Asc-Seurat: analytical single-cell Seurat-based web application.

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a peripheral blood mononuclear cell dataset. CONCLUSIONS: Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

Determining the value of the abdominal core health quality collaborative to support regulatory decisions.

PURPOSE: The study objective is to document value created by real-world evidence from the Abdominal Core Health Quality Collaborative (ACHQC) for regulatory decisions. The ACHQC is a national effort that generates data on hernia repair techniques and devices. METHODS: Two retrospective cohort evaluations compared cost and time of ACHQC analyses to traditional postmarket studies. The first analysis was based on 25 reports submitted to the European Medicines Agency of 20 mesh products for post-market surveillance. A second analysis supported label expansion submitted to the Food and Drug Administration, Center for Devices and Radiological Health for a robotic-assisted surgery device to include ventral hernia repair. Estimated costs of counterfactual studies, defined as studies that might have been done if the registry had not been available, were derived from a model described in the literature. Return on investment, percentage of cost savings, and time savings were calculated. RESULTS: 45,010 patients contributed to the two analyses. The cost and time differences between individual 25 ACHQC analyses (41,112 patients) and traditional studies ranged from $1.3 to $2.2 million and from 3 to 4.8 years, both favoring use of the ACHQC. In the second label expansion analysis (3,898 patients), the estimated return on investment ranged from 11 to 461% with time savings of 5.1 years favoring use of the ACHQC. CONCLUSIONS: Compared to traditional postmarket studies, use of ACHQC data can result in cost and time savings when used for appropriate regulatory decisions in light of key assumptions.

Initial Experiences with Amyloid-Related Imaging Abnormalities in Patients Receiving Aducanumab Following Accelerated Approval.

Aducanumab is the first FDA-approved amyloid-lowering immunotherapy for Alzheimer's disease. There is little real-world data to guide management of amyloid-related imaging abnormalities (ARIA), a potentially serious side-effect which requires surveillance with magnetic resonance imaging. We report our experiences in managing ARIA in patients receiving aducanumab at the Butler Hospital Memory and Aging Program during the year following FDA approval. We followed the Appropriate Use Recommendations for aducanumab to guide patient selection, detection, and management of ARIA (1). ARIA-E occurred in 6 out of 24 participants treated; all APOE-ε4 carriers. Treatment was discontinued in 4 cases of moderate-severe ARIA-E, temporarily held in 1 moderate case, and dosed through in 1 mild case (mean duration = 3 months, range, 1-6 months). No participants required hospitalization or high dose corticosteroids. Participants on anticoagulation were excluded and no macrohemorrhages occurred. These data support the measured approaches to treatment outlined in the Appropriate Use Recommendations.

Epidemiological and clinical aspects of human Brucella suis infection in Polynesia.

High brucellosis seroprevalence rates in domestic swine herds have been reported in Wallis and Futuna Islands and are associated with a significant burden of human infection by Brucella suis, a species that is rarely incriminated in human disease. Between 2003 and 2010, seven patients had a positive blood culture for B. suis biovar 1, 11 symptomatic patients had a positive Rose Bengal test (RBT) and a positive serum agglutination test (SAT) and three asymptomatic cases were found to be positive for RBT, SAT or ELISA IgM (after systematic screening of 52 family members of 15 index cases). Overall, Brucella infection was diagnosed in 21 people, corresponding to a mean annual incidence of 19 cases/100 000 inhabitants. Compared to series of patients infected with other more commonly encountered Brucella spp. such as B. melitensis and B. abortus, clinical presentation and percentage and distribution of complications were similar, apart from a marked observation of significantly increased median alanine aminotransferase levels, 20 times greater than upper normal rates, but not accompanied by any particular hepatic pathology. Wallis and Futuna, where people live in close proximity to animals and where the cultural significance of pig-raising precludes the implementation of adequate veterinary preventive measures, thus represents one of the few known B. suis foci worldwide and allows for evaluation of the peculiarities of this infection.

