Miracle-dz/UniFAR-FTUs huggingface dataset:
Software Fault Tolerance in the Application Layer

By software fault tolerance in the application layer, we mean a set of application level software components to detect and recover from faults that are not handled in the hardware or operating system layers of a computer system. We consider those faults that cause an application process to crash or hang; they include application software faults as well as faults in the underlying hardware and operating system layers if they are undetected in those layers. We dene four levels of software fault tolerance based on availability and data consistency of an application in the presence of such faults. We describe three reusable software components that provide up to the third level of software fault tolerance. Those components perform automatic detection and restart of failed processes, periodic checkpointing and recovery of critical volatile data, and replication and synchronization of persistent data in an application software system. These components have been ported to a number of UNIX 2 platforms and can be used in any application with minimal programming effort. Some telecommunications products in AT&T have already been enhanced for faulttolerance capability using these three components. Experience with those products to date indicates that these modules provide efcient and economical means to increase the level of fault tolerance in a software system. The performance overhead due to these components depends on the level and varies from 0.1% to 14% based on the amount of critical data being checkpointed and replicated.
Automated testing of refactoring engines

Refactorings are behavior-preserving program transformations that improve the design of a program. Refactoring engines are tools that automate the application of refactorings: first the user chooses a refactoring to apply, then the engine checks if the transformation is safe, and if so, transforms the program. Refactoring engines are a key component of modern IDEs, and programmers rely on them to perform refactorings. A bug in the refactoring engine can have severe consequences as it can erroneously change large bodies of source code. We present a technique for automated testing of refactoring engines. Test inputs for refactoring engines are programs. The core of our technique is a framework for iterative generation of structurally complex test inputs. We instantiate the framework to generate abstract syntax trees that represent Java programs. We also create several kinds of oracles to automatically check that the refactoring engine transformed the generated program correctly. We have applied our technique to testing Eclipse and NetBeans, two popular open-source IDEs for Java, and we have exposed 21 new bugs in Eclipse and 24 new bugs in NetBeans.
Relevance of the Mention of Antioxidant Properties in Yogurt Labels: In Vitro Evaluation and Chromatographic Analysis

The purpose of the inclusion of fruit (natural additives) in yogurt aims to increase its antioxidant activity and functionality. Herein, a comparative study of the antioxidant potential of yogurts with pieces of various fruits was performed, including yogurts with mention of antioxidant properties in the label. Free radicals scavenging activity, reducing power and inhibition of lipid peroxidation were evaluated by in vitro assays, as were the contents in antioxidants such as phenolics, flavonoids, sugars and tocopherols. After analyzing thirteen yogurts containing fruit pieces and a natural one (control), the most interesting were yogurts with pieces of berries (for phenolics, flavonoids and 2,2-dipheny-1-picrylhydrazyl (DPPH) scavenging activity), pineapple (for reducing power), blackberry (for β-carotene bleaching inhibition), blackberry “antioxidant” (for tocopherols) and cherry (for sugars). The mention of “antioxidant” in the label was relevant for tocopherols, sugars, DPPH scavenging activity and reducing power. No synergisms were observed in yogurts prepared with pieces of different fruits. Nevertheless, the addition of fruit pieces to yogurt was favorable for antioxidant content, increasing the protection of the consumer against diseases related to oxidative stress.
Additional File 1: Additional Documentation for Dynamic Properties of Independent Chromatin Domains Measured by Correlation Spectroscopy in Living Cells Content

Supplementary Figure S1: Profile-based peak detection for genomic contact probability maps Supplementary Figure S2: Structural analysis of 5C data Supplementary Figure S3: Structural analysis of T2C data Supplementary Figure S4: Multiscale properties of simulated domain topologies Supplementary Figure S5: Experimental and simulated 5C data and domain structure Supplementary Figure S6: Experimental and simulated T2C data and domain structure Supplementary Figure S7: Image intensity analysis and classification Supplementary Figure S8: FCS in the presence of photobleaching Supplementary Figure S9: Confocal and light-sheet FCS on different scales Supplementary Figure S10: FCS in fixed HeLa cells expressing H2A-EGFP Supplementary Figure S11: Strip profile analysis of FRAP experiments Supplementary Figure S12: Simulated FRAP experiments
Molecular epidemiology of Neisseria gonorrhoeae– identification of the first presumed Swedish transmission chain of an azithromycin‐resistant strain

