Miracle-dz/UniFAR-FTUs huggingface dataset:
EFFECT OF CHILLING STRESS ON THE PHOTOSYNTHETIC PERFORMANCE OF YOUNG PLANTS FROM TWO MAIZE (ZEA MAYS) HYBRIDS

: In the climate conditions of Bulgaria, early stages of maize plants development often go under suboptimal temperatures. Chilling stress is known to cause different physiological disturbances in young maize plants during the transition period from heterotrophic to autotrophic nutrition. However, the effect of chilling may differ among maize hybrids. Photosynthetic performance could be a good indicator for the hybrid tolerance to chilling. The aim of our study was to evaluate the tolerance of young maize plants from two hybrids – the new Bulgarian hybrid - Kneza 307 and the hybrid P9528 using as criteria the changes in their photosynthetic performance. Plants at the third leaf stage were exposed for seven days to chilling stress. At the end of the experimental period, growth, leaf lipid peroxidation, and several photosynthetic parameters were measured. We found that chilling stress reduced the fresh mass accumulation, increased lipid peroxidation, diminished net photosynthetic rate and chlorophyll content, and enhanced non-photochemical quenching of chlorophyll fluorescence. Although the responses of both hybrids were similar, some specificity were observed and discussed.
Sodium–Calcium Exchanger Reverse Mode Sustains Dichotomous Ion Fluxes Required for Procoagulant COAT Platelet Formation

Abstract Procoagulant collagen-and-thrombin (COAT)-activated platelets represent a subpopulation of activated platelets, which retain a coat of prohemostatic proteins and express phosphatidylserine on their surface. Dichotomous intracellular signaling generating procoagulant platelet activity instead of traditional aggregating endpoints is still not fully elucidated. It has been demonstrated that secondary messengers such as calcium and sodium play a critical role in platelet activation. Therefore, we developed a flow cytometric analysis to investigate intracellular ion fluxes simultaneously during generation of aggregating and procoagulant platelets. Human platelets were activated by convulxin-plus-thrombin. Cytosolic calcium, sodium, and potassium ion fluxes were visualized by specific ion probes and analyzed by flow cytometry. We observed high and prolonged intracellular calcium concentration, transient sodium increase, and fast potassium efflux in COAT platelets, whereas aggregating non-COAT platelets rapidly decreased their calcium content, maintaining higher cytosolic sodium, and experiencing lower and slower potassium depletion. Considering these antithetical patterns, we investigated the role of the sodium–calcium exchanger (NCX) during convulxin-plus-thrombin activation. NCX inhibitors, CBDMB and ORM-10103, dose-dependently reduced the global calcium mobilization induced by convulxin-plus-thrombin activation and dose-dependently prevented formation of procoagulant COAT platelets. Our data demonstrate that both NCX modes are used after convulxin-plus-thrombin-induced platelet activation. Non-COAT platelets use forward-mode NCX, thus pumping calcium out and moving sodium in, while COAT platelets rely on reverse NCX function, which pumps additional calcium into the cytosol, by extruding sodium. In conclusion, we described for the first time the critical and dichotomous role of NCX function during convulxin-plus-thrombin-induced platelet activation.
Evaluation of the probiotic and functional potential of Lactobacillus agilis 32 isolated from pig manure

Escherichia coli is a symbiotic bacterium in humans and animals and an important pathogen of humans and animals. Prevention and suppression of E. coli infection is of great concern. In this study, we isolated a strain of Lactobacillus agilis 32 from pig manure and evaluated its biological characteristics, and found that its bacterial survival rate was 25% after 4 h of treatment at pH 2, and under the condition of 0·5% bile concentration, its survival rate exceeds 30%. In addition, L. agilis 32 has a cell surface hydrophobicity of 77·8%, and exhibits 67·1% auto‐aggregation and 63·2% aggregation with Enterotoxigenic E. coli 10 (ETEC 10). FITC fluorescence labelling showed that the fluorescence intensity of cecum was significantly higher than that of duodenum, jejunum or colon (P < 0·05), but no significant difference from ileum. Lactobacillus agilis 32 bacterial culture and CFS showed average inhibition zone diameters of 14·2 and 15·4 mm respectively. Lactobacillus agilis 32 CFS treatment can significantly reduce the pathogenicity of ETEC 10. These results show that L. agilis 32 is an active and potential probiotic, and it has a good antibacterial effect on ETEC10, which provides basic research for probiotics to prevent and treat intestinal diarrhoea pathogen infection.
Expression of miR-34 family of microRNA and clinical outcome of neuroblastoma

