Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterogeneous view integration and its automation

Software systems are characterized by unprecedented complexity. One effective means of dealing with that complexity is to consider a system from a particular perspective, or view (e.g., architecture or design diagram). Views enable software developers to reduce the amount of information they have to deal with at any given time. They enable this by utilizing a divide-and-conquer strategy that allows large-scale software development problems to be broken up into smaller, more comprehensible pieces. Individual development issues can then be evaluated without the need of access to the whole body of knowledge about a given software system. The major drawback of views is that development concerns cannot truly be investigated by themselves, since concerns tend to affect one another. Successful and precise product development supported via multiple views requires that common assumptions and definitions are recognized and maintained in a consistent fashion. In other words, having views with inconsistent assumptions about a system's expected environment reduces their usefulness and possibly renders invalid solutions based on them. Developing software systems therefore requires more than what general-purpose software development models can provide today. Development is about modeling, solving, and interpreting, and in doing so a major emphasis is placed on mismatch identification and reconciliation within and among diagrammatic and textual views. Our work introduces a view integration framework and demonstrates how its activities enable view comparison in a more scalable and reliable fashion. Our framework extends the comparison activity with mapping and transformation to define the ‘what’ and the ‘how’ of view integration. We will demonstrate the use of our framework on the Unified Modeling Language (UML), which has become a de-facto standard for object-oriented software development. In this context we will describe causes of model inconsistencies among UML views, and show how integration techniques can be applied to identify and resolve them in a more automated fashion. Our framework is tool supported.
Challenges for Autonomic Network Management

The improvement in the management capabilities and available bandwidth offered by next generation of networks is accelerating the development of a new kind of applications, interfaces and services. The ultimate goal of such networks is to automatically adapt their services and resources in accordance with changing environmental conditions and user needs. Such ‘autonomic’ capabilities imply the usage of sophisticated technologies in order to integrate every object of our environment that would be enabled with important computational power and storage capabilities. The challenge behind such implementation is to simplify the administrators’ task by automating the decision making process, and enabling the users to seamlessly find their way in such pervasive environments. This paper gives an overview of the different architectures that support the design, implementation and deployment of autonomic systems.
On Helberg's Generalization of the Levenshtein Code for Multiple Deletion/Insertion Error Correction

A proof that the Helberg code is capable of correcting multiple deletion/insertion errors is presented. This code is a generalization of the number-theoretic Levenshtein code which is capable of correcting a single deletion/insertion. However, apart from exhaustive testing of short codes, no proof was hitherto given to verify that the Helberg code is indeed capable of correcting multiple deletions and insertions.
Advances and challenges in the management of essential thrombocythemia

The new World Health Organization (WHO) diagnostic criteria for essential thrombocythemia (ET) issued in 2008 made an important distinction between true ET and early myelofibrosis (MF), which has helped to identify a more homogenous population for the diagnosis with longer survival and much less transformation to overt MF. The recent finding of a new mutation (CALR), which is mutually exclusive with JAK2 and MPL mutations, adds to the characterization of ET patients, since there are important phenotypic differences between the mutation types. CALR patients are younger, have lower white blood cell counts (WBC) and a lower thrombosis incidence. A growing field of interest is the state of hypercoagulation due to dysfunction of hemostatic systems, cell–cell interaction and hereditary prothrombotic traits. Activation of platelets, WBC and endothelial cells has been found, making the whole intravascular milieu prothrombotic. Several risk score models, based on retrospective studies, have been developed lately, distinguishing patient groups with graded risk for complications and death. Even if these may be helpful in evaluating patients, they have not been validated in prospective studies and there are not enough data to support their use as a basis for treatment algorithms. The traditional risk factors age, previous thrombosis and platelets >1500 × 109/l are still recommended for the distinction between high risk and low risk ET and the decision to give cytoreductive therapy. However, cardiovascular (CV) risk factors add to thrombosis risk and should be considered both for specific treatment in any risk group and for upgrading low risk patients with high CV risk to an intermediary group where active therapy with aspirin and cytoreduction may be considered. First-line cytoreductive therapy differs with age; in younger patients interferon (IFN) or anagrelide are preferable, in older patients hydroxycarbamide (HC). Second-line therapy for younger patients is HC, for older patients IFN or anagrelide (ANA). JAK2 inhibitors may be suitable in rare cases with symptoms not responding to other therapy.
Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all‐atom force field and the surface generalized born solvent model

