gebhart/patrepeval huggingface dataset:
Synthesis and antiviral activity of certain 4-substituted and 2,4-disubstituted 7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3-d]pyrimidines (1988)

Treatment of the sodium salt of 4-chloro-2-(methylthio)pyrrolo[2,3-d]pyrimidine (2) with (2-acetoxyethoxy)methyl bromide (3) has provided 4-chloro-2-(methylthio)-7[(2-acetoxyethoxy)methyl]pyrrolo[2,3- d]pyrimidine (4). Ammonolysis of 4 at room temperature gave 4-chloro-2-(methylthio)-7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3- d]pyrimidine (5). However, ammonolysis of 5 at 130 degrees C furnished 4-amino-2-(methylthio)-7-[(2-hydroxyethoxy)methyl]-pyrrolo[2,3- d]pyrimidine (6), which on desulfurization with Raney Ni yielded 4-amino-7-[(2-hydroxyethoxy)-methyl]pyrrolo[2,3-d]pyrimidine (7) (acyclic analogue of tubercidin). The oxidation of 6 with m-chloroperbenzoic acid provided the sulfone derivative 8. A nucleophilic displacement of the 2-methylsulfonyl group from 8 with methoxide anion provided 4-amino-2-methoxy-7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3-d]pyrimidine (9). Demethylation of 9 with iodotrimethylsilane gave 4-amino-2-hydroxy-7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3-d]pyrimidine (10). Treatment of 2,4-dichloropyrrolo[2,3-d]pyrimidine (11) with 3 gave the protected acyclic compound 12, which on deacetylation and ammonolysis under controlled reaction conditions gave 2,4-dichloro-7-[(2-hydroxyethoxy)-methyl]pyrrolo[2,3-d]pyrimidine (13) and 4-amino-2-chloro-7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3- d]pyrimidine (14), respectively. The condensation of 2-acetamido-4-chloropyrrolo[2,3-d]pyrimidine (15) with 3 gave the protected acyclic compound 16, which on concomitant deacetylation and ammonolysis with methanolic ammonia at an elevated temperature yielded 2,4-diamino-7-[(2-hydroxyethoxy)methyl]pyrrolo[2,3-d]pyrimidine (17) in moderate yield. In tests involving human cytomegalovirus (HCMV) and herpes simplex virus type 1 (HSV-1), only slight activity and cytotoxicity were observed. The most active compounds (12 and 13) were slightly more active against HCMV than acyclovir, but both compounds were inactive against HSV-1. The activity against HCMV, however, was not well separated from cytotoxicity leading to the conclusion that these compounds did not merit further study.
Sister telomeres rendered dysfunctional by persistent cohesion are fused by NHEJ (2009)

Telomeres protect chromosome ends from being viewed as double-strand breaks and from eliciting a DNA damage response. Deprotection of chromosome ends occurs when telomeres become critically short because of replicative attrition or inhibition of TRF2. In this study, we report a novel form of deprotection that occurs exclusively after DNA replication in S/G2 phase of the cell cycle. In cells deficient in the telomeric poly(adenosine diphosphate ribose) polymerase tankyrase 1, sister telomere resolution is blocked. Unexpectedly, cohered sister telomeres become deprotected and are inappropriately fused. In contrast to telomeres rendered dysfunctional by TRF2, which engage in chromatid fusions predominantly between chromatids from different chromosomes (Bailey, S.M., M.N. Cornforth, A. Kurimasa, D.J. Chen, and E.H. Goodwin. 2001. Science. 293:2462-2465; Smogorzewska, A., J. Karlseder, H. Holtgreve-Grez, A. Jauch, and T. de Lange. 2002. Curr. Biol. 12:1635-1644), telomeres rendered dysfunctional by tankyrase 1 engage in chromatid fusions almost exclusively between sister chromatids. We show that cohered sister telomeres are fused by DNA ligase IV-mediated nonhomologous end joining. These results demonstrate that the timely removal of sister telomere cohesion is essential for the formation of a protective structure at chromosome ends after DNA replication in S/G2 phase of the cell cycle.
MIMO Broadcast Channels with Digital Channel Feedback (2006)