In the present study, 10 azithromycin‐resistant Neisseria gonorrhoeae isolates from 6 Swedish male patients in 2004, 3 sporadic Swedish azithromycin‐resistant N. gonorrhoeae isolates from recent years and one Swedish N. gonorrhoeae isolate from 2003 that was susceptible to azithromycin but assigned the same serological variant (serovar), i.e. IB‐37, as the isolates from 2004 were included. The isolates were characterized phenotypically using antibiograms and serovar determination and genetically with pulsed‐field gel electrophoresis (PFGE), entire porB gene sequencing and N. gonorrhoeae multiantigen sequence typing (NG‐MAST). The epidemiological information and the results of the thorough phenotypic characterisation and genetic characterisation identified the first presumed domestic transmission of one azithromycin‐resistant N. gonorrhoeae strain in Sweden in 2004. This stresses the need for continuous surveillance of the antibiotic susceptibility of N. gonorrhoeae in order to identify emergence of new resistance, monitor the changing patterns of the susceptibility, and be able to update treatment recommendations on a regular basis.
Treatment of Acute Silicoproteinosis by Whole-Lung Lavage

Acute silicoproteinosis is a rare disease that occurs following a heavy inhalational exposure to silica dusts. Clinically, it resembles pulmonary alveolar proteinosis (PAP); silica exposure is thought to be a cause of secondary PAP. We describe a patient with biopsy-confirmed acute silicoproteinosis whose course was complicated by acute hypoxemic respiratory failure requiring mechanical ventilation. Without clinical improvement despite antibiotic and steroid treatment, the patient was scheduled for whole-lung lavage under general anesthesia. Anesthetic challenges included double-lumen tube placement and single-lung ventilation in a hypoxic patient, facilitating lung lavage, and protecting the contralateral lung from catastrophic spillage.
Functional Cooperation between Snail1 and Twist in the Regulation of ZEB1 Expression during Epithelial to Mesenchymal Transition*

Snail1 and Zeb1 are E-cadherin-transcriptional repressors induced during epithelial mesenchymal transition (EMT). In this article we have analyzed the factors controlling Zeb1 expression during EMT. In NMuMG cells treated with TGF-β, Snail1 RNA and protein are induced 1 h after addition of the cytokine preceding Zeb1 up-regulation that requires 6–8 h. Zeb1 gene expression is caused by increased RNA levels but also by enhanced protein stability and is markedly dependent on Snail1 because depletion of this protein prevents Zeb1 protein and RNA up-regulation. In addition to Snail1, depletion of the Twist transcriptional factor retards Zeb1 stimulation by TGF-β or decreases Zeb1 expression in other cellular models indicating that this factor is also required for Zeb1 expression. Accordingly, Snail1 and Twist cooperate in the induction of Zeb1: co-transfection of both cDNAs is required for the maximal expression of ZEB1 mRNA. Unexpectedly, the expression of Snail1 and Twist shows a mutual dependence although to a different extent; whereas Twist depletion retards Snail1 up-regulation by TGF-β, Snail1 is necessary for the rapid increase in Twist protein and later up-regulation of Twist1 mRNA induced by the cytokine. Besides this effect on Twist, Snail1 also induces the nuclear translocation of Ets1, another factor required for Zeb1 expression. Both Twist and Ets1 bind to the ZEB1 promoter although to different elements: whereas Ets1 interacts with the proximal promoter, Twist does it with a 700-bp sequence upstream of the transcription start site. These results indicate that Snail1 controls Zeb1 expression at multiple levels and acts cooperatively with Twist in the ZEB1 gene transcription induction.
Ensemble Manifold Regularization

