gebhart/patrepeval huggingface dataset:
Temporal causal modeling with graphical granger methods (2007)

The need for mining beyond mere statistical correlations, for real world problems has been recognized widely. Many of these applications naturally involve temporal data, which raises the challenge of how best to leverage the temporal information for causal modeling. Recently graphical modeling with the concept of causality, based on the intuition that a cause helps predict its effects in the future, has gained attention in many domains involving time series data analysis. With the surge of interest in model selection methodologies for regression, such as the Lasso, as practical alternatives to solving structural learning of graphical models, the question arises whether and how to combine these two notions into a practically viable approach for temporal causal modeling. In this paper, we examine a host of related algorithms that, loosely speaking, fall under the category of graphical Granger methods, and characterize their relative performance from multiple viewpoints. Our experiments show, for instance, that the Lasso algorithm exhibits consistent gain over the canonical pairwise graphical Granger method. We also characterize conditions under which these variants of graphical Granger methods perform well in comparison to other benchmark methods. Finally, we apply these methods to a real world data set involving key performance indicators of corporations, and present some concrete results.
An Arg307 to Gln Polymorphism within the ATP-binding Site Causes Loss of Function of the Human P2X7 Receptor (2004)

The P2X(7) receptor is a ligand-gated channel that is highly expressed on mononuclear cells of the immune system and that mediates ATP-induced apoptosis. Wide variations in the function of the P2X receptor have been observed, explained in part by (7)loss-of-function polymorphisms that change Glu(496) to Ala (E496A) and Ile(568) to Asn (I568N). In this study, a third polymorphism, which substitutes an uncharged glutamine for the highly positively charged Arg(307) (R307Q), has been found in heterozygous dosage in 12 of 420 subjects studied. P2X(7) function was measured by ATP-induced fluxes of Rb(+), Ba(2+), and ethidium(+) into peripheral blood monocytes or various lymphocyte subsets and was either absent or markedly decreased. Transfection experiments showed that P2X(7) carrying the R307Q mutation lacked either channel or pore function despite robust protein synthesis and surface expression of the receptor. The monoclonal antibody (clone L4) that binds to the extracellular domain of wild type P2X(7) and blocks P2X(7) function failed to bind to the R307Q mutant receptor. Differentiation of monocytes to macrophages up-regulated P2X(7) function in cells heterozygous for the R307Q to a value 10-40% of that for wild type macrophages. However, macrophages from a subject who was double heterozygous for R307Q/I568N remained totally non-functional for P2X(7), and lymphocytes from the same subject also lacked ATP-stimulated phospholipase D activity. These data identify a third loss-of-function polymorphism affecting the human P2X(7) receptor, and since the affected Arg(307) is homologous to those amino acids essential for ATP binding to P2X(1) and P2X(2), it is likely that this polymorphism abolishes the binding of ATP to the extracellular domain of P2X(7).
Hepatitis D: Scenario in the Asia-Pacific region (2010)

Hepatitis D virus (HDV) infection is present worldwide and affects all age groups. Around 18 million people are estimated to be infected with HDV. An important trend in HDV infection is global decline. HDV prevalence has decreased significantly in Europe since the 1970s and 1980s when it was first reported. The Asia-Pacific region now seems to be where HDV is a major health concern. There is a lack of available data from most of the countries from this region; hence, the true status of HDV cannot be determined. In South Asia, most of the countries have conditions that are favorable for the spread of hepatitis B and other related infections. Countries like Pakistan and Iran have shown an increase in HDV prevalence over a period of time. Other countries and region like China, Turkey, Australia, Japan, India and Taiwan, some of which had very high HDV prevalence in the past, have shown a decline in the incidence, but high prevalence persists in some. Intravenous drug abusers, homosexual men and women, prostitutes, and people on hemodialysis are the groups with very high HDV prevalence.
Prediction of relapse and survival in breast cancer patients by pS2 protein status. (1990)

