| 171. |
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| 172. |
- Aarrestad, Thea, et al.
(author)
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Benchmark data and model independent event classification for the large hadron collider
- 2022
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In: SciPost Physics. - 2542-4653. ; 12:1
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Journal article (peer-reviewed)abstract
- We describe the outcome of a data challenge conducted as part of the Dark Machines (https://www.darkmachines.org) initiative and the Les Houches 2019 workshop on Physics at TeV colliders. The challenged aims to detect signals of new physics at the Large Hadron Collider (LHC) using unsupervised machine learning algorithms. First, we propose how an anomaly score could be implemented to define model-independent signal regions in LHC searches. We define and describe a large benchmark dataset, consisting of > 1 billion simulated LHC events corresponding to 10 fb−1 of proton-proton collisions at a center-of-mass energy of 13 TeV. We then review a wide range of anomaly detection and density estimation algorithms, developed in the context of the data challenge, and we measure their performance in a set of realistic analysis environments. We draw a number of useful conclusions that will aid the development of unsupervised new physics searches during the third run of the LHC, and provide our benchmark dataset for future studies at https://www.phenoMLdata.org. Code to reproduce the analysis is provided at https://github.com/bostdiek/DarkMachines-UnsupervisedChallenge.
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| 173. |
- Aartolahti, Eeva, et al.
(author)
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Perceived opportunities for physical activity and willingness to be more active in older adults with different physical activity levels
- 2021
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In: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 18:11
-
Journal article (peer-reviewed)abstract
- This study examined equity in physical activity (PA) by investigating whether perceived opportunity for PA was associated with willingness to be more active. Among community residents (75, 80, or 85 years old, n = 962) perceived opportunity for PA (poor and good), willingness to be more active (not at all, a bit, and a lot), and level of PA (low, moderate, and high) were assessed via questionnaires. Multinomial logistic regression showed that physical activity moderated the association between poor opportunity and willingness to increase PA. Among those with moderate PA, poor opportunity for PA increased the odds of willingness to be a lot more active (multinomial odds ratio, mOR 3.90, 95% confidence interval 2.21–6.87) than not wanting to be more active compared to those perceiving good opportunities. Associations were similar at high PA levels (p < 0.001), but were not found at low PA levels. Those with moderate or high PA wish to increase their activity particularly when the perceived opportunities for activity are not optimal. Among those with low PA, perceived opportunities are not associated with a perceived need to increase physical activity. Increasing equity in physical activity in old age requires provision of support and opportunities at every level of physical activity.
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| 174. |
- Aastrup, Christian, et al.
(author)
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Jackdaw nestlings rapidly increase innate immune function during the nestling phase but no evidence for a trade-off with growth
- 2021
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In: Developmental and Comparative Immunology. - : Elsevier BV. - 0145-305X. ; 117
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Journal article (peer-reviewed)abstract
- Although animals are born with a protective immune system, even the innate immune system is under development from birth to adulthood and this development may be affected by sex and growth. However, most knowledge comes from captive animals or long-lived slow growing species. Moreover, little is known about how innate immune function, the important first line of defence, develops during early life in fast-growing animals such as free-living passerines. We studied development of innate baseline immune function in nestlings of free-living jackdaws Corvus monedula. We measured four immune parameters (hemolysis, hemagglutination, bacterial-killing capacity, haptoglobin concentration) and structural body size (body mass, wing length, tarsus length) at day 12 and day 29 post-hatching. We found that three out of four immune parameters (hemolysis, hemagglutination, bacterial-killing capacity) substantially increased with nestling age and had roughly reached adult levels shortly prior to fledging. We found little differences in immune development between males and females despite them differing in structural development. We also found no evidence that the nestlings traded off immune development with growth. That nestlings rapidly increase innate baseline immune function during early life and similarly in males and females indicates the importance of a well-functioning immune system already during the nestling phase.
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| 175. |
- Aastrup, Christian, et al.
