Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B Virus Capsid-like Particles Can Display the Complete, Dimeric Outer Surface Protein C and Stimulate Production of Protective Antibody Responses against Borrelia burgdorferi Infection*

Hepatitis B virus capsid-like particles (CLPs), icosahedral assemblies formed by 90 or 120 core protein dimers, hold promise as immune-enhancing vaccine carriers for heterologous antigens. Insertions into the immunodominant c/e1 B cell epitope, a surface-exposed loop, are especially immunogenic. However, display of whole proteins, desirable to induce multispecific and possibly neutralizing antibody responses, can be restrained by an unsuitable structure of the foreign protein and by its propensity to undergo homomeric interactions. Here we analyzed CLP formation by core fusions with two distinct variants of the dimeric outer surface lipoprotein C (OspC) of the Lyme disease agent Borrelia burgdorferi. Although the topology of the termini in the OspC dimer does not match that of the insertion sites in the carrier dimer, both fusions, coreOspCa and coreOspCb, efficiently formed stable CLPs. Electron cryomicroscopy clearly revealed the surface disposition of the OspC domains, possibly with OspC dimerization occurring across different core protein dimers. In mice, both CLP preparations induced high-titered antibody responses against the homologous OspC variant, but with substantial cross-reactivity against the other variant. Importantly, both conferred protection to mice challenged with B. burgdorferi. These data show the principal applicability of hepatitis B virus CLPs for the display of dimeric proteins, demonstrate the presence in OspC of hitherto uncharacterized epitopes, and suggest that OspC, despite its genetic variability, may be a valid vaccine candidate.
On model reduction of hybrid systems

The ever-increasing need for accurate mathematical modelling of physical as well as artificial processes for simulation and control leads to models of high complexity. The complexity appears as high order describing dynamical system or complex nonlinear structure. This problem demands efficient computational prototyping tools to replace such complex models by approximate simpler models, which are capable of capturing dynamical behaviour and preserving essential properties of the complex one. Due to this fact model reduction methods have become increasingly popular over the last two decades. On the other hand, most of the methods that are proposed so far for control and analysis of hybrid and switched systems are suffering from high computational burden when dealing with large-scale dynamical systems. Because of the weakness of nonlinear model reduction techniques and due to pressing needs for efficient analysis and control of large-scale dynamical hybrid and switched systems; it is essential to study model reduction of hybrid and switched systems in particular. This fact has motivated the researchers in hybrid systems to study model reduction. To the best of our knowledge just few research works on model reduction of hybrid systems have been reported in the literature [1]-[4]. Therefore this problem is still largely open. We will start the talk with giving a brief walk-trough the previous methods, their advantages and disadvantages concerning computations and conservatism and also from system and control theoretic technical viewpoint. We will proceed with the classification of hybrid and switched systems and we will mainly concentrate on switched systems with autonomous switching and state-based switched systems.The generalized gramian framework for model reduction of switched systems with autonomous switches will be presented then. This framework is based on the generalized gramians instead of gramians [5]. In order to compute the generalized gramians , one should solve Lyapunov inequalities instead of Lyapunov equations. This method is used to devise a technique for structure preserving model reduction methods in [6]. We first show that the generalized method in [5] can be extended to various gramian based reduction methods. We have modified the original method in [5] to avoid numerical instability and to achieve more numerical efficiency by building Petrov-Galerkin projection
Multi-view Multi-illuminant Intrinsic Dataset

This paper proposes a novel high-resolution multi-view dataset of complex multiilluminant scenes with precise reflectance and shading ground-truth as well as raw depth and 3D point cloud. Our dataset challenges the intrinsic image methods by providing complex coloured cast shadows, highly textured and colourful surfaces, and specularity. This is the first publicly available multi-view real-photo dataset at such complexity with pixel-wise intrinsic ground-truth. In the effort to help evaluating different intrinsic image methods, we propose a new perception-inspired metric based on the reflectance consistency. We provide the evaluation of three intrinsic image methods using our dataset and metric.
CARD15 gene polymorphisms in patients with spondyloarthropathies identify a specific phenotype previously related to Crohn’s disease

