gebhart/patrepeval huggingface dataset:
A resiliency model for high performance infrastructure based on logical encapsulation (2012)

An emerging trend in distributed systems is the creation of dynamically provisioned heterogeneous high performance platforms that include the co-allocation of both virtualized computing and network attached storage volumes offering NAS and SAN level data services. These high performance computing environments support parallel applications performing traditional file system operations. As with any parallel platform the ability to continue computation in the face of component failures is an important characteristic. Achieving resiliency in heterogeneous environments presents unique challenges and opportunities not found in homogeneous aggregations of computing resources. We present a logical encapsulation model for heterogeneous high performance infrastructure, which enables a reactive resiliency approach for federations of virtual machines and externally hosted physical storage volumes. Asynchronous state capture and restoration models are presented for individual resources, which are composed into non-blocking resiliency models for logical encapsulations. We perform an evaluation that demonstrates our methodology has greater overall flexibility and significant performance improvements when compared to current resiliency approaches in virtualized distributed execution environments.
Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast (2004)

We demonstrate the efficacy of a genome-wide protocol in yeast that allows the identification of those gene products that functionally interact with small molecules and result in the inhibition of cellular proliferation. Here we present results from screening 10 diverse compounds in 80 genome-wide experiments against the complete collection of heterozygous yeast deletion strains. These compounds include anticancer and antifungal agents, statins, alverine citrate, and dyclonine. In several cases, we identified previously known interactions; furthermore, in each case, our analysis revealed novel cellular interactions, even when the relationship between a compound and its cellular target had been well established. In addition, we identified a chemical core structure shared among three therapeutically distinct compounds that inhibit the ERG24 heterozygous deletion strain, demonstrating that cells may respond similarly to compounds of related structure. The ability to identify on-and-off target effects in vivo is fundamental to understanding the cellular response to small-molecule perturbants.
An infogeometric approach to telerobotics (2002)

'Infogeometrics' is the application of low unit cost, multimode digital/RF hardware and structured algorithm firmware that provide remotely maneuvering platforms with: (a) instrumentation quality location tracking, and (b) high bandwidth communications capability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The crystal structures of reduced pseudoazurin from Alcaligenes faecalis S‐6 at two pH values (1994)

The structures of the reduced (Cu1+) blue-copper protein pseudoazurin from Alcaligenes faecalis strain S-6 are refined at pH 7.8 and 4.4 using X-ray diffraction data to 1.8 A resolution. The final R-factors for the high and low pH structures are 0.178 and 0.177, respectively. Comparing the reduced pseudoazurin at pH 7.8 with the oxidised (Cu2+) molecule, small changes are observed in the vicinity of the copper site and on the protein surface. At pH 4.4 the copper substituent imidazole of His81 rotates away from the metal with a concurrent movement of the latter towards the plane of the remaining three ligands (S gamma-Cys78, N delta 1-His40 and S delta-Met86) thus the geometry of the copper site becomes planar trigonal.
In Vitro Analysis of Virus Particle Subpopulations in Candidate Live-Attenuated Influenza Vaccines Distinguishes Effective from Ineffective Vaccines (2010)

Two effective (vac+) and two ineffective (vac-) candidate live-attenuated influenza vaccines (LAIVs) derived from naturally selected genetically stable variants of A/TK/OR/71-delNS1[1-124] (H7N3) that differed only in the length and kind of amino acid residues at the C terminus of the nonstructural NS1 protein were analyzed for their content of particle subpopulations. These subpopulations included total physical particles (measured as hemagglutinating particles [HAPs]) with their subsumed biologically active particles of infectious virus (plaque-forming particles [PFPs]) and different classes of noninfectious virus, namely, interferon-inducing particles (IFPs), noninfectious cell-killing particles (niCKPs), and defective interfering particles (DIPs). The vac+ variants were distinguished from the vac- variants on the basis of their content of viral subpopulations by (i) the capacity to induce higher quantum yields of interferon (IFN), (ii) the generation of an unusual type of IFN-induction dose-response curve, (iii) the presence of IFPs that induce IFN more efficiently, (iv) reduced sensitivity to IFN action, and (v) elevated rates of PFP replication that resulted in larger plaques and higher PFP and HAP titers. These in vitro analyses provide a benchmark for the screening of candidate LAIVs and their potential as effective vaccines. Vaccine design may be improved by enhancement of attributes that are dominant in the effective (vac+) vaccines.
KDM1 is a novel therapeutic target for the treatment of gliomas (2012)

