Miracle-dz/UniFAR-FTUs huggingface dataset:
Alex - a Global Filesystem

The Alex filesystem provides users and applications transparent read access to files in Internet anonymous FTP sites. Today there are thousands of anonymous FTP sites with a total of a few million files and roughly a terabyte of data. The standard approach to accessing these files involves logging in to the remote machine. This means that an application can not access remote files and that users do not have any of their aliases or local tools available when connected to a remote site. Users who want to use an application on a remote file must first manually make a local copy of the file. Not only is this inconvenient, it creates two more problems. First, there is no mechanism for automatically updating this local copy when the remote file changes. The users must keep track of where they get their files from and check to see if there are updates, and then fetch these. Second, many different users at the same site may have made copies of the same remote file, thus wasting disk space. Alex addresses the problems with the above approach while maintaining compatibility with the existing FTP protocol so that the large collection of currently available files can be accessed. To get reasonable performance, long term file caching must be used. Thus consistency must be addressed. Traditional solutions to the cache consistency problem do not work in the Internet FTP domain: callbacks are not an option as the FTP protocol has no provisions for this, and polling over the Internet is slow. Fortunately, the usage of these files is also not traditional and lends itself to a new approach. Alex relaxes file cache consistency semantics, on a per file basis, and uses special caching algorithms that take into account the properties of the files and of the network. This approach allows a simple stateless filesystem to scale to the size of the Internet. This research was sponsored in part by The Defense Advanced Research Projects Agency, Information Science and Technology Office, under the title “Research on Parallel Computing”, ARPA Order No. 7330, issued by DARPA/CMO under Contract MDA972-90-C-0035 and in part by the National Science Foundation under grant number ECD-8907068. The views and conclusions contained in this document are those of the author and should not be interpreted as representing the official policies, either expressed or implied, of the U.S. Government. Alex a Global Filesystem Vincent Cate vac@cs.cmu. edu
22nd European Society for Animal Cell Technology (ESACT) Meeting on Cell Based Technologies Vienna, Austria. 15-18 May 2011. Abstracts.

s Peniscola, Spain 2007, 123-136. 3. Weibo C, et al: Applications of gold nanoparticles in cancer nanotechnology. Review, Nanotechnology, Science and Applications 2008, 27-32. 4. Lihua W, et al: Gold nanoparticlebased optical probes for targetresponsive DNA structures. Gold Bulletin 2008, 41(1):37-42. 5. Harris N, et al: Tunable integrated absorption by metal nanoparticles: the case for gold rods and shells. Gold Bulletin 2008, 41(1):5-14. 6. NCI Alliance for Nanotechnology in Cancer. nanoUtah, Piotr Grodzinski,
Lightweight and Privacy-Friendly Spatial Data Aggregation for Secure Power Supply and Demand Management in Smart Grids

The concept of smart metering allows real-time measurement of power demand which in turn is expected to result in more efficient energy use and better load balancing. However, finely granular measurements reported by smart meters can lead to starkly increased exposure of sensitive information, including various personal attributes and activities. Even though several security solutions have been proposed in recent years to address this issue, most of the existing solutions are based on public-key cryptographic primitives, such as homomorphic encryption and elliptic curve digital signature algorithms which are ill-suited for the resource constrained smart meters. On the other hand, to address the computational inefficiency issue, some masking-based solutions have been proposed. However, these schemes cannot ensure some of the imperative security properties, such as consumer’s privacy and sender authentication. In this paper, we first propose a lightweight and privacy-friendly masking-based spatial data aggregation scheme for secure forecasting of power demand in smart grids. Our scheme only uses lightweight cryptographic primitives, such as hash functions and exclusive-OR operations. Subsequently, we propose a secure billing solution for smart grids. As compared with existing solutions, our scheme is simple and can ensure better privacy protection and computational efficiency, which are essential for smart grids.
Path-based Graph Indexing for Keyword Search on RDF data - Discovering Concepts Through Community Detection