(author)
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Size and immune function as predictors of predation risk in nestling and newly fledged jackdaws
- 2023
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In: Animal Behaviour. - : Elsevier BV. - 0003-3472. ; 198, s. 73-84
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Journal article (peer-reviewed)abstract
- Prey choice by predators may be based on the potential prey's condition, for example resulting in substandard individuals running a higher risk of being predated. Over 5 years, we studied young jackdaws, Corvus monedula, to determine whether size and innate baseline immune function may predict predation risk by goshawks, Accipiter gentilis, during the nestling and early fledging phases. We measured body mass, wing length, tarsus length and four innate immune indices two to four times when nestlings were 12–29 days old. To determine which individuals had been predated during the nestling phase and shortly after fledging, we searched for metal rings of the jackdaws in the only goshawk territory close to the jackdaw colony. Nestling mortality before 12 days of age was entirely due to starvation, whereas between 12 days of age and fledging, mortality was mainly due to predation. Nestlings with smaller size (mass, wing, tarsus) and low lysis titre and haptoglobin concentrations were at a higher risk of being predated before fledging. Directly after fledging, individuals with short wings were preferentially predated, with no effects of body mass, tarsus length or any of the four immune indices measured at day 29 (i.e. shortly before fledging). That lower immune function and smaller size predict predation risk in nestlings may reflect that these individuals are of poor quality and/or lag behind in development. We hypothesize that hunger makes these nestlings sit closest to the entrance hole and hence become the first to be predated. For fledglings, our results suggest that poor flight ability makes individuals with short wings the easiest targets for avian predators.
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| 176. |
- Aazami, J., et al.
(author)
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Evaluation of three environmental flow techniques in Shoor wetland of Golpayegan, Iran
- 2022
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In: International Journal of Environmental Science and Technology. - : Springer Science and Business Media LLC. - 1735-1472 .- 1735-2630. ; 19:8, s. 7885-7898
-
Journal article (peer-reviewed)abstract
- Shoor wetland, in south central Iran, is a unique ecosystem which plays an important role in maintaining stability of this eco-region. The most important function of Shoor is dust control. Environmental flow releases are a tool for wetland restoration, but their success has not been consistent. We utilized Justin (Watershed), Flow Duration Curve (FDC), and Water Resources Balance (WRB) methods to determine optimal environmental flow for Shoor wetland, which can help in its preservation. Data pertaining to Golpayegan River flow, reported by Chamesfand Hydrometric Station between 1985 and 2017 were used for FDC analysis. FDC results say that 60% of flow frequency occurrence in to Shoor is < 2 m3/s, and 20% is > 5 m3/s. Water resource balance analysis indicates that between May and November, environmental flow to Shoor is negative, and the wetland is in desiccation mode. Suggesting that, at this time, surface water charges are essential for health of the wetland. The average monthly environmental flow rate (l/s) for each method are as follows: Justin (1282), FDC (1397.5), and WRB (5373). Environmental flow assessed by WRB is the highest. To protect health of Shoor and prevent further degradation of this wetland, we recommend shutting down agricultural drains. This action will safeguard appropriate groundwater levels and protect areas of Shoor that are prone to dust creation. Better well water management will also help restore Shoor ecosystem. We highly recommend these measures.
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| 177. |
- Ababneh, Nidaa A., et al.
(author)
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Identification of APTX disease-causing mutation in two unrelated Jordanian families with cerebellar ataxia and sensitivity to DNA damaging agents
- 2020
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:8
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Journal article (peer-reviewed)abstract
- BACKGROUND: Ataxia with oculomotor apraxia type 1 (AOA1) is a rare autosomal recessive cerebellar ataxia, caused by mutations in the APTX gene. The disease is characterized by early-onset cerebellar ataxia, oculomotor apraxia and severe axonal polyneuropathy. The aim of this study was to detect the disease-causing variants in two unrelated consanguineous Jordanian families with cerebellar ataxia using whole exome sequencing (WES), and to correlate the identified mutation(s) with the clinical and cellular phenotypes. METHODS: WES was performed in three affected individuals and segregation analysis of p.W279* APTX candidate variant was performed. Expression levels of APTX were measured in patients' skin fibroblasts and peripheral blood mononuclear cells, followed by western blot analysis in skin fibroblasts. Genotoxicity assay was performed to detect the sensitivity of APTX mutated cells to H2O2, MMC, MMS and etoposide. RESULTS: A recurrent homozygous nonsense variant in APTX gene (c.837G>A, p.W279*) was revealed in all affected individuals. qRT-PCR showed normal APTX levels in peripheral blood and lower levels in fibroblast cells. However, western blot showed the absence of APTX protein in patients' skin fibroblasts. Significant hypersensitivity to H2O2, MMC and etoposide and lack of sensitivity to MMS were noted. CONCLUSIONS: This is the first study to report the identification of a nonsense variant in the APTX gene (c.837G>A; p.W279*) in AOA1 patients within the Jordanian population. This study confirmed the need of WES to assist in the diagnosis of cerebellar ataxia and it emphasizes the importance of studying the pathophysiology of the APTX gene.
