gebhart/patrepeval huggingface dataset:
Effects of the Introduction of L-Nucleotides into DNA. Solution Structure of the Heterochiral Duplex d(G-C-G-(L)T-G-C-G).cntdot.d(C-G-C-A-C-G-C) Studied by NMR Spectroscopy (1994)

The effect of the substitution of a L-nucleoside for a D-nucleoside in the duplex d(G-C-G-T-G-C-G).d(C-G-C-A-C-G-C) was studied by UV and NMR spectroscopy. These unnatural oligonucleotides have potential for antisense DNA technology [Damha, M. J., Giannaris, P. A., & Marfey, P. (1994) Biochemistry (preceding paper in this issue)]. The thermal stability of such duplexes is lower than that of the natural one and is dependent on the nucleotide type and/or sequence. Interestingly, inversion of the chirality of thymidine but not adenosine coincides with a large stabilizing enthalpy change. The structure of the heterochiral duplex d(G1-C2-G3-(L)T4-G5-C6-G7).d(C8-G9-C10-A11-C12-G13- C14), where (L)T denotes the mirror image of the natural thymidine, has been determined by NMR spectroscopy. The sugar conformation was determined using the sum of coupling constants and the distances using a model free relaxation matrix approach. The torsion angles of the backbone follow from 3JHH, 3JHP, and 4JHP coupling constants. The structure of the duplex was calculated by metric matrix distance geometry followed by simulated annealing. The structure is close to that of B-DNA. The base pair formed by (L)T and A is of the Watson-Crick type. All sugars adopt an S-type pucker. The incorporation of the L-sugar in the duplex is accomplished by changes in the backbone torsion angles around the phosphates and the glycosidic torsion angle of (L)T. The modification induces changes in the natural strand as well. The structure exhibits an unusual interaction between the aromatic rings of the (L)T4.A11 and G3.C12 base pairs, which provides a plausible explanation of the unusual thermodynamic properties of the duplex.
Gabapentin for acute and chronic post-surgical pain (2007)

Pain after surgery remains a significant clinical problem as it impairs recovery adversely and may lead to the transition to chronic pain. Opioid medications are far from ideal agents in suppressing postoperative pain. Gabapentin –an anticonvul-sant with antihyperalgesic properties- originally efficacious against neuropathic pain seems to be very promising for the management of pain after surgery as well. Gabapentin, by decreasing noxious stimulus-induced excitatory neurotransmitter release at the spinal cord, may attenuate central sensitization, and eventually decrease postoperative late pain. Furthermore, different sites of action may be pertinent to a synergistic effect with opioids. Both actions (antihyperalgesic effect and syn-ergy with opioid analgesia) may manifest as analgesia and/or opioid-sparing effect after surgery. This has been confirmed by a variety of clinical studies, in a variety of settings. Most of these studies have shown that either single preoperative or repeated doses of gabapentin, continued for up to a few days after surgery, decrease acute postoperative pain and/or need for postoperative opioids. This has been shown for procedures such as abdominal and vaginal hysterectomy, breast surgery for cancer (mastectomy or lumpectomy), lumbar discectomy and spinal fusion, laparoscopic cholecystectomy and other, such as ENT surgery. Finally, a few studies indicate that perioperative gabapentin may as well decrease chronic pain several weeks after surgery.
Deoxyribonucleic Acid Nucleases (1968)

Abstract The effect of different metals on the hydrolysis of DNA by DNase I was studied with the assay previously described which depends upon the release of large fragments of isotopically labeled DNA from a gel. With Mg2+, an initial lag in the rate of release occurred. This lag was eliminated when Mn2+, Ca2+, Co2+, or Mg2+ plus Ca2+ was used. Na1+ added to Mn2+, to Ca2+, or to Mg2+ plus Ca2+ reestablished the lag. The presence of the lag was related to a double hit mechanism of hydrolysis, while the absence was related to a single hit mechanism. This interpretation was confirmed by viscometry and ultracentrifuge experiments.
A combination of cyclosporin-A (CsA) and interferon-gamma (INF-gamma) induces apoptosis in human gastric carcinoma cells. (2001)

