gebhart/patrepeval huggingface dataset:
Interrelations between C4 Ketogenesis, C5 Ketogenesis, and Anaplerosis in the Perfused Rat Liver (2009)

We investigated the interrelations between C(4) ketogenesis (production of beta-hydroxybutyrate + acetoacetate), C(5) ketogenesis (production of beta-hydroxypentanoate + beta-ketopentanoate), and anaplerosis in isolated rat livers perfused with (13)C-labeled octanoate, heptanoate, or propionate. Mass isotopomer analysis of C(4) and C(5) ketone bodies and of related acyl-CoA esters reveal that C(4) and C(5) ketogenesis share the same pool of acetyl-CoA. Although the uptake of octanoate and heptanoate by the liver are similar, the rate of C(5) ketogenesis from heptanoate is much lower than the rate of C(4) ketogenesis from octanoate. This results from the channeling of the propionyl moiety of heptanoate into anaplerosis of the citric acid cycle. C(5) ketogenesis from propionate is virtually nil because acetoacyl-CoA thiolase does not favor the formation of beta-ketopentanoyl-CoA from propionyl-CoA and acetyl-CoA. Anaplerosis and gluconeogenesis from heptanoate are inhibited by octanoate. The data have implications for the design of diets for the treatment of long chain fatty acid oxidation disorders, such as the triheptanoin-based diet.
Reliability Performance of ETOX Based Flash Memories (1988)

The reliability performance of a 64 K flash memory based on a single-transistor, floating-gate memory cell is considered. The reliability performance of these memories, before program/erase cycling, matches that of UV EPROMs. Cycling generally does not introduce defect-related failures common to some EEPROMs. However, it may aggravate two intrinsic instabilities found in the UV EPROM (intrinsic charge loss and the DC program disturb mechanism). Experience shows that these are related effects caused by injection of holes during the erase step of the cycle. High source-to-substrate electric fields, during erase, generate these holes. Channel hot electron injection, for programming, plays no significant role in the observed degradation. These cycling effects can be addressed through incorporation of additional margin into the flash cell. Through such cell optimization, the reliability of these memories is made equivalent to that of conventional UV EPROMs, even after hundreds of program/erase cycles. >
Metal–Organic Frameworks Incorporating Copper‐Complexed Rotaxanes (2012)

MOFs on the move: A copper-coordinated [2]pseudorotaxanate which reacts with zinc nitrate to form threefold interpenetrated networks retains most of its solution-state chemistry, including its ability to undergo electronic switching of some of the copper(I) ions under redox control. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Mutation analysis of NPHP6/CEP290 in patients with Joubert syndrome and Senior–Løken syndrome (2007)

Six novel and six known truncating mutations, one known missense mutation and one novel 3 bp pair in-frame deletion were identified in a total of seven families with JBTS, two families with SLSN and one family with isolated NPHP.
Peptidomimetics via copper-catalyzed azide–alkyne cycloadditions (2007)

This critical review concerns the impact of copper-mediated alkyne-azide cycloadditions on peptidomimetic studies. It discusses how this reaction has been used to insert triazoles into peptide chains, to link peptides to other functionalities (e.g. carbohydrates, polymers, and labels), and as a basis for evolution of less peptidic compounds as pharmaceutical leads. It will be of interest to those studying this click reaction, peptidomimetic secondary structure and function, and to medicinal chemists.
Two‐photon Fluorescence Light Microscopy (2001)

Abstract Two‐photon fluorescence microscopy allows three‐dimensional imaging of biological specimens in vivo . Compared with confocal microscopy, it offers the advantages of deeper tissue penetration and less photodamage but has the disadvantage of slightly lower resolution.
Use of plant‐derived protein hydrolysates for enhancing growth ofBombyx mori(silkworm) insect cells in suspension culture (2005)

