Miracle-dz/UniFAR-FTUs huggingface dataset:
Salmonella och verotoxinproducerande E. coli i färdigsallader Salmonella and verotoxin producing E. coli in ready-made salads

Ready-to-eat salads are an increasingly popular commodity. It displays a convenient way to prepare a meal. However, in recent years there have been a number of disease outbreaks caused by enteric bacteria such as Salmonella spp. and E. coli. One example is the recent outbreak of E. coli O104:H4, which was caused by contaminated sprouts. The aim of this thesis was to find out which pathotypes of Salmonella and E. coli, which are the most dangerous and also to try to find ways to deal with them to decrease their numbers. The main focus will be on verotoxin-producing E. coli as they can cause potentially life threatening symptoms apart from the other pathotypes which usually cause less severe symptoms. The conclusions are that the most important measure to take is to make sure that a high level of hygiene is maintained throughout the postharvest chain. It is here the main transmission of bacteria between, for example, field grown leafy vegetables may occur. Innehallsforteckning Sida
Colonization of grapes berries by Alternaria sp. and their ability to produce mycotoxins

Our research focused on identify the Alternaria species from grapes (surface sterilized berries and non-surface sterilized berries) of Slovak origin and characterize their toxinogenic potential in in vitro conditions. We analyzed 47 samples of grapes, harvested in years 2011, 2012 and 2013 from various wine-growing regions. For the isolation of species, the method of direct plating berries and surface-sterilized berries (using 1 % freshly pre-pared chlorine) on DRBC (Dichloran Rose Bengal Chloramphenicol agar) was used. For each analysis was used 50 berries. Only undamaged berries have been used for analysis. The cultivation was carried at 25 ±1°C, for 5 to 7 days in dark. After incubation, the colonies of Alternaria were transferred on PCA - potato-carrot agar and CYA - Czapek-yeast extract agar and cultured for 7 days at room temperature and natural light. A total 4 species-groups of the genus Alternaria were isolated from grapes berries: Alternaria alternata (1369 isolates), Alternaria arborescens (734 isolates), Alternaria infectoria (143 isolates), and Alternaria tenuissima (3579 isolates). According to European Union legislation mycotoxins produced by species genus Alternaria are not monitored in foods and food commodities. Mycotoxins such as alternariol and alternariol monomethylether are mutagenic and genotoxic in various in vitro systems. Selected strains were tested for production of altenuene, alternariol monomethylether and alternariol. In neither case of A. infectoria species-group isolates was confirmed the production of tested mycotoxins in in vitro conditions by TLC method. The ability to produce altenuene, alternariol monomethylether and alternariol in in vitro conditions was detected in isolates of Alternaria alternata , Alternaria arborescens and Alternaria tenuissima species-groups. Isolates of Alternaria alternata species-group (44 tested isolates) were able to produce altenuene (24 isolates), alternariol monomethyleter (42 isolates) and alternariol (43 isolates). Only one isolate did not produce any mycotoxins. Isolates of Alternaria arborescens species-group (38 tested isolates) were able to produce altenuene (24 isolates), alternariol monomethyleter (33 isolates) and alternariol (36 isolates). Only two isolates did not produce any mycotoxins. Isolates of Alternaria tenuissima species-group (87 tested isolates) were able to produce altenuene (42 isolates), alternariol monomethyleter (41 isolates) and alternariol (73 isolates). Thirteen isolates did not produce any mycotoxins.
The role of phosphoinositides in mast cell exocytosis

