| 1. |
- Klionsky, Daniel J., et al.
(author)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 2. |
- Akkoyun, S., et al.
(author)
-
AGATA - Advanced GAmma Tracking Array
- 2012
-
In: Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. - : Elsevier BV. - 0168-9002 .- 0167-5087 .- 1872-9576. ; 668, s. 26-58
-
Journal article (peer-reviewed)abstract
- The Advanced GAmma Tracking Array (AGATA) is a European project to develop and operate the next generation γ-ray spectrometer. AGATA is based on the technique of γ-ray energy tracking in electrically segmented high-purity germanium crystals. This technique requires the accurate determination of the energy, time and position of every interaction as a γ ray deposits its energy within the detector volume. Reconstruction of the full interaction path results in a detector with very high efficiency and excellent spectral response. The realisation of γ-ray tracking and AGATA is a result of many technical advances. These include the development of encapsulated highly segmented germanium detectors assembled in a triple cluster detector cryostat, an electronics system with fast digital sampling and a data acquisition system to process the data at a high rate. The full characterisation of the crystals was measured and compared with detector- response simulations. This enabled pulse-shape analysis algorithms, to extract energy, time and position, to be employed. In addition, tracking algorithms for event reconstruction were developed. The first phase of AGATA is now complete and operational in its first physics campaign. In the future AGATA will be moved between laboratories in Europe and operated in a series of campaigns to take advantage of the different beams and facilities available to maximise its science output. The paper reviews all the achievements made in the AGATA project including all the necessary infrastructure to operate and support the spectrometer. © 2011 Elsevier B.V. All rights reserved.
|
|
| 3. |
- Bullock, Garrett S., et al.
(author)
-
Kinesiophobia, Knee Self-Efficacy, and Fear Avoidance Beliefs in People with ACL Injury: A Systematic Review and Meta-Analysis
- 2022
-
In: Sports Medicine. - : ADIS INT LTD. - 0112-1642 .- 1179-2035. ; 52, s. 3001-3019
-
Research review (peer-reviewed)abstract
- Background To improve the understanding of the psychological impacts of anterior cruciate ligament (ACL) injury, a systematic review synthesizing the evidence on knee self-efficacy, fear avoidance beliefs and kinesiophobia following ACL injury is needed. Objective The aim of this systematic review was to investigate knee self-efficacy, fear avoidance beliefs and kinesiophobia following ACL injury, and compare these outcomes following management with rehabilitation alone, early and delayed ACL reconstruction (ACLR). Methods Seven databases were searched from inception to April 14, 2022. Articles were included if they assessed Tampa Scale of Kinesiophobia (TSK), Knee Self-Efficacy Scale (KSES), or Fear Avoidance Beliefs Questionnaire (FABQ). Risk of bias (RoB) was assessed using domain-based RoB tools (ROBINS-1, RoB 2, RoBANS), and GRADE-assessed certainty of evidence. Random-effects meta-analyses pooled outcomes, stratified by time post-injury (pre-operative, 3-6 months, 7-12 months, > 1-2 years, > 2-5 years, > 5 years). Results Seventy-three studies (70% high RoB) were included (study outcomes: TSK: 55; KSES: 22; FABQ: 5). Meta-analysis demonstrated worse kinesiophobia and self-efficacy pre-operatively (pooled mean [95% CI], TSK-11: 23.8 [22.2-25.3]; KSES: 5.0 [4.4-5.5]) compared with 3-6 months following ACLR (TSK-11: 19.6 [18.7-20.6]; KSES: 19.6 [18.6-20.6]). Meta-analysis suggests similar kinesiophobia > 3-6 months following early ACLR (19.8 [4.9]) versus delayed ACLR (17.2 [5.0]). Only one study assessed outcomes comparing ACLR with rehabilitation only. Conclusions Knee self-efficacy and kinesiophobia improved from pre-ACLR to 3-6 months following ACLR, with similar outcomes after 6 months. Since the overall evidence was weak, there is a need for high-quality observational and intervention studies focusing on psychological outcomes following ACL injury.
|
|
| 4. |
- Cederwall, B., et al.
