7,164 research outputs found
Pollution-induced community tolerance in freshwater biofilms – from molecular mechanisms to loss of community functions
Exposure to herbicides poses a threat to aquatic biofilms by affecting their community structure, physiology and function. These changes render biofilms to become more tolerant, but on the downside community tolerance has ecologic costs. A concept that addresses induced community tolerance to a pollutant (PICT) was introduced by Blanck and Wängberg (1988). The basic principle of the concept is that microbial communities undergo pollution-induced succession when exposed to a pollutant over a long period of time, which changes communities structurally and functionally and enhancing tolerance to the pollutant exposure. However, the mechanisms of tolerance and the ecologic consequences were hardly studied up to date. This thesis addresses the structural and functional changes in biofilm communities and applies modern molecular methods to unravel molecular tolerance mechanisms.
Two different freshwater biofilm communities were cultivated for a period of five weeks, with one of the communities being contaminated with 4 μg L-1 diuron. Subsequently, the communities were characterized for structural and functional differences, especially focusing on their crucial role of photosynthesis. The community structure of the autotrophs was assessed using HPLC-based pigment analysis and their functional alterations were investigated using Imaging-PAM fluorometry to study photosynthesis and community oxygen profiling to determine net primary production. Then, the molecular fingerprints of the communities were measured with meta-transcriptomics (RNA-Seq) and GC-based community metabolomics approaches and analyzed with respect to changes in their molecular functions. The communities were acute exposed to diuron for one hour in a dose-response design, to reveal a potential PICT and uncover related adaptation to diuron exposure. The combination of apical and molecular methods in a dose-response design enabled the linkage of functional effects of diuron exposure and underlying molecular mechanisms based on a sensitivity analysis.
Chronic exposure to diuron impaired freshwater biofilms in their biomass accrual. The contaminated communities particularly lost autotrophic biomass, reflected by the decrease in specific chlorophyll a content. This loss was associated with a change in the molecular fingerprint of the communities, which substantiates structural and physiological changes. The decline in autotrophic biomass could be due to a primary loss of sensitive autotrophic organisms caused by the selection of better adapted species in the course of chronic exposure. Related to this hypothesis, an increase in diuron tolerance has been detected in the contaminated communities and molecular mechanisms facilitating tolerance have been found. It was shown that genes of the photosystem, reductive-pentose phosphate cycle and arginine metabolism were differentially expressed among the communities and that an increased amount of potential antioxidant degradation products was found in the contaminated communities. This led to the hypothesis that contaminated communities may have adapted to oxidative stress, making them less sensitive to diuron exposure. Moreover, the photosynthetic light harvesting complex was altered and the photoprotective xanthophyll cycle was increased in the contaminated communities. Despite these adaptation strategies, the loss of autotrophic biomass has been shown to impair primary production. This impairment persisted even under repeated short-term exposure, so that the tolerance mechanisms cannot safeguard primary production as a key function in aquatic systems.:1. The effect of chemicals on organisms and their functions .............................. 1
1.1 Welcome to the anthropocene .......................................................................... 1
1.2 From cellular stress responses to ecosystem resilience ................................... 3
1.2.1 The individual pursuit for homeostasis ....................................................... 3
1.2.2 Stability from diversity ................................................................................. 5
1.3 Community ecotoxicology - a step forward in monitoring the effects of chemical
pollution? ................................................................................................................. 6
1.4 Functional ecotoxicological assessment of microbial communities ................... 9
1.5 Molecular tools – the key to a mechanistic understanding of stressor effects
from a functional perspective in microbial communities? ...................................... 12
2. Aims and Hypothesis ......................................................................................... 14
2.1 Research question .......................................................................................... 14
2.2 Hypothesis and outline .................................................................................... 15
2.3 Experimental approach & concept .................................................................. 16
2.3.1 Aquatic freshwater biofilms as model community ..................................... 16
2.3.2 Diuron as model herbicide ........................................................................ 17
2.3.3 Experimental design ................................................................................. 18
3. Structural and physiological changes in microbial communities after chronic
exposure - PICT and altered functional capacity ................................................. 21
3.1 Introduction ..................................................................................................... 21
3.2 Methods .......................................................................................................... 23
3.2.1 Biofilm cultivation ...................................................................................... 23
