gebhart/patrepeval huggingface dataset:
Mismatch cleavage by single-strand specific nucleases (2004)

We have investigated the ability of single-strand specific (sss) nucleases from different sources to cleave single base pair mismatches in heteroduplex DNA templates used for mutation and single-nucleotide polymorphism analysis. The TILLING (Targeting Induced Local Lesions IN Genomes) mismatch cleavage protocol was used with the LI-COR gel detection system to assay cleavage of amplified heteroduplexes derived from a variety of induced mutations and naturally occurring polymorphisms. We found that purified nucleases derived from celery (CEL I), mung bean sprouts and Aspergillus (S1) were able to specifically cleave nearly all single base pair mismatches tested. Optimal nicking of heteroduplexes for mismatch detection was achieved using higher pH, temperature and divalent cation conditions than are routinely used for digestion of single-stranded DNA. Surprisingly, crude plant extracts performed as well as the highly purified preparations for this application. These observations suggest that diverse members of the S1 family of sss nucleases act similarly in cleaving non-specifically at bulges in heteroduplexes, and single-base mismatches are the least accessible because they present the smallest single-stranded region for enzyme binding. We conclude that a variety of sss nucleases and extracts can be effectively used for high-throughput mutation and polymorphism discovery.
Human and Mouse Monoclonal Antibodies to Blood Group A Substance, Which Are Nearly Identical Immunochemically, Use Radically Different Primary Sequences (1995)

A human monoclonal antibody (HuA) specific for blood group A substance with two fucose groups was found to be immunochemically almost identical with that of a previously characterized mouse monoclonal anti-A, AC-1001. The VH and VL chain cDNAs of HuA were sequenced and compared with those of AC-1001. The human and mouse antibodies used VH and Vk genes that came from different families and shared minimal nucleotide and amino acid sequence identity. Thus, two antibodies from two different species can use evolutionarily unrelated sequences to bind the same carbohydrate epitope. The cloned HuA VH and VL genes were then transfected into a mouse myeloma cell line and re-expressed, together, and each separately with an irrelevant VH or VL. Only the original HuA VH and Vk had anti-A activity, demonstrating that both the heavy and light chains contributed to specificity.
Isolation and structure of .DELTA.+- tetrahydrocannabinol and other neutral cannabinoids from hashish (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsolation and structure of .DELTA.+- tetrahydrocannabinol and other neutral cannabinoids from hashishYechiel Gaoni and Raphael MechoulamCite this: J. Am. Chem. Soc. 1971, 93, 1, 217–224Publication Date (Print):January 1, 1971Publication History Published online1 May 2002Published inissue 1 January 1971https://pubs.acs.org/doi/10.1021/ja00730a036https://doi.org/10.1021/ja00730a036research-articleACS PublicationsRequest reuse permissionsArticle Views2259Altmetric-Citations276LEARN 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
Long-term cryopreservation of bone marrow for autologous transplantation. (1996)

Little is known about the effect of long-term cryopreservation on the viability of hematopoietic stem cells (HSC) or on the success of autologous bone marrow transplantation. Although progenitor cell assays such as culture of CFU-GM after thawing can be predictive of engraftment, the most rigorous assay for the cryosurvival of HSC is engraftment after reinfusion of stem cells. We retrospectively evaluated the engraftment data for 36 patients with hematologic malignancies or solid tumors treated at the Fred Hutchinson Cancer Research Center between 1981 and 1993 who received bone marrows stored for 2 years or more. The median duration of cryopreservation for this study group was 2.7 years (range 2.0-7.8). Ninety-seven percent of patients in the study group achieved a granulocyte count of > or = 0.5 x 1.0(9)/1 at a median of 19 days (range 10-115) vs 86% of control group (selected by diagnosis and date of storage) at a median of 20 days (P = 0.14). Seventy percent of patients in the study group achieved a platelet count > or = 20 x 10(9)/1 at a median of 27 days (range 9-69) vs 74% of control group at a median of 23 days (P = 0.47). Also, samples of 28 marrows cryopreserved for a median of 4.4 years (range 2.0-7.8) were cultured to determine if a loss of hematopoietic progenitors relative to duration of storage could be detected. The storage length was not predictive for the quantity of colonies formed (P = 0.57 for BFU-E-derived colonies; P = 0.65 for CFU-GM-derived colonies). We found no consistent detrimental effect of long-term cryopreservation on the success rate of autologous bone marrow transplantation. This report confirms previous reports that marrow cells cryopreserved for several years are capable of engrafting. Therefore, bone marrow cells may be stored at an early appropriate time before the side-effects of multiple cycles of chemotherapy and radiotherapy on hematopoietic tissues are incurred.
Simple BM25 extension to multiple weighted fields (2004)