The successful suspension culture of the Bombyx mori (silkworm) cell lines Bm5 and BmN4 without FBS (fetal-bovine serum) was first realized in Sf-900 II SFM (serum-free medium) (Gibco BRL, Rockville, MD, U.S.A.) supplemented with a plant-derived protein hydrolysate. The addition of 0.5% HyPep 1510 (Difco Co., Detroit, MI, U.S.A.) and 10 mM glutamine to Sf-900 II SFM at 4 days of culture was found effective in increasing the cell concentration to 8.5x10(6) cells/ml. The replacement of medium with Sf-900 II SFM supplemented with 0.5% HyPep 1510 at 6 days of culture increased the cell concentration by 1.1x10(7) cells/ml. When Sf-900 II SFM was supplemented with 0.5% Hypep 1510, 16 days, which was half of the conventional adaptation time, was sufficient for the B. mori cell line to adapt to SFM and shear stress while maintaining a stable viability. The beta-galactosidase activity in Sf-900 II SFM supplemented with 0.5% Hypep 1510 was 4.9x10(3) units/ml, which was 2-fold higher than that of the FBS-supplemented medium. By SDS/PAGE, only the band corresponding to beta-galactosidase was detected in the sample from the media supplemented with plant-derived protein hydrolysates, while thick bands corresponding to proteins having lower molecular masses than beta-galactosidase were detected in samples from the FBS-supplemented media. These results suggest that plant-derived protein hydrolysates are promising FBS substitutes for enhancing the growth of B. mori cells and facilitating the purification of recombinant proteins produced by baculovirus infection.
Synthesis, Thermotropic Behavior, and Permeability Properties of Vesicular Membranes Composed of Cationic Mixed-Chain Surfactants (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Thermotropic Behavior, and Permeability Properties of Vesicular Membranes Composed of Cationic Mixed-Chain SurfactantsSantanu Bhattacharya and Saubhik HaldarCite this: Langmuir 1995, 11, 12, 4748–4757Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/la00012a028https://doi.org/10.1021/la00012a028research-articleACS PublicationsRequest reuse permissionsArticle Views305Altmetric-Citations51LEARN 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-Alertsclose Get e-Alerts
Loss distribution measurement of silica-based waveguidesby using a jaggedness-free optical low coherence reflectometer (1994)

The loss distributions in silica-based waveguides are successfully measured using a jaggedness-free optical low coherence reflectometer (OLCR). The OLCR reduces the unavoidable jagged fluctuations which appear in Rayleigh backscattering measurements undertaken with conventional OLCRs to within ± 1 dB by averaging the wavelength-dependent Rayleigh backscatter signals. Constant loss distributions and a step-like loss increase in the waveguides were clearly observed.
Predicting CIN2+ when detecting HPV mRNA and DNA by PreTect HPV‐proofer and consensus PCR: A 2‐year follow‐up of women with ASCUS or LSIL pap smear (2005)

It has been suggested that human papillomavirus (HPV) testing improves follow-up of atypical cells of undetermined significance (ASCUS) and low-grade squamous intraepithelial lesion (LSIL) in cervical cancer screening programs. To evaluate the prognostic value of including HPV testing as an adjunct to cytology, we carried out a 2-year follow-up study of 77 women with ASCUS or LSIL Papanicolaou (Pap) smear in the Norwegian Cervical Cancer Screening Program (NCCSP) for detection of histological cervical intraepithelial neoplasia (CIN) 2+. The study includes a comparison between viral mRNA and DNA detection. PreTect HPV-Proofer was used for HPV E6/E7 mRNA detection from the 5 high-risk types 16, 18, 31, 33 and 45, and Gp5+/6+ consensus PCR was used for HPV DNA detection. Twice as many women were positive for HPV DNA (54.6%) than for HPV mRNA (23.4%). PreTect HPV-Proofer and consensus PCR had a sensitivity of 85.7% (95% confidence interval [CI] = 42.1-99.6) for detecting CIN2+ during follow-up. The specificity was significantly higher for PreTect HPV-Proofer, 84.9% (95% CI = 73.9-92.5), than for consensus PCR, 50.0% (95% CI = 37.4-62.6). PreTect HPV-Proofer positive women were 69.8 times (95% CI = 4.3-1137.3) more likely to be diagnosed with CIN2+ within 2 years than PreTect HPV-Proofer negative women. Consensus PCR-positive women were 5.7 times (95% CI = 0.6-52.0) more likely to be diagnosed with CIN2+ within 2 years than PCR-negative women. With equal sensitivity and higher specificity than consensus PCR, the PreTect HPV-Proofer might offer an improvement for the triage of women with ASCUS or LSIL Pap smear.
Restoration of the Majority of the Visual Spectrum by Using Modified Volvox Channelrhodopsin-1 (2014)

