Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of organ-confined prostate cancer: incremental value of MR imaging and MR spectroscopic imaging to staging nomograms.

PURPOSE To assess retrospectively the incremental value of endorectal coil magnetic resonance (MR) imaging and combined endorectal MR imaging-MR spectroscopic imaging to the staging nomograms for predicting organ-confined prostate cancer (OCPC). MATERIALS AND METHODS The institutional review board approved this HIPAA-compliant study and issued a waiver of informed consent for review of the MR reports and clinical data. Between November 1, 1999, and November 1, 2004, 229 patients underwent endorectal MR imaging and 383 underwent combined endorectal MR imaging-MR spectroscopic imaging before radical prostatectomy. Mean patient age was 58 years (range, 32-74 years). MR studies were interpreted prospectively by 12 radiologists who were informed of patients' clinical data. On the basis of the MR reports, the risks of extracapsular extension, seminal vesicle invasion, and lymph node metastasis were scored retrospectively from 1 to 5; the highest score was subtracted from 6 to determine a score (from 1 to 5) for the likelihood of OCPC on MR studies. The staging nomograms were used to calculate the likelihood of OCPC on the basis of serum prostate-specific antigen level, Gleason grade at biopsy, and clinical stage. Histopathologic findings constituted the reference standard. Logistic regression was used to estimate the multivariable relations between OCPC and MR findings. The area under the receiver operator characteristic curve was calculated for each model. The jackknife method was used for bias correction. RESULTS MR findings contributed significant incremental value (P </= .02) to the nomograms in the overall study population. The contribution of MR findings was significant in all risk groups but was greatest in the intermediate- and high-risk groups (P < .01 for both). Accuracy in the prediction of OCPC with MR was higher when MR spectroscopic imaging was used, but the difference was not significant. CONCLUSION Endorectal MR imaging and combined endorectal MR imaging-MR spectroscopic imaging contribute significant incremental value to the staging nomograms in predicting OCPC.
Homing in on mechanisms linking breast density to breast cancer risk.

I n probably the best-known finding from the Women’s Health Initiative, postmenopausal hormone therapy with estrogen and progestin was linked to a substantial increase in breast cancer risk. Now researchers think that the increase may be explained by an associated rise in breast density. Among women taking hormone therapy in the large, prospective women’s health study, both the density found on baseline mammograms and the change in density were statistically signifi cantly associated with breast cancer risk, according to Celia Byrne, Ph.D., assistant professor at Georgetown University’s Lombardi Comprehensive Cancer Center. Byrne discussed the results of this new analysis of Women’s Health Initiative data at the 2010 American Association of Cancer Research meeting in April. Researchers now consider mammographic density — the amount of white, radiodense area compared with the amount of gray, radiolucent area on a mammogram — one of the strongest independent risk factors for breast cancer ( see “Breast Density Gains Acceptance as Breast Cancer Risk Factor,” J. Natl. Cancer Inst. 2010;102:374 – 5). But researchers do not fully understand just how breast density increases breast cancer risk. Research into the biological mechanisms underlying breast density and linking it to breast cancer risk has been an understudied area, according to Paolo Provenzano, Ph.D. , a research associate at Seattle’s Fred Hutchinson Cancer Research Center. That situation is changing as Provenzano and others have begun to identify some of the complex biological processes that account for breast density and to explain how they affect breast tissue. “Direct studies to begin to address a causal relationship between breast tissue density and cancer have only started to emerge,” Provenzano said. “While there is still much work to be done, I believe that high breast tissue density is causal for the increasing risk of developing breast cancer. ”
Multi-instanton calculus in N=2 supersymmetric gauge theory. II. Coupling to matter.

