gebhart/patrepeval huggingface dataset:
A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity (2010)

At least two components that modulate plant resistance against the fungal powdery mildew disease are ancient and have been conserved since the time of the monocot-dicot split (≈ 200 Mya). These components are the seven transmembrane domain containing MLO/MLO2 protein and the syntaxin ROR2/PEN1, which act antagonistically and have been identified in the monocot barley (Hordeum vulgare) and the dicot Arabidopsis thaliana, respectively. Additionally, syntaxin-interacting N-ethylmaleimide sensitive factor adaptor protein receptor proteins (VAMP721/722 and SNAP33/34) as well as a myrosinase (PEN2) and an ABC transporter (PEN3) contribute to antifungal resistance in both barley and/or Arabidopsis. Here, we show that these genetically defined defense components share a similar set of coexpressed genes in the two plant species, comprising a statistically significant overrepresentation of gene products involved in regulation of transcription, posttranslational modification, and signaling. Most of the coexpressed Arabidopsis genes possess a common cis-regulatory element that may dictate their coordinated expression. We exploited gene coexpression to uncover numerous components in Arabidopsis involved in antifungal defense. Together, our data provide evidence for an evolutionarily conserved regulon composed of core components and clade/species-specific innovations that functions as a module in plant innate immunity.
Augmentation of GG2EE macrophage cell line-mediated anti-Candida activity by gamma interferon, tumor necrosis factor, and interleukin-1 (1990)

The expression of anti-Candida activity in the GG2EE macrophage cell line, generated by immortalization of fresh bone marrow with v-raf and v-myc oncogenes, was studied. GG2EE cells spontaneously inhibited the growth of an agerminative mutant of Candida albicans in vitro. The anti-Candida activity was maximal after 8 h of coculture and was proportional to the effector-to-target ratio. Gamma interferon (IFN-gamma), interleukin-1 (IL-1), and tumor necrosis factor (TNF) all significantly enhanced the anti-Candida activity of GG2EE cells. In contrast, IL-3, IL-4, and colony-stimulating factor 1 were ineffective. The augmentation of anti-Candida activity was not always concomitant with enhancement of phagocytosis, since IFN-gamma and colony-stimulating factor 1, but not IL-1 or TNF, augmented the phagocytic ability of GG2EE cells. Furthermore, the augmentation of anti-Candida activity in GG2EE cells did not correlate with the acquisition of antitumor activity. In fact, none of the cytokines alone were able to induce antitumor activity in GG2EE cells, which, however, could be activated to a tumoricidal stage by IFN-gamma plus heat-killed Listeria monocytogenes. These findings demonstrate that GG2EE cells exhibit spontaneous anti-Candida activity and that such activity is enhanced by TNF, IL-1, and IFN-gamma.
Glucocorticoid-Induced Osteoporosis (1983)

The most surprising thing about the study by Adinoff and Hollister in this issue of the Journal is that such a study needed to be performed at all.1 It has been known for several years that supraphysiologic doses of glucocorticoids can cause osteoporosis. As long ago as 1932, Harvey Cushing noted that an excess of endogenous glucocorticoid was accompanied by osteoporosis.2 Why then was it necessary for Adinoff and Hollister to determine whether osteoporosis develops in glucocorticoid-treated asthmatics? Eight years ago, Mueller measured bone mass at the distal radius and reported that glucocorticoid therapy resulted in loss of bone in . . .
On Scalability for MPI Runtime Systems (2011)

The future of high performance computing, as being currently foretold, will gravitate toward hundreds of thousands to million node machines, harnessing the computing power of billions of cores. While the hardware part is well covered, the software infrastructure at that scale is vague. However, no matter what the infrastructure will be, efficiently running parallel applications on such large machines will require optimized runtime environments that are scalable and resilient. More particularly, considering a future where Message Passing Interface (MPI) remains a major programming paradigm, the MPI implementations will have to seamlessly adapt to launching and managing large scale applications on resources several levels of magnitude larger than today. In this paper, we present a modified version of the Open MPI runtime that has been adapted towards a scalability goal. We evaluate the performance and compare it with two widely used runtime systems: the default version of Open MPI and MPICH2; using various underlying launching systems. The performance evaluation demonstrates a significant improvement over the state of the art. We also discuss the basic requirements for an exascale-ready parallel runtime.
Prevalence of and Risk Factors for Dry Eye Syndrome (2000)