We previously showed that blind rats whose vision was restored by gene transfer of Chlamydomonas channelrhodopsin-2 (ChR2) could only detect wavelengths less than 540 nm because of the action spectrum of the transgene product. Volvox-derived channelrhodopsin-1, VChR1, has a broader spectrum than ChR2. However, the VChR1 protein was mainly localized in the cytoplasm and showed weak ion channel properties when the VChR1 gene was transfected into HEK293 cells. We generated modified Volvox channelrhodopsin-1 (mVChR1), which is a chimera of Volvox channelrhodopsin-1 and Chlamydomonas channelrhodopsin-1 and demonstrated increased plasma membrane integration and dramatic improvement in its channel properties. Under whole-cell patch clamp, mVChR1-expressing cells showed a photo-induced current upon stimulation at 468-640 nm. The evoked currents in mVChR1-expressing cells were ~30 times larger than those in VChR1-expressing cells. Genetically, blind rats expressing mVChR1 via an adeno-associated virus vector regained their visual responses to light with wavelengths between 468 and 640 nm and their recovered visual responses were maintained for a year. Thus, mVChR1 is a candidate gene for gene therapy for restoring vision, and gene delivery of mVChR1 may provide blind patients access to the majority of the visible light spectrum.
Classification of European mtDNAs From an Analysis of Three European Populations (1996)

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations.
Subsets of Human Dendritic Cell Precursors Express Different Toll-like Receptors and Respond to Different Microbial Antigens (2001)

Toll-like receptors (TLRs) are ancient microbial pattern recognition receptors highly conserved from Drosophila to humans. To investigate if subsets of human dendritic cell precursors (pre-DC), including monocytes (pre-DC1), plasmacytoid DC precursors (pre-DC2), and CD11c(+) immature DCs (imDCs) are developed to recognize different microbes or microbial antigens, we studied their TLR expression and responses to microbial antigens. We demonstrate that whereas monocytes preferentially express TLR 1, 2, 4, 5, and 8, plasmacytoid pre-DC strongly express TLR 7 and 9. In accordance with these TLR expression profiles, monocytes respond to the known microbial ligands for TLR2 (peptidoglycan [PGN], lipoteichoic acid) and TLR4 (lipopolysaccharide), by producing tumor necrosis factor (TNF)-alpha and interleukin (IL)-6. In contrast, plasmacytoid pre-DCs only respond to the microbial TLR9-ligand, CpG-ODNs (oligodeoxynucleotides [ODNs] containing unmethylated CpG motifs), by producing IFN-alpha. CD11c(+) imDCs preferentially express TLR 1, 2, and 3 and respond to TLR 2-ligand PGN by producing large amounts of TNF-alpha, and to viral double-stranded RNA-like molecule poly I:C, by producing IFN-alpha and IL-12. The expression of distinct sets of TLRs and the corresponding difference in reactivity to microbial molecules among subsets of pre-DCs and imDCs support the concept that they have developed through distinct evolutionary pathways to recognize different microbial antigens.
Family and Line Selection for Seed Yield of Soybean (2001)

