Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence Analysis and Characterization of Recombinant Enzymes from the Thermoacidophilic Archaeon Picrophilus torridus

Picrophilus torridus is a thermo- and acidophilic archaeon which grows optimally at 60°C and pH 0.7 and thus represents the most acidophilic organism known so far. In the frame of the current work the complete genome sequence of P. torridus was determined followed by analysis of the identified genes and the possible metabolic pathways which they possibly encode. The information obtained from the genome was further interpreted with respect to the unique characteristics of the organism. In particular, it was anticipated that the genome sequence of P.torridus would allow a more intense examination of the evolutionary relations among organisms that share similar extreme growth conditions under the special consideration of lateral gene transfer. In order to further investigate the adaptation mechanisms allowing the organism to survive at low pH values, several P. torridus open reading frames were selected for heterologous expression. Standard (E. coli) as well as alternative (S. solfataricus and S. cerevisiae) expression systems were used. Two recombinant enzymes were produced and purified, i.e., α-glucosidase (MalP) and glucose-1-dehydrogenase (GdhA), and biochemically characterised.
Advanced magnetic resonance spectroscopic neuroimaging: Experts' consensus recommendations

Magnetic resonance spectroscopic imaging (MRSI) offers considerable promise for monitoring metabolic alterations associated with disease or injury; however, to date, these methods have not had a significant impact on clinical care, and their use remains largely confined to the research community and a limited number of clinical sites. The MRSI methods currently implemented on clinical MRI instruments have remained essentially unchanged for two decades, with only incremental improvements in sequence implementation. During this time, a number of technological developments have taken place that have already greatly benefited the quality of MRSI measurements within the research community and which promise to bring advanced MRSI studies to the point where the technique becomes a true imaging modality, while making the traditional review of individual spectra a secondary requirement. Furthermore, the increasing use of biomedical MR spectroscopy studies has indicated clinical areas where advanced MRSI methods can provide valuable information for clinical care. In light of this rapidly changing technological environment and growing understanding of the value of MRSI studies for biomedical studies, this article presents a consensus from a group of experts in the field that reviews the state‐of‐the‐art for clinical proton MRSI studies of the human brain, recommends minimal standards for further development of vendor‐provided MRSI implementations, and identifies areas which need further technical development.
Mapping brain–behavior networks using functional and structural connectome fingerprinting in the HCP dataset

Connectome analysis of the human brain's structural and functional architecture provides a unique opportunity to understand the organization of the brain's functional architecture. In previous studies, connectome fingerprinting using brain functional connectivity profiles as an individualized trait was able to predict an individual's neurocognitive performance from the Human Connectome Project (HCP) neurocognitive datasets.
Enabling Tools for Modern Breeding of Cowpea for Biotic Stress Resistance

This chapter summarizes recent advances in genomic resources, technologies, breeding platforms, and molecular markers that are being used to expedite delivery of cowpea cultivars with resistance to important biotic stresses. The genomic resources available in cowpea include high-throughput single nucleotide polymorphism (SNP) genotyping platforms, a high-density consensus genetic map with more than 1,100 markers, a whole genome sequence assembly, bacterial artificial chromosomes (BACs), and a physical map anchored to the genetic map. Markers linked to important biotic resistance traits, including resistance to foliar and flower thrips, Fusarium wilt, root-knot nematode, bacterial blight, ashy stem blight (Macrophomina), Striga, and viruses are described, together with tools developed to integrate SNP genotypes, genetic maps, and trait information to guide breeding. A genetic transformation system has been developed for cowpea and breeding lines developed with resistance to cowpea weevil and Maruca pod borer. Some examples of initial work in evaluating and optimizing marker-assisted backcross and marker-assisted pedigree breeding are described. Major challenges that must be overcome to allow for the adoption of modern marker-assisted breeding (MAB) in cowpea include human and precision phenotyping capacity issues. Further, as essentially all cowpea breeding is being conducted by the public sector with modest resources, efficient strategies are needed to minimize running costs.
Integrating predictive analysis in self-adaptive pervasive systems. (Intégration de l'analyse prédictive dans des systèmes auto-adaptatifs)

In this thesis we proposed a proactive self-adaptation by integrating predictive analysis into two phases of the software process. At design time, we propose a predictive modeling process, which includes the activities: define goals, collect data, select model structure, prepare data, build candidate predictive models, training, testing and cross-validation of the candidate models and selection of the ''best'' models based on a measure of model goodness. At runtime, we consume the predictions from the selected predictive models using the running system actual data. Depending on the input data and the time allowed for learning algorithms, we argue that the software system can foresee future possible input variables of the system and adapt proactively in order to accomplish middle and long term goals and requirements.
FAK Inhibition Induces Glioblastoma Cell Senescence-Like State through p62 and p27

