gebhart/patrepeval huggingface dataset:
Binding of Myc Proteins to Canonical and Noncanonical DNA Sequences (1993)

Using an in vitro binding-site selection assay, we have demonstrated that c-Myc-Max complexes bind not only to canonical CACGTG or CATGTG motifs that are flanked by variable sequences but also to noncanonical sites that consist of an internal CG or TG dinucleotide in the context of particular variations in the CA--TG consensus. None of the selected sites contain an internal TA dinucleotide, suggesting that Myc proteins necessarily bind asymmetrically in the context of a CAT half-site. The noncanonical sites can all be bound by proteins of the Myc-Max family but not necessarily by the related CACGTG- and CATGTG-binding proteins USF and TFE3. Substitution of an arginine that is conserved in these proteins into MyoD (MyoD-R) changes its binding specificity so that it recognizes CACGTG instead of the MyoD cognate sequence (CAGCTG). However, like USF and TFE3, MyoD-R does not bind to all of the noncanonical c-Myc-Max sites. Although this R substitution changes the internal dinucleotide specificity of MyoD, it does not significantly alter its wild-type binding sequence preferences at positions outside of the CA--TG motif, suggesting that it does not dramatically change other important amino acid-DNA contacts; this observation has important implications for models of basic-helix-loop-helix protein-DNA binding.
Post-conflict reconstuction : Bosnia and Herzegovina - case study summary (1998)

The World Bank's response to post-conflict needs in Bosnia and Herzegovina (BIH) was early and comprehensive. Its role in reconstruction and economic recovery is widely perceived to have been successful by BIH authorities, other donors, nongovernmental organizations, and beneficiaries. The Bank's non-lending activities, including providing a framework for reconstruction and guidance to donors, are generally appreciated. There is wide-spread recognition that Bank -supported projects were implemented quickly. Other elements of success include: a wide dispersion of benefits, both geographically and to a broad range of beneficiaries, involvement of stakeholders; and early and balanced inclusion of social sector projects to rebuild human and social capital; and a contribution to local implementation capacity. BIH authorities particularly appreciated the sense of ownership afforded them by Bank projects.
Apoptosis and Mitochondrial Dysfunction in Lymphocytes of Patients With Systemic Lupus Erythematosus (2004)

Systemic lupus erythematosus (SLE) is characterized by abnormal activation and cell death signaling within the immune system. Activation, proliferation, or death of cells of the immune system are dependent on controlled reactive oxygen intermediate (ROI) production and ATP synthesis in mitochondria. The mitochondrial transmembrane potential (Delta(Psi)m) reflects the energy stored in the electrochemical gradient across the inner mitochondrial membrane, which in turn is used by F0F1-ATPase to convert adenosine 5'-diphosphate to ATP during oxidative phosphorylation. Mitochondrial hyperpolarization and transient ATP depletion represent early and reversible steps in T-cell activation and apoptosis. By contrast, T lymphocytes of patients with SLE exhibit elevated Delta(Psi)m, that is, persistent mitochondrial hyperpolarization, cytoplasmic alkalinization, increased ROI production, as well as diminished levels of intracellular glutathione and ATP. Oxidative stress affects signaling through the T-cell receptor as well as the activity of redox-sensitive caspases. ATP depletion may be responsible for diminished activation-induced apoptosis and sensitize lupus T cells to necrosis. Mitochondrial dysfunction is identified as a key mechanism in the pathogenesis of SLE.
A picosecond passively mode-locked vertical extended cavity surface emitting diode laser (2005)

We demonstrate multi-GHz rate picosecond pulse generation by passive mode- locking of an extended surface emitting diode laser which permits the incorporation of a saturable Bragg reflector mirror into a device, here designed for large aperture operation as a high power 980 nm InGaAs multiple quantum-well vertical cavity source? 2002 Optical Society of America OClS Codes: 120.5700,320.7120 Modelocking of lasers is a technique for generation of psec optical pulses. For potential applications ranging from high-speed chipscale optical clocks to nonlinear optical imaging in biology, passive mode-locking of a compact source such as a VCSEL is of interest. Keller and co-workers (I), in particular, have achieved high power psec pulse generation at multi-GHz repetition rates from optically pumped InGaAs MQW-based external cavity VCSELs, incorporating a semiconductor saturable Bragg absorber mirror (SESAM) for passive modelocking. Here we demonstrate the modelocking of a compact vertical extended cavity surface emitting diode laser (VECSEL) by using specific device design ideas.
A Randomized Trial of Combined Citalopram and Naltrexone for Nonabstinent Outpatients With Co-Occurring Alcohol Dependence and Major Depression (2015)

