Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

SUMMARY Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes. Thus, the interactions between bacteria and fungi are of central importance to numerous biological questions in agriculture, forestry, environmental science, food production, and medicine. Here we present a structured review of bacterial-fungal interactions, illustrated by examples sourced from many diverse scientific fields. We consider the general and specific properties of these interactions, providing a global perspective across this emerging multidisciplinary research area. We show that in many cases, parallels can be drawn between different scenarios in which bacterial-fungal interactions are important. Finally, we discuss how new avenues of investigation may enhance our ability to combat, manipulate, or exploit bacterial-fungal complexes for the economic and practical benefit of humanity as well as reshape our current understanding of bacterial and fungal ecology.
Ecology, Diversity, and Evolution of Magnetotactic Bacteria

SUMMARY Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.
Biological Diversity of Prokaryotic Type IV Secretion Systems

SUMMARY Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction.
Ecological Genomics of Marine Picocyanobacteria

SUMMARY Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.
The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

SUMMARY The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
Propofol and barbiturates for the anesthesia of refractory convulsive status epilepticus: pros and cons

Abstract Objective: To discuss mainly the use of propofol and barbiturates in the anesthesia of refractory status epilepticus (RSE). Methods: Review of literature. Results: There are no prospective, randomized works comparing the effects of anesthetics in the treatment of RSE. Recently, the use of propofol has increased in the treatment of RSE. Propofol terminates both clinical and electric seizures quickly, but the maintenance of burst-suppression EEG pattern requires repetitive titration of doses. Relapses of seizures have occurred in 19–33% of patients, especially when tapering of dose. The advantages of barbiturates are lower frequency of short-term treatment failures, breakthrough seizures and changes to a different anesthetic agent. On the other hand, prolonged recovery leads to prolonged duration of mechanical ventilation, intensive care and hospital stay. Discussion: The use of propofol, barbiturates or midazolam in the anesthesia of RSE can be justified. When using propofol, the duration of high doses should be limited to 48 hours and the risk of propofol infusion syndrome should be kept in mind. High doses of barbiturates terminate effectively seizures but recovery from anesthesia prolongs ventilator treatment and intensive care.
Regulatory Circuitry Governing Fungal Development, Drug Resistance, and Disease

SUMMARY Pathogenic fungi have become a leading cause of human mortality due to the increasing frequency of fungal infections in immunocompromised populations and the limited armamentarium of clinically useful antifungal drugs. Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus are the leading causes of opportunistic fungal infections. In these diverse pathogenic fungi, complex signal transduction cascades are critical for sensing environmental changes and mediating appropriate cellular responses. For C. albicans, several environmental cues regulate a morphogenetic switch from yeast to filamentous growth, a reversible transition important for virulence. Many of the signaling cascades regulating morphogenesis are also required for cells to adapt and survive the cellular stresses imposed by antifungal drugs. Many of these signaling networks are conserved in C. neoformans and A. fumigatus, which undergo distinct morphogenetic programs during specific phases of their life cycles. Furthermore, the key mechanisms of fungal drug resistance, including alterations of the drug target, overexpression of drug efflux transporters, and alteration of cellular stress responses, are conserved between these species. This review focuses on the circuitry regulating fungal morphogenesis and drug resistance and the impact of these pathways on virulence. Although the three human-pathogenic fungi highlighted in this review are those most frequently encountered in the clinic, they represent a minute fraction of fungal diversity. Exploration of the conservation and divergence of core signal transduction pathways across C. albicans, C. neoformans, and A. fumigatus provides a foundation for the study of a broader diversity of pathogenic fungi and a platform for the development of new therapeutic strategies for fungal disease.
An approach for mobile agent security and fault tolerance using distributed transactions

Mobile agents are no longer a theoretical issue since different architectures for their realization have been proposed. With the increasing market of electronic commerce it becomes an interesting aspect to use autonomous mobile agents for electronic business transactions. Being involved in money transactions, supplementary security features for mobile agent systems have to be ensured. In this paper we present an architecture for a mobile agent system which guarantees security for the host as well as security for the agent. This architecture additionally offers fault tolerance for the whole agent system at a high level. To handle these issues for mobile agents we use various encryption mechanisms and we apply a novel method for mobile agent systems by using distributed transactions processing based on the OMG Object Transaction Service in our architecture. With this security architecture an agent will be enabled to do money transactions.
Plasticity after acute ischaemic stroke studied by transcranial magnetic stimulation.

