Miracle-dz/UniFAR-FTUs huggingface dataset:
Formal Certification of ElGamal Encryption A Gentle Introduction to CertiCrypt

CertiCrypt [1] is a framework that assists the construction of machine-checked cryptographic proofs that can be automatically verified by third parties. To date, CertiCrypt has been used to prove formally the exact security of widely studied cryptographic systems, such as the OAEP padding scheme and the Full Domain Hash digital signature scheme. The purpose of this article is to provide a gentle introduction to CertiCrypt. For concreteness, we focus on a simple but illustrative example, namely the semantic security of the Hashed ElGamal encryption scheme in both, the standard and the random oracle model.
Application of adaptive probing for fault diagnosis in computer networks

This dissertation presents an adaptive probing based tool for fault diagnosis in computer networks by addressing the problems of probe station selection and probe selection. We first present algorithms to place probe stations to monitor the network in the presence of various failures in the network. We then present algorithms for probe selection in an adaptive manner to perform fault diagnosis. We present algorithms considering both deterministic as well as non-deterministic environments. We present evaluation of the proposed algorithms through comprehensive simulation studies. The dissertation is available at http://www.cis. udel.edu/~natu/papers/dissertation.pdf.
Optimal density of sensors for distributed detection in single-hop wireless sensor networks

In this paper we study the problem of determining the optimal spatial node density for deployment of a Wireless Sensor Network (WSN) for detection of a randomly located target in a sensing field. We formulate an optimization problem for the single-hop scenario and account for factors such as the Medium Access Control (MAC) protocol that is used, the wireless channel's propagation characteristics, a randomized sleep/wake-up scheduling protocol, network coverage constraints, the energy consumed, the time to reach a decision, and the total number of nodes available. We show that the optimal node density that minimizes the average Decision Error Probability (DEP) at the CH is a function of the network parameters such as average wake-up rate, propagation path-loss exponent and the lifetime of the network. Simulations are used to study the many optimal trade-offs that are possible.
Visualization of Mad2 Dynamics at Kinetochores, along Spindle Fibers, and at Spindle Poles in Living Cells

The spindle checkpoint prevents errors in chromosome segregation by inhibiting anaphase onset until all chromosomes have aligned at the spindle equator through attachment of their sister kinetochores to microtubules from opposite spindle poles. A key checkpoint component is the mitotic arrest–deficient protein 2 (Mad2), which localizes to unattached kinetochores and inhibits activation of the anaphase-promoting complex (APC) through an interaction with Cdc20. Recent studies have suggested a catalytic model for kinetochore function where unattached kinetochores provide sites for assembling and releasing Mad2–Cdc20 complexes, which sequester Cdc20 and prevent it from activating the APC. To test this model, we examined Mad2 dynamics in living PtK1 cells that were either injected with fluorescently labeled Alexa 488-XMad2 or transfected with GFP-hMAD2. Real-time, digital imaging revealed fluorescent Mad2 localized to unattached kinetochores, spindle poles, and spindle fibers depending on the stage of mitosis. FRAP measurements showed that Mad2 is a transient component of unattached kinetochores, as predicted by the catalytic model, with a t 1/2 of ∼24–28 s. Cells entered anaphase ∼10 min after Mad2 was no longer detectable on the kinetochores of the last chromosome to congress to the metaphase plate. Several observations indicate that Mad2 binding sites are translocated from kinetochores to spindle poles along microtubules. First, Mad2 that bound to sites on a kinetochore was dynamically stretched in both directions upon microtubule interactions, and Mad2 particles moved from kinetochores toward the poles. Second, spindle fiber and pole fluorescence disappeared upon Mad2 disappearance at the kinetochores. Third, ATP depletion resulted in microtubule-dependent depletion of Mad2 fluorescence at kinetochores and increased fluorescence at spindle poles. Finally, in normal cells, the half-life of Mad2 turnover at poles, 23 s, was similar to kinetochores. Thus, kinetochore-derived sites along spindle fibers and at spindle poles may also catalyze Mad2 inhibitory complex formation.
Publication of NIH funded trials registered in ClinicalTrials.gov: cross sectional analysis

Objective To review patterns of publication of clinical trials funded by US National Institutes of Health (NIH) in peer reviewed biomedical journals indexed by Medline. Design Cross sectional analysis. Setting Clinical trials funded by NIH and registered within ClinicalTrials.gov (clinicaltrials.gov), a trial registry and results database maintained by the US National Library of Medicine, after 30 September 2005 and updated as having been completed by 31 December 2008, allowing at least 30 months for publication after completion of the trial. Main outcome measures Publication and time to publication in the biomedical literature, as determined through Medline searches, the last of which was performed in June 2011. Results Among 635 clinical trials completed by 31 December 2008, 294 (46%) were published in a peer reviewed biomedical journal, indexed by Medline, within 30 months of trial completion. The median period of follow-up after trial completion was 51 months (25th-75th centiles 40-68 months), and 432 (68%) were published overall. Among published trials, the median time to publication was 23 months (14-36 months). Trials completed in either 2007 or 2008 were more likely to be published within 30 months of study completion compared with trials completed before 2007 (54% (196/366) v 36% (98/269); P<0.001). Conclusions Despite recent improvement in timely publication, fewer than half of trials funded by NIH are published in a peer reviewed biomedical journal indexed by Medline within 30 months of trial completion. Moreover, after a median of 51 months after trial completion, a third of trials remained unpublished.
Validated Continuation for Equilibria of PDEs

