gebhart/patrepeval huggingface dataset:
Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community (1996)

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene segments was used to profile microbial populations inhabiting different temperature regions in the microbial mat community of Octopus Spring, Yellowstone National Park. DGGE allowed a rapid evaluation of the distributions of amplifiable sequence types. Profiles were essentially identical within regions of the mat defined by one temperature range but varied between sites with different temperature ranges. Individual DGGE bands were sequenced, and the sequences were compared with those previously obtained from the mat by cloning and from cultivated Octopus Spring isolates. Two known cyanobacterial populations and one known green nonsulfur bacterium-like population were detected by DGGE, as were many new cyanobacterial and green nonsulfur and green sulfur bacterium-like populations and a novel bacterial population of uncertain phylogenetic affiliation. The distributions of several cyanobacterial populations compared favorably with results obtained previously by oligonucleotide probe analyses and suggest that adaptation to temperature has occurred among cyanobacteria which are phylogenetically very similar.
7  Structure and rheology of aqueous gels (2003)

The experimental techniques of scattering and rheology are discussed, in the context of determining the structure and mechanical response of aqueous physical gels. In particular simultaneous scattering and rheology studies are discussed. This review paper covers the rheology and structure of gels of poly(oxyethylene) based copolymers, poly(vinyl alcohol), gelatin and starch.
A man-interactive simulator system for above-knee prosthetics studies. (1973)

Massachusetts Institute of Technology. Dept. of Mechanical Engineering. Thesis. 1973. Ph.D.
N-Substituted Adenosines as Novel Neuroprotective A1 Agonists with Diminished Hypotensive Effects (1999)

The synthesis and pharmacological profile of a series of neuroprotective adenosine agonists are described. Novel A(1) agonists with potent central nervous system effects and diminished influence on the cardiovascular system are reported and compared to selected reference adenosine agonists. The novel compounds featured are derived structurally from two key lead structures: 2-chloro-N-(1-phenoxy-2-propyl)adenosine (NNC 21-0041, 9) and 2-chloro-N-(1-piperidinyl)adenosine (NNC 90-1515, 4). The agonists are characterized in terms of their in vitro profiles, both binding and functional, and in vivo activity in relevant animal models. Neuroprotective properties assessed after postischemic dosing in a Mongolian gerbil severe temporary forebrain ischemia paradigm, using hippocampal CA1 damage endpoints, and the efficacy of these agonists in an A(1) functional assay show similarities to some reference adenosine agonists. However, the new compounds we describe exhibit diminished cardiovascular effects in both anesthetized and awake rats when compared to reference A(1) agonists such as (R)-phenylisopropyladenosine (R-PIA, 5), N-cyclopentyladenosine (CPA, 2), 4, N-[(1S,trans)-2-hydroxycyclopentyl]adenosine (GR 79236, 26), N-cyclohexyl-2'-O-methyladenosine (SDZ WAG 994, 27), and N-[(2-methylphenyl)methyl]adenosine (Metrifudil, 28). In mouse permanent middle cerebral artery occlusion focal ischemia, 2-chloro-N-[(R)-[(2-benzothiazolyl)thio]-2-propyl]adenosine (NNC 21-0136, 12) exhibited significant neuroprotection at the remarkably low total intraperitoneal dose of 0.1 mg/kg, a dose at which no cardiovascular effects are observed in conscious rats. The novel agonists described inhibit 6, 7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate-induced seizures, and in mouse locomotor activity higher doses are required to reach ED(50) values than for reference A(1) agonists. We conclude that two of the novel adenosine derivatives revealed herein, 12 and 5'-deoxy-5'-chloro-N-[4-(phenylthio)-1-piperidinyl]adenosine (NNC 21-0147, 13), representatives of a new series of P(1) ligands, reinforce the fact that novel selective adenosine A(1) agonists have potential in the treatment of cerebral ischemia in humans.
Oligoribonucleotides containing 2′,5′-phosphodiester linkages exhibit binding selectivity for 3′,5′-RNA over 3′,5′-ssDNA (1993)