Plant‐row‐yield tests (PRYT) are used by soybean [ Glycine max (L.) Merr.] breeders for the initial evaluation of experimental lines. The highest yielding lines in the PRYT are advanced for additional testing in replicated tests. The objective of this study was to determine the reliability of selection for seed yield in unreplicated plots by the family and line methods of selection. Four F 3 ‐derived lines from each of 21 F 2 families from four populations were grown in a PRYT during 1995 and in replicated tests at four environments in 1996. For the family method, the mean seed yield of the four F 3 ‐derived lines of each F 2 family was used to identify superior families from which to select individual lines. For the line method, lines were selected without regard to the family structure. The seed yield of the selected and unselected lines on the basis of data from the PRYT was compared with their mean seed yield in the 1996 environments. The total number of lines selected by the family method was less than for the line method in all populations. The percentage of selected lines that were correctly classified was similar for both methods. There was a greater percentage of lines incorrectly rejected by the family method than by the line method. The use of replication at an individual location did not improve the selection of lines by the family or line methods of selection. For the selection of lines for seed yield in unreplicated plots, breeding methods that rely on family performance would not be more effective or efficient than methods that ignore family structure. To obtain lines for yield tests at multiple locations, selection of lines by the line method on the basis of their performance in a PRYT would be better than the use of random lines.
Resizing by symmetry-summarization (2010)

Image resizing can be achieved more effectively if we have a better understanding of the image semantics. In this paper, we analyze the translational symmetry, which exists in many real-world images. By detecting the symmetric lattice in an image, we can summarize, instead of only distorting or cropping, the image content. This opens a new space for image resizing that allows us to manipulate, not only image pixels, but also the semantic cells in the lattice. As a general image contains both symmetry & non-symmetry regions and their natures are different, we propose to resize symmetry regions by summarization and non-symmetry region by warping. The difference in resizing strategy induces discontinuity at their shared boundary. We demonstrate how to reduce the artifact. To achieve practical resizing applications for general images, we developed a fast symmetry detection method that can detect multiple disjoint symmetry regions, even when the lattices are curved and perspectively viewed. Comparisons to state-of-the-art resizing techniques and a user study were conducted to validate the proposed method. Convincing visual results are shown to demonstrate its effectiveness.
Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA (2000)

The synthesis of a 5'-O-BzH-2'- O -ACE-protected pseudouridine phosphoramidite is reported [BzH, benzhydryloxy-bis(trimethylsilyloxy)silyl; ACE, bis(2-acetoxyethoxy)methyl]. The availability of the phosphoramidite allows for reliable and efficient syntheses of hairpin RNAs containing single or multiple pseudouridine modifications in the stem or loop regions. Five 19-nt hairpin RNAs representing the 1920-loop region (G(1906)-C(1924)) of Escherichia coli 23S rRNA were synthesized with pseudouridine residues located at positions 1911, 1915 and 1917. Thermodynamic parameters, circular dichroism spectra and NMR data are presented for all five RNAs. Overall, three different structural contexts for the pseudouridine residues were examined and compared with the unmodified RNA. Our main findings are that pseudouridine modifications exhibit a range of effects on RNA stability and structure, depending on their locations. More specifically, pseudouridines in the single-stranded loop regions of the model RNAs are slightly destabilizing, whereas a pseudo-uridine at the stem-loop junction is stabilizing. Furthermore, the observed effects on stability are approximately additive when multiple pseudouridine residues are present. The possible relationship of these results to RNA function is discussed.
Analysis of Factors Controlling Soil Organic Matter Levels in Great Plains Grasslands (1987)