Background: The association between spondyloarthropathy and Crohn’s disease is well known. A risk for evolution to Crohn’s disease has already been shown in the subgroup of patients with spondyloarthropathy associated with chronic gut inflammation. Objective: To investigate whether the reported polymorphisms in the CARD15 gene, a susceptibility gene for Crohn’s disease, are associated with the presence of preclinical intestinal inflammation observed in spondyloarthropathies. Methods: 104 patients with spondyloarthropathies were studied. All underwent ileocolonoscopy with biopsies between 1983 and 2004. The prevalence of three single nucleotide polymorphisms in the CARD15 gene (R702W, G908R, and 1007fs) was assessed using restriction fragment length polymorphism–polymerase chain reaction (RFLP-PCR); the patients were compared with an ethnically matched Crohn’s disease population and a control population. Results: The carrier frequency of R702W, G908R, or 1007fs variants in the spondyloarthropathy populations (20%) was similar to the control population (17%), but increased to 38% in the spondyloarthropathy subgroup with chronic gut inflammation. This frequency was significantly higher than in the other spondyloarthropathy subgroups (p = 0.001) or the control group (p = 0.006), but not different from the Crohn’s disease group (49%) (NS). This indicates that CARD15 polymorphisms are associated with a higher risk for development of chronic gut inflammation. Conclusions:CARD15 gene polymorphisms clearly identify a subgroup of patients with spondyloarthropathies associated with chronic intestinal inflammation.
Verifying read-copy-update in a logic for weak memory

Read-Copy-Update (RCU) is a technique for letting multiple readers safely access a data structure while a writer concurrently modifies it. It is used heavily in the Linux kernel in situations where fast reads are important and writes are infrequent. Optimized implementations rely only on the weaker memory orderings provided by modern hardware, avoiding the need for expensive synchronization instructions (such as memory barriers) as much as possible. Using GPS, a recently developed program logic for the C/C++11 memory model, we verify an implementation of RCU for a singly-linked list assuming "release-acquire" semantics. Although release-acquire synchronization is stronger than what is required by real RCU implementations, it is nonetheless significantly weaker than the assumption of sequential consistency made in prior work on RCU verification. Ours is the first formal proof of correctness for an implementation of RCU under a weak memory model.
Enterprise Systems Implementations in NewZealand: A Practitioners' Perspective

The market for enterprise systems (ES), continues to grow despite much speculation on its future after the slow down in the early 2000s. This study looks at the current ES implementation scenario in New Zealand (NZ). The purpose of the study is to gain insights into what is a typical case of ES implementation, to understand the current practices of ES implementations, and to do so through a “practitioners’ perspective" of ES vendors, ES consultants and IT research firms in a NZ context. Key findings indicate that although most large ES implementations have been completed by now, the ES market still shows progressive growth in the small to mediumsized enterprise sector for new implementations and upgrades or add-ons in all sectors. Many ES implementations in New Zealand are several years old now, however companies have only recently started tracking benefits through analytical processes to optimize and realize business value from their enterprise systems investment. Implications for practice in implementation processes, implementation models and organizational contexts are discussed.
Considerations on Selecting Fractional-Slot Nonoverlapped Coil Windings

This paper focuses on the selection of a fractional-slot winding for permanent-magnet (PM) machines. The choice of the proper combination of the number of slots and number of poles, together with the corresponding winding layout, has a strong impact on the PM machine performance, in terms of torque density, torque ripple, magnetomotive force harmonic content, and induced rotor losses, as well as the capability to limit the short-circuit current and other fault-tolerance features. Considering these characteristics, this paper aims to help the PM machine designer to select the proper winding configuration, giving useful indications. The winding choice criteria are given using analytical equations, so that their implementation is easy. In this way, the collection of such criteria becomes a helpful tool in the design process.
Galactose Metabolism by the Mouse with Galactose-1-Phosphate Uridyltransferase Deficiency

The ability of mice deficient in galactose-1-phosphate uridyltransferase (GALT) to metabolize galactose was determined in animals weaned to a mouse chow diet for a 4-wk period. When given [14C]galactose intraperitoneally, these animals slowly oxidized the sugar, excreting only 5.5% of the dose as 14CO2 in 4 h, whereas normal animals excreted 39.9%. These results mimic those seen in human galactosemic patients given isotopic galactose. When given 10 μmol of [1-13C]galactose, normal animals excrete small amounts of labeled galactose and galactonate but no galactitol in urine whereas GALT-deficient mice excrete significant amounts of all of these as labeled compounds in urine. When challenged with galactose, only about 20% of the dose is excreted in urine, and even on the chow diet, significant amounts of galactose, galactonate, and galactitol are excreted in urine. These compounds are also found to be present in liver, kidney, and brain, except that galactonate is not found in brain. Galactose-1-phosphate accumulates in red blood cells to levels found in humans exposed to large amounts of galactose, and galactose-1-phosphate is found in increased amounts in liver, kidney, and brain of GALT-deficient animals. There was no difference in the hepatic concentration of uridine diphosphate galactose and uridine diphosphate glucose between normal and GALT-deficient mice. The explanation for the presence of galactose and its conversion products in tissues and urine of affected mice appears to be related to the presence of approximately 1.75% of galactose-containing carbohydrates in the chow, which becomes bioavailable to mice. Despite the presence of galactose and its metabolites in tissues and urine and impaired ability to oxidize the sugar, the GALT-deficient animals are indistinguishable from normal animals and do not exhibit the phenotype of humans with GALT-deficiency galactosemia.
INFLUENCE OF MICROHABITAT HETEROGENEITY ON GENE FREQUENCY DISTRIBUTION AND GAMETIC PHASE DISEQUILIBRIUM IN AVENA BARBATA