Glioma development is a multistep process, involving alterations in genetic and epigenetic mechanisms. Understanding the mechanisms and enzymes that promote epigenetic changes in gliomas are urgently needed to identify novel therapeutic targets. We examined the role of histone demethylase KDM1 in glioma progression. KDM1 was overexpressed in gliomas and its expression positively correlated with histological malignancy. Knockdown of KDM1 expression or its pharmacological inhibition using pargyline or NCL-1 significantly reduced the proliferation of glioma cells. Inhibition of KDM1 promoted up regulation of the p53 target genes p21 and PUMA. Patient-derived primary GBM cells expressed high levels of KDM1 and pharmacological inhibition of KDM1 decreased their proliferation. Further, KDM1 inhibition reduced the expression of stemness markers CD133 and nestin in GBM cells. Mouse xenograft assays revealed that inhibition of KDM1 significantly reduced glioma xenograft tumor growth. Inhibition of KDM1 increased levels of H3K4-me2 and H3K9-Ac histone modifications, reduced H3K9-me2 modification and promoted expression of p53 target genes (p21 and PUMA), leading to apoptosis of glioma xenograft tumors. Our results suggest that KDM1 is overexpressed in gliomas and could be a potential therapeutic target for the treatment of gliomas.
Full 360 degrees phase shifting of injection-locked oscillators (1993)

A design is presented to produce analog phase shift of 0 degrees to 360 degrees in optically controlled oscillators which are subharmonically injection-locked. The proposed concept was analytically described and experimentally demonstrated by producing 360 degrees of phase shift in an 8-GHz oscillator that is indirect optically injection-locked to a 4-GHz subharmonic frequency. This design concept could eliminate the need for switched delay-line phase shifters in the T/R modules of optically controlled phased array antennas, thus making T/R modules more compact and efficient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hematopoietic progenitor kinase 1 is a critical component of prostaglandin E2-mediated suppression of the anti-tumor immune response (2009)

Lung cancer is the leading cause of cancer-related mortality in the world, resulting in over a million deaths each year. Non-small cell lung cancers (NSCLCs) are characterized by a poor immunogenic response, which may be the result of immunosuppressive factors such as prostaglandin E2 (PGE(2)) present in the tumor environment. The effect of PGE(2) in the suppression of anti-tumor immunity and its promotion of tumor survival has been established for over three decades, but with limited mechanistic understanding. We have previously reported that PGE(2) activates hematopoietic progenitor kinase 1 (HPK1), a hematopoietic-specific kinase known to negatively regulate T-cell receptor signaling. Here, we report that mice genetically lacking HPK1 resist the growth of PGE(2)-producing Lewis lung carcinoma (LLC). The presence of tumor-infiltrating lymphocytes (TILs) and T-cell transfer into T cell-deficient mice revealed that tumor rejection is T cell mediated. Further analysis demonstrated that this may be significantly due to the ability of HPK1 (-/-) T cells to withstand PGE(2)-mediated suppression of T-cell proliferation, IL-2 production, and apoptosis. We conclude that PGE(2) utilizes HPK1 to suppress T cell-mediated anti-tumor responses.
Stink Bugs of Economic Importance in America North of Mexico (2000)

Many scientists have reported an extensive amount of information on the biology, life history, and damage potential of stink bugs. However, this information is scattered among numerous journals, periodicals, and other publications. Stink Bugs of Economic Importance in America North of Mexico brings together the applied and nonapplied literature in
Use of synthetic peptides to confirm that the Pseudomonas aeruginosa PAK pilus adhesin and the Candida albicans fimbrial adhesin possess a homologous receptor‐binding domain (1996)