Protein decoy data sets provide a benchmark for testing scoring functions designed for fold recognition and protein homology modeling problems. It is commonly believed that statistical potentials based on reduced atomic models are better able to discriminate native‐like from misfolded decoys than scoring functions based on more detailed molecular mechanics models. Recent benchmark tests on small data sets, however, suggest otherwise. In this work, we report the results of extensive decoy detection tests using an effective free energy function based on the OPLS all‐atom (OPLS‐AA) force field and the Surface Generalized Born (SGB) model for the solvent electrostatic effects. The OPLS‐AA/SGB effective free energy is used as a scoring function to detect native protein folds among a total of 48,832 decoys for 32 different proteins from Park and Levitt's 4‐state‐reduced, Levitt's local‐minima, Baker's ROSETTA all‐atom, and Skolnick's decoy sets. Solvent electrostatic effects are included through the Surface Generalized Born (SGB) model. All structures are locally minimized without restraints. From an analysis of the individual energy components of the OPLS‐AA/SGB energy function for the native and the best‐ranked decoy, it is determined that a balance of the terms of the potential is responsible for the minimized energies that most successfully distinguish the native from the misfolded conformations. Different combinations of individual energy terms provide less discrimination than the total energy. The results are consistent with observations that all‐atom molecular potentials coupled with intermediate level solvent dielectric models are competitive with knowledge‐based potentials for decoy detection and protein modeling problems such as fold recognition and homology modeling. Proteins 2002;48:404–422. © 2002 Wiley‐Liss, Inc.
Variation in the heritability of body mass index based on diverse twin studies: a systematic review

Over the past three decades, twin studies have shown variation in the heritability of obesity. This study examined the difference of body mass index (BMI) heritability (BMI‐H) by population characteristics, such as sex, age, time period of observation and average BMI, as well as by broad social‐environmental factors as indicated by country‐level gross domestic product (GDP) per capita and GDP growth rate.
BOSSA: Extended bow formalism for image classification

In image classification, the most powerful statistical learning approaches are based on the Bag-of-Words paradigm. In this article, we propose an extension of this formalism. Considering the Bag-of-Features, dictionary coding and pooling steps, we propose to focus on the pooling step. Instead of using the classical sum or max pooling strategies, we introduced a density function-based pooling strategy. This flexible formalism allows us to better represent the links between dictionary codewords and local descriptors in the resulting image signature. We evaluate our approach in two very challenging tasks of video and image classification, involving very high level semantic categories with large and nuanced visual diversity.
Geometric primitive extraction using a genetic algorithm

A genetic algorithm based on a minimal subset representation of a geometric primitive is used to perform primitive extraction. A genetic algorithm is an optimization method that uses the metaphor of evolution, and a minimal subset is the smallest number of points necessary to define a unique instance of a geometric primitive. The approach is capable of extracting more complex primitives than the Hough transform. While similar to a hierarchical merging algorithm, it does not suffer from the problem of premature commitment. <<ETX>>
Running throughout middle‐age improves memory function, hippocampal neurogenesis, and BDNF levels in female C57BL/6J mice

Age‐related memory loss is considered to commence at middle‐age and coincides with reduced adult hippocampal neurogenesis and neurotrophin levels. Consistent physical activity at midlife may preserve brain‐derived neurotrophic factor (BDNF) levels, new cell genesis, and learning. In the present study, 9‐month‐old female C57Bl/6J mice were housed with or without a running wheel and injected with bromodeoxyuridine (BrdU) to label newborn cells. Morris water maze learning, open field activity and rotarod behavior were tested 1 and 6 months after exercise onset. Here we show that long‐term running improved retention of spatial memory and modestly enhanced rotarod performance at 15 months of age. Both hippocampal neurogenesis and mature BDNF peptide levels were elevated after long‐term running. Thus, regular exercise from the onset and during middle‐age may maintain brain function. © 2011 Wiley Periodicals, Inc. Develop Neurobiol 72: 943–952, 2012
Near-Optimum Online Ad Allocation for Targeted Advertising

Motivated by Internet targeted advertising, we address several ad allocation problems. Prior work has established these problems admit no randomized online algorithm better than (1-1/e)-competitive ([Karp et al. 1990; Mehta et al. 2007]), yet simple heuristics have been observed to perform much better in practice. We explain this phenomenon by studying a generalization of the bounded-degree inputs considered by [Buchbinder et al. 2007), graphs which we call (k,d)-bounded. In such graphs the maximal degree on the online side is at most d and the minimal degree on the offline side is at least k. We prove that for such graphs, these problems' natural greedy algorithms attain competitive ratio 1-(d-1)/(k+d-1), tending to one as d/k tends to zero. We prove this bound is tight for these algorithms. Next, we develop deterministic primal-dual algorithms for the above problems achieving competitive ratio 1-(1-1/d)k>1-1/ek/d, or exponentially better loss as a function of k/d, and strictly better than 1-1/e whenever k ≥ d. We complement our lower bounds with matching upper bounds for the vertex-weighted problem. Finally, we use our deterministic algorithms to prove by dual-fitting that simple randomized algorithms achieve the same bounds in expectation. Our algorithms and analysis differ from previous ad allocation algorithms, which largely scale bids based on the spent fraction of their bidder's budget, whereas we scale bids according to the number of times the bidder could have spent as much as her current bid. Our algorithms differ from previous online primal-dual algorithms, as they do not maintain dual feasibility, but only primal-to-dual ratio, and only attain dual feasibility upon termination. We believe our techniques could find applications to other well-behaved online packing problems.
Space of K\"ahler metrics (IV)--On the lower bound of the K-energy