The phosphoinositides (Pin) are a family of phospholipids that contain myo inositol as their headgroup. Despite being present in eukaryotic membranes with low abundance, their high rates of metabolic turnover allow them to control a plethora of cellular functions. In particular, phosphatidylinositol 4,5-&wphosphate (PtdIns(4,5)P2) regulates several processes, including preparing secretory organelles to undergo fusion with the plasma membrane in response to a stimulus (regulated exocytosis), budding and fission of vesicular cargo from the plasma membrane (endocytosis), and controlling the cortical actin cytoskeleton. In this thesis, the role of Pin in regulated exocytosis is examined in mast cells, since these undergo an acute, massive and rapid exocytosis, without any immediate endocytosis. Using a reconstitution approach, it was not possible to define which Pin are involved in exocytosis, although it was concluded that at least one Pin that is not PtdIns(4,5)P2 is required. In order to study PtdIns(4,5)P2 dynamics in primary mast cells, a novel quantitative immunofluoescence technique for Pin was established. Using this technique, PtdIns(4,5)P2 was identified at the plasma membrane of mast cells, but was depleted almost entirely during exocytosis the latter observation was confirmed using biochemical approaches. This depletion was blocked by inhibitors of phospholipase C (PLC), an enzyme that breaks down PtdIns(4,5)P2 into diacylglycerol (DAG) and the calcium mobilising messenger, inositol 1,4,5-frisphosphate (Ins(l,4,5)P3). Although PLC activity was required for initiation of calcium signalling in mast cells, experiments whereby the Ins(l,4,5)P3/calcium pathway was bypassed demonstrated further requirements for PLC activity. These were not precisely defined, but simple elimination of plasma membrane PtdIns(4,5)P2 or production of DAG were not sufficient. Both events may be required in conjunction, however. A model is proposed whereby elimination of plasma membrane PtdIns(4,5)P2 together with production of DAG may activate the protein machinery for membrane fusion during exocytosis.
MODIS and VIIRS Calibration and Characterization in Support of Producing Long-Term High-Quality Data Products

Terra and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) have successfully operated since their launches in 1999 and 2002, respectively, and generated various data products to support the Earth remote sensing disciplines and users worldwide for their research activities and applications, including studies of the Earth system, and its changes over time and geographic regions. The MODIS data have also significantly contributed to the continuity of multi-decadal satellite data records and led to major advances in the Earth remote sensing field. The long-term data records from MODIS observations have been and will continue to be extended by the Visible Infrared Imaging Radiometer Suite (VIIRS) instruments, currently operated aboard the Suomi-National Polar-Orbiting Partnership (NPP) and NOAA-20 satellites. The data quality of satellite instruments strongly depends on their calibration accuracy and stability. In order to help scientists and users gain a better understanding of MODIS and VIIRS data quality, this paper provides an overview of their on-orbit calibration methodologies, approaches, and results derived from instrument on-board calibrators and lunar observations, as well as select Earth view targets. What is also discussed is the calibration consistency between MODIS and VIIRS and its potential impact on producing multi-sensor long-term data records. As illustrated, the overall performance of both MODIS and VIIRS continues to meet their design requirements.
Coculture with marine bacteria confers resistance to complete viral lysis of diatom cultures

Supplement. The following information supports the ‘Materials and methods’ section of the main text for testing the possibility of viral genome integration into the host genome DNA, i.e. latent or lysogenic infection, and for the effects of all bacterial isolates on the host–virus system. These results are shown in Figs. S1 & S2, respectively. Furthermore, the results of the BLAST analysis based on the bacterial 16S rDNA sequence data are shown in Table S1
The detrimental effect of microplastics on critical periods of development in the neuroendocrine system

As a result of human socio‐economic activity, industrial wastes have increased alarmingly. Plastic pollution is globally distributed across the world due to its properties of buoyancy and durability. Two broad classes of plastic‐related chemicals are of critical concern for human health—bisphenol‐A or BPA, and additives used in the synthesis of plastics, which are known as phthalates. Our exposure to them is ubiquitous because they are used in the production of materials that we use daily such as polycarbonate plastics, epoxy resins, flooring, automotive parts, medical devices, dental sealants, and children's toys. Since these compounds are not covalently bound to the products, they easily leach from them, leading to high human exposure. Both, BPA and phthalates, are endocrine‐disruptor compounds (EDCs) with steroidogenic activity, and can bind to different receptors, such as estrogen, androgen, PPAR‐γ, and AhR. These pathways are part of the complex regulatory neuroendocrine network, since its cellular components not only express neuroendocrine receptors, but synthesize and respond to several hormones and other endocrine ligands. On the other hand, the effects of BPA and phthalates on neuroendocrine diseases have been poorly studied and the available data are inconclusive. This can be attributed to the enormous variety of animal models and the different doses used in experiments or levels found in humans. However, what is clear is that exposure to both EDCs during critical life stages induces many changes in the neuroendocrine system of exposed humans that are correlated with different reproductive and neurological diseases.
Human Evolutionary Genetics

