A Closed-Form, Consistent and Robust Solution to Uncalibrated Photometric Stereo Via Local Diffuse Reflectance Maxima

Images of an object under different illumination are known to provide strong cues about the object surface. A mathematical formalization of how to recover the normal map of such a surface leads to the so-called uncalibrated photometric stereo problem. In the simplest instance, this problem can be reduced to the task of identifying only three parameters: the so-called generalized bas-relief (GBR) ambiguity. The challenge is to find additional general assumptions about the object, that identify these parameters uniquely. Current approaches are not consistent, i.e., they provide different solutions when run multiple times on the same data. To address this limitation, we propose exploiting local diffuse reflectance (LDR) maxima, i.e., points in the scene where the normal vector is parallel to the illumination direction (see Fig. 1). We demonstrate several noteworthy properties of these maxima: a closed-form solution, computational efficiency and GBR consistency. An LDR maximum yields a simple closed-form solution corresponding to a semi-circle in the GBR parameters space (see Fig. 2); because as few as two diffuse maxima in different images identify a unique solution, the identification of the GBR parameters can be achieved very efficiently; finally, the algorithm is consistent as it always returns the same solution given the same data. Our algorithm is also remarkably robust: It can obtain an accurate estimate of the GBR parameters even with extremely high levels of outliers in the detected maxima (up to 80 % of the observations). The method is validated on real data and achieves state-of-the-art results.

High-resolution sequence stratigraphic correlation in the Upper Jurassic (Kimmeridgian)–Upper Cretaceous (Cenomanian) peritidal carbonate deposits (Western Taurides, Turkey)

Upper Jurassic (Kimmeridgian)±Upper Cretaceous (Cenomanian) inner platform carbonates in the Western Taurides are composed of metre-scale upward-shallowing cyclic deposits (parasequences) and important karstic surfaces capping some of the cycles. Peritidal cycles (shallow subtidal facies capped by tidal-¯at laminites or fenestrate limestones) are regressive- and transgressive-prone (upward-deepening followed by upward-shallowing facies trends). Subtidal cycles are of two types and indicate incomplete shallowing. Submerged subtidal cycles are composed of deeper subtidal facies overlain by shallow subtidal facies. Exposed subtidal cycles consist of deeper subtidal facies overlain by shallow subtidal facies that are capped by features indicative of prolonged subaerial exposure. Subtidal facies occur characteristically in the Jurassic, while peritidal cycles are typical for the Lower Cretaceous of the region. Within the foraminiferal and dasyclad algal biostratigraphic framework, four karst breccia levels are recognized as the boundaries of major second-order cycles, introduced for the ®rst time in this study. These levels correspond to the Kimmeridgian±Portlandian boundary, mid-Early Valanginian, mid-Early Aptian and mid-Cenomanian and represent important sea level falls which affected the distribution of foraminiferal fauna and dasyclad ¯ora of the Taurus carbonate platform. Within the Kimmeridgian±Cenomanian interval 26 third-order sequences (types 1 and 2) are recognized. These sequences are the records of eustatic sea level ¯uctuations rather than the records of local tectonic events because the boundaries of the sequences representing 1±4 Ma intervals are correlative with global sea level falls. Third-order sequences and metre-scale cyclic deposits are the major units used for long-distance, high-resolution sequence stratigraphic correlation in the Western Taurides. Metre-scale cyclic deposits (parasequences) in the Cretaceous show genetical stacking patterns within third-order sequences and correspond to fourth-order sequences representing 100±200 ka. These cycles are possibly the E2 signal (126 ka) of the orbital eccentricity cycles of the Milankovitch band. The slight deviation of values, calculated for parasequences, from the mean value of eccentricity cycles can be explained by the currently imprecise geochronology established in the Cretaceous and missed sea level oscillations when the platform lay above fluctuating sea level.

Sedimentary evolution and environmental history of Lake Van (Turkey) over the past 600,000 years

The lithostratigraphic framework of Lake Van, eastern Turkey, has been systematically analysed to document the sedimentary evolution and the environmental history of the lake during the past ca 600,000 years. The lithostratigraphy and chemostratigraphy of a 219 m long drill core from Lake Van serves to separate global climate oscillations from local factors caused by tectonic and volcanic activity. An age model was established based on the climatostratigraphic alignment of chemical and lithological signatures, validated by 40Ar/39Ar ages. The drilled sequence consists of ca 76% lacustrine carbonaceous clayey silt, ca 2% fluvial deposits, ca 17% volcaniclastic deposits and 5% gaps. Six lacustrine lithotypes were separated from the fluvial and event deposits, such as volcaniclastics (ca 300 layers) and graded beds (ca 375 layers), and their depositional environments are documented. These lithotypes are: (i) graded beds frequently intercalated with varved clayey silts reflect rising lake-levels during the terminations; (ii) varved clayey silts reflect strong seasonality and an intralake oxic–anoxic boundary, for example, lake-level highstands during interglacials/interstadials; (iii) CaCO3-rich banded sediments are representative of a lowering of the oxic-anoxic boundary, for example, lake-level decreases during glacial inceptions; (iv) CaCO3-poor banded and mottled clayey silts reflect an oxic–anoxic boundary close to the sediment-water interface, for example, lake-level low-stands during glacials/stadials; (v) diatomaceous muds were deposited during the early beginning of the lake as a fresh water system; and (vi) fluvial sands and gravels indicate the initial flooding of the lake basin. The recurrence of lithologies (i) to (iv) follows the past five glacial/interglacial cycles. A 20 m thick disturbed unit reflects an interval of major tectonic activity in Lake Van at ca 414 ka BP.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Combined systemic and local morpholino treatment rescues the phenotype of the SMA Delta 7 mouse model