One of the most efficient methods for determining the equilibria of a continuous parameterized family of differential equations is to use predictor-corrector continuation techniques. In the case of partial differential equations this procedure must be applied to some finite-dimensional approximation, which of course raises the question of the validity of the output. We introduce a new technique that combines the information obtained from the predictor-corrector steps with ideas from rigorous computations and verifies that the numerically produced equilibrium for the finite-dimensional system can be used to explicitly define a set which contains a unique equilibrium for the infinite-dimensional partial differential equation. Using the Cahn-Hilliard and Swift-Hohenberg equations as models we demonstrate that the cost of this new validated continuation is less than twice the cost of the standard continuation method alone.
Parental Leave -a Policy Evaluation of the Swedish "daddy-month" Reform Parental Leave – a Policy Evaluation of the Swedish " Daddy-month " Reform

Any opinions expressed here are those of the author(s) and not those of the institute. Research disseminated by IZA may include views on policy, but the institute itself takes no institutional policy positions. The Institute for the Study of Labor (IZA) in Bonn is a local and virtual international research center and a place of communication between science, politics and business. IZA is an independent nonprofit company supported by Deutsche Post World Net. The center is associated with the University of Bonn and offers a stimulating research environment through its research networks, research support, and visitors and doctoral programs. IZA engages in (i) original and internationally competitive research in all fields of labor economics, (ii) development of policy concepts, and (iii) dissemination of research results and concepts to the interested public. IZA Discussion Papers often represent preliminary work and are circulated to encourage discussion. Citation of such a paper should account for its provisional character. A revised version may be available directly from the author. ABSTRACT Parental Leave – A Policy Evaluation of the Swedish " Daddy-Month " Reform * Many countries are trying to incentivize fathers to increase their share in parental leave and in household work to improve female labor market opportunities. Our unique data set stems from a natural experiment in Sweden. The data comprises all children born before (control group) and after the reform (treatment group) in cohorts of up to 27,000 newborns, mothers and fathers. We find strong short term effects of incentives on male parental leave. However, we find no learning-by doing, or specialization, effects: fathers in the treatment group do not have larger shares in the leave taken for care of sick children, which is our measure for household work. from SITE is gratefully acknowledged. All errors are ours.
Different doses of micafungin for prophylaxis of invasive fungal diseases in hemato‐oncological high‐risk patients: a web‐based non‐interventional trial in four large university hospitals in Germany

Treatment indications of new antifungals in clinical practice often deviate from the strict criteria used in controlled clinical trials. Under routine clinical conditions, beneficial and adverse effects, not previously described in clinical trials may be observed. The aim of this study was to describe customary prescription and treatment strategies of micafungin (MCFG).
Dual wavelength laser damage testing for high energy lasers

As high energy laser systems evolve towards higher energies, fundamental material properties such as the laserinduced damage threshold (LIDT) of the optics limit the overall system performance. The Z-Backlighter Laser Facility at Sandia National Laboratories uses a pair of such kiljoule-class Nd:Phosphate Glass lasers for x-ray radiography of high energy density physics events on the Z-Accelerator. These two systems, the Z-Beamlet system operating at 527nm/ 1ns and the Z-Petawatt system operating at 1054nm/ 0.5ps, can be combined for some experimental applications. In these scenarios, dichroic beam combining optics and subsequent dual wavelength high reflectors will see a high fluence from combined simultaneous laser exposure and may even see lingering effects when used for pump-probe configurations. Only recently have researchers begun to explore such concerns, looking at individual and simultaneous exposures of optics to 1064 and third harmonic 355nm light from Nd:YAG [1]. However, to our knowledge, measurements of simultaneous and delayed dual wavelength damage thresholds on such optics have not been performed for exposure to 1054nm and its second harmonic light, especially when the pulses are of disparate pulse duration. The Z-Backlighter Facility has an instrumented damage tester setup to examine the issues of laser-induced damage thresholds in a variety of such situations [2] . Using this damage tester, we have measured the LIDT of dual wavelength high reflectors at 1054nm/0.5ps and 532nm/7ns, separately and spatially combined, both co-temporal and delayed, with single and multiple exposures. We found that the LIDT of the sample at 1054nm/0.5ps can be significantly lowered, from 1.32J/cm2 damage fluence with 1054/0.5ps only to 1.05 J/cm2 with the simultaneous presence of 532nm/7ns laser light at a fluence of 8.1 J/cm2. This reduction of LIDT of the sample at 1054nm/0.5ps continues as the fluence of 532nm/7ns laser light simultaneously present increases. The reduction of LIDT does not occur when the 2 pulses are temporally separated. This paper will also present dual wavelength LIDT results of commercial dichroic beam-combining optics simultaneously exposed with laser light at 1054nm/2.5ns and 532nm/7ns.
SME e-readiness in Malaysia: Implications for Planning and Implementation

