Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Data Structures for Approximate Nearest Neighbor Search

Similarity searching has a vast range of applications in various fields of computer science. Many methods have been proposed for exact search, but they all suffer from the curse of dimensionality and are, thus, not applicable to high dimensional spaces. Approximate search methods are considerably more efficient in high dimensional spaces. Unfortunately, there are few theoretical results regarding the complexity of these methods and there are no comprehensive empirical evaluations, especially for non-metric spaces. To fill this gap, we present an empirical analysis of data structures for approximate nearest neighbor search in high dimensional spaces. We provide a comparison with recently published algorithms on several data sets. Our results show that small world approaches provide some of the best tradeoffs between efficiency and effectiveness in both metric and non-metric spaces. Keywords–nearest neighbor search; metric space; non-metric search, approximate search; small world graphs
Extent of Bilateral Neuronal Network Reorganization and Functional Recovery in Relation to Stroke Severity

Remodeling of neuronal structures and networks is believed to significantly contribute to (partial) restoration of functions after stroke. However, it has been unclear to what extent the brain reorganizes and how this correlates with functional recovery in relation to stroke severity. We applied serial resting-state functional MRI and diffusion tensor imaging together with behavioral testing to relate longitudinal modifications in functional and structural connectivity of the sensorimotor neuronal network to changes in sensorimotor function after unilateral stroke in rats. We found that gradual improvement of functions is associated with wide-ranging changes in functional and structural connectivity within bilateral neuronal networks, particularly after large stroke. Both after medium and large stroke, brain reorganization eventually leads to (partial) normalization of neuronal signal synchronization within the affected sensorimotor cortical network (intraregional signal coherence), as well as between the affected and unaffected sensorimotor cortices (interhemispheric functional connectivity). Furthermore, the bilateral network configuration shifts from subacutely increased “small-worldness,” possibly reflective of initial excessive neuronal clustering and wiring, toward a baseline small-world topology, optimal for global information transfer and local processing, at chronic stages. Cortical network remodeling was accompanied by recovery of initially disrupted structural integrity in corticospinal tract regions, which correlated positively with retrieval of sensorimotor functions. Our study demonstrates that the degree of functional recovery after stroke is associated with the extent of preservation or restoration of ipsilesional corticospinal tracts in combination with reinstatement of interhemispheric neuronal signal synchronization and normalization of small-world cortical network organization.
Scale‐up of mouse embryonic stem cell expansion in stirred bioreactors

The aim of this study was to develop a robust, quality controlled and reproducible large‐scale culture system using serum‐free (SF) medium to obtain vast numbers of embryonic stem (ES) cells as a starting source for potential applications in tissue regeneration, as well as for drug screening studies. Mouse ES (mES) cells were firstly cultured on microcarriers in spinner flasks to investigate the effect of different parameters such as the agitation rate and the feeding regimen. Cells were successfully expanded at agitation rates up to 60 rpm using the SF medium and no significant differences in terms of growth kinetics or metabolic profiles were found between the two feeding regimens evaluated: 50% medium renewal every 24 h or 25% every 12 h. Overall, cells reached maximum concentrations of (4.2 ± 0.4) and (5.6 ± 0.8) ×106 cells/mL at Day 8 for cells fed once or twice per day; which corresponds to an increase in total cell number of 85 ± 7 and 108 ± 16, respectively. To have a more precise control over culture conditions and to yield a higher number of cells, the scale‐up of the spinner flask culture system was successfully accomplished by using a fully controlled stirred tank bioreactor. In this case, the concentration of mES cells cultured on microcarriers increased 85 ± 15‐fold over 11 days. Importantly, mES cells expanded under stirred conditions, in both spinner flask and fully controlled stirred tank bioreactor, using SF medium, retained the expression of pluripotency markers such as Oct‐4, Nanog, and SSEA‐1 and their differentiation potential into cells of the three embryonic germ layers. © 2011 American Institute of Chemical Engineers Biotechnol. Prog. ,, 2011
Evolving better representations through selective genome growth