We further discuss the {ital N}=2 superinstantons in SU(2) gauge theory, obtained from the general self-dual solutions of topological charge {ital n} constructed by Atiyah, Drinfeld, Hitchin, and Manin (ADHM). We realize the {ital N}=2 supersymmetry algebra as actions on the superinstanton moduli. This allows us to recast in concise superfield notation our previously obtained expression for the exact classical interaction between {ital n} ADHM superinstantons mediated by the adjoint Higgs bosons, and, moreover, to incorporate {ital N}{sub {ital F}} flavors of hypermultiplets. We perform explicit one- and two-instanton checks of the Seiberg-Witten prepotentials for all {ital N}{sub {ital F}} and arbitrary hypermultiplet masses. Our results for the low-energy couplings are all in precise agreement with the predictions of Seiberg and Witten except for {ital N}{sub {ital F}}=4, where we find a finite renormalization of the coupling which is absent in the proposed solution. {copyright} {ital 1996 The American Physical Society. }
Two strains of Epstein-Barr virus (B95-8 and a P3HR-1 subclone) that lack defective genomes induce early antigen and cause abortive infection of Raji cells

The heterogeneity of Epstein-Barr virus (EBV) obtained from P3HR-1 cells has permitted derivation of a distinct subclone of P3HR-1 (L. Heston, M. Rabson, N. Brown, and G. Miller, Nature (London) 295:160-163, 1982). We have analyzed the biologic properties and genomic structure of this subclonal virus (clone 13) compared with those of parental P3HR-1 and B95-8 viruses. Synthesis of EBV compared with those of parental P3HR-1 and B95-8 viruses. Synthesis of EBV proteins in Raji cells superinfected with virus derived from P3HR-1, clone 13, and B95-8 was analyzed both by fluorography of radiolabeled proteins and by immunoblotting. Highly concentrated preparations of clone 13 and B95-8 virus induced most of the spectrum of EBV proteins in Raji cells with the exception of the 145,000-, 140,000-, and 110,000-molecular-weight proteins, which were either undetectable or reduced. Moreover, both clone 13 and B95-8 viruses also induced the same patterns of early antigen diffuse components as the parental P3HR-1 virus did. However, only P3HR-1 virus could induce EBV DNA synthesis in superinfected Raji cells, as determined both by buoyant density centrifugation and by in situ cytohybridization with biotinylated recombinant EBV DNA probes. Defective heterogeneous molecules present in P3HR-1 virus have been implicated in early antigen induction after superinfection of Raji cells. Therefore, Southern blots of clone 13, P3HR-1, and B95-8 viruses were hybridized to recombinant EBV fragments representing the sequences contained within the defective molecules in P3HR-1. The parental P3HR-1 contained the previously described defective molecules. No evidence for defective molecules was found in clone 13 or B95-8 viruses. These data indicate that concentrated preparations of both clone 13 and B95-8 viruses can induce abortive infection in Raji cells, but while the defective molecules are not needed for induction of early antigen diffuse components, they may be required for the induction of viral DNA synthesis.
NONINVASIVE ANALYSIS OF CARDIAC FUNCTION OF ELITE DISTANCE RUNNERS—ECHOCARDIOGRAPHY, VECTORCARDIOGRAPHY, AND CARDIAC INTERVALS

A number of variables have been described pertaining to the phenomenon of the "athlete's heart. " Electrocardiographic, vectorcardiographic, radiographic, and recently echocardiographic variables have been analyzed, and conflicting reports have been generated suggesting that the athlete's heart may be diseased or that it may exhibit superior We had the opportunity to perform noninvasive cardiac evaluation of a group of world class distance runners during active training. We assessed them for evidence of chamber hypertrophy and dilatation, and we also looked for evidence of diminished or increased cardiac function by a variety of parameters.
Crossover: Online Pests Plaguing the Offline World

During the past 10 years, several technological trends have emerged that significantly and positively affected today's world. Two in particular are noteworthy: the apparently unbounded desire to network any and all devices and deployment of Microsoft's operating systems in everything from consumer PCs and business servers to embedded devices. We could well see the telecommunications boom; the rise of the Internet, and the rush to connect everything to it as one of humanity's milestones, not far removed from, that of the invention of the telephone or telegraph. Computer networking, over the Internet, particularly, has democratized the publishing of information, made massive amounts of information and services accessible to the general public, and enabled new business models. But everything has a dark side. Along with its benefits, the Internet has brought about such things as cybercrime, computer worms, online fraud, spam, and denial-of-service attacks, among other online unpleasantness. This down side is considered in the article.
US Presidential Election: What Engaged People on Facebook

We study Facebook posts published by major news organizations in the 10-month period leading to the 2016 presidential election. Our goal is to explore the topics related to the two major party candidates, Hillary Clinton and Donald Trump, and identify the ones that engaged the Facebook users the most. The engagement is measured by the total number of reactions, comments, and shares. Using topic modeling with Linear Dirichlet Allocation (LDA) on the Facebook posts, we identify the top 10 topics related to each candidate and then assess the audience engagement for these topics across 10 different news organizations. We use Hierarchical Bayesian Models (HBMs) to analyze the data, which allow us to partially pool the information across different sources.
Is there beauty in ontologies?