The results suggest several factors, such as smoking, caffeine use, and multivitamin use, could be studied for preventive or therapeutic efficacy. Arch Ophthalmol. 2000;118:1264-1268
Optimized Adeno-Associated Viral-Mediated Human Factor VIII Gene Therapy in Cynomolgus Macaques (2018)

Hemophilia A is a common hereditary bleeding disorder that is characterized by a deficiency of human blood coagulation factor VIII (hFVIII). Previous studies with adeno-associated viral (AAV) vectors identified two liver-specific promoter and enhancer combinations (E03.TTR and E12.A1AT) that drove high level expression of a codon-optimized, B-domain-deleted hFVIII transgene in a mouse model of the disease. This study further evaluated these enhancer/promoter combinations in cynomolgus macaques using two different AAV capsids (AAVrh10 and AAVhu37). Each of the four vector combinations was administered intravenously at a dose of 1.2 × 10<sup>13</sup> genome copy/kg into five macaques per group. Delivery of the hFVIII transgene via the AAVhu37 capsid resulted in a substantial increase in hFVIII expression compared to animals administered with AAVrh10 vectors. Two weeks after administration of E03.TTR packaged within the AAVhu37 capsid, average hFVIII expression was 20.2 ± 5.0% of normal, with one animal exhibiting peak expression of 37.1% of normal hFVIII levels. The majority of animals generated an anti-hFVIII antibody response by week 8-10 post vector delivery. However, two of the five macaques administered with AAVhu37.E03.TTR were free of a detectable antibody response for 30 weeks post vector administration. Overall, the study supports the continued development of AAV-based gene therapeutics for hemophilia A using the AAVhu37 capsid.
Liver-associated toxicity of the HSV-tk/GCV approach and adenoviral vectors. (1997)

Intravenous injection of immunodeficient mice with adenoviral vectors carrying the HSV-tk gene led to preferential transduction of liver tissue. Subsequent application of ganciclovir (GCV) resulted in extremely high toxicity with negligible survival rates. This toxicity was only seen when GCV was applied in addition to the adenoviral vector and not if combined with the Ad-beta gal control vector. This indicates a specific Ad-tk/GCV-related toxicity. Low survival rates were seen not only after intravenous administration but also after injection of the vectors into the portal vein, the liver tissue and liver tumors, but not during the treatment of subcutaneous tumors. This, together with extensive signs of liver degeneration occurring as early as one day after the initiation of GCV treatment, strongly suggests a specific liver-associated toxicity. Severe toxicity was observed when animals received GCV treatment as late as 7 weeks after vector administration. Moreover, in vitro survival rates of resting primary hepatocytes treated with Ad-tk and GCV were very low. We therefore suppose a mechanism of toxicity of phosphorylated GCV which is independent from cellular proliferation. Since our results indicate that the Ad-HSV-tk/GCV approach is toxic for the resting liver, additional safety features such as tumor-restricted transgene expression should be included in adenoviral vectors.
Functional Role of Fatty Acyl-Coenzyme A Synthetase in the Transmembrane Movement and Activation of Exogenous Long-chain Fatty Acids (2002)