Pseudomonas aeruginosa PAK pili and Candida albicans fimbriae are adhesins present on the microbial cell surfaces which mediate binding to epithelial cell-surface receptors. The receptor-binding domain (adhesintope) of the PAK pilus adhesin has been shown previously to reside in the carboxy-terminal disulphide-bonded region of P. aeruginosa pilin (PAK128-144). The delineation of the C. albicans fimbrial adhesintope was investigated in these studies using synthetic peptides which correspond to the whole (PAK128-144) or part of (PAK134-140) adhesintope of the PAK pilus and their respective anti-peptide antisera and biotinylated PAK pili (Bt-PAK pili), fimbriae (Bt-fimbriae), P. aeruginosa whole cells (Bt-P. aeruginosa) and C. albicans whole cells (Bt-C. albicans). The results from these studies confirmed that a structurally conserved motif akin to the PAK(128-144) peptide sequence is present in C. albicans fimbrial adhesin and that the seven-amino-acid residue PAK(134-140) sequence plays an important role in forming the adhesintope for both P. aeruginosa PAK pilus and C. albicans fimbrial adhesins.
A Patient-Specific in silico Model of Inflammation and Healing Tested in Acute Vocal Fold Injury (2008)

The development of personalized medicine is a primary objective of the medical community and increasingly also of funding and registration agencies. Modeling is generally perceived as a key enabling tool to target this goal. Agent-Based Models (ABMs) have previously been used to simulate inflammation at various scales up to the whole-organism level. We extended this approach to the case of a novel, patient-specific ABM that we generated for vocal fold inflammation, with the ultimate goal of identifying individually optimized treatments. ABM simulations reproduced trajectories of inflammatory mediators in laryngeal secretions of individuals subjected to experimental phonotrauma up to 4 hrs post-injury, and predicted the levels of inflammatory mediators 24 hrs post-injury. Subject-specific simulations also predicted different outcomes from behavioral treatment regimens to which subjects had not been exposed. We propose that this translational application of computational modeling could be used to design patient-specific therapies for the larynx, and will serve as a paradigm for future extension to other clinical domains.
Normalization of Left Ventricular Parameters Following Combined Pimobendan and Carvedilol Treatment in a Case of Unclassified Cardiomyopathy with Longstanding Refractory Status. (2002)

A 58-year-old man with a 64-month history of unclassified cardiomyopathy developed congestive heart failure (CHF) and had been dependent on long-term intravenous positive inotropes. Combined pimobendan and carvedilol administration resulted in marked symptomatic improvement from New York Heart Association functional class IV to I. Echocardiograms showed improvement of left ventricular (LV) ejection fraction from 15 to 48%, and LV end-diastolic diameter from 6.7 to 4.9 cm. This mode of therapy not only improved LV contractile function but also normalized LV volume, which was an unusual clinical course compared with the general course of advanced CHF.
Hexamethyl-p-terphenyl poly(benzimidazolium): a universal hydroxide-conducting polymer for energy conversion devices (2016)

A benchmark hydroxide-conducting polymer is utilized in alkaline hydrogen fuel cell and water electrolyzer devices at 60 °C for &gt;100 hours.
Unequalisation of electrode capacitances for enhanced energy capacity in asymmetrical supercapacitors (2010)

An increase beyond 70% in specific energy of an asymmetrical supercapacitor of carbon (−) and composite of carbon nanotubes and polyaniline (+) was achieved by firstly identifying the ‘cell voltage limiting electrode’, and then adjusting the capacitance ratio of the ±electrodes from 1.0 to 1.3.
INTERLEUKIN-2 AND INTERFERON-?? DOUBLE KNOCKOUT MICE REJECT HETEROTOPIC CARDIAC ALLOGRAFTS (2000)

The combined absence of IL-2 and IFN-gamma in the setting of Th2 deviation does not prevent allograft rejection.
Coagulation and Fibrinolysis Markers and Risk of Dementia (1998)

We performed a cross-sectional case-control study among 277 subjects with dementia and 298 control subjects drawn from participants of the Rotterdam Study, a population-based cohort study among subjects aged 55 years or over, and from participants of the Rotterdam Stroke Databank, a hospital-based stroke registry, with the objective to evaluate the association of indicators of coagulability, fibrinogen, prothrombin fragments 1+2, thrombin-antithrombin complex (TAT), and indicators of fibrinolysis, plasmin-inhibitor complex, D-dimer and tissue-type plasminogen activator (t-PA) with dementia. Increased levels of TAT, D-dimer and t-PA activity were associated with an increased risk of dementia. Additional stratified analyses indicated that an increased TAT level was the primary factor related to dementia. The present study provides evidence that predominantly increased thrombin generation is associated with dementia.
Intrinsic mitochondrial dysfunction in ATM-deficient lymphoblastoid cells (2007)

