Miracle-dz/UniFAR-FTUs huggingface dataset:
The interplay between polymerase organization and nucleosome occupancy along DNA : How dynamic roadblocks on the DNA induce the formation of RNA polymerase pelotons

During transcription RNA polymerase (RNAP) moves along a DNA molecule to copy the information on the DNA to an RNA molecule. Many textbook pictures show an RNAP sliding along empty DNA, but in reality it is crowded on the DNA and RNAP competes for space with many proteins such as other RNAP’s and histones. Coverage of DNA by histones is essential for DNA protection and signaling. However, during transcription RNAP evicts histones, which then rebind quickly or are replaced by other proteins. How does crowding of RNAP and histones on the DNA affects transcription dynamics on the one hand, and how does transcription activity change the density and exchange of histones along the DNA on the other hand? Those are the central questions of this thesis.
Effect of GAN-based image standardization on MR knee bone-tissue classification performance

Due to their sensitivity to acquisition parameters, medical images such as magnetic resonance images (MRI), Positron Emission tomography (PET) or Computed Tomography (CT) images often suffer from a kind of variability unrelated to diagnostic power, known as the center effect (CE) or domain shift. This is especially true in MRI, where units are arbitrary and image values can strongly depend on subtle variations in the pulse sequences [2]. Due to the CE it is particularly difficult in various medical imaging applications to 1) pool data coming from several centers or 2) train machine learning algorithms requiring large homogeneous training sets. There is therefore a clear need for image standardization techniques aiming at reducing this effect. Considerable improvements in image synthesis have been achieved over the recent years using (deep) machine learning. Models based on generative adversarial neural networks (GANs) now enable the generation of high definition images capable of fooling the human eye [5]. These methods are being increasingly used in medical imaging for various cross-modality (image-to-image) applications such as MR to CT synthesis [3]. However, they have been seldom used for the purpose of image standardization, i.e. for reducing the CE [4]. In this work, we explore the potential advantage of embedding a standardization step using GANs prior to knee bone tissue classification in MRI. We consider image standardization as a within-domain image synthesis problem, where our objective is to learn a mapping between a domain D constituted of heterogeneous images and a reference domain R showing one or several images of desired image characteristics.
Hakkâri İlinde Gıda Olarak Tüketilen Yabani Bitki ve Yabancı Ot Türlerinin Güncel Durumu

Bu calismada Hakkâri ili ve ilcelerinde yore halki tarafindan dogal alanlar ve tarimsal ekosistemlerden toplanarak gida ve/veya tibbi amac icin kullanilan bitkiler ele alinmistir. Bolgede asiri toplama sonucu olarak bazi bitkilere rastlanmadigi ve neredeyse neslinin yok olmaya yuz tuttugu kamuoyuna yansiyan bu bitkilerin guncel durumunun ortaya konulmasi hedeflenmistir. Arastirma kapsaminda, 2018 yili ilkbahar doneminde bitkileri dogada toplayan kisiler ile mulakatlar yapilmis, yerel pazarlarda halktan insanlarla gorusulmus ve arazi surveyleri gerceklestirilmistir. Ayrica daha once bolgede yapilan etnobotanik calismalar da dikkate alinarak konuya iliskin degerlendirmeler yapilmistir. Yapilan arastirmalar sonucunda bolgede en fazla toplanip tuketilen Kose otu/Siyabo (Diplotaenia cachrydifolia Boiss.), Yayla muzu/Rrevas (Rheum ribes L.), Kenger/Kengir (Gundelia tournefortii L. var. tournefortii), Tarak otu/Mendi (Chaerophyllum macrospermum (Willd. ex Sprengel), Ters lale/Guldexin (Fritillaria imperialis L.), Cayir salebi/Şepizek (Orchis palustris jacq) ve Yabani mantar/Kivark (Pleurotus eryngii var. ferulae (Lanzi) Sacc. ) gibi bitki turlerinin dogada rastlanma sikliklarinin ve yogunluklarinin onemli olcude azaldigi saptanmistir. Bunun bir sonucu olarak yorede bitki toplayan ve ticari olarak bunlardan gelir elde eden kisilerin toplama isi icin cok daha fazla mesafe kat etikleri ve zaman harcadiklari bu nedenle de bu bitkilerin piyasa fiyatlarinin da surekli artigi da saptanmistir. Bolgede dogal olarak yetisen ve ekonomik degeri son derece yuksek olan bu bitkilerin korunmasi ve surdurulebilir bir sekilde toplanabilmeleri icin yore halkina yonelik bilgilendirme ve bilinclendirme calismalarinin yapilmasi gerektigi sonucuna varilmistir. Bu durum bolgedeki biyolojik cesitliligin korunmasina da buyuk katkilar saglayacaktir. Ayrica en azindan bazi turlerin kulture alinmasinin dogal flora ustundeki baskiyi azaltabilecegi kanaatine varilmistir.
Twinned power: formations of cloud-edge control

