gebhart/patrepeval huggingface dataset:
Bacterial endophytes in agricultural crops (1997)

Endophytic bacteria are ubiquitous in most plant species, residing latently or actively colonizing plant tissues locally as well as systemically. Several definitions have been proposed for endophytic bacteria; in this review endophytes will be defined as those bacteria that can be isolated from surface-disinfested plant tissue or extracted from within the plant, and that do not visibly harm the plant. While this definition does not include nonextractable endophytic bacteria, it is a practical definition based on experimental limitations and is inclusive of bacterial symbionts, as well as internal plant-colonizing nonpathogenic bacteria with no known beneficial or detrimental effects on colonized plants. Historically, endophytic bacteria have been thought to be weakly virulent plant pathogens but have recently been discovered to have several beneficial effects on host plants, such as plant growth promotion and increased resistance against plant pathogens and parasites. In general, endophytic bacteria originate from the epiphytic bacterial communities of the rhizosphere and phylloplane, as well as from endophyte-infested seeds or planting materials. Besides gaining entrance to plants through natural openings or wounds, endophytic bacteria appear to actively penetrate plant tissues using hydrolytic enzymes like cellulase and pectinase. Since these enzymes are also produced by pathogens, more knowledge on their regulation and expression is needed to distinguish endophytic bacteria from plant pathogens. In general, endophytic bacteria occur at lower population densities than pathogens, and at least some of them do not induce a hypersensitive response in the plant, indicating that they are not recognized by the plant as pathogens. Evolutionarily, endophytes appear to be intermediate between saprophytic bacteria and plant pathogens, but it can only be speculated as to whether they are saprophytes evolving toward pathogens, or are more highly evolved than plant pathogens and conserve protective shelter and nutrient supplies by not killing their host. Overall, the endophytic microfloral community is of dynamic structure and is influenced by biotic and abiotic factors, with the plant itself constituting one of the major influencing factors. Since endophytic bacteria rely on the nutritional supply offered by the plant, any parameter affecting the nutritional status of the plant could consequently affect the endophytic community. This review summarizes part of the work being done on endophytic bacteria, including their methodology, colonization, and establishment in the host plant, as well as their role in plant–microbe interactions. In addition, speculative conclusions are raised on some points to stimulate thought and research on endophytic bacteria.Key words: endophytic bacteria, methods, localization, diversity, biological control.
Cyclooxygenase-2 in prostate cancer (2000)

Prostate cancer (pc) is the most commonly diagnosed adenocarcinoma and the second leading cause of cancer death after lung cancer in men in the Western world. In 1998 alone, it was estimated that about 185,000 new cases (30% of all new cancers in men) were diagnosed and more than 39,000 patients died from PC in the United States.1 Approximately 50% of patients present with or develop incurable, metastatic disease.2 Although most patients with advanced PC initially respond to androgen ablation treatment, relapse to an androgen-independent state occurs after a period of approximately two years, followed by death about six months later.3 Therefore, much research is being directed toward understanding the mechanisms involved in development and progression of PC and developing new strategies for prevention and cure. The present article reviews the role of cyclooxygenase-2 (COX-2) in the development and progression of PC.
The Role of Human Papillomavirus in Oral Carcinogenesis (2004)

Human papillomavirus (HPV) infection with high-risk types 16 and 18 has widely been reported as one of the prominent mechanisms behind the development of cervical squamous cell carcinoma. Links between HPV and oral cavity cancer have been suggested as well, based on epidemiologic and molecular means, though the association is less well-established. It is likely that HPV plays a role in oral cavity carcinogenesis, though only in a small subset of cases. The difficulty in providing true causal evidence of HPV's role in oral cancer lies in our lack of understanding of the significance of mechanisms by which HPV leads to oral carcinogenesis, as well as limitations in the molecular analysis of HPV. Further studies are necessary for the contribution of HPV in oral cavity malignancy to be better demonstrated.
Mechanism and swimming experiment of micro mobile robot in water (2002)