Focal adhesion kinase (FAK) is a central component of focal adhesions that regulate cancer cell proliferation and migration. Here, we studied the effects of FAK inhibition in glioblastoma (GBM), a fast growing brain tumor that has a poor prognosis. Treating GBM cells with the FAK inhibitor PF-573228 induced a proliferative arrest and increased cell size. PF-573228 also reduced the growth of GBM neurospheres. These effects were associated with increased p27/CDKN1B levels and β-galactosidase activity, compatible with acquisition of senescence. Interestingly, FAK inhibition repressed the expression of the autophagy cargo receptor p62/SQSTM-1. Moreover, depleting p62 in GBM cells also induced a senescent-like phenotype through transcriptional upregulation of p27. Our results indicate that FAK inhibition arrests GBM cell proliferation, resulting in cell senescence, and pinpoint p62 as being key to this process. These findings highlight the possible therapeutic value of targeting FAK in GBM.
Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure–function relationships

The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or “movement” of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure–function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work‐flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev
Symptoms of Malignant Fungating Wounds and Functional Performance among Patients with Advanced Cancer: An Integrative Review from 2000 to 2019.

Introduction: Malignant fungating wounds (MFWs), non-healing wounds caused by aggressive proliferation of malignant tumors, afflict 5%-14.5% of patients with advanced cancer. We conducted an integrative review to evaluate the level of evidence of peer-reviewed literature published from 2000 to 2019 on symptoms of MFWs, and the impact of the symptoms on functional performance among patients with advanced cancer. Methods: Four electronic databases were searched and 1506 articles were retrieved. A total of 1056 abstracts were screened for relevance and a full review of the 26 articles was performed. A total of 12 articles met inclusion criteria. An established quality assessment tool was used to rate the quality of the included studies. Results: The overall quality of the included 12 studies was adequate. This integrative review of the literature provided strong evidence that patients with MFWs suffered multiple symptoms, including pain, odor, exudate, bleeding, pruritus, perceived wound status, perceived bulk effect and lymphedema. Quantitative research was not able to capture the occurrence and characteristics of all the identified symptoms. There was a lack of quantitative research on the impact of MFWs and symptoms on patients' functional performance. Yet, qualitative studies provided vivid description of how the symptoms negatively affected patients' functional performance. Future research should develop a clinical tool that enables the comprehensive assessment of symptoms of MFWs. Well-designed quantitative research is needed to delineate the impact of symptoms of MFWs on patients' functional performance to ensure quality palliative care.
Lipoylation and assembly of a 2-oxoacid dehydrogenase multienzyme complex from thermoplasma acidophilum

Energy generating processes like the citric acid cycle are a pivotal part of metabolism. Members of the 2-oxoacid dehydrogenase multienzyme complex (OADHC) superfamily feed into and act within the citric acid cycle. OADHCs are composed of three enzymes: 2-oxoacid decarboxylase (E1), dihydrolipoamide acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Covalent attachment of lipoic acid (LA) to E2 is essential for overall OADHC activity. Although thought to be absent in Archaea, it has recently been found that Thermoplasma acidophilum has all the components for an active recombinant OADHC (Heath et al., 2007). Recent studies have further suggested that Tp. acidophilum may have an enzyme to covalently attach LA to E2 (Sun et al., 2007; McManus et al., 2006). This work describes the cloning and recombinant expression of the Thermoplasma lipoate protein ligase (Tp. LplA), its C-terminal domain and a fusion protein composed of the above two proteins. Both proteins are required for lipoylation of E2 in vitro. For the first time, in vivo lipoylation of E2 in Tp. acidophilum cell cultures is also being reported. The effect of lipoylation and temperature on the Thermoplasma OADHC assembly has also been studied. This study revealed the temperature dependence of the E2 core and the whole complex assembly. These findings are in line with the optimum growth temperature of Tp. acidophilum. Dynamic light scattering and analytical ultracentrifugation were used to determine the molecular mass of whole OADHC. The molecular mass was determined to be 5 MDa with an octahedral geometry of the E2 core. The results of this work strengthen the assumption that these enzyme systems may have had or potentially have a role in the Archaea. This may hold further clues to the evolutionary relationship between the three kingdoms of life and the role of OADHCs/lipoylation in the Archaea. The temperature dependent assembly of the complex and thermostability of these proteins may also provide a model to study thermostability and protein-protein interactions at high temperatures.
Emergence ecology of Orthetrum cancellatum: temporal pattern and microhabitat selection (Odonata: Libellulidae)

