gebhart/patrepeval huggingface dataset:
First Report of Dodder Transmission of Huanglongbing from Naturally Infected Murraya paniculata to Citrus (2007)

Huanglongbing (HLB) or "greening" disease of citrus is caused by phloem-limited, uncultured bacteria in the genus "Candidatus Liberibacter". HLB is one of the most destructive diseases of citrus worldwide and is considered so dangerous to a U.S. citrus production that the USDA has listed "Ca. Liberibacter species" as a Select Agent. HLB is spread by the Asian citrus psyllid, Diaphorina citri, which was intercepted 40 times by APHIS/PPQ at U.S. ports between 1985 and 1998, became established in Florida by 1998, and more recently in Texas (1). HLB was first detected in the United States near Miami, FL during August 2005, and to date has been confirmed to have spread to 12 Florida counties. In addition to citrus, Murraya paniculata (orange jasmine) is a preferred host of D. citri, and retail trade in this ornamental shrub is strongly implicated in the distribution of D. citri (1). M. paniculata is reported to be a cryptic or largely asymptomatic host of "Ca. Liberibacter" (4), but another report concludes that the bacteria cannot replicate in M. paniculata (2). The epidemiological significance of murraya as a host for the HLB pathogen is therefore unclear. We report here the transmission of "Ca. Liberibacter asiaticus" from M. paniculata to citrus. Two M. paniculata plants, suspected of harboring "Ca. Liberibacter" because of their proximity to HLB-infected citrus and infested with D. citri, were removed from the field, treated with insecticide, and transferred to a quarantine facility. Both plants tested positive for "Ca. Liberibacter" by nested PCR using primers OI1 and OI2 (3) as the first set and primers CGO3F (RGG GAA AGA TTT TAT TGG AG) and CGO5R (GAA AAT AYC ATC TCT GAT ATC GT) as the second set. Two, young, sweet orange plants (Citrus sinensis) grown and maintained in psyllid-free greenhouses in Gainesville, FL were infected by dodder (Cuscuta pentagona) grown from seed. After the dodder had become well established on the orange plants, the orange plants were moved adjacent to the two murraya plants and the dodder from the citrus was draped over the murraya. Coinfection of murraya by dodder occurred within a few days. Sixty days later, both murraya plants, both sweet orange plants, and the connecting dodder all repeatedly tested positive for "Ca. Liberibacter" by nested PCR. Beginning 2 weeks later, the orange plants tested positive by standard PCR using primer set OI1 and OI2 or CGO3F and CGO5R, but remained without typical greening symptoms. Sequencing of the PCR products confirmed amplification of "Ca. L. asiaticus" DNA. We conclude that M. paniculata can serve as an infection source of a Select Agent since it can host the HLB pathogen for at least 2 months and the HLB pathogen can be transmitted to sweet orange during this time. References: (1) S. E. Halbert and K. L. Manjunath. Florida Entomol. 87:330, 2004. (2) T. H. Hung et al. J. Phytopathol. 148:321, 2000. (3) S. Jagoueix et al. Mol. Cell Probes 10:43, 1996. (4) T. Li and C. Ke. Acta Phytophylacica Sin. 29:31, 2002.
Temperature-jump Studies on Benzeneboronic Acid-Serine Protease Interactions (1975)

The interactions of benzeneboronic acid (BBA) as a transition state analog with subtilisin (EC 3.4.21.4) and with alpha-chymotrypsin (EC 3.4.21.1) were investigated kinetically by the temperature-jump method using pH indicators. For both enzymes, the concentration dependence of the relaxation time was consistent with a two-step mechanism involving a fast bimolecular association followed by a slow, unimolecular process. The possibility of a trigonal-tetrahedral interconversion of BBA at the active site of the enzyme is discussed.
TNFa and IL-1B are separate targets in chronic arthritis (1999)