This position paper presents an introduction to the special issue of Applied Ontology on “Beautiful Ontologies”. It discusses the relevance of considering the notion of beauty when building and evaluating ontologies, making a parallel with other disciplines such as physics and software engineering. It also discusses the difference between the beauty of an ontology and the notion of quality generally considered in ontology evaluation. Finally, it discusses examples included in the articles of the special issue, to show that a beautiful ontology can be seen as one that integrates contradictory requirements.
The IARC Monographs: a resource for precaution and prevention? The new Preamble does not fit.

In the last issue of the Journal, Cogliano presented the International Agency for Research on Cancer (IARC) Monographs as a tool both for precaution and prevention ( Occup Environ Med 2008; 64 :572). If true in the past, the new Preamble severely impairs this potential. In fact, a new task for the working group has been introduced: “the target organ(s) or tissue(s) in which an increase in cancer was observed is identified” and “a statement that there is sufficient evidence is followed by a separate sentence that identifies the target organ(s) or tissue(s) in which an increase in cancer was observed in humans. Identification of a specific target organ or tissue does not preclude the possibility that the agent may cause cancer …
Contribution of the Helicobacter pylori Thiol Peroxidase Bacterioferritin Comigratory Protein to Oxidative Stress Resistance and Host Colonization

ABSTRACT Peroxiredoxins, the enzymes that catalyze the reduction of hydrogen peroxide and organic hydroperoxides, are ubiquitous proteins that protect organisms from damage by reactive oxygen species. Helicobacter pylori contains three members of the peroxiredoxin family: AhpC (alkyl hydroperoxide reductase), Tpx (thiol-specific peroxidase), and bacterioferritin comigratory protein (BCP). In this study, we characterized H. pylori bcp mutant strains and wild-type BCP. Compared to the parent strain and the ahpC mutant strain, the bcp mutant showed moderate sensitivity to the superoxide-generating agent paraquat and to organic hydroperoxides. Upon exposure of 108 cells to air for 10 h, 106 wild-type cells survived but none of the 108bcp mutant cells were recovered. Introduction of an intact bcp gene at an unrelated locus in the bcp strain restored the wild-type-like oxidative stress resistance phenotype. Purified BCP was shown to be a thiol peroxidase that depends on the reducing activity of thioredoxin and thioredoxin reductase. Among a series of peroxides tested, linoleic acid hydroperoxide was the preferred substrate of BCP. By examining the profiles of protein expression within H. pylori cells, we confirmed that AhpC is much more abundant than BCP. The overlapping functions and activities of BCP and AhpC probably explain why the bcp mutant displayed a relatively weak oxidative stress resistance phenotype. The bcp mutant strain could colonize mouse stomachs, although colonization by the wild-type strain was slightly better than that by the mutant strain at 1 week after host inoculation. However, at 3 weeks after inoculation, the colonization ability of the wild type was significantly greater than that of the bcp mutant; for example, H. pylori was recovered from 10 of 11 mouse stomachs inoculated with the wild-type strain but from only 4 of 12 mice that were inoculated with the bcp mutant strain. This indicates that H. pylori BCP plays a significant role in efficient host colonization.
Osteoblast regulation via ligand-activated nuclear trafficking of the oxytocin receptor