Summary. Knowledge of both phenology and habitat selection are important assets for conservation and management purposes. Generally, aquatic insect species have an optimal season and larval microhabitat in which their survival and reproductive success are high. In odonates, emergence is usually a seasonal-restricted process during which the insect has to find a good timing and a convenient microhabitat to carry out the final ecdysis out of the water. We investigated temporal emergence pattern and microhabitat choice in Orthetrum cancellatum in northeast Algeria, which represents the southern limit of its distribution range. The emergence season lasted 56 days starting from 30.IV and ended on 25.VI, showing a peak on 19.V. The time by which 50% of the annual population has emerged (EM50) was 20 days and the sex ratio was slightly male-biased, with 51.53%. Final instar larvae chose areas with relatively dense vegetation, and this selection was positively dependent on the mean vegetation height and not on sex or body size. Height selection was positively dependent only on the support height that the larva chose. We suggest that larvae consider both predation risks and mainly local microclimate to select their emergence site.
The role of SOSTDC1 in interactions between myeloma and cells of osteoblast lineage

Rationale and Hypothesis: Multiple myeloma (MM) is characterised by destructive bone disease, mediated by an increase in osteoclastic bone resorption and impaired osteoblastic bone formation. The canonical Wingless-type (Wnt) and Bone Morphogenic Protein (BMP) signalling pathways have both been implicated in the regulation of bone formation. Our data show that SOSTDC1 is upregulated in the bone marrow (BM) of mice with osteolytic bone disease associated with myeloma. It is unclear whether SOSTDC1 regulates signalling in bone directly, and also which cells in the BM express SOSTDC1. We hypothesise that SOSTDC1 disrupts Wnt and BMP signalling in bone and is expressed by both myeloma cells (MC) and osteoblasts (OB) as a result of myeloma cell/osteoblast interaction. The objectives of this study were to (i) assess the effect of SOSTDC1 on mouse primary osteoblast (pOB) differentiation in the presence of activated BMP and Wnt signalling and (ii) to determine the conditions under which myeloma cells express SOSTDC1. Materials and Methods: Mouse pOB were treated with recombinant SOSTDC1 protein, in the presence or absence of BMP2, BMP7 or Wnt3a. The effects of SOSTDC1 treatment on BMP and Wnt signalling were determined by measuring BMP-activated Smad phosphorylation and phosphorylated β-catenin respectively, using western blot. qPCR was used to assess the effects of SOSTDC1 on the regulation of genes involved in pOB differentiation. Flow-cytometry, immunofluorescence and western blot analysis were used to determine the distribution of SOSTDC1 in MC/OB cultures and co-cultures. Results: SOSTDC1 suppressed BMP2- and BMP7-induced Smad phosphorylation and also Wnt3a-induced β-catenin phosphorylation in pOB (P<0.05). Both Runx2a and total β-catenin expression (qPCR) were reduced following treatment with SOSTDC1, suggesting that SOSTDC1 suppresses Wnt3a-induced pOB differentiation (P<0.05). Flow-cytometry, immunofluorescence and western blot data all suggest that SOSTDC1 is switched on in OB and increased in MC, when these two cells are cultured together. Conclusions: Our findings suggest that increased SOSTDC1 levels may result from OB/MC contact and that this may result in suppression of OB differentiation. Taken together these results suggest that targeting SOSTDC1 may reduce osteolytic bone disease observed in MM.
On the definition of finite operator quantities in quantum electrodynamics

Field equations for finite quantized fields are obtained by including a limiting process in the definition of the non-linear terms, generalizing thereby a method of Dirac and Heisenberg.The equations are deduced from an action integral, the compensating terms of which are defined by means of vacuum expectation values of operators.The compensating functions depend on several off-diagonal distances, and are expressed in terms of space-time averages, without reference to Fourier transforms.The concept of renormalization and its possible arbitrariness are discussed. In the determination of finite quantities the use of the commutation relations of incoming free fields is assumed. Since the commutation relations of (renormalized) field quantities, for equal time arguments, are related to infinities for physical reasons, the form of the canonical formalism which relates the concept of a state-vector to a given space-like surface, does not seem suitable as a basis for a consistent finite field theory.
Selección de genotipos de caña de azúcar usando características de cultivo de callos