Chronic arthritis is characterized by persistent joint inflammation and concomitant joint destruction. Using murine arthritis models and neutralizing antibodies as well as cytokine-specific knockout conditions, it was found that tumor necrosis factor α (TNFα) is important in joint swelling, whereas a direct role in tissue destruction is unlikely. Interleukin-1 (IL-1) is not a dominant cytokine in early joint swelling, but has a pivotal role in sustained cell infiltration and erosive cartilage damage. TNFa-independent IL-1 production is a prominent feature in murine arthritis models, implying that IL-1 as well as TNFα are appropriate targets for therapy. These observations provide evidence for the potential uncoupling of joint inflammation and erosive changes and underline the need for TNFα /IL-1 directed combination-therapy approaches.
High Frequency of TP53 Mutation in BRCA1 and Sporadic Basal-like Carcinomas but not in BRCA1 Luminal Breast Tumors (2009)

Breast tumors with a germ-line mutation of BRCA1 (BRCA1 tumors) and basal-like carcinoma (BLC) are associated with a high rate of TP53 mutation. Because BRCA1 tumors frequently display a basal-like phenotype, this study was designed to determine whether TP53 mutations are correlated with the hereditary BRCA1 mutated status or the particular phenotype of these tumors. The TP53 gene status was first investigated in a series of 35 BRCA1 BLCs using immunohistochemistry, direct sequencing of the coding sequence, and functional analysis of separated alleles in yeast, and compared with the TP53 status in a series of 38 sporadic (nonhereditary) BLCs. Using this sensitive approach, TP53 was found to be frequently mutated in both BRCA1 (34 of 35, 97%) and sporadic (35 of 38, 92%) BLCs. However, the spectrum of mutation was different, particularly with a higher rate of complex mutations, such as insertion/deletion, in BRCA1 BLCs than in the sporadic group [14 of 33 (42%) and 3 of 34 (9%), [corrected] respectively; P = 0.002]. Secondly, the incidence of TP53 mutations was analyzed in 19 BRCA1 luminal tumors using the same strategy. Interestingly, only 10 of these 19 tumors were mutated (53%), a frequency similar to that found in grade-matched sporadic luminal tumors. In conclusion, TP53 mutation is highly recurrent in BLCs independently of BRCA1 status, but not a common feature of BRCA1 luminal tumors.
Vanadate-resistant yeast mutants are defective in protein glycosylation. (1991)

Spontaneous recessive orthovanadate-resistant mutants of Saccharomyces cerevisiae were obtained in five complementation groups, and all show defects in protein glycosylation that mimic the previously isolated mnn mutants. Three of the groups are allelic to the known mnn8, mnn9, and mnn10 mutants, whereas the other two groups show other glycosylation defects. The vanadate-resistant phenotype was associated with enhanced hygromycin B sensitivity. The glycosylation phenotypes of the mutants are all reflections of defects in glycoprotein trafficking, and the easy isolation of vanadate-resistant or hygromycin B-sensitive mutants should facilitate the study of this process.
Radioimmunodetection of lymph node invasion in prostatic cancer. The use of iodine 123 (123I)-labeled monoclonal anti-prostatic acid phosphatase (PAP) 227 A F(ab′l)2 antibody fragments in vivo (1989)

The therapeutic indications in prostatic cancer depend on the regional and distant extension of the cancer and are difficult to assess before lymphadenectomy. Radioimmunodetection of lymph node involvement with monoclonal anti-prostatic acid phosphatase (PAP) antibodies can be proposed as a noninvasive alternative to lymphadenectomy. Fifteen patients with various stages of histologically proven prostatic cancer were examined by immunolymphoscintigraphy (ILS) before treatment to detect lymph node metastases. These patients had Stage A (n = 7), Stage B (n = 3), Stage C (n = 2), and Stage D (n = 3) tumors. They received between 100 and 400 micrograms of monoclonal antibody 227 A in the form of F(ab')2 fragments labeled with iodine 123 (123I). The antibody was injected directly into the periprostatic area. ILS images were obtained after 1, 3, 6, and 24 hours. Three days later, each patient underwent a lymphadenectomy for histologic examination. The results of the histologic examination and ILS were compared. In ten patients, the examination did not show any images capable of being interpreted as lymphadenopathy and histologic examination confirmed the integrity of the nodes examined. In five cases, scintigraphy suggested the presence of lymph node invasion by prostatic cancer and this was confirmed by histologic examination in three of the five cases. Overall, in terms of lymphadenopathy, this examination had a sensitivity of 100% and a specificity of 83%. Therefore, ILS appears to be capable of detecting lymph node metastases in prostatic cancer.
Cyclooxygenase-2 Expression in Macrophages: Modulation by Protein Kinase C-α (2000)