Fatty acyl-CoA synthetase (FACS, fatty acid:CoA ligase, AMP forming; EC ) plays a central role in intermediary metabolism by catalyzing the formation of fatty acyl-CoA. In Escherichia coli this enzyme, encoded by the fadD gene, is required for the coupled import and activation of exogenous long-chain fatty acids. The E. coli FACS (FadD) contains two sequence elements, which comprise the ATP/AMP signature motif ((213)YTGGTTGVAKGA(224) and (356)GYGLTE(361)) placing it in the superfamily of adenylate-forming enzymes. A series of site-directed mutations were generated in the fadD gene within the ATP/AMP signature motif site to evaluate the role of this conserved region to enzyme function and to fatty acid transport. This approach revealed two major classes of fadD mutants with depressed enzyme activity: 1) those with 25-45% wild type activity (fadD(G216A), fadD(T217A), fadD(G219A), and fadD(K222A)) and 2) those with 10% or less wild-type activity (fadD(Y213A), fadD(T214A), and fadD(E361A)). Using anti-FadD sera, Western blots demonstrated the different mutant forms of FadD that were present and had localization patterns equivalent to the wild type. The defect in the first class was attributed to a reduced catalytic efficiency although several mutant forms also had a reduced affinity for ATP. The mutations resulting in these biochemical phenotypes reduced or essentially eliminated the transport of exogenous long-chain fatty acids. These data support the hypothesis that the FACS FadD functions in the vectorial movement of exogenous fatty acids across the plasma membrane by acting as a metabolic trap, which results in the formation of acyl-CoA esters.
Survival and Prognostic Factors of Invasive Aspergillosis After Allogeneic Bone Marrow Transplantation (1999)

To determine prognostic factors for survival in bone marrow transplant recipients with invasive aspergillosis (IA), we retrospectively reviewed 27 IA cases observed in our bone marrow transplantation unit between January 1994 and October 1994. On 30 September 1997, six patients were alive and disease-free. The median survival after IA diagnosis was 36 days. Of eight variables found to be related to survival according to the univariate analysis, graft-versus-host disease (GVHD) status at IA diagnosis (P = .0008) and the cumulative prednisolone dose taken during the week preceding IA diagnosis (CPDlw) (P < .0001) were selected by a backward stepwise Cox regression model. A three-stage classification was established: CPD1w of < or =7 mg/kg (3 of 8 patients died; 60-day survival rate, 88%), CPD1w of >7 mg/kg and no GVHD (9 of 10 patients died; 60-day survival rate, 20%), and CPD1w of >7 mg/kg and active acute grade 2 or more or extensive chronic GVHD (9 of 9 patients died; 30-day survival rate, 0) (P < .0001).
Improving cache behavior of dynamically allocated data structures (1998)

Poor data layout in memory may generate weak data locality and poor performance. Code transformations such as loop blocking or interchanging and array padding have addressed this issue for scientific applications. However many generalist applications do not use data arrays, but dynamically allocated heterogeneous data structures. In this paper, we explore two data layout techniques for dynamically allocated data structures: field reorganization, and instance interleaving. The application of these techniques may be guided by program profiling. This allows significant cache behavior improvements on some applications. To support instance interleaving, we developed a specific memory allocation library called ialloc. An ialloc-like library may be of great help in a toolbox for performance tuning of general-purpose applications.
Affinity Purification of RNA: Sequence-Specific Capture by Nonionic Morpholino Probes (1997)

Nucleic acid isolation for amplification-based diagnostics requires techniques that do not co-purify inhibitors of DNA polymerases. Also, other requirements for an ideal sample preparation technology include ease of use, capability for automation, high recovery and the use of nontoxic reagents. Affinity purification techniques provide high purification factor with minimal sample processing. Hybridization is the affinity interaction specific to nucleic acids and thus provides a uniquely advantageous method for purifying DNA or RNA for subsequent manipulation. Nonionic (morpholino) probes (Neu-Probes, AntiVirals, Corvallis, OR, USA) have several unique hybridization properties, including resistance to nucleases and the ability to hybridize independently of salt concentration. Therefore, such probes provide advantages over DNA probes for sample preparation by hybridization capture. Three formats for hybridization-based purification of human immunodeficiency virus (HIV) RNA were evaluated using RNA transcripts spiked into crude lysates of normal human plasma. Indirect capture used streptavidin-coated microparticles to capture hybrids of biotinylated capture probes and HIV RNA. Direct capture used particles precoated with probes. In addition, a novel method for acceleration of sequence-specific hybridization was developed and shown to give consistently high recoveries.
Discussion of “Will Harmonizing Accounting Standards Really Harmonize Accounting? Evidence from Non-U.S. Firms Adopting U.S. GAAP” (2008)