Oligoribonucleotides containing 2',5'-phosphodiester linkages have been synthesized on a solid support by the 'silyl-phosphoramidite' method. The stability of complexes formed between these oligonucleotides and complementary 3',5'-RNA strands have been studied using oligoadenylates and a variety of oligonucleotides of mixed base sequences including phosphorothioate backbones. In many cases, particularly for 2',5'-linked adenylates, the UV melting profiles are quite sharp and exhibit large hyperchromic changes. Substituting a few 3',5'-linkages with the 2',5'-linkage within an oligomer lowers the Tm of the complex and the degree of destabilization depends on the neighboring residues and neighboring linkages. The 2',5'-linked oligoribonucleotides prepared in this study exhibited remarkable selectivity for complementary single stranded RNA over DNA. For example, in 0.01 M phosphate buffer--0.10 M NaCl (pH 7.0), no association was observed between 2',5'-r(CCC UCU CCC UUC U) and its Watson-Crick DNA complement 3',5'-d(AGAAGGGAGAGGG). However, 2',5'-r(CCC UCU CCC UUC U) with its RNA complement 3',5'-r(AGAAGGGAGAGGG) forms a duplex which melts at 40 degrees C. The decamer 2',5'-r(Ap)9A forms a complex with both poly dT and poly rU but the complex [2',5'-r(Ap)9A]:[poly dT] is unstable (Tm, -1 degree C) and is seen only at high salt concentrations. In view of their unnatural character and remarkable selectivity for single stranded RNA, 2',5'-oligo-RNAs and their derivatives may find use as selective inhibitors of viral mRNA translation, and as affinity ligands for the purification of cellular RNA.
Microfabricated Sensor Arrays Sensitive to pH and K+ for Ionic Distribution Measurements in the Beating Heart (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrofabricated Sensor Arrays Sensitive to pH and K+ for Ionic Distribution Measurements in the Beating HeartVasile V. Cosofret, Miklos. Erdosy, Timothy A. Johnson, Richard P. Buck, R. Bruce. Ash, and Michael R. NeumanCite this: Anal. Chem. 1995, 67, 10, 1647–1653Publication Date (Print):May 15, 1995Publication History Published online1 May 2002Published inissue 15 May 1995https://pubs.acs.org/doi/10.1021/ac00106a001https://doi.org/10.1021/ac00106a001research-articleACS PublicationsRequest reuse permissionsArticle Views782Altmetric-Citations124LEARN 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
IEEE 802.11 MAC Protocol over Wireless Mesh Networks: Problems and Perspectives (2005)

The wireless mesh network has been an emerging technology in recent years. Because the transmission medium used in networking backhaul APs is radio, the wireless mesh network is not only easy and cost effective in deployment, but also has good scalability in coverage area and capacity. The IEEE 802.11 MAC protocol has been adopted as the de-facto medium access control. In this paper, we assess the fitness of the IEEE 802.11 over wireless mesh networks. We focus on the question: Does the backhaul networking of a wireless mesh network have the capability to support multimedia transport? The backhaul must guarantee the throughput and the latency. Furthermore, the QoS guarantee is required for multimedia applications. We contend that it is really necessary to consider what the key is to be changed in the IEEE 802.11 so that it can adapt the IEEE 802.11 MAC protocol to wireless mesh networks. Through the study of existing solutions, we analyze the previous work and sketch the contours of the directions to achieve our goal in this article.
Text Detection and Character Recognition in Scene Images with Unsupervised Feature Learning (2011)

Reading text from photographs is a challenging problem that has received a significant amount of attention. Two key components of most systems are (i) text detection from images and (ii) character recognition, and many recent methods have been proposed to design better feature representations and models for both. In this paper, we apply methods recently developed in machine learning -- specifically, large-scale algorithms for learning the features automatically from unlabeled data -- and show that they allow us to construct highly effective classifiers for both detection and recognition to be used in a high accuracy end-to-end system.
GRP78/BiP/HSPA5/Dna K is a universal therapeutic target for human disease (2014)