(author)
-
Isospin Properties of Nuclear Pair Correlations from the Level Structure of the Self-Conjugate Nucleus Ru-88
- 2020
-
In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 124:6
-
Journal article (peer-reviewed)abstract
- The low-lying energy spectrum of the extremely neutron-deficient self-conjugate (N = Z) nuclide Ru-88(44)44 has been measured using the combination of the Advanced Gamma Tracking Array (AGATA) spectrometer, the NEDA and Neutron Wall neutron detector arrays, and the DIAMANT charged particle detector array. Excited states in Ru-88 were populated via the Fe-54(Ar-36, 2n gamma)Ru-88* fusion-evaporation reaction at the Grand Accelerateur National d'Ions Lourds (GANIL) accelerator complex. The observed gamma-ray cascade is assigned to Ru-88 using clean prompt gamma-gamma-2-neutron coincidences in anticoincidence with the detection of charged particles, confirming and extending the previously assigned sequence of low-lying excited states. It is consistent with a moderately deformed rotating system exhibiting a band crossing at a rotational frequency that is significantly higher than standard theoretical predictions with isovector pairing, as well as observations in neighboring N > Z nuclides. The direct observation of such a "delayed" rotational alignment in a deformed N = Z nucleus is in agreement with theoretical predictions related to the presence of strong isoscalar neutron-proton pair correlations.
|
|
| 5. |
- Cederwall, Bo, 1964-, et al.
(author)
-
Isospin Properties of Nuclear Pair Correlations from the Level Structure of the Self-Conjugate Nucleus Ru 88
- 2020
-
In: Physical Review Letters. - : American Physical Society (APS). - 0031-9007 .- 1079-7114. ; 124:6
-
Journal article (peer-reviewed)abstract
- The low-lying energy spectrum of the extremely neutron-deficient self-conjugate (N = Z) nuclide 88Ru has been measured using the combination of the Advanced Gamma Tracking Array (AGATA)spectrometer, the NEDA, and Neutron Wall neutron detector arrays, and the DIAMANT charged particle detector array. Excited states in 88 Ru were populated via the 54 Feð 36 Ar; 2nγÞ 88 Ru fusion-evaporationreaction at the Grand Accélérateur National d’Ions Lourds (GANIL) accelerator complex. The observed γ-ray cascade is assigned to 88 Ru using clean prompt γ-γ-2-neutron coincidences in anticoincidence with the detection of charged particles, confirming and extending the previously assigned sequence of low-lying excited states. It is consistent with a moderately deformed rotating system exhibiting a band crossing at a rotational frequency that is significantly higher than standard theoretical predictions with isovector pairing, as well as observations in neighboring N > Z nuclides. The direct observation of such a “delayed” rotational alignment in a deformed N 1⁄4 Z nucleus is in agreement with theoretical predictions related to the presence of strong isoscalar neutron-proton pair correlations.
|
|
| 6. |
- Ciemala, M., et al.
(author)
-
Testing ab initio nuclear structure in neutron-rich nuclei : Lifetime measurements of second 2(+) state in C-16 and O-20
- 2020
-
In: Physical Review C. - : AMER PHYSICAL SOC. - 2469-9985 .- 2469-9993. ; 101:2
-
Journal article (peer-reviewed)abstract
- To test the predictive power of ab initio nuclear structure theory, the lifetime of the second 2(+) state in neutron-rich O-20, tau(2(2)(+)) = 150(-30)(+80) fs, and an estimate for the lifetime of the second 2(+) state in C-16 have been obtained for the first time. The results were achieved via a novel Monte Carlo technique that allowed us to measure nuclear state lifetimes in the tens-to-hundreds of femtoseconds range by analyzing the Doppler-shifted gamma-transition line shapes of products of low-energy transfer and deep-inelastic processes in the reaction O-18 (7.0 MeV/u) + Ta-181. The requested sensitivity could only be reached owing to the excellent performances of the Advanced gamma-Tracking Array AGATA, coupled to the PARIS scintillator array and to the VAMOS++ magnetic spectrometer. The experimental lifetimes agree with predictions of ab initio calculations using two- and three-nucleon interactions, obtained with the valence-space in-medium similarity renormalization group for O-20 and with the no-core shell model for C-16. The present measurement shows the power of electromagnetic observables, determined with high-precision gamma spectroscopy, to assess the quality of first-principles nuclear structure calculations, complementing common benchmarks based on nuclear energies. The proposed experimental approach will be essential for short lifetime measurements in unexplored regions of the nuclear chart, including r-process nuclei, when intense beams, produced by Isotope Separation On-Line (ISOL) techniques, become available.
|
|
| 7. |
- Crespi, F. C. L., et al.