Transcranial magnetic stimulation (TMS) is an established technique in which a painless pulse of fast rising magnetic field is used to induce an electric current intracranially, causing depolarisation of nerve membranes and the generation of action potentials. It produces early motor responses trans-synaptically via the pyramidal tract. There are other effects, which are subject to changes in the GABAergic and monoaminergic systems and in sodium and calcium channel properties,1 the first of these showing particular relevance to human plasticity.2 In addition to the familiar clinical studies of central motor conduction time, TMS is used for single motor unit studies, mapping of the motor cortex, the determination of motor threshold or cortical excitability, intracortical inhibition and facilitation studies (using a paired pulse protocol, to express interneuronal connectivity involving the motor cortex), stimulus-response recruitment curves, sensory studies (including the production of phosphenes), and for the targeted disruption of motor or cognitive task performance. Triple stimulation protocols can provide quantitative data on central conduction failure and mapping studies with TMS can be coregistered with structural and functional MRI, or used for the study of functional connectivity across brain regions when combined with simultaneous PET.3 4 A combination of these approaches have now converged on several themes, including the study of excitability changes and plasticity after stroke. Transcranial magnetic stimulation has started to provide support for at least two models of reactive motor changes, in which adaptive reorganisation seems to involve cortical areas that may or may not have been implicated originally in the function of the infarcted area (vicariation and substitution, respectively). These models have stood the test of time but now require thorough re-examination, in parallel with recent elegant work in the monkey.5 The seeds of these two processes are identified within the studies reviewed briefly here, from …
Acupuncture manipulation enhances anti-nociceptive effect on formalin-induced pain in rats

Abstract Objectives: In order to apply appropriate acupuncture stimulation, different needle manipulation techniques are required. These manipulations are performed in many ways such as twirling the needle, varying the insertion angle, etc. The present study was designed to evaluate the antinociceptive effect of these manipulations to the acupuncture point ST36 on formalin-induced pain in rats. Methods: Animals were divided into four groups: non-treated control (CON), acupuncture without manipulation (AT), acupuncture with twirling manipulation (TM) and acupuncture with lifting–thrusting manipulation (LM) group. Level of pain was measured in formalin-injected rats in the early (0–10 minutes) and the late (10–60 minutes) phase. Several pain-related gene expressions were investigated in the spinal cord using reverse transcriptase-polymerase chain reaction analysis. Results: Formalin-induced pain was significantly reduced in the TM and the LM groups, compared with the CON and the AT groups. TM was more effective than LM in both phases. Needle manipulation was also effective in suppressing the mRNA expression of pain-related genes such as Fos, opioid receptor-like 1, tachykinin 1, tachykinin receptor 1, μ-opioid receptor and 5-hydroxytryptamine receptor 2A in the spinal cord. Discussion: The TM and the LM groups showed enhanced analgesia, compared with the AT group. This effect might be related to the suppression of the transcription of pain-related genes.
Cell Biology of Cnidarian-Dinoflagellate Symbiosis

SUMMARY The symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genus Symbiodinium is of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidarian-dinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between green Hydra and its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future.
Inter-Frequency Re-Selection for CSG Cell Interference Avoidance in LTE Network