The chaperone GRP78/Dna K is conserved throughout evolution down to prokaryotes. The GRP78 inhibitor OSU-03012 (AR-12) interacted with sildenafil (Viagra) or tadalafil (Cialis) to rapidly reduce GRP78 levels in eukaryotes and as a single agent reduce Dna K levels in prokaryotes. Similar data with the drug combination were obtained for: HSP70, HSP90, GRP94, GRP58, HSP27, HSP40 and HSP60. OSU-03012/sildenafil treatment killed brain cancer stem cells and decreased the expression of: NPC1 and TIM1; LAMP1; and NTCP1, receptors for Ebola/Marburg/Hepatitis A, Lassa fever, and Hepatitis B viruses, respectively. Pre-treatment with OSU-03012/sildenafil reduced expression of the coxsakie and adenovirus receptor in parallel with it also reducing the ability of a serotype 5 adenovirus or coxsakie virus B4 to infect and to reproduce. Similar data were obtained using Chikungunya, Mumps, Measles, Rubella, RSV, CMV, and Influenza viruses. OSU-03012 as a single agent at clinically relevant concentrations killed laboratory generated antibiotic resistant E. coli and clinical isolate multi-drug resistant N. gonorrhoeae and MRSE which was in bacteria associated with reduced Dna K and Rec A expression. The PDE5 inhibitors sildenafil or tadalafil enhanced OSU-03012 killing in N. gonorrhoeae and MRSE and low marginally toxic doses of OSU-03012 could restore bacterial sensitivity in N. gonorrhoeae to multiple antibiotics. Thus, Dna K and bacterial phosphodiesterases are novel antibiotic targets, and inhibition of GRP78 is of therapeutic utility for cancer and also for bacterial and viral infections.
Field-evolved resistance by western corn rootworm to multipleBacillus thuringiensistoxins in transgenic maize (2014)

The widespread planting of crops genetically engineered to produce insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) places intense selective pressure on pest populations to evolve resistance. Western corn rootworm is a key pest of maize, and in continuous maize fields it is often managed through planting of Bt maize. During 2009 and 2010, fields were identified in Iowa in which western corn rootworm imposed severe injury to maize producing Bt toxin Cry3Bb1. Subsequent bioassays revealed Cry3Bb1 resistance in these populations. Here, we report that, during 2011, injury to Bt maize in the field expanded to include mCry3A maize in addition to Cry3Bb1 maize and that laboratory analysis of western corn rootworm from these fields found resistance to Cry3Bb1 and mCry3A and cross-resistance between these toxins. Resistance to Bt maize has persisted in Iowa, with both the number of Bt fields identified with severe root injury and the ability western corn rootworm populations to survive on Cry3Bb1 maize increasing between 2009 and 2011. Additionally, Bt maize targeting western corn rootworm does not produce a high dose of Bt toxin, and the magnitude of resistance associated with feeding injury was less than that seen in a high-dose Bt crop. These first cases of resistance by western corn rootworm highlight the vulnerability of Bt maize to further evolution of resistance from this pest and, more broadly, point to the potential of insects to develop resistance rapidly when Bt crops do not achieve a high dose of Bt toxin.
A substance P receptor (NK1) antagonist can reverse vascular and nociceptive abnormalities in a rat model of complex regional pain syndrome type II (2003)

Sciatic nerve section in rats evokes chronic hindlimb edema, pain behavior, and hyperalgesia, a syndrome resembling complex regional pain syndrome (CRPS II) in man. Furthermore, there is an increase in spontaneous protein extravasation in the hindpaw skin of rats after sciatic transection, similar to the increased protein extravasation observed in the edematous limbs of CRPS patients. Now we demonstrate that sciatic nerve section also generates chronic hindlimb warmth, distal articular tenderness, allodynia, and periarticular osteoporosis, sequelae of nerve injury resembling those observed in CRPS. We postulated that facilitated substance P signaling may contribute to these vascular and nociceptive abnormalities and attempted to reverse these changes with the long acting substance P receptor (NK(1)) antagonist LY303870. Hindpaw spontaneous extravasation was inhibited by LY303870. Systemic administration of LY303870 also reversed hindpaw edema and cutaneous warmth. Intrathecal, but not systemic administration of LY303870 reversed soft tissue and articular mechanical hyperalgesia in the hindpaw. Collectively, these data further support the hypothesis that the sciatic nerve transection model closely resembles CRPS and that substance P contributes to the spontaneous extravasation, edema, warmth, and mechanical hyperalgesia observed in this model.
Cross-talk Between Retinoic Acid and STAT3 Signaling Pathways in Acute Promyelocytic Leukemia (2003)

