A Geant Study of the Scintillating Optical Fiber (SOFCAL) Cosmic Ray Detector

Recent energy measurements by balloon-borne passive emulsion chambers indicate that the flux ratios of protons to helium nuclei and of protons to all heavy nuclei decrease as the primary cosmic ray energy per nucleon increases above approx. 200 GeV/n, and suggest a "break" in the proton spectrum between 200 GeV and 5 TeV. However, these passive emulsion chambers are limited to a lower energy threshold of approx. 5 TeV/n, and cannot fully explore this energy regime. Because cosmic ray flux and composition details may be significant to acceleration models, a hybrid detector system called the Scintillating Optical Fiber Calorimeter (SOFCAL) has been designed and flown. SOFCAL incorporates both conventional passive emulsion chambers and an active calorimeter utilizing scintillating plastic fibers as detectors. These complementary types of detectors allow the balloon-borne SOFCAL experiment to measure the proton and helium spectra from approx. 400 GeV/n to approx. 20 TeV. The fundamental purpose of this study is to use the GEANT simulation package to model the hadronic and electromagnetic shower evolution of cosmic rays incident on the SOFCAL detector. This allows the interpretation of SOFCAL data in terms of charges and primary energies of cosmic rays, thus allowing the determinations of cosmic ray flux and composition as functions of primary energy

Prospects for Supersymmetry at LEP2

Working within the framework of the minimal supergravity model with gauge coupling unification and radiative electroweak symmetry breaking (SUGRA), we map out regions of parameter space explorable by experiments at LEP2, for center of mass energy options of $\sqrt{s}=150,\ 175$, $190$ and 205 GeV. We compute signals from all accessible $2 \rightarrow 2$ SUSY pair production processes using the ISAJET simulation program, and devise cuts that enhance the signal relative to Standard Model backgrounds, and which also serve to differentiate various supersymmetric processes from one another. We delineate regions of SUGRA parameter space where production of neutralino pairs, chargino pairs, slepton pairs and the production of the light Higgs scalar of SUSY is detectable above Standard Model backgrounds and distinguishable from other SUSY processes. In addition, we find small regions of SUGRA parameter space where \te\te, \tz_2\tz_2 and \tnu_L\tnu_L production yields spectacular events with up to four isolated leptons. The combined regions of parameter space explorable by LEP2 are compared with the reach of Tevatron Main Injector era experiments. Finally, we comment on how the reach via the neutralino pair channel is altered when the radiative electroweak symmetry breaking constraint is relaxed.Comment: 22 page REVTEX file + 9 uuencoded figures; a uuencoded PS file with PS figures is available via anonymous ftp at ftp://hep.fsu.edu/preprints/baer/FSUHEP950501.u

Biomarker Discovery in Subclinical Mycobacterial Infections of Cattle

BACKGROUND: Bovine tuberculosis is a highly prevalent infectious disease of cattle worldwide; however, infection in the United States is limited to 0.01% of dairy herds. Thus detection of bovine TB is confounded by high background infection with M. avium subsp. paratuberculosis. The present study addresses variations in the circulating peptidome based on the pathogenesis of two biologically similar mycobacterial diseases of cattle. METHODOLOGY/PRINCIPAL FINDINGS: We hypothesized that serum proteomes of animals in response to either M. bovis or M. paratuberculosis infection will display several commonalities and differences. Sera prospectively collected from animals experimentally infected with either M. bovis or M. paratuberculosis were analyzed using high-resolution proteomics approaches. iTRAQ, a liquid chromatography and tandem mass spectrometry approach, was used to simultaneously identify and quantify peptides from multiple infections and contemporaneous uninfected control groups. Four comparisons were performed: 1) M. bovis infection versus uninfected controls, 2) M. bovis versus M. paratuberculosis infection, 3) early, and 4) advanced M. paratuberculosis infection versus uninfected controls. One hundred and ten differentially elevated proteins (P < or = 0.05) were identified. Vitamin D binding protein precursor (DBP), alpha-1 acid glycoprotein, alpha-1B glycoprotein, fetuin, and serine proteinase inhibitor were identified in both infections. Transthyretin, retinol binding proteins, and cathelicidin were identified exclusively in M. paratuberculosis infection, while the serum levels of alpha-1-microglobulin/bikunin precursor (AMBP) protein, alpha-1 acid glycoprotein, fetuin, and alpha-1B glycoprotein were elevated exclusively in M. bovis infected animals. CONCLUSIONS/SIGNIFICANCE: The discovery of these biomarkers has significant impact on the elucidation of pathogenesis of two mycobacterial diseases at the cellular and the molecular level and can be applied in the development of mycobacterium-specific diagnostic tools for the monitoring progression of disease, response to therapy, and/or vaccine based interventions

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10−8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 x 10(-8)), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution. A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.Peer reviewe