The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

Dynamic impacts of the inhibition of the molecular chaperone hsp90 on the T-cell proteome have implications for anti-cancer therapy.

The molecular chaperone Hsp90-dependent proteome represents a complex protein network of critical biological and medical relevance. Known to associate with proteins with a broad variety of functions termed clients, Hsp90 maintains key essential and oncogenic signalling pathways. Consequently, Hsp90 inhibitors are being tested as anti-cancer drugs. Using an integrated systematic approach to analyse the effects of Hsp90 inhibition in T-cells, we quantified differential changes in the Hsp90-dependent proteome, Hsp90 interactome, and a selection of the transcriptome. Kinetic behaviours in the Hsp90-dependent proteome were assessed using a novel pulse-chase strategy (Fierro-Monti et al., accompanying article), detecting effects on both protein stability and synthesis. Global and specific dynamic impacts, including proteostatic responses, are due to direct inhibition of Hsp90 as well as indirect effects. As a result, a decrease was detected in most proteins that changed their levels, including known Hsp90 clients. Most likely, consequences of the role of Hsp90 in gene expression determined a global reduction in net de novo protein synthesis. This decrease appeared to be greater in magnitude than a concomitantly observed global increase in protein decay rates. Several novel putative Hsp90 clients were validated, and interestingly, protein families with critical functions, particularly the Hsp90 family and cofactors themselves as well as protein kinases, displayed strongly increased decay rates due to Hsp90 inhibitor treatment. Remarkably, an upsurge in survival pathways, involving molecular chaperones and several oncoproteins, and decreased levels of some tumour suppressors, have implications for anti-cancer therapy with Hsp90 inhibitors. The diversity of global effects may represent a paradigm of mechanisms that are operating to shield cells from proteotoxic stress, by promoting pro-survival and anti-proliferative functions. Data are available via ProteomeXchange with identifier PXD000537.

Use of a dynamic foot pressure index to monitor the effects of treatment for equinus gait in children with cerebral palsy.

The purpose of this study is to introduce and describe a newly developed index using foot pressure analysis to quantify the degree of equinus gait in children with cerebral palsy before and after injection with botulinum toxin. Data were captured preinjection and 12 weeks postinjection. Ten children aged 2(1/2) to 6(1/2) years took part (5 boys and 5 girls). Three of them had a diagnosis of spastic diplegia and 7 of congenital hemiplegia. In total, 13 limbs were analyzed. After orientation and segmentation of raw pedobarographic data, we determined a dynamic foot pressure index graded 0 to 100 that quantified the relative degree of heel and forefoot contact during stance. These data were correlated (Pearson correlation) with clinical measurements of dorsiflexion at the ankle (on a slow and fast stretch) and video observation (using the Observational Gait Scale). Pedobarograph data were strongly correlated with both the Observational Gait Scale scores (R = 0.79, P < 0.005) and clinical measurements of dorsiflexion on a fast stretch, which is reflective of spasticity (R = 0.70, P < 0.005). We demonstrated the index's sensitivity in detecting changes in spasticity and good correlation with video observations seems to indicate this technique's potential validity. When manipulated and segmented appropriately, and with the development of a simple ordinal index, we found that foot pressure data provided a useful tool in tracking changes in patients with spastic equinus.

Owl pellets as a source of DNA for genetic studies of small mammals.

Owl pellets contain a good skeletal record of the small mammals consumed, and correspond to the undigested portions of prey which are regurgitated. These pellets are easy to find at the roosting site of owls. As it has been demonstrated that amplifiable DNA can be isolated from ancient bone remains, the possibility of using owl pellets as a source of DNA for small mammal genetics studies via the polymerase chain reaction has been investigated. The main uncertainties when isolating DNA from such a material are firstly the possibility that the extracted DNA would be too degraded during the digestion in the stomach of the owl, and secondly that extensive cross-contaminations could occur among the different prey consumed. The results obtained clearly demonstrate that cross-contamination does not occur, and that mitochondrial and nuclear DNA can be amplified using skulls of small mammals found in owl pellets as a source of DNA. The relative efficiency of two methods of DNA extraction is estimated and discussed. Thus, owl pellets represent a non-invasive sampling technique which provides a valuable source of DNA for studying population genetics of small mammals.