Description Theories and methods of molecular population genetics, with emphasis on human examples. How DNA sequence variation is analyzed to infer population history and to identity genes recently subject to selection. Laboratory exercises develop elementary programming skills using Python to show how computation is used in research to connect models and data. Satisfies Quantitative Intensive Requirement.
Callus Induction and Plantlet Regeneration in Orthosiphon aristatus (Blume) Miq.-A Potent Medicinal Herb

An efficient protocol was devised for rapid callus induction and plantlet regeneration from the leaves of Orthosiphon aristatus. For callus induction, auxins such as 2, 4-D, IAA, NAA alone and in combination with cytokinin BAP were used. The most effective medium for callus induction and shoot regeneration was M S medium fortified with 8mg/l BAP and 2mg/l NAA, on which multiple shoots were obtained after 15 days of callus induction. All the in vitro raised shoots with length of 3-5 cm were transferred to rooting medium supplemented with different concentrations of IBA. The best rooting response was observed on half strength M S liquid medium supplemented with 3mg/l IBA. The established plantlets obtained were subjected to hardening and acclimatisation by transferring to polycups containing sterile soil for 3-4 weeks and then to the field, where 85% survived to maturity.
Crude ethanolic extracts of different parts of Gallesia integrifolia (Phytolaccaceae) for the control of Rhipicephalus microplus

ABSTRACT The ectoparasite Rhipicephalus microplus has caused huge economic losses in livestock, and its synthetic chemical control resulted in acaricidal resistant ticks, environmental damages and residues in bovine products. Therefore, it is important to search for alternative products to control this parasite. This study aimed to characterize the crude extracts of different parts of Gallesia integrifolia by GC and MS, and to evaluate the acaricidal activity against R. microplus by adult immersion test (AIT) and larval packet immersion test (LPIT). The acaricidal activity was verified by adult immersion test and larval packet test, while the anticholinesterase activity was done by bioautographic method. The results showed greater larvicidal activity of crude extracts from flowers (LC99.9 = 15.82 mg/mL) and fruits (LC99.9 = 16.13 mg/mL), when compared to the leaf crude extract (LC99.9 = 18.39 mg/mL). Product efficiency of flower and fruit extracts at 12.5 mg/mL was 96.9% and 96.2%, respectively, probably due to the greater amount of sulphur compounds in flowers (21.7%) mainly disulphide, bis(2-sulphhydryl ethyl (12.8%), and in fruits (9.1%), mostly 2,3,5-trithiahexane (5.0%). Thus, G. integrifolia is an alternative to be exploited for the control cattle tick. Graphical abstract
Spatial control of nucleoporin condensation by fragile X‐related proteins

Nucleoporins (Nups) build highly organized nuclear pore complexes (NPCs) at the nuclear envelope (NE). Several Nups assemble into a sieve‐like hydrogel within the central channel of the NPCs. In the cytoplasm, the soluble Nups exist, but how their assembly is restricted to the NE is currently unknown. Here, we show that fragile X‐related protein 1 (FXR1) can interact with several Nups and facilitate their localization to the NE during interphase through a microtubule‐dependent mechanism. Downregulation of FXR1 or closely related orthologs FXR2 and fragile X mental retardation protein (FMRP) leads to the accumulation of cytoplasmic Nup condensates. Likewise, models of fragile X syndrome (FXS), characterized by a loss of FMRP, accumulate Nup granules. The Nup granule‐containing cells show defects in protein export, nuclear morphology and cell cycle progression. Our results reveal an unexpected role for the FXR protein family in the spatial regulation of nucleoporin condensation.
A Quantitative Monitoring Method for Determining Maize Lodging in Different Growth Stages

