V-NeuroStack: Open-source 3D time stack software for identifying patterns in neuronal data

Understanding functional correlations between the activities of neuron populations is vital for the analysis of neuronal networks. Analyzing large-scale neuroimaging data obtained from hundreds of neurons simultaneously poses significant visualization challenges. We developed V-NeuroStack, a novel network visualization tool to visualize data obtained using calcium imaging of spontaneous activity of neurons in a mouse brain slice as well as in vivo using two-photon imaging. V-NeuroStack creates 3D time stacks by stacking 2D time frames for a time-series dataset. It provides a web interface to explore and analyze data using both 3D and 2D visualization techniques. Previous attempts to analyze such data have been limited by the tools available to visualize large numbers of correlated activity traces. V-NeuroStack's 3D view is used to explore patterns in dynamic large-scale correlations between neurons over time. The 2D view is used to examine any timestep of interest in greater detail. Furthermore, a dual-line graph provides the ability to explore the raw and first-derivative values of activity from an individual or a functional cluster of neurons. V-NeuroStack can scale to datasets with at least a few thousand temporal snapshots. It can potentially support future advancements in in vitro and in vivo data capturing techniques to bring forth novel hypotheses by allowing unambiguous visualization of massive patterns in neuronal activity data.

Nosocomial SARS-CoV-2 transmission in postoperative infection and mortality: analysis of 14 798 procedures

This study used a national administrative database to estimate perioperative SARS-CoV-2 infection risk, and associated mortality, relative to nosocomial transmission rates. The impact of nosocomial transmission was greatest after major emergency surgery, whereas laparoscopic surgery may be protective owing to reduced duration of hospital stay. Procedure-specific risk estimates are provided to facilitate surgical decision-making and informed consent. Estimated risks.

Bilateral Scapulothoracic Fusions Fixed with High-Strength Suture Tapes for Facioscapulohumeral Dystrophy: A Case Report

CASE

A 32-year-old male right-hand dominant school-bus driver with facioscapulohumeral dystrophy (FSHD) was referred to an upper limb specialist for consideration for scapulothoracic fusion (STF) because of limited upper limb function and cosmetic issues. Staged bilateral STFs were performed with seven high-strength suture tapes tensioned to secure a standard tubular plate in situ.

CONCLUSION

STF may be a desirable treatment option for patients with FSHD. The use of high-strength suture tapes in cases of STF allows for secure fixation of the scapulothoracic joint. This potentially confers a reduction in operative time while ensuring adequate tensioned fixation and minimizing the risk of iatrogenic pneumothorax.

Enhanced expression of transferrin receptor 1 contributes to oncogenic signalling by sphingosine kinase 1

Sphingosine kinase 1 (SK1) is a lipid kinase that catalyses the formation of sphingosine-1-phosphate (S1P). Considerable evidence has implicated elevated cellular SK1 in tumour development, progression and disease severity. In particular, SK1 has been shown to enhance cell survival and proliferation and induce neoplastic transformation. Although S1P has been found to have both cell-surface G-protein-coupled receptors and intracellular targets, the specific downstream pathways mediating oncogenic signalling by SK1 remain poorly defined. Here, using a gene expression array approach, we have demonstrated a novel mechanism whereby SK1 regulates cell survival, proliferation and neoplastic transformation through enhancing expression of transferrin receptor 1 (TFR1). We showed that elevated levels of SK1 enhanced total as well as cell-surface TFR1 expression, resulting in increased transferrin uptake into cells. Notably, we also found that SK1 activation and localization to the plasma membrane, which are critical for its oncogenic effects, are necessary for regulation of TFR1 expression specifically through engagement of the S1P G-protein coupled receptor, S1P2. Furthermore, we showed that blocking TFR1 function with a neutralizing antibody inhibits SK1-induced cell proliferation, survival and neoplastic transformation of NIH3T3 fibroblasts. Similar effects were observed following antagonism of S1P2. Together these findings suggest that TFR1 has an important role in SK1-mediated oncogenesis.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

Robotics and virtual reality: the development of a life-sized 3-D system for the rehabilitation of motor function

We have been developing and combining state-of-art devices that allow humans to visualize and feel synthetic objects superimposed on the real world. This effort stems from the need of platform for extending experiments on motor control and learning to realistic human motor tasks and environments, not currently represented in the practice of research. This paper's goal is to outline our motivations, progress, and objectives. Because the system is a general tool, we also hope to motivate researchers in related fields to join in. The platform under development, an augmented reality system combined with a haptic-interface robot, will be a new tool for contributing to the scientific knowledge base in the area of human movement control and rehabilitation robotics. Because this is a prototype, the system will also guide new methods by probing the levels of quality necessary for future design cycles and related technology. Inevitably, it should also lead the way to commercialization of such systems.

