@phdthesis{Brinkmann2024, author = {Brinkmann, Charlotte}, title = {Molecular characterisation of the Xanthomonas type III effector XopM}, doi = {10.25932/publishup-64898}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-648985}, school = {Universit{\"a}t Potsdam}, pages = {VII, 96}, year = {2024}, abstract = {Due to their sessile lifestyle, plants are constantly exposed to pathogens and possess a multi-layered immune system that prevents infection. The first layer of immunity called pattern-triggered immunity (PTI), enables plants to recognise highly conserved molecules that are present in pathogens, resulting in immunity from non-adaptive pathogens. Adapted pathogens interfere with PTI, however the second layer of plant immunity can recognise these virulence factors resulting in a constant evolutionary battle between plant and pathogen. Xanthomonas campestris pv. vesicatoria (Xcv) is the causal agent of bacterial leaf spot disease in tomato and pepper plants. Like many Gram-negative bacteria, Xcv possesses a type-III secretion system, which it uses to translocate type-III effectors (T3E) into plant cells. Xcv has over 30 T3Es that interfere with the immune response of the host and are important for successful infection. One such effector is the Xanthomonas outer protein M (XopM) that shows no similarity to any other known protein. Characterisation of XopM and its role in virulence was the focus of this work. While screening a tobacco cDNA library for potential host target proteins, the vesicle-associated membrane protein (VAMP)-associated protein 1-2 like (VAP12) was identified. The interaction between XopM and VAP12 was confirmed in the model species Nicotiana benthamiana and Arabidopsis as well as in tomato, a Xcv host. As plants possess multiple VAP proteins, it was determined that the interaction of XopM and VAP is isoform specific. It could be confirmed that the major sperm protein (MSP) domain of NtVAP12 is sufficient for binding XopM and that binding can be disrupted by substituting one amino acid (T47) within this domain. Most VAP interactors have at least one FFAT (two phenylalanines [FF] in an acidic tract) related motif, screening the amino acid sequence of XopM showed that XopM has two FFAT-related motifs. Substitution of the second residue of each FFAT motif (Y61/F91) disrupts NtVAP12 binding, suggesting that these motifs cooperatively mediate this interaction. Structural modelling using AlphaFold further confirmed that the unstructured N-terminus of XopM binds NtVAP12 at its MSP domain, which was further confirmed by the generation of truncated XopM variants. Infection of pepper leaves, with a XopM deficient Xcv strain did not result in a reduction of virulence in comparison to the Xcv wildtype, showing that the function of XopM during infection is redundant. Virus-induced gene silencing of NbVAP12 in N. benthamiana plants also did not affect Xcv virulence, which further indicated that interaction with VAP12 is also non-essential for Xcv virulence. Despite such findings, ectopic expression of wildtype XopM and XopMY61A/F91A in transgenic Arabidopsis seedlings enhanced the growth of a non-pathogenic Pseudomonas syringae pv. tomato (Pst) DC3000 strain. XopM was found to interfere with the PTI response allowing Pst growth independent of its binding to VAP. Furthermore, transiently expressed XopM could suppress reactive oxygen species (ROS; one of the earliest PTI responses) production in N. benthamiana leaves. The FFAT double mutant XopMY61A/F91A as well as the C-terminal truncation variant XopM106-519 could still suppress the ROS response while the N-terminal variant XopM1-105 did not. Suppression of ROS production is therefore independent of VAP binding. In addition, tagging the C-terminal variant of XopM with a nuclear localisation signal (NLS; NLS-XopM106-519) resulted in significantly higher ROS production than the membrane localising XopM106-519 variant, indicating that XopM-induced ROS suppression is localisation dependent. To further characterise XopM, mass spectrometry techniques were used to identify post-translational modifications (PTM) and potential interaction partners. PTM analysis revealed that XopM contains up to 21 phosphorylation sites, which could influence VAP binding. Furthermore, proteins of the Rab family were identified as potential plant protein interaction partners. Rab proteins serve a multitude of functions including vesicle trafficking and have been previously identified as T3E host targets. Taking this into account, a model of virulence of XopM was proposed, with XopM anchoring itself to VAP proteins to potentially access plasma membrane associated proteins. XopM possibly interferes with vesicle trafficking, which in turn suppresses ROS production through an unknown mechanism. In this work it was shown that XopM targets VAP proteins. The data collected suggests that this T3E uses VAP12 to anchor itself into the right place to carry out its function. While more work is needed to determine how XopM contributes to virulence of Xcv, this study sheds light onto how adapted pathogens overcome the immune response of their hosts. It is hoped that such knowledge will contribute to the development of crops resistant to Xcv in the future.