Significance We have shown previously that oxytocin (Oxt), other than regulating lactation and social bonding, is a potent stimulator of bone formation by the osteoblast. Here, we present evidence that this action is exerted through the nuclear localization of the Oxt receptor (Oxtr). Our findings prompt additional studies into the contribution of nuclear Oxtr signaling in regulating lactation and social bonding. We report that oxytocin (Oxt) receptors (Oxtrs), on stimulation by the ligand Oxt, translocate into the nucleus of osteoblasts, implicating this process in the action of Oxt on osteoblast maturation. Sequential immunocytochemistry of intact cells or isolated nucleoplasts stripped of the outer nuclear membrane showed progressive nuclear localization of the Oxtr; this nuclear translocation was confirmed by monitoring the movement of Oxtr–EGFP as well as by immunogold labeling. Nuclear Oxtr localization was conclusively shown by Western immunoblotting and MS of nuclear lysate proteins. We found that the passage of Oxtrs into the nucleus was facilitated by successive interactions with β-arrestins (Arrbs), the small GTPase Rab5, importin-β (Kpnb1), and transportin-1 (Tnpo1). siRNA-mediated knockdown of Arrb1, Arrb2, or Tnpo1 abrogated Oxt-induced expression of the osteoblast differentiation genes osterix (Sp7), Atf4, bone sialoprotein (Ibsp), and osteocalcin (Bglap) without affecting Erk phosphorylation. Likewise and again, without affecting pErk, inhibiting Arrb recruitment by mutating Ser rich clusters of the nuclear localization signal to Ala abolished nuclear import and Oxtr-induced gene expression. These studies define a previously unidentified mechanism for Oxtr action on bone and open possibilities for direct transcriptional modulation by nuclear G protein-coupled receptors.
Detectors with Low-Barrier Schottky Diodes for Millimeter-Wave Imaging Array

The principles of millimeter-wave detectors based on planar slot antennas and low-barrier Schottky diodes are discussed. 94 GHz slot antenna with 8-GHz wide frequency band and 800 Omega impedance has been developed. Detector characteristics of antenna coupled with diodes of various junction resistances within the range Rj=1divide1000 kOmega at zero bias is investigated. Based on experimental investigations, the optimal values of diode resistance for obtaining high value of voltage sensitivity>104 V/W and NEPap10-12 W/Hz1/2have been determined
Rescue of epithelial HCO3− secretion in murine intestine by apical membrane expression of the cystic fibrosis transmembrane conductance regulator mutant F508del

• Cystic fibrosis (CF) is a lethal disease characterized by low rates of epithelial Cl− and HCO3− secretion and obstruction of the airways and gastrointestinal and reproductive organs by sticky mucus. HCO3− secretion has recently been demonstrated to be necessary for mucus hydration. • The most frequent CF mutation is F508del. This mutant protein is usually degraded in the proteasome. New therapeutic strategies have been developed which deliver F508del to the plasma membrane. • Utilizing transgenic F508del mutant and cystic fibrosis transmembrane conductance regulator (CFTR) knockout mice, apical membrane expression of F508del protein was found to be associated with enhanced stimulation of intestinal HCO3− secretion. • The predominant molecular mechanism for enhanced F508del HCO3− stimulation appeared to be the activation of a Cl− recycling pathway, with Cl− exit via membrane‐resident F508del protein and Cl− entry in exchange for HCO3− by apical Cl−/HCO3− exchange. In contrast, the predominant molecular mechanism for cAMP‐activated HCO3− secretion in WT intestine appears to be HCO3− exit via CFTR itself.
Physical mapping of a 670-kb region of chromosomes XVI and XVII from the human protozoan parasite Trypanosoma cruzi encompassing the genes for two immunodominant antigens.

As part of the Trypanosoma cruzi Genome Initiative, we have mapped a large portion of the chromosomal bands XVI (2.3 Mb) and XVII (2.6 Mb) containing the highly repetitive and immunodominant antigenic gene families h49 and jl8. Restriction mapping of the isolated chromosomal bands and hybridization with chromosome specific gene probes showed that genes h49 and jl8 are located in a pair of size-polymorphic homologous chromosomes. To construct the integrated map of the chromosomes harboring the h49 and jl8 loci, we used YAC, cosmid, and lambda phage overlapping clones, and long range restriction analysis using a variety of probes (i.e., known gene sequences, ESTs, polymorphic repetitive sequences, anonymous sequences, STSs generated from the YAC ends). The total length covered by the YAC contig was approximately 670 kb, and its map agreed and was complementary to the one obtained by long-range restriction fragment analysis. Average genetic marker spacing in a 105 kb region around h49 and jl8 genes was estimated to be 6.2 kb/marker. We have detected some polymorphism in the H49/JL8 antigens-encoding chromosomes, affecting also the coding regions. The physical map of this region, together with the isolation of specific chromosome markers, will contribute in the global effort to sequence the nuclear genome of this parasite.
Cross-sectional and longitudinal effects of racism on mental health among residents of Black neighborhoods in New York City.

