gebhart/patrepeval huggingface dataset:
SCAA mask exposures and Phase Phirst designs for 100 nm and below (2001)

The Sidewall Chrome Alternating Aperture (SCAA) mask has now successftilly printed resist images with k1 factors as low as 0.20, without significant focus-dependent spacewidth alternation or other anomalies that affect common alternating-PSM structures. The SCAA mask process (reported at BACUS 2000') etches the phase topography first and then forms the transparent openings that define the image in a conformal chrome layer deposited afterwards. This process minimizes the differences between the 3-dimensional environments ofthe phase shifted and unshifted mask features. With all chrome supported and all quartz walls covered, only the size of a chrome aperture determines its transmission and only the height difference ofthe quartz surface affects the phase shift. SCAA masks are more stable mechanically than alt-PSM structures in which the quartz walls are undercut beneath the chrome edges to minimize the french walls effects. The chrome covering the phase edges also buries entire classes ofunrepairable phase defects. Initial experiments on Canon ES2 and ES3 exposure tools confirm that KrF SCAA masks project acceptable images of isolated line and line-space patterns down to lOOnm in 280mn thick JSR M1O8Y resist. The process windows, however, were limited by resist collapse, and there were strong optical proximity effects. Comparing the resist results to SEM scans of the masks confirmed the insensitivity ofthe image to overlay errors, so long as the phase steps were covered by chrome. The Phase Phirst paradigm exploits the SCAA mask structure to enable low cost strong PSMs. The key is to mass produce SCAA mask substrates with generally useful phase topographies using wafer fab techniques. These Phase Phirst substrates would arrive at the mask houses ready to write and guaranteed to be free ofphase-defects. At design houses, Phase Phirstenabled EDA tools would lay out the chips in such a way that all fme dark features lie at the predetermined phase shift locations on the Phase Phirst substrate while the larger-dimension structures appear on a more conventional trim-mask. Once the GDS-II tapes arrive at the mask house, the chip design would be matched to the specified Phase Phirst substrate and printed in the chrome. Cost and turn around time should be similar to those of a COG mask pair. The wafer yield and resolution, however, would be enhanced by the well-known advantages of strong phase-shifting.
Sequence-Specific Interactions of Methylene Blue with Polynucleotides and DNA: A Spectroscopic Study (1994)

The modes of binding of the phenothiazinium dye methylene blue (1) to alternating and nonalternating polynucleotides and to calf thymus (CT) DNA have been characterized using linear dichroism (LD) and circular dichroism (CD) spectroscopy. With the polynucleotide [poly(dG-dC)](2) the interaction at low binding ratios is shown to be purely intercalative and the binding mode is insensitive to changes in ionic strength. The observed CD spectrum is bisignate, which may be due to intercalation at the different base-pair steps (5'G-C3' and 5'C-G3'), giving rise to CD signals of different sign and shape, By contrast, a single intercalative binding mode with the alternating AT polynucleotide [poly(dA-dT)](2) is likely only at very low ionic strength; at high ionic strength (200 mM phosphate, pH 6.9), a second binding mode is also manifest which is attributed to groove binding of the dye. The absorption and linear dichroism spectroscopic features of the methylene blue/CT-DNA (42% GC) complex reflect those of complexes of the dye with both [poly(dA-dT)](2) and [poly(dG-dC)](2); the circular dichroism spectrum of the methylene blue/CT-DNA complex and its variation with ionic strength reflect the complexity of even this simple system where numerous possible binding sites exist. Comparative binding to the nonalternating polynucleotides poly(dA).poly(dT) and poly(da).poly(dC), which each possess only one base-pair step, was also examined. On the basis of the combined LD and CD evidence, it is proposed that the dye is loosely bound with poly(dA).poly(dT), probably in the major groove, and intercalated with poly(dG).poly(dC).
Activation of a G Protein–coupled Inwardly Rectifying K+Current and Suppression of I hContribute to Dexmedetomidine-induced Inhibition of Rat Hypothalamic Paraventricular Nucleus Neurons (2007)