This paper deals with a micro-mobile robot in water utilizing PZT(Pb(Zr, Ti)O/sub 3/) as an actuator. A robot driven by PZT requires a magnification mechanism and the effects of the resonance condition to enlarge the displacement of the PZT to some extent. In this paper, we show a prototype micro-mobile robot in water (double-fin-fish robot), which possesses a pair of fins and moves them symmetrically. Therefore, the momentum of this robot is canceled and the tendency to move straight ahead is improved. The size of the robot is 50 mm in length. We propose a structure for the magnification mechanism, which is made by the wire cut method. The magnification ratio is 326 geometrically. This robot has many possible applications, such as small pipeline inspections and biomedical fields.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The use of a one-stage dynamic programming algorithm for connected word recognition (1984)

This paper is of tutorial nature and describes a one-stage dynamic programming algorithm for file problem of connected word recognition. The algorithm to be developed is essentially identical to one presented by Vintsyuk [1] and later by Bridle and Brown [2] ; but the notation and the presentation have been clarified. The derivation used for optimally time synchronizing a test pattern, consisting of a sequence of connected words, is straightforward and simple in comparison with other approaches decomposing the pattern matching problem into several levels. The approach presented relies basically on parameterizing the time warping path by a single index and on exploiting certain path constraints both in the word interior and at the word boundaries. The resulting algorithm turns out to be significantly more efficient than those proposed by Sakoe [3] as well as Myers and Rabiner [4], while providing the same accuracy in estimating the best possible matching string. Its most important feature is that the computational expenditure per word is independent of the number of words in the input string. Thus, it is well suited for recognizing comparatively long word sequences and for real-time operation. Furthermore, there is no need to specify the maximum number of words in the input string. The practical implementation of the algorithm is discussed; it requires no heuristic rules and no overhead. The algorithm can be modified to deal with syntactic constraints in terms of a finite state syntax.
Microelectromechanical systems (MEMS): fabrication, design and applications (2001)

Micromachining and micro-electromechanical system (MEMS) technologies can be used to produce complex structures, devices and systems on the scale of micrometers. Initially micromachining techniques were borrowed directly from the integrated circuit (IC) industry, but now many unique MEMS-specific micromachining processes are being developed. In MEMS, a wide variety of transduction mechanisms can be used to convert real-world signals from one form of energy to another, thereby enabling many different microsensors, microactuators and microsystems. Despite only partial standardization and a maturing MEMS CAD technology foundation, complex and sophisticated MEMS are being produced. The integration of ICs with MEMS can improve performance, but at the price of higher development costs, greater complexity and a longer development time. A growing appreciation for the potential impact of MEMS has prompted many efforts to commercialize a wide variety of novel MEMS products. In addition, MEMS are well suited for the needs of space exploration and thus will play an increasingly large role in future missions to the space station, Mars and beyond.
A Mathematical Programming Approach to the Kernel Fisher Algorithm (2000)

We investigate a new kernel-based classifier: the Kernel Fisher Discriminant (KFD). A mathematical programming formulation based on the observation that KFD maximizes the average margin permits an interesting modification of the original KFD algorithm yielding the sparse KFD. We find that both, KFD and the proposed sparse KFD, can be understood in an unifying probabilistic context. Furthermore, we show connections to Support Vector Machines and Relevance Vector Machines. From this understanding, we are able to outline an interesting kernel--regression technique based upon the KFD algorithm. Simulations support the usefulness of our approach.
The slow component of Vo2in professional cyclists (2000)

A significant but small VO2 slow component was shown in professional cyclists during constant load heavy exercise. The results suggest that the primary origin of the slow component is not neuromuscular factors in these subjects, at least for exercise intensities up to 80% of VO2MAX.
Making greed work in mobile ad hoc networks (2002)