PATRIC: the VBI PathoSystems Resource Integration Center

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: ‘breadth first’ beginning with whole-genome and proteome curation using standardized protocols, a ‘targeted’ approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website () will continually grow with the addition of data, analysis and functionality over the course of the project.

SETTING STANDARDS FOR TRAINING AND COMPETENCE: THE UK ALCOHOL TREATMENT TRIAL

AIMS

To examine factors that influence the recruitment and training of therapists and their achievement of competence to practise two psychological therapies for alcohol dependence, and the resources required to deliver this.

METHODS

The protocol for the UK Alcohol Treatment Trial required trial therapists to be competent in one of the two trial treatments: Social Behaviour and Network Therapy (SBNT) or Motivational Enhancement Therapy (MET). Therapists were randomised to practise one or other type of therapy. To ensure standardisation and consistent delivery of treatment in the trial, the trial training centre trained and supervised all therapists.

RESULTS

Of 76 therapists recruited and randomised, 72 commenced training and 52 achieved competence to practise in the trial. Length of prior experience did not predict completion of training. However, therapists with a university higher qualification, and medical practitioners compared to other professionals, were more likely to complete. The average number of clients needed to be treated before the trainee achieved competence was greater for MET than SBNT, and there was a longer duration of training for MET.

CONCLUSIONS

Training therapists of differing professional backgrounds, randomised to provide a specific therapy type, is feasible. Supervision after initial training is important, and adds to the training costs.

The influence of an immersive virtual environment on the segmental organization of postural stabilizing responses

We examined the effect of a 3-dimensional stereoscopic scene on segmental stabilization. Eight subjects participated in static sway and locomotion experiments with a visual scene that moved sinusoidally or at constant velocity about the pitch or roll axes. Segmental displacements, Fast Fourier Transforms, and Root Mean Square values were calculated. In both pitch and roll, subjects exhibited greater magnitudes of motion in head and trunk than ankle. Smaller amplitudes and frequent phase reversals suggested control of the ankle by segmental proprioceptive inputs and ground reaction forces rather than by the visual-vestibular signals. Postural controllers may set limits of motion at each body segment rather than be governed solely by a perception of the visual vertical. Two locomotor strategies were also exhibited, implying that some subjects could override the effect of the roll axis optic flow field. Our results demonstrate task dependent differences that argue against using static postural responses to moving visual fields when assessing more dynamic tasks.

Analysis of candidate gene co-amplification with MYCN in neuroblastoma

Previous studies have revealed that the MYCN gene spans approximately 7kb, while the amplicon has been estimated to be 100 kb to 1 Mb long [1-3]. This implies that several other genes may be present on the MYCN amplicon. Such co-amplified genes could contribute to the malignant phenotype and might provide an explanation for why not all patients with MYCN amplification have a poor outcome. We investigated 7 neuroblastoma cell lines and 167 primary tumours for the co-amplification of candidate genes known to be present near the MYCN locus: ornithine decarboxylase, ribonucleotide reductase, syndecan-1 and a DEAD box protein gene, DDX1. We also investigated further the pG21 expressed sequence previously reported to be co-amplified with MYCN. No co-amplification with the first 3 genes was found in any of the cell lines or tumour samples. DDX1 was found to be amplified along with MYCN in 4/6 (67%) cell lines and 18/38 (47%) of the MYCN amplified tumours. No amplification of DDX1, ODC1, RRM2 or syndecan-1 was found in the absence of MYCN amplification. DDX1 co-amplification was observed to occur mainly in stage 4 or 4S patients. With the exclusion of those with 4S disease, patients with DDX1 co-amplification had a significantly shorter mean (+/- SE) disease-free interval (4.1 +/- 1.4, n = 8 months) compared with patients with MYCN amplification alone (19.6 +/- 4.5, n = 17) (P = 0.04, Welch's unpaired t-test). The pG21 sequence was identical to part of the DDX1 gene. These observations indicate that there is at least 1 other gene co-amplified with MYCN in a proportion of cases and that those patients with DDX1 co-amplification tend to relapse more quickly. It also implies that the MYCN amplicon is of varied size and/or position relative to the MYCN gene.