Los programas para obtener nuevos genotipos de cana de azucar (Saccharum officinarum) duran de 10 a 15 anos y la etapa de seleccion es la que consume mas tiempo. Por tanto, se realizo un estudio para determinar la relacion entre las caracteristicas de los cultivos de callos y variables agronomicas de plantas derivadas de callos de cuatro genotipos de cana de azucar cultivados en Mexico. Se encontro que el peso fresco de los callos se correlaciono con el tallo industrializable, con el numero de entrenudos y numero de tallos. El contenido de sacarosa en los callos se correlaciono con la longitud del tallo industrializable y el diametro de los entrenudos El peso fresco y el contenido de sacarosa en los callos son dos caracteristicas de los cultivos in vitro que deben estudiarse con mas genotipos antes de usarse para seleccionar genotipos de cana de azucar en programas de mejoramiento
Molecular Cytogenetic Analysis: Applications in Cancer

Molecular cytogenetics has played an important role in the rapid and precise characterisation of chromosome anomalies, which can serve as hallmarks of different types of cancer. The authors have considerably advanced their understanding of the molecular events involved in the initiation and progression of various cancers, with the aid of molecular cytogenetic technologies. Techniques such as fluorescence in situ hybridisation, as well as recent high-throughput sequencing methods that give a comprehensive insight into cancer genomics, have helped in the early identification of at-risk individuals. These techniques also allow for an earlier detection of cancer, prognosis optimisation and the opportunity for a cure. This article highlights the application of molecular cytogenetics analysis in various cancers. Key Concepts: All cancers display at least one numerical or structural chromosome aberration. Molecular cytogenetics enables a clinician to decide the best testing strategy for cancer patients. Molecular cytogenetic techniques provide a snapshot of all the molecular activities in a tumour sample facilitating the discovery of totally novel and unexpected functional roles of genes. Techniques such as fluorescence in situ hybridisation is highly recommended for identifying key biomarkers in various cancers. DNA microarray technology has led to identification of certain anomalies in cancer that were once thought to be non-traceable. Next generation sequencing has enabled to catalogue the genomic landscape of thousands of cancer genomes across many disease types. Molecular cytogenetic methods have subclassified tumours that are important in identifying or tailoring responsiveness to targeted therapies. The high sensitivity and specificity of the molecular cytogenetic techniques make them useful adjuvants to conventional banding in the screening for all types of chromosomal aberration. A new era of bridging molecular cytogenetics and personalised medicine has emerged that will help to monitor disease progression and molecularly guided therapies. Keywords: molecular cytogenetics; genomics; cancer; fluorescence in situ hybridisation; spectral karyotyping; M-FISH; CGH; array-CGH; next generation sequencing
Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal‐restriction fragment length polymorphisms

1. T‐RFLP is an established tool for high‐throughput studies of microbial communities, which can, with care and practical validation, be enhanced to aid identification of specific organisms in a community by associating T‐RFs from experimental runs with predicted T‐RFs from a set of existing sequences. A barrier to this approach is the laborious process of selecting diagnostic restriction enzyme(s) for further validation.
Initial preference for plant species and state during oviposition site selection by an odonate

Endophytic egg‐laying odonates use an ovipositor to insert their eggs inside plant tissues. Before egg deposition, oviposition site selection consists of two crucial steps: (i) the initial choice, typically decided in species that oviposit in tandem within vertical substrates by the male when landing and then by the female by staying on the substrate or flying to another; and (ii) the insertion site choice, made by the female who uses her ovipositor to palpate the substrate. Some odonates prefer to deposit their eggs within specific plant species. Some are able to discriminate between living and dead substrates during the initial choice. However, the extent to which odonates discriminate among distinct plant species during the initial choice is unknown. We studied the initial site preference in Lestes macrostigma (Odonata: Lestidae) to determine whether the males and/or females show a distinct preference among five types of shoots when landing on or when palpating the substrate, respectively. Male L. macrostigma preferred to land on Bolboschoenus maritimus and dead Juncus spp. When focusing on J. maritimus, females preferentially palpated the substrate when the male landed on dead shoots. We suggest that the male preference for these substrates is consistent with that of the female during insertion site choice but also during egg deposition. Such behavior should reduce the duration of oviposition, with benefits of reducing the predation risk and increasing available time for foraging. The advantage in preferring these substrates should be linked to a selection pressure acting on egg development and/or survival.
Protein phosphorylation in the nervous system

Protein Kinases. Protein Phosphatases. Substrate Proteins. Direct Evidence for a Role of Protein Phosphorylation in Neuronal Function. Applications of Protein Phosphorylation Systems to Other Areas of Neuroscience. Initial Studies of the Molecular Biology of Protein Phosphorylation Systems. General Themes. Interactions Among Protein Phosphorylation Systems.