Since its introduction into California some two-hundred years ago the slender wild oat (Avena barbata) has become established in a wide variety of habitats. While it is generally restricted to regions with a Mediterranean climate, A. barbata may be found on sites whose environments range from rich, mesic agricultural conditions to infertile, xeric ridgetop conditions. In some areas such as the Napa Valley of Northern California A. barbata may be found growing in environmentally diverse habitats which are located in close physical proximity to one another. Using five genetically determined allozyme loci, Hamrick and Allard (1972) demonstrated that spatial variation in allele frequencies was closely associated with environmental variation in Napa Valley populations of A. barbata. Populations which occur on infertile, xeric sites are usually monomorphic for a specific set of alleles (the xeric combination) while plants growing on fertile, mesic sites are typically monomorphic for a specific complementary combination
Twinning Strains in Synfolding Calcite, Proterozoic Sinian System, China

Synfolding calcite was precipitated between layers of Neoproterozoic sandy dolomite and striated parallel to the fold axis of an open anticline with a shallow plunge during folding. The fold had limb dips of 45° and plunged 20° to the south. The synfolding calcite had sub-horizontal grooves that trended parallel to the fold. Limb-hinge-limb calcite samples (3 samples; n = 100 grains) preserved a layer-parallel shortening strain that trended at an acute (45°) angle to the trend of the fold axis and fold lineations. Extension axes were vertical and there was no strain overprint (low NEVs). Shortening strain magnitudes were −2.9% and the differential stress responsible for twinning was −38 MPa. The commonly observed structures were layer-parallel slip striations normal to the fold axis: sub-horizontal interlayer slip surfaces parallel to a fold axis (parallel to bedding strike) were unreported; as was a sub-horizontal shortening strain at an acute angle to the axis of a plunging fold.
Randomised Language Modelling for Statistical Machine Translation

A Bloom filter (BF) is a randomised data structure for set membership queries. Its space requirements are significantly below lossless information-theoretic lower bounds but it produces false positives with some quantifiable probability. Here we explore the use of BFs for language modelling in statistical machine translation. We show how a BF containing n-grams can enable us to use much larger corpora and higher-order models complementing a conventional n-gram LM within an SMT system. We also consider (i) how to include approximate frequency information efficiently within a BF and (ii) how to reduce the error rate of these models by first checking for lower-order sub-sequences in candidate ngrams. Our solutions in both cases retain the one-sided error guarantees of the BF while takingadvantageof theZipf-likedistribution of word frequencies to reduce the space requirements.
Quantitative recovery planning: understanding how human activities in watersheds can influence population dynamics and genetic structuring of diadromous fishes.

Developing quantitative relationships that link human-induced environmental change with changes in population dynamics for species of conservation concern is hindered by: (1) a limited understanding of the cumulative effect (and relative importance) of population regulation, spatial dynamics, and demographic processes, (2) issues with detectability for species-environment interactions owing to data characteristics and (3) the cumulative or confounding nature of multiple threats. Taking a single-species approach based on endangered Atlantic salmon, I have partially addressed these challenges in my four research chapters. In chapter two, I characterized the conditions under which metapopulation structure would be expected to benefit a population assemblage and found that straying can reduce abundance and heighten extinction risk when productivity is low. For species of conservation concern, I would expect that remediation actions designed to influence demographic rates (e.g. mortality rates) would be more beneficial than actions influencing spatial dynamics. In chapter three, I accounted for the effects of observation and measurement error when quantifying relationships between hydrological variation and survival. Beyond the potential to change our interpretation of ecological relationships, I was able to infer the types of threats affecting juveniles in specific watersheds. In chapter four, I used patterns of effective dispersal to surmise the behavioural mechanism leading to watershed choice among straying adult salmon as well as the relative importance of multiple concurrent threats. My conclusions contradict some current perceptions on threats and suggest new directions for future research. In chapter five, I was able to develop a spatial tool that could inform management decisions or identify priority areas for restoration efforts. However, I was unable to fully characterize how environmental variation influences habitat utilization, distribution patterns, or population-level responses to human activities at multiple spatial extents. The relationships I describe are among the first to be developed for endangered Atlantic salmon in Nova Scotia at a population level. Several of the analyses represent novel applications to conservation questions and have the potential to be extended or more widely applied. Because freshwater fishes, including diadromous fishes, are collectively one of the most imperiled species groups in the world, such research represents a timely contribution to conservation biology.
Who is Who and What is What: Experiments in Cross-Document Co-Reference