Modulation of interferon-gamma effect by other drug may enhance its tumor specific activity. The apoptosis inducing effect of interferon-gamma and its modulation by cyclosporin-A or tacrolimus (FK-506) were investigated in in vitro and ex vivo experiments. We found that a combination of cyclosporin-A (CsA) and recombinant interferon-gamma (rIFN-gamma) induced significant apoptosis in all four types of human gastric carcinoma cells tested but not in normal cells such as human peripheral blood mononuclear cells (PBMCs), human omentum-derived mesothelial cells, or human umbilical vein endothelial cells (HUVECs) in vitro. Apoptosis was also induced by a combination of rIFN-gamma with FK-506 but not with rapamycin. Next, the apoptosis-inducing effect of endogenous IFN-gamma combined with cyclosporin-A was examined using clinical samples. A streptococcal preparation, OK-432, was administered intraperitoneally for the management of 12 gastric cancer patients with malignant ascites. None of the gascitic fluids obtained before the OK-432 injection showed detectable IFN-gamma level. The OK-432 injection induced a detectable IFN-gamma production ranging from 6 to 89 pg/mL in ascitic fluids from 9 out of the 12 patients. A combination of CsA with ascitic fluids collected after but not before OK-432 injection induced significant apoptosis in MK-1 cells, a gastric carcinoma cell line. A positive correlation was found between the IFN-gamma level and CsA-induced apoptosis. The CsA-induced apoptosis was also blocked by a specific antibody against human IFN-gamma. These results indicated that both recombinant and endogenous IFN-gamma can induce potent tumor-apoptosis when combined with CsA.
Local induction of calcium phosphate formation on TiO<sub>2</sub> coatings on titanium via surface treatment with a CO<sub>2</sub> laser (2003)

Sol-gel-derived TiO(2) coatings are known to promote bonelike hydroxyapatite formation on their surfaces in vitro and in vivo. Hydroxyapatite integrates into bone tissue. In some clinical applications, the surface of an implant is simultaneously interfaced with soft and hard tissues, so it should match the properties of both. A new method is introduced for treating the coatings locally in a controlled manner. The local densification of sol-gel-derived titania coatings on titanium substrates with a CO(2) laser was studied in terms of the in vitro calcium phosphate-inducting properties. CO(2)-laser-treated multilayer coatings were compared with furnace-fired coatings prepared with the same recipe and previously shown to be bioactive. Additionally, local areas of furnace-fired multilayer coatings (previously shown to be bioactive in vitro) were further laser-treated to achieve various properties in the same implant. Topological surface properties were examined with atomic force microscopy. The formation of hydroxyapatite was studied with Fourier transform infrared and scanning electron microscopy energy-dispersive X-ray analysis. The results show that calcium phosphate formation can be adjusted locally by laser treatment. Calcium phosphate is a bonelike hydroxyapatite. The local treatment of sol-gel-derived coatings with a CO(2) laser is a promising technique for creating implants with various properties to interface different tissues and a possible way of coating implants that do not tolerate furnace firing.
An email application with active spoof monitoring and control (2016)

Spoofing is a serious security issue for email applications. Although several anti-email spoofing techniques have been developed, most of them do not provide users with sufficient control and information on spoof attacks. In this paper a web-based client oriented anti-spoofing email application is proposed which actively detects, monitors and controls email spoofing attacks. When the application detects a spoofed message, it triggers an alert message and sends the spoofed message into a spoof filter. Moreover, the user who has received the spoofed message is given the option of notifying the real sender of the spoofing attack. In this way an active spoof control is achieved. The application is hosted using the HTTPS protocol and uses notification messages that are sent in parallel with email messages via a channel that has been secured by the Secure Socket Layer (SSL) protocol. The notification messages allows the application to detect spoofed emails. The application has been developed in PHP using the Netbeans IDE and provides a user-friendly interface which is easily deployable over the web.
Interventional Applications of Intravascular Ultrasound Imaging: Initial Experience and Future Perspectives (1990)