Despite the high rate of co-occurrence of major depression and alcohol dependence, the role of pharmacotherapy in their treatment remains unclear. In the new era of naltrexone for alcohol dependence, it is notable that only 1 study to date has examined the efficacy of antidepressant medication prescribed concurrently with naltrexone. We aimed to determine whether combining naltrexone with citalopram produced better treatment outcomes than naltrexone alone in patients with co-occurring alcohol dependence and depression, and to investigate whether either sex or depression type (independent or substance-induced depression) moderated treatment response. Participants were 138 depressed alcohol-dependent adults who were not required to be abstinent at the commencement of the trial. They were randomized to 12 weeks of citalopram or placebo, plus naltrexone and clinical case management. Treatment was well attended, and medications were reasonably well tolerated with high adherence rates. Substantial improvements in both mood and drinking occurred in both groups, with no significant differences between groups on any of the mood or drinking outcome measures, whether or not other variables were controlled for. No interaction effect was found for independent/substance-induced depression status, whereas there was a marginal effect found by sex, with greater improvement in 1 drinking outcome measure (percent days abstinent) in women taking citalopram. These findings suggest that citalopram is not a clinically useful addition to naltrexone and clinical case management in this treatment population. Independent/substance-induced depression status did not predict treatment response. Findings for sex were equivocal.
Percutaneous biportal endoscopic decompression for lumbar spinal stenosis: a technical note and preliminary clinical results (2016)

From a surgical point of view, percutaneous biportal endoscopy is very similar to microscopic spinal surgery, permitting good visualization of the contralateral sublaminar and medial foraminal areas. The authors suggest that the PBED, which is a minimally invasive procedure, is an alternative treatment option for degenerative lumbar stenosis.
Gigabit ethernet: migrating to high-bandwidth LANs (1998)

1. Introduction. Overview of This Book. Ethernet Origins. 2. The First Generation: 10 Mb/s Ethernet. Overview. Media Access Control Frame Format. Functional Overview of the 802.3 Model. Operation of an Ethernet Node. Repeater Definition. Bridge Definition. Router Definition. Media and Topology Options. Management. Technology Advantages of 10BASE-T. User Benefits of 10BASE-T. 3. The Second Generation: 100 Mb/s and Switched Ethernet. Overview. Functional Overview of the 802.3u Standard Suite. Media and Topology Options. Switched Ethernet. Full Duplex and Flow Control. VLAN Tagging. 10/100 Mb/s Capable Devices. 4. The Third Generation: 1000 Mb/s (Gigabit). Overview. Layer 3 Switch Definition. Gigabit Ethernet Technology: Introduction. Gigabit MAC Operation. Full-Duplex Operation. Reconciliation Sublayer (RS) and Gigabit Medium-Independent Interface (GMII) (Clause 35). Physical-Layer Technology. Physical Coding Sublayer (PCS) (Clause 36). Physical Medium Attachment (PMA) Sublayer (Clause 36). Auto-Negotiation for 1000BASE-X (Clause 37). Physical Medium Dependent (PMD) Sublayer (Clauses 38, 39). Repeater Operation (Clause 41). Topology (Clause 42). Management (Clause 30). 5. Gigabit Ethernet Applications. Networking Evolution. Gigabit Ethernet Meets the Challenge. Gigabit Ethernet Migration. Switched or Shared 100 Mb/s Ethernet and FDDI Upgrade. Shared, Switched and Routed Networks. Layer 3 Switching. Gigabit Ethernet vs. Other Technologies. 6. Looking to the Future. Overview. Industry Trends and Technologies. Network Challenges to Support Gigabit Ethernet. Scaling Gigabit Ethernet. Summary. Appendix A. 802.3 Document Cross Reference. Section/Clause Cross Reference. Appendix B. 802.3 Ethernet Frame and Address Formats. Appendix. Glossary. Index.
Biology of multiple drug resistance in acute leukemia. (2000)