Spinal muscular atrophy (SMA) is a childhood fatal motor neuron disease caused by mutations in the Survival Motor Neuron 1 (SMN1) gene, currently without effective treatment. One possible therapeutic approach is the use of antisense oligonucleotides (ASOs) to redirect the splicing of a paralogous gene, SMN2, to increase the production of functional SMN protein. A range of ASOs with different chemical properties is suitable for these applications, including a morpholino (MO) variant, which has a particularly excellent safety, and efficacy profile. We used a 25- nt MO oligomer sequence against the ISS-N1 region of SMN2 (HSMN2Ex7D(-10-34)) with superior efficacy to previously described sequences also in transgenic SMA Δ7 mice. The combined local and systemic administration of MO (bare or conjugated to octa-guanidine) is necessary to increase full-length SMN expression, leading to robust neuropathological features improvement and survival rescue. Additionally, several snRNA levels that are dysregulated in SMA mice could be restored by MO treatment. These results demonstrate that MO therapy is efficacious and can result in phenotypic rescue. These data provide important insights for the development of therapeutic strategies in SMA patients.

Effect of Combined Systemic and Local Morpholino Treatment on the Spinal Muscular Atrophy Δ7 Mouse Model Phenotype

BACKGROUND: Spinal muscular atrophy (SMA) is a fatal motor neuron disease of childhood that is caused by mutations in the SMN1 gene. Currently, no effective treatment is available. One possible therapeutic approach is the use of antisense oligos (ASOs) to redirect the splicing of the paralogous gene SMN2, thus increasing functional SMN protein production. Various ASOs with different chemical properties are suitable for these applications, including a morpholino oligomer (MO) variant with a particularly excellent safety and efficacy profile. OBJECTIVE: We investigated a 25-nt MO sequence targeting the negative intronic splicing silencer (ISS-N1) 10 to 34 region. METHODS: We administered a 25-nt MO sequence against the ISS-N1 region of SMN2 (HSMN2Ex7D[-10-34]) in the SMAΔ7 mouse model and evaluated the effect and neuropathologic phenotype. We tested different concentrations (from 2 to 24 nM) and delivery protocols (intracerebroventricular injection, systemic injection, or both). We evaluated the treatment efficacy regarding SMN levels, survival, neuromuscular phenotype, and neuropathologic features. RESULTS: We found that a 25-nt MO sequence against the ISS-N1 region of SMN2 (HSMN2Ex7D[-10-34]) exhibited superior efficacy in transgenic SMAΔ7 mice compared with previously described sequences. In our experiments, the combination of local and systemic administration of MO (bare or conjugated to octaguanidine) was the most effective approach for increasing full-length SMN expression, leading to robust improvement in neuropathologic features and survival. Moreover, we found that several small nuclear RNAs were deregulated in SMA mice and that their levels were restored by MO treatment. CONCLUSION: These results indicate that MO-mediated SMA therapy is efficacious and can result in phenotypic rescue, providing important insights for further development of ASO-based therapeutic strategies in SMA patients.

Assessing the Potential of Multiple Imputation in Sequence Analysis

Sequence analysis and optimal matching are useful heuristic tools for the descriptive analysis of heterogeneous individual pathways such as educational careers, job sequences or patterns of family formation. However, to date it remains unclear how to handle the inevitable problems caused by missing values with regard to such analysis. Multiple Imputation (MI) offers a possible solution for this problem but it has not been tested in the context of sequence analysis. Against this background, we contribute to the literature by assessing the potential of MI in the context of sequence analyses using an empirical example. Methodologically, we draw upon the work of Brendan Halpin and extend it to additional types of missing value patterns. Our empirical case is a sequence analysis of panel data with substantial attrition that examines the typical patterns and the persistence of sex segregation in school-to-work transitions in Switzerland. The preliminary results indicate that MI is a valuable methodology for handling missing values due to panel mortality in the context of sequence analysis. MI is especially useful in facilitating a sound interpretation of the resulting sequence types.