RDF graphs are structured data that is designed to be used by computers for reasoning. However, such data may be of interest to people as well. Therefore has keyword search on RDF graphs been introduced. The current approaches to keyword search, on both RDF graphs and other graphs, typically finds solutions that connects keyword matching nodes with minimal cost. Minimal costs could, for instance, be the shortest paths between the nodes. Minimal solutions, however, may not always be the most informative answers to a query. Returning parts of the graph that constitute concepts corresponding to how humans conceptualize the world, could give answers that better satisfies the information need. This thesis has explored if such concepts can be discovered automatically in an RDF graph. To this end, we have employed algorithms for finding closely connected groups of nodes in a graph. These groups of nodes are called communities, and finding them is called community detection. A state of the art review examining approaches to keyword search on graphs in general, and RDF graphs in particular, was carried out. Additionally, we performed a review on current algorithms for finding overlapping communities in a graph. Based on this review, we did a preliminary study where the most relevant of these algorithms were applied to some RDF graphs. Through the study, we found some weaknesses in the direct application on RDF graphs, with regard to our stated objective of finding concepts. This was related to the special nature of RDF graphs, compared to other graphs. In particular, we found inconsistencies in the discovered communities with regard to class information, and the meaning that is found in predicate edges. These inconsistencies prevented us from describing the found communities as logical concepts. To eliminate these weaknesses, we developed a novel community detection algorithm for finding concepts in an RDF graph. This new algorithm defines communities in RDF graphs as a set of paths, not as a collection of nodes. We run our community detection algorithm on a sample of the nodes in the graph to find the paths included in communities, and then aggregate the results. The paths that are most frequently included in a community are kept, and used to build concepts. Our algorithm ensures that the concepts are both consistent internally in a community, and consistent across the dataset. The feasibility of our approach were shown through experiments. Furthermore, the usefulness of the approach is argued through a proof-of-concept search solution that uses the concepts found by the community detection algorithm. We find that the concepts discovered by our algorithm can enhance the answers to queries, when compared to corresponding minimal solutions.
Improving Availability of Multicore Real-Time Systems Suffering Both Permanent and Transient Faults

CMOS scaling has greatly increased concerns for both lifetime reliability due to permanent faults and soft-error reliability due to transient faults. Most existing works only focus on one of the two reliability concerns, but often times techniques used to increase one type of reliability may adversely impact the other type. A few efforts do consider both types of reliability together and use two different metrics to quantify the two types of reliability. However, for many systems, the user's concern is to maximize system availability by improving the mean time to failure (MTTF), regardless of whether the failure is caused by permanent or transient faults. Addressing this concern requires a uniform metric to measure the effect due to both types of faults. This paper introduces a novel analytical expression for calculating the MTTF due to transient faults. Using this new formula and an existing method to evaluate system MTTF, we tackle the problem of maximizing availability for multicore real-time systems with consideration of permanent and transient faults. A framework is proposed to solve the system availability maximization problem. Experimental results on a hardware board and simulation results of synthetic tasks show that our scheme significantly improves system MTTF (and hence availability) compared with existing techniques.
Research advances in Alzheimer's disease and related disorders

Partial table of contents: EPIDEMIOLOGY. The Epidemiology of Alzheimer's Disease: Beyond Risk Factors (J. Mortimer). GENETICS. Apolipoprotein E and Alzheimer's Disease (A. Roses, et al.). DIAGNOSIS. Impaired Vasodilation of Skin Vessels in Alzheimer's Disease (A. Algotsson, et al.). CLINICAL COURSE. Behavioral Changes in Early Alzheimer's Disease (L. Harrell, et al.). TREATMENT STRATEGIES. Drug Development must be Optimized in Order to Choose the Correct Strategy (N. Cutler & J. Sramek). NEUROPATHOLOGY. The Pathological Lesions of Alzheimer's Disease: Form and Formation (D. Mann). CYTOSKELETAL PATHOLOGY. What have we Learned from Paired Helical Filaments? (Y. Ihara). AMLOIDOGENESIS. Amyloids, Genes and Chaperons in Alzheimer's Disease (B. Frangione, et al.). APP BIOLOGY. Biological Function and Processing of APP (N. Robakis, et al.). MODEL SYSTEMS. Fibrillar and Non-Fibrallar Amyloid in the Brain of Aged Dogs (F. Wegiel, et al.). PRION DISEASES. Molecular Biology, Genetics and Protein Chemistry of Prion Disease (M. Baldwin & S. Prusiner). Index.
New records of Neogene Xenarthra (Mammalia) from eastern Puna (Argentina): diversity and biochronology

Abstract. Xenarthra is an endemic South American lineage of mammals, probably the sister clade of the other placental mammals. The oldest records of Xenarthra are from the latest Paleocene, although its current diversity is much lower than that recorded in some intervals of the Cenozoic Era. A new Neogene Xenarthra (Pilosa and Cingulata) assemblage from two localities of the Argentine Eastern Puna (Calahoyo and Casira) is described. The newly recorded taxa—Cingulata, Dasypodidae, Eutatini: Stenotatus sp. indet. and Eutatini indet. , Euphractini: Macrochorobates scalabrinii (Moreno and Mercerat, 1891), and Tardigrada, Mylodontinae: cf. Simomylodon sp. indet. and Simomylodon cf. S. uccasamamensis Saint-André et al., 2010—and those already published from Calahoyo—Cingulata: Macrochorobates chapadmalensis (Ameghino, 1908), Eosclerocalyptus sp. indet. , and Tardigrada, Megatheriidae: Pyramiodontherium bergi (Moreno and Mercerat, 1891)—suggest a middle–late Miocene age for the fossil-bearing levels. In Calahoyo, the presence of Stenotatus sp. indet. , in addition to some rodents currently under study in the lower levels, suggest a closer similarity with the palaeofauna of Cerdas (southern Bolivia), probably involving the last part of the Miocene Climatic Optimum. The Xenarthra recorded in the middle and upper levels of Calahoyo and Casira suggest a late Miocene–Pliocene age. A comparative analysis between Calahoyo and Casira highlights the absence of Cingulata in the latter and a high diversity in the former. This situation probably indicates different paleoenvironmental conditions. Finally, we present the first certain record of the genus Simomylodon Saint-André et al., 2010 in Argentina, which includes the oldest record of dermal ossicles for sloths in South America.
Deletions associated with stabilization of the Top1 cleavage complex in yeast are products of the nonhomologous end-joining pathway