Application of systemic adjuvant therapy for primary breast cancer patients requires a more accurate identification of patients at high risk for recurrence. We have quantitatively assessed the cytosolic levels of estrogen-regulated pS2 protein in tumors of 205 breast cancer patients (median follow-up, 47 mo). There were no significant associations between the level of pS2 protein and tumor size, lymph node status, and differentiation grade. Using length of relapse-free survival (RFS) and overall survival (OS) as end points, 11 ng of pS2 protein/mg of cytosol protein were found as the best cutoff level to discriminate between positive (pS2+) and negative (pS2-). Patients with pS2- tumors showed significantly shorter RFS and OS (P less than 0.0001) than patients with pS2+ tumors. Also after adjustment for tumor size, lymph node status, and estrogen receptor (ER) status, pS2 negativity was associated with earlier recurrence and death. Tumors positive for pS2 (55 of 205, 27%) were almost exclusively confined to the subclass of ER+ tumors (53 of 55, 96%). The death rate for patients with pS2+ tumors was one-tenth of the death rate for patients with pS2-/ER- tumors. In the patients with ER+ tumors, the prognostic power of the pS2 status was especially present in patients whose tumors were also positive for the progesterone receptor (5-yr RFS and OS, 85% and 97% for ER+/PgR+/pS2+ tumors compared with 50% and 54% for the patients with ER+/PgR+/pS2- tumors). In patients with axillary lymph node involvement (N+), pS2 status could discriminate strongly between a good and bad prognosis group (5-yr RFS and OS, 65% and 88% for N+/pS2+ compared with 32% and 34% for N+/pS2-). A similar phenomenon was observed in patients without axillary lymph node involvement (5-yr RFS and OS, 89% and 95% for N0/pS2+ compared with 58% and 82% for N0/pS2-). We conclude that the pS2 status of human primary breast tumors is an important variable for the identification of patients at high risk for recurrence and death. Knowledge of the cytosolic pS2 status appeared of particular importance to identify patients at high risk in the ER+/PgR+ subclass of tumors, and in both the N0 and N+ subclasses of patients.
Tuning Selectivity in Propylene Epoxidation by Plasmon Mediated Photo-Switching of Cu Oxidation State (2013)

Oxidation of functioning copper has restricted its applicability as a catalyst for commercially important epoxidation of propylene to form propylene oxide. Here, we report that steady-state selectivity in propylene epoxidation on copper (Cu) nanoparticles increases sharply when the catalyst is illuminated with visible light. The selectivity increase is accompanied by light-induced reduction of the surface Cu atoms, which is brought about by photoexcitation of the localized surface plasmon resonance (LSPR) of Cu. We discuss multiple mechanisms by which Cu LSPR weakens the Cu-O bonds, reducing Cu2O.
Signal transduction for nuclear factor-kappa B activation. Proposed location of antioxidant-inhibitable step. (1994)

Reactive oxygen species are thought to be messengers for nuclear factor (NF)-kappa B activation because its activation can be abrogated by antioxidants. However, this study identifies, for the first time, NF-kappa B activators that are insensitive to antioxidants. NF-kappa B activation that is induced by either calyculin A or okadaic acid (inhibitors of serine/threonine protein phosphatases 1 and 2A) is not blocked by N-acetylcysteine or dihydrolipoate in Jurkat and U937 cells. Nonetheless, these antioxidants block induction by TNF-alpha, lymphotoxin, and PMA. Unlike okadaic acid and calyculin A, neither TNF-alpha, lymphotoxin, nor PMA inhibited activities of phosphatases 1 and 2A. NF-kappa B activation induced by okadaic acid or calyculin A was not blocked by a myosin light chain kinase inhibitor, but was prevented by a protease inhibitor. The mitochondrial inhibitor, rotenone, also inhibited NF-kappa B activation by calyculin A; however, this inhibition was accompanied by a depletion of cellular ATP. These results suggest that 1) phosphatase inhibitors either target a component of signal transduction, which occurs downstream to an antioxidant-sensitive step or use distinct signaling pathways; 2) inhibition of phosphatases 1 and 2A is not a step in the pathway of TNF-alpha-, lymphotoxin-, or PMA-induced NF-kappa B activation; 3) myosin light chain kinase does not participate in NF-kappa B activation; and 4) activation of NF-kappa B by phosphatase inhibitors is controlled by proteases.
Chromosome 9 deletion mapping reveals interferon alpha and interferon beta-1 gene deletions in human glial tumors. (1991)