We partially confirm an old conjecture of Donaldson that if there exists a cscK metrics in a given K\"ahler class, then there is no degenerated geodesic ray which is tamed by a bounded ambient geometry unless it parallels to a holomorphic line consists of cscK metrics only. We also prove that for simple test configuration where the central fibre has a cscK metric, the K energy functionals in the nearby fibre must also have a uniform lower bound in its underlying K\"ahler class.
Inhibition of dynamin completely blocks compensatory synaptic vesicle endocytosis

The ability of synapses to sustain signal propagation relies on rapid recycling of transmitter-containing presynaptic vesicles. Clathrin- and dynamin-mediated retrieval of vesicular membrane has an undisputed role in synaptic vesicle recycling. There is also evidence for other modes of vesicle retrieval, including bulk retrieval and the so-called kiss-and-run recycling. Whether dynamin in required for these other modes of synaptic vesicle endocytosis remains unclear. Here, we have tested the role of dynamin in synaptic vesicle endocytosis by using a small molecule called dynasore, which rapidly inhibits the GTPase activity of dynamin with high specificity. Endocytosis after sustained or brief stimuli was completely and reversibly blocked by dynasore in cultured hippocampal neurons expressing the fluorescent tracer synaptopHluorin. By contrast, dynasore had no effect on exocytosis. In the presence of dynasore, low-frequency stimulation led to sustained accumulation of synaptopHluorin and other vesicular proteins on the surface membrane at a rate predicted from net exocytosis. These vesicular components remained on surface membranes even after the stimulus was terminated, suggesting that all endocytic events rely on dynamin during low-frequency activity as well as in the period after it. Ultrastructural analysis revealed a reduction in the density of synaptic vesicles and the presence of endocytic structures only at synapses that were stimulated in the presence of dynasore. In sum, our data indicate that dynamin is essential for all forms of compensatory synaptic vesicle endocytosis including any kiss-and-run events.
Loss of Cdx2 Expression in Primary Tumors and Lymph Node Metastases is Specific for Mismatch Repair-Deficiency in Colorectal Cancer

Background: Approximately 20% of all colorectal cancers are hypothesized to arise from the “serrated pathway” characterized by mutation in BRAF, high-level CpG Island Methylator Phenotype, and microsatellite instability/mismatch repair (MMR)-deficiency. MMR-deficient cancers show frequent losses of Cdx2, a homeodomain transcription factor. Here, we determine the predictive value of Cdx2 expression for MMR-deficiency and investigate changes in expression between primary cancers and matched lymph node metastases. Methods: Immunohistochemistry for Cdx2, Mlh1, Msh2, Msh6, and Pms2 was performed on whole tissue sections from 201 patients with primary colorectal cancer and 59 cases of matched lymph node metastases. Receiver operating characteristic curve analysis and Area under the Curve (AUC) were investigated; association of Cdx2 with clinicopathological features and patient survival was carried out. Results: Loss of Cdx2 expression was associated with higher tumor grade (p = 0.0002), advanced pT (p = 0.0166), and perineural invasion (p = 0.0228). Cdx2 loss was an unfavorable prognostic factor in univariate (p = 0.0145) and multivariate [p = 0.0427; HR (95% CI): 0.58 (0.34–0.98)] analysis. The accuracy (AUC) for discriminating MMR-proficient and – deficient cancers was 87% [OR (95% CI): 0.96 (0.95–0.98); p < 0.0001]. Specificity and negative predictive value for MMR-deficiency was 99.1 and 96.3%. One hundred and seventy-four patients had MMR-proficient cancers, of which 60 (34.5%) showed Cdx2 loss. Cdx2 loss in metastases was related to MMR-deficiency (p < 0.0001). There was no difference in expression between primary tumors and matched metastases. Conclusion: Loss of Cdx2 is a sensitive and specific predictor of MMR-deficiency, but is not limited to these tumors, suggesting that events “upstream” of the development of microsatellite instability may impact Cdx2 expression.
Potassium Ions and the Inhibitory Process in the Crayfish Stretch Receptor

The effect of the absence of potassium in the bathing solution on the synaptic inhibitory potentials of the crayfish stretch receptor has been studied. The inhibitory potentials were increased in size, i.e. became more hyperpolarizing, in the absence of potassium. Since the resting potential of the cell is increased in the absence of potassium, the alteration of the inhibitory potentials implies that the potassium conductance of the membrane is increased. While other ions, e.g. Cl-, may also be involved, it seems that the membrane potential during inhibition is mainly dominated by K+.
Measurements of Film-Substrate Bond Strength by Laser Spallation