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| 178. |
- Abalo, Kossi, et al.
(author)
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Secondary malignancies among mantle cell lymphoma patients
- 2023
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In: European Journal of Cancer. - : Elsevier. - 0959-8049 .- 1879-0852. ; 195
-
Journal article (peer-reviewed)abstract
- Purpose:With modern treatments, mantle cell lymphoma (MCL) patients more frequently experience long-lasting remission resulting in a growing population of long-term survivors. Follow-up care includes identification and management of treatment-related late-effects, such as secondary malignancies (SM). We conducted a populationbased study to describe the burden of SM in MCL patients.Methods:All patients with a primary diagnosis of MCL, aged >= 18 years and diagnosed between 2000 and 2017 in Sweden were included along with up to 10 individually matched population comparators. Follow-up was from twelve months after diagnosis/matching until death, emigration, or December 2019, whichever occurred first. Rates of SM among patients and comparators were estimated using the Anderson-Gill method (accounting for repeated events) and presented as hazard ratios (HR) with 95% confidence intervals (CI) adjusted for age at diagnosis, calendar year, sex, and the number of previous events.Results:Overall, 1 452 patients and 13 992 comparators were followed for 6.6 years on average. Among patients, 230 (16%) developed at least one SM, and 264 SM were observed. Relative to comparators, patients had a higher rate of SM, HRadj= 1.6 (95%CI:1.4-1.8), and higher rates were observed across all primary treatment groups: the Nordic-MCL2 protocol, R-CHOP, R-bendamustine, ibrutinib, lenalidomide, and R-CHOP/Cytarabine. Compared to Nordic-MCL2, treatment with R-bendamustine was independently associated with an increased risk of SM, HRadj= 2.0 (95%CI:1.3-3.2). Risk groups among patients were those with a higher age at diagnosis (p < 0.001), males (p = 0.006), and having a family history of lymphoma (p = 0.009). Patients had preferably higher risk of melanoma, other neoplasms of the skin and other hematopoietic and lymphoid malignancies.Conclusions:MCL survivors have an increased risk of SM, particularly if treated with R-bendamustine. The intensive treatments needed for long-term remissions are a concern, and transition to treatment protocols with sustained efficacy but with a lower risk of SM is needed.
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| 179. |
- Abalos, Javier, et al.
(author)
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No evidence for differential sociosexual behavior and space use in the color morphs of the European common wall lizard (Podarcis muralis)
- 2020
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10:20, s. 10986-11005
-
Journal article (peer-reviewed)abstract
- Explaining the evolutionary origin and maintenance of color polymorphisms is a major challenge in evolutionary biology. Such polymorphisms are commonly thought to reflect the existence of alternative behavioral or life-history strategies under negative frequency-dependent selection. The European common wall lizard Podarcis muralis exhibits a striking ventral color polymorphism that has been intensely studied and is often assumed to reflect alternative reproductive strategies, similar to the iconic “rock–paper–scissors” system described in the North American lizard Uta stansburiana. However, available studies so far have ignored central aspects in the behavioral ecology of this species that are crucial to assess the existence of alternative reproductive strategies. Here, we try to fill this gap by studying the social behavior, space use, and reproductive performance of lizards showing different color morphs, both in a free-ranging population from the eastern Pyrenees and in ten experimental mesocosm enclosures. In the natural population, we found no differences between morphs in site fidelity, space use, or male–female spatial overlap. Likewise, color morph was irrelevant to sociosexual behavior, space use, and reproductive success within experimental enclosures. Our results contradict the commonly held hypothesis that P. muralis morphs reflect alternative behavioral strategies, and suggest that we should instead turn our attention to alternative functional explanations.
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| 180. |
- Abalos, Javier, et al.
(author)
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Viability, behavior, and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs
- 2021
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In: Current Zoology. - : Oxford University Press (OUP). - 1674-5507 .- 2396-9814. ; 68:1, s. 41-55
-
Journal article (peer-reviewed)abstract
- Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.
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