Cellular source and mechanisms of high transcriptome complexity in the Mammalian testis.

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein-coding and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

A dynamic model of keratinocyte stem cell renewal and differentiation: role of the p21WAF1/Cip1 and Notch1 signaling pathways.

We present here a dynamic model of functional equilibrium between keratinocyte stem cells, transit amplifying populations and cells that are reversibly versus irreversibly committed to differentiation. According to this model, the size of keratinocyte stem cell populations can be controlled at multiple levels, including relative late steps in the sequence of events leading to terminal differentiation and by the influences of a heterogeneous extra-cellular environment. We discuss how work in our laboratory, on the interconnection between the cyclin/CDK inhibitor p21WAF1/Cip1 and the Notch1 signaling pathways, provides strong support to this dynamic model of stem cell versus committed and/or differentiated keratinocyte populations.

Proton NMR of (15)N-choline metabolites enhanced by dynamic nuclear polarization.

Chemical shifts of protons can report on metabolic transformations such as the conversion of choline to phosphocholine. To follow such processes in vivo, magnetization can be enhanced by dynamic nuclear polarization (DNP). We have hyperpolarized in this manner nitrogen-15 spins in (15)N-labeled choline up to 3.3% by irradiating the 94 GHz electron spin resonance of admixed TEMPO nitroxide radicals in a magnetic field of 3.35 T during ca. 3 h at 1.2 K. The sample was subsequently transferred to a high-resolution magnet, and the enhanced polarization was converted from (15)N to methyl- and methylene protons, using the small (2,3)J((1)H,(15)N) couplings in choline. The room-temperature lifetime of nitrogen polarization in choline, T(1)((15)N) approximately 200 s, could be considerably increased by partial deuteration of the molecule. This procedure enables studies of choline metabolites in vitro and in vivo using DNP-enhanced proton NMR.

A new conservative-dynamic treatment for the acute ruptured Achilles tendon.

INTRODUCTION: There is a trend towards surgical treatment of acute ruptured Achilles tendon. While classical open surgical procedures have been shown to restore good functional capacity, they are potentially associated with significant complications like wound infection and paresthesia. Modern mini-invasive surgical techniques significantly reduce these complications and are also associated with good functional results so that they can be considered as the surgical treatment of choice. Nevertheless, there is still a need for conservative alternative and recent studies report good results with conservative treatment in rigid casts or braces. PATIENTS/METHOD: We report the use of a dynamic ankle brace in the conservative treatment of Achilles tendon rupture in a prospective non-randomised study of 57 consecutive patients. Patients were evaluated at an average follow-up time of 5 years using the modified Leppilahti Ankle Score, and the first 30 patients additionally underwent a clinical examination and muscular testing with a Cybex isokinetic dynamometer at 6 and 12 months. RESULTS: We found good and excellent results in most cases. We observed five complete re-ruptures, almost exclusively in case of poor patient's compliance, two partial re-ruptures and one deep venous thrombosis complicated by pulmonary embolism. CONCLUSION: Although prospective comparison with other modern treatment options is still required, the functional outcome after early ankle mobilisation in a dynamic cast is good enough to ethically propose this method as an alternative to surgical treatment.

Detection of hemorrhage source: the diagnostic value of post-mortem CT-angiography.

The aim of this study was to compare the diagnostic value of post-mortem computed tomography angiography (PMCTA) to conventional, ante-mortem computed tomography (CT)-scan, CT-angiography (CTA) and digital subtraction angiography (DSA) in the detection and localization of the source of bleeding in cases of acute hemorrhage with fatal outcomes. The medical records and imaging scans of nine individuals who underwent a conventional, ante-mortem CT-scan, CTA or DSA and later died in the hospital as a result of an acute hemorrhage were reviewed. Post-mortem computed tomography angiography, using multi-phase post-mortem CTA, as well as medico-legal autopsies were performed. Localization accuracy of the bleeding was assessed by comparing the diagnostic findings of the different techniques. The results revealed that data from ante-mortem and post-mortem radiological examinations were similar, though the PMCTA showed a higher sensitivity for detecting the hemorrhage source than did ante-mortem radiological investigations. By comparing the results of PMCTA and conventional autopsy, much higher sensitivity was noted in PMCTA in identifying the source of the bleeding. In fact, the vessels involved were identified in eight out of nine cases using PMCTA and only in three cases through conventional autopsy. Our study showed that PMCTA, similar to clinical radiological investigations, is able to precisely identify lesions of arterial and/or venous vessels and thus determine the source of bleeding in cases of acute hemorrhages with fatal outcomes.