Since the early 1970s, multiple drug resistance (MDR) has been known to exist in cancer cells and is thought to be attributable to a membrane-bound, energy-dependent pump protein (P-glycoprotein [P-gp]) capable of extruding various related and unrelated chemotherapeutic drugs. P-gp is coded for by the MDR1 gene, which in the human genome is located on the long arm of chromosome 7 (7q21-31). At the cellular level, the function of P-gp has been extensively investigated in human cancer. Although innumerable reports have been published in which P-gp has been shown to confer MDR to malignant (including leukemia) cells, so far, large-scale studies in the clinical setting have not convincingly proven that MDR1 plays a major role in clinical drug resistance when the influence of other known prognostic factors in human leukemia are taken into account. At present, results from phase 3 clinical trials evaluating the efficiency of inhibiting (or reversing) the function of P-gp in hematologic malignancies are eagerly awaited. Moreover, the horizon of cellular drug resistance in human cancer has during recent years widened dramatically. Thus, an array of different molecules and mechanisms by which resistant cells can escape the cytotoxic effect of anticancer drugs has now been identified. These molecules and mechanisms include apoptosis-related proteins. In this article, we review the different methods for determining MDR and, in particular, methods for determining P-gp/MDR1, with special reference to their potential importance for therapeutic strategies in human acute leukemia.
A supervisor-based semi-centralized network surveillance scheme and the fault detection latency bound (2002)

Network surveillance (NS) schemes facilitate fast learning by each interested fault free node in the system of the faults or repair completion events occurring in other parts of the system. Currently concrete real time NS schemes effective in distributed computer systems based on point to point network architectures are scarce. We present a semi centralized real time NS scheme effective in a variety of point to point networks, called the supervisor based NS (SNS) scheme. This scheme is highly scalable and can be implemented entirely in software using commercial off the shelf (COTS) components without requiring any special purpose hardware support. An efficient execution support for the scheme has been designed as a new extension of the DREAM kernel, a timeliness guaranteed operating system kernel model developed in the authors' laboratory. This design can be viewed as an implementation model which can be easily adapted to various commercial operating system kernels. The paper also presents an analysis of the SNS scheme on the basis of the implementation model to obtain some tight bounds on the fault detection latency.
Syntheses and Antibacterial Activities of New Quinolones Containing cis- or trans-3-Amino-4-methylthiomethylpyrrolidino Moiety (2003)

7번 위치에 하롤겐이 치환된 여로종류의 퀴놀론 모핵과 시스 또는 트란스-3-아미노-4-메틸오메틸피롤리딘을 반응시켜 7-(시스 또는 트란스-3-아미노-4-메틸티오메틸피롤리디닐) 퀴롤론-3-카르복실산의 신규 항균제를 합성하였다. 새롭게 합성된 퀴놀론의 약효는 그람양성균에 대해 대조물질인 시프로플로삭신보다 매우 탁월하였고, 녹농균이외의 그람음성균에 대해서도 대조물질과 거의 유사하였다. 그리고 임상에서 문제가 되고 있는 메티실린 내성 포도상구균(MRSA)에 대한 신규 퀴놀론의 약효는 더욱더 향상되어진 것으로 나타났다. New quinolone derivatives of 7-(cis- or trans-3-amino-4-mehtylthiomethylpyrrolidinyl) quinolone-3-carboxylic acids were synthesized by condensation of 7-halo substituted quinolone-3-carboxylic acids with cis- or trans-3-amino-4-mehtylthiomethylpyrrolidine. Some of these compounds showed broad spectra of antibacterial activities against Gram-positive and Gram-negative organisms except Pseudomonas aeruginosa, and exhibited much stronger activity against MRSA.
[Effect of various nutrient solutions on quality of Gastrodia elata]. (1998)