This study hoped to answer 2 main objectives. The first objective was to assess the level of e-readiness of SMEs in Northern Malaysia. The second objective was to investigate the factors contributing to the e-readiness of SMEs in Northern Malaysia. Questionnaires were distributed using a simple random sampling method to 300 SMEs in Penang, Kedah and Perlis. The findings of this study show that SMEs in Northern Malaysia are ready to go for e-business, e-commerce and Internet in general. The findings also showed that in general top management commitment and infrastructure and technology have significant impact on SMEs’ e-readiness. However, human capital, resistance to change, and information security do not have significant impact or contribution on e-readiness in SMEs.
Percutaneous vertebroplasty for spinal metastases: complications.

PURPOSE To retrospectively evaluate complications of percutaneous vertebroplasty (PV) performed with polymethylmethacrylate cement to treat pain in patients with metastases to the spine. MATERIALS AND METHODS This study had institutional review board approval; patient informed consent for the review of records and images was not required. In 2 years, 117 patients (38 men [32.5%] and 79 women [67.5%]; mean age, 58.2 years) underwent 159 fluoroscopy-guided PV procedures to treat 304 vertebrae. Spinal metastases included osteolytic, osteoblastic, and mixed lesions. Complications were characterized as local or systemic. Evaluated data included immediate imaging findings (on radiographs and computed tomographic scans) and clinical findings at 30-day follow-up. Chi2 or Fisher exact testing was performed for univariate analysis of variables. RESULTS The primary cancers were breast cancers (45.3%), lung cancers (14.5%), myeloma (7.7%), or other cancers (32.5%). Among the 423 cement leakages identified, 332 (78.5%) were vascular and 91 (21.5%) were nonvascular. Vascular leaks were classified as venous epidural leaks, paravertebral and foraminal plexus leaks, and leaks to the vena cava, while nonvascular leaks included puncture trajectory leaks, paravertebral soft tissue leaks, and diskal leaks. Patients with nonvascular leaks were asymptomatic. Eight (6.8%) patients experienced complications, and seven of these complications were symptomatic. Among these eight patients, six (5.1%) had local complications (puncture site hematoma in two patients and radicular pain [successfully treated with nonsteroidal anti-inflammatory drugs or corticosteroids] in four patients), and two (1.7%) had systemic complications (pulmonary embolism resulting from cement migration through the vena cava). One of the latter patients died. Univariate analyses revealed a significant association between cement migration through the vena cava and pulmonary embolism (P = .001) but not between foraminal venous leakage and radicular pain (P = .123). CONCLUSION Despite numerous technical incidents (leaks), PV-induced complications were rare, leading to the hypothesis that systemic complications are a consequence of intravascular leakage while local complications are a consequence of cement-related irritation, compression and/or ischemia, and/or needle-induced trauma.
Deficiency of Angulin-2/ILDR1, a Tricellular Tight Junction-Associated Membrane Protein, Causes Deafness with Cochlear Hair Cell Degeneration in Mice

Tricellular tight junctions seal the extracellular spaces of tricellular contacts, where the vertices of three epithelial cells meet, and are required for the establishment of a strong barrier function of the epithelial cellular sheet. Angulins and tricellulin are known as specific protein components of tricellular tight junctions, where angulins recruit tricellulin. Mutations in the genes encoding angulin-2/ILDR1 and tricellulin have been reported to cause human hereditary deafness DFNB42 and DFNB49, respectively. To investigate the pathogenesis of DFNB42, we analyzed mice with a targeted disruption of Ildr1, which encodes angulin-2/ILDR1. Ildr1 null mice exhibited profound deafness. Hair cells in the cochlea of Ildr1 null mice develop normally, but begin to degenerate by two weeks after birth. Tricellulin localization at tricellular contacts of the organ of Corti in the cochlea was retained in Ildr1 null mice, but its distribution along the depth of tricellular contacts was affected. Interestingly, compensatory tricellular contact localization of angulin-1/LSR was observed in the organ of Corti in Ildr1 null mice although it was hardly detected in the organ of Corti in wild-type mice. The onset of hair cell degeneration in Ildr1 null mice was earlier than that in the reported Tric mutant mice, which mimic one of the tricellulin mutations in DFNB49 deafness. These results indicate that the angulin-2/ILDR1 deficiency causes the postnatal degenerative loss of hair cells in the cochlea, leading to human deafness DFNB42. Our data also suggest that angulin family proteins have distinct functions in addition to their common roles of tricellulin recruitment and that the function of angulin-2/ILDR1 for hearing cannot be substituted by angulin-1/LSR.
Characterization of the cooperative function of inhibitory sequences in Ets-1