Cyclooxygenase-2 (COX-2) is an inducible enzyme responsible for high levels of PG production during inflammation and immune responses. Previous studies with pharmacological inhibitors suggested a role for protein kinase C (PKC) in PG production possibly by regulating COX-2 expression. In this study, we addressed the role of PKC-alpha in the modulation of COX-2 expression and PGE2 synthesis by the overexpressing of a dominant-negative (DN) mutant of this isoenzyme in the mouse macrophage cell line RAW 264.7. We investigated the effect of various stimuli on COX-2 expression, namely, LPS, IFN-gamma, and the intracellular parasite Leishmania donovani. Whereas LPS-induced COX-2 mRNA and protein expression were down-regulated in DN PKC-alpha-overexpressing clones, IFN-gamma-induced COX-2 expression was up-regulated in DN PKC-alpha-overexpressing clones with respect to normal RAW 264.7 cells. Measurements of PGE2 levels revealed a strong correlation between PGE2 secretion and IFN-gamma-induced COX-2 mRNA and protein levels in DN PKC-alpha-overexpressing clones. Taken together, these results suggest a role for PKC-alpha in the modulation of LPS- and IFN-gamma-induced COX-2 expression, as well as in IFN-gamma-induced PGE2 secretion.
Clinical use of anti-TNF-alpha biological agents--a guide for GPs. (2007)

TNF-alpha inhibitors may have a potent effect in reducing inflammation and possibly inducing remission where conventional disease modifying drugs have failed to do so. These drugs are associated with an increased risk of infection as well as other potentially serious side effects. Their use is restricted to the relevant specialist prescribing the drug and are only available on the Pharmaceutical Benefits Scheme under strict prescribing criteria. The role of the GP is critical in identifying patients suitable for referral to consider commencing treatment and in monitoring patients on long term therapy.
Synthesis and bioactivation of bis(aroyloxymethyl) and mono(aroyloxymethyl) esters of benzylphosphonate and phosphonoacetate (1993)

The bis(aroyloxymethyl) esters of benzylphosphonate 8(XPh, ArPh, 2-MeC6H4 or 2,4,6-Me3C6H2) and methoxycarbonylmethylphosphonate 8(XMeO2C, ArPh, 2-MeC6H4 or 2,4,6-Me3C6H2) have been prepared by reaction of 2 equiv. of the appropriate aroyloxymethyl iodide with the disilver salt of either benzylphosphonate or methoxycarbonylmethylphosphonate. The cyclohexylammonium salts of the mono(aroyloxymethyl) esters of benzylphosphonate 12(XPh, ArPh, 2-MeC6H4 or 2,4,6-Me3C6H2, M+C6H11NH3+) were prepared by reaction of silver benzyl benzylphosphonate with the appropriate aroyloxymethyl iodide, with subsequent hydrogenolysis to remove the P-O-benzyl group. The bis(aroyloxymethyl) esters 8(XPh or MeO2C, ArPh, 2-MeC6H4 or 2,4,6-Me3C6H2) and the mono(aroyloxymethyl) salts 12(XPh, ArPh, 2MeC6H4 or 2,4,6-Me3C6H2, M+C6H11NH3+) were stable towards chemical hydrolysis at 37 °C at physiological pH. In the presence of porcine liver carboxyesterase, the bis(aroyloxymethyl) esters of benzylphosphonate 8(XPh, ArPh or 2-MeC6H4) degraded to the mono(aroyloxymethyl) esters 12(XPh, ArPh or 2-MeC6H4,), which showed slow hydrolysis to benzylphosphonate. For the bis(aroyloxymethyl) esters of methoxycarbonylmethylphosphonate 8(XMeO2C, ArPh or 2MeC6H4) there was competition between the esterase-catalysed hydrolyses of the aroyloxymethyl and methoxycarbonyl groups. For the triester 8(XMeO2C, Ar2,4,6-Me3C6H2) cleavage of the methoxycarbonyl group was observed and hydrolysis of the sterically hindered 2,4,6-trimethylbenzoyl group (Ar2,4,6-Me3C6H2) was not detected for any compound.
Transfer of dendritic cells (DC)ex vivostimulated with interferon-gamma (IFN-γ) down-modulates autoimmune diabetes in non-obese diabetic (NOD) mice (1999)