}, language = {en} } @article{WittekToumaNitezkietal.2023, author = {Wittek, Laura and Touma, Chadi and Nitezki, Tina and Laeger, Thomas and Kr{\"a}mer, Stephanie and Raila, Jens}, title = {Reduction in cold stress in an innovative metabolic cage housing system increases animal welfare in laboratory mice}, series = {Animals}, volume = {13}, journal = {Animals}, number = {18}, publisher = {MDPI}, address = {Basel}, issn = {2076-2615}, doi = {10.3390/ani13182866}, pages = {21}, year = {2023}, abstract = {Housing in metabolic cages can induce a pronounced stress response. Metabolic cage systems imply housing mice on metal wire mesh for the collection of urine and feces in addition to monitoring food and water intake. Moreover, mice are single-housed, and no nesting, bedding, or enrichment material is provided, which is often argued to have a not negligible impact on animal welfare due to cold stress. We therefore attempted to reduce stress during metabolic cage housing for mice by comparing an innovative metabolic cage (IMC) with a commercially available metabolic cage from Tecniplast GmbH (TMC) and a control cage. Substantial refinement measures were incorporated into the IMC cage design. In the frame of a multifactorial approach for severity assessment, parameters such as body weight, body composition, food intake, cage and body surface temperature (thermal imaging), mRNA expression of uncoupling protein 1 (Ucp1) in brown adipose tissue (BAT), fur score, and fecal corticosterone metabolites (CMs) were included. Female and male C57BL/6J mice were single-housed for 24 h in either conventional Macrolon cages (control), IMC, or TMC for two sessions. Body weight decreased less in the IMC (females—1st restraint: -6.94\%; 2nd restraint: -6.89\%; males—1st restraint: -8.08\%; 2nd restraint: -5.82\%) compared to the TMC (females—1st restraint: -13.2\%; 2nd restraint: -15.0\%; males—1st restraint: -13.1\%; 2nd restraint: -14.9\%) and the IMC possessed a higher cage temperature (females—1st restraint: 23.7 °C; 2nd restraint: 23.5 °C; males—1st restraint: 23.3 °C; 2nd restraint: 23.5 °C) compared with the TMC (females—1st restraint: 22.4 °C; 2nd restraint: 22.5 °C; males—1st restraint: 22.6 °C; 2nd restraint: 22.4 °C). The concentration of fecal corticosterone metabolites in the TMC (females—1st restraint: 1376 ng/g dry weight (DW); 2nd restraint: 2098 ng/g DW; males—1st restraint: 1030 ng/g DW; 2nd restraint: 1163 ng/g DW) was higher compared to control cage housing (females—1st restraint: 640 ng/g DW; 2nd restraint: 941 ng/g DW; males—1st restraint: 504 ng/g DW; 2nd restraint: 537 ng/g DW). Our results show the stress potential induced by metabolic cage restraint that is markedly influenced by the lower housing temperature. The IMC represents a first attempt to target cold stress reduction during metabolic cage application thereby producing more animal welfare friendlydata.}, language = {en} } @phdthesis{Wilke2024, author = {Wilke, Heinrich}, title = {The order of destruction}, series = {Transdisciplinary souths}, journal = {Transdisciplinary souths}, publisher = {Routledge}, address = {London}, isbn = {978-1-032-51416-1}, doi = {10.4324/9781003465935}, pages = {ix, 224}, year = {2024}, abstract = {This book studies sugarcane monoculture, the dominant form of cultivation in the colonial Caribbean, in the later 1600s and 1700s up to the Haitian Revolution. Researching travel literature, plantation manuals, Georgic poetry, letters, and political proclamations, this book interprets texts by Richard Ligon, Henry Drax, James Grainger, Janet Schaw, and Toussaint Louverture. As the first extended investigation into its topic, this book reads colonial Caribbean monoculture as the conjunction of racial capitalism and agrarian capitalism in the tropics. Its eco-Marxist perspective highlights the dual exploitation of the soil and of enslaved agricultural producers under the plantation regime, thereby extending Marxist analysis to the early colonial Caribbean. By focusing on textual form (in literary and non-literary texts alike), this study discloses the bearing of monoculture on contemporary writers' thoughts. In the process, it emphasizes the