Abstract We analyzed climatic and textural controls of soil organic C and N for soils of the U.S. Great Plains. We used a model of soil organic matter (SOM) quantity and composition to simulate steady‐state organic matter levels for 24 grassland locations in the Great Plains. The model was able to simulate the effects of climatic gradients on SOM and productivity. Soil texture was also a major control over organic matter dynamics. The model adequately predicted aboveground plant production and soil C and N levels across soil textures (sandy, medium, and fine); however, the model tended to overestimate soil C and N levels for fine textured soil by 10 to 15%. The impact of grazing on the system was simulated and showed that steady‐state soil C and N levels were sensitive to the grazing intensity, with soil C and N levels decreasing with increased grazing rates. Regional trends in SOM can be predicted using four site‐specific variables, temperature, moisture, soil texture, and plant lignin content. Nitrogen inputs must also be known. Grazing intensity during soil development is also a significant control over steady‐state levels of SOM, and since few data are available on presettlement grazing, some uncertainty is inherent in the model predictions.
Selective apoptosis of natural killer‐cell tumours by l‐asparaginase (2005)

Summary We examined the effectiveness of various anti‐tumour agents to natural killer (NK)‐cell tumour cell lines and samples, which are generally resistant to chemotherapy, using flow cytometric terminal deoxynucleotidyl transferase‐mediated dUTP‐biotin nick end‐labelling (TUNEL) assay. Although NK‐YS and NK‐92 were highly resistant to various anti‐tumour agents, l ‐asparaginase induced apoptosis in these two NK‐cell lines. NK‐cell leukaemia/lymphoma and acute lymphoblastic leukaemia (ALL) samples were selectively sensitive to l ‐asparaginase and to doxorubicin (DXR) respectively. Samples of chronic NK lymphocytosis, an NK‐cell disorder with an indolent clinical course, were resistant to both drugs. Our study clearly separated two major categories of NK‐cell disorders and ALL according to the sensitivity to DXR and l ‐asparaginase. We examined asparagine synthetase levels by real‐time quantitative polymerase chain reaction (RQ‐PCR) and immunostaining in these samples. At least in nasal‐type NK‐cell lymphoma, there was a good correlation among asparagine synthetase expression, in vitro sensitivity and clinical response to l ‐asparaginase. In aggressive NK‐cell leukaemia, although asparagine synthetase expression was high at both mRNA and protein levels, l ‐asparaginase induced considerable apoptosis. Furthermore, samples of each disease entity occupied a distinct area in two‐dimensional plotting with asparagine synthetase mRNA level (RQ‐PCR) and in vitro l ‐asparaginase sensitivity (TUNEL assay). We confirmed rather specific anti‐tumour activity of l ‐asparaginase against NK‐cell tumours in vitro , which provides an experimental background to the clinical use of l ‐asparaginase for NK‐cell tumours.
Discovery of Piragliatin—First Glucokinase Activator Studied in Type 2 Diabetic Patients (2012)

Glucokinase (GK) activation as a potential strategy to treat type 2 diabetes (T2D) is well recognized. Compound 1, a glucokinase activator (GKA) lead that we have previously disclosed, caused reversible hepatic lipidosis in repeat-dose toxicology studies. We hypothesized that the hepatic lipidosis was due to the structure-based toxicity and later established that it was due to the formation of a thiourea metabolite, 2. Subsequent SAR studies of 1 led to the identification of a pyrazine-based lead analogue 3, lacking the thiazole moiety. In vivo metabolite identification studies, followed by the independent synthesis and profiling of the cyclopentyl keto- and hydroxyl- metabolites of 3, led to the selection of piragliatin, 4, as the clinical lead. Piragliatin was found to lower pre- and postprandial glucose levels, improve the insulin secretory profile, increase β-cell sensitivity to glucose, and decrease hepatic glucose output in patients with T2D.
Chromium picolinate and biotin combination improves glucose metabolism in treated, uncontrolled overweight to obese patients with type 2 diabetes (2007)

These results suggest that the chromium picolinate/biotin combination, administered as an adjuvant to current prescription anti-diabetic medication, can improve glycaemic control in overweight to obese individuals with type 2 diabetes; especially those patients with poor glycaemic control on oral therapy.