Countermeasures against node misbehavior and selfishness are mandatory requirements in mobile ad hoc networks. Selfishness that causes lack of node activity cannot be solved by classical security means that aim at verifying the correctness and integrity of an operation. In this paper we outline an original security mechanism (CORE) based on reputation that is used to enforce cooperation among the nodes of a MANET. We then investigate on its robustness using an original approach: we use game theory to model the interactions between the nodes of the ad hoc network and we focus on the strategy that a node can adopt during the network operation. As a first result, we obtained the guidelines that should be adopted when designing a cooperative security mechanism that enforces mobile nodes cooperation. Furthermore, we were able to show that when no countermeasures are taken against misbehaving nodes, network operation can be heavily jeopardized. We then showed that the CORE mechanism is compliant with guidelines provided by the game theoretic model and that, under certain conditions, it assures the cooperation of at least half of the nodes of a MANET Keywords. Security, Denial of Service Attacks, Simulation, Game Theory. Table of Contents .
Policies and Polls: Elections and Land Conflicts in Paser, Indonesia (2019)

This paper deals with the impact of direct bupati (district head) elections on local politics with regard to land confl icts in the district of Paser, Indonesia. I discuss the position and infl uence of non-governmental organizations (NGOs) in this process and their usage of adat-based land claims. The paper is concerned with the internal political context of government-NGO power relations as well as with the position and profi ling of these parties in Paserese society at large. The subject is approached through a discussion of two ‘land’ occupations (one in fact being a sea occupation) by groups claiming adat rights, and of the measures taken by the local government and NGOs alike. The new importance of regional politics and local responsibility of those in power in Paser are reviewed against the background of Indonesian political reform. I argue that results are likely to be determined by a specifi c local context and momentum rather than by nationwide developments.
Kinetics of inhibition of human plasma kallikrein by a site-specific modified inhibitor Arg15-aprotinin: evaluation using a microplate system and comparison with other proteases (1987)

Human plasma kallikrein, a product of contact-activated plasma proteolysis, is moderately inhibited by aprotinin, a small polypeptide from bovine lung that has been used as an experimental drug in human disease states. Aprotinin has a Lys residue in the P1 (reactive center) position occupying residue 15. Since kallikrein is an arginine-directed serine protease, we hypothesized that an altered form of aprotinin, Arg15-aprotinin, might be a better inhibitor. Kinetic evaluations were performed in 96-well microplates. We found that the KL (loose or Michaelis-Menten complex) was unchanged by the modification. However, the association rate constant was increased from 1.14 X 10(4) (mol/L)- 1s-1 to 1.5 X 10(5) (mol/L)-1s1, thus indicating that the inhibition rate was increased 14-fold for the modified protein. The Ki (at equilibrium) was decreased from 3.2 X 10(-7) mol/L to 1.5 X 10(-8) mol/L after substituting Arg for Lys in the P1 position. Therefore, the modified inhibitor binds to plasma kallikrein more tightly than the natural protein. We also investigated the effect of Arg15-aprotinin on tissue kallikrein, plasmin, factor XIIa, factor XIa, and thrombin and found that the Ki slightly decreased from 5.1 X 10(-7) mol/L to 1.2 X 10(-7) mol/L for tissue kallikrein and slightly decreased from 2 X 10(- 8) mol/L to 1 X 10(-8) mol/L for plasmin. Arg15-aprotinin did not inhibit thrombin or factor XIIa, even though both enzymes are arginine- directed serine proteases. However, factor XIa, although it was not inhibited by aprotinin, had a Ki of 3.4 X 10(-8) mol/L for Arg15- aprotinin. Therefore, Arg15-aprotinin is a more effective inhibitor of plasma kallikrein as well as factor XIa but shows minimal preference for plasmin and tissue kallikrein. This study also indicates that it is possible and practical to perform kinetic analyses directly in microplates.
Efficient gene transfer into primary murine lymphocytes obviating the need for drug selection (1993)