The choice of how to represent the search space for a genetic algorithm (GA) is critical to the GA's performance. Representations are usually engineered by hand and fixed for the duration of the GA run. Here a new method is described in which the degrees of freedom of the representation-i.e. the genes-are increased incrementally. The phenotypic effects of the new genes are randomly drawn from a space of different functional effects. Only those genes that initially increase fitness are kept. The genotype-phenotype map that results from this selection during the construction of the genome allows better adaptation. This effect is illustrated with the NK landscape model. The resulting genotype-phenotype maps are much less epistatic than unselected maps would be, having extremely low values of "K"-the number of fitness components affected by each gene. Moreover, these maps are exquisitely tuned to the specifics of the epistatic fitness function, creating adaptive landscapes that are much smoother than generic NK landscapes with the same genotype-phenotype maps, with fitness peaks many standard deviations higher. Thus a caveat should be made when making arguments about the applicability of generic properties of complex systems to evolved systems. This method may help to solve the problem of choice of representations in genetic algorithms. <<ETX>>
Structure control of La/B multilayer systems by partial nitridation

This PhD thesis contains a selection of thin film research results on the structure control of La/B multilayer mirrors with nm- and sub nm-thick layers, used at normal and grazing incidence of XUV radiation. Topics investigated include an improvement of the optical layer contrast, the reflectivity at 6.x nm wavelength, and the thermal stability. The approaches presented deal with in situ growth studies, deposition control and high resolution X-ray analysis.
Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets

Avian flu can acquire the capacity for airborne transmission between mammals without recombination in an intermediate host. Highly pathogenic avian influenza A/H5N1 virus can cause morbidity and mortality in humans but thus far has not acquired the ability to be transmitted by aerosol or respiratory droplet (“airborne transmission”) between humans. To address the concern that the virus could acquire this ability under natural conditions, we genetically modified A/H5N1 virus by site-directed mutagenesis and subsequent serial passage in ferrets. The genetically modified A/H5N1 virus acquired mutations during passage in ferrets, ultimately becoming airborne transmissible in ferrets. None of the recipient ferrets died after airborne infection with the mutant A/H5N1 viruses. Four amino acid substitutions in the host receptor-binding protein hemagglutinin, and one in the polymerase complex protein basic polymerase 2, were consistently present in airborne-transmitted viruses. The transmissible viruses were sensitive to the antiviral drug oseltamivir and reacted well with antisera raised against H5 influenza vaccine strains. Thus, avian A/H5N1 influenza viruses can acquire the capacity for airborne transmission between mammals without recombination in an intermediate host and therefore constitute a risk for human pandemic influenza.
MIGHT WE EVENTUALLY UNDERSTAND THE ORIGIN OF THE DARK MATTER VELOCITY ANISOTROPY?

The density profile of simulated dark matter structures is fairly well-established, and several explanations for its characteristics have been put forward. In contrast, the radial variation of the velocity anisotropy has still not been explained. We suggest a very simple origin, based on the shapes of the velocity distribution functions, which are shown to differ between the radial and tangential directions. This allows us to derive a radial variation of the anisotropy profile which is in good agreement with both simulations and observations. One of the consequences of this suggestion is that the velocity anisotropy is entirely determined once the density profile is known. We demonstrate how this explains the origin of the γ–β relation, which is the connection between the slope of the density profile and the velocity anisotropy. These findings provide us with a powerful tool, which allows us to close the Jeans equations.
K-Means Clustering with Distributed Dimensions ( Supplement )

1. Proof of Theorem 4 Proof. It is easy to verify the communication cost, and thus we focus on the proof for the approximation ratio below. Similar to the proof of Theorem 1, the grid G is rewritten as {g1, · · · , gm} where m = (k + z) , and for each gj , its corresponding intersection ⋂T l=1Mlil is rewritten as Sj . Meanwhile, we denote the index-set indicating the outliers obtained by our algorithm as Z. Furthermore, we denote the optimal k cluster centers as {c1, · · · , ck} and the indexset indicating the outliers in the optimal solution as Zopt. We have the same definitions for N (pi) and N(gj) from the proof of Theorem 1 as well. Also, we denote by Γ(Z) = ∑(k+z)T j=1 ∑ i∈Sj\Z ‖pi − N(gj)‖ the cost of our solution, by Γopt(Z) = ∑ i∈[n]\Z ‖pi − N (pi)‖ the cost of the optimal solution. Let ∑(k+z)T j=1 ∑ i∈Sj\Z ‖pi − gj‖ 2 be Γa(Z), and ∑(k+z)T j=1 |Sj \Z|‖gj −N(gj)‖ be Γb(Z), respectively. Using the similar manner of proving the inequality (2) in our paper, we have Γ(Z) ≤ Γa(Z) + Γb(Z) + 2 √ Γa(Z)Γb(Z). (1)
Correction: Circulating Levels of Human Salusin-β, a Potent Hemodynamic and Atherogenesis Regulator