A comprehensive discussion of HMBC pulse sequences. III. Solving the problem of missing and weakly observed long-range correlations

The intensity of long-range correlations observed with the classical HMBC pulse sequence using static optimization of the long-range coupling delay is directly related to the size of the coupling constant and is often set as a compromise. As such, some long-range correlations might appear with a reduced intensity or might even be completely absent from the spectra. After a short introduction, this third manuscript will give a detailed review of some selected HMBC variants dedicated to improve the detection of long-range correlations, such as the ACCORD-HMBC, CIGAR-HMBC, and Broadband HMBC experiments. Practical details about the accordion optimization, which affords a substantial improvement in both the number and intensity of the long-range correlations observed, but introduces a modulation in F1, will be discussed. The incorporation of the so-called constant time variable delay in the CIGAR-HMBC experiment, which can trigger or even completely suppress 1H–1H coupling modulation inherent to the utilization of the accordion principle, will be also discussed. The broadband HMBC scheme, which consists of recording a series of HMBC spectra with different delays set as a function of the long-range heteronuclear coupling constant ranges and transverse relaxation times T2, is also examined.

A first chironomid-based summer temperature reconstruction (13–5 ka BP) around 49°N in inland Europe compared with local lake development

Temperature reconstructions for the end of the Pleistocene and the first half of the Holocene based on biotic proxies are rare for inland Europe around 49°N. We analysed a 7 m long sequence of lake deposits in the Vihorlat Mts in eastern Slovakia (820 m a.s.l.). Chironomid head capsules were used to reconstruct mean July temperature (TJuly), other proxies (diatoms, green algae, pollen, geochemistry) were used to reconstruct local environmental changes that might have affected the climate reconstruction, such as epilimnetic total phosphorus concentrations (TP), lake level changes and development of surrounding vegetation. During the Younger Dryas (YD), temperature fluctuated between 7 and 11 °C, with distinct, decadal to centennial scale variations, that agree with other palaeoclimate records in Europe such as δ18O content in stalagmites or Greenland ice cores. The results indicate that the site was somewhat colder than expected from the general south-to-north YD temperature gradient within Europe, possibly because of north-facing exposition. The warmer phases of the YD were characterised by low water level or even complete desiccation of the lake (12,200-12,400 cal yr BP). At the Late-Glacial/Holocene transition TJuly steeply increased from from 11 to 15.5 °C (11,700-11,400 cal yr BP) - the highest TJuly for entire sequence. This rapid climate change was reflected by all proxies as a compositional change and increasing species diversity. The open woodlands of Pinus, Betula, Larix and Picea were replaced by broad-leaved temperate forests dominated by Betula, later by Ulmus and finally by Corylus (ca 9700 cal yr BP). At the same time, input of eroded coarse-grained material into the lake decreased and organic matter (LOI) and biogenic silica increased. The Early-Holocene climate was rather stable till 8700 cal yr BP, with temporary decrease in TJuly around 11,200 cal yr BP. The lake was productive with a well-developed littoral, as indicated by both diatoms and chironomids. A distinct decline of TJuly to 10 °C between 8700 and 8000 cal yr BP was associated with decreasing chironomid diversity and increasing climate moistening indicated by pollen. Tychoplanktonic and phosphorus-demanding diatoms increased which might be explained by hydrological and land-cover changes. Later, a gradual warming started after 7000 cal yr BP and representation of macrophytes, periphytic diatoms and littoral chironomids increased. Our results suggest that the Holocene thermal maximum was taking place unusually early in the Holocene at our study site, but its timing might be affected by topography and mesoclimate. We further demonstrated that temperature changes had coincided with variations in local hydrology

Fiscal Federalism and Tax Equalization: The potential for progressive local taxes

We construct an empirically informed computational model of fiscal federalism, testing whether horizontal or vertical equalization can solve the fiscal externality problem in an environment in which heterogeneous agents can move and vote. The model expands on the literature by considering the case of progressive local taxation. Although the consequences of progressive taxation under fiscal federalism are well understood, they have not been studied in a context with tax equalization, despite widespread implementation. The model also expands on the literature by comparing the standard median voter model with a realistic alternative voting mechanism. We find that fiscal federalism with progressive taxation naturally leads to segregation as well as inefficient and inequitable public goods provision while the alternative voting mechanism generates more efficient, though less equitable, public goods provision. Equalization policy, under both types of voting, is largely undermined by micro-actors' choices. For this reason, the model also does not find the anticipated effects of vertical equalization discouraging public goods spending among wealthy jurisdictions and horizontal encouraging it among poor jurisdictions. Finally, we identify two optimal scenarios, superior to both complete centralization and complete devolution. These scenarios are not only Pareto optimal, but also conform to a Rawlsian view of justice, offering the best possible outcome for the worst-off. Despite offering the best possible outcomes, both scenarios still entail significant economic segregation and inequitable public goods provision. Under the optimal scenarios agents shift the bulk of revenue collection to the federal government, with few jurisdictions maintaining a small local tax.