum computation (2015)

Abstract We provide a current perspective on the rapidly developing field of Majorana zero modes (MZMs) in solid-state systems. We emphasise the theoretical prediction, experimental realisation and potential use of MZMs in future information processing devices through braiding-based topological quantum computation (TQC). Well-separated MZMs should manifest non-Abelian braiding statistics suitable for unitary gate operations for TQC. Recent experimental work, following earlier theoretical predictions, has shown specific signatures consistent with the existence of Majorana modes localised at the ends of semiconductor nanowires in the presence of superconducting proximity effect. We discuss the experimental findings and their theoretical analyses, and provide a perspective on the extent to which the observations indicate the existence of anyonic MZMs in solid-state systems. We also discuss fractional quantum Hall systems (the 5/2 state), which have been extensively studied in the context of non-Abelian anyons and TQC. We describe proposed schemes for carrying out braiding with MZMs as well as the necessary steps for implementing TQC.
.eta.1-Benzene coordination: the synthesis and x-ray crystal structure of a novel silver salt of the weakly coordinating carborane anion B11CH12- (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.eta.1-Benzene coordination: the synthesis and x-ray crystal structure of a novel silver salt of the weakly coordinating carborane anion B11CH12-Kenneth Shelly, David C. Finster, Young Ja Lee, W. Robert Scheidt, and Christopher A. ReedCite this: J. Am. Chem. Soc. 1985, 107, 21, 5955–5959Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/ja00307a021https://doi.org/10.1021/ja00307a021research-articleACS PublicationsRequest reuse permissionsArticle Views824Altmetric-Citations160LEARN 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
Isolation of alcohol oxidase and two other methanol regulatable genes from the yeast Pichia pastoris. (1985)

The oxidation of methanol follows a well-defined pathway and is similar for several methylotrophic yeasts. The use of methanol as the sole carbon source for the growth of Pichia pastoris stimulates the expression of a family of genes. Three methanol-responsive genes have been isolated; cDNA copies have been made from mRNAs of these genes, and the protein products from in vitro translations have been examined. The identification of alcohol oxidase as one of the cloned, methanol-regulated genes has been made by enzymatic, immunological, and sequence analyses. Methanol-regulated expression of each of these three isolated genes can be demonstrated to occur at the level of transcription. Finally, DNA subfragments of two of the methanol-responsive genomic clones from P. pastoris have been isolated and tentatively identified as containing the control regions involved in methanol regulation.
Range of validity of field emission equations (2008)

The analytical equations for field emission current density and total energy distribution are compared with a rigorous numerical solution of the fundamental emission equations over a wide range of electric field, work function, and temperature. In particular, the range of the latter parameters where agreement occurs between the analytical and numerical results is established. Some interesting periodic deviations with applied electric field are observed for the numerically calculated current density and total energy distributions.
An easily synthesized, photolyzable luciferase substrate for in vivo luciferase activity measurement. (1993)

Many reporter gene assays require killing the cell by fixation or lysis. For assays in living cells, the substrate delivery is inefficient and cannot be supplied in situ in a bolus, which makes assays highly variable. We report a simple synthesis of a luciferin ester that is both photolyzable and cleaved by endogenous esterases such that luciferase activity in living cells is easily monitored. Although the photolyzed substrate can be delivered in bolus, the rapid equilibration of the luciferin ester in the cell and the continuous delivery by the endogenous esterases allow stable, long-term measurements of luciferase activity.
Utilizing Memory Content Similarity for Improving the Performance of Replicated Virtual Machines (2011)

Checkpoint-recovery based Virtual Machine (VM) replication is an emerging approach towards accommodating VM installations with high availability. However, it comes with the price of significant performance degradation of the application executed in the VM due to the large amount of state that needs to be synchronized between the primary and the backup machines. It is therefore critical to find new ways for attaining good performance, and at the same time, maintaining fault tolerant execution. In this paper, we present a novel approach to improve the performance of services deployed over replicated virtual machines by exploiting data similarity within the VM's memory image to reduce the network traffic during synchronization. For identifying similar memory areas, we propose a bit density based hash function, upon which, we build a content addressable hash table. We present a quantitative analysis on the degree of similarity we found in various workloads, and introduce a lightweight compression method, which, compared to existing replication techniques, reduces network traffic by up to 80% and yields a performance improvement over 90% for certain latency sensitive applications.
Blind separation of auditory event-related brain responses into independent components (1997)

Averaged event-related potential (ERP) data recorded from the human scalp reveal electroencephalographic (EEG) activity that is reliably time-locked and phase-locked to experimental events. We report here the application of a method based on information theory that decomposes one or more ERPs recorded at multiple scalp sensors into a sum of components with fixed scalp distributions and sparsely activated, maximally independent time courses. Independent component analysis (ICA) decomposes ERP data into a number of components equal to the number of sensors. The derived components have distinct but not necessarily orthogonal scalp projections. Unlike dipole-fitting methods, the algorithm does not model the locations of their generators in the head. Unlike methods that remove second-order correlations, such as principal component analysis (PCA), ICA also minimizes higher-order dependencies. Applied to detected-and undetected-target ERPs from an auditory vigilance experiment, the algorithm derived ten components that decomposed each of the major response peaks into one or more ICA components with relatively simple scalp distributions. Three of these components were active only when the subject detected the targets, three other components only when the target went undetected, and one in both cases. Three additional components accounted for the steady-state brain response to a 39-Hz background click train. Major features of the decomposition proved robust across sessions and changes in sensor number and placement. This method of ERP analysis can be used to compare responses from multiple stimuli, task conditions, and subject states.
Development of a bile acid–based newborn screen for Niemann-Pick disease type C (2016)

Niemann-Pick disease type C (NPC) is a fatal, neurodegenerative, cholesterol storage disorder. With new therapeutics in clinical trials, it is imperative to improve diagnostics and facilitate early intervention. We used metabolomic profiling to identify potential markers and discovered three unknown bile acids that were increased in plasma from NPC but not control subjects. The bile acids most elevated in the NPC subjects were identified as 3β,5α,6β-trihydroxycholanic acid and its glycine conjugate, which were shown to be metabolites of cholestane-3β,5α,6β-triol, an oxysterol elevated in NPC. A high-throughput mass spectrometry-based method was developed and validated to measure the glycine-conjugated bile acid in dried blood spots. Analysis of dried blood spots from 4992 controls, 134 NPC carriers, and 44 NPC subjects provided 100% sensitivity and specificity in the study samples. Quantification of the bile acid in dried blood spots, therefore, provides the basis for a newborn screen for NPC that is ready for piloting in newborn screening programs.
Single Chirality Extraction of Single-Wall Carbon Nanotubes for the Encapsulation of Organic Molecules (2012)

The hollow inner spaces of single-wall carbon nanotubes (SWCNTs) can confine various types of molecules. Many remarkable phenomena have been observed inside SWCNTs while encapsulating organic molecules (peapods). However, a mixed electronic structure state of the surrounding SWCNTs has impeded a detailed understanding of the physical/chemical properties of peapods and their device applications. We present a single-chirality purification method for SWCNTs that can encapsulate organic molecules. A single-chiral state of (11,10) SWCNTs with a diameter of 1.44 nm, which is large enough for molecular encapsulation, was obtained after a two-step purification method: metal-semiconductor sorting and cesium-chloride sorting. The encapsulation of C(60) to the (11,10) SWCNTs was also succeeded, promising a route toward single-chirality peapod devices.