significance of a literary tradition that, despite its ideological importance, is frequently neglected in (postcolonial) literary studies and the environmental humanities. Located at a crossroads of disciplines and perspectives, this study will be of interest to literary critics and historians working in the early Americas, to students and scholars of agriculture, colonialism, and (racial) capitalism, to those working in the environmental humanities, and to Marxist academics. It will be of great interest to scholars and researchers of language and literature, post-colonial studies, cultural studies, diaspora studies, and the Global South studies}, language = {en} } @article{MonteroCrucifixCoupletetal.2022, author = {Montero, Marina Mart{\´i}nez and Crucifix, Michel and Couplet, Victor and Brede, Nuria and Botta, Nicola}, title = {SURFER v2.0: a flexible and simple model linking anthropogenic CO2 emissions and solar radiation modification to ocean acidification and sea level rise}, series = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, volume = {15}, journal = {Geoscientific model development : an interactive open access journal of the European Geosciences Union}, number = {21}, publisher = {Copernicus}, address = {Katlenburg-Lindau}, issn = {1991-959X}, doi = {10.5194/gmd-15-8059-2022}, pages = {8059 -- 8084}, year = {2022}, abstract = {We present SURFER, a novel reduced model for estimating the impact of CO2 emissions and solar radiation modification options on sea level rise and ocean acidification over timescales of several thousands of years. SURFER has been designed for the analysis of CO2 emission and solar radiation modification policies, for supporting the computation of optimal (CO2 emission and solar radiation modification) policies and for the study of commitment and responsibility under uncertainty. The model is based on a combination of conservation laws for the masses of atmospheric and oceanic carbon and for the oceanic temperature anomalies, and of adhoc parameterisations for the different sea level rise contributors: ice sheets, glaciers and ocean thermal expansion. It consists of 9 loosely coupled ordinary differential equations, is understandable, fast and easy to modify and calibrate. It reproduces the results of more sophisticated, high-dimensional earth system models on timescales up to millennia.}, language = {en} } @article{VanonciniHoehlElsneretal.2023, author = {Vanoncini, Monica and H{\"o}hl, Stefanie and Elsner, Birgit and Wallot, Sebastian and Boll-Avetisyan, Natalie and Kayhan, Ezgi}, title = {Mother-infant social gaze dynamics relate to infant brain activity and word segmentation}, series = {Developmental cognitive neuroscience : a journal for cognitive, affective and social developmental neuroscience}, volume = {65}, journal = {Developmental cognitive neuroscience : a journal for cognitive, affective and social developmental neuroscience}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1878-9293}, doi = {10.1016/j.dcn.2023.101331}, pages = {8}, year = {2023}, abstract = {The 'social brain', consisting of areas sensitive to social information, supposedly gates the mechanisms involved in human language learning. Early preverbal interactions are guided by ostensive signals, such as gaze patterns, which are coordinated across body, brain, and environment. However, little is known about how the infant brain processes social gaze in naturalistic interactions and how this relates to infant language development. During free-play of 9-month-olds with their mothers, we recorded hemodynamic cortical activity of ´social brain` areas (prefrontal cortex, temporo-parietal junctions) via fNIRS, and micro-coded mother's and infant's social gaze. Infants' speech processing was assessed with a word segmentation task. Using joint recurrence quantification analysis, we examined the connection between infants' ´social brain` activity and the temporal dynamics of social gaze at intrapersonal (i.e., infant's coordination, maternal coordination) and interpersonal (i.e., dyadic coupling) levels. Regression modeling revealed that intrapersonal dynamics in maternal social gaze (but not infant's coordination or dyadic coupling) coordinated significantly with infant's cortical activity. Moreover, recurrence quantification analysis revealed that intrapersonal maternal social gaze dynamics (in terms of entropy) were the best predictor of infants' word segmentation. The findings support the importance of social interaction in language development, particularly highlighting maternal social gaze dynamics.