The efficient introduction of exogenous genes into primary lymphocytes is potentially important both for somatic cell gene therapy and for studying lymphocyte biology. We describe the use of retroviral vectors to efficiently introduce exogenous genes into primary, mature murine lymph node T and B cells, and primary, immature murine CD4- CD8- double- negative (DN) thymocytes. Efficient infection of primary cells was achieved by cocultivation of target cells with lethally irradiated helper cells that produce high titers of retroviral vectors containing either the neomycin phosphotransferase II (neo) gene, or both the neo and the human adenosine deaminase (ADA) genes, in the presence of lymphokines and/or mitogens. Two days postinfection, without neomycin selection, one to five copies of the exogenous genes per cell were detected by Southern blot analysis. Expression of the exogenous human ADA protein was detected at levels comparable to the endogenous murine ADA protein in the mature T and B lymphocytes, and was somewhat lower for the immature DN thymocytes.
Chronic Reversible Cerebral Ischemia (1980)

The authors describe their experience with a baboon model of reversible cerebral ischemia. Middle cerebral artery occlusion was achieved by external compression with an implantable, inflatable balloon cuff in awake, unanesthetized baboons. Selective cerebral angiography confirmed consistent, reliable occlusion. Computed tomography demonstrated early density changes after ischemia, which were reversible with reperfusion. Neurological evaluation demonstrated a "recruitment response" of increasingly persistent deficit with repeated occlusion. Permanent deficits were noted after extensive angiography during periods of occlusion. This was accompanied by the dropout of small vessels in the middle cerebral artery distribution. The results of pathological examinations were consistent with the clinical examinations. No gross or microscopic changes were noted after repeated occlusions that caused deficits like those of transient ischemic attacks. Consistent infarctions were noted in animals with permanent deficits after permanent occlusion or after repeated occlusion and extensive angiography.
Experience-dependent regulation of adult hippocampal neurogenesis: Effects of long-term stimulation and stimulus withdrawal (1999)

Exposure to an enriched environment has been shown to cause an increase in neurogenesis in the dentate gyrus of adult mice. In this study we examined how this experience-dependent response in adult hippocampal neurogenesis of C57BL/6 mice is modulated under the conditions of long-term stimulation and of withdrawal from the enriched environment. We found that a group which experienced withdrawal from the enriched environment 3 months earlier, had more than twice as many proliferating cells in the subgranular zone as controls and mice experiencing long-term stimulation. We propose that the greater number of proliferating cells after withdrawal reflects a survival-promoting effect on the dividing neuronal stem and progenitor cells during the earlier period of stimulation. No differences between the groups were observed in the number of surviving progeny or their phenotypes. Therefore, the existence of more dividing cells in the withdrawal group did not translate into a significant net increase in neurogenesis in the absence of continued stimulation. Similarly, the finding in the group experiencing long-term stimulation showing no clear benefit over controls could be interpreted as a diminished efficiency of continued environmental stimuli to elicit a neurogenic response. Thus, we propose as a working hypothesis that: 1) stimulation early in life may preserve the neurogenic potential in the dentate gyrus, and 2) the novelty of complex stimuli rather than simply continued exposure to complex stimuli elicits the environmental effects on adult hippocampal neurogenesis.
c-Myc inhibition prevents leukemia initiation in mice and impairs the growth of relapsed and induction failure pediatric T-ALL cells (2014)

Although prognosis has improved for children with T-cell acute lymphoblastic leukemia (T-ALL), 20% to 30% of patients undergo induction failure (IF) or relapse. Leukemia-initiating cells (LICs) are hypothesized to be resistant to chemotherapy and to mediate relapse. We and others have shown that Notch1 directly regulates c-Myc, a known regulator of quiescence in stem and progenitor populations, leading us to examine whether c-Myc inhibition results in efficient targeting of T-ALL-initiating cells. We demonstrate that c-Myc suppression by small hairpin RNA or pharmacologic approaches prevents leukemia initiation in mice by eliminating LIC activity. Consistent with its anti-LIC activity in mice, treatment with the BET bromodomain BRD4 inhibitor JQ1 reduces C-MYC expression and inhibits the growth of relapsed and IF pediatric T-ALL samples in vitro. These findings demonstrate a critical role for c-Myc in LIC maintenance and provide evidence that MYC inhibition may be an effective therapy for relapsed/IF T-ALL patients.
The negative costimulatory molecule PD‐1 modulates the balance between immunity and tolerance via miR‐21 (2011)