Many studies have achieved efficient and accurate methods for identifying crop lodging under homogeneous field surroundings. However, under complex field conditions, such as diverse fertilization methods, different crop growth stages, and various sowing periods, the accuracy of lodging identification must be improved. Therefore, a maize plot featuring different growth stages was selected in this study to explore an applicable and accurate lodging extraction method. Based on the Akaike information criterion (AIC), we propose an effective and rapid feature screening method (AIC method) and compare its performance using indexed methods (i.e., variation coefficient and relative difference). Seven feature sets extracted from unmanned aerial vehicle (UAV) images of lodging and nonlodging maize were established using a canopy height model (CHM) and the multispectral imagery acquired from the UAV. In addition to accuracy parameters (i.e., Kappa coefficient and overall accuracy), the difference index (DI) was applied to search for the optimal window size of texture features. After screening all feature sets by applying the AIC method, binary logistic regression classification (BLRC), maximum likelihood classification (MLC), and random forest classification (RFC) were utilized to discriminate among lodging and nonlodging maize based on the selected features. The results revealed that the optimal window sizes of the gray-level cooccurrence matrix (GLCM) and the gray-level difference histogram statistical (GLDM) texture information were 17 × 17 and 21 × 21, respectively. The AIC method incorporating GLCM texture yielded satisfactory results, obtaining an average accuracy of 82.84% and an average Kappa value of 0.66 and outperforming the index screening method (59.64%, 0.19). Furthermore, the canopy structure feature (CSF) was more beneficial than other features for identifying maize lodging areas at the plot scale. Based on the AIC method, we achieved a positive maize lodging recognition result using the CSFs and BLRC. This study provides a highly robust and novel method for monitoring maize lodging in complicated plot environments.
Draft Genome Sequence of a Potential Commercial Biocellulose Producer, Strain Komagataeibacter europaeus GH1

In this work, we present the draft genome sequence of Komagataeibacter europaeus strain GH1 which is an extremely efficient biocellulose producer. ABSTRACT In this work, we present the draft genome sequence of Komagataeibacter europaeus strain GH1, which is an extremely efficient biocellulose producer.
Complete Genome Sequence of an Acetic Acid Bacterium, Acetobacter aceti JCM20276

Acetobacter aceti is used in industry to produce vinegar by converting ethanol into acetic acid. We determined the complete genome sequence of A. aceti JCM20276, which is composed of one chromosome and four plasmids. This study may contribute to a better understanding of the genes necessary for acetic acid production. ABSTRACT Acetobacter aceti is used in industry to produce vinegar by converting ethanol into acetic acid. We determined the complete genome sequence of A. aceti JCM20276, which is composed of one chromosome and four plasmids. This study may contribute to a better understanding of the genes necessary for acetic acid production.
Comparison of TEC Calculations Based on Trimble, Javad, Leica, and Septentrio GNSS Receiver Data

A Global Navigation Satellite System (GNSS) receiver is, to some extent, a “black box” when its data is used for ionospheric studies. Our results based on Javad, Septentrio, Trimble, and Leica GNSS receivers have proven that the accuracy of the slant Total Electron Content (TEC) calculation can differ significantly depending on the GNSS receiver type/model, because TEC measurements depend on the carrier phase tracking technique applied in a receiver. The correlation coefficient between carrier phase noise in L1 and L2 channels is considered as a possible indicator that shows if the L1-aided tracking technique or independent tracking is applied inside a receiver. An empirical model of the TEC noise component was provided to determine the TEC noise value in different types/models of GNSS receivers.
Genetic risk for Alzheimer disease affects the brain throughout the lifespan