This paper dealed with the effect of media fertilization on the quality of Gastrodia eleta according to the results of tissue culture. The results showed that contents of nutrient elements, gastrodin and free amino acids in G. elata were affected by various nutrients solutions. The result of comprehensive analysis showed that the 1/2 MS medium was the fittest treatment of fertilization.
Detection of Trypanosoma cruzi in blood specimens of chronic chagasic patients by polymerase chain reaction amplification of kinetoplast minicircle DNA: comparison with serology and xenodiagnosis (1993)

A panel of 114 blood samples from chronic chagasic patients and nonchagasic patients was screened for Trypanosoma cruzi by xenodiagnostic, serologic, and polymerase chain reaction (PCR) amplification tests. Blood samples were preserved in a guanidine-EDTA buffer, and total blood DNA was isolated after chemical nuclease cleavage with 1,10-phenanthroline-copper ion and used as a template for PCR amplification of the conserved and variable regions of T. cruzi minicircle molecules. The PCR products were screened by Southern blot hybridization with a digoxigenin-labeled oligonucleotide probe specific for the conserved region of the minicircle. The method showed a sensitivity of 100% compared with the serologic test. In addition, all of the serology-positive, xenodiagnosis-negative samples were positive by PCR. This demonstrates that PCR amplification of T. cruzi kinetoplast minicircle DNA could replace xenodiagnosis for evaluation of parasitemia in chronic chagasic patients and could serve as a complement for serologic testing in the screening of blood bank donors.
Synergistic inhibition of T cell proliferation by gold sodium thiomalate and auranofin. (1994)

Our results demonstrate that GSTM and AF exert distinct effects on T cell responsiveness and together synergistically inhibit mitogen induced T cell proliferation. These results suggest the possibility that the combination of GSTM and AF may exert a heightened therapeutic effect in RA compared to the action of either agent alone.
Biological significance of chemokine receptor expression by normal human megakaryoblasts. (2001)

The aim of this study was to learn more on the role of chemokines in the regulation of human megakryopoiesis. Normal human megakaryoblasts were expanded in serum-free liquid cultures and subsequently (1) phenotyped for expression of various chemokine receptors, (2) evaluated if chemokine receptors which they express are functional after stimulation by chemokines (calcium flux assay, chemotaxis, phosphorylation of MAPK-p42/44 and AKT proteins), and (3) investigated for expression and secretion of selected chemokines by employing RT-PCR and ELISA assays, respectively. In addition we also phenotyped peripheral blood platelets for expression of chemokine receptors and chemokines. We found that while human megakaryoblasts express several chemokine receptors (CXCR4, CCR6, CCR8, CCR5, CCR2 and CXCR3), CXCR4 was the only receptor detectable by FACS on human platelets. Moreover, among various chemokines tested, only SDF-1 (CXCR4 ligand) stimulated calcium flux and chemotaxis in normal human megakaryoblasts and phosphorylated MAPK-p42/44 and AKT in these cells. Although mRNAs for several chemokines were detectable by RT-PCR in normal human megakaryoblasts, only RANTES, IL-8, MCP-1 and PF-4 were found to be secreted by these cells. Finally we noticed that no chemokine tested in this study affected CFU-Meg colony formation by human CD34+ cells in serum-free cultures. We conclude that from all the chemokine receptor-chemokine axes tested, only SDF-1-CXCR4 axis was functional in assays employed in our studies, which further support the view that this axis plays a privileged role in regulating normal human megakaryopoiesis.
A high speed, postprocessing free, quantum random number generator (2008)

A quantum random number generator (QRNG) based on gated single photon detection of an In–GaAs photodiode at gigahertz frequency is demonstrated. Owing to the extremely long coherence time of each photon, each photons’ wave function extends over many gating cycles of the photodiode. The collapse of the photon wave function on random gating cycles as well as photon random arrival time detection events are used to generate sequences of random bits at a rate of 4.01Mbit∕s. Importantly, the random outputs are intrinsically biasfree and require no postprocessing procedure to pass random number statistical tests, making this QRNG an extremely simple device.
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing (2008)

Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating the transmission of human immunodeficiency virus type 1 (HIV-1) and in developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach to analyze HIV-1 env genes as intact genetic units amplified from plasma virion RNA by single-genome amplification (SGA), followed by direct sequencing of uncloned DNA amplicons. We show that this strategy precludes in vitro artifacts caused by Taq-induced nucleotide substitutions and template switching, provides an accurate representation of the env quasispecies in vivo, and has an overall error rate (including nucleotide misincorporation, insertion, and deletion) of less than 8 x 10(-5). Applying this method to the analysis of virus in plasma from 12 Zambian subjects from whom samples were obtained within 3 months of seroconversion, we show that transmitted or early founder viruses can be identified and that molecular pathways and rates of early env diversification can be defined. Specifically, we show that 8 of the 12 subjects were each infected by a single virus, while 4 others acquired more than one virus; that the rate of virus evolution in one subject during an 80-day period spanning seroconversion was 1.7 x 10(-5) substitutions per site per day; and that evidence of strong immunologic selection can be seen in Env and overlapping Rev sequences based on nonrandom accumulation of nonsynonymous mutations. We also compared the results of the SGA approach with those of more-conventional bulk PCR amplification methods performed on the same patient samples and found that the latter is associated with excessive rates of Taq-induced recombination, nucleotide misincorporation, template resampling, and cloning bias. These findings indicate that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately.
Activation of Leukocytes During the Uteroplacental Passage in Preeclampsia (2002)

Endothelial dysfunction and inflammation appear to play a major role in the pathogenesis of preeclampsia. We hypothesize that a chronic inflammation in the decidua and placenta during preeclampsia may lead to a local leukocyte activation in this compartment. Venous blood was sampled simultaneously from antecubital and uterine veins during cesarean sections in 30 women with preeclampsia, 29 with uncomplicated pregnancies, and from 17 nonpregnant women. The expression of adhesion molecules and complement-related markers on neutrophils and monocytes was analyzed by flow cytometry. In patients with preeclampsia, neutrophil expression of the integrins CD11a, CD11b, and CD11c and of the complement related markers CD35 and CD59 was significantly higher in samples from uterine than from antecubital veins. No differences were found in nonpregnant women. On monocytes the expression of the Sialyl Lewis(x) antigen, the integrins CD11a, CD11c, and CD49d, and the complement-related markers CD46 and CD59 was higher in samples from uterine than from antecubital veins during preeclampsia, but not in uncomplicated pregnancies, whereas in nonpregnant women CD31 was decreased. Our findings suggest activation of neutrophils and monocytes taking place during the uteroplacental passage in preeclamptic, but not in normal pregnancies. Such a local inflammatory response involving enhanced leukocyte/endothelial interaction may contribute to the pathogenesis of this disorder.
Failure Of <i>klebsiella pneumoniae</i> antibodies to cross‐react with peripheral blood mononuclear cells from patients with ankylosing spondylitis (1987)

Cross-reactivity between antibodies to 2 strains of Klebsiella pneumoniae (K43 and F77) and the peripheral blood lymphocytes of patients with ankylosing spondylitis (AS) was examined in 3 separate antibody binding and cytotoxicity assays. Using K pneumoniae antisera in a chromium release cytotoxicity assay, we found no difference in the reactions of cells from AS patients and those from control subjects. This result contrasts with the results of previous studies. Similarly, using an enzyme-linked immunosorbent assay, we detected no significant increase in antibody binding to peripheral blood mononuclear cells (PBMC) in HLA-B27 positive patients with AS. Low levels of antibody binding were detected by a fluoresceinated antibody binding assay; however, normal rabbit serum, which was used as a control, was shown to have a binding affinity for PBMC that was significantly greater than that of specific K pneumoniae antisera. The results of our present study do not support the concept of a specific cross-reactivity between antibodies to K pneumoniae and the PBMC of patients with AS who are HLA-B27 positive.
Notation (2003)

Introduction Notation is the visual means of representing music, which can be either graphic or linguistic, or a combination of the two. Examples of notation are provided by scores using five-line staves, and by guitar tablature. One purpose of notation is to convey instructi