We propose an automatic approximation of the intrinsic manifold for general semi-supervised learning (SSL) problems. Unfortunately, it is not trivial to define an optimization function to obtain optimal hyperparameters. Usually, cross validation is applied, but it does not necessarily scale up. Other problems derive from the suboptimality incurred by discrete grid search and the overfitting. Therefore, we develop an ensemble manifold regularization (EMR) framework to approximate the intrinsic manifold by combining several initial guesses. Algorithmically, we designed EMR carefully so it 1) learns both the composite manifold and the semi-supervised learner jointly, 2) is fully automatic for learning the intrinsic manifold hyperparameters implicitly, 3) is conditionally optimal for intrinsic manifold approximation under a mild and reasonable assumption, and 4) is scalable for a large number of candidate manifold hyperparameters, from both time and space perspectives. Furthermore, we prove the convergence property of EMR to the deterministic matrix at rate root-n. Extensive experiments over both synthetic and real data sets demonstrate the effectiveness of the proposed framework.
Performance bounds for λ policy iteration and application to the game of Tetris

We consider the discrete-time infinite-horizon optimal control problem formalized by Markov decision processes (Puterman, 1994; Bertsekas and Tsitsiklis, 1996). We revisit the work of Bertsekas and Ioffe (1996), that introduced λ policy iteration--a family of algorithms parametrized by a parameter λ--that generalizes the standard algorithms value and policy iteration, and has some deep connections with the temporal-difference algorithms described by Sutton and Barto (1998). We deepen the original theory developed by the authors by providing convergence rate bounds which generalize standard bounds for value iteration described for instance by Puterman (1994). Then, the main contribution of this paper is to develop the theory of this algorithm when it is used in an approximate form. We extend and unify the separate analyzes developed by Munos for approximate value iteration (Munos, 2007) and approximate policy iteration (Munos, 2003), and provide performance bounds in the discounted and the undiscounted situations. Finally, we revisit the use of this algorithm in the training of a Tetris playing controller as originally done by Bertsekas and Ioffe (1996). Our empirical results are different from those of Bertsekas and Ioffe (which were originally qualified as "paradoxical" and "intriguing"). We track down the reason to be a minor implementation error of the algorithm, which suggests that, in practice, l policy iteration may be more stable than previously thought.
Risks and Benefits of Physical Activity among Breast Cancer Survivors who have Completed Treatment

Worldwide, over 1 million cases of breast cancer are diagnosed each year. In the USA, approximately 185,000 women are newly diagnosed annually. Nearly 90% of newly diagnosed cancer patients in the USA will live for 5 years beyond diagnosis and there are estimated to be 2.4 million breast cancer survivors currently living in the USA. There are unique challenges in meeting the medical needs of these survivors. Persistent impairment and increased medical risks can occur as a result of treatment, including changes to the cardiovascular, pulmonary, endocrine, immune, musculoskeletal, neurological and lymphatic systems. Physical activity can cause positive changes in each of these body systems. However, physiologic impairments and altered risks for cardiopulmonary, bone health, neurosensory and other outcomes among breast cancer survivors can cause confusion regarding the safety of returning to exercise after treatment. In this article, we review the adverse effects of cancer treatments on the body systems affected by and used to perform exercise, the risks of exercise among breast cancer survivors, the effects of exercise on persistent treatment toxicities, whether exercise may prevent recurrence or mortality, as well as providing guidance for exercise testing and prescription among breast cancer survivors.
Physicochemical and sensory properties of peanut spreads fortified with soy flour.

The physicochemical and sensory properties of peanut spreads fortified with soy flour were studied. Peanut spreads were replaced by whole soybean flour and soy nut flour at 0, 5, 15, 20 and 30% (w/w). All samples were analyzed for fat, protein, sugar, moisture content, adhesiveness, cohesiveness, hardness and sensory characteristics. Replacing peanut spread with soy flour had significant effect (p<0.05) on physicochemical and sensory properties of peanut soy spreads. Replacing peanut spread by soy flour at 30% resulted in the lowest fat content. Regardless of type of flour used, replacing peanut spreads by soy flour increased the protein content of spreads. As the amount of soy flour increased, the average hardness increased. All peanut soy spreads received flavor ratings similar to control, while spreads containing 20% soy nut flour (Psn20) received the highest score for flavor and even more than control.
Increased condom use without other major changes in sexual behavior among the general population in Switzerland.