Neuronal cell death and loss of synapses are hallmarks of the pathology of Alzheimer disease (AD). The incidence of AD increases with age, and both regional and global brain atrophies have been identified as pathological correlates. Thus, AD can, in many respects, be regarded as a paradigmatic neurodegenerative disorder. However, disrupted function of the presenilin genes, the most common cause of early-onset familial AD (FAD), can also affect brain development, including early processes of neuronal migration and morphogenesis.1
Spatial and Temporal Pasture Biomass Estimation Integrating Electronic Plate Meter, Planet CubeSats and Sentinel-2 Satellite Data

There is a substantial opportunity to lift feed utilization and profitability on pasture-based dairy systems through both increased pasture monitoring accuracy and frequency. The first objective of this experiment was to determine the impact of the number of electronic rising plate meter (RPM) readings and walking pattern on the accuracy of the RPM to determine pasture biomass. The second objective was to evaluate current satellite technology (i.e., small CubeSats and traditional large satellites) in combination with the electronic RPM as an accurate tool for systematic pasture monitoring. The experiment was conducted from October to December 2019 at Camden, Australia. Two experimental paddocks, each of 1.1 ha, were sown with annual ryegrass and monitored with an electronic RPM integrated with Global Navigation Satellite System and with two different satellites (Planet CubeSats and Sentinel-2 satellite). Here we show that 70 RPM readings achieve a ± 5% error in the pasture biomass estimations (kg DM/ha), with no effect of the walking pattern on accuracy. The normalized difference vegetation index (NDVI) derived from satellites showed a good correlation with pasture biomass estimated using the electronic RPM (R2 0.74–0.94). Satellite pasture biomass and growth rate estimations were similar to RPM in one regrowth period but underestimated by ≈20% in the other. Our results also reveal that the accuracy of uncalibrated satellites (i.e., biomass estimated using NDVI to kg DM/ha standard equations) is low (R2 0.61, RMSE 566–1307 kg DM/ha). However, satellites calibrated with a RPM showed greater accuracy in the estimations (R2 0.72, RMSE 255 kg DM/ha). Current satellite technology, when used with the electronic RPM, has the potential to not only reduce the time required to monitor pasture biomass manually but provide finer scale measurements of pasture biomass within paddocks. Further work is required to test this hypothesis, both spatially and temporally.
Applying Deep Learning for Prediction Sleep Quality from Wearable Data

Sleep is not only very important for physical health but also the mental health of human, that was addressed by many previous studies. Today, with the development of technology, which opens in the application for improving quality of sleep, such as wearable devices, artificial intelligence, neural network. In this study, we applied deep learning (DL) neural networks and smart wearable devices to predict the quality of sleep. The data was collected on students (mean age = 20.79) during 106 days by Fitbit Charge HR™ device. The results showed DL models could predict sleep quality base on physical activities in awake time.
A Priority Data Association Policy for Multitarget Tracking on Intelligent Vehicle Risk Assessment

In order to conduct risk assessment for collision-free decision making of intelligent vehicles in a complex road traffic environment, it is essential to conduct stable tracking and state estimation of multiple vehicle targets. Therefore, this paper proposes a multitarget tracking method in line with the priority data association rule. Firstly, a standard coordinate turn process model is deduced as the existence of translation and rotation of the vehicle on the two-dimensional ground plane. Secondly, an unscented Kalman filter algorithm is developed due to the nonlinear radar measurement model. Thirdly, a priority data association rule, which puts the targets in a priority queue according to the number of times they are associated, is designed to filter out noise, given that it is unlikely for a vehicle target as an inertial system to appear or disappear instantly in practice. In addition, the data association rule specifies that the closer the target is to the front of the queue, the more prioritized the association with the newly observed target would be. Finally, the track management algorithm is constructed. On this basis, a series of real vehicle tests were conducted on real roads with four typical scenarios. According to the test results, the proposed algorithm is effective in filtering out noise and is suboptimal as the nearest neighbor data association.