3.2.2 Dry weight and autotrophic index ............................................................. 23
3.2.4 Pigment analysis of periphyton ................................................................. 23
3.2.4.1 In-vivo pigment analysis for community characterization ....................... 24
3.2.4.2 In-vivo pigment analysis based on Imaging-PAM fluorometry ............... 24
3.2.4.3 In-vivo pigment fluorescence for tolerance detection ............................. 26
3.2.4.4 Ex-vivo pigment analysis by high-pressure liquid-chromatography ....... 27
3.2.5 Community oxygen metabolism measurements ....................................... 28
3.3 Results and discussion ................................................................................... 29
3.3.1 Comparison of the structural community parameters ............................... 29
3.3.2 Photosynthetic activity and primary production of the communities after
selection phase ................................................................................................. 33
3.3.3 Acquisition of photosynthetic tolerance .................................................... 34
3.3.4 Primary production at exposure conditions ............................................... 36
3.3.5 Tolerance detection in primary production ................................................ 37
3.4 Summary and Conclusion ........................................................................... 40
4. Community gene expression analysis by meta-transcriptomics ................... 41
4.1 Introduction to meta-transcriptomics ............................................................... 41
4.2. Methods ......................................................................................................... 43
4.2.1 Sampling and RNA extraction................................................................... 43
4.2.2 RNA sequencing analysis ......................................................................... 44
4.2.3 Data assembly and processing................................................................. 45
4.2.4 Prioritization of contigs and annotation ..................................................... 47
4.2.5 Sensitivity analysis of biological processes .............................................. 48
4.3 Results and discussion ................................................................................... 48
4.3.1 Characterization of the meta-transcriptomic fingerprints .......................... 49
4.3.2 Insights into community stress response mechanisms using trend analysis
(DRomic’s) ......................................................................................................... 51
4.3.3 Response pattern in the isoform PS genes .............................................. 63
4.5 Summary and conclusion ................................................................................ 65
5. Community metabolome analysis ..................................................................... 66
5.1 Introduction to community metabolomics ........................................................ 66
5.2 Methods .......................................................................................................... 68
5.2.1 Sampling, metabolite extraction and derivatisation................................... 68
5.2.2 GC-TOF-MS analysis ............................................................................... 69
5.2.3 Data processing and statistical analysis ................................................... 69
5.3 Results and discussion ................................................................................... 70
5.3.1 Characterization of the metabolic fingerprints .......................................... 70
5.3.2 Difference in the metabolic fingerprints .................................................... 71
5.3.3 Differential metabolic responses of the communities to short-term exposure
of diuron ............................................................................................................ 73
5.4 Summary and conclusion ................................................................................ 78
6. Synthesis ............................................................................................................. 79
6.1 Approaches and challenges for linking molecular data to functional
measurements ...................................................................................................... 79
6.2 Methods .......................................................................................................... 83
6.2.1 Summary on the data ............................................................................... 83
6.2.2 Aggregation of molecular data to index values (TELI and MELI) .............. 83
6.2.3 Functional annotation of contigs and metabolites using KEGG ................ 83
6.3 Results and discussion ................................................................................... 85
6.3.1 Results of aggregation techniques ........................................................... 85
6.3.2 Sensitivity analysis of the different molecular approaches and endpoints 86
6.3.3 Mechanistic view of the molecular stress responses based on KEGG
functions ............................................................................................................ 89
6.4 Consolidation of the results – holistic interpretation and discussion ............... 93
6.4.1 Adaptation to chronic diuron exposure - from molecular changes to
community effects.............................................................................................. 93
6.4.2 Assessment of the ecological costs of Pollution-induced community
tolerance based on primary production ............................................................. 94
6.5 Outlook ............................................................................................................ 9
Coincidental Generation