This paper describes a simple way of adapting the BM25 ranking formula to deal with structured documents. In the past it has been common to compute scores for the individual fields (e.g. title and body) independently and then combine these scores (typically linearly) to arrive at a final score for the document. We highlight how this approach can lead to poor performance by breaking the carefully constructed non-linear saturation of term frequency in the BM25 function. We propose a much more intuitive alternative which weights term frequencies before the non-linear term frequency saturation function is applied. In this scheme, a structured document with a title weight of two is mapped to an unstructured document with the title content repeated twice. This more verbose unstructured document is then ranked in the usual way. We demonstrate the advantages of this method with experiments on Reuters Vol1 and the TREC dotGov collection.
Y2 receptors for peptide YY and neuropeptide Y on dispersed chief cells from guinea pig stomach (1992)

Peptide YY (PYY) and neuropeptide Y (NPY) inhibit agonist-induced adenosine 3',5'-cyclic monophosphate (cAMP) production and pepsinogen secretion from chief cells. We used radiolabeled PYY and NPY to characterize receptors on chief cells from guinea pig stomach. Binding of 125I-labeled PYY was rapid (70% maximal within 10 min) and specific (not inhibited by secretin, vasoactive intestinal peptide, cholecystokinin, carbachol, prostaglandin E2, forskolin, or cholera toxin). Measurement of the ability of PYY to inhibit binding of 125I-PYY indicated the presence of 1.8 x 10(3) high-affinity [dissociation constant (Kd) = 1.7 nM] and 5.1 x 10(4) low-affinity (Kd = 83.3 nM) sites/cell. Internalization of bound 125I-PYY was suggested by slow and incomplete dissociation in the presence of unlabeled PYY (50% after 2 h) and was examined further by measuring residual binding after washing with acetic acid (pH 2.5), glycine (pH 10.5), or trypsin. After 30 min at 37 degrees C, internalization of radioligand was evidenced by the failure of washing with these solutions to remove 50-65% of bound radioactivity. At 4 degrees C, internalization of 125I-PYY was nearly abolished. Binding of 125I-PYY and 125I-NPY was inhibited by NPY-(13-36) but not by [Leu31,Pro34]NPY indicating that these are Y2 receptors. In guinea pig chief cells, PYY and NPY modulate cAMP-mediated pepsinogen secretion by interacting with specific high-affinity Y2 receptors.
Phase I Trial of Intraperitoneal Injection of the E1B-55-kd-Gene-Deleted Adenovirus ONYX-015 (dl1520) Given on Days 1 Through 5 Every 3 Weeks in Patients With Recurrent/Refractory Epithelial Ovarian Cancer (2002)

This article therefore describes the first clinical experience with the intraperitoneal delivery of any replication-competent/-selective virus in cancer patients.
The 72K IE1 and 80K IE2 proteins of human cytomegalovirus independently trans-activate the c-fos, c-myc and hsp70 promoters via basal promoter elements (1992)