Bradshaw and Miller (2007) study a sample of non-U.S. firms that voluntarily adopted U.S. Generally Accepted Accounting Principles (GAAP) during the period from 1980 to 2001. They document that the voluntary U.S. GAAP adopters move significantly closer to U.S. firms in terms of compliance with U.S. GAAP and various accounting earnings properties, although they have not fully converged with U.S. firms. This paper is an interesting and comprehensive study of voluntary U.S. GAAP adopters. The paper's research setting, however, limits its ability to address the question raised in its title.
The relationship between soft tissue attachment, epithelial downgrowth and surface porosity (1981)

Millipore filters with pore sizes ranging from 0.025 μm to 8.0 μm were implanted in the backskin of pigs for periods up to 8 weeks. Measurements of the rate of epithelial migration along the filters showed an inverse relationship with pore size although the extent of migration was significantly less along filters with pore sizes of 3‐ μm and above than along those with smaller pore sizes. Histological examination revealed a difference in the extent of connective tissue infiltration which corresponded to the differences in the rate of migration; filters of pore size 3 μm or more were extensively infiltrated with cell and tissue elements whereas there was little infiltration of filters of 1 μm pore size and none of smaller pore size filters. It is suggested that 3 μm is the minimum pore size that permits connective tissue penetration into the filter and that when infiltration does occur the resulting soft tissue attachment markedly restricts the extent of epithelial downgrowth. These results support therapeutic attempts to modify the cemental surface and thereby facilitate soft tissue reattachment to the tooth.
Facile One-Pot Procedure for Et3Al-Promoted Asymmetric Pinacol-Type Rearrangement (2003)

A facile procedure for the synthesis of enantiomerically pure α-substituted ketones is described. The pinacol-type 1,2-shift of sec-tert 1,2-diols could be effected by performing the following two processes in a one pot procedure, (1) regioselective methanesulfonylation, and (2) direct treatment of the resulting mesylate with Et3Al. This procedure allowed 1,2-shift reactions of various groups, including vinyl, aryl, and heteroaromatic groups, giving enantiomerically pure ketones in high yields.
Serial in vitro bone marrow fibroblast culture in human leukemia (1983)

Human fibroblast colony formation from bone marrow was performed in liquid culture. Fetal calf serum was used as a stimulator of the fibroblast colony formation. The colony formation took place not only in normal donors, but also in patients with acute leukemia and chronic myelocytic leukemia. At the diagnosis of the disease, significant colony suppression was observed in most cases of acute leukemia, while the number of colonies increased in half of the cases of chronic myelocytic leukemia. However, there was no correlation between the colony-forming efficiency and the initial number of peripheral platelets or bone marrow megakaryocytes that contained growth-promoting factor. The number of colonies increased after chemotherapy, recovered at the stage of complete remission, and then decreased to low levels at relapse in the patients with acute leukemia; it decreased after treatment with busulfan in the patients with chronic myelocytic leukemia. This fibroblast culture method is useful for counting fibroblast colony-forming cells in the bone marrow of human leukemia.
Molecular Characterization of an Alpha Interferon Receptor 1 Subunit (IFNaR1) Domain Required for TYK2 Binding and Signal Transduction (1996)

Binding of alpha interferon (IFNalpha) to its receptors induces rapid tyrosine phosphorylation of the receptor subunits IFNaR1 and IFNaR2, the TYK2 and JAK1 tyrosine kinases, and the Stat1 and Stat2 transcription factors. Previous studies have demonstrated that TYK2 directly and specifically binds to and tyrosine phosphorylates IFNaR1 in vitro. We now report a detailed analysis of the TYK2 binding domain on the IFNaR1 subunit. First, we used an in vitro binding assay to identify the TYK2 binding motif in IFNaR1 as well as the critical residues within this region. The most striking feature is the importance of a number of hydrophobic and acidic residues. A minor role is also ascribed to a region resembling the proline-rich "box 1" sequence. In addition, mutations which disrupt in vitro binding also disrupt the coimmunoprecipitation of the receptor and TYK2. We also provide direct evidence that the binding region is both necessary and sufficient to activate TYK2 in vivo. Specifically, mutations in the binding domain act in a dominant-negative fashion to inhibit the IFNalpha-induced tyrosine phosphorylation of TYK2 and Stat2. Further, introduction of dimerized glutathione S-transferase-IFNaR1 fusion proteins into permeabilized cells is sufficient to induce phosphorylation of TYK2 and the receptor, confirming the role of the binding domain in IFNalpha signal transduction. These studies provide clues to the sequences determining the specificity of the association between JAK family tyrosine kinases and cytokine receptors as well as the functional role of these kinases in cytokine signal transduction.
Defects associated with the accommodation of misfit between crystals (1975)

