Miracle-dz/UniFAR-FTUs huggingface dataset:
A Three-tier Hierarchical Model for Capturing and Rendering of 3D Geometry and Appearance from 2D Images

We propose a three-scale hierarchical representation of scenes and objects and show how this representation is suitable for both computer vision capture of models from images and efficient photo-realistic graphics rendering. The mode l consists of: (1) a conventional triangulated geometry on th e macro-scale; (2) a displacement map, introducing pixel-wi se depth with respect to each planar model facet (triangle) on the meso level; (3) a photo-realistic micro-structure repr esented by an appearance basis spanning viewpoint variation in texture space. We implement a capture and rendering system for this model. Conventional Shape-From-Silhouette or Structure-From-Motion is used to capture the coarse macro geometry, variational shape and reflectance estimation for the meso-level, and texture basis optimization for the micr o level. For efficiency the meso and micro level routines are both HW accelerated. Photo-realistic capture of complex scenes is thus possible in a few minutes using budget cameras and PC’s, and rendering is real-time. Experimental results and videos show models from regular images of humans and objects.
Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA

The time course of polysome formation was studied in a long-term wheat germ cell-free translation system using sedimentation and electron microscopy techniques. The polysomes were formed on uncapped luciferase mRNA with translation-enhancing 5′ and 3′ UTRs. The formation of fully loaded polysomes was found to be a long process that required many rounds of translation and proceeded via several phases. First, short linear polysomes containing no more than six ribosomes were formed. Next, folding of these polysomes into short double-row clusters occurred. Subsequent gradual elongation of the clusters gave rise to heavy-loaded double-row strings containing up to 30–40 ribosomes. The formation of the double-row polysomes was considered to be equivalent to circularization of polysomes, with antiparallel halves of the circle being laterally stuck together by ribosome interactions. A slow exchange with free ribosomes and free mRNA observed in the double-row type polysomes, as well as the resistance of translation in them to AMP-PNP, provided evidence that most polysomal ribosomes reinitiate translation within the circularized polysomes without scanning of 5′ UTR, while de novo initiation including 5′ UTR scanning proceeds at a much slower rate. Removal or replacements of 5′ and 3′ UTRs affected the initial phase of translation, but did not prevent the formation of the double-row polysomes during translation.
Interferon-γ Release Assays for the Diagnosis of Mycobacterium Tuberculosis Infection in Children: A Literature Review

The role of Interferon-gamma release assays (IGRAs) for immunologic diagnosis of tuberculosis in children is under debate. We carried out a narrative review on the studies on IGRAs in paediatric populations. A literature search was conducted using multiple keywords and standardized terminology in Medline, EMBASE and Cochrane databases, up to January 27th, 2011. Study quality was assessed using the MOOSE checklist and results of relevant studies were summarized. Sixty-seven paediatric studies (study population ranging from 14 to 5,244 children) were identified. Non-commercial ELISPOT assay (by means of ESAT-6 and CFP-10 antigens) had been carried out in 11 studies. QuantiFERON-TB Gold (QFT-G), QuantiFERON-TB Gold In-tube (QFT-G-IT), and T-SPOT.TB assays had been performed in 10, 44 and 18 studies, respectively. Most studies reported higher specificity of IGRA than tuberculin skin test (TST), but interpretation of the results is complicated by the fact that a gold standard for the diagnosis of latent TB is lacking. The reported sensitivity for active TB ranged from 51–93% for QFT-G/QFT-G-IT and 40–100% for ELISPOT assays, suggesting that a negative IGRA result may not exclude tuberculosis. Combining TST and IGRA results increased the diagnostic sensitivity. Rates of indeterminate results largely varied (0 to 35%). Most of the studies on young (< 5 years) or immune-compromised children reported a proportion of indeterminate results exceeding 4%. Agreement among TST and IGRA, assessed by the k statistics, ranged from −0.03 to 0.87. Higher rates of discordance were reported in BCG-vaccinated than in non-BCG-vaccinated children. Studies on children <5 years and immunocompromised children reported conflicting results, as did studies on serial IGRA determinations. Despite the large amount of literature data, the role of IGRA in the pediatric population is still unclear, especially in young children. Combined use of TST/IGRA may increase diagnostic sensitivity but interpretation of discordant results remains a challenging issue.
Contingency and entrenchment in protein evolution under purifying selection