Generative AI models are emerging as a versatile tool across diverse
industries with applications in synthetic data generation computational art
personalization of products and services and immersive entertainment Here we
introduce a new privacy concern in the adoption and use of generative AI models
that of coincidental generation Coincidental generation occurs when a models
output inadvertently bears a likeness to a realworld entity Consider for
example synthetic portrait generators which are today deployed in commercial
applications such as virtual modeling agencies and synthetic stock photography
We argue that the low intrinsic dimensionality of human face perception implies
that every synthetically generated face will coincidentally resemble an actual
person all but guaranteeing a privacy violation in the form of a
misappropriation of likeness
Hi4D: 4D Instance Segmentation of Close Human Interaction
We propose Hi4D, a method and dataset for the automatic analysis of
physically close human-human interaction under prolonged contact. Robustly
disentangling several in-contact subjects is a challenging task due to
occlusions and complex shapes. Hence, existing multi-view systems typically
fuse 3D surfaces of close subjects into a single, connected mesh. To address
this issue we leverage i) individually fitted neural implicit avatars; ii) an
alternating optimization scheme that refines pose and surface through periods
of close proximity; and iii) thus segment the fused raw scans into individual
instances. From these instances we compile Hi4D dataset of 4D textured scans of
20 subject pairs, 100 sequences, and a total of more than 11K frames. Hi4D
contains rich interaction-centric annotations in 2D and 3D alongside accurately
registered parametric body models. We define varied human pose and shape
estimation tasks on this dataset and provide results from state-of-the-art
methods on these benchmarks.Comment: Project page: https://yifeiyin04.github.io/Hi4D
Central-provincial Politics and Industrial Policy-making in the Electric Power Sector in China
In addition to the studies that provide meaningful insights into the complexity of technical and economic issues, increasing studies have focused on the political process of market transition in network industries such as the electric power sector. This dissertation studies the central–provincial interactions in industrial policy-making and implementation, and attempts to evaluate the roles of Chinese provinces in the market reform process of the electric power sector. Market reforms of this sector are used as an illustrative case because the new round of market reforms had achieved some significant breakthroughs in areas such as pricing reform and wholesale market trading. Other policy measures, such as the liberalization of the distribution market and cross-regional market-building, are still at a nascent stage and have only scored moderate progress. It is important to investigate why some policy areas make greater progress in market reforms than others. It is also interesting to examine the impacts of Chinese central-provincial politics on producing the different market reform outcomes. Guangdong and Xinjiang are two provinces being analyzed in this dissertation. The progress of market reforms in these two provinces showed similarities although the provinces are very different in terms of local conditions such as the stages of their economic development and energy structures. The actual reform can be understood as the outcomes of certain modes of interactions between the central and provincial actors in the context of their particular capabilities and preferences in different policy areas. This dissertation argues that market reform is more successful in policy areas where the central and provincial authorities are able to engage mainly in integrative negotiations than in areas where they engage mainly in distributive negotiations
Examples of works to practice staccato technique in clarinet instrument
Klarnetin staccato tekniğini güçlendirme aşamaları eser çalışmalarıyla uygulanmıştır. Staccato
geçişlerini hızlandıracak ritim ve nüans çalışmalarına yer verilmiştir. Çalışmanın en önemli amacı
sadece staccato çalışması değil parmak-dilin eş zamanlı uyumunun hassasiyeti üzerinde de
durulmasıdır. Staccato çalışmalarını daha verimli hale getirmek için eser çalışmasının içinde etüt
çalışmasına da yer verilmiştir. Çalışmaların üzerinde titizlikle durulması staccato çalışmasının ilham
verici etkisi ile müzikal kimliğe yeni bir boyut kazandırmıştır. Sekiz özgün eser çalışmasının her
aşaması anlatılmıştır. Her aşamanın bir sonraki performans ve tekniği güçlendirmesi esas alınmıştır.
Bu çalışmada staccato tekniğinin hangi alanlarda kullanıldığı, nasıl sonuçlar elde edildiği bilgisine
yer verilmiştir. Notaların parmak ve dil uyumu ile nasıl şekilleneceği ve nasıl bir çalışma disiplini
içinde gerçekleşeceği planlanmıştır. Kamış-nota-diyafram-parmak-dil-nüans ve disiplin
kavramlarının staccato tekniğinde ayrılmaz bir bütün olduğu saptanmıştır. Araştırmada literatür
taraması yapılarak staccato ile ilgili çalışmalar taranmıştır. Tarama sonucunda klarnet tekniğin de
kullanılan staccato eser çalışmasının az olduğu tespit edilmiştir. Metot taramasında da etüt
çalışmasının daha çok olduğu saptanmıştır. Böylelikle klarnetin staccato tekniğini hızlandırma ve
güçlendirme çalışmaları sunulmuştur. Staccato etüt çalışmaları yapılırken, araya eser çalışmasının
girmesi beyni rahatlattığı ve istekliliği daha arttırdığı gözlemlenmiştir. Staccato çalışmasını yaparken
doğru bir kamış seçimi üzerinde de durulmuştur. Staccato tekniğini doğru çalışmak için doğru bir
kamışın dil hızını arttırdığı saptanmıştır. Doğru bir kamış seçimi kamıştan rahat ses çıkmasına
bağlıdır. Kamış, dil atma gücünü vermiyorsa daha doğru bir kamış seçiminin yapılması gerekliliği
vurgulanmıştır. Staccato çalışmalarında baştan sona bir eseri yorumlamak zor olabilir. Bu açıdan
çalışma, verilen müzikal nüanslara uymanın, dil atış performansını rahatlattığını ortaya koymuştur.