Intravascular ultrasound imaging offers the potential to provide more detailed information about vessel and lesion morphology and physiology than is currently available from angiography. The greatest impact of intravascular ultrasound upon clinical decisions may be in the area of cardiac and vascular interventions. To evaluate the utility of intravascular ultrasound, we prospectively studied 45 patients, 11 of whom underwent interventional procedures. Intravascular ultrasound imaging was performed before and after interventions using a 20 MHz, mechanically rotating transducer on either 6.5 Fr or 8.0 Fr catheter systems. Interventions included seven peripheral vessel balloon angioplasties (Femoral artery-two, Renal artery-two, Arteriovenous fistula-two, Aortic coarctation-one), two Femoral artery rotational atherectomies, and two balloon valvuloplasties (Pulmonic valve-1, Mitral valve-1). Intravascular ultrasound and digital angiography provided similar information about vessel size. However, morphological information about the vessel wall, plaque composition, plaque topography, luminal thrombus, and vessel dissections was better appreciated by intravascular ultrasound. Intravascular ultrasound was determined to have provided unique and clinically useful information in 10/11 (91%) interventions. These preliminary data illustrate the potential value of intravascular ultrasound for the evaluation of the vascular system and in particular its value in interventional procedures.
Une étude critique de la hausse des prix à l'ère ramesside (1991)

La hausse des prix en Égypte ancienne à l'époque Ramesside est étudiée ici avec un regard d'économistes. Les interprétations habituelles de ce phénomène présupposent souvent une prédominance des mécanismes de marché qui reste hypothétique. Cette confrontation entre histoire et économie politique ne débouche pas sur une explication globale du phénomène mais permet de soulever des interrogations que les auteurs espèrent fécondes.
Desulfovirga adipica gen. nov., sp. nov., an adipate-degrading, gram-negative, sulfate-reducing bacterium. (2000)

A novel, mesophilic, Gram-negative bacterium was isolated from an anaerobic digestor for municipal wastewater. The bacterium degraded adipate in the presence of sulfate, sulfite, thiosulfate and elemental sulfur. (E)-2-Hexenedioate accumulated transiently in the degradation of adipate. (E)-2-Hexenedioate, (E)-3-hexenedioate, pyruvate, lactate, C1-C12 straight-chain fatty acids and C2-C10 straight-chain primary alcohols were also utilized as electron donors. 3-Phenylpropionate was oxidized to benzoate. The G + C content of the DNA was 60 mol%. 16S rDNA sequence analysis revealed that the new isolate clustered with species of the genus Syntrophobacter and Desulforhabdus amnigenus. Strain TsuAS1T resembles Desulforhabdus amnigenus DSM 10338T with respect to the ability to utilize acetate as an electron donor and the inability to utilize propionate without sulfate in co-culture with Methanospirillum hungatei DSM 864. Strains TsuAS1T and DSM 10338T form a 'non-syntrophic subcluster' within the genus Syntrophobacter. Desulfovirga adipica gen. nov., sp. nov. is proposed for the newly isolated bacterium, with strain TsuAS1T (= DSM 12016T) as the type strain.
The Enzymatic Cleavage of Phosphate Termini from Polynucleotides (1967)