Identification of genes encoding hypothetical proteins in open-reading frame expressed sequence tags from mammalian stages of Trypanosoma cruzi.

Approximately 50% of the predicted protein-coding genes of the Trypanosoma cruzi CL Brener strain are annotated as hypothetical or conserved hypothetical proteins. To further characterize these genes, we generated 1161 open-reading frame expressed sequence tags (ORESTES) from the mammalian stages of the VL10 human strain. Sequence clustering resulted in 435 clusters, consisting of 339 singletons and 96 contigs. Significant matches to the T. cruzi predicted gene database were found for ~94% contigs and ~69% singletons. These included genes encoding surface proteins, known to be intensely expressed in the parasite mammalian stages and implicated in host cell invasion and/or immune evasion mechanisms. Among 151 contigs and singletons with similarity to predicted hypothetical protein-coding genes and conserved hypothetical protein-coding genes, 83% showed no match with T. cruzi EST and/or proteome databases. These ORESTES are the first experimental evidence that the corresponding genes are in fact transcribed. Sequences with no significant match were searched against several T. cruzi and National Center for Biotechnology Information non-redundant sequence databases. The ORESTES analysis indicated that 124 predicted conserved hypothetical protein-coding genes and 27 predicted hypothetical protein-coding genes annotated in the CL Brener genome are transcribed in the VL10 mammalian stages. Six ORESTES annotated as hypothetical protein-coding genes showing no match to EST and/or proteome databases were confirmed by Northern blot in VL10. The generation of this set of ORESTES complements the T. cruzi genome annotation and suggests new stage-regulated genes encoding hypothetical proteins.

Vaccine third dose and cancer patients: necessity or luxury?

The current state of the SARS-CoV-2 pandemic is an equilibrium between expanding vaccine coverage on the one hand, and emergence of variants of concern which compromise vaccine effectiveness and enhance viral transmission on the other. Inequity in vaccine distribution, primarily an ethical issue, challenges this equilibrium, as industrialized countries prepare to administer a third booster dose to their population. Solid tumor cancer patients typically respond well to initial full vaccination and someone could argue that they should not be prioritized for an adjuvant third dose, since protection from severe disease has largely been achieved with the two-dose regimen. Nevertheless, their immune status is dynamic and not all of them exhibit an adequate immune response. A booster third dose is necessary for the inadequate responders, while it will result in better protection of all patients from mild disease as well, which if presented could have ominous consequences due to their overall frailty, and their need to adhere to strict therapeutic schemes. International scientific and public health communities should develop approaches that allow for wide immediate vaccination coverage of the developing world, in parallel with administration of adjuvant doses to solid tumor cancer patients (and other at-risk categories) of the developed nations, in order to avoid prolonging the pandemic, which will be prospectively against cancer patients' best interest.

Decreasing trends of ultrasonographic prevalence of cystic echinococcosis in a rural Greek area.

Greece is considered as one of the endemic European countries for cystic echinococcosis (CE). We evaluated the prevalence trends of CE in the rural area of Trikala, Central Greece, through ultrasound records for the period 2001-2008. Of the 47,045 total number of abdominal ultrasound tests performed in the period 2001-2008, a total of 153 individuals had abdominal CE. Despite this generally high figure, significantly lower prevalence rates were noted during the second half of the study period. The implementation of a national campaign for CE control, started in 1984, has led to decreasing annual detection rates of CE in Central Greece.

Cilia formation in the adult cat brain after pargyline treatment.

The brains of four adult cats treated with pargyline (a nonhydrazide monoaminoxidase inhibitor) were examined at both the light and electron microscopic levels. Formation of typical mature cilia with the 9 + 2 pattern was observed in neural cells in the following areas: habenula nuclei, interpeduncular nuclei, hippocampus, mammillary bodies, thalamus, and caudate nucleus. The most marked ciliation occurs in the habenula nuclei. In general, glial cells greatly predominate in the formation of cilia. It is not clear whether ciliation in the central nervous system is the direct result of pargyline or if it occurs indirectly as a result of inhibition of monoaminoxidase. These findings are compared with the serotonin effect on ciliation in the embryogenesis of lower forms. It is suggested that pharmacological stimulation of centriolar reproduction without subsequent mitosis may lead to ciliary formation.