Significance How large a role does history play in evolution? Do later events depend critically on specific earlier events, or do all events occur more or less independently? If a change occurs early in evolution, does it become easier or harder to revert the change as time proceeds? Here, we explore these ideas in the context of protein evolution, by simulating sequence evolution under purifying selection and then systematically permuting the order of amino acid substitutions. Our results suggest that the amino acid substitutions that occur in evolution are typically contingent on the presence of prior substitutions, and that substitutions that occur early in evolution become entrenched and difficult to modify as subsequent substitutions accrue. The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background.
Centaur: A Framework for Hybrid CPU-FPGA Databases

Accelerating relational databases in general and SQL in particular has become an important topic given thechallenges arising from large data collections and increasinglycomplex workloads. Most existing work, however, has beenfocused on either accelerating a single operator (e.g., a join) orin data reduction along the data path (e.g., from disk to CPU). In this paper we focus instead on the system aspects of accelerating a relational engine in hybrid CPU-FPGA architectures. In particular, we present Centaur, a framework running on theFPGA that allows the dynamic allocation of FPGA operatorsto query plans, pipelining these operators among themselveswhen needed, and the hybrid execution of operator pipelinesrunning on the CPU and the FPGA. Centaur is fully compatiblewith relational engines as we demonstrate through its seamlessintegration with MonetDB, a popular column store database. Inthe paper, we describe how this integration is achieved, andempirically demonstrate the advantages of such an approach. The main contribution of the paper is to provide a realisticsolution for accelerating SQL that is compatible with existingdatabase architectures, thereby opening up the possibilities forfurther exploration of FPGA based data processing.
Interference analysis of a total frequency hopping GSM cordless telephony system

We present an interference analysis which reveals capacity reserves for a hierarchical GSM radio network. In the investigated concept a low-power cordless telephony system reuses the frequencies of a cellular GSM system based on total frequency hopping (T-FH) multiple access. Based on a novel simulation method, which considers the dynamics of a T-FH cellular network, we present results for different cordless user densities and numbers of T-FH frequencies which exhibit the benefits of our CTS concept. Moreover, we show two possible ways to further improve the CTS downlink performance in case of difficult scenarios.
Renal failure in cirrhosis.

Renal failure, a challenging complication of cirrhosis, is one of the most important risk factors for liver transplantation. In recent years, substantial progress has been made toward understanding the pathogenesis and natural history of renal failure in cirrhosis. This review discusses recently identified information about renal failure in cirrhosis and clinical interventions that may assist in the prevention and management of this complication.
Evaluating automatic cross-domain Dutch semantic role annotation

In this paper we present the first corpus where one million Dutch words from a variety of text genres have been annotated with semantic roles. 500K have been completely manually verified and used as training material to automatically label another 500K. All data has been annotated following an adapted version of the PropBank guidelines. The corpus's rich text type diversity and the availability of manually verified syntactic dependency structures allowed us to experiment with an existing semantic role labeler for Dutch. In order to test the system's portability across various domains, we experimented with training on individual domains and compared this with training on multiple domains by adding more data. Our results show that training on large data sets is necessary but that including genre-specific training material is also crucial to optimize classification. We observed that a small amount of in-domain training data is already sufficient to improve our semantic role labeler.
Roads, Interrupted Dispersal, and Genetic Diversity in Timber Rattlesnakes

Abstract: Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine‐scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic‐assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads.
Monitoring of human herpesvirus‐6 and ‐7 genomes in saliva samples of healthy adults by competitive quantitative PCR

Human herpesviruses‐6 and ‐7 (HHV‐6 and HHV‐7) are thought to be transmitted during early infancy through saliva. However, the kinetics of the virus shedding in saliva of healthy adults, from whom children are assumed to acquire the viruses, is mostly unknown. This study was conducted to determine how many copies of the genome are secreted in saliva of healthy adults and to clarify the relationship between viral DNA load and virus isolation of HHV‐6 and HHV‐7. Competitive PCR was performed using primer sets in the U42 gene of each viral genome. In saliva samples from 29 healthy adults, HHV‐6 and HHV‐7 DNA was detected in 41.4% and 89.7%, respectively. The average copy number of the HHV‐7 genome in the positive samples was higher than that of the HHV‐6 genome. Follow‐up studies of six seropositive individuals for 3 months showed that the amount of HHV‐7 DNA was constant in each individual and that “high producers” and “low producers” could be distinguished. By contrast, the amount of HHV‐6 DNA varied drastically over time in each individual. Although HHV‐6 was never isolated from the saliva of any of the six individuals during the follow‐up period, HHV‐7 was isolated from each individual several times. The amount of HHV‐7 DNA tended to be higher at the times when the virus was isolated than at the times when the virus was not isolated. These data demonstrate a striking contrast between HHV‐6 and HHV‐7 in the kinetics of genome and virus shedding. J. Med. Virol. 61:208–213, 2000. © 2000 Wiley‐Liss, Inc.
Plasticity, not genetic variation, drives infection success of a fungal parasite