This paper summarizes recent results on the multiple antenna broadcast (downlink) channel in which limited- rate digital feedback is used to convey channel state information from each mobile (receiver), each of which is assumed to have perfect channel information, to the transmitter. The transmitter employs linear precoding based on this feedback, and the effect of imperfect channel state information is multi-user interference, which can significantly degrade throughput if the channel information is not sufficiently accurate. Feedback requirements are studied for systems with single antenna mobiles in both the small system regime, i.e., number of mobiles equal to the number of transmit antennas, as well as in the large system regime, where user selection is performed on the basis of digital feedback. In addition, two different methods for utilizing multiple mobile antennas are described and compared in the small system regime.
Aminoacyl Esterase Activity of the Tetrahymena Ribozyme (1992)

Several classes of ribozymes (catalytic RNA's) catalyze reactions at phosphorus centers, but apparently no reaction at a carbon center has been demonstrated. The active site of the Tetrahymena ribozyme was engineered to bind an oligonucleotide derived from the 3' end of N-formyl-methionyl-tRNA(fMet). This ribozyme catalyzes the hydrolysis of the aminoacyl ester bond to a modest extent, 5 to 15 times greater than the uncatalyzed rate. Catalysis involves binding of the oligonucleotide to the internal guide sequence of the ribozyme and requires Mg2+ and sequence elements of the catalytic core. The ability of RNA to catalyze reactions with aminoacyl esters expands the catalytic versatility of RNA and suggests that the first aminoacyl tRNA synthetase could have been an RNA molecule.
Evaluation of Multiplex Flow Cytometric Opsonophagocytic Assays for Determination of Functional Anticapsular Antibodies to Streptococcus pneumoniae (2006)

ABSTRACT The determination of functional antipneumococcal capsular polysaccharide antibodies by sequential testing of pre- and postvaccination serum samples one serotype at a time is sample-intensive and time-consuming and has a relatively low throughput. We tested several opsonophagocytic assay (OPA) formats, including the reference killing method, a monovalent bacterium-based flow method, a trivalent bacterium-based flow method, and a tetravalent bead-based flow method using a panel of sera (4 prevaccination and 16 postvaccination, from healthy adults immunized with the 23-valent pneumococcal polysaccharide vaccine). The trivalent and tetravalent methods allow simultaneous measurements of opsonic antibodies to multiple pneumococcal serotypes. The trivalent bacterial-flow OPA had significant correlation to the reference OPA method and to a previously published flow cytometric OPA ( r values ranged from 0.61 to 0.91, P &lt; 0.05) for serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F. The tetravalent OPA had significant correlation to all OPA method formats tested ( r values from 0.68 to 0.92, P &lt; 0.05) for all seven serotypes tested. This tetravalent OPA is an alternative to other OPA methods for use during vaccine evaluation and clinical trials. Further, the flow cytometric multiplex OPA format has the potential for expansion beyond the current four serotypes to eight or more serotypes, which would further increase relative sample throughput while reducing reagent and sample volumes used.
Delivery of Biologically Active Anti-Inflammatory Cytokines IL-10 and IL-1ra In Vivo by the Shigella Type III Secretion Apparatus (2008)

Pathogenicity of many Gram-negative bacteria relies on a type III secretion (T3S) apparatus, which is used for delivery of bacterial effectors into the host cell cytoplasm allowing the bacteria to manipulate host cell cytoskeleton network as well as to interfere with intracellular signaling pathways. In this study, we investigated the potential of the Shigella flexneri T3SA as an in vivo delivery system for biologically active molecules such as cytokines. The anti-inflammatory cytokines IL-10 and IL-1 receptor antagonist (IL-1ra) were genetically fused to the first 30 or 60 residues of the Shigella T3S effector IpaH9.8 or to the first 50 residues of the Yersinia enterocolitica effector YopE and the recombinant fusion proteins were expressed in S. flexneri. YopE(50)-IL-10, IpaH(60)-IL-10, and IpaH(60)-IL-1ra were efficiently secreted via the T3S apparatus of Shigella. Moreover, these recombinant proteins did not impair the invasive ability of the bacteria in vitro. In a murine model, Shigella strains expressing YopE(50)-IL-10, IpaH(60)-IL-10, and IpaH(60)-IL-1ra induced a lower mortality in mice that was associated with reduced inflammation and a restricted localization of bacteria within the lung tissues as compared with wild-type Shigella. Moreover, the level of TNF-alpha and IL-1beta mRNA were reduced in the lungs following infection by IL-10- and IL-1ra-secreting Shigella, respectively. These findings demonstrate that the Shigella T3S apparatus can deliver biologically active cytokines in vivo, thus opening new avenues for the use of attenuated bacteria to deliver proteins for immunomodulation or gene therapy purposes.
Further studies by immunofluorescence of the monoclonal antibodies associated with experimental non-A, non-B hepatitis in chimpanzees and their relation to D hepatitis (1986)