OBJECTIVES We investigated the impact of reported racism on the mental health of African Americans at cross-sectional time points and longitudinally, over the course of 1 year. METHODS The Black Linking Inequality, Feelings, and the Environment (LIFE) Study recruited Black residents (n = 144) from a probability sample of 2 predominantly Black New York City neighborhoods during December 2011 to June 2013. Respondents completed self-report surveys, including multiple measures of racism. We conducted assessments at baseline, 2-month follow-up, and 1-year follow-up. Weighted multivariate linear regression models assessed changes in racism and health over time. RESULTS Cross-sectional results varied by time point and by outcome, with only some measures associated with distress, and effects were stronger for poor mental health days than for depression. Individuals who denied thinking about their race fared worst. Longitudinally, increasing frequencies of racism predicted worse mental health across all 3 outcomes. CONCLUSIONS These results support theories of racism as a health-defeating stressor and are among the few that show temporal associations with health.
EFFECT OF RECOMBINANT HUMAN GRANULOCYTE COLONY‐ STIMULATING FACTOR ON HEMODYNAMIC AND CYTOKINE RESPONSE IN A PORCINE MODEL OF PSEUDOMONAS SEPSIS

To investigate the effect of recombinant human granulocyte colony-stimulating factor (rhG-CSF) on sepsis, chronically catheterized conscious pigs were challenged with Pseudomonas aeruginosa (8 ± 107 colony-forming units kg-1 h-1) for 84 h (Group A, n = 8). Group B (n = 7) also received rhG-CSF at 5 μg kg-1 d-1, the first dose being given 30 min before starting bacterial infusion. Two of the animals in Group A died from pulmonary failure, whereas all those treated with rh-GCSF survived. Fever, severe pulmonary hypertension and systemic hypotension-the latter accompanied at first by a transient hypodynamic, and later a hyperdynamic response-were observed in all of the animals. In Group B, however, the rise in temperature, mean pulmonary arterial pressure (at a later stage of the observation), plasma levels of tumor necrosis factor, and endotoxin were significantly less than in Group A. In the rhG-CSF-treated pigs, an initial leukopenia completely recovered within 24 h (p < .05 vs. Group A). These data suggest that rhG-CSF might be beneficial in the treatment of sepsis.
Effect of membrane potential on acetylcholine‐induced inward current in guinea‐pig ileum.

1. The whole‐cell patch clamp technique with caesium aspartate internal solution was used with single isolated cells from the longitudinal muscle layer of guinea‐pig ileum, to investigate the voltage‐dependent gating of ACh‐induced inward current. 2. In voltage clamp experiments, at holding potentials ranging from ‐80 to ‐30 mV, ACh (300 microM) produced a slow sustained inward current in physiological salt bath solution (PSS). The measurements of the reversal potentials on substituting Na+ by other monovalent and divalent cations showed that this current is through non‐selective cation channels (Ins, ACh). 3. During hyperpolarizations, Ins, ACh instantaneously increased in amplitude and then relaxed to a new steady‐state level. The I‐V relationship of the instantaneous peak was linear with a reversal potential of 0 mV, while that of the steady state was bell‐shaped. The time course of relaxation appeared to be monoexponential and its time constants were reduced by stronger hyperpolarizations. 4. These results were not affected by the organic Ca2+ antagonists D600 or nitrendipine (10 microM). Under this condition, maximal chord conductance of Ins, Ach which was observed at 0 mV was about 1.5 nS. The steady‐state activation relationship was well fitted by Boltzmann's equation with a half‐maximal activation (Vh) of ‐50 mV and a slope factor (k) of ‐15 mV at membrane potentials negative to 0 mV, but over 0 mV the degree of activation was again decreased. The time constants for relaxation also appeared to follow a sigmoid curve. 5. In current clamp experiments, superfusion of ACh (300 microM) depolarized the membrane up to ‐10 to 0 mV. Inward current injection resulting in the moderate hyperpolarization of the membrane (‐70 to ‐80 mV) attenuated ACh‐induced depolarization and stronger hyperpolarization (less than ‐80 mV) abolished it. 6. These results show that ACh‐induced depolarization is controlled by the membrane potential, which is explained by the voltage‐dependent gating of Ins, Ach.