We have applied restriction fragment length polymorphism analysis to a 30-member panel of primary glioma DNAs, which had been previously examined for loss of genetic information (C. D. James, E. Carlbom, J. P. Dumanski, M. Hansen, M. Nordenskjold, V. P. Collins, and W. K. Cavenee, Cancer Res., 48:5546-5551, 1988), to determine the frequency and sublocalization of loss of genetic information from chromosome 9. We have also utilized scanning densitometry for dosage determination of the 9p-localized interferon alpha and interferon beta-1 genes among these same tumors. Our results reveal the following: (a) for those cases in which loss has occurred, the region of common loss lies on the short (p) arm of the chromosome; (b) loss of genetic information from the short arm of chromosome 9 occurs frequently in glial tumors of intermediate (anaplastic, grade III) and high (glioblastoma, grade IV) histological malignancy (10 of 20 cases) but not in tumors of low (grade II) histological malignancy (0 of 10 cases); (c) tumors with 9p deletions are hemi- or nullizygous for interferon beta-1 and the interferon alpha gene cluster; (d) cases of interferon nullizygosity occur exclusively among tumors of highest histological malignancy (glioblastoma). These data, especially the determination of a region of nullizygosity, suggest proximity to or residence within a gene(s) whose function(s) is (are) critical to the suppression of the malignant evolution of glial tumors.
Location-aware computing comes of age (2004)

At the core of invisible computing is context awareness, the concept of sensing and reacting to dynamic environments and activities. Location is a crucial component of context, and much research in the past decade has focused on location-sensing technologies, location-aware application support, and location-based applications. With numerous factors driving deployment of sensing technologies, location-aware computing may soon become a part of everyday life.
Eradication of polymerase chain reaction-detectable chronic lymphocytic leukemia cells is associated with improved outcome after bone marrow transplantation (1996)

In chronic lymphocytic leukemia (CLL), clonal rearrangement of the immunoglobulin heavy chain locus (IgH) provides a useful marker for the detection of minimal residual disease (MRD) after treatment. At the time of initial presentation, DNA from patients with CLL was polymerase chain reaction (PCR)-amplified using consensus Variable (VH) and Joining (JH) region primers using complementarity determining region III consensus region primers or a panel of VH family-specific framework region 1 (FR1) primers. The clonal product was directly sequenced and patient-specific probes constructed using N region nucleotide sequences. We amplified and sequenced the CDRIII region and designed patient specific oligonucleotide probes for the detection of MRD in 55 of 66 patients (84%, 90% Confidence Intervals (CI): 74% to 90%) with poor prognosis CLL referred for autologous and allogeneic bone marrow transplantation (BMT). To determine the clinical utility of this technique, PCR amplification was performed on patient samples at the time of and following autologous (21 patients) and allogeneic (10 patients) BMT in whom serial bone marrow samples obtained after BMT were available for analysis. We show that the persistence of MRD after BMT is associated with increased probability of relapse. In all cases that have relapsed to date, the IgH CDRII region was identical at the time of initial presentation and at relapse suggesting that clonal evolution of the IgH locus is unusual in this disease. The finding that a significant number of patients remain disease free and with no evidence of PCR-detectable MRD after BMT suggests that high-dose therapy may contribute to improved outcome in selected patients with CLL.
Multispectral Thin Film Biosensing and Quantitative Imaging Using 3D Plasmonic Crystals (2009)

This work provides plasmonic crystal platforms for quantitative imaging mode biosensing and multispectral immunoassays, establishing and validating both the optical and equilibrium bases for their operation. We investigated the distance-dependent refractive index sensitivity of full 3D plasmonic crystals to thin polymeric films formed using layer by layer (LbL) assembly of polyelectrolytes as a model system. LbL was also used to determine the preferred gold thickness and plasmonic crystal design rules (nanowell diameter and periodicity) for improved thin-film sensitivity, and full 3D finite-difference time-domain (FDTD) calculations were used to quantitatively model and confirm the experimentally observed thin film sensitivities. The integrated multispectral response of the crystals increases approximately linearly with film thickness for values <70 nm, which enables the use of molecular rulers with known thicknesses (such as self-assembled monolayers of alkanethiols on gold) to calibrate these optics for quantitative detection and speciation of surface binding events in a multiplexed imaging format. The utility of these sensors and multispectral analysis for applications in quantitative biosensing was further demonstrated by measuring the equilibrium response curve of an antibody/antigen pair (rabbit antigoat IgG/goat IgG) at increasing antigen concentrations. Fitting the integrated response to a Langmuir isotherm yielded a calculated binding constant on the order of approximately 10(7) M(-1), which is in agreement with the affinity constants reported in the literature for anti-IgG/IgG binding pairs and provides intrinsic detection limits of approximately 400 pM for such unamplified assays.
Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis (2003)