Atypical gap junctions in the ciliary epithelium of the albino rabbit eye.

Gap junctions are present between nonpigmented and pigmented epithelial cells layers, as well as between the adjacent pigmented cells, but not between the nonpigmented epithelial cells which face the posterior chamber. The unusual feature of these gap junctions is a dark banding which regularly appears every three rows of subunits. This dark band is the equivalent width of two rows of facets.

Morphological correlates of increased coupling resistance at an electrotonic synapse.

Close appositions between axonal membranes are present in the septum between adjacent axonal segments of the septate or lateral giant axons of the crayfish Procambarus. In sections the closely apposed membranes appear separated by a space or gap. The use of lanthanum indicates that there may be structures connecting the apposed membranes. The apparent gap is actually a network of channels continuous with the extracellular space. Adjacent axonal segments are electrotonically coupled at the septa. The coupling resistance is increased by mechanical injury of an axon, immersion in low Cl(-) solutions, and immersion in low Ca(++) solutions, followed by a return to normal physiological solution. Septa at which coupling resistance had been measured were examined in the electron microscope. The induced increases in coupling resistance are associated with separation of the junctional membranes (with the exception of the moderate increases during immersion in low Ca(++) solutions). Schwann cell processes are present between the separated axonal membranes. When nerve cords in low Cl(-) solutions are returned to normal physiological solution, coupling, i.e., electrotonic synapses. A model of an electrotonic synapse is proposed in which tween axonal membranes are again found. The association between the morphological and physiological findings provides further evidence that the junctions are the sites of electrotonic coupling, i.e., electrotonic, synapses. A model of an electrotonic synapse is proposed in which intercytoplasmic channels not open to the extracellular space are interlaced with a hexagonal network of extracellular channels between the apposed junctional membranes.

Membrane specializations of dentritic spines and glia in the weaver mouse cerebellum: a freeze-fracture study.

Electron microscopy of thin-sectioned and freeze-fractured preparations of the cerebellum of the weaver mouse indicates that the dendritic spines are morphologically identical to those of their normal littermates. The weaver dendritic spines have been characterized as "unattached" since the synaptic input from the parallel fibers is absent (8-10). The entire region around the dendritic spines is taken up by astrocytic processes in the weaver. The outer fracture face of a normal dendritic spine contains aggregations of 10-nm wide particles in the immediate postsynaptic region. Similar particle aggregations occur in the unattached spines of the weaver. Freeze-fracture preparations reveal rectilinear arrays of particles, having a 7-nm center-to-center distance in the glial membranes. Rectilinear arrays are apparently distributed throughout the astrocyte membrane.

The fine structure of a rectifying electrotonic synapse.

The synapses between the lateral giant axon and the giant motor axon found in the abdominal ganglia of the ventral nerve cord of the crayfish Procambarus clarkii are electronic. The junctional membrane rectifies, favoring impulse transmission from lateral giant fiber to giant motor fiber. This rectifying electronic junction consists of closely apposed membranes indistinguishable from ordinary arthropod gap junctions. The apposed membranes contain intramembrane particles that are approximately 12.5 nm in width. These particles have a central depression and are arranged in a loosely ordered array with a center-to-center spacing of about 20 nm. The only obvious morphological evidence of asymmetry is the presence of vesicles (about 80 nm in diameter) in the cytoplasm adjacent to the junctional region of the presynaptic lateral giant fiber. Vesicles are not present in the adjacent cytoplasm of the postsynaptic giant motor fiber; however, mitochondria and smooth tubular endoplasmic reticulum are more frequent in the cytoplasm of the giant motor fiber.