To further investigate the specificity of the monoclonal antibodies (48-1 and S-1) associated with non-A, non-B hepatitis, extensive immunofluorescence studies were performed on liver biopsy specimens from chimpanzees with experimental hepatitis A, B, non-A, non-B or delta, or from normal chimpanzees. Both 48-1 and S-1 antibodies reacted in the same manner with liver biopsy specimens from 47 of 50 (94%) chimpanzees with acute or chronic non-A, non-B hepatitis and 15 of 18 (83%) chimpanzees with type D hepatitis. Examinations of serial liver biopsy specimens revealed that the duration of expression of the antigen reacting with the antibodies in hepatocytes of chimpanzees infected with non-A, non-B viruses appeared to be longer than that of chimpanzees infected with the hepatitis delta-virus. By thin-section electron microscopy, the presence of the microtubular aggregates, identical to those previously described for chimpanzees with non-A, non-B hepatitis and shown by immunoelectron microscopy to react with the antibodies, was noted in hepatocytes during the acute phase of hepatitis delta-virus. The antibodies did not react with liver biopsy specimens from chimpanzees acutely or chronically infected with hepatitis B virus or hepatitis A virus, or from normal chimpanzees. The present results confirm our previous observations with the 48-1 and S-1 antibodies. Furthermore, the finding that these two antibodies were also associated with hepatitis D would support the possibility that non-A, non-B agents and the hepatitis delta-virus may have a similar nature or may elicit a similar host response.
An introduction to coil array design for parallel MRI (2006)

The basic principles of radiofrequency coil array design for parallel MRI are described from both theoretical and practical perspectives. Because parallel MRI techniques rely on coil array sensitivities to provide spatial information about the sample, a careful choice of array design is essential. The concepts of coil array spatial encoding are first discussed from four qualitative perspectives. These qualitative descriptions include using coil arrays to emulate spatial harmonics, choosing coils with selective sensitivities to aliased pixels, using coil sensitivities with broad k-space reception profiles, and relying on detector coils to provide a set of generalized projections of the sample. This qualitative discussion is followed by a quantitative analysis of coil arrays, which is discussed in terms of the baseline SNR of the received images as well as the noise amplifications (g-factor) in the reconstructed data. The complications encountered during the experimental evaluation of coil array SNR are discussed, and solutions are proposed. A series of specific array designs are reviewed, with an emphasis on the general design considerations that motivate each approach. Finally, a set of special topics is discussed, which reflect issues that have become important, especially as arrays are being designed for more high-performance applications of parallel MRI. These topics include concerns about the depth penetration of arrays composed of small elements, the use of adaptive arrays for systems with limited receiver channels, the management of inductive coupling between array elements, and special considerations required at high field strengths. The fundamental limits of spatial encoding using coil arrays are discussed, with a primary emphasis on how the determination of these limits impacts the design of optimized arrays. This review is intended to provide insight into how arrays are currently used for parallel MRI and to place into context the new innovations that are to come.
EVOLVING FEDERATIONS AND SUBCENTRAL DEFICITS: TESTING THE BAILOUT HIPÓTESIS IN THE SPANISH CASE (2004)