Laser spallation is a technique for detaching thin films from substrates by impinging a pulsed, high-energy laser beam onto the back side of a substrate (made opaque in the case of transparent substrates). The explosive evaporation of absorbing material on the back side sends a recoil compressive shock wave through the substrate toward the film-substrate interface. The substrate then snaps back in tension. Threshold values for film detachment can yield information about the film-substrate bonds without contact with or disturbance of the film surface. Thus damage propagated to the interface from film surface disturbance is eliminated. In some cases it is possible to examine [for example, by Auger electron spectroscopy (AES)] the spalled dot and the region of the substrate from which it was spalled to determine the locus of failure and to obtain information about interface formation.
Suppression of genome instability by redundant S-phase checkpoint pathways in Saccharomyces cerevisiae

Cancer cells show increased genome rearrangements, although it is unclear what defects cause these rearrangements. Previous studies have implicated the Saccharomyces cerevisiae replication checkpoint in the suppression of spontaneous genome rearrangements. In the present study, low doses of methyl methane sulfonate that activate the intra-S checkpoint but not the G1 or G2 DNA damage checkpoints were found to cause increased accumulation of genome rearrangements in both wild-type strains and to an even greater extent in strains containing mutations causing defects in the intra-S checkpoint. The rearrangements were primarily translocations or events resulting in deletion of a portion of a chromosome arm along with the addition of a new telomere. Combinations of mutations causing individual defects in the RAD24 or SGS1 branches of the intra-S checkpoint or the replication checkpoint showed synergistic interactions with regard to the spontaneous genome instability rate. PDS1 and the RAD50–MRE11–XRS2 complex were found to be important members of all the S-phase checkpoints in suppressing genome instability, whereas RAD53 only seemed to play a role in the intra-S checkpoints. Combinations of mutations that seem to result in inactivation of the S-phase checkpoints and critical effectors resulted in as much as 12,000–14,000-fold increases in the genome instability rate. These data support the view that spontaneous genome rearrangements result from DNA replication errors and indicate that there is a high degree of redundancy among the checkpoints that act in S phase to suppress such genome instability.
Social Affordances for People with Lifelong Disability through Using Virtual Worlds

In the information age, information and communication technology (ICT) is an asset for supporting people with disability to participate and be included in society. Research indicates that virtual worlds may help this group to gain independence and improve social participation. The aim of the present research was to explore the role that virtual worlds play in facilitating people with disability to experience a self-perceived improvement of social participation, independence and well-being. Using qualitative methods our results indicate that people with lifelong disability perceive that they reach a larger and more diverse network through the use of virtual worlds. Based on identified Quality of Life factors, we found that people with lifelong disability perceived that they obtained increased independence, social participation and well-being. The social affordances offered by virtual worlds are promising for improving these identified factors. This area of research warrants further empirical investigation to understand the implications in a broader social context.
Flaw Selection Strategies for Partial-Order Planning

Several recent studies have compared the relative efficiency of alternative flaw selection strategies for partial-order causal link (POCL) planning. We review this literature, and present new experimental results that generalize the earlier work and explain some of the discrepancies in it. In particular, we describe the Least-Cost Flaw Repair (LCFR) strategy developed and analyzed by Joslin and Pollack (1994), and compare it with other strategies, including Gerevini and Schubert's (1996) ZLIFO strategy. LCFR and ZLIFO make very different, and apparently conflicting claims about the most effective way to reduce search-space size in POCL planning. We resolve this conflict, arguing that much of the benefit that Gerevini and Schubert ascribe to the LIFO component of their ZLIFO strategy is better attributed to other causes. We show that for many problems, a strategy that combines least-cost flaw selection with the delay of separable threats will be effective in reducing search-space size, and will do so without excessive computational overhead. Although such a strategy thus provides a good default, we also show that certain domain characteristics may reduce its effectiveness.
Benchmarking Eventual Consistency: Lessons Learned from Long-Term Experimental Studies

Cloud storage services and NoSQL systems typically guarantee only Eventual Consistency. Knowing the degree of inconsistency increases transparency and comparability, it also eases application development. As every change to the system implementation, configuration, and deployment may affect the consistency guarantees of a storage system, long-term experiments are necessary to analyze how consistency behavior evolves over time. Building on our original publication on consistency benchmarking, we describe extensions to our benchmarking approach and report the surprising development of consistency behavior in Amazon S3 over the last two years. Based on our findings, we argue that consistency behavior should be monitored continuously and that deployment decisions should be reconsidered periodically. For this purpose, we propose a new method called Indirect Consistency Monitoring which allows to track all application-relevant changes in consistency behavior in a much more cost-efficient way compared to continuously running consistency benchmarks.