}, language = {en} } @phdthesis{Wamwanduka2024, author = {Wamwanduka, Leo}, title = {Examining the Translation of Gender Norms in Southern Africa}, school = {Universit{\"a}t Potsdam}, pages = {359}, year = {2024}, language = {en} } @phdthesis{Gladkaya2024, author = {Gladkaya, Margarita}, title = {Essays on the digitization of the individual}, pages = {188}, year = {2024}, language = {en} } @article{LaunDuffusKumaretal.2022, author = {Laun, Konstantin and Duffus, Benjamin R. and Kumar, Hemant and Oudsen, Jean-Pierre H. and Karafoulidi-Retsou, Chara and Waffo, Armel Tadjoung and Hildebrandt, Peter and Ly, Khoa Hoang and Leimk{\"u}hler, Silke and Katz, Sagie and Zebger, Ingo}, title = {A minimal light-driven system to study the enzymatic CO2 reduction of formate dehydrogenase}, series = {ChemCatChem : the European Society Journal for Catalysis}, volume = {14}, journal = {ChemCatChem : the European Society Journal for Catalysis}, number = {24}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1867-3880}, doi = {10.1002/cctc.202201067}, pages = {7}, year = {2022}, abstract = {A minimal light-driven approach was established for studying enzymatic CO2 conversion spectroscopically. The system consists of a photosensitizer Eosin Y, EDTA as a sacrificial electron donor and substrate source, and formate dehydrogenase from Rhodobacter capsulatus (RcFDH) as a biocatalyst. This simplified three-component system provides a photo-triggered control for in situ characterization of the entire catalytic reaction. Direct reduction of RcFDH by the photosensitizer without additional electron carriers was confirmed via UV-Vis spectroscopy, while GC-MS and IR spectroscopy were used to follow photoinduced CO2 generation from EDTA and its subsequent enzymatic reduction, yielding the product formate. Photo-driven and in vitro, dye-based CO2 reduction was inhibited by azide under a mixed (competitive-non-competitive) inhibition mode. IR spectroscopy reveals displacement of the competitively-bound azide by CO2, reflecting an interaction of both with the active site cofactor. This work comprises a proof-of-concept for a new approach to employ light for regulating the reaction of formate dehydrogenases and other CO2 reductases.}, language = {en} } @article{BoginHermanussenScheffler2022, author = {Bogin, Barry and Hermanussen, Michael and Scheffler, Christiane}, title = {Bergmann's rule is a "just-so" story of human body size}, series = {Journal of physiological anthropology}, volume = {41}, journal = {Journal of physiological anthropology}, number = {1}, publisher = {BMC}, address = {London}, issn = {1880-6805}, doi = {10.1186/s40101-022-00287-z}, pages = {13}, year = {2022}, abstract = {Carl Bergmann was an astute naturalist and physiologist. His ideas about animal size and shape were important advances in the pre-Darwinian nineteenth century. Bergmann's rule claims that that in cold climates, large body mass increases the ratio of volume-to-surface area and provides for maximum metabolic heat retention in mammals and birds. Conversely, in warmer temperatures, smaller body mass increases surface area relative to volume and allows for greater heat loss. For humans, we now know that body size and shape are regulated more by social-economic-political-emotional (SEPE) factors as well as nutrition-infection interactions. Temperature has virtually no effect. Bergmann's rule is a "just-so" story and should be relegated to teaching and scholarship about the history of science. That "rule" is no longer acceptable science and has nothing to tell us about physiological anthropology.}, language = {en} } @article{YarmanKurbanoglu2022, author = {Yarman, Aysu and Kurbanoglu, Sevinc}, title = {Molecularly imprinted polymer-based sensors for SARS-CoV-2}, series = {Biomimetics}, volume = {7}, journal = {Biomimetics}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2313-7673}, doi = {10.3390/biomimetics7020058}, pages = {17}, year = {2022}, abstract = {Since the first reported case of COVID-19 in 2019 in China and the official declaration from the World Health Organization in March 2021 as a pandemic, fast and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played a major role worldwide. For this reason, various methods have been developed, comprising reverse transcriptase-polymerase chain reaction (RT-PCR), immunoassays, clustered regularly interspaced short palindromic repeats (CRISPR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and bio(mimetic)sensors. Among the developed methods, RT-PCR is so far the gold standard. Herein, we give an overview of the MIP-based sensors utilized since the beginning of the pandemic.