Morphological correlates of functional differentiation of nodes of Ranvier along single fibers in the neurogenic electric organ of the knife fish Stern archus.

Electric organs in Sternarchidae are of neural origin, in contrast to electric organs in other fish, which are derived from muscle. The electric organ in Sternarchus is composed of modified axons of spinal neurons. Fibers comprising the electric organ were studied by dissection and by light- and electron microscopy of sectioned material. The spinal electrocytes descend to the electric organ where they run anteriorly for several segments, turn sharply, and run posteriorly to end blindly at approximately the level where they enter the organ. At the level of entry into the organ, and where they turn around, the axons are about 20 micro in diameter; the nodes of Ranvier have a typical appearance with a gap of approximately 1 micro in the myelin. Anteriorly and posteriorly running parts of the fibers dilate to a diameter of approximately 100 micro, and then taper again. In proximal and central regions of anteriorly and posteriorly running parts, nodal gaps measure approximately 1 micro along the axon. In distal regions of anteriorly and posteriorly running parts are three to five large nodes with gaps measuring more than 50 micro along the fiber axis. Nodes with narrow and with wide gaps are distinguishable ultrastructurally; the first type has a typical structure, whereas the second type represents a new nodal morphology. At the typical nodes a dense cytoplasmic material is associated with the axon membrane. At large nodes, the unmyelinated axon membrane is elaborated to form a closely packed layer of irregular polypoid processes without a dense cytoplasmic undercoating. Electrophysiological data indicate that typical nodes in proximal regions of anteriorly and posteriorly running segments actively generate spikes, whereas large distal nodes are inactive and act as a series capacity. Increased membrane surface area provides a morphological correlate for this capacity. This electric organ comprises a unique neural system in which axons have evolved so as to generate external signals, an adaptation involving a functionally significant structural differentiation of nodes of Ranvier along single nerve fibers.

An electron microscopic study of the development of synapses in cultured fetal mouse cerebrum continuously exposed to xylocaine.

Explants of fetal mouse cerebral cortex, continuously exposed to the local anesthetic Xylocaine from the time of explantation to the time of fixation, were examined in the electron microscope to determine whether morphologically normal synapses and potentially functional interneuronal synaptic networks can form in the absence of electrical impulse activity. Morphological differentiation of complex synaptic networks proceeds normally, and the drug does not alter the fine structure of the formed synapses. These observations are consonant with the electrophysiological data which show that the potential for complex bioelectric activity can develop in the absence of its expression. The development and maturation of functional synaptic networks, then, is not contingent upon prior electrical impulse activity. These data support the concept that organized neuronal assemblies are formed in forward reference to their ultimate function.

Permeability and structure of junctional membranes at an electrotonic synapse.

The dye Procion Yellow M4RS crosses junctional membranes from cytoplasm to cytoplasm at electrotonic synapses between segments of the crayfish septate axon. The dye does not enter the cells from extracellular space. Thus permeability of junctional membranes is qualitatively different from that of nonjunctional membranes. Electron microscopy after fixation in the presence of lanthanum hydroxide indicates that these synapses are "gap junctions" and that there is a network of channels continuous with extracellular space between apposed junctional membranes. These channels must be interlaced with intercytoplasmic channels that are not open to extracellular space.

Temperature-dependence of resistance at an electrotonic synapse.

The junctional resistance at septa of the crayfish lateral giant axon is inversely related to temperature with a Q(1l), of about 3 over the range from 5 degrees to 20 degrees C. Nonjunctional axonal membrane is much less affected. Resistance changes occur rapidly with temperature changes. No correlates in ultrastructure of the synapses have been found.

Oculomotor neurons in fish: electrotonic coupling and multiple sites of impulse initiation.