Significance The separation of DNA strands during replication and transcription creates torsional stress (supercoiling) that requires resolution by topoisomerases. Topoisomerase 1 (Top1) removes supercoils by transiently nicking one DNA strand, which allows its rotation around the intact, complementary strand. Stabilization of the covalent Top1–DNA cleavage intermediate results in potentially toxic DNA damage during replication, making this enzyme an attractive target of chemotherapeutic drugs. We find that genetic or chemical Top1 stabilization gives rise to large deletions that require the nonhomologous end-joining pathway and most likely reflect the joining of nonadjacent ends. Furthermore, the relevant Top1-mediated damage accumulates in nondividing cells, suggesting a potential mechanism for genetic change that occurs outside the context of replication. Topoisomerase I (Top1) resolves supercoils by nicking one DNA strand and facilitating religation after torsional stress has been relieved. During its reaction cycle, Top1 forms a covalent cleavage complex (Top1cc) with the nicked DNA, and this intermediate can be converted into a toxic double-strand break (DSB) during DNA replication. We previously reported that Top1cc trapping in yeast increases DSB-independent, short deletions at tandemly repeated sequences. In the current study, we report a type of DSB-dependent mutation associated with Top1cc stabilization: large deletions (median size, ∼100 bp) with little or no homology at deletion junctions. Genetic analyses demonstrated that Top1cc-dependent large deletions are products of the nonhomologous end-joining (NHEJ) pathway and require Top1cc removal from DNA ends. Furthermore, these events accumulated in quiescent cells, suggesting that the causative DSBs may arise outside the context of replication. We propose a model in which the ends of different, Top1-associated DSBs are joined via NHEJ, which results in deletion of the intervening sequence. These findings have important implications for understanding the mutagenic effects of chemotherapeutic drugs that stabilize the Top1cc.
Challenges faced by peer support workers during the integration into hospital-based mental health-care teams: Results from a qualitative interview study

Background: Being aware of the challenges that may occur during the implementation of peer support work in psychiatry is important to facilitate the integration of peer support workers (PSWs) into multidisciplinary mental health-care teams. Aim: The purpose of this study is to explore the challenges faced by PSWs during their integration into hospital-based mental health-care teams. Methods: Qualitative content analysis of nine open-ended, semi-structured interviews with PSWs is undertaken in five adult psychiatric hospitals in North Rhine-Westphalia, Germany. Results: The analysis of the data revealed three themes: (1) ‘Pioneers and the pressure to succeed’; (2) ‘a colleague, a rival or yet another patient? ’ and (3) ‘sharing of information, boundaries and professionalism’. All three themes relate to several concrete challenges on different systemic levels and have the potential to impede the PSWs’ integration process. Conclusion: Specific implementation strategies which address potential barriers on the different systemic levels should be developed and applied prior to the start of the integration of PSWs into multidisciplinary mental health-care teams.
Efficient Exploration in Constrained Environments with Goal-Oriented Reference Path

In this paper, we consider the problem of building learning agents that can efficiently learn to navigate in constrained environments. The main goal is to design agents that can efficiently learn to understand and generalize to different environments using high-dimensional inputs (a 2D map), while following feasible paths that avoid obstacles in obstacle-cluttered environment. To achieve this, we make use of traditional path planning algorithms, supervised learning, and reinforcement learning algorithms in a synergistic way. The key idea is to decouple the navigation problem into planning and control, the former of which is achieved by supervised learning whereas the latter is done by reinforcement learning. Specifically, we train a deep convolutional network that can predict collision-free paths based on a map of the environment– this is then used by an reinforcement learning algorithm to learn to closely follow the path. This allows the trained agent to achieve good generalization while learning faster. We test our proposed method in the recently proposed Safety Gym suite that allows testing of safety-constraints during training of learning agents. We compare our proposed method with existing work and show that our method consistently improves the sample efficiency and generalization capability to novel environments.
Regulation of transcription and translation : a tale of crystallins and small heat shock proteins