most common cancers in children that arises from sympathetic nervous system tissue with a high rate of incidence in of decrease of survival rates in groups of patients with MDM2 overexpression and MYCN not-amplified low expressed MDM2 neuroblastoma. Taking this into account, analysis of mir-34a expression can help to improve personalized therapy strategy and serve as additional marker for the stratification optimization in patients with neuroblastoma.
Computational modelling of attentional bias towards threat in paediatric anxiety

Abstract Computational modelling can be used to precisely characterize the cognitive processes involved in attentional biases towards threat, yet so far has only been applied in the context of adult anxiety. Furthermore, studies investigating attentional biases in childhood anxiety have largely used tasks that conflate automatic and controlled attentional processes. By using a perceptual load paradigm, we separately investigate contributions from automatic and controlled processes to attentional biases towards negative stimuli and their association with paediatric anxiety. We also use computational modelling to investigate these mechanisms in children for the first time. In a sample of 60 children (aged 5‐11 years) we used a perceptual load task specifically adapted for children, in order to investigate attentional biases towards fearful (compared with happy and neutral) faces. Outcome measures were reaction time and percentage accuracy. We applied a drift diffusion model to investigate the precise cognitive mechanisms involved. The load effect was associated with significant differences in response time, accuracy and the diffusion modelling parameters drift rate and extra‐decisional time. Greater anxiety was associated with greater accuracy and the diffusion modelling parameter ‘drift rate’ on the fearful face trials. This was specific to the high load condition. These findings suggest that attentional biases towards fearful faces in childhood anxiety are driven by increased perceptual sensitivity towards fear in automatic attentional systems. Our findings from computational modelling suggest that current attention bias modification treatments should target perceptual encoding directly rather than processes occurring afterwards.
Dispersal of semi-fleshy fruits to rock crevices by a rock-restricted rodent

Seed dispersal allows successive generations of plants to be mobile in space and time. Heeria argentea’s unusual fruit and its ubiquity in extremely rocky habitats, suggests that this tree requires a specialist disperser. We therefore investigated the dispersal ecology of H. argentea and Hartogiella schinoides. We found M. namaquensis rapidly removed H. argentea and H. schinoides fruits, moving them short distances within and between rock outcrops, and consumed only the pericarps. Birds were observed consuming H. schinoides, but not H. argentea fruits, suggesting M. namaquensis is its sole, specialist disperser. Most H. argentea seeds (65%) with removed pericarps germinated successfully, while intact fruits did not. We show rock outcrops represent fire refugia, allowing H. argentea trees to grow to large sizes, with small stems and a co-occurring, wind-dispersed tree, Widdringtonia nodiflora found away from these sites. This rodent–tree mutualism is perhaps the clearest global example of directed dispersal and shows that these endemic trees are highly adapted for survival in the southwestern Cape habitat and are not tropical relicts. Significance: The fruits of rock-restricted Cape trees are directly dispersed by rock rats to rock outcrops. This is the first description of rodent dispersal of fleshy fruits in South Africa. This species-specific interaction allows for rapid germination of seeds and protection from frequent fires for adults. This rodent–tree mutualism is perhaps the clearest global example of directed seed dispersal. Supplementary Video 1: https://youtu.be/qOgylIJSKpI Supplementary Video 2: https://youtu.be/4jWIUrtzpUk Supplementary Video 3: https://youtu.be/FtBmh-3oYi4
Premature termination codons signal targeted gene repair by nonsense-mediated gene editing in E. coli