Normal Vestibular Function in Chicks After Partial Exposure to Microgravity During Development

Sixty-four fertilized chicken eggs, half at developmental Day 2 and half at Day 9, were exposed to micro-gravity for 5 days aboard the shuttle. Postflight examination showed that none of the Day 2 flight embryos had survived, whereas the Day 9 flight group and both groups of synchronous ground control embryos appeared viable. One-half of the Day 9 flight and ground control embryos were dissected and the temporal bones preserved in acetone for morphological examination. The other half was allowed to hatch to examine vestibularly related behavioral changes. Morphology of the lagenar otoconia was evaluated by scanning electron microscopy. Behavioral changes were accessed by a battery of reflex tests and recordings of spontaneous and vestibularly driven head movements. The results from both the morphological and behavioral studies showed no consistent difference between the flight and the control animals. Several hypotheses may account for this negative result. Because all the Day 2 embryos failed to survive, the remaining Day 9 chicks may have passed the critical developmental period of the chick’s vestibular system. Also, the reexposure of the developing chick embryo to earth’s 1-g environment may have masked any adverse behavioral effects that exposure to Microgravity may have caused.

Injections of calmidazolium chloride into the ipsilateral medial vestibular nucleus or fourth ventricle reduce spontaneous ocular nystagmus following unilateral labyrinthectomy in guinea pigs

The effects of three injections (0.5-4.5 h post-operation) of 1-[bis-(p-chlorophenyl)methyl]-3-[2,4-dichloro-beta-(2,4- dichlorobenzyloxy)phenethyl]-imidazolium chloride (calmidazolium chloride, R24571), into the ipsilateral medial vestibular nucleus or fourth ventricle, on vestibular compensation for unilateral labyrinthectomy was studied in guinea pigs. R24571, a calmodulin antagonist and inhibitor of several Ca(2+)-dependent enzymes, caused a significant reduction in the average frequency of spontaneous ocular nystagmus (spontaneous nystagmus) during the first 53 h following unilateral labyrinthectomy (n = 5), compared with vehicle-injected animals (n = 5). Although a statistical analysis was not performed on the yaw head tilt and roll head tilt data because of the large variability between animals over the 53-h period of compensation, most R24571-treated animals had less yaw head tilt (4/4 animals) and roll head tilt (4/5 animals) at 9-11 h post-labyrinthectomy than the average values for the vehicle groups at that time. The decrease in the frequency of spontaneous nystagmus following R24571 treatment was not associated with general ataxia or sedation. These results are consistent with recent biochemical studies in suggesting that intracellular pathways associated with Ca2+ may be involved in the neuronal mechanisms of vestibular compensation following unilateral labyrinthectomy.

Four- versus five-day estrous cycles in rats: vaginal cycling and pregnancy

Five- compared to four-day cycling rats had earlier onsets and prolonged periods of full vaginal cornification at estrus, and similar times of the first appearance of the "pavement" cells that signal the end of estrus. In mating tests, a larger proportion of five- compared to four-day cyclers became either pregnant or progestational after mating to one ejaculation by the male. As groups, four- and five-day cyclers did not differ in measures of male or female sexual behavior during the mating test. The observed differences between four- and five-day cyclers in the progestational response to one ejaculatory series and in cyclic vaginal cytology are consistent with previously reported hormonal differences between four- and five-day cycling female rats.

Coagulation and complement studies in Rocky Mountain spotted fever

A patient with laboratory-acquired Rocky Mountain spotted fever (RMSF) and concomitant influenza virus infection was studied from the third day of clinical illness. The course of his illness was marked by petechial rash, thrombocytopenia, and elevation of fibrin split products. No evidence of complement activation was observed. Plasma proteins were elevated in a pattern characteristic of the "acute phase reaction." The patient recovered completely, and vascular collapse or clinically important disseminated intravascular coagulation had developed. In febrile patients who had influenza or a clinically similar noninfluenzal respiratory syndrome, no changes in coagulation, complement, or plasma proteins developed. We conclude that aberrations in the patient's laboratory values reflected RMSF, and that complement played no critical role in his illness.

Dynamic and static violations of Hering's law of equal innervation

Hering's Law of Equal Innervation treats the double eye as a single organ. Normal humans often execute saccadic eye movements that are dynamic violations of Hering's Law. These infractions are produced by differences in the neural controller signals sent to each eye and are exemplified by monocular movements, such as dynamic overshoot, glissades, and double saccades; these dynamic violations occur more frequently in fatigued subjects. In contrast to dynamic violations, static violations of Hering's Law are usually indicative of pathological conditions.