The DNA sequences of many genomes have been elucidated in the last years. The challenge now is to predict first the genotype and then the phenotype from the genomic sequences. To predict expression patterns of the genes located on the genome, not only regulation at the level of transcription, but also at the level of translation is important. To obtain more information about regulation of transcription, the promoter and its regulatory elements need to be mapped. In this thesis a conventional search for known and active regulatory elements in the B2-crystallin promoter was performed. For the intergenic region between aB-crystallin and HspB2, an alternative approach was taken to determine which elements are likely to be important for gene regulation, and the evolutionary conservation of sequence elements in this region was studied. Alignments of this region of many species lead to the confirmation of importance of known regulatory elements and the finding of new sites. A good example of regulation of gene expression mediated by regulation of translation, is translation after stress. During and after heat shock, cap-dependent translation is inhibited, while cap-independent translation can still take place. After heat shock translation of (s)Hsps is increased, these (s)Hsps are thought to protect cells from stress. We show that two of the sHsps, aB-crystallin and Hsp27 protect cap-dependent, but not cap-independent translation after heat shock. Inhibition of translation is thought to be mediated by a decrease in activity of the translation factors. However, the protection of translation mediated by sHsps does not seem to affect translation factors directly, but overexpression of aB-crystallin seems to increase the dispersal of stress granules that contain the stalled translation initiation complexes. We propose that aB-crystallin, probably together with other Hsps, resolubilizes the stress granule components and that translational thermotolerance is a cooperative effect of different Hsps.
ExSample: Efficient Searches on Video Repositories through Adaptive Sampling

Capturing and processing video is increasingly common as cameras become cheaper to deploy. At the same time, rich video-understanding methods have progressed greatly in the last decade. As a result, many organizations now have massive repositories of video data, with applications in mapping, navigation, autonomous driving, and other areas. Because state-of-the-art object-detection methods are slow and expensive, our ability to process even simple ad-hoc object search queries (“find 100 traffic lights in dashcam video”) over this accumulated data lags far behind our ability to collect the data. Processing video at reduced sampling rates is a reasonable default strategy for these types of queries; however, the ideal sampling rate is both data and query dependent. We introduce ExSample, a low cost framework for object search over un-indexed video that quickly processes search queries by adapting the amount and location of sampled frames to the particular data and query being processed. ExSample prioritizes the processing of frames in a video repository so that processing is focused in portions of video that most likely contain objects of interest. It approaches searching in a similar way to a multi-arm bandit problem where each arm corresponds to a portion of a video. On large, real-world datasets, ExSample reduces processing time by 1.9x on average and up to 6x over an efficient random sampling baseline. Moreover, we show ExSample finds many results long before sophisticated, state-of-the-art baselines based on proxy scores can begin producing their first results.
Genome Rearrangement Distance with Reversals, Transpositions, and Indels

The rearrangement distance is a well-known problem in the field of comparative genomics. Given two genomes, the rearrangement distance is the minimum number of rearrangements in a set of allowed rearrangements (rearrangement model), which transforms one genome into the other. In rearrangement distance problems, a genome is modeled as a string, where each element represents a conserved region within the two genomes. When the orientation of the genes is known, it is represented by (plus or minus) signs assigned to the elements of the string. Two of the most studied rearrangements are reversals, which invert a segment of the genome, and transpositions, which exchange the relative positions of two adjacent segments of the genome. The first works in genome rearrangements considered that the genomes being compared had the same genetic material and that rearrangement events were restricted to reversals, transpositions, or both. El-Mabrouk extended the reversal model on signed strings to include the operations of insertion and deletion of segments in the genome, which allowed the comparison of genomes with different genetic material. Other studies also addressed this problem and, recently, this problem was proved to be solvable in polynomial time by Willing et al. For unsigned strings, we still observe a lack of results. That said, in this study we prove that computing the rearrangement distance for the following models is NP-Hard: reversals and indels on unsigned strings; transpositions and indels on unsigned strings; and reversals, transpositions, and indels on signed and unsigned strings. Along with the NP-hardness proofs, we present a 2-approximation algorithm for reversals on unsigned strings and 3-approximation algorithms for the other models.
Novel aspects of the real paracrystal

A revision of the mathematical concept of paracrystals is proposed. Hermann's [Z. Electrochem. (1940), 46, 425-436] early theory of mesophases represents a special case of a paracrystal where the statistical parameters introduced were merely crystalline or gas-like. The theory of paracrystals removes the black-white picture of crystalline and amorphous phases by introducing 18 new statistical parameters into conventional crystallography. It is shown that a real paracrystal can be defined by a three-dimensional convolution polynomial in combination with an empirically derived α* law. Hence, a missing corner-stone of colloid science is established.