| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Aktas, A, et al.
(author)
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A direct search for stable magnetic monopoles produced in positron-proton collisions at HERA
- 2005
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In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 41, s. 133-141
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Journal article (peer-reviewed)abstract
- A direct search has been made for magnetic monopoles produced in e(+)p collisions at a centre of mass energy of 300 GeV at HERA. The beam pipe surrounding the interaction region in 1995-1997 was investigated using a SQUID magnetometer to look for stopped magnetic monopoles. During this time an integrated luminosity of 62 pb(-1) was delivered. No magnetic monopoles were observed and charge and mass dependent upper limits on the e(+)p production cross section are set.
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| 3. |
- Aktas, A, et al.
(author)
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Search for leptoquark bosons in ep collisions at HERA
- 2005
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 629:1, s. 9-19
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Journal article (peer-reviewed)abstract
- A search for scalar and vector leptoquarks coupling to first generation fermions is performed using the e(+) p and e(-) p scattering data collected by the H1 experiment between 1994 and 2000. The data correspond to a total integrated luminosity of 117 pb(-1). No evidence for the direct or indirect production of such particles is found in data samples with a large transverse momentum final state electron or with large missing transverse momentum. Constraints on leptoquark models are established. For leptoquark couplings of electromagnetic strength, leptoquarks with masses up to 275-325 GeV are ruled out at 95% confidence level. These limits improve and supercede earlier H1 limits based on subsamples of the data used here.
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| 4. |
- Aktas, A, et al.
(author)
-
A determination of electroweak parameters at HERA
- 2006
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 632:1, s. 35-42
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Journal article (peer-reviewed)abstract
- Using the deep inelastic e(+) p and e(-) p charged and neutral current scattering cross sections previously published, a combined electroweak and QCD analysis is performed to determine electroweak parameters accounting for their correlation with parton distributions. The data used have been collected by the HI experiment in 1994-2000 and correspond to an integrated luminosity of 117.2 pb(-1). A measurement is obtained of the W propagator mass in charged current ep scattering. The weak mixing angle sin(2)theta w is determined in the on-mass-shell renormalisation scheme. A first measurement at HERA is made of the light quark weak couplings to the Z(0) boson and a possible contribution of right-handed isospin components to the weak couplings is investigated. (c) 2005 Elsevier B.V. All rights reserved.
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| 5. |
- Aktas, A, et al.
(author)
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Measurement of Fc(c)over-bar(2) and Fb(b)over-bar(2) at low Q(2) and x using the H1 vertex detector at HERA
- 2006
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In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 45:1, s. 23-33
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Journal article (peer-reviewed)abstract
- Measurements are presented of inclusive charm and beauty cross sections in e(+)p collisions at HERA for values of photon virtuality 12 <= Q(2) = 60 GeV2 and of the Bjorken scaling variable 0.0002 <= x <= 0.005. The fractions of events containing charm and beauty quarks are determined using a method based on the impact parameter, in the transverse plane, of tracks to the primary vertex, as measured by the H1 vertex detector. Values for the structure functions F-2(cc) and F-2(bb) are obtained. This is the first measurement of F-2(bb) in this kinematic range. The results are found to be compatible with the predictions of perturbative quantum chromodynamics and with previous measurements of F-2(cc).
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| 6. |
- Aktas, A, et al.
(author)
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First measurement of charged current cross sections at HERA with longitudinally polarised positrons
- 2006
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 634:2-3, s. 173-179
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Journal article (peer-reviewed)abstract
- Data taken with positrons of different longitudinal polarisation states in collision with unpolarised protons at HERA are used to measure the total cross sections of the charged current process, e(+) p -> nu X, for negative four-momentum transfer squared Q(2) > 400 GeV2 and inelasticity gamma < 0.9. Together with the corresponding cross section obtained from the previously published unpolarised data, the polarisation dependence of the charged current cross section is measured for the first time at high Q(2) and found to be in agreement with the Standard Model prediction. (c) 2006 Elsevier B.V. All rights reserved.
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| 7. |
- Aktas, A, et al.
(author)
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Measurement of charm and beauty photoproduction at HERA using D*mu correlations
- 2005
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 621:1-2, s. 56-71
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Journal article (peer-reviewed)abstract
- A measurement of charm and beauty photoproduction at the electron proton collider HERA is presented based on the simultaneous detection of a D*(+/-) meson and a muon. The correlation between the D* meson and the muon serves to separate the charm and beauty contributions and the analysis provides comparable sensitivity to both. The total and differential experimental cross sections are compared to LO and NLO QCD calculations. The measured charm cross section is in good agreement with QCD predictions including higher order effects while the beauty cross section is higher.
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| 8. |
- Aktas, A, et al.
(author)
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Measurement of deeply virtual Compton scattering at HERA
- 2005
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In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 44:1, s. 1-11
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Journal article (peer-reviewed)abstract
- A measurement is presented of elastic deeply virtual Compton scattering gamma* p -> gamma p made using e(+) p collision data corresponding to a luminosity of 46.5 pb(-1), taken with the H1 detector at HERA. The cross section is measured as a function of the photon virtuality, Q(2), the invariant mass of the gamma* p system, W, and for the first time, differentially in the squared momentum transfer at the proton vertex, t, in the kinematic range 2 < Q(2) < 80 GeV2, 30 < W < 140 GeV and vertical bar t vertical bar < 1 GeV2. QCD based calculations at next-to-leading order using generalized parton distributions can describe the data, as can colour dipole model predictions.
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| 9. |
- Aktas, A, et al.
(author)
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Search for bosonic stop decays in R-parity violating supersymmetry in e(+)p collisions at HERA
- 2004
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 599:3-4, s. 159-172
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Journal article (peer-reviewed)abstract
- A search for scalar top quarks in R-parity violating supersymmetry is performed in e(+)p collisions at HERA using the H1 detector. The data, taken at roots = 319 GeV and 301 GeV, correspond to an integrated luminosity of 106 pb(-1). The resonant production of scalar top quarks t in positron quark fusion via an R-parity violating Yukawa coupling lambda' is considered with the subsequent bosonic stop decay t --> BW. The R-parity violating decay of the sbottom quark b --> dv(e) and leptonic and hadronic W decays are considered. No evidence for stop production is found in the search for bosonic stop decays nor in a search for the direct R-parity violating decay t --> eq. Mass dependent limits on lambda' are obtained in the framework of the minimal supersymmetric Standard Model. Stop quarks with masses up to 275 GeV can be excluded at the 95% confidence level for a Yukawa coupling of electromagnetic strength. (C) 2004 Elsevier B.V. All rights reserved.
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| 10. |
- Aktas, A, et al.
(author)
-
A general search for new phenomena in ep scattering at HERA
- 2004
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In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - 0370-2693. ; 602:1-2, s. 14-30
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Journal article (peer-reviewed)abstract
- A model-independent search for deviations from the Standard Model prediction is performed in e(+) p and e(-) p collisions at HERA using H1 data corresponding to an integrated luminosity of 117 pb(-1). For the first time all event topologies involving isolated electrons, photons, muons, neutrinos and jets with high transverse momenta are investigated in a single analysis. Events are assigned to exclusive classes according to their final state. A statistical algorithm is developed to search for deviations from the Standard Model in the distributions of the scalar sum of transverse momenta or invariant mass of final state particles and to quantify their significance. A good agreement with the Standard Model prediction is observed in most of the event classes. The most significant deviation is found for a topology containing an isolated muon, missing transverse momentum and a jet, consistent with a previously reported observation.
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