There were multiple errors in the title. The correct title is: "Circulating Levels of Human Salusin-β, a Potent Hemodynamic and Atherogenesis Regulator. " The correct citation is: Fujimoto K, Hayashi A, Kamata Y, Ogawa A, Watanabe T, et al. (2013) Circulating Levels of Human Salusin-β, a Potent Hemodynamic and Atherogenesis Regulator. PLoS ONE 8(10): e76714. doi:10.1371/journal.pone. 0076714.
Implementation of the EXI Schema on Wireless Sensor Nodes Using Contiki

The current trend in Wireless Sensor Networks (WSN) is to use the Internet Protocol (IP) and open standards to achieve native connectivity between smart objects and the Internet, contributing to consolidate the Internet of Things (IoT). Emerging standards such as 6LoWPAN/IPv6 and CoRE/CoAP will play a very important role in a Restful Web of Things, where each node has its own IPv6 address and is able to provide information and control about itself. Data exchanging in Machine To Machine (M2M) applications and communication with Web services require the use of structured data. XML is a possible solution, but its verbosity is not suitable for a WSN (e.g. based on IEEE 802.15.4) characterized by limited packet size. This paper investigates the benefits of Efficient XML Interchange (EXI) in a real scenario, considering sensor nodes running on the Contiki RTOS. For this purpose, the authors have implemented an extremely lightweight version of EXI for Contiki running on application boards with just 8 Kbyte RAM memory.
Evolutionary history shapes patterns of mutualistic benefit in Acacia–rhizobial interactions

The ecological and evolutionary factors that drive the emergence and maintenance of variation in mutualistic benefit (i.e., the benefits provided by one partner to another) in mutualistic symbioses are not well understood. In this study, we evaluated the role that host and symbiont phylogeny might play in determining patterns of mutualistic benefit for interactions among nine species of Acacia and 31 strains of nitrogen‐fixing rhizobial bacteria. Using phylogenetic comparative methods we compared patterns of variation in mutualistic benefit (host response to inoculation) to rhizobial phylogenies constructed from housekeeping and symbiosis genes; and a multigene host phylogeny. We found widespread genotype‐by‐genotype variation in patterns of plant growth. A relatively large component of this variation (21–28%) was strongly influenced by the interacting evolutionary histories of both partners, such that phylogenetically similar host species had similar growth responses when inoculated with phylogenetically similar rhizobia. We also found a relatively large nonphylogenetic effect for the average mutualistic benefit provided by rhizobia to plants, such that phylogenetic relatedness did not predict the overall benefit provided by rhizobia across all hosts. We conclude that phylogenetic relatedness should frequently predict patterns of mutualistic benefit in acacia‐rhizobial mutualistic interactions; but that some mutualistic traits also evolve independently of the phylogenies.
Indictment of the microglia as the villain in multiple sclerosis