ABSTRACT From smart vehicles to smart city sensors, the millions of new devices connected over the next few years will generate huge amounts of highly personal data that needs to be processed in real time. Transmitting this data to the cloud, with its centralized data centers and high latency, is both economically and technically unviable. As a result, the industry is moving towards processing data closer to the source, a major shift from the cloud to the so-called edge. This new architecture is understood as a necessary augmentation to the cloud. Indeed, in many ways, the edge is the polar opposite of the cloud: ad hoc networks, composed of resource-poor devices, that function at the hyperlocal level of the home, office, or neighborhood. However, this article argues that such technical supplementation is also about control, filling a critical void in contemporary formations of power. Coupled together, this cloud-edge formation is both centralized and decentralized, resource intense yet geographically dispersed. Drawing on Foucauldian theory, such power augments heavy, situated force with a more flexible, economic architecture – conforming to a trajectory of ‘intensification’ while also complicating it. While each mode of power has certain strengths and weaknesses, combining their operations forms a twinned power with new capacities for subjectivation and governance.
Adjustments of Socially Vulnerable Populations in Galveston County, Texas USA Following Hurricane Ike

The role of socio-demographic vulnerability to hazards is an increasingly important aspect for consideration in disaster mitigation and adaptation. This paper examines the spatial adjustments of populations to the 2008 Hurricane Ike by estimating the effects of damage on the changes of socially vulnerable populations pre- and post-Hurricane Ike. Multivariate regression models are used to understand household-level adjustments in different flood zones and inundation levels at the block-group level in Galveston county. In contrast to past literature that suggests that vulnerable populations remain or move into hazardous areas post-disaster, our results indicate that socially vulnerable populations have moved out of highly damaged areas. The tremendous investment opportunity post-disaster and the slow distribution of funds to recover public housing on Galveston Island provide potential explanation of the estimated adjustment patterns. Analyzing post disaster adjustments offers important insights into the “resilient” recovery of Galveston County post-Hurricane Ike. Our results also point to potential vulnerabilities that may arise in the future because of the change in community identity and the loss of social memory. Understanding disaster-driven changes in community make-up will help inform potential recovery trajectories from future catastrophes.
IL4, IL13, GSTM1 and T1 variants and susceptibility to Schistosomiasis and associated bladder pathologies in Eggua, Nigeria

Failure of the human host to elicit adequate immune responses to the adult Schistosoma haematobium worm and continuous strong inflammatory responses to the eggs have been the main causes of bladder pathology in chronic Schistosomiasis. Identification of susceptibility biomarkers for schistosomiasisassociated bladder pathology is necessary in order to detect genetic factors responsible for the infection and spread of the disease. The aim of this study was to identify candidate-biomarkers for susceptibility to schistosomiasis and its associated pathologies. A total of 371 adult participants, comprising 130 males and 241 females from Eggua community, Ogun State, Nigeria, were randomly recruited into a cross sectional study from August 2012 to May 2014. They were screened for S. haematobium ova and bladder pathologies by microscopy and ultrasonography, respectively. Human host susceptibility to schistosomiasis and its associated bladder pathologies were determined by PCR genotyping of Interleukin (IL4 and IL13) genes, and glutathione-S-transferase (GSTT1 and GSTM1) genes. The overall prevalence of S. haematobium in the population was 29.3% (108/369). Bladder pathologies were observed in 32.3% (117/362) of the population. Polymorphisms in IL 4-590 and IL 13-1055 were observed in 24.1% and 9.3% schistosomiasis cases, respectively. The IL 13-1055 polymorphism did not indicate susceptibility to schistosomiasis in males (OR 0.7, 95% CI 0.3-2.1) but a slight risk was found in females (OR 1.1, 95% CI 0.7-1.7). Participants with GSTM1 and GSTT1 polymorphisms expressed elevated risks of bladder pathologies (OR = 4.3, 95% CI 2.0 9.2 and OR = 4.2, 95% CI 1.5 – 12.0, respectively), with the pathology and schistosomiasis group having more GST polymorphisms than bladder pathologies.
Biological Control of Potato Brown Leaf Spot Disease Caused by Alternaria alternata Using Brevibacillus formosus Strain DSM 9885 and Brevibacillus brevis Strain NBRC 15304