One of the characteristic features of cells from patients with ataxia telangiectasia (A-T) is that they are in a state of continuous oxidative stress and exhibit constitutive activation of pathways that normally respond to oxidative damage. In this report, we investigated whether the oxidative stress phenotype of A-T cells might be a reflection of an intrinsic mitochondrial dysfunction. Mitotracker Red staining showed that the structural organization of mitochondria in A-T cells was abnormal compared to wild-type. Moreover, A-T cells harbored a much larger population of mitochondria with decreased membrane potential (DeltaPsi) than control cells. In addition, the basal expression levels of several nuclear DNA-encoded oxidative damage responsive genes whose proteins are targeted to the mitochondria--polymerase gamma, mitochondrial topoisomerase I, peroxiredoxin 3 and manganese superoxide dismutase--are elevated in A-T cells. Consistent with these results, we found that overall mitochondrial respiratory activity was diminished in A-T compared to wild-type cells. Treating A-T cells with the antioxidant, alpha lipoic acid (ALA), restored mitochondrial respiration rates to levels approaching those of wild-type. When wild-type cells were transfected with ATM-targeted siRNA, we observed a small but significant reduction in the respiration rates of mitochondria. Moreover, mitochondria in A-T cells induced to stably express full-length ATM, exhibited respiration rates approaching those of wild-type cells. Taken together, our results provide evidence for an intrinsic mitochondrial dysfunction in A-T cells, and implicate a requirement for ATM in the regulation of mitochondrial function.
The Endothelial Cell as a Regulator of T‐Cell Function (1990)

These studies have analyzed the antigen-presenting capacities of EC. EC can transcribe, translate and express MHC class II molecules in response to IFN-gamma as well as express class I molecules. The class II dimeric structure is functional, in that allospecific CTL can efficiently kill IFN-gamma-treated EC or fibroblasts, an outcome that can be blocked by antibody to non-polymorphic regions of the class II molecule. Moreover, EC can present antigen in an MHC-restricted manner to resting T cells as well as to antigen-specific cloned T-cell lines. This ability to stimulate primary as well as secondary responses has been further confirmed by experiments using purified populations of naive and memory T cells. In this regard, EC differ from fibroblasts and other non-immune cell types in that they possess costimulator activities necessary for activation of resting T cells. As the local concentration of IL-2 has been shown to be critical in determining the fate of T cells--whether they become activated or anergic--we have investigated the ability of EC to modulate T-cell IL-2 production, believing that this may underlie their ability to act as costimulatory cells. Using PHA-stimulated peripheral blood mononuclear cells or purified CD4+ T cells we have found that EC can augment IL-2 production, typically by 3- to 8-fold. This increased IL-2 production is functional as OKT3-stimulated or sub-optimally PHA-stimulated T cells proliferate more in the presence of EC than in their absence. The major pathway by which EC augment T-cell IL-2 production is cell contact-dependent and involves the CD2:LFA-3 ligand pair. However, use of blocking mAb to CD2 and LFA-3, of PI-LFA-3, and of the immunosuppressive drug CsA has allowed us to reveal the presence of a second signalling pathway. This pathway confers a certain degree of CsA resistance on T cells, but the ligands involved have not yet been identified. We do not find a role for CD28, LFA-1:ICAM-1, VLA-4:VCAM-1 or CD44 in this system. Augmentation is independent of EC metabolism or soluble factors, as fixed cells are almost as efficient as living cells. Similar mechanisms seem also to be involved in more physiological settings, such as alloresponses. Here, proliferation can be blocked by antibodies to CD2 or LFA-3, presumably by blocking of augmented IL-2 production.(ABSTRACT TRUNCATED AT 400 WORDS)
Knee acoustic emission: A potential biomarker for quantitative assessment of joint ageing and degeneration (2011)