Acute promyelocytic leukemia (APL) is a form of acute myelogenous leukemia characterized by chromosomal alterations involving the retinoic acid receptor-alpha (RARalpha) gene that generate unique chimeric proteins (N-RARalpha) and by clinical responsiveness to all-trans-retinoic acid (ATRA) treatment. APL cells are notable for differentiation block and resistance to apoptosis. While increasing evidence suggests that N-RARalpha fusion proteins interfere with normal RARalpha transcription function at retinoic acid response elements (RAREs) resulting in inhibition of normal myeloid differentiation, the mechanism for apoptosis resistance remains unexplained. Recently, we and others have reported that APL-fusion proteins can augment STAT3 transcriptional activity. Constitutive STAT3 activation has been observed in a number of hematopoietic and non-hematopoietic malignancies where it contributes to apoptosis resistance. In this review, we summarize a series of recent observations concerning cross talk between the retinoic acid and STAT3 signaling pathways in APL cells. These findings support the hypothesis that apoptosis resistance in APL may be mediated through the effects of APL fusion proteins on STAT3 signaling and suggest that targeting of STAT3 may be a useful adjunctive treatment strategy in APL.
Hydrolysis of lysine peptides by plasmin. (1974)

The syntheses of L-leucyl-L-lysine amide, glycyl-L-lysyl-L-lysine, glycyl-L-lysyl-L-lysine amide, glycyl-L-lysyl-L-arginine and L-lysyl-L-lysyl-L-arginine were described. All dipeptides and dipeptide amides examined were resistant to plasmin, while glycyl-L-lysine amide and L-leucyl-L-lysine amide were cleaved by trypsin although dipeptides were not. Tetrapeptide, glycyl-L-lysyl-L-lysyl-L-arginine, was hydrolyzed by plasmin to glycyl-L-lysine and L-lysyl-L-arginine, as well as by trypsin. L-Lysyl-L-lysyl-L-arginine was cleaved on lysyllysine bond by plasmin, however, no reaction occurred by trypsin. The other hand, L-lysyl-L-lysyl-L-lysine was hydrolyzed by trypsin to L-lysyl-L-lysine and L-lysine, although this tripeptide was not attacked by plasmin. Also glycyl-L-lysyl-L-lysine amide was not to be the substrate for plasmin, while this amide was attacked by trypsin, yielding glycyl-L-lysine and L-lysine amide in addition, to glycyl-L-lysyl-L-lysine, ammonia and L-lysine.
A vitamin E analogue suppresses malignant mesothelioma in a preclinical model: A future drug against a fatal neoplastic disease? (2004)

Malignant mesothelioma is a fatal type of neoplasia of the pleura and the peritoneum with currently no known cure. Therefore, discovery of an efficient antimesothelioma drug with low deleterious side effects is desirable. Here, we studied in vivo the effect of alpha-tocopheryl succinate, a semisynthetic vitamin E analogue with proapoptotic and anticancer activity and selectivity for malignant cells, on experimental peritoneal mesothelioma using immunocompromised mice. Compared to untreated animals, the agent increased their survival >3-fold. Our finding warrants further testing of vitamin E analogues as potential antimesothelioma drugs.
Analysis of adenovirus transforming proteins from early regions 1A and 1B with antisera to inducible fusion antigens produced in Escherichia coli (1984)

Plasmid vectors were constructed which expressed three adenovirus tumor antigens fused to a portion of the trpE protein of Escherichia coli. Insertion of adenovirus type 2 DNA from early region 1A (E1A) into such a plasmid led to a fusion protein which contained the C-terminal 266 amino acids of the 289-amino acid protein encoded by the viral 13S mRNA. Similarly, insertion of adenovirus type 5 DNA corresponding to the E1B 55- and 21-kilodalton proteins led to production of fusion proteins containing amino acid sequences from these proteins. After induction with indoleacrylic acid, fusion proteins accumulated stably in the E. coli cells. By using a simple extraction of insoluble protein, 1 to 10 mg of fusion protein per liter of culture was obtained. The fusion proteins were purified on preparative polyacrylamide gels and used to immunize rabbits. Specific antisera for the E1A 289- and closely related 243-amino acid proteins and the E1B 55- and 21-kilodalton proteins were obtained. These sera were used to immunoprecipitate the tumor antigens in cells infected with wild-type and various mutants of adenovirus or to analyze them by an immunoblotting procedure. Mutant E1A proteins in which the C-terminal 70 amino acids are deleted were phosphorylated to much lower extents than the wild-type E1A proteins. This indicates that the deleted region is important for the process of phosphorylation. The E1A proteins were extracted, sedimented in glycerol gradients, analyzed by immunoprecipitation, and found to sediment primarily as monomers.
Free electrons and ionic liquids: study of excited states by means of electron-energy loss spectroscopy and the density functional theory multireference configuration interaction method (2015)