(author)
-
Isospin Character of Low-Lying Pygmy Dipole States in Pb-208 via Inelastic Scattering of O-17 Ions
- 2014
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 113:1, s. 012501-
-
Journal article (peer-reviewed)abstract
- The properties of pygmy dipole states in Pb-208 were investigated using the Pb-208(O-17, O-17'gamma) reaction at 340 MeV and measuring the gamma decay with high resolution with the AGATA demonstrator array. Cross sections and angular distributions of the emitted gamma rays and of the scattered particles were measured. The results are compared with (gamma, gamma') and (p, p') data. The data analysis with the distorted wave Born approximation approach gives a good description of the elastic scattering and of the inelastic excitation of the 2(+) and 3(-) states. For the dipole transitions a form factor obtained by folding a microscopically calculated transition density was used for the first time. This has allowed us to extract the isoscalar component of the 1(-) excited states from 4 to 8 MeV.
|
|
| 8. |
- Delafosse, C., et al.
(author)
-
Pseudospin Symmetry and Microscopic Origin of Shape Coexistence in the Ni-78 Region : A Hint from Lifetime Measurements
- 2018
-
In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 121:19
-
Journal article (peer-reviewed)abstract
- Lifetime measurements of excited states of the light N = 52 isotones Kr-88, Se-86, and Ge-84 have been performed, using the recoil distance Doppler shift method and VAMOS and AGATA spectrometers for particle identification and gamma spectroscopy, respectively. The reduced electric quadrupole transition probabilities B(E2; 2(+)-> 0(+)) and B(E2; 4(+)-> 2(+)) were obtained for the first time for the hard-to-reach 84Ge. While the B(E2; 2(+)-> 0(+) ) values of Kr-88, Se-86 saturate the maximum quadrupole collectivity offered by the natural valence (3s, 2d, 1g(7/2), 1h(11/2)) space of an inert Ni-78 core, the value obtained for Ge-84 largely exceeds it, suggesting that shape coexistence phenomena, previously reported at N less than or similar to 49, extend beyond N = 50. The onset of collectivity at Z = 32 is understood as due to a pseudo-SU(3) organization of the proton single-particle sequence reflecting a clear manifestation of pseudospin symmetry. It is realized that the latter provides actually reliable guidance for understanding the observed proton and neutron single particle structure in the whole medium-mass region, from Ni to Sn, pointing towards the important role of the isovector-vector rho field in shell-structure evolution.
|
|
| 9. |
- Hadynska-Klek, K., et al.
(author)
-
Quadrupole collectivity in Ca-42 from low-energy Coulomb excitation with AGATA
- 2018
-
In: Physical Review C. - : AMER PHYSICAL SOC. - 2469-9985 .- 2469-9993. ; 97:2
-
Journal article (peer-reviewed)abstract
- ACoulomb-excitation experiment to study electromagnetic properties of Ca-42 was performed using a 170-MeV calcium beam from the TANDEM XPU facility at INFN Laboratori Nazionali di Legnaro. gamma rays from excited states in Ca-42 were measured with the AGATA spectrometer. The magnitudes and relative signs of ten E2 matrix elements coupling six low-lying states in Ca-42, including the diagonal E2 matrix elements of 2(1)(+) and 2(2)(+) states, were determined using the least-squares code GOSIA. The obtained set of reduced E2 matrix elements was analyzed using the quadrupole sum rule method and yielded overall quadrupole deformation for 0(1),(+)(2) and 2(1,2)(+) states, as well as triaxiality for 0(1,2)(+) states, establishing the coexistence of a weakly deformed ground-state band and highly deformed slightly triaxial sideband in Ca-42. The experimental results were compared with the state-of-the-art large-scale shell-model and beyond-mean-field calculations, which reproduce well the general picture of shape coexistence in Ca-42.
|
|
| 10. |
- Hadynska-Klek, K., et al.
(author)
-
Superdeformed and Triaxial States in Ca-42
- 2016
-
In: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 117:6
-
Journal article (peer-reviewed)abstract
- Shape parameters of a weakly deformed ground-state band and highly deformed slightly triaxial sideband in Ca-42 were determined from E2 matrix elements measured in the first low-energy Coulomb excitation experiment performed with AGATA. The picture of two coexisting structures is well reproduced by new state-of-the-art large-scale shell model and beyond-mean-field calculations. Experimental evidence for superdeformation of the band built on 0(2)(+) has been obtained and the role of triaxiality in the A similar to 40 mass region is discussed. Furthermore, the potential of Coulomb excitation as a tool to study superdeformation has been demonstrated for the first time.
|
|