Dexmedetomidine inhibited PVN magnocellular neurons by activation of the G protein-coupled inwardly rectifying K current and inhibited PVN parvocellular neurons by suppression of Ih.
Endoglycan, a Member of the CD34 Family, Functions as an L-selectin Ligand through Modification with Tyrosine Sulfation and Sialyl Lewis x (2003)

During lymphocyte homing to secondary lymphoid organs and instances of inflammatory trafficking, the rolling of leukocytes on vascular endothelium is mediated by transient interactions between L-selectin on leukocytes and several carbohydrate-modified ligands on the endothelium. Most L-selectin ligands such as CD34 and podocalyxin present sulfated carbohydrate structures (6-sulfated sialyl Lewis x or 6-sulfo-sLex) as a recognition determinant within their heavily glycosylated mucin domains. We recently identified endoglycan as a new member of the CD34 family. We report here that endoglycan, like the two other members of this family (CD34 and podocalyxin) can function as a L-selectin ligand. However, endoglycan employs a different binding mechanism, interacting with L-selectin through sulfation on two tyrosine residues and O-linked sLex structures that are presented within its highly acidic amino-terminal region. Our analysis establishes striking parallels with PSGL-1, a leukocyte ligand that interacts with all three selectins, mediating leukocyte-endothelial, leukocyte-leukocyte, and platelet-leukocyte interactions. Since the distribution of endoglycan includes hematopoietic precursors and leukocyte subpopulations, in addition to endothelial cells, our findings suggest several potential settings for endoglycan-mediated adhesion events.
Two Modes of Ligand Binding in Maltose-binding Protein ofEscherichia coli (1997)

In the preceding two papers (Hall, J. A., Gehring, K., and Nikaido, H. (1997) J. Biol. Chem. 272, 17605-17609; Hall, J. A., Thorgeirson, T. E., Liu, J., Shin, Y.-E., and Nikaido, H. (1997) J. Biol. Chem. 272, 17610-17614), we showed that ligands that bind to the Escherichia coli maltose-binding protein (MBP) without producing the closure of its two lobes are not transported into the cytoplasm. Here, we examine various combinations of ligands, MBPs, and membrane-associated transporters, by utilizing reconstituted proteoliposomes, right side-out membrane vesicles, and intact cells. Closed forms of wild type MBP, complexed with maltose or maltodextrins, interacted with wild type transporter complex to stimulate the hydrolysis of ATP by MalK ATPase located on the other side of the membrane, as shown earlier for the maltose-MBP complex (Davidson, A. L., Shuman, H. A., and Nikaido, H. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 2360-2364). In contrast, open forms of liganded MBPs, such as the complex containing wild type MBP and reduced, oxidized, or cyclic maltodextrins or the complex containing the mutant MBP MalE254 and unmodified maltodextrins, did not stimulate ATP hydrolysis, suggesting that the proper interaction between the ligand-MBP complex and the external surface of the transporter requires the former to be in the closed conformation. However, when a mutant transporter containing MalG511 was used, the already significant basal level of ATP hydrolysis was further stimulated not only by ligand MBPs in the closed form but also by those in the open form (except that containing beta-cyclodextrin), data suggesting that the mutant transporter does not always require the closed MBP complex presumably because of its exceptionally strong affinity to MBP, described earlier (Dean, D. A., Hor, L.-I., Shuman, H. A., and Nikaido, H. (1992) Mol. Microbiol. 6, 2033-2040). Furthermore, this mutant transporter was able to transport reduced maltodextrin, and cells expressing the transporter were able to grow by using reduced maltodextrin, if the periplasmic concentrations of MBP were kept low so as not to inhibit the transport process.
Boron Containing Macromolecules and Nanovehicles as Delivery Agents for Neutron Capture Therapy† (2006)