OBJECTIVES This study is part of a continuous evaluation of the Swiss AIDS prevention strategy from 1987 through 1994. METHODS Annual telephone surveys of samples representative of the general population aged 17 through 45 years have been conducted since 1987 to monitor behavioral change. RESULTS No major changes in level of sexual activity (lifetime number of partners, frequency of sexual encounters in the past week) or potential exposure to risk of HIV transmission (acquisition of a new steady partner during the year or of casual partners in the last 6 months) were observed. Systematic condom use with a new steady partner increased between 1988 and 1994, from 40% to 64% among 17- to 30-year-olds and from 57% to 72% among those aged 31 to 45. Systematic condom use with casual partners increased from 8% to 56% between 1987 and 1994 among 17- to 30-year-olds and from 22% to 42% between 1989 and 1994 among those aged 31 to 45. Condom use was higher among those with multiple partners. CONCLUSIONS A general-population approach to AIDS prevention was able to achieve large-scale improvements in condom-based protection against HIV infection without inducing other major changes in sexual behavior.
ESHAP and G-CSF is a superior blood stem cell mobilizing regimen compared to cyclophosphamide 1.5 g m−2 and G-CSF for pre-treated lymphoma patients: a matched pairs analysis of 78 patients

Cyclophosphamide 1.5 g m–2 followed by granulocyte colony-stimulating factor (G-CSF) is an effective peripheral blood stem cell (PBSC) mobilizing regimen, but has limited anti-lymphoma activity. We therefore assessed the mobilizing potential of ESHAP (etoposide, ara-C, methylprednisolone and cisplatin), a potent second-line lymphoma regimen followed by G-CSF. The results were compared in 78 patients with relapsed or resistant lymphomas with the use of cyclophosphamide 1.5 g m−2 followed by G-CSF in a matched pairs analysis, matching the ESHAP recipients (for predetermined prognostic factors) from a cohort of 178 lymphoma patients mobilized with cyclophosphamide and G-CSF. The total numbers of mononuclear cells collected at apheresis was similar with both regimens but ESHAP plus G-CSF resulted in a significantly higher percentage of CD34+ cells, absolute number of CD34+ cells and GM-CFC (all with P -values < 0.001). The number of patients requiring only one apheresis harvest to achieve a CD34+ cell yield of > 2.0 × 106kg–1 was greatly increased in the ESHAP recipients (56/78 vs 17/78, P< 0.001). The total number of progenitor cells collected was not significantly different with the two mobilization regimens because of this higher number of apheresis in the cyclophosphamide group. The proportion of patients who failed to achieve a minimum CD34+ cell target of 1 × 106kg–1 with the pooled harvests was less in the ESHAP arm (four patients vs nine patients) despite an increased number of aphereses in the cyclophosphamide recipients. ESHAP plus G-CSF is well tolerated and is an excellent mobilization regimen in patients with pre treated lymphoma. © 2000 Cancer Research Campaign
Phase Transitions in Partially Structured Random Graphs

We study a one parameter family of random graph models that spans a continuum between traditional random graphs of the Erd\H{o}s-R\'enyi type, where there is no underlying structure, and percolation models, where the possible edges are dictated exactly by a geometry. We find that previously developed theories in the fields of random graphs and percolation have, starting from different directions, covered almost all the models described by our family. In particular, the existence or not of a phase transition where a giant cluster arises has been proved for all values of the parameter but one. We prove that the single remaining case behaves like a random graph and has a single linearly sized cluster when the expected vertex degree is greater than one.
Combinatorial Administration of Molecules That Simultaneously Inhibit Angiogenesis and Invasion Leads to Increased Therapeutic Efficacy in Mouse Models of Malignant Glioma