High debt autonomy and low tax autonomy often characterize evolving federations, making the bailout hypothesis very attractive when explaining subcentral governments deficits. In order to test it in the case of Spanish regional governments, I analyze relationships among observable variables suggested in the literature on the bailout hypothesis. The main conclusion is that deficit seems to be better explained by a more traditional model of fiscal choices than by bailout expectations.
Improved outcome in HLA-identical sibling hematopoietic stem-cell transplantation for acute myelogenous leukemia predicted by KIR and HLA genotypes (2005)

Inhibitory killer immunoglobulin (Ig)-like receptors (KIRs) recognize HLA-C and -B epitopes on target cells, thereby regulating natural killer (NK) cell activity. In 178 patients receiving T-cell-depleted HLA-identical sibling transplants for acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL), or myelodysplastic syndrome (MDS), analysis of donor KIR genotype with HLA genotype demonstrated that 62.9% of the patients lacked an HLA ligand for donor-inhibitory KIR. Lack of HLA ligand for donor-inhibitory KIR (missing KIR ligand) had no effect on disease-free survival (DFS), overall survival (OS), or relapse in patients receiving transplants for CML and ALL. In patients with AML and MDS, however, there was a significant missing KIR ligand effect on DFS (P = .014; hazard ratio [HR], 0.53; 95% confidence interval [95% CI], 0.28-0.88) and OS (P = .03; HR, 0.53; 95% CI, 0.3-0.93). Incidence of relapse was also lower in patients with AML and MDS who lacked the HLA ligand for donor-inhibitory KIR (P = .04; HR, 0.41; 95% CI, 0.18-0.97). AML and MDS patients lacking 2 HLA ligands for donor-inhibitory KIR had the highest DFS (P = .002) and OS (P = .003). There was no significant contribution of donor-activating KIR to transplantation outcome in these patients. These data indicate that the absence of class I ligand in the recipient for donor-inhibitory KIR can be a prognostic factor for transplantation outcome in HLA-identical sibling transplantation and that the lack of HLA-C or -B ligands for donor-inhibitory KIR can contribute to improved outcomes for patients with AML and MDS.
The reverse transcriptase component of the Tetrahymena telomerase ribonucleoprotein complex (1998)

Telomerase is a eukaryotic reverse transcriptase that adds simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. We describe here the identification of a Tetrahymena telomerase protein with reverse transcriptase motifs, p133. This subunit is associated with the previously identified Tetrahymena telomerase RNA and the telomerase proteins p80 and p95 in immunoprecipitation assays. Therefore, all four known Tetrahymena telomerase components are present in a single complex. Expressed in rabbit reticulocyte lysate, recombinant p133 and telomerase RNA alone catalyze a reverse transcriptase activity with some similarities to and some differences from native Tetrahymena telomerase. These experiments suggest a complexity of telomerase structure and function.
Testosterone prevents the heat shock-induced overactivation of glycogen synthase kinase-3β but not of cyclin-dependent kinase 5 and c-Jun NH 2 -terminal kinase and concomitantly abolishes hyperphosphorylation of τ: Implications for Alzheimer's disease (2002)

We have shown previously that glycogen synthase kinase-3 beta (GSK-3 beta), cyclin-dependent kinase 5, and c-Jun NH(2)-terminal kinase become overactivated and hyperphosphorylate tau in heat-shocked female rats. This hyperphosphorylation of tau is estrogen-independent, prevented by androgens, and similar to Alzheimer's disease. In this study, ovariectomized (OVX) Sprague-Dawley rats (n = 75) received daily injections of 10 microg of 17 beta-estradiol benzoate (EB), or 250 microg of testosterone propionate (TP), or both EB and TP, or sesame oil (SO) vehicle for 4-6 weeks. In kinase assays of forebrain homogenates, overactivation of GSK-3 beta at 0-6 h after heat shock toward human recombinant tau, bovine tau, and phosphoglycogen synthase peptide 2 was prevented in OVX + TP and OVX + (EB + TP) but not in sham-OVX + SO, OVX + SO, and OVX + EB. Abs against inactive (pSer(9)) and activity-enhanced (pTyr(216)) GSK-3 beta showed marked increase of pSer(9)- and decrease of pTyr(216)-GSK-3 beta in both OVX + TP and OVX + (EB + TP) but not in sham-OVX + SO, OVX + SO, and OVX + EB. EB enhanced the overactivation of cyclin-dependent kinase 5. The activity of c-Jun NH(2)-terminal kinase was gonadal hormone-independent. The serum concentrations of testosterone and 17 beta-estradiol were 2.53 ng/ml and 201 pg/ml in OVX + TP and OVX + EB, respectively. These findings demonstrate that testosterone prevents the hyperphosphorylation of tau by inhibiting the heat shock-induced overactivation of GSK-3 beta and suggest that androgens given to aging men or, in combination with estrogens, to postmenopausal women could prevent or delay Alzheimer's disease.
A Mechanochemical Model of Growth Termination in Vertical Carbon Nanotube Forests (2008)