Growth-regulating cellular genes or genes encoding proteins involved in cell cycle control are likely to be major targets of viral gene products in the establishment of a cellular state favourable for a permissive infection. We have examined whether infection of permissive fibroblasts with human cytomegalovirus (HCMV) results in trans-regulation of such cellular genes. Here we have shown that the proto-oncogenes c-fos and c-myc are specifically induced during immediate early (IE) and early times of HCMV infection, as has recently been shown for the heat shock protein 70 gene (hsp70). Deletion analyses and transfection assays of all three promoters showed that previously defined control sequences upstream of the constitutive promoters and downstream of the mRNA cap site are not required for this up-regulation by HCMV, such that the minimal inducible promoters of c-fos, c-myc and the hsp70 gene contained only 50 to 60 bp upstream of the transcription start site. Cotransfection assays with vectors expressing HCMV major IE cDNAs showed that the 72K IE1 and 80K IE2 proteins are involved in the up-regulation of these promoters. IE1 and IE2 products independently were able to up-regulate the minimal constitutive promoters of the constructs tested here, but trans-activation by IE1 and IE2 together was synergistic. In the case of the hsp70 promoter, promoter constructs containing a variety of different TATA elements could be activated by the 72K IE1 and 80K IE2 proteins.
Iliac and femoral artery stenoses and occlusions: treatment with intravascular stents. (1989)

Forty-five patients with atherosclerotic stenoses and occlusions of the iliac and superficial femoral arteries were treated with a flexible, self-expanding, metallic intravascular stent. Of these patients, 37 were treated immediately after inadequate angioplasty. At a follow-up period of 2-12 months, intravenous digital subtraction angiograms demonstrated patency of the vessels with stents in 40 of 45 patients. The mean Doppler ankle/arm index increased from 0.60 to 0.92 immediately after treatment and was 0.89 at follow-up. Early thrombotic stent occlusion occurred in two patients. Intimal hyperplasia was a late effect and led to stent stenoses in three patients after 5-9 months and stent occlusion in one patient after 6 months. In three patients, percutaneous recanalization with balloon and Simpson catheters was successful. Intravascular stents proved particularly useful for maintenance of patency after angioplasty in occlusions of the iliac and femoral arteries and in treatment of stenoses due to eccentric and severely ulcerated plaques. The stents also helped manage complications after angioplasty. Long-term results will depend on the degree, frequency, and progression of intimal hyperplasia narrowing the vascular lumen.
Transcription activator‐like type III effector AvrXa27 depends on OsTFIIAγ5 for the activation of Xa27 transcription in rice that triggers disease resistance to Xanthomonas oryzae pv. oryzae (2009)

The transcription activator-like (TAL) type III effector AvrXa27 from Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99(A) activates the transcription of the host resistance gene Xa27, which results in disease resistance to bacterial blight (BB) in rice. In this study, we show that AvrXa27-activated Xa27 transcription requires host general transcription factor OsTFIIAgamma5. The V39E substitution in OsTFIIAgamma5, encoded by the recessive resistance gene xa5 in rice, greatly attenuates this activation in xa5 and Xa27 double homozygotes on inoculation with Xa27-incompatible strains. The xa5 gene also causes attenuation in the induction of Xa27 by AvrXa27 expressed in rice. The xa5-mediated attenuation of Xa27-mediated resistance to PXO99(A) is recessive. Intriguingly, xa5-mediated resistance to xa5-incompatible strains is also down-regulated in the xa5 and Xa27 double homozygotes. In addition, AvrXa27 expressed in planta shows weak virulence activity in the xa5 genetic background and causes enhanced susceptibility of the plants to BB inoculation. The results suggest that TAL effectors target host general transcription factors to directly manipulate the host transcriptional machinery for virulence and/or avirulence. The identification of xa5-mediated attenuation of Xa27-mediated resistance to Xoo provides a guideline for breeding resistance to BB when pyramiding xa5 with other resistance genes.
Deterministic Diagnostic Pattern Generation (DDPG) for Compound Defects (2008)

Scan chain failure diagnosis has become an important means for silicon debug and yield improvement. Although plenty of prior work discussed how to perform scan chain diagnosis, most of the previously proposed techniques made an assumption that the system logic is fault-free, which could be an impractical assumption leading to incorrect diagnostic results. In this paper, we propose a scan chain deterministic diagnostic pattern generation (DDPG) method that can tolerate the faults in the system logic without degradation of chain diagnostic resolution and precision. The entire flow includes three steps. In the first step, patterns are created to propagate the state of a targeted scan cell to as many reliable observation points as possible. In the second step, the load error probability of each targeted scan cell is calculated based on the hamming distances between the observed responses and the expected good or faulty responses. In the last step, a suspect profile is plotted, which can be used to identify the suspect scan cell(s) based on ranking scores. Experimental results show that the diagnostic resolution and precision are not degraded even with dozens of faults injected into the system logic.
Polysaccharides (2004)