Gelecek nesillere edinilen bilgi ve birikimlerin aktarılması ve geliştirici olması teşvik edilmiştir.
Çıkacak eserlerin nasıl çözüleceği, staccato tekniğinin nasıl üstesinden gelinebileceği anlatılmıştır.
Staccato tekniğinin daha kısa sürede çözüme kavuşturulması amaç edinilmiştir. Parmakların
yerlerini öğrettiğimiz kadar belleğimize de çalışmaların kaydedilmesi önemlidir. Gösterilen azmin ve
sabrın sonucu olarak ortaya çıkan yapıt başarıyı daha da yukarı seviyelere çıkaracaktır
A scalable solution for the extended multi-channel facility location problem
We study the extended version of the non-uniform, capacitated facility
location problem with multiple fulfilment channels between the facilities and
clients, each with their own channel capacities and service cost. Though the
problem has been extensively studied in the literature, all the prior works
assume a single channel of fulfilment, and the existing methods based on linear
programming, primal-dual relationships, local search heuristics etc. do not
scale for a large supply chain system involving millions of decision variables.
Using the concepts of sub-modularity and optimal transport theory, we present a
scalable algorithm for determining the set of facilities to be opened under a
cardinality constraint. By introducing various schemes such as: (i) iterative
facility selection using incremental gain, (ii) approximation of the linear
program using novel multi-stage Sinkhorn iterations, (iii) creation of
facilities one for each fulfilment channel etc., we develop a fast but a tight
approximate solution, requiring
instances of optimal transport problems to select k facilities from m options,
each solvable in linear time. Our algorithm is implicitly endowed with all the
theoretical guarantees enjoyed by submodular maximisation problems and the
Sinkhorn distances. When compared against the state-of-the-art commercial MILP
solvers, we obtain a 100-fold speedup in computation, while the difference in
objective values lies within a narrow range of 3%
The cosmic waltz of Coma Berenices and Latyshev 2 (Group X). Membership, phase-space structure, mass, and energy distributions
Context. Open clusters (OCs) are fundamental benchmarks where theories of
star formation and stellar evolution can be tested and validated. Coma Ber and
Latyshev 2 (Group X) are the second and third OCs closest to the Sun, making
them excellent targets to search for low-mass stars and ultra-cool dwarfs. In
addition, this pair will experience a flyby in 10-16 Myr which makes it a
benchmark to test OCs pair interactions. Aims. We aim at analysing the
membership, luminosity, mass, phase-space (i.e., positions and velocities), and
energy distributions for Coma Ber and Latyshev 2 and test the hypothesis of the
mixing of their populations at the encounter time. Methods. We develop a new
phase-space membership methodology and apply it to Gaia data. With the
recovered members we infer the phase-space, luminosity and mass distributions
using publicly available Bayesian inference codes. Then, with a publicly
available orbit integration code and members' positions and velocities, we
integrate their orbits 20 Myr into the future. Results. In Coma Ber, we
identify 302 candidate members distributed in the core and tidal tails. The
tails are dynamically cold and asymmetrically populated. The stellar system
called Group X is made of two structures: the disrupted OC Latyshev 2 (186
candidate members) and a loose stellar association called Mecayotl 1 (146
candidate members), both of them will fly by Coma Ber in Myr and
Myr, respectively, and each other in Myr. Conclusions.