DNA binding by the eukaryotic transcription factor Ets-1 is negatively regulated by an intramolecular mechanism. Quantitative binding assays compared the DNA-binding activities of native Ets-1, three deletion mutants, and three tryptic fragments. Ets-1 and activated Ets-1 polypeptides differed in DNA-binding affinity as much as 23-fold. Inhibition was mediated by two regions flanking the minimal DNA-binding domain. Both regions regulated affinity by enhancing dissociation of the protein-DNA complex. Three lines of evidence indicated that inhibition requires cooperative interaction between the two regions: first, the two inhibitory regions acted through a common mechanism; second, neither region functioned independently of the other; finally, mutation of the C-terminal inhibitory region altered the conformation of the N-terminal inhibitory region. In addition, partial proteolysis detected an identical altered conformation in the N-terminal inhibitory region of Ets-1 bound to DNA. This finding suggested that repression is transiently disrupted during DNA binding. These results provide evidence that the two inhibitory regions of Ets-1 are structurally, as well as functionally, coupled. In addition, conformational change is shown to be a critical component of the inhibition mechanism. A cooperative, allosteric model of autoinhibition is described. Autoinhibition of Ets-1 could be relieved by either protein partner(s) or posttranslational modifications.
Knowledge Capturing Tools for Domain Experts

The success of the Semantic Web depends on the availability of content marked up using its description languages. Although the idea has been around for nearly a decade, the amount of Semantic Web content available is still fairly small. This is despite the existence of many digital archives containing lots of high quality collections which would, appropriately marked up, greatly enhance the reach of the Semantic Web. The archives themselves would benefit as well, by improved opportunities for semantic search, navigation and interconnection with other archives. The main challenge lies in the fact that ontology creation at the moment is a very detailed and complicated process. It mostly requires the service of an ontology engineer, who designs the ontology in accordance with domain experts. The software tools available, be it from the text engineering or the ontology creation disciplines, reflect this: they are built for engineers, not for domain experts. In order to really tap the potential of the digital collections, tools are needed that support the domain experts in marking up the content they understand better than anyone else. This paper presents an integrated approach to knowledge capturing and subsequent ontology creation, called WIKINGER, that aims at empowering domain experts to prepare their content for inclusion into the Semantic Web. This is done by largely automating the process through the use of named entity recognition and relation discovery.
Semantic Instance Segmentation with a Discriminative Loss Function

Semantic instance segmentation remains a challenging task. In this work we propose to tackle the problem with a discriminative loss function, operating at the pixel level, that encourages a convolutional network to produce a representation of the image that can easily be clustered into instances with a simple post-processing step. The loss function encourages the network to map each pixel to a point in feature space so that pixels belonging to the same instance lie close together while different instances are separated by a wide margin. Our approach of combining an off-the-shelf network with a principled loss function inspired by a metric learning objective is conceptually simple and distinct from recent efforts in instance segmentation. In contrast to previous works, our method does not rely on object proposals or recurrent mechanisms. A key contribution of our work is to demonstrate that such a simple setup without bells and whistles is effective and can perform on par with more complex methods. Moreover, we show that it does not suffer from some of the limitations of the popular detect-and-segment approaches. We achieve competitive performance on the Cityscapes and CVPPP leaf segmentation benchmarks.
Selection of Suitable Reference Genes for RT-qPCR Analyses in Cyanobacteria

Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR) is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works.
Muppet: MapReduce-Style Processing of Fast Data

MapReduce has emerged as a popular method to process big data. In the past few years, however, not just big data, but fast data has also exploded in volume and availability. Examples of such data include sensor data streams, the Twitter Firehose, and Facebook updates. Numerous applications must process fast data. Can we provide a MapReduce-style framework so that developers can quickly write such applications and execute them over a cluster of machines, to achieve low latency and high scalability? In this paper we report on our investigation of this question, as carried out at Kosmix and WalmartLabs. We describe MapUpdate, a framework like MapReduce, but specifically developed for fast data. We describe Muppet, our implementation of MapUpdate. Throughout the description we highlight the key challenges, argue why MapReduce is not well suited to address them, and briefly describe our current solutions. Finally, we describe our experience and lessons learned with Muppet, which has been used extensively at Kosmix and WalmartLabs to power a broad range of applications in social media and e-commerce.