RNA interference (RNAi) can achieve sequence-selective inactivation of gene expression in a wide variety of eukaryotes by introducing double-stranded RNA corresponding to the target gene. Here we explore the potential of RNAi as a therapy for amyotrophic lateral sclerosis (ALS) caused by mutations in the Cu, Zn superoxide dismutase (SOD1) gene. Although the mutant SOD1 is toxic, the wild-type SOD1 performs important functions. Therefore, the ideal therapeutic strategy should be to selectively inhibit the mutant, but not the wild-type SOD1 expression. Because most SOD1 mutations are single nucleotide changes, to selectively silence the mutant requires single-nucleotide specificity. By coupling rational design of small interfering RNAs (siRNAs) with their validation in RNAi reactions in vitro and in vivo, we have identified siRNA sequences with this specificity. A similarly designed sequence, when expressed as small hairpin RNA (shRNA) under the control of an RNA polymerase III (pol III) promoter, retains the single-nucleotide specificity. Thus, RNAi is a promising therapy for ALS and other disorders caused by dominant, gain-of-function gene mutations.
Long-term acid control and proton pump inhibitors: interactions and safety issues in perspective. (1997)

Concerns have been raised regarding the safety of proton pump inhibitors in the long-term management of acid-related peptic disease, especially with regard to the physiological effects of prolonged hypochlorhydria. Of special consideration is the potential for development of enterochromaffin-like cell hyperplasia and gastric carcinoids, colorectal adenocarcinoma and polyps, and bacterial overgrowth as a result of achlorhydria. However, the magnitude of hypergastrinemia associated with the administration of proton pump inhibitors is comparable to that observed after vagotomy and is 3- to 6-fold lower than that observed with pernicious anemia. Only minimal morphological changes in gastric endocrine cells have been observed after the long-term daily administration of proton pump inhibitors, and these changes appear to be self-limiting, nondysplastic, and nonneoplastic. All current evidence suggests that the hypergastrinemia observed during proton pump inhibitor therapy has little clinical significance. However, longer-term results are necessary so that one can appreciate the full implications of acid suppression by proton pump inhibitors.
Ecalectin/Galectin-9, a Novel Eosinophil Chemoattractant: Its Function and Production (2000)

We have recently succeeded in purifying and cloning a novel eosinophil chemoattractant, ecalectin/galectin-9, which belong to a rapidly growing galectin family. The eosinophil chemoattractant activity of ecalectin is potent and selective for eosinophils. The cellular source of ecalectin has been thought to be antigen-stimulated T cells. Herein, we will review the significance of its divalent galactoside-binding activity in ecalectin-induced eosinophil chemoattraction and the regulation of ecalectin expression in immune cells.
Low-frequency electroacupuncture and physical exercise decrease high muscle sympathetic nerve activity in polycystic ovary syndrome (2009)