Boron neutron capture therapy (BNCT) is based on the nuclear capture and fission reactions that occur when non-radioactive boron-10 is irradiated with low energy thermal neutrons to yield high linear energy transfer (LET) alpha particles ((4)He) and recoiling lithium -7((7)Li) nuclei. For BNCT to be successful, a sufficient number of (10)B atoms ( approximately 10(9) atoms/cell) must be selectively delivered to the tumor and enough thermal neutrons must be absorbed by them to sustain a lethal (10)B(n, alpha) (7)Li capture reaction. BNCT primarily has been used to treat patients with brain tumors, and more recently those with head and neck cancer. Two low molecular weight (LMW) boron delivery agents currently are being used clinically, sodium borocaptate and boronophenylalanine. However, a variety of high molecular weight (HMW) agents consisting of macromolecules and nanovehicles have been developed. This review will focus on the latter which include: monoclonal antibodies, dendrimers, liposomes, dextrans, polylysine, avidin, folic acid, and epidermal and vascular endothelial growth factors (EGF and VEGF). Procedures for introducing boron atoms into these HMW agents and their chemical properties will be discussed. In vivo studies on their biodistribution will be described, and the efficacy of a subset of them, which have been used for BNCT of tumors in experimental animals, will be discussed. Since brain tumors currently are the primary candidates for treatment by BNCT, delivery of these HMW agents across the blood-brain barrier presents a special challenge. Various routes of administration will be discussed including receptor-facilitated transcytosis following intravenous administration, direct intratumoral injection and convection enhanced delivery by which a pump is used to apply a pressure gradient to establish bulk flow of the HMW agent during interstitial infusion. Finally, we will conclude with a discussion relating to issues that must be addressed if these HMW agents are to be used clinically.
The Selective Reaction of Aryl Halides with KOH:  Synthesis of Phenols, Aromatic Ethers, and Benzofurans (2006)

The direct and selective synthesis of phenols from aryl/heteroaryl halides and KOH has been achieved through the use of highly active monophosphine-based catalysts derived from Pd(2)dba(3) and ligands L1 or L2 and the biphasic solvent system 1,4-dioxane/H(2)O. We have also demonstrated a one-pot method of phenol formation/alkylation for the preparation of alkyl aryl ethers from aryl halides. In many instances, this protocol overcomes limitations in existing Pd-catalyzed coupling reactions of aliphatic alcohols with aryl halides. Finally, we demonstrate that substituted benzofurans can be prepared efficiently via a Pd-catalyzed phenol formation/cyclization protocol starting from 2-chloroaryl alkynes.
Sortase A-Catalyzed Transpeptidation of Glycosylphosphatidylinositol Derivatives for Chemoenzymatic Synthesis of GPI-Anchored Proteins (2010)

Several peptides/small proteins and glycosylphosphatidylinositol (GPI) derivatives were synthesized and compared as substrates of sortase A (SrtA), a bacterial transpeptidase, for enzymatic coupling. It was observed that peptides containing the LPKTGGS and LPKTGGRS sequences as sorting signals at the peptide C-terminus were effectively coupled to GPI derivatives having one or two glycine residues attached to the phosphoethanolamine group at the nonreducing end. This reaction was employed to prepare several analogues of the human CD52 and CD24 antigens, which are naturally GPI-anchored glycopeptides/glycoproteins. It was further observed that the trisaccharide GPI analogues 5 and 6 were better SrtA substrates than monosaccharide GPI analogue 4, suggesting that steric hindrance of the GPI analogues does not affect their peptidation reaction mediated by SrtA. Therefore, this synthetic strategy may be useful for the preparation of more complex GPI-anchored peptides, glycopeptides, proteins, and glycoproteins.
Bruton's Tyrosine Kinase as an Inhibitor of the Fas/CD95 Death-inducing Signaling Complex (1999)