Brown leaf spot is one of the prevalent diseases caused by Alternaria alternata in different growing areas of potato worldwide. Eight A. alternata isolates were screened from forty-two isolates collected from different potato growing regions in four Egyptian governorates viz, North Sinai (Baloza), Beheira (El-Nubaria and Wadi El-Natrun), Ismailia (Abu Suweir, Fayed and Tell El-Kebir), Sharqia (New Salheya and El-Husseiniya). The virulence of the isolates was tested based on the Per cent of Disease Index (PDI) which ranged from 28.2% to 70.3% PDI by Alternaria isolates of Baloza and Fayed respectively. Two bacterial strains “Brevibacillus formosus strain DSM 9885, and Brevibacillus brevis strain NBRC 15304 were selected to control of A. alternata. The bacterial strains have a higher inhibitory effect on mycelial development and spore germination of A. alternata. To determine the effects of the bacterial strains on disease index and severity, the most virulent of A. alternata isolates were selected for greenhouse experiments where the potato plants were sprayed with bacterial strains individually and mixture treatments. Superior effect of treatments in disease reduction was observed when the two bacterial strains were combined. The effect of leaf age was studied where the leaf position has significant effect on disease progress. The changes of soluble protein in potato leaves due to Brevibacillus strains application were studied. Protein profiling by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) revealed that the plant treated with mixture of biocontrol agents able to synthesize some new proteins with maximum number of bands followed by treatment by B. formosus strain. The presence or absence of the bands in protein profiling might be responsible for resistance response against A. alternata in potato. The present work suggests that use of B. formosus strain DSM 9885, and B. brevis strain NBRC 15304 could be considered as potential management tools for reducing the impact of A. alternata causing brown leaf spot disease on potato.
Linking bio-cultural diversity to markets: The niche for locally fermented foods

Marketing of agro-related products is a known problem. This situation is worse for fermented traditional foods. Interest is growing for these foods. The situation is ripe for research and development effort to markets and marketing of these foods. This paper draws attention to this need and beyond. The paper was written based on a desk study with limited triangulation using a checklist. The findings are that fermented foods have received very little research and development attention. They have very limited markets and market opportunities. In the worldviews of Africans, markets have a more holistic perspective beyond just a place for buying and selling and these markets have their own structures and systems and also cultures. The write-up recommended “market mapping” as one investigating strategy that conforms to a holistic approach to developing the market for fermented products. It further recommended bringing onboard all stakeholders using an endogenous development approach.
First record of the ectoparasitic mite Spinturnix scuticornis (Acari: Spinturnicidae) from the Himalayan whiskered bat Myotis siligorensis (Chiroptera: Vespertilionidae) in Vietnam

ABSTRACT Here we report the ectoparasitic mite Spinturnix scuticornis Dusbábek, 1970 collected from the Himalayan whiskered bat, Myotis siligorensis Horsfield, 1855 (Chiroptera: Vespertilionidae), in the Quang Binh province, Vietnam. Previously this mite species have been recorded from Myotis longipes, Miniopterus fuliginosus in Afghanistan and Taiwan and presumably from Eptesicus serotinus in Azerbaijan. This is the southernmost record and new host record for S. scuticornis.
Study of bursting events and effect of hole-size on turbulent bursts triggered by the fluid and mid-channel bar interaction