Dynamic models of energy allocation and investment

In dynamic models of energy allocation, assimilated energy is allocated to reproduction, somatic growth, maintenance or storage, and the allocation pattern can change with age. The expected evolutionary outcome is an optimal allocation pattern, but this depends on the environment experienced during the evolutionary process and on the fitness costs and benefits incurred by allocating resources in different ways. Here we review existing treatments which encompass some of the possibilities as regards constant or variable environments and their predictability or unpredictability, and the ways in which production rates and mortality rates depend on body size and composition and age and on the pattern of energy allocation. The optimal policy is to allocate resources where selection pressures are highest, and simultaneous allocation to several body subsystems and reproduction can be optimal if these pressures are equal. This may explain balanced growth commonly observed during ontogeny. Growth ceases at maturity in many models; factors favouring growth after maturity include non-linear trade-offs, variable season length, and production and mortality rates both increasing (or decreasing) functions of body size. We cannot yet say whether these are sufficient to account for the many known cases of growth after maturity and not all reasonable models have yet been explored. Factors favouring storage are also reviewed.

Assimilation des expériences problématiques: une étude de cas de psychothérapie psychodynamique limitée dans le temps [Assimilation of problematic experiences: a case study on short-term dynamic psychotherapy].

The assimilation model is a qualitative and integrative approach that enables to study change processes that occur in psychotherapy. According to Stiles, this model conceives the individual's personality as constituent of different voices; the concept of voice is used to describe traces left by past experiences. During the psychotherapy, we can observe the progressive integration of the problematic voices into the patient's personality. We applied the assimilation model to a 34-session-long case of an effective short-term dynamic psychotherapy. We've chosen eight sessions we transcribed and analyzed by establishing points of contact between the case and the theory. The results are presented and discussed in terms of the evolution of the main voices in the patient.

Working memory in schizophrenia: dynamic visuo-spatial information processing

Working memory, commonly defined as the ability to hold mental representations on line transiently and to manipulate these representations, is known to be a core deficit in schizophrenia. The aim of the present study was to investigate the visuo-spatial component of the working memory in schizophrenia, and more precisely to what extent the dynamic visuo-spatial information processing is impaired in schizophrenia patients. For this purpose we used a computerized paradigm in which 29 patients with schizophrenia (DSMIV, Diagnostic Interview for Genetic Studies) and 29 age and sex matched control subjects (DIGS) had to memorize a plane moving across the computer screen and to identify the observed trajectory among 9 plots proposed together. Each trajectory could be seen max. 3 times if needed. The results showed no difference between schizophrenia patients and controls regarding the number of correct trajectory identified after the first presentation. However, when we determine the mean number of correct trajectories on the basis of 3 trials, we observed that schizophrenia patients are significantly less performant than controls (Mann-Whitney, p _ 0.002). These findings suggest that, although schizophrenia patients are able to memorize some dynamic trajectories as well as controls, they do not profit from the repetition of the trajectory presentation. These findings are congruent with the hypothesis that schizophrenia could induce an unbalance between local and global information processing: the patients may be able to focus on details of the trajectory which could allow them to find the right target (bottom-up processes), but may show difficulty to refer to previous experience in order to filter incoming information (top-down processes) and enhance their visuo-spatial working memory abilities.