Bruton's tyrosine kinase (BTK) is a member of the Src-related Tec family of protein tyrosine kinases. Mutations in the btk gene have been linked to severe developmental blocks in human B-cell ontogeny leading to X-linked agammaglobulinemia. Here, we provide unique biochemical and genetic evidence that BTK is an inhibitor of the Fas/APO-1 death-inducing signaling complex in B-lineage lymphoid cells. The Src homology 2, pleckstrin homology (PH), and kinase domains of BTK are all individually important and apparently indispensable, but not sufficient, for its function as a negative regulator of Fas-mediated apoptosis. BTK associates with Fas via its kinase and PH domains and prevents the FAS-FADD interaction, which is essential for the recruitment and activation of FLICE by Fas during the apoptotic signal. Fas-resistant DT-40 lymphoma B-cells rendered BTK-deficient through targeted disruption of the btk gene by homologous recombination knockout underwent apoptosis after Fas ligation, but wild-type DT-40 cells or BTK-deficient DT-40 cells reconstituted with wild-type human btk gene did not. Introduction of an Src homology 2 domain, a PH domain, or a kinase domain mutant human btk gene into BTK-deficient cells did not restore the resistance to Fas-mediated apoptosis. Introduction of wild-type BTK protein by electroporation rendered BTK-deficient DT-40 cells resistant to the apoptotic effects of Fas ligation. BTK-deficient RAMOS-1 human Burkitt's leukemia cells underwent apoptosis after Fas ligation, whereas BTK-positive NALM-6-UM1 human B-cell precursor leukemia cells expressing similar levels of Fas did not. Treatment of the anti-Fas-resistant NALM-6-UM1 cells with the leflunomide metabolite analog alpha-cyano-beta-methyl-beta-hydroxy-N-(2, 5-dibromophenyl)propenamide, a potent inhibitor of BTK, abrogated the BTK-Fas association without affecting the expression levels of BTK or Fas and rendered them sensitive to Fas-mediated apoptosis. The ability of BTK to inhibit the pro-apoptotic effects of Fas ligation prompts the hypothesis that apoptosis of developing B-cell precursors during normal B-cell ontogeny may be reciprocally regulated by Fas and BTK.
Building high-level features using large scale unsupervised learning (2011)

We consider the problem of building high-level, class-specific feature detectors from only unlabeled data. For example, is it possible to learn a face detector using only unlabeled images? To answer this, we train a 9-layered locally connected sparse autoencoder with pooling and local contrast normalization on a large dataset of images (the model has 1 billion connections, the dataset has 10 million 200x200 pixel images downloaded from the Internet). We train this network using model parallelism and asynchronous SGD on a cluster with 1,000 machines (16,000 cores) for three days. Contrary to what appears to be a widely-held intuition, our experimental results reveal that it is possible to train a face detector without having to label images as containing a face or not. Control experiments show that this feature detector is robust not only to translation but also to scaling and out-of-plane rotation. We also find that the same network is sensitive to other high-level concepts such as cat faces and human bodies. Starting with these learned features, we trained our network to obtain 15.8% accuracy in recognizing 20,000 object categories from ImageNet, a leap of 70% relative improvement over the previous state-of-the-art.
ChemInform Abstract: Synthesis of Conformationally Restricted Substrate Analogues and Their Interaction with 3‐Isopropylmalate Dehydrogenase Derived from Thermus thermophilus. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Rapid biochemical test to identify verocytotoxin-positive strains of Escherichia coli serotype O157 (1990)