SUMMARY Hosts strongly influence parasite fitness. However, it is challenging to disentangle host effects on genetic vs plasticity-driven traits of parasites, since parasites can evolve quickly. It remains especially difficult to determine the causes and magnitude of parasite plasticity. In successive generations, parasites may respond plastically to better infect their current type of host, or hosts may produce generally ‘good’ or ‘bad’ quality parasites. Here, we characterized parasite plasticity by taking advantage of a system in which the parasite (the yeast Metschnikowia bicuspidata, which infects Daphnia) has no detectable heritable variation, preventing rapid evolution. In experimental infection assays, we found an effect of rearing host genotype on parasite infectivity, where host genotypes produced overall high or low quality parasite spores. Additionally, these plastically induced differences were gained or lost in just a single host generation. Together, these results demonstrate phenotypic plasticity in infectivity driven by the within-host rearing environment. Such plasticity is rarely investigated in parasites, but could shape epidemiologically important traits.
MAV-swarms: Unmanned aerial vehicles stabilized along a given path using onboard relative localization

A novel approach for stabilization and navigation of swarms of Micro Aerial Vehicles (MAVs) along a predefined path through a complex environment with obstacles is introduced in this paper. The method enables to control large MAV swarms (in literature also called UAV swarms) based only on onboard sensors and without any inter-vehicle communication. The proposed method relies on visual localization modules carried by all MAVs, which provide estimation of the relative positions of neighbours in the swarm. Guess on the positions of the neighbouring MAVs and information on the relative positions of obstacles are integrated into swarm stabilization via Reynolds' Boids model. The performance of the complex system is shown in various numerical simulations and in experiments with a fleet of MAVs in the paper. Presented experimental results with the multi-MAV swarm were conducted in indoor and outdoor environment, and without using any external global localization system such as Vicon motion capture system or GPS localization.
Biochemical Aspects of a Serine Protease from Caesalpinia echinata Lam. (Brazilwood) Seeds: A Potential Tool to Access the Mobilization of Seed Storage Proteins

Several proteins have been isolated from seeds of leguminous, but this is the first report that a protease was obtained from seeds of Caesalpinia echinata Lam. , a tree belonging to the Fabaceae family. This enzyme was purified to homogeneity by hydrophobic interaction and anion exchange chromatographies and gel filtration. This 61-kDa serine protease (CeSP) hydrolyses H-D-prolyl-L-phenylalanyl-L-arginine-p-nitroanilide (K m 55.7 μM) in an optimum pH of 7.1, and this activity is effectively retained until 50°C. CeSP remained stable in the presence of kosmotropic anions (PO4 3−, SO4 2−, and CH3COO−) or chaotropic cations (K+ and Na+). It is strongly inhibited by TLCK, a serine protease inhibitor, but not by E-64, EDTA or pepstatin A. The characteristics of the purified enzyme allowed us to classify it as a serine protease. The role of CeSP in the seeds cannot be assigned yet but is possible to infer that it is involved in the mobilization of seed storage proteins.
An enhanced correlation-based method for stereo correspondence with subpixel accuracy

The invariance of the similarity measure in photometric distortions as well as its capability in producing subpixel accuracy are two desired and often required features in most stereo vision applications. In this paper we propose a new correlation-based measure which incorporates both mentioned requirements. Specifically, by using an appropriate interpolation scheme in the candidate windows of the matching image, and using the classical zero mean normalized cross correlation function, we introduce a suitable measure. Although the proposed measure is a nonlinear function of the sub-pixel displacement parameter, its maximization results in a closed form solution, resulting in reduced complexity for its use in matching techniques. Application of the proposed measure in a number of benchmark stereo pair images reveals its superiority over existing correlation-based techniques used for subpixel accuracy.
The factors affecting on estimation of carbohydrate content of meals in carbohydrate counting