}, language = {en} } @article{MitzscherlingMacLeanLipusetal.2022, author = {Mitzscherling, Julia and MacLean, Joana and Lipus, Daniel and Bartholom{\"a}us, Alexander and Mangelsdorf, Kai and Lipski, Andre and Roddatis, Vladimir and Liebner, Susanne and Wagner, Dirk}, title = {Paenalcaligenes niemegkensis sp. nov., a novel species of the family Alcaligenaceae isolated from plastic waste}, series = {International journal of systematic and evolutionary microbiology}, volume = {72}, journal = {International journal of systematic and evolutionary microbiology}, number = {4}, publisher = {Microbiology Society}, address = {London}, issn = {1466-5026}, doi = {10.1099/ijsem.0.005333}, pages = {9}, year = {2022}, abstract = {Strain NGK35T is a motile, Gram-stain-negative, rod-shaped (1.0-2.1 mu m long and 0.6-0.8 mu m wide), aerobic bacterium that was isolated from plastic-polluted landfill soil. The strain grew at temperatures between 6 and 37 degrees C (optimum, 28 degrees C), in 0-10 \% NaCl (optimum, 1 \%) and at pH 6.0-9.5 (optimum, pH 7.5-8.5). It was positive for cytochrome c oxidase, catalase as well as H2S production, and hydrolysed casein and urea. It used a variety of different carbon sources including citrate, lactate and pyruvate. The predominant membrane fatty acids were C-16:1 cis9 and C-16:0, followed by C-17:0 cyclo and C-18:1 cis11. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine, followed by diphosphatidyglycerol. The only quinone was ubiquinone Q-8. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK35(T) belongs to the genus Paenalcaligenes (family Alcaligenaceae), appearing most closely related to Paenalcaligenes hominis CCUG 53761A(T) (96.90 \%) and Paenalcaligenes suwonensis ABC02-12(T) (96.94 \%). The genomic DNA G+C content of strain NGK35(T) was 52.1 mol\%. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Paenalcaligenes. Based on phenotypic and molecular characterization, strain NGK35(T) can clearly be differentiated from its phylogenetic neighbours establishing a novel species, for which the name Paenalcaligenes niemegkensis sp. nov. is proposed. The type strain is NGK35T (=DSM 113270(T)=NCCB 100854(T)).}, language = {en} } @article{MiddelanisWillnerOttoetal.2022, author = {Middelanis, Robin and Willner, Sven N. and Otto, Christian and Levermann, Anders}, title = {Economic losses from hurricanes cannot be nationally offset under unabated warming}, series = {Environmental research letters}, volume = {17}, journal = {Environmental research letters}, number = {10}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1748-9326}, doi = {10.1088/1748-9326/ac90d8}, pages = {11}, year = {2022}, abstract = {Tropical cyclones range among the costliest of all meteorological events worldwide and planetary scale warming provides more energy and moisture to these storms. Modelling the national and global economic repercussions of 2017's Hurricane Harvey, we find a qualitative change in the global economic response in an increasingly warmer world. While the United States were able to balance regional production failures by the original 2017 hurricane, this option becomes less viable under future warming. In our simulations of over 7000 regional economic sectors with more than 1.8 million supply chain connections, the US are not able to offset the losses by use of national efforts with intensifying hurricanes under unabated warming. At a certain warming level other countries have to step in to supply the necessary goods for production, which gives US economic sectors a competitive disadvantage. In the highly localized mining and quarrying sector-which here also comprises the oil and gas production industry-this disadvantage emerges already with the original Hurricane Harvey and intensifies under warming. Eventually, also other regions reach their limit of what they can offset. While we chose the example of a specific hurricane impacting a specific region, the mechanism is likely applicable to other climate-related events in other regions and other sectors. It is thus likely that the regional economic sectors that are best adapted to climate change gain significant advantage over their competitors under future warming.}, language = {en} } @article{PawlitzkiAcarMasannecketal.2022, author = {Pawlitzki, Marc and Acar, Laura and Masanneck, Lars and Willison, Alice and Regner-Nelke, Liesa and Nelke, Christopher and L'hoest, Helmut and Marschall, Ursula and Schmidt, Jens and Meuth, Sven G. and Ruck, Tobias}, title = {Myositis in Germany: epidemiological insights over 15 years from 2005 to 2019}, series = {Neurological research and practice : official journal of the German Neurological Society}, volume = {4}, journal = {Neurological research and practice : official journal of the German Neurological Society}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {2524-3489}, doi = {10.1186/s42466-022-00226-4}, pages = {11}, year = {2022}, abstract = {Background: The medical care of patients with myositis is a great challenge in clinical practice. This is due to the rarity of these disease, the complexity of diagnosis and management as well as the lack of systematic analyses. Objectives: Therefore, the aim of this project was to obtain an overview of the current care of myositis patients in Germany and to evaluate epidemiological trends in recent years. Methods: In collaboration with BARMER Insurance, retrospective analysis of outpatient and inpatient data from an average of approximately 8.7 million insured patients between January 2005 and December 2019 was performed using ICD-10 codes for myositis for identification of relevant data. In addition, a comparative analysis was performed between myositis patients and an age-matched comparison group from other populations insured by BARMER. Results: 45,800 BARMER-insured individuals received a diagnosis of myositis during the observation period, with a relatively stable prevalence throughout. With regard to comorbidities, a significantly higher rate of cardiovascular disease as well as neoplasm was observed compared to the control group within the BARMER-insured population. In addition, myositis patients suffer more frequently from psychiatric disorders, such as depression and somatoform disorders. However, the ICD-10 catalogue only includes the specific coding of "dermatomyositis" and "polymyositis" and thus does not allow for a sufficient analysis of all idiopathic inflammatory myopathies subtypes. Conclusion: The current data provide a comprehensive epidemiological analysis of myositis in Germany, highlighting the multimorbidity of myositis patients. This underlines the need for multidisciplinary management. However, the ICD-10 codes currently still in use do not allow for specific analysis of the subtypes of myositis. The upcoming ICD-11 coding may improve future analyses in this regard.}, language = {en} } @article{AndjelkovicMarjanovicChenetal.2022, author = {Andjelkovic, Marko and Marjanovic, Milos and Chen, Junchao and Ilic, Stefan and Ristic, Goran and Krstic, Milos}, title = {PS-BBICS: Pulse stretching bulk built-in current sensor for on-chip measurement of single event transients}, series = {Microelectronics reliability}, volume = {138}, journal = {Microelectronics reliability}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {0026-2714}, doi = {10.1016/j.microrel.2022.114726}, pages = {6}, year = {2022}, abstract = {The bulk built-in current sensor (BBICS) is a cost-effective solution for detection of energetic particle strikes in integrated circuits. With an appropriate number of BBICSs distributed across the chip, the soft error locations can be identified, and the dynamic fault-tolerant mechanisms can be activated locally to correct the soft errors in the affected logic. In this work, we introduce a pulse stretching BBICS (PS-BBICS) constructed by connecting a standard BBICS and a custom-designed pulse stretching cell. The aim of PS-BBICS is to enable the on-chip measurement of the single event transient (SET) pulse width, allowing to detect the linear energy transfer (LET) of incident particles, and thus assess more accurately the radiation conditions. Based on Spectre simula-tions, we have shown that for the LET from 1 to 100 MeV cm2 mg -1, the SET pulse width detected by PS-BBICS varies by 620-800 ps. The threshold LET of PS-BBICS increases linearly with the number of monitored inverters, and it is around 1.7 MeV cm2 mg- 1 for ten monitored inverters. On the other hand, the SET pulse width is in-dependent of the number of monitored inverters for LET > 4 MeV cm2 mg -1. It was shown that supply voltage, temperature and process variations have strong impact on the response of PS-BBICS.}, language = {en} } @article{CheshmehElahiGhayyemetal.2022, author = {Cheshmeh, Sahar and Elahi, Negin and Ghayyem, Maysa and Mosaieby, Elaheh and Moradi, Shima and Pasdar, Yahya and Tahmasebi, Susan and Moradinazar, Mehdi}, title = {Effect of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with polycystic ovary syndrome}, series = {Genes \& nutrition}, volume = {17}, journal = {Genes \& nutrition}, number = {1}, publisher = {Springer}, address = {Berlin}, issn = {1865-3499}, doi = {10.1186/s12263-022-00719-6}, pages = {11}, year = {2022}, abstract = {Background: Polycystic ovary syndrome (PCOS) is an endocrine disease in which related to obesity, metabolic disorders and is considered as one of the main causes of infertility in women. This trial was investigated the effects of green cardamom on the expression of genes implicated in obesity and diabetes among obese women with PCOS. Methods: One hundred ninety-four PCOS women were randomly divided two groups: intervention (n = 99; 3 g/day green cardamom) and control groups (n = 95). All of them were given low calorie diet. Anthropometric, glycemic and androgen hormones were assessed before and after 16-week intervention. The reverse transcription-polymerase chain reaction (RT-PCR) method was used to measure fat mass and obesity-associated (FTO), peroxisome proliferative activating receptor- (PPAR-), carnitine palmitoyltransferase 1A (CPT1A), acetyl-CoA carboxylase beta (ACAB), leptin receptor (LEPR), ghrelin, and lamin A/C (LAMIN) genes expression in each group. Results: Anthropometric indices were significantly decreased after intervention in both two studied groups. Glycemic indices and androgen hormones were significantly improved in the intervention group compared to the control group. The expression levels of FTO, CPT1A, LEPR, and LAMIN were significantly downregulated compared to control group (P < 0.001), as well as, PPAR-y was significantly upregulated in the intervention group after intervention with green cardamom compared to control group (P < 0.001). Conclusion: This current study showed that the administration of green cardamom is a beneficial approach for improving anthropometric, glycemic, and androgen hormones, as well as obesity and diabetes genes expression in PCOS women under the low-calorie diet.}, language = {en} } @article{GrzesiukPietrzakWackeretal.2022, author = {Grzesiuk, Malgorzata and Pietrzak, Barbara and Wacker, Alexander and Pijanowska, Joanna}, title = {Photosynthetic activity in both algae and cyanobacteria changes in response to cues of predation}, series = {Frontiers in plant science}, volume = {13}, journal = {Frontiers in plant science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2022.907174}, pages = {8}, year = {2022}, abstract = {A plethora of adaptive responses to predation has been described in microscopic aquatic producers. Although the energetic costs of these responses are expected, with their consequences going far beyond an individual, their underlying molecular and metabolic mechanisms are not fully known. One, so far hardly considered, is if and how the photosynthetic efficiency of phytoplankton might change in response to the predation cues. Our main aim was to identify such responses in phytoplankton and to detect if they are taxon-specific. We exposed seven algae and seven cyanobacteria species to the chemical cues of an efficient consumer, Daphnia magna, which was fed either a green alga, Acutodesmus obliquus, or a cyanobacterium, Synechococcus elongatus (kairomone and alarm cues), or was not fed (kairomone alone). In most algal and cyanobacterial species studied, the quantum yield of photosystem II increased in response to predator fed cyanobacterium, whereas in most of these species the yield did not change in response to predator fed alga. Also, cyanobacteria tended not to respond to a non-feeding predator. The modal qualitative responses of the electron transport rate were similar to those of the quantum yield. To our best knowledge, the results presented here are the broadest scan of photosystem II responses in the predation context so far.}, language = {en} } @article{JarajapuRathinasamyAgarwaletal.2022, author = {Jarajapu, Deva Charan and Rathinasamy, Maheswaran and Agarwal, Ankit and Bronstert, Axel}, title = {Design flood estimation using extreme Gradient Boosting-based on Bayesian optimization}, series = {Journal of hydrology}, volume = {613}, journal = {Journal of hydrology}, number = {Part A}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0022-1694}, doi = {10.1016/j.jhydrol.2022.128341}, pages = {16}, year = {2022}, abstract = {Regional Flood Frequency Analysis (RFFA) is one of the widely used approaches for estimating design floods in the ungauged basins. We developed an eXtreme Gradient Boost (XGB) machine learning model for RFFA and flood estimation. Our approach relies on developing a regression model between flood quantiles and the commonly available catchment descriptors. We used CAMELs data for 671 catchments from the USA to test the approach's efficacy. The results were compared with the traditional Multiple Linear Regression methods and Artificial Neural Networks. Results revealed that the XGB-based approach estimated design flood with the highest accuracy during training and validation with minor mean absolute error, root mean square error values, and percentage bias ranging from -10 to + 10. The importance of each catchment feature is visualized by three different approaches Gini Impurity, Permutation, and Dropout Loss Feature Ranking. We observed that the most dominating variables are rainfall intensity, slope, snow fraction, soil porosity, and temperature. It is observed that the importance of these variables is a function of the hydroclimatic regions and varies with space. In contrast, mean annual areal potential evapotranspiration, mean annual rainfall, fraction forest area, and soil conductivity have low significance in estimating design flood for an ungauged catchment. Indeed, the proposed XGB-based approach has broader applicability and replicability.