A substantial fraction of the defects in epitaxial thin films are formed to accommodate part of the misfit between the stress−free lattice parameters of film and substrate. This paper describes some of the complete dislocations, partial dislocations, and cracks that are made for this purpose. Also described are the optimum division of misfit between dislocations and elastic strain, and the modification of this division caused by the Peierls stress and the barrier to nucleation of dislocation half−loops. The use of misfit strain to remove dislocations, the effect of misfit strain on the mode of film growth, and the evidence for dislocation sources in epitaxial layers are discussed in brief.
REPEATED ADMINISTRATION OF A F(ab′)2 FRAGMENT OF AN ANTI-TUMOR NECROSIS FACTOR α MONOCLONAL ANTIBODY IN PATIENTS WITH SEVERE SEPSIS (1994)

In an uncontrolled clinical trial the effects of repeated administration of the F(ab')2 fragment of a murine monoclonal anti-tumor necrosis factor alpha (TNF alpha)-antibody (MAK 195F) on cytokine levels and the cardiovascular system were studied in 20 patients with severe sepsis. Patients were treated with a total of 11 single dosages of the anti-TNF alpha-antibody intravenously over 5 days using either 1 mg/kg (n = 10) or 3 mg/kg (n = 10). The anti-TNF alpha-antibody was well tolerated in all patients without signs of toxicity and without development of anti-murine antibodies. As assessed by cytokine levels (TNF alpha, Interleukin-6) and hemodynamics there was no evidence that the higher dosage of the anti-TNF alpha-antibody (3 mg/kg per dose) was more effective than the lower dosage (1 mg/kg per dose). Comparison of our data with recent data from phase I or II trials using a complete murine monoclonal anti-TNF alpha-antibody suggest that the F(ab')2 fragments of the murine monoclonal anti-TNF alpha-antibody may be of similar efficacy. Definitive conclusions, however, with respect to improvement of mortality and improvement of the cardiovascular system, await the results of larger ongoing placebo-controlled trials.
Metabolic pathways as regulators of HIV infection (2013)

The availability and use of energy resources in fluctuating environments regulate T-cell function and susceptibility to HIV-1 infection. Identification of the targets coordinating the selected metabolic pathways will advance new strategic avenues for controlling HIV-1 disease progression.
Stop-line detection and localization method for intersection scenarios (2011)

This paper presents a method for the detection and localization of stop-lines and other horizontal road markings as bicycle or pedestrian crossings encountered in road environments. The few existing stop-line detection approaches found in literature are based on monocular vision, and therefore cannot infer high accuracy information from the visual data. The proposed solution uses a hybrid approach that combines 2D detections in grayscale images with stereo-vision based 3D validations in order to increase the robustness and accuracy of the results. Model based reasoning is also used to eliminate false positive situations and to detect exactly the objects of interest (stop-lines, pedestrian or bicycle crossings). The detected horizontal road markings can be used as landmarks for a very accurate longitudinal localization of the ego vehicle within intersection scenarios compensating missing GPS data or its lack of accuracy.
Li2MnO3-stabilized LiMO2 (M = Mn, Ni, Co) electrodes for lithium-ion batteries (2007)

A strategy used to design high capacity (>200 mAh g−1), Li2MnO3-stabilized LiMO2 (M = Mn, Ni, Co) electrodes for lithium-ion batteries is discussed. The advantages of the Li2MnO3 component and its influence on the structural stability and electrochemical properties of these layered xLi2MnO3·(1 − x)LiMO2 electrodes are highlighted. Structural, chemical, electrochemical and thermal properties of xLi2MnO3·(1 − x)LiMO2 electrodes are considered in the context of other commercially exploited electrode systems, such as LiCoO2, LiNi0.8Co0.15Al0.05O2, Li1+xMn2−xO4 and LiFePO4.