Over the past decade, considerable attention has focused on the theory that MS is an autoimmune disease mediated by T cells specific for neural autoantigens. [1,2] Infectious agents may play a role in triggering an autoimmune process in a susceptible individual. [3,4] If so, this would reconcile the roles of environmental and genetic factors in the development of MS. The existence of structural similarities between viral antigens and autoantigens (viral mimicry) and the possibility that viral products (super antigens) can amplify T-cell populations have suggested mechanisms by which an infectious agent such as a virus can initiate an autoimmune process. [5,6] An essential element of both hypotheses (molecular mimicry and superantigens) is the expansion and targeting of autoreactive CD4+ T cells to the CNS. Hence, understanding T-cell receptor (TCR) gene usage of autoreactive T cells and their cytokine secretion profile has been a central focus of interest. We propose a model of CNS demyelination that is not predicated upon the continued presence of autoreactive T cells. Instead, we suggest that microglial activation is a central element in CNS demyelination and that the oligodendrocyte-myelin unit is the target. Understanding the nature of microglial activation is likely to offer therapeutic insights to the treatment of MS. In contrast to autoantibody-mediated autoimmune disease, evidence for the role of autoreactive T cells in autoimmune disease has been difficult to prove. This is in part because T-cell reactivity to autoantigens is present in the normal healthy population and there is no system to test the pathogenicity of autoreactive T cells. Nonetheless, rheumatoid arthritis, MS, inflammatory bowel disease, and insulin-dependent diabetes mellitus are thought to represent T-cell-mediated autoimmune disease. In this paradigm, the end-organ damage is not the result of antibodies to self-antigens but due in part to a delayed type hypersensitivity, cytokines, and cytotoxic T-cell …
Optimal Investment Strategies for Product-Flexible and Dedicated Manufacturing Systems under Demand Uncertainty ∗

This paper studies the optimal investment strategy of a firm having the managerial freedom to acquire both flexible or dedicated production capacity. Flexible Capacity is more expensive but allows the firm to switch costlessly between products and handle changes in relative volumes among products in a given product mix. Dedicated capacities restrict to manufacture one specific product but for lower acquisition cost. Specifically, I model the investment decision of a monopolistic firm selling two products in a market characterized by price-dependent and uncertain demand, in a continuous time setting. The paper takes a real option approach to consider optimal capacity investment decisions under uncertainty. Besides the timing of the investment, the firm can choose the optimal capacity level and is free to undergo investment in flexible or dedicated capacity. The sensitivity of the firm’s optimal capacity investment considering flexible and dedicated capacity to key problem components is analyzed. The main focus is on the effect of demand variability a key driver of flexibility as well as substitutability and product profitability effects. I find that if uncertainty goes up the firm invests later in higher capacity. Flexibility especially pays off when uncertainty is high, substitutability low, and profit levels between the two products are substantially different. In the flexible case, under high demand the firm just produces the most profitable product, if demand is low the firm produces both products to make total market demand bigger. In the dedicated case the firm invests in both capacities only if the substitutability rate is low and profitability I would like to thank my supervisors Prof. Peter M. Kort and Dr. Kuno J.M. Huisman for many interesting and fruitful discussions about this topic. Furthermore I would like to thank participants of the Economics Workshops Seminar at Tilburg University for helpful discussions and comments.
A Platform for Heterogeneous Interconnection Network Management

A comprehensive network management function built into the interconnection network provides a means of meeting user needs of fault tolerance, performance, accounting, and security. However, meeting these needs on a heterogeneous interconnection network is several levels more complex than on a homogeneous network because of the existence of multiple protocol stacks for communication. An architecture that will solve this problem by analyzing the heterogeneous interconnection network as a single entity is proposed. The authors present the design issues evaluated in choosing this approach and establish the need for the various components in this architecture. An overview is presented of each of the components, and their place in the architecture is pointed out. >
An Efficient Scheme for Encrypted Data Aggregation on Sensor Networks

It is an open problem of how to protect the traffics and at the same time, to support in-network processing in sensor networks. This paper tackles the problem by proposing an efficient model of categorizing encrypted data transmitted on sensor networks. An aggregator, an intermediate sensor node in our setting, is embedded with a set of searching keywords in encrypted format. Upon receiving an encrypted message, it matches the message with the keywords and then processes the message based on certain policies such as forwarding the original message to the next hop, updating it and forwarding or simply dropping it on detecting duplicates. The messages are encrypted before being sent out and decrypted only at their destination. Although the intermediate classifiers can categorize the messages, they learn nothing about the encrypted messages except several encrypted keywords, even the statistic information. The secure and efficient aggregation SEA scheme uses Bloom filter to further reduce transmission cost. The performance analysis shows that the computational cost and communication cost are well balanced
Impact of Multidrug Resistance