This paper describes a language-independent, scalable system for both challenges of cross-document co-reference: name variation and entity disambiguation. We provide system results from the ACE 2008 evaluation in both English and Arabic. Our English system's accuracy is 8.4% relative better than an exact match baseline (and 14.2% relative better over entities mentioned in more than one document). Unlike previous evaluations, ACE 2008 evaluated both name variation and entity disambiguation over naturally occurring named mentions. An information extraction engine finds document entities in text. We describe how our architecture designed for the 10K document ACE task is scalable to an even larger corpus. Our cross-document approach uses the names of entities to find an initial set of document entities that could refer to the same real world entity and then uses an agglomerative clustering algorithm to disambiguate the potentially co-referent document entities. We analyze how different aspects of our system affect performance using ablation studies over the English evaluation set. In addition to evaluating cross-document co-reference performance, we used the results of the cross-document system to improve the accuracy of within-document extraction, and measured the impact in the ACE 2008 within-document evaluation.
Load Balanced Spanning Tree in Metro Ethernet Networks

Spanning Tree Protocol (STP) is a link management standard that provides loop free paths in Ethernet networks. Deploying STP in metro area networks is inadequate because it does not meet the requirements of these networks. STP blocks redundant links, causing the risk of congestion close to the root. As a result, STP provides poor support for load balancing in metro Ethernet networks. A solution for this problem is using multi-criteria spanning tree by considering criterions related to load balancing over links and switches. In our previous work, an algorithm named Best Spanning Tree (BST) is proposed to find the best spanning tree in a metro Ethernet network. BST is based on the computation of total cost for each possible spanning tree; therefore, it is very time consuming especially when the network is large. In this paper, two heuristic algorithms named Load Balanced Spanning Tree (LBST) and Modified LBST (MLBST) will be proposed to find the near-optimal balanced spanning tree in metro Ethernet networks. The computational complexity of the proposed algorithms is much less than BST algorithm. Furthermore, simulation results show that the spanning tree obtained by proposed algorithms is the same or similar to the spanning tree obtained by BST algorithm.
Fixation pattern and macular sensitivity in eyes with subfoveal choroidal neovascularization secondary to age-related macular degeneration. A microperimetry study

Purpose. To investigate the effects of subfoveal choroidal neovascularizzation (CNV) secondary to age-related macular degeneration (AMD) on macular functional parameters quantified with an automatic fundus perimeter. Methods. 118 eyes of 98 consecutive patients with subfoveal CNV secondary to AMD were evaluated. Best corrected visual acuity (ETDRS charts), fundus photography, and fluorescein angiography were performed. Microperimetry (fundus-related perimetry) was used to quantify macular sensitivity and fixation pattern (location and stability). Results. Of 118 eyes: 26 (21.9%) had central, 18 (15.1%) poor central and 74 (63.0%) eccentric fixation; 31 (26.0%) had stable, 42 (35.6%) relatively unstable and 45 (38.4%) unstable fixation. In 75 eyes (63.4%) a dense central scotoma was found. Angiographic classification of subfoveal CNV (occult versus classic) was not significantly related to fixation pattern (location: P = 0.274; stability: P = 0.385), and presence of dense scotoma (P = 0.41). Conclusion. Microperimetric quantification of macular sensitivity and fixation pattern in eyes with subfoveal CNV secondary to AMD offers new data about the impact of visual impairment in these eyes. Moreover, microperimetry improves the functional evaluation of subfoveal CNV in AMD.
Efficient diversity-aware search

Typical approaches of ranking information in response to a user's query that return the most relevant results ignore important factors contributing to user satisfaction; for instance, the contents of a result document may be redundant given the results already examined. Motivated by emerging applications, in this work we study the problem of Diversity-Aware Search, the essence of which is ranking search results based on both their relevance, as well as their dissimilarity to other results reported. Diversity-Aware Search is generally a hard problem, and even tractable instances thereof cannot be efficiently solved by adapting existing approaches. We propose DIVGEN, an efficient algorithm for diversity-aware search, which achieves significant performance improvements via novel data access primitives. Although selecting the optimal schedule of data accesses is a hard problem, we devise the first low-overhead data access prioritization scheme with theoretical quality guarantees, and good performance in practice. A comprehensive evaluation on real and synthetic large-scale corpora demonstrates the efficiency and effectiveness of our approach.
Tough life: the case of a young coastal common bottlenose dolphin repeatedly entangled

We report the case of a young coastal bottlenose dolphin (Tursiops truncatus) hooked and entangled in artisanal fishing gear on two occasions in a period of six months. In both occasions the animal managed to get rid of the gear by itself. The case occurred in the inner estuary of Gulf of Guayaquil, Ecuador. The animal survived both events, but scars remained in various parts of the body and missed fluke tips. Photographs of the individual after the events allowed to evaluate the healing process. This case demonstrated that longlines represents a threat for this population.