At the mononucleotide level, the purified E. coli C enzyme also showed 5'-nucleotidase activity on substrates without a 3'.phosphate substitution.A third unique phosphatase activity was also encountered in extracts of phage-infected cells.An enzyme, purified extensively from this source, was found capable of removing the 5'-phosphate groups of ribo-and deoxyribopolynucleotides.With polynucleotides labeled specifically with 3*P at their 5'-termini as subst,rates, this reaction proceeds as follows.In this communication, procedures for the isolation and characterization of these three enzymes are described.EXPERIMENTAL PROCEDURE Enzymes 5'-Nucleotidase of Crotalus adamanteus was further purified from a commercial source (Sigma) by the procedure of Lehman, ROUSSOS, and Pratt (6).Prostatic phosphomonoesterase was prepared according to Ostrowski and Tsugita (7).Micrococcal nuclease, crystalline pancreatic DNase, RNase, alkaline phosphatase, spleen phosphodiesterase, and venom phosphodiesterase were purchased from Worthington.E. coli endonuclease I, exonuclease I, and exonuclease III were generous gifts of Dr. I. R. Lehman.5'-TMP kinase was the kind gift of Dr. M. J. Bessman.5'-Hydroxylpolynucleotide kinase was purified from T4 am 82.infected E. coli B by the procedure of Novogrodsky and Hurwitz (4). Nucleic Acids and NucleotidesCalf thymus DNA was either isolated by the method of Kay, Simmons, and Dounce (8) or obtained commercially (Worthington).z2P-Labeled E. coli DNA (specific activity 10,000 to 18,000 cpm per mpmole of nucleotide residue) was prepared as described by Lehman (9).Bacterial DNA was prepared by the method of Marmur (10); phage DNA was prepared as described by Mandell and Hershey (11).Soluble RNA and ribosomal RNA of E. coli were prepared as described elsewhere (12, 5).Unlabeled pTp, pT, 5'-, 3'-, and 2'ribomononucleotides were purchased from Calbiochem, as were p-nitrophenylphosphate and p-nitrophenyl-5'-thymidylate.2', 3'-Cyclic guanylate was the gift of Dr. J. Winter.y-s2P-Labeled ATP (specific activity 1,000 to 8,000 cpm per ppmole) was synthesized according to the method of Penefsky et al. ( 13).Unlabeled and 32P-labeled 3'-deoxymononucleotides were prepared from nonradioactive and 32P-labeled DNA from E. coli B by the sequential action cf micrococcal nuclease and spleen phosphodiesterase followed by chromatography on Dowex l-Cl-as described by Josse, Kaiser, and Kornberg (14).32P-Labeled Tp (specific activity 500 cpm per mpmole) was prepared in large quantities according to the method of Tener (15).3',5'-dTDP, labeled with 32P specifically in position 5', was synthesized by Mr. 111.Gefter and kindly donated by him.32P-Labeled 5'-dTMP was purchased from the International Chemical and Nuclear Corporation, and was further purified by chromatography on Dowex I-Cl-.2'(3')-and 5'-phosphoryl-terminat,ed polyuridylate oligonucleo-
Transforming growth factor-beta and IL-4 cause helper T cell precursors to develop into distinct effector helper cells that differ in lymphokine secretion pattern and cell surface phenotype (1991)

We have investigated the effects of TGF-beta on the in vitro development of different subsets of Th cells and find that addition of TGF-beta results in the generation of cell populations with distinct characteristics that resemble those of memory cells. Resting, short-lived CD4+ precursor T cells can be induced by mitogen stimulation to proliferate and differentiate in in vitro cultures and after 4 to 7 days will generate a population of cells that, when restimulated, synthesize and secrete high titers of a wide variety of lymphokines. It has been previously reported that the presence of the lymphokine IL-4 during in vitro culture results in the generation of a population of "effector" cells that can be rapidly induced by mitogen to synthesize and secrete high titers of IL-4, IL-5, IL-3, IFN-gamma, and granulocyte-macrophage-CSF. We find that TGF-beta added to CD4+ precursors, suppresses the development of IL-4/IL-5 secreting effectors and results instead in the development of cells secreting IL-2 and IFN-gamma. CD4 T cells generated in the presence of TGF-beta show little or no expression of CD45RB, in contrast to those developed in IL-4 (or in IL-2 alone) that express high surface densities of CD45RB. The kinetics of cell recovery also differs when TGF-beta rather than IL-4 is present during culture. Cultures of effectors generated in TGF-beta, initially have low cell recoveries but cells expand dramatically between 4 to 7 days in the presence of IL-2 whereas IL-4 induces optimum cell recovery at day 4 and cell recoveries decrease with further culture. The properties of cells grown in TGF-beta thus show several attributes in common with memory or highly differentiated CD4+ cells, i.e., IL-2 as a predominant cytokine, easy propagation and low expression of CD45RB. Therefore, we propose the hypothesis that TGF-beta favors the development of a population(s) of Th cells that is likely to give rise to memory cells although IL-4 favors development of a short-lived effector population that secretes Th2 lymphokines.
SODA: a service-on-demand architecture for application service hosting utility platforms (2004)

The grid is realizing the vision of providing computation as utility: computational jobs can be scheduled on-demand at grid hosts based on available computational capacity. In this project, we study another emerging usage of grid utility: the hosting of application services. Different from a computational job, an application service such as an e-Laboratory or an on-line business has longer lifetime, and performs multiple jobs requested by its clients. A service hosting utility platform (HUP) is formed by a set of hosts in the grid, and multiple application services will be hosted on the HUP. SODA is a service-on-demand architecture that enables on-demand creation of application services on a HUP. With SODA, an application service will be created in the form of a set of virtual service nodes; each node is a virtual machine which is physically a 'slice' of a real host in the HUP. SODA involves both OS and middleware techniques, and has the following salient capabilities: (1) on-demand service priming: the image of an application service as well as the OS on which it runs will be created on-demand and bootstrapped automatically; (2) better service isolation: services sharing the same HUP host are isolated with respect to administration, faults, intrusion, and resources; (3) integrated service load management: for each service, a service switch will be created to direct client requests to appropriate virtual service nodes. Moreover, the application service provider can replace the default request switching policy with a service-specific policy.
Polymorphism in the <i>CETP</i> Gene Region, HDL Cholesterol, and Risk of Future Myocardial Infarction (2009)