Completely revised and expanded to reflect the latest advancements in the field, Polysaccharides: Structural Diversity and Functional Versatility, Second Edition outlines fundamental concepts in the structure, function, chemistry, and stability of polysaccharides and reveals new analytical techniques and applications currently impacting the cosmeti
Recent applications of the hetero Diels–Alder reaction in the total synthesis of natural products (2015)

The synthetic utility and potential power of the Diels–Alder (D–A) reaction in organic chemistry is evident.
Biosynthesis of gliotoxin. Synthesis of sulfur-bridged dioxopiperazines from N-hydroxyamino acids (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBiosynthesis of gliotoxin. Synthesis of sulfur-bridged dioxopiperazines from N-hydroxyamino acidsJacobus D. M. Herscheid, Rutger J. F. Nivard, Marian W. Tijhuis, and Harry C. J. OttenheijmCite this: J. Org. Chem. 1980, 45, 10, 1885–1888Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://pubs.acs.org/doi/10.1021/jo01298a024https://doi.org/10.1021/jo01298a024research-articleACS PublicationsRequest reuse permissionsArticle Views399Altmetric-Citations24LEARN 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
Redox‐Mediated Regulation of p21Waf1/Cip1 Expression Involves a Post‐Transcriptional Mechanism and Activation of the Mitogen‐Activated Protein Kinase Pathway (1997)

p21(waf1/cip1) gene expression is induced by DNA damage in cells with wild-type p53 and contributes to the arrest of cell growth. It was demonstrated that under many experimental conditions, including oxidative stress, p21(waf1/cip1) expression can be induced through p53-independent pathways. Since most of these experimental conditions induce the phosphorylation of mitogen-activated protein kinase (MAPK) and thus its activation, we evaluated p21(waf1/cip1) mRNA levels in cells exposed to an oxidative stress, induced by diethylmaleate (Et2Mal), and in which the MAPK pathway was blocked. The expression of a dominant-negative mutant of MEK, the MAPK kinase that phosphorylates and activates MAPK, and of a dominant-negative [Asn17]Ras mutant prevented the Et2Mal-induced accumulation of p21(waf1/cip1) mRNA. Similarly, the expression of MEK- and of [Asn17]Ras mutants decreased the 12-O-tetradecanoyl-phorbol 13-acetate (TPA)-mediated p21(waf1/cip1) induction. Furthermore, TPA-induced and serum-induced p21(waf1/cip1) mRNA accumulation was blocked by pretreating the cells with the antioxidant compound N-acetylcysteine, suggesting that oxidative stress is involved in these responses. p21(waf1/cip1) mRNA levels reached a maximum within 2 h of adding Et2Mal or TPA; however, the rate of transcription from a p21(waf1/cip1)-promoter construct did not increase during this period. In contrast, cells treated with actinomycin D show an increase of p21(waf1/cip1) mRNA stability after Et2Mal treatment. This result suggests that the increase in p21(waf1/cip1) mRNA at early times results from post-transcriptional regulatory events. Longer exposure to TPA may activate p21(waf1/cip1) gene transcription through an Sp1-dependent mechanism, while Et2Mal treatment gradually inhibits p21(waf1/cip1) gene transcription through oxidative changes that affect Sp1 binding to DNA.
Dexmedetomidine Diminishes Halothane Anesthetic Requirements in Rats Through a Postsynaptic Alpha2 Adrenergic Receptor (1988)