We have recently shown that polycystic ovary syndrome (PCOS) is associated with high muscle sympathetic nerve activity (MSNA). Animal studies support the concept that low-frequency electroacupuncture (EA) and physical exercise, via stimulation of ergoreceptors and somatic afferents in the muscles, may modulate the activity of the sympathetic nervous system. The aim of the present study was to investigate the effect of these interventions on sympathetic nerve activity in women with PCOS. In a randomized controlled trial, 20 women with PCOS were randomly allocated to one of three groups: low-frequency EA (n = 9), physical exercise (n = 5), or untreated control (n = 6) during 16 wk. Direct recordings of multiunit efferent postganglionic MSNA in a muscle fascicle of the peroneal nerve before and following 16 wk of treatment. Biometric, hemodynamic, endocrine, and metabolic parameters were measured. Low-frequency EA (P = 0.036) and physical exercise (P = 0.030) decreased MSNA burst frequency compared with the untreated control group. The low-frequency EA group reduced sagittal diameter (P = 0.001), while the physical exercise group reduced body weight (P = 0.004) and body mass index (P = 0.004) compared with the untreated control group. Sagittal diameter was related to MSNA burst frequency (Rs = 0.58, P < 0.005) in the EA group. No correlation was found for body mass index and MSNA in the exercise group. There were no differences between the groups in hemodynamic, endocrine, and metabolic variables. For the first time we demonstrate that low-frequency EA and physical exercise lowers high sympathetic nerve activity in women with PCOS. Thus, treatment with low-frequency EA or physical exercise with the aim to reduce MSNA may be of importance for women with PCOS.
Immunomodulating Therapy: New Treatment Modality in Congestive Heart Failure (2003)

Accumulating evidence indicates that inflammatory cytokines play a pathogenic role in congestive heart failure (CHF) by influencing heart contractility, inducing hypertrophy, and promoting apoptosis or fibrosis, contributing to the continuous myocardial remodeling process. Traditional cardiovascular drugs seem to have little influence on the overall cytokine network, and immunomodulatory therapy has emerged as a possible new treatment modality in CHF. Several animal studies have suggested that modulation of inflammatory cytokines may improve cardiac performance. The authors have recently demonstrated that intravenous immunoglobulin enhances the left ventricular ejection fraction in CHF patients, and that this is significantly correlated with anti-inflammatory effects of such therapy. While intravenous immunoglobulin is not necessarily the drug of choice, this study suggests a potential role for immunomodulatory therapy in CHF in addition to optimal cardiovascular treatment regimens. Further research will more precisely identify the most important actors in the immunopathogenesis of CHF and contribute to the development of more specific immunomodulating agents for this disorder.
N-channel Si/SiGe MODFETs: effects of rapid thermal activation on the DC performance (1993)

Si/SiGe MODFETs with P- and As-implanted source and drain contacts were fabricated. The effect of rapid thermal activation (RTA) on the DC performance of those devices was studied. The RTA temperature determines the device operation, i.e. a 550-750 degrees C treatment yields enhancement and a 900 degrees C annealing results in depletion mode. Extremely high ratios of the 77- to the 300 K transconductance ( approximately=4.5) were found. Low thermal budget RTA ( approximately=600 degrees C) is essential to eliminate degradation of the channel mobility and to achieve a significant increase of the 77 K transconductance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
IL-12, IFN-gamma, and T cell proliferation to measles in immunized infants. (1999)

Measles infection in infants is associated with severe complications, and secondary infections are attributed to generalized immunosuppression. Measles binding to its monocyte receptor down-regulates IL-12 which is expected to diminish Th1-like cytokine responses, including IFN-gamma. Whether young infants can be immunized effectively against measles is an important public health issue. We evaluated Ag-specific IL-12, IFN-gamma, and T cell responses of infants at 6 (n = 60), 9 (n = 46), or 12 mo (n = 56) of age and 29 vaccinated adults. IL-12 and IFN-gamma release by PBMC stimulated with measles Ag increased significantly after measles immunization in infants. IL-12 and IFN-gamma concentrations were equivalent in younger and older infants, but IL-12 concentrations were significantly lower in infants than in adults (p = 0.04). IL-12 production by monocytes was down-regulated by measles; the addition of recombinant human IL-12 enhanced IFN-gamma production by PBMC stimulated with measles Ag, but infant T cells released significantly less IFN-gamma than adult T cells under this condition. Of particular interest, the presence of passive Abs to measles had no effect on the specific T cell proliferation or IFN-gamma production after measles stimulation. Cellular immunity to measles infection and vaccination may be limited in infants compared with adults as a result of less effective IFN-gamma and IL-12 production in response to measles Ags. These effects were not exaggerated in younger infants compared with effects in infants who were immunized at 12 mo. In summary, infant T cells were primed with measles Ag despite the presence of passive Abs, but their adaptive immune responses were limited compared with those of adults.