Purpose: We investigated the ability of the combinatorial administration of different inhibitors with activities on glioma angiogenesis, migration, and proliferation to produce a prolonged inhibition of glioma growth. Experimental Design: We combined inhibitors affecting solely tumor angiogenesis (PF-4/CTF, cyclo-VEGI) or inhibitors affecting both angiogenesis and invasion together (PEX, PF-4/DLR). Results: When administered in combination, these drugs produced a prolonged and increased inhibition of glioma growth independently from the type of inhibitor used. The combinatory administration was more effective than the administration of a single inhibitor alone, and a strong therapeutic response was reached with a significantly lower amount of protein. The strongest inhibition was observed when human PEX and PF-4/DLR, which affect both glioma angiogenesis and invasion by separate mechanisms, were combined. Conclusions: This supports the concept that prolonged glioma growth inhibition can be achieved by simultaneous delivery of molecules that target both tumor and endothelial cells and acting by separate mechanisms.
A Combined Photolithographic and Molecular‐Assembly Approach to Produce Functional Micropatterns for Applications in the Biosciences

Chemical patterns have attracted substantial interest for applications in the field of biosensors, fundamental cell–surface interaction studies, tissue engineering, and biomaterials. A novel micropatterning technique is proposed here that combines a top–down approach based on photolithography and a bottom–up strategy through self‐organization of multifunctional molecules. The development of the molecular‐assembly patterning by lift‐off (MAPL) has been driven by the need to economically produce patches incorporating a controlled surface density of bioligands while inhibiting non‐specific adsorption. In the MAPL process, a photoresist pattern is transferred into the desired biochemical pattern by means of spontaneous adsorption of biologically relevant species and photoresist lift‐off. The surface between the interactive patches is subsequently rendered non‐fouling through immobilization of a polycationic poly(ethylene glycol) (PEG)‐graft polymer. We demonstrate that surface density of biotin molecules inside adhesive islands can be tailored quantitatively and that cells grow selectively on cell‐adhesive peptide patterns. MAPL is considered to be a valuable addition to the toolbox of soft‐lithography techniques for life‐science applications combining simplicity (no clean‐room equipment needed), cost‐effectiveness, reproducibility on the scale of whole wafer surfaces, and flexibility in terms of pattern geometry, chemistry, and substrate choice.
Dopaminergic Neuronal Loss, Reduced Neurite Complexity and Autophagic Abnormalities in Transgenic Mice Expressing G2019S Mutant LRRK2

Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene cause late-onset, autosomal dominant familial Parkinson's disease (PD) and also contribute to idiopathic PD. LRRK2 mutations represent the most common cause of PD with clinical and neurochemical features that are largely indistinguishable from idiopathic disease. Currently, transgenic mice expressing wild-type or disease-causing mutants of LRRK2 have failed to produce overt neurodegeneration, although abnormalities in nigrostriatal dopaminergic neurotransmission have been observed. Here, we describe the development and characterization of transgenic mice expressing human LRRK2 bearing the familial PD mutations, R1441C and G2019S. Our study demonstrates that expression of G2019S mutant LRRK2 induces the degeneration of nigrostriatal pathway dopaminergic neurons in an age-dependent manner. In addition, we observe autophagic and mitochondrial abnormalities in the brains of aged G2019S LRRK2 mice and markedly reduced neurite complexity of cultured dopaminergic neurons. These new LRRK2 transgenic mice will provide important tools for understanding the mechanism(s) through which familial mutations precipitate neuronal degeneration and PD.
The Continuous Cold-start Problem in e-Commerce Recommender Systems

Many e-commerce websites use recommender systems to recommend items to users. When a user or item is new, the system may fail because not enough information is available on this user or item. Various solutions to this `cold-start problem' have been proposed in the literature. However, many real-life e-commerce applications suffer from an aggravated, recurring version of cold-start even for known users or items, since many users visit the website rarely, change their interests over time, or exhibit different personas. This paper exposes the `Continuous Cold Start' (CoCoS) problem and its consequences for content- and context-based recommendation from the viewpoint of typical e-commerce applications, illustrated with examples from a major travel recommendation website, Booking.com. Keywords: Recommender systems, continous cold-start problem, industrial applications