The technique of low energy (0-30 eV) electron impact spectroscopy, originally developed for gas phase molecules, is applied to room temperature ionic liquids (IL). Electron energy loss (EEL) spectra recorded near threshold, by collecting 0-2 eV electrons, are largely continuous, assigned to excitation of a quasi-continuum of high overtones and combination vibrations of low-frequency modes. EEL spectra recorded by collecting 10 eV electrons show predominantly discrete vibrational and electronic bands. The vibrational energy-loss spectra correspond well to IR spectra except for a broadening (∼0.04 eV) caused by the liquid surroundings, and enhanced overtone activity indicating a contribution from resonant excitation mechanism. The spectra of four representative ILs were recorded in the energy range of electronic excitations and compared to density functional theory multireference configuration interaction (DFT/MRCI) calculations, with good agreement. The spectra up to about 8 eV are dominated by π-π* transitions of the aromatic cations. The lowest bands were identified as triplet states. The spectral region 2-8 eV was empty in the case of a cation without π orbitals. The EEL spectrum of a saturated solution of methylene green in an IL band showed the methylene green EEL band at 2 eV, indicating that ILs may be used as a host to study nonvolatile compounds by this technique in the future.
Hybrid Silicon Photonics for Low‐Cost High‐Bandwidth Link Applications (2008)

Current discrete optical solutions for high data‐rate link applications, even with potentially high manufacturing volumes, are too costly. Highly integrated, multifunction modules are a key part of the solution, reducing size and cost while providing improved reliability. Silicon, with its proven manufacturability and reliability, offers a solid foundation for building a cost‐efficient path to successful products. In this paper, recent work on the development of silicon photonic enabling components for multichannel high data‐rate links is presented.
Pyridinyl Imidazole Inhibitors of p38 Mitogen-activated Protein Kinase Bind in the ATP Site (1997)

The site of action of a series of pyridinyl imidazole compounds that are selective inhibitors of p38 mitogen-activated protein kinase in vitro and block proinflammatory cytokine production in vivo has been determined. Using Edman sequencing, 125I-SB206718 was shown to cross-link to the nonphosphorylated Escherichia coli-expressed p38 kinase at Thr175, which is proximal to the ATP binding site. Titration calorimetric studies with E. coli-expressed p38 kinase showed that SB203580 bound with a stoichiometry of 1:1 and that binding was blocked by preincubation of p38 kinase with the ATP analogue, FSBA (5'-[p-(fluorosulfonyl)benzoyl]adenosine), which covalently modifies the ATP binding site. The intrinsic ATPase activity of the nonphosphorylated enzyme was inhibited by SB203580 with a Km of 9.6 mM. Kinetic studies of active, phosphorylated yeast-expressed p38 kinase using a peptide substrate showed that SB203580 was competitive with ATP with a Ki of 21 nM and that kinase inhibition correlated with binding and biological activity. Mutagenesis indicated that binding of 125I-SB206718 was dependent on the catalytic residues K53 and D168 in the ATP pocket. These findings indicate that the pyridinyl imidazoles act in vivo by inhibiting p38 kinase activity through competition with ATP and that their selectivity is probably determined by differences in nonconserved regions within or near the ATP binding pocket.
Multiple Abnormalities in Glucose and Energy Metabolism and Coordinated Changes in Levels of Adiponectin, Cytokines, and Adhesion Molecules in Subjects With Metabolic Syndrome (2004)

The metabolic syndrome is characterized by an excess of intra-abdominal fat, hypoadiponectinemia, insulin resistance in skeletal muscle and adipose tissue, multiple defects in glucose and energy metabolism, and elevated levels of cytokines and adhesion molecules.