Fluorogenic procedures were used with the substrate 4-methylumbelliferyl-beta-D-glucuronide (MUG) to identify Escherichia coli. Most strains produced beta-glucuronidase and, thus, were MUG positive. A 20-min procedure was developed to detect glucuronidase activity in 1,295 bacterial cultures, representing 23 genera, of strains that were isolated from clinical specimens. Very few organisms other than E. coli were MUG positive. Of 682 E. coli strains that were isolated, 630 (92.4%) were MUG positive. When an additional 188 E. coli serotype O157 isolates were examined, 155 E. coli O157:H7, 10 E. coli O157:H-, and 1 E. coli O157:H (rough) isolate were MUG negative. All 166 cultures were verocytotoxin positive. Of the remaining 22 E. coli O157 isolates, 2 isolates were O157:H-, 1 isolate was O157:H (rough), and 19 isolates were other H types (H6, H16, H19, H25, H42, and H45); these 22 isolates were MUG positive. All 22 cultures were verocytotoxin negative. The rapid MUG procedure can be used to predict verocytotoxin-positive isolates of E. coli O157; that is, there is a very good likelihood that MUG-negative E. coli O157 isolates are verocytotoxin positive.
Preparation and properties of (S,S)-[Ti((R,R)-cyclacene)Cl2], a chiral strapped bent metallocene (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and properties of (S,S)-[Ti((R,R)-cyclacene)Cl2], a chiral strapped bent metalloceneT. Keith Hollis, Arnold L. Rheingold, N. P. Robinson, John Whelan, and B. BosnichCite this: Organometallics 1992, 11, 8, 2812–2816Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://pubs.acs.org/doi/10.1021/om00044a020https://doi.org/10.1021/om00044a020research-articleACS PublicationsRequest reuse permissionsArticle Views197Altmetric-Citations39LEARN 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
Comparative Sequence Analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and Proposal for Creation of a New Genus, Alicyclobacillus gen. nov. (1992)

Comparative 16S rRNA (rDNA) sequence analyses performed on the thermophilic Bacillus species Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus revealed that these organisms are sufficiently different from the traditional Bacillus species to warrant reclassification in a new genus, Alicyclobacillus gen. nov. An analysis of 16S rRNA sequences established that these three thermoacidophiles cluster in a group that differs markedly from both the obligately thermophilic organisms Bacillus stearothermophilus and the facultatively thermophilic organism Bacillus coagulans, as well as many other common mesophilic and thermophilic Bacillus species. The thermoacidophilic Bacillus species B. acidocaldarius, B. acidoterrestris, and B. cycloheptanicus also are unique in that they possess omega-alicylic fatty acid as the major natural membranous lipid component, which is a rare phenotype that has not been found in any other Bacillus species characterized to date. This phenotype, along with the 16S rRNA sequence data, suggests that these thermoacidophiles are biochemically and genetically unique and supports the proposal that they should be reclassified in the new genus Alicyclobacillus.
The challenge of overactive bladder therapy: alternative to antimuscarinic agents (2006)

Contemporary, the management of overactive bladder (OAB), a medical condition characterized by urgency, with or without urge urinary incontinence, frequency and nocturia, in absence of genitourinary pathologies or metabolic factors that could explain these symptoms, is complex, and a wide range of conservative treatments has been offered, including bladder training, biofeedback, behavioral changes, oral or intravesical anticholinergic agents, S3 sacral neuromodulation and peripheral electrical stimulation. Clinical efficacy of these treatments remains an open issue and several experimental and clinical studies were carried out in the last years improving the results of medical treatment. Here we review the pathophysiology of micturition reflex, the current therapies for OAB and the rationale for alternative treatments. Furthermore we critically address the potential use of medications targeting the central nervous system (CNS) and the primary sensory nerves of the bladder wall, we review the use of agonists of nociceptin/orphanin protein (NOP) receptor and finally we report the results obtained by intradetrusor injection of botulinum toxin.
WOOD HYDROLYSIS INDUSTRY IN THE SOVIET UNION AND RUSSIA: A MINI-REVIEW (2010)

The main objectives, feedstock, processes and spectra of products (commodities, specialties, fine chemicals, including pharmaceuticals as by-products of lignin) manufactured by the Soviet and Russian hydrolysis industry for over 75 years are briefly overviewed. The limitations and the difficulties that might have affected this type of industry are also considered. The history of the Soviet/Russian hydrolysis industry clearly shows that, without state subsidies, the production of commodities, such as ethanol or fodder yeast, from lignocellulosic raw materials, can survive only if it also involves the production of heat and electric power from lignin and value-added products, which requires special techniques and equipment, along with a pre-developed market niche.