We study the dynamical properties of the core and tails of Coma Ber and also
confirm the existence of the OC Latyshev 2 and its neighbour stellar
association Mecayotl 1. Although these three systems will experience encounters
we find no evidence supporting the mixing of their populations.Comment: 25 pages, 19 figures, accepted for publication in Astronomy &
Astrophysic
Evaluation of DNA extraction methods and direct PCR in metabarcoding of mock and marine bacterial communities
Recent advances in new molecular biology methods and next-generation sequencing (NGS) technologies have revolutionized metabarcoding studies investigating complex microbial communities from various environments. The inevitable first step in sample preparation is DNA extraction which introduces its own set of biases and considerations. In this study, we assessed the influence of five DNA extraction methods [B1: phenol/chloroform/isoamyl extraction, B2 and B3: isopropanol and ethanol precipitations, respectively—both modifications of B1, K1: DNeasy PowerWater Kit (QIAGEN), K2: modified DNeasy PowerWater Kit (QIAGEN) and direct PCR approach (P) that completely circumvents this step on community composition and DNA yield of mock and marine sample communities from the Adriatic Sea]. B1–B3 methods generally produced higher DNA yields and more similar microbial communities, but with higher interindividual variability. Each method demonstrated significant differences in a specific community structure, where rare taxa seem to play a crucial role. There was not one superior method closest to the theoretically expected mock community composition, they all demonstrated skewed ratios, but in a similar way which might be attributed to other factors, such as primer bias or 16S rRNA gene count for specific taxa. Direct PCR represents an interesting approach when high throughput in sample processing is required. We emphasize the importance of making a cautious decision about the choice of the extraction method or direct PCR approach, but even more importantly its consistent application throughout the study
Innate immunity and metabolism in the bovine ovarian follicle
Postpartum uterine disease in dairy cows is associated with reduced fertility. One of the first and most prevalent bacteria associated with uterine disease is Escherichia coli. The bacterial endotoxin, lipopolysaccharide (LPS), accumulates in the ovarian follicular fluid of animals with uterine disease. The granulosa cells of the ovarian follicle respond to LPS by secreting pro-inflammatory cytokines, such as interleukin (IL)-1a, IL-1b and IL-8, and oocyte health is perturbed. Dairy cows also experience metabolic energy stress in the postpartum period, which is associated with an increased risk of developing uterine disease and ovarian dysfunction. This thesis explored the crosstalk between innate immunity and metabolic energy stress in bovine granulosa cells and cumulus-oocyte complex. Firstly, we found that glycolysis, AMP-activated protein kinase and the mechanistic target of rapamycin, regulate the innate immune responses to LPS in granulosa cells isolated from bovine ovarian follicles. Activation of AMP-activated protein kinase decreased the LPS-induced secretion of IL-1a, IL-1b, and IL8, and was associated with shortened duration of ERK1/2 and JNK phosphorylation. Next, we found that decreasing the availability of cholesterol or inhibiting cholesterol biosynthesis using short-interfering RNA impaired the LPS-induced secretion of IL-1a and IL-1b by granulosa cells. Furthermore, metabolic energy stress or inhibiting cholesterol biosynthesis in the bovine cumulus-oocyte complex modulated the innate immune responses to LPS, and perturbed meiotic progression during in vitro maturation. Finally, we explored an in vivo model of uterine disease in heifers, using RNAseq to investigate alterations to the transcriptome of the reproductive tract. We found that uterine disease altered the transcriptome of the endometrium, oviduct, granulosa cells and oocyte, several months after bacterial infusion; these changes were most evident in the granulosa cells and oocyte of the ovarian follicle. The findings from this thesis imply that there is crosstalk between innate immunity and metabolism in the bovine ovarian follicle
High stakes online assessments: A case study of National Benchmark Tests during COVID-19
Owing to the COVID-19 pandemic, paper-based delivery of the National Benchmark Tests (NBTs) was not possible during the 2020 testing cycle. The NBTs, being a large-scale national assessment project, did not have alternative options, other than to offer the tests online. Moving these high-stakes tests online meant that certain considerations had to be considered to retain the credibility and security of the tests, without compromising the validity and reliability of the scores. Digitising the paper-based NBTs required an innovative, flexible and robust solution, which promotes fairness and ensures the quality of testing is maintained, while in many ways remains comparable to the paper-based implementation. To deliver the NBTs online, the following important considerations needed to be addressed: test security and integrity, test candidate identification processes, the prevention of dishonest behaviour, test scheduling and timing and technical support. The online testing solution chosen integrates the following aspects: it 1) enables all candidates to take the same test at the same time; 2) ensures the quality and similarity in experience of test delivery for all candidates as far as possible; 3) prevents candidates from accessing other applications and devices during the test; 4) enables proctoring before, during and after the tests to encourage appropriate behaviour similar to that expected during paper-based tests; 5) provides live support to assist candidates to deal with technical challenges and to guide them through the test sessions and 6) processes and presents data and scores in the same way as for the paper-based tests. In this article, we analyse the integration and complexity of the online NBTs solution, the opportunities and challenges associated with this form of delivery and reflect on test candidates’ and the team’s experiences. We discuss components of online assessment and wish to argue that this is also relevant to high-stakes course assessments. This case study should help to refine the scope of further research and development in the use of online high-stakes assessments
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