Turbulent structures of flow around the mid-channel braid bar have not been adequately investigated so far. Of late, the intrinsic fluvial hydraulics associated with the formation of braided rivers interspersed with sand bars have been vital topics of research. In this paper, the findings yielded from a research foray on the aforementioned underlying processes are presented. For obtaining the requisite experimental data, the three-dimensional flow velocity components are measured with the help of acoustic Doppler velocimetry (ADV) and these velocity data are analyzed using quadrant bursting techniques. The flow characteristics are greatly affected by the presence of a mid-channel bar. The depth-averaged contours of turbulent parameters are analyzed in the present study. Herein, the hole size concept is adopted for separating the bursting events. The effect of hole size on the quadrant events is also studied. The experiments are performed for different submergence ratios. A new parameter, Bursting Index (BI), is proposed in this research to reflect a quantitative measure of the turbulent bursting effect on streambed elevation changes. The parameter BI is the ratio of the odd event occurrence probability to the even event occurrence probability. The high values of correlation coefficients signify that the BI is profoundly influenced by streambed elevation changes, which makes it an ideal parameter for analyzing scour and deposition phenomena in real-life water management projects. The prime focus on performing the experiments has been to analyze the impact of bar height on flow structure in the vicinity of the mid-channel bar.
The information phase of accountability: The role of management boards in European Union agencies

The creation of European Union agencies has prompted normative and theoretical discussions about their accountability and democratic legitimacy. This study examines the extent to which different features concerning the institutional design of agencies incentivize information provision on their performance. To do so, it measures four aspects for which their governing bodies are expected to provide information: governance decisions, policy performance, financial issues, and interactions with stakeholders. Using a new data set of informative statements included in 199 annual activity reports of 29 agencies during the period 2010–2016, this study demonstrates that formal accountability positively affects information provision on governance and policy issues, and that the establishment of scientific bodies within agencies improves information provision on governance aspects, policy performance and their interactions with stakeholders. Finally, this article finds that agencies that perform more direct regulation are subject to greater transparency demands about their governance decisions and stakeholder interactions. Points for practitioners The study provides practitioners with an analytical tool for assessing the provision of information about the decisions and actions of management boards on governance issues, policy performance, financial aspects and their interactions with stakeholders.
Total pain in a patient with lung cancer diagnosis

Pain is experienced by most cancer patients. According to the definition of the International Society for the Study of Pain (IASP), pain is an unpleasant sensory and emotional experience associated with, or resembling that associated with, actual or potential tissue damage. This very “medical” definition indicates that pain is a mental, subjective, sensual, emotional, and unpleasant phenomenon. In palliative care, there is often a need for a better and deeper understanding of what “total” pain can be. The case of a young patient with lung cancer diagnosis presented an opportunity to describe characteristics of such pain, which encompasses physical, mental, social and spiritual suffering.
An investigation of the role of glucose and fructose in non-alcoholic fatty liver disease using systems approaches

Whether or not dietary fructose exacerbate hepatic lipogenesis and non-alcoholic fatty liver disease (NAFLD) pathogenesis remains an unresolved question. Furthermore, few studies have utilised systems approaches, notably at a genome-scale level, to investigate specific monosaccharides on hepatic steatosis. Therefore, the aim of this work was to develop a predictive, multi-scale computational model of hepatic monosaccharide transport, signalling and metabolism; validated experimentally to an in vitro model of steatosis. Utilising quasi-steady state Petri nets (QSSPN), a dynamic network of hepatic glucose and fructose transport was reconstructed and integrated with a human hepatocyte-specific genome scale metabolic network constrained by in vitro flux data. Additionally, a regulatory, kinetic model of hepatic insulin signalling was reconstructed and successfully integrated in QSSPN. Together with our novel simulation method, dynamic flux variability analysis, simulations predicted minimum and maximum flux rates allowing the calculation of extracellular glucose and fructose, and triacylglycerol production over time, while also satisfying the demands of a ‘healthy hepatocyte’. Immortalised hepatic cells, HepG2, treated with fatty acids were confirmed as an in vitro model of NAFLD after the characterisation of both viability, as measured by LDH and MTT assays, and intracellular lipid by Nile red staining. Differential effects of glucose and fructose on lipid metabolism were also investigated in an in vitro mixed-nutrient model of glucose, fructose and oleate. Intracellular lipid was assessed by Nile red and the gold standard, gas chromatography mass spectrometry. While oleate induced intracellular lipid (P < 0.05), no statistical differences were detected between sugar treatments. Additionally, intracellular lipid by Nile red was measured in HepG2 cells treated with glucose or fructose ± insulin. Notably, while hepatic monosaccharide uptake in vitro was reproduced by our in silico model, differential lipogenic effects of fructose were not found experimentally, nor predicted by our in silico model. In conclusion, in vitro hepatic monosaccharide uptake and intracellular lipid was reproduced in our in silico model with no differential lipogenic effects of fructose detected. This highlights existing concerns of current public health recommendations targeting single nutrients, e.g. fructose, to combat lifestyle-related metabolic diseases such as NAFLD. Future work should aim to predict the outcomes and investigate underlying molecular and regulatory mechanisms of sugar and lipid metabolism in response to mixed meals containing physiological levels of glucose and fructose without confounding excess energy.
Effect of forest litter depth on seed germination efficacy of Rhododendron ponticum.