Dynamic Modelling of Material Flows and Sustainable Resource Use: Case Studies in Regional Metabolism and Space Life Support Systems

Sustainable resource use is one of the most important environmental issues of our times. It is closely related to discussions on the 'peaking' of various natural resources serving as energy sources, agricultural nutrients, or metals indispensable in high-technology applications. Although the peaking theory remains controversial, it is commonly recognized that a more sustainable use of resources would alleviate negative environmental impacts related to resource use. In this thesis, sustainable resource use is analysed from a practical standpoint, through several different case studies. Four of these case studies relate to resource metabolism in the Canton of Geneva in Switzerland: the aim was to model the evolution of chosen resource stocks and flows in the coming decades. The studied resources were copper (a bulk metal), phosphorus (a vital agricultural nutrient), and wood (a renewable resource). In addition, the case of lithium (a critical metal) was analysed briefly in a qualitative manner and in an electric mobility perspective. In addition to the Geneva case studies, this thesis includes a case study on the sustainability of space life support systems. Space life support systems are systems whose aim is to provide the crew of a spacecraft with the necessary metabolic consumables over the course of a mission. Sustainability was again analysed from a resource use perspective. In this case study, the functioning of two different types of life support systems, ARES and BIORAT, were evaluated and compared; these systems represent, respectively, physico-chemical and biological life support systems. Space life support systems could in fact be used as a kind of 'laboratory of sustainability' given that they represent closed and relatively simple systems compared to complex and open terrestrial systems such as the Canton of Geneva. The chosen analysis method used in the Geneva case studies was dynamic material flow analysis: dynamic material flow models were constructed for the resources copper, phosphorus, and wood. Besides a baseline scenario, various alternative scenarios (notably involving increased recycling) were also examined. In the case of space life support systems, the methodology of material flow analysis was also employed, but as the data available on the dynamic behaviour of the systems was insufficient, only static simulations could be performed. The results of the case studies in the Canton of Geneva show the following: were resource use to follow population growth, resource consumption would be multiplied by nearly 1.2 by 2030 and by 1.5 by 2080. A complete transition to electric mobility would be expected to only slightly (+5%) increase the copper consumption per capita while the lithium demand in cars would increase 350 fold. For example, phosphorus imports could be decreased by recycling sewage sludge or human urine; however, the health and environmental impacts of these options have yet to be studied. Increasing the wood production in the Canton would not significantly decrease the dependence on wood imports as the Canton's production represents only 5% of total consumption. In the comparison of space life support systems ARES and BIORAT, BIORAT outperforms ARES in resource use but not in energy use. However, as the systems are dimensioned very differently, it remains questionable whether they can be compared outright. In conclusion, the use of dynamic material flow analysis can provide useful information for policy makers and strategic decision-making; however, uncertainty in reference data greatly influences the precision of the results. Space life support systems constitute an extreme case of resource-using systems; nevertheless, it is not clear how their example could be of immediate use to terrestrial systems.

Organic geochemistry of Jurassic-Cretaceous source rocks and oil seeps from the profile across the Adriatic-Dinaric carbonate platform

Organic geochemical and stable isotope investigations were performed to provide an insight into the depositional environments, origin and maturity of the organic matter in Jurassic and Cretaceous formations of the External Dinarides. A correlation is made among various parameters acquired from Rock-Eval, gas chromatography-mass spectrometry data and isotope analysis of carbonates and kerogen. Three groups of samples were analysed. The first group includes source rocks derived from Lower Jurassic limestone and Upper Jurassic ``Leme'' beds, the second from Upper Cretaceous carbonates, while the third group comprises oil seeps genetically connected with Upper Cretaceous source rocks. The carbon and oxygen isotopic ratios of all the carbonates display marine isotopic composition. Rock-Eval data and maturity parameter values derived from biomarkers define the organic matter of the Upper Cretaceous carbonates as Type I-S and Type II-S kerogen at the low stage of maturity up to entering the oil-generating window. Lower and Upper Jurassic source rocks contain early mature Type III mixed with Type IV organic matter. All Jurassic and Cretaceous potential source rock extracts show similarity in triterpane and sterane distribution. The hopane and sterane distribution pattern of the studied oil seeps correspond to those from Cretaceous source rocks. The difference between Cretaceous oil seeps and potential source rock extracts was found in the intensity and distribution of n-alkanes, as well as in the abundance of asphaltenes which is connected to their biodegradation stage. In the Jurassic and Cretaceous potential source rock samples a mixture of aromatic hydrocarbons with their alkyl derivatives were indicated, whereas in the oil seep samples extracts only asphaltenes were observed.