The NOD mouse has been used to explore the many features of insulin-dependent diabetes mellitus (IDDM) that is caused by the destruction of insulin-producing beta cells in the islets of Langerhans of the pancreas. Self-reactive T cells have been considered to mediate IDDM in the NOD mouse, and antigen-presenting cells like DC and macrophages are expected to be involved in the processes from their role in generating regulatory or effector T cells. The present study shows that transfer of IFN-gamma-stimulated DC of the NOD or ICR mouse into the NOD mouse did not accelerate IDDM onset but afforded long-lasting protection against clinical and histological signs of IDDM in the recipient mice. The anti-diabetogenic ability was unique to IFN-gamma-stimulated DC when compared with unstimulated DC. A considerable proportion of the injected IFN-gamma-stimulated DC was demonstrated to migrate into the pancreas and its associated lymphoid tissues, suggesting the DC exert their anti-diabetogenic effects there. These findings suggest that development of autoimmune diabetes in the NOD mouse is under the control of DC, and that IDDM onset could be controlled by appropriately manipulating DC systems in vivo, which may open the gate for the therapeutic application of ex vivo-conditioned DC to human IDDM.
Cancer cells. 3: Growth factors and transformation (1985)

Working memory (WM) is a distributed cognitive process that employs communication between prefrontal cortex and posterior brain regions in the form of cross-frequency coupling between theta ( θ) and high-alpha ( α2) brain waves. A novel method for deriving causal interactions between brain waves of different frequencies is essential for a better understanding of the neural dynamics of such complex cognitive process. Here, we proposed a novel method to estimate transfer entropy ( TE) through a symbolization scheme, which is based on neural-gas algorithm (NG) and encodes a bivariate time series in the form of two symbolic sequences. Given the symbolic sequences, the delay symbolic transfer entropy ( dSTE<sup>NG</sup>) is defined. Our approach is akin to standard symbolic transfer entropy ( STE) that incorporates the ordinal pattern (OP) symbolization technique. We assessed the proposed method in a WM-invoked paradigm that included a mental arithmetic task at various levels of difficulty. Effective interactions between Frontal<sup>θ</sup> ( F<sup>θ</sup> ) and [Formula: see text] ( PO<sup>α2</sup>) brain waves were detected in multichannel EEG recordings from 16 subjects. Compared with conventional methods, our technique was less sensitive to noise and demonstrated improved computational efficiency in quantifying the dominating direction of effective connectivity between brain waves of different spectral content. Moreover, we discovered an efferent F<sup>θ</sup> connectivity pattern and an afferent PO<sup>α2</sup> one, in all the levels of the task. Further statistical analysis revealed an increasing dSTE<sup>NG</sup> strength following the task's difficulty.
Screening of Maternal Serum for Fetal Down's Syndrome in the First Trimester (1998)

Screening for Down's syndrome in the first trimester is feasible, with use of measurements of pregnancy-associated protein A and either hCG or its free beta subunit in maternal serum.
Resource Allocation for Real-Time Tasks Using Cloud Computing (2011)

This paper presents a method to allocate resources for real-time tasks using the "Infrastructure as a Service" model offered by cloud computing. Real-time tasks have to be completed before deadlines, and cloud computing offers selection of resources with different speeds and costs. In cloud computing, resource allocations can be scaled up based on the requirements; this is called elasticity and is the key difference from existing multiprocessor task allocation. Scalable resources make economical allocation of resources an important problem. We analyze the problem of allocating resources for a set of realtime tasks such that the economic cost is minimized and all the deadlines are met. We formulate the problem as a constrained optimization problem and propose a polynomial-time solution to allocate resources efficiently. We compare the economic costs and performance provided by our solution with the optimal solution and an EDF (earliest deadline first) method. We show how the cost varies based on the distribution of the tasks.
Mixed osmolytes: The degree to which one osmolyte affects the protein stabilizing ability of another (2006)