In this prospective cohort of initially healthy women, SNPs at the CETP locus impact on future risk of myocardial infarction, supporting a causal role for CETP in atherothrombosis, possibly through an HDL-C mediated pathway.
Digital Microfluidics: An Emerging Sample Preparation Platform for Mass Spectrometry (2013)

Mass spectrometry (MS) has become an indispensable tool for laboratory science, but a drawback is the laborious sample processing required before MS analysis. Digital microfluidics (DMF), a microscale liquid handling technique characterized by the manipulation of fluid droplets on open electrode arrays, presents a potential solution to this problem. In DMF, discrete droplets can be made to merge, mix, split, and dispense from reservoirs. Since droplets are manipulated individually and act as discrete microreactors, DMF is well suited for microscale sample processing. Coupling the versatility of MS analysis with DMF sample handling has been beneficial for a number of DMF-based applications, including proteomics, chemical synthesis, and clinical diagnostics. In this review, we provide a summary of efforts to integrate these two technologies, focusing on examples of both off-line and in-line MS analysis for DMF sample processing.
Syntheses and Oligonucleotide Incorporation of Nucleoside Analogues Containing Pendant Imidazolyl or Amino Functionalities – The Search for Sequence‐Specific Artificial Ribonucleases (2005)

Abstract Oligonucleotide derivatives containing imidazolyl and amino functionalities have been proposed as artificial ribonucleases that might mimic the activities of RNase A but with greater sequence specificity. Such oligonucleotide reagents would have important applications as enhanced antisense reagents that obviate the need to recruit a cellular nuclease or nuclease complex. We present the syntheses of six nucleoside phosphoramidite analogues containing pendant protected imidazolyl or amino groups and their incorporation into oligonucleotides. We show that the six functionalised phosphoramidites have similar efficiencies of incorporation and present mass spectral evidence that the composition of an oligonucleotide library of 81 components is consistent with the expected mass mixture distribution. Such phosphoramidites are thus suitable starting materials for construction of mixed oligonucleotide libraries containing a region of imidazolyl and amino‐modified nucleotides ready for screening for sequence‐specific ribonuclease activity. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Transferrin-Conjugated Micelles: Enhanced Accumulation and Antitumor Effect for Transferrin-Receptor-Overexpressing Cancer Models (2012)

As the transport protein for iron, transferrin can trigger cellular endocytosis once binding to its receptor (TfR) on the cell membrane. Using this property, we conjugated transferrin onto the surface of biodegradable polymeric micelles constructed from amphiphilic block copolymers. The core of micelle was either labeled with a near-infrared dye (NIR) or conjugated with a chemotherapeutic drug paclitaxel (PTX) to study the biodistribution or antitumor effect in nude mice bearing subcutaneous TfR-overexpressing cancers. DLS and TEM showed that the sizes of Tf-conjugated and Tf-free micelles were in the range of 85-110 nm. Confocal laser scanning microscopy and flow cytometry experiments indicated that the uptake efficiency of the micelles by the TfR-overexpressing cells was enhanced by Tf conjugation. Semiquantitative analysis of the NIR signals collected from the tumor site showed that the maximum accumulation was achieved at 28 h in the M(NIR) group, while at 22 h in Tf-M(NIR) groups; and the area under the intensity curve in the Tf-M(NIR) groups was more than that in M(NIR) group. Finally, the tumor inhibition effects of targeting micelles were studied with the gastric carcinoma model which overexpressed TfR. The analysis of tumor volumes and the observation of H&E-stained tumor sections showed that Tf-M(PTX) had the best antitumor effect compared with the control groups (saline, PTX, and M(PTX)). The results of this study demonstrated the potential application of Tf-conjugated polymeric micelles in the treatment of TfR-overexpressing cancers.