Oculomotor neurons are electrotonically coupled in three teleosts. Electron microscopy revealed axosomatic synapses with close appositions of pre- and postynaptic membranes. Similar junctions are associated with electrotonic coupling in many other cases. Stimulation of the ipsilateral eighth nerve usually initiated impulses at sites distant from the cell bodies; stimulation of the ipsilateral ophthalmic nerve initiated impulses close to the cell bodies. Electrotonic coupling may synchronize impulses arising near the, cell bodies to generate synchronous muscle contractions. Impulses arising distant from the cell bodies may lead to contractions of graded strength.

Bacterial diversity associated with the Brazilian endemic reef coral Mussismilia braziliensis.

AIMS: We performed the first characterization of the microbiota associated with the reef coral Mussismilia braziliensis by means of a culture-independent approach. METHODS AND RESULTS: The main groups were Proteobacteria, Cyanobacteria and unclassified bacteria according to the 16S rDNA libraries. Most of the sequences of the mucus of healthy and diseased M. braziliensis did not find close matches in GenBank (i.e. >97% 16S rDNA similarity). Most of the sequences of seawater and mucus of healthy coral fell into tight clusters (17 and 15 clusters respectively). In contrast, most of the sequences of mucus of diseased coral did not form clusters. The rarefaction curves indicate saturation in the recovery of higher taxa (approximately 40 phyla). However, the number of species in the coral mucus (n = 130-170) and seawater (n = 170) did not reach a plateau. CONCLUSIONS: The coral microbiota encompasses several potentially novel species and higher taxa. The microbiota of M. braziliensis appears to be species-specific. Diseased coral may have provided a suitable place for colonization by opportunistic bacteria, resulting in a greater bacterial diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: The first study on the diversity of the microbiota of the endemic and endangered of extinction coral M. braziliensis.

Vaccination of asplenic or hyposplenic adults.

BACKGROUND: Sepsis is a feared complication in patients with an absent or dysfunctioning spleen. METHODS: A literature search was undertaken to identify recommendations for vaccination in asplenic or hyposplenic adults, and published data regarding the effectiveness of the vaccines in reducing the incidence of infections, and vaccine failures. RESULTS: Various committees and organizations recommend that the pneumococcal, meningococcal and Haemophilus influenza vaccine, plus booster doses, should be administered to patients with an absent or dysfunctional spleen. However, adherence to such recommendations varies. Furthermore, vaccine failures still occur in a subset of properly immunized individuals. Immunocompromised individuals, in particular, have a greater risk of inadequate antibody response. CONCLUSION: Immunization is partially responsible for the observed reduction in sepsis after splenectomy.

Characterization of Aspergillus flavus strains from Brazilian Brazil nuts and cashew by RAPD and ribosomal DNA analysis.

AIMS: The aim of this study was to determine the genetic variability in Aspergillus flavus populations from Brazil nut and cashew and develop a polymerase chain reaction (PCR) detection method. METHODS AND RESULTS: Chomatography analysis of 48 isolates identified 36 as aflatoxigenic (75%). One hundred and forty-one DNA bands were generated with 11 random amplified polymorphic DNA (RAPD) primers and analysed via unweighted pair group analysis, using arithmetic means (UPGMA). Isolates grouped according to host, with differentiation of those from A. occidentale also according to geographical origin. Aspergillus flavus-specific PCR primers ASPITSF2 and ASPITSR3 were designed from ribosomal DNA internal transcribed spacers (ITS 1 and 2), and an internal amplification control was developed, to prevent false negative results. Specificity to only A. flavus was confirmed against DNA from additional aspergilli and other fungi. CONCLUSIONS: RAPD-based characterization differentiated isolates according to plant host. The PCR primer pair developed showed specificity to A. flavus, with a detection limit of 10 fg. SIGNIFICANCE AND IMPACT OF THE STUDY: Genetic variability observed in A. flavus isolates from two Brazilian agroecosystems suggested reproductive isolation. The PCR detection method developed for A. flavus represents progress towards multiplex PCR detection of aflatoxigenic and nonaflatoxigenic strains in Hazard Analysis Critical Control Point systems.