Frameshift mutations yield truncated proteins, leading to loss-of-function, genetic disorders or even death. Reverse mutations, which restore the wild-type phenotype of a mutant, have been assumed to be far rarer than forward mutations. However, in this study, screening tests showed that the revertants of a frameshift mutation are detected more frequently than expected in E. coli. Sanger sequencing of the revertants revealed that the reversion of the frameshift mutation is not caused by random mutagenesis but by active targeted gene repair. Molecular studies suggest that premature termination codons (PTCs) in the nonsense mRNAs signal the repair of the frameshift mutation. Genome survey indicate that the genome sequence of a revertant is stable, confirming that the DNA replication proofreading/mismatch repair system of the revertant is not defective. Transcriptome profiling identified dozens of upregulated genes/pathways that possibly involve in frameshift repair, including DNA replication, RNA processing, RNA editing, mismatch repair and homologous recombination. Introducing synthetic DNA or RNA oligonucleotides into the frameshift can promote the gene repair. Based on these data and an in-depth review of previous studies, we hypothesized a molecular model for frameshift repair referred to as nonsense-mediated gene editing (NMGE): nonsense mRNAs are recognized by mRNA surveillance by PTC signaling, edited by RNA editing and then used to direct the repair of their defective coding gene through mismatch repair and homologous recombination. Moreover, NMGE may also serve as a driving force for molecular evolution and a new source of genetic diversity, leads to a widespread existence of frameshift homologs.
EXAMINATION OF OPTICAL COORDINATE MEASUREMENT SYSTEMS IN THE CONDITIONS OF THEIR OPERATION

Intense advancement of optical measurement techniques, which is accompanied by the development of new calibration technologies and accuracy assessment methods determine new fields of necessary research and verification tests. In the Laboratory of Coordinate Metrology of the Cracow University of Technology (LCM CUT), works have been conducted for years dedicated to optical coordinate measurements. It was observed that certain external factors have a dominating influence in the context of value of received results. As a result, a cycle of research in operational conditions was performed, and the most important of them undergo a thorough analysis for exerting influence on the measurement result. Badanie optycznych współrzędnościowych systemów pomiarowych w warunkach ich eksploatacji Słowa kluczowe: współrzędnościowe systemy optyczne, skanery optyczne, triangulacja laserowa, światło strukturalne, algorytmy do pracy z chmurą punktów, rozdzielczość strukturalna. Streszczenie: Intensywny rozwój techniki pomiarów optycznych, któremu towarzyszy opracowywanie nowych technologii wzorcowania oraz metod oceny dokładności pomiaru, wyznacza nowe obszary koniecznych badań i testów weryfikacyjnych. W Laboratorium Metrologii Współrzędnościowej na Politechnice Krakowskiej (LMW PK) od lat trwają prace poświęcone współrzędnościowym pomiarom optycznym, podczas których zaobserwowano dominację pewnych czynników zewnętrznych w kontekście wartości otrzymanego wyniku. W następstwie przeprowadzono cykl badań w warunkach eksploatacyjnych i poddano szczegółowej analizie kluczowe z nich pod kątem wywierania wpływu na wynik pomiaru. p. 7–19
Deep Learning in Data Annotation: Projection-based 2.5D U-net Structure for Biomedical Volumetric Segmentation

This master thesis has been written in collaboration with the Group of Applied Mathematics Innsbruck and the Department of Neuroradiology Innsbruck. We give an introduction to the problem of image segmentation and discuss the idea of fully convolutional networks [16], which provided one of the first network structures to achieve state-of-the-art 2D segmentation masks. Based on them, we stepwise derive the U-net-architecture [18], which constitutes a fully automated method for very accurate semantic segmentation, especially for biomedical images. Additionally, given 3D MRA scans of 119 different patients, we apply all discussed models to them using 2D maximum intensity projections. Furthermore, we extend the U-net to construct volumetric segmentation masks using 3D convolutions [6, 10, 17]. Volumetric convolutions have huge storage requirements and therefore, end-to-end training is limited by GPU memory and data size. To overcome this issue, we introduce a network structure for volumetric data without 3D convolutional layers. The main idea is to include projections (e.g. maximum intensity projections or Radontransforms [7]) from different random directions to transform the volumetric data to a sequence of images, where each image contains information of the full data. We then apply 2D convolutions to these projection images and lift them to volumetric data using a trainable reconstruction algorithm. The proposed network architecture can be applied to arbitrary big data volumes without cropping or sliding-window techniques, which is not possible for network structures using 3D convolutions. For the targeted volumetric binary segmentation of MRA scans, it even shows better performance than the 3D U-net and is much more consistent in terms of accuracy of the output segmentations. Every network in this thesis is constructed with the programming language Python v3.6. 8 (https://www.anaconda.com/download/#linux) using the machine learning library Keras [5] v2.2. 4 with TensorFlow -backend [2] v1.13. 1. We assume that the reader owns good knowledge about the construction and training process of neural networks. Especially understanding the building blocks of convolutional neural networks (i.e. convolutional layers, pooling layers, fully-connected layers et cetera) and the training process of such networks (i.e. loss functions, optimizers et cetera) is important. Information and background on these issues are given in [1, 3, 14].
Towards Automatic Coding of Collaborative Learning Data with Deep Learning Technology