}, language = {en} } @article{RoseWei2022, author = {Rose, Christian and Wei, Guofang}, title = {Eigenvalue estimates for Kato-type Ricci curvature conditions}, series = {Analysis \& PDE}, volume = {15}, journal = {Analysis \& PDE}, number = {7}, publisher = {Mathematical Sciences Publishers}, address = {Berkeley}, issn = {1948-206X}, doi = {10.2140/apde.2022.15.1703}, pages = {1703 -- 1724}, year = {2022}, abstract = {We prove that optimal lower eigenvalue estimates of Zhong-Yang type as well as a Cheng-type upper bound for the first eigenvalue hold on closed manifolds assuming only a Kato condition on the negative part of the Ricci curvature. This generalizes all earlier results on Lp-curvature assumptions. Moreover, we introduce the Kato condition on compact manifolds with boundary with respect to the Neumann Laplacian, leading to Harnack estimates for the Neumann heat kernel and lower bounds for all Neumann eigenvalues, which provides a first insight in handling variable Ricci curvature assumptions in this case.}, language = {en} } @article{Grebenkov2022, author = {Grebenkov, Denis S.}, title = {Statistics of diffusive encounters with a small target}, series = {Journal of statistical mechanics: theory and experiment}, volume = {2022}, journal = {Journal of statistical mechanics: theory and experiment}, number = {8}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1742-5468}, doi = {10.1088/1742-5468/ac85ec}, pages = {34}, year = {2022}, abstract = {Diffusive search for a static target is a common problem in statistical physics with numerous applications in chemistry and biology. We look at this problem from a different perspective and investigate the statistics of encounters between the diffusing particle and the target. While an exact solution of this problem was recently derived in the form of a spectral expansion over the eigenbasis of the Dirichlet-to-Neumann operator, the latter is generally difficult to access for an arbitrary target. In this paper, we present three complementary approaches to approximate the probability density of the rescaled number of encounters with a small target in a bounded confining domain. In particular, we derive a simple fully explicit approximation, which depends only on a few geometric characteristics such as the surface area and the harmonic capacity of the target, and the volume of the confining domain. We discuss the advantages and limitations of three approaches and check their accuracy. We also deduce an explicit approximation for the distribution of the first-crossing time, at which the number of encounters exceeds a prescribed threshold. Its relations to common first-passage time problems are discussed.}, language = {en} } @article{PompaGarciaCastillaMetzleretal.2022, author = {Pompa-Garcia, Ivan and Castilla, Rodrigo and Metzler, Ralf and Dagdug, Leonardo}, title = {First-passage times in conical varying-width channels biased by a transverse gravitational force}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {106}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {6}, publisher = {American Physical Society}, address = {College Park}, issn = {2470-0045}, doi = {10.1103/PhysRevE.106.064137}, pages = {8}, year = {2022}, abstract = {We study the crossing time statistic of diffusing point particles between the two ends of expanding and narrowing two-dimensional conical channels under a transverse external gravitational field. The theoretical expression for the mean first-passage time for such a system is derived under the assumption that the axial diffusion in a two-dimensional channel of smoothly varying geometry can be approximately described as a one-dimensional diffusion in an entropic potential with position-dependent effective diffusivity in terms of the modified Fick-Jacobs equation. We analyze the channel crossing dynamics in terms of the mean first-passage time, combining our analytical results with extensive two-dimensional Brownian dynamics simulations, allowing us to find the range of applicability of the one-dimensional approximation. We find that the effective particle diffusivity decreases with increasing amplitude of the external potential. Remarkably, the mean first-passage time for crossing the channel is shown to assume a minimum at finite values of the potential amplitude.}, language = {en} }