Based on a single time-point study of 34 healthy and 19 osteoarthritic knees in three different age groups (early, middle and late adulthood), this paper reports the potential of knee acoustic emission as a biomarker to monitor joint ageing and degeneration. Measurements were made of short transient high frequency acoustic emission signals generated by knee joints under stress during repeated sit-stand-sit movements along with joint angle. A statistically significant feature profile was established using a four-phase model of sit-stand-sit movements and two waveform features. The four-phase movement model is derived from joint angle measurement during repeated sit-stand-sit movements, and it consists of the ascending-acceleration and ascending-deceleration phases in the sit-to-stand movement, followed by the descending-acceleration and descending-deceleration phases in the stand-to-sit movement. The two statistically significant waveform features are extracted from AE measurement during repeated sit-stand-sit movements, and they consist of the peak magnitude value and average signal level of each AE burst. In addition to the use of bilateral plots, statistical distributions and 2D colour histograms to visualise the differences and similarities among participants, use of principal component analysis showed not only distinct data clusters corresponding to participating groups, but also an age- and disease-related trajectory progressing from the early adulthood healthy group to the late adulthood healthy group followed by the middle adulthood osteoarthritic group to the late adulthood osteoarthritic group. Furthermore, this trajectory shows increasing areas for each data cluster, with a highly compact cluster for the early adulthood healthy group at one end and a widely spread cluster for the late adulthood osteoarthritic group at the other end. From these results, a strong basis is formed for further development of knee acoustic emission as a convenient and non-invasive biomarker for quantitative assessment of joint ageing and degeneration.
Control of T Cell-mediated Autoimmunity by Metabolite Flux to N-Glycan Biosynthesis (2007)

Autoimmunity is a complex trait disease where the environment influences susceptibility to disease by unclear mechanisms. T cell receptor clustering and signaling at the immune synapse, T cell proliferation, CTLA-4 endocytosis, T(H)1 differentiation, and autoimmunity are negatively regulated by beta1,6GlcNAc-branched N-glycans attached to cell surface glycoproteins. Beta1,6GlcNAc-branched N-glycan expression in T cells is dependent on metabolite supply to UDP-GlcNAc biosynthesis (hexosamine pathway) and in turn to Golgi N-acetylglucosaminyltransferases Mgat1, -2, -4, and -5. In Jurkat T cells, beta1,6GlcNAc-branching in N-glycans is stimulated by metabolites supplying the hexosamine pathway including glucose, GlcNAc, acetoacetate, glutamine, ammonia, or uridine but not by control metabolites mannosamine, galactose, mannose, succinate, or pyruvate. Hexosamine supplementation in vitro and in vivo also increases beta1,6GlcNAc-branched N-glycans in naïve mouse T cells and suppresses T cell receptor signaling, T cell proliferation, CTLA-4 endocytosis, T(H)1 differentiation, experimental autoimmune encephalomyelitis, and autoimmune diabetes in non-obese diabetic mice. Our results indicate that metabolite flux through the hexosamine and N-glycan pathways conditionally regulates autoimmunity by modulating multiple T cell functionalities downstream of beta1,6GlcNAc-branched N-glycans. This suggests metabolic therapy as a potential treatment for autoimmune disease.
Potential for gene transfer between wheat (Triticum aestivum) and jointed goatgrass (Aegilops cylindrica) (1998)

Jointed goatgrass is a major weed in the wheat-producing areas of the western U.S. It shares the D genome with wheat, and interspecific hybrids between the two species occur in the field. The objective of this research was to determine if wheat X jointed goatgrass hybrids could serve to transfer genes from wheat to jointed goatgrass. A backcrossing program was initiated in the greenhouse between wheat X jointed goatgrass hybrids and either jointed goatgrass or wheat to determine the potential for seed set and the restoration of self-fertility. Seed was set by backcrossing with either species as the recurrent parent. Female fertility increased from 2% in the hybrid to 37% in the BC 2 plants with jointed goatgrass as the recurrent parent. Partial self-fertility was restored in the second backcross (BC 2 ) generation using jointed goatgrass as the recurrent parent. This indicates that genes could be transferred between wheat and jointed goatgrass after only two backcrosses. The number of bivalents observed in the plants during meiosis appeared to be key to increasing female fertility and self-fertility. Based on the results of this study, it is possible for genes to move from wheat to jointed goatgrass. Any release of a herbicide-resistant wheat should be accompanied by a management plan that would minimize the potential for gene movement between these species.