— In Computer Supported Collaborative Learning (CSCL) research, gaining a guideline to carry out appropriate scaffolding by analyzing mechanism of successful collaborative interaction and extracting indicators to identify groups where collaborative process is not going well, can be considered as the most important preoccupation, both for research and for educational implementation. And to study this collaborative learning process, different approaches have been tried. In this paper, we opt for the verbal data analysis; its advantage of this method is that it enables quantitative processing while maintaining qualitative perspective, with collaborative learning data of considerable size. However, coding large scale educational data is extremely time consuming and sometimes goes beyond men’s capacity. So, in recent years, there have also been attempts to automate complex coding by using machine learning technology. In this background, with large scale data generated in our CSCL system, we have tried to implement automation of high precision coding utilizing deep learning methods, which are derived from the leading edge technology of machine learning. The results indicate that our approach with deep learning methods is promising, outperforming the machine learning baselines, and that the prediction accuracy could be improved by constructing models more sensitive to the context of conversation.
Faktori koji utječu na efikasnost genomskih predviđanja u testrižancima biparentalne populacije

Genomic prediction accuracy (r_MP) is affected by many factors, such as the trait heritability, training population size and structure, and the number of markers. This study’s objective was to investigate the factors associated with r_MP for the ear height and the plant height in two planting densities in testcrosses of maize (Zea mays L.) IBM population. Genetic correlations between the training and validation populations were calculated. The high heritability estimates and correlations between the traits were observed. The non-zero estimates of r_MP for all trait-density combinations implied an efficiency of genomic selection. The lower than expected values of genetic correlations were observed between the training and validation populations. However, a strong correlation was observed between a genetic correlation of training and the validation population and r_MP in all three sizes of training populations assessed (20-40%, 40-60%, and 60-80%), suggesting that the size of the training population can be kept low by an appropriate selection while maintaining a high r_MP. Further studies of relationships between the training and validation populations with larger effective population sizes are suggested, as reducing the size of training population while maintaining a high r_MP can facilitate a more effective allocation of resources in a maize breeding program.
WELL-DISPERSED MULTI-WALLED CARBON NANOTUBE/PEEK NANO-COMPOSITES AND THEIR PHOTOLUMINESCENCE PROPERTIES

Photoluminescence (PL) effects have never been observed on multiwalled carbon nanotubes (MWNTs) due to their complex structures. Here, a nanocomposite film composed of 6.5 wt% multi-walled carbon nanotubes (MWNTs) and PEEK polymer was prepared and the individualization of MWNTs was achieved. PL effects were observed from this nanocomposite film which cannot be ascribed solely to either PEEK or MWNTs, but are likely be an unusual property of the nanocomposite generated from its unique composite structure.
OSTROWSKI FOR NUMBER FIELDS

In 1916, Ostrowski [6] classified the nontrivial absolute values on Q: up to equivalence, they are the usual (archimedean) absolute value and the p-adic absolute values for different primes p, with none of these being equivalent to each other. We will see how this theorem extends to a number field K, giving a list of all the nontrivial absolute values on K up to equivalence: for each nonzero prime ideal p in OK there is a p-adic absolute value, real embeddings of K and complex embeddings of K up to conjugation lead to archimedean absolute values on K, and every nontrivial absolute value on K is equivalent to a p-adic, real, or complex absolute value.
Six unusual Cladotanytarsus Kieffer: towards a systematics of the genus and resurrection of Lenziella Kieffer (Diptera: Chironomidae: Tanytarsini)