Mixtures of organic osmolytes occur in cells of many organisms, raising the question of whether their actions on protein stability are independent or synergistic. To investigate this question it is desirable to develop a system that permits evaluation of the effect of one osmolyte on the efficacy of another to either force-fold or denature a protein. A means of evaluating the efficacy of an osmolyte is provided by its m-value, an experimental quantity that measures the ability of the osmolyte to force a protein to unfold or fold. An experimental system is presented that enables evaluations of the m-values of osmolytes in the presence and absence of a second osmolyte. The experimental system involves use of a marginally stable protein in 10 mM buffer (pH 7, 200 mM salt, and 34 degrees C) that is at the midpoint of its native to denatured transition. These conditions enable determination of m-values for protecting and denaturing osmolytes in the presence and absence of a second osmolyte, permitting assessment of the extent to which the two osmolytes affect each other's efficacy. The two osmolytes investigated in this work are the denaturing osmolyte, urea, and the protecting osmolyte, sarcosine. Results show unequivocally that neither osmolyte alters the efficacy of the other in forcing the protein to fold or unfold-the osmolytes act independently on the protein despite their combined concentrations being in the multi-molar range. These osmolytes avoid altering one another's efficacy at these high concentrations because the number of osmolyte interaction sites on the protein is large and the binding constants are quite small. Consequently, the site occupancies are low enough in number that the two osmolytes neither compete nor cooperate in interacting with the protein.
Adoptive T‐cell therapy as a therapeutic option for chronic hepatitis B (2007)

The human hepatitis B virus is a small, enveloped and non-cytopathic virus, with a very narrow host range and a strong liver tropism causing acute and chronic liver disease. Although a well-tolerated vaccine is available, more than 350 million people are chronically infected worldwide. Available therapies for chronic hepatitis B only rarely eliminate the virus. Although new antivirals are being developed, long-term treatment is required, which may be limited by the selection of resistant viruses. Therefore, immunotherapies are investigated as an approach to eliminate persistently infected cells. Besides therapeutic vaccination, adoptive T-cell therapy is an interesting option, which is discussed in this review.
Coenzyme Q10 Can in Some Circumstances Block Apoptosis, and This Effect Is Mediated through Mitochondria (1999)

The mitochondrial component coenzyme Q10 (CoQ10) has been used for many years as a dietary supplement intended to promote good health by trapping free radicals, thus preventing lipid peroxidation and DNA damage. We have tested its use as a generic anti-apoptotic compound and have found that its ability to protect against apoptosis varies depending on both cell type and mode of cell death induction. We have further established that this protection may be mediated by its effect on mitochondrial function and viability. We provide additional evidence that CoQ10's protective effect on mitochondrial membrane potential does not always result in altered mitochondrial enzyme activity and neither does it guarantee survival. These observations open the way for further investigations into the mechanisms involved in mitochondrial control of apoptosis.
For the Grid and Through the Grid: The Role of Power Line Communications in the Smart Grid (2011)

Are Power Line Communications (PLC) a good candidate for Smart Grid applications? The objective of this paper is to address this important question. To do so, we provide an overview of what PLC can deliver today by surveying its history and describing the most recent technological advances in the area. We then address Smart Grid applications as instances of sensor networking and network control problems and discuss the main conclusions one can draw from the literature on these subjects. The application scenario of PLC within the Smart Grid is then analyzed in detail. Because a necessary ingredient of network planning is modeling, we also discuss two aspects of engineering modeling that relate to our question. The first aspect is modeling the PLC channel through fading models. The second aspect we review is the Smart Grid control and traffic modeling problem which allows us to achieve a better understanding of the communications requirements. Finally, this paper reports recent studies on the electrical and topological properties of a sample power distribution network. Power grid topological studies are very important for PLC networking as the power grid is not only the information source but also the information delivery system-a unique feature when PLC is used for the Smart Grid.
Iron-catalysed green synthesis of carboxylic esters by the intermolecular addition of carboxylic acids to alkenes (2007)

Iron triflate, in situ-formed from FeCl3 and triflic acid, or FeCl3 and silver triflate efficiently catalyse the intermolecular addition of carboxylic acids to various alkenes to yield carboxylic esters; the reaction is applicable to the synthesis of unstable esters, such as acrylates.