Understanding the mechanisms by which vertical arrays of carbon nanotube (CNT) forests terminate their growth may lead to the production of aligned materials of infinite length. We confirm through calculation of the Thiele modulus that several prominent systems reported in the literature to date are not stunted by diffusion limitations. Evidence also suggests that, for many systems, the growth-termination mechanism is spatially correlated among nanotubes, making spontaneous, random catalytic poisoning unlikely as a dominant mechanism. We propose that a mechanical coupling of the top surface of the film creates an energetic barrier to the relative displacement between neighboring nanotubes. A Monte Carlo simulation based on this premise is able to qualitatively reproduce characteristic deflections of the top surface of single- and doubled-walled CNT (SWNT and DWNT) films near the edges and corners. The analysis asserts that the coupling is limited by the enthalpy of the carbon-forming reaction. We show that for patterned domains, the resulting top surface of the pillars is approximately conic with hyperbolic cross sections that allow for empirical calculation of a threshold force (F(max) = 34-51 nN for SWNTs, 25-27 nN for DWNTs) and elastic constant (k, 384-547 N/m for SWNTs and 157-167 N/m for DWNTs) from the images of experimentally synthesized films. Despite differences in nanotube type and precursor chemistry, the values appear consistent supporting the validity of the model. The possible origin of the mechanical coupling is discussed.
Angelman Syndrome: Clinical Profile (1992)

To further delineate the clinical and developmental features of Angelman syndrome, we collected data through three sources of information: (1) physical examinations; (2) laboratory data and family questionnaire data of affected individuals; and (3) literature review. The questionnaire data describes a generally normal prenatal and birth history. Feeding difficulties, developmental delay, or seizures were the presenting problems in all infants. The diagnosis of Angelman syndrome, however, was not made in any infant prior to 1 year of age. Except for seizures, no medical or surgical complication was common, although a variety of visual complaints or findings were common. Sixty percent of Angelman syndrome children had a cytogenetically demonstrated deletion of chromosome 15q11-q13. The individuals with and without a deletion could not be differentiated clinically. Diagnosis in early childhood is therefore difficult, and a high index of suspicion is recommended.
Nano Meets Security: Exploring Nanoelectronic Devices for Security Applications (2015)

Information security has emerged as an important system and application metric. Classical security solutions use algorithmic mechanisms that address a small subset of emerging security requirements, often at high-energy and performance overhead. Further, emerging side-channel and physical attacks can compromise classical security solutions. Hardware security solutions overcome many of these limitations with less energy and performance overhead. Nanoelectronics-based hardware security preserves these advantages while enabling conceptually new security primitives and applications. This tutorial paper shows how one can develop hardware security primitives by exploiting the unique characteristics such as complex device and system models, bidirectional operation, and nonvolatility of emerging nanoelectronic devices. This paper then explains the security capabilities of several emerging nanoelectronic devices: memristors, resistive random-access memory, contact-resistive random-access memory, phase change memories, spin torque-transfer random-access memory, orthogonal spin transfer random access memory, graphene, carbon nanotubes, silicon nanowire field-effect transistors, and nanoelectronic mechanical switches. Further, the paper describes hardware security primitives for authentication, key generation, data encryption, device identification, digital forensics, tamper detection, and thwarting reverse engineering. Finally, the paper summarizes the outstanding challenges in using emerging nanoelectronic devices for security.