This dataset contains the digitized treatments in Plazi based on the original journal article Gilka, Wojciech (2011): Six unusual Cladotanytarsus Kieffer: towards a systematics of the genus and resurrection of Lenziella Kieffer (Diptera: Chironomidae: Tanytarsini). Zootaxa 3100: 1-34, DOI: 10.5281/zenodo.202994
Systemic therapy for advanced cholangiocarcinoma: new options on the horizon

Patients with unresectable cholangiocarcinoma (CCA) face a poor prognosis, and there are few effective treatment options for the disease. The standard of care for patients with locally advanced or metastatic CCA is chemotherapy with a gemcitabine-based doublet. Unfortunately, the clinical benefit obtained with these regimens is modest, with a median overall survival of about one year. For CCA that is chemotherapy-refractory or recurs after first-line chemotherapy, the treatment options are even more limited, and no relevant randomized controlled data are available. In recent years, molecular profiling has shed light on the molecular basis of CCA and identified subgroups of patients that might benefit from a personalized treatment approach. These efforts resulted in the recent FDA approval of the fibroblast growth factor receptor (FGFR) inhibitor, pemigatinib, as a second-line treatment for patients with advanced CCA harboring an FGFR2-fusion or rearrangement. Several other targeted agents also are under evaluation in patients with CCA, of which the isocitrate dehydrogenase inhibitor has had the most promising results. Finally, immunotherapy is being explored as a new treatment approach for advanced CCA patients; indeed, the immune checkpoint inhibitor pembrolizumab can already be used to treat CCAs that are mismatch repair deficient. This review is a comprehensive overview of the treatment options for CCA and offers a glimpse into what the future could hold for these patients.
Amyloid β-Protein Oligomerization

Assembly of the amyloid β-protein (Aβ) into neurotoxic oligomers and fibrils is a seminal event in Alzheimer's disease. Understanding the earliest phases of Aβ assembly, including prenucleation and nucleation, is essential for the development of rational therapeutic strategies. We have applied a powerful new method, photoinduced cross-linking of unmodified proteins (PICUP), to the study of Aβ oligomerization. Significant advantages of this method include an extremely short reaction time, enabling the identification and quantification of short lived metastable assemblies, and the fact that no pre facto structural modification of the native peptide is required. Using PICUP, the distribution of Aβ oligomers existing prior to assembly was defined. A rapid equilibrium was observed involving monomer, dimer, trimer, and tetramer. A similar distribution was seen in studies of an unrelated amyloidogenic peptide, whereas nonamyloidogenic peptides yielded distributions indicative of a lack of monomer preassociation. These results suggest that simple nucleation-dependent polymerization models are insufficient to describe the dynamic equilibria associated with prenucleation phases of Aβ assembly.
Methodological Artefacts in Consciousness Science The Case Against the Global Workspace Theory

Consciousness is scientifically challenging to study because of its subjective aspect. This leads researchers to rely on report-based experimental paradigms in order to discover neural correlates of consciousness (NCCs). I argue that the reliance on reports has biased the search for NCCs, thus creating what I call ‘methodological artefacts’. This paper has three main goals: first, describe the measurement problem in consciousness science and argue that this problem led to the emergence of methodological artefacts. Second, provide a critical assessment of the NCCs put forward by the global neuronal workspace theory. Third, provide the means of dissociating genuine NCCs from methodological artefacts.
Advanced concepts for satellite reception of AIS messages

— This paper addresses the problem of demodulating messages received by a low-orbit satellite (altitude between 700 and 800 km) and transmitted by vessels using the Automatic Identification System (AIS). AIS is a Self-Organized Time Division Multiple Access (SO-TDMA) system, in which vessels periodically transmit information (mainly including MMSI – identification code of the ship– and its GPS position). The main application of the actual AIS system is collision avoidance between ships but a satellite reception would lead to a global supervision of maritime traffic, which could be of great interest for a lot of applications (military but also civil applications as fleet surveillance and monitoring).