Disruption of the programmed death-1 (PD-1) pathway leads to breakdown of peripheral tolerance and initiation of autoimmunity. The molecular pathways that mediate this effect remain largely unknown. We report here that PD-1 knockout (PD-1(-/-) ) mice develop more severe and sustained Ag-induced arthritis (AIA) than WT animals, which is associated with increased T-cell proliferation and elevated levels of IFN-γ and IL-17 secretion. MicroRNA analysis of Ag-specific CD4(+) T cells revealed a significant upregulation of microRNA 21 (miR-21) in PD-1(-/-) T cells compared with WT controls. In addition, PD-1 inhibition, via siRNA, upregulated miR-21 expression and enhanced STAT5 binding in the miR-21 promoter area. Computational analysis confirmed that miR-21 targets directly the expression of programmed cell death 4 (PDCD4) and overexpression of miR-21 in cells harboring the 3'UTR of PDCD4 resulted in reduced transcription and PDCD4 protein expression. Importantly, in vitro delivery of antisense-miR-21 suppressed the Ag-specific proliferation and cytokine secretion by PD-1(-/-) T cells, whereas adoptive transfer of Ag-specific T cells, overexpressing miR-21, induced severe AIA. Collectively, our data demonstrate that breakdown of tolerance in PD-1(-/-) mice activates a signaling cascade mediated by STAT5, miR-21, and PDCD4 and establish their role in maintaining the balance between immune activation and tolerance.
Proton pump inhibitors and traditional nonsteroidal anti‐inflammatory drugs and the risk of acute interstitial nephritis and acute kidney injury (2012)

Proton pump inhibitor exposure may increase the odds of AIN, but this result was not definitive and should be confirmed in a dataset with more AIN cases to allow for increased statistical precision. tNSAIDs, yet not PPIs, were associated with a significantly increased odds of AKI.
Mucosal immunization with Salmonella typhimurium expressing Lassa virus nucleocapsid protein cross-protects mice from lethal challenge with lymphocytic choriomeningitis virus. (2001)

The LAS recombinant Salmonella vector is comparable to the LAS recombinant vaccinia vector in its ability to cross-protect mice from lethal challenge. Nucleocapsid protein is an inadequate immunogen on its own, but provides sufficient cross-protection to make it a useful component of a broadly reactive arenavirus vaccine.
Crucial Role for Nuclear Factor of Activated T Cells in T Cell Receptor-mediated Regulation of Human Interleukin-17 (2004)

The biological activities of the inflammatory cytokine interleukin (IL)-17 have been widely studied. However, comparatively little is known about how IL-17 expression is controlled. Here, we examined the basis for transcriptional regulation of the human IL-17 gene. IL-17 secretion was induced in peripheral blood mononuclear cells following anti-CD3 cross-linking to activate the T cell receptor (TCR), and costimulatory signaling through CD28 strongly enhanced CD3-induced IL-17 production. To define cis-acting elements important for IL-17 gene regulation, we cloned 1.25 kb of genomic sequence upstream of the transcriptional start site. This putative promoter was active in Jurkat T cells following CD3 and CD28 cross-linking, and its activity was inhibited by cyclosporin A and MAPK inhibitors. The promoter was also active in Hut102 T cells, which we have shown to secrete IL-17 constitutively. Overexpression of nuclear factor of activated T cells (NFAT) or Ras enhanced IL-17 promoter activity, and studies in Jurkat lines deficient in specific TCR signaling pathways provided supporting evidence for a role for NFAT. To delineate the IL-17 minimal promoter, we created a series of 5' truncations and identified a region between -232 and -159 that was sufficient for inducible promoter activity. Interestingly, two NFAT sites were located within this region, which bound to NFATc1 and NFATc2 in nuclear extracts from Hut102 and Jurkat cells. Moreover, mutations of these sites dramatically reduced both specific DNA binding and reporter gene activity, and chromatin immunoprecipitation assays showed occupancy of NFAT at this region in vivo. Together, these data show that NFAT is the crucial sensor of TCR signaling in the IL-17 promoter.