In Ireland one of the most serious invasive alien species which poses threats to local biodiversity is Rhododendron ponticum L. Once established on a susceptible site, R. ponticum can kill other plant species in the ground vegetation layer and prevent the regeneration of trees and shrubs, thereby also indirectly affecting the local fauna. Forest floor litter negatively impacts on the germination success of many plant species, and both the amount and distribution of forest litter can influence the establishment of invasive alien species. Many land management practices, particularly in forestry, disturb ground cover leading to soil exposure, which may increase the risk of R. ponticum invasion. In this study, the effect of forest floor litter on the germination of R. ponticum seeds in five different litter types was assessed. The treatments included bare soil; 1 cm, 3 cm and 5 cm depths of broadleaved litter; and 2 cm conifer litter depth. The results showed a clear relationship between litter type and seed germination success with seeds having poorer success rates in deeper forest litter. This study demonstrated that even small decreases in forest litter depth, sufficient to expose bare soil, facilitates R. ponticum seedling establishment. These findings will inform guidelines and standard operating procedures for future forest management plans, particularly in areas that are sensitive to R. ponticum invasion.
Pandemia na necroeconomia neoliberal

Estamos vivendo, desde meados de marco de 2020, no Brasil, uma situacao excepcional, gerada pela pandemia do coronavirus, cientificamente codificada em suas siglas como doenca, classificada como substantivo feminino, a Covid-19 A propria definicao de pandemia implica uma questao mundial, que atinge de alguma maneira a todas e todos: Oriente e Ocidente;Norte e Sul;pobres e ricos;mulheres e homens, cis e trans, homossexuais e heterossexuais;pessoas indigenas, negras, brancas, orientais Entretanto, como Boaventura de Souza Santos (2020) e tantas autoras e autores tem argumentado, essa ideia de uma “igualdade” frente ao virus e uma ficcao, ja que a doenca nao atinge a todas da mesma forma e com a mesma intensidade Se algumas/ uns de nos podem estar em isolamento nos espacos domesticos, trabalhando com seus computadores e internet, outras pessoas nao tem essa possibilidade Segundo este autor, a pandemia e o confinamento como prevencao para a mesma promovem e revelam as cisoes perversas das sociedades, que tornam alguns grupos sociais mais suscetiveis em razao de suas condicoes socioeconomicas e da falta de politicas publicas adequadas, visibilizando os que estao “ao sul da quarentena”: mulheres, trabalhadoras e trabalhadores precarios ou informais, moradoras e moradores de rua, de periferias pobres e de favelas, as/os internadas/os em campos de refugiados e prisoes, idosas/os, deficientes fisicos (SANTOS, 2020, p 15-21) Esses “grupos vulneraveis” formam a maioria das pessoas no planeta, aquela maioria que nao esta protegida pela redoma dos planos de saude, das casas com internet rapida, dos empregos em instituicoes e empresas que permitem home office e continuam pagando salarios, das pessoas que podem comprar alimentos e refeicoes por delivery