Abstract. The objective of this study was to identify factors affecting on errors in carbohydrate (CHO) content estimation during CHO counting. Thirty-seven type 1 diabetes patients and 22 of their parents and 28 physicians/dieticians were enrolled in this study. CHO counting was counted in “Carb”, with 1 Carb defined as 10 g of CHO. To evaluate the accuracy of CHO counting, 80 real-size photographs of cooked meals were presented to the subjects for Carb estimation. Carbs tended to be overestimated for foods containing relatively small amounts of Carbs. On the other hands, Carbs tended to be underestimated for foods with higher than 6 Carbs. Accurate estimation of the Carbs in food containing a large amount of rice was particularly difficult even in the subjects having the CHO counting experience. The Carb contents of high-calorie foods such as meats, fried foods, and desserts tended to be overestimated. This error was smaller in subjects having the CHO counting experience. In conclusion, misunderstanding of high-calorie dishes containing high amounts of CHO was observed in inexperienced subjects, indicating the efficacy of the current methodology of CHO counting. On the other hand it was difficult even for experienced subjects to assess the amount of seasoned rice, suggesting the need for a new methodology for accurate estimation.
Conceptual design, kinematics and dynamics of swimming robotic structures using ionic polymeric gel muscles

The structural design, kinematics and swimming dynamics of autonomous swimming robotic structures which utilize an arrangement of electrically controlled ionic polymeric gel muscles are discussed. The general structural design of such swimming robotic structures is considered to be in the form of a submarine structure which is partially encapsulated in an elastic or flexible membrane filled with a counterionic electrolyte such as water+acetone. In such an encapsulated portion of the robotic swimming structure there exist specifically arranged polyacrylamide or PVA-AAA polymeric cylindrical fibres or bundles. The arrangement of, say, polyacrylamide fibres is such that it is capable of generating microprocessor-based electrically controlled propagating transverse waves to propel the partially encapsulated membrane structure in any direction and in any desired manner. A brief description of the governing equations is also presented.
Layer-by-layer nanoassembly of iridium oxide/platinum-black for low impedance, high charge injecting microelectrode applications

We report an electrode device with a low impedance and high charge injecting characteristics for a powerful application to micro/nano-scale electrophysiological measurements of neuron/cells. Due to the small effective electrode area, conventional microelectrodes exhibit high interfacial electrode impedance (~10 MΩ at 1 kHz) and low charge injection characteristics, making the targeted cells impossible to record/stimulate. To overcome these limitations, we propose enhanced surface-area of an electrode with a low impedance material, based on layer-by-layer assembled iridium oxide (IrOx)/platinum-black (Pt-black) with nano-scale roughness. The assembled nanorough-IrOx/Pt-black electrode exhibits 2 times lower impedance and 2.4 times larger injection delivery capacity (QCDC) compared to a planer-IrOx electrode with the same size. Additionally, we fabricated nanorough-Ir/Pt-black tipped microprobes and demonstrated in saline, while improved stimulating currents were observed.
Safety and Reactogenicity of Canarypox ALVAC-HIV (vCP1521) and HIV-1 gp120 AIDSVAX B/E Vaccination in an Efficacy Trial in Thailand

Background A prime-boost vaccination regimen with ALVAC-HIV (vCP1521) administered intramuscularly at 0, 4, 12, and 24 weeks and gp120 AIDSVAX B/E at 12 and 24 weeks demonstrated modest efficacy of 31.2% for prevention of HIV acquisition in HIV-uninfected adults participating in a community-based efficacy trial in Thailand. Methodology/Principal Findings Reactogenicity was recorded for 3 days following vaccination. Adverse events were monitored every 6 months for 3.5 years, during which pregnancy outcomes were recorded. Of the 16,402 volunteers, 69% of the participants reported an adverse event any time after the first dose. Only 32.9% experienced an AE within 30 days following any vaccination. Overall adverse event rates and attribution of relatedness did not differ between groups. The frequency of serious adverse events was similar in vaccine (14.3%) and placebo (14.9%) recipients (p = 0.33). None of the 160 deaths (85 in vaccine and 75 in placebo recipients, p = 0.43) was assessed as related to vaccine. The most common cause of death was trauma or traffic accident. Approximately 30% of female participants reported a pregnancy during the study. Abnormal pregnancy outcomes were experienced in 17.1% of vaccine and 14.6% (p = 0.13) of placebo recipients. When the conception occurred within 3 months (estimated) of a vaccination, the majority of these abnormal outcomes were spontaneous or elective abortions among 22.2% and 15.3% of vaccine and placebo pregnant recipients, respectively (p = 0.08). Local reactions occurred in 88.0% of vaccine and 61.0% of placebo recipients (p<0.001) and were more frequent after ALVAC-HIV than AIDSVAX B/E vaccination. Systemic reactions were more frequent in vaccine than placebo recipients (77.2% vs. 59.8%, p<0.001). Local and systemic reactions were mostly mild to moderate, resolving within 3 days. Conclusions/Significance The ALVAC-HIV and AIDSVAX B/E vaccine regimen was found to be safe, well tolerated and suitable for potential large-scale use in Thailand. Trial Registration ClinicalTrials.gov NCT00223080