In 3GPP Rel'8 access to a Home eNodeB may be restricted to only UEs belonging to a Closed Subscriber Group (CSG). These cells are called CSG cells and a UE with CSG subscription would have an Allowed CSG List containing CSG Identities associated with the CSG cells on which the UE is allowed access. This however, can be problematic for the users located near the CSG cells, but who are not allowed to access them. The interference caused by the CSG cell can be devastating if the UE is connected to a macro cell using the same frequency. Some solutions for these interference problems have been proposed in 3GPP standardization and in this study we have evaluated the performance of different options for handling the interference issues related to mixed carrier CSG deployments. The proposals utilize different details of the LTE re-selection algorithm and suggestion on the best solution is also given.
The therapeutic effects of providing patient progress information to therapists and patients

Patient-focused research systems have been developed to monitor and inform therapists of patients' treatment progress in psychotherapy as a method of enhancing outcome. The current study examined the effects of providing treatment progress information to only therapists and to both patients and therapists during the course of psychotherapy. Outpatients (N = 201) at a hospital-based psychotherapy clinic were randomly assigned to 1 of 3 treatment groups: treatment as usual, therapist feedback, and patient–therapist feedback. Patients in the 2 feedback conditions demonstrated significantly greater improvement at termination than those in the treatment-as-usual condition, with no average increase in sessions attended. These findings suggest that providing feedback to patients and therapists may be a viable approach to enhancing patient outcomes.
Anemia and transfusions in geriatric patients: a time for evaluation

Abstract Anemia is common in the elderly, especially in very old patients who are often frail and may be institutionalized. Senescence, the ageing process, puts the elderly at risk of developing anemia for multiple reasons, but anemia may not be attributed to senescence unless a thorough diagnostic workup has excluded other etiologies. Nutritional deficiencies are common and need to be identified and treated appropriately. Inflammatory diseases and renal failure are also frequent etiological factors and tend to be chronic. Myelodysplastic syndromes increase in frequency with age and may be difficult to diagnose and only a minority of cases respond to appropriate treatment. Anemia is associated with poor outcome and symptomatic treatment with transfusions frequently has to be considered. Red blood cell transfusion has a high therapeutic index and is likely to be effective only if anemia is symptomatic or particularly severe, as a consequence, its use has been restricted to this group. Much of the evidence on usage is limited to younger adults and specific clinical situations. Geriatricians have to deal with a large number of patients with significant anemia but with an absence of well constructed guidelines for the frail and the very old. The object of the present article is to raise awareness that anemia in the geriatric group is multi-factorial and that the patients are more than merely older than those included in most studies, that the results of ongoing trials should be appropriately interpreted and will be important in guiding future practice.
Proposal of a score combining red blood cell indices for early differentiation of beta‐thalassemia minor from iron deficiency anemia

Abstract This study evaluates the diagnostic reliability of 11 red blood cells indices, together with our new index, referred to as ‘11T’, in differentiation of beta‐thalassemia minor (BTm) from iron deficiency anemia (IDA). A total of 129 patients with microcytic anemia were involved in a retrospective study, 80 with IDA and 49 with BTm. Using an automatic program, we calculated 11 discrimination indices and a new score, 11T, based on the results of these 11 tests. To confirm the interest of 11T, we performed a prospective study with 53 patients. 11T was most effective in differentiating BTm from IDA: 11T had the highest Youden’s index (83%) and the best percentage of correctly identified patients (93%) and gave optimal performance in our prospective study. We proposed a score, 11T, which is able to discriminate between IDA and BTm with high specificity and high sensitivity in order to conduct the appropriate confirmatory examination.
Revisiting the relationship between code smells and refactoring

Refactoring is a critical technique in evolving software systems. Martin Fowler presented a catalogue of refactoring patterns that defines a list of code smells and their corresponding refactoring patterns. This list aimed at supporting programmers in finding suitable refactoring patterns that remove code smells from their systems. However, a recent empirical study by Bavota et al. shows that refactoring rarely removes code smells which do not align with Fowler's catalog. To bridge the gap between them, we revisit the relationship between code smells and refactorings. In this study, we investigate whether developers apply appropriate refactoring patterns to fix code smells in three open source software systems.