The effect of 4(5)-[1-(2,3-dimethylphenyl)ethyl]imidazole (medetomidine), the alpha 2 adrenergic agonist, on anesthetic requirements was investigated in rats anesthetized with halothane. Halothane MAC was determined before and after either dexmedetomidine (d-enantiomer) or levomedetomidine (l-enantiomer) 10, 30, and 100 micrograms/kg or vehicle ip. There was a dose-dependent decrease in MAC with the d-, but not the l-, stereoisomer. At the highest dose of dexmedetomidine (100 micrograms/kg), halothane could be discontinued for up to 30 min with no response to tail clamping. To determine whether alpha 2 adrenoreceptors mediated this effect of dexmedetomidine on MAC, cohorts of rats were pretreated with idazoxan, 10 mg/kg ip, a highly selective alpha 2 antagonist. This completely prevented the reduction of MAC caused by dexmedetomidine. To determine whether the reduction of MAC caused by dexmedetomidine was mediated in part through either opiate or adenosine receptors, groups of rats were pretreated with either naltrexone, 5 mg/kg ip, an opiate antagonist, or 8-phenyltheophylline, 2.5 mg/kg ip, an A1 adenosine antagonist. These two pretreatments did not alter the reduction of MAC by dexmedetomidine. To determine whether postsynaptic mechanisms mediate the anesthetic effect of dexmedetomidine, rats were depleted of central catecholamine stores with either n-(2-chloroethyl)-n-ethyl-2-bromobenzylamine (DSP-4) or reserpine and alpha-methyl-para-tyrosine and MAC was determined before and after each dose of dexmedetomidine. While the catecholamine-depleted rats had a lower basal MAC than the vehicle controls, there was still a profound reduction in halothane MAC after administration of dexmedetomidine. The reduction of MAC by dexmedetomidine was blocked with idazoxan in the catecholamine depleted rats.(ABSTRACT TRUNCATED AT 250 WORDS)
The role of NF-kappaB in the angiogenic response of coronary microvessel endothelial cells. (1996)

The activation of nuclear factor (NF)-kappaB by 12(R)-hydroxyeicosatrienoic acid [12(R)-HETrE], an arachidonic acid metabolite with potent stereospecific proinflammatory and angiogenic properties, was examined and its role in the angiogenic response was determined in capillary endothelial cells derived from coronary microvessels. Electrophoretic mobility-shift assay of nuclear protein extracts from cells treated with 12(R)-HETrE demonstrated a rapid and stereospecific time- and concentration-dependent increase in the binding activity of NF-kappaB, which was inhibitable by the antioxidants N-acetylcysteine, butylated hydroxyanisole, and pyrrolidine dithiocarbamate and was partially attenuated by the protein kinase C inhibitors, staurosporine and calphostin C. Neither 12(S)-HETrE nor other related eicosanoids--e.g., 12(R)-HETE, 12(S)-HETE, and leukotriene B4--stimulated the activation of NF-kappaB relative to 12(R)-HETrE, substantiating the claim for a specific receptor-mediated mechanism. 12(R)-HETrE stimulated the formation of capillary-like cords of microvessel endothelial cells distinguishable from a control; this effect was comparable to that observed with basic fibroblast growth factor (bFGF). Inhibition of NF-kappaB activation resulted in inhibition of capillary-like formation of endothelial cells treated with 12(R)-HETrE by 80% but did not affect growth observed with bFGF. It is suggested that 12(R)-HETrE's angiogenic activity involves the activation of NF-kappaB, possibly via protein kinase C stimulation and the generation of reactive oxygen intermediates for downstream signaling.
Tensile-strained, n-type Ge as a gain medium for monolithic laser integration on Si (2007)

We analyze the optical gain of tensile-strained, n-type Ge material for Si-compatible laser applications. The band structure of unstrained Ge exhibits indirect conduction band valleys (L) lower than the direct valley (Gamma) by 136 meV. Adequate strain and n-type doping engineering can effectively provide population inversion in the direct bandgap of Ge. The tensile strain decreases the difference between the L valleys and the Gamma valley, while the extrinsic electrons from n-type doping fill the L valleys to the level of the Gamma valley to compensate for the remaining energy difference. Our modeling shows that with a combination of 0.25% tensile strain and an extrinsic electron density of 7.6x10(19)/cm(3) by n-type doping, a net material gain of ~400 cm(-1) can be obtained from the direct gap transition of Ge despite of the free carrier absorption loss. The threshold current density for lasing is estimated to be ~6kA cm(-2) for a typical edgeemitting double heterojunction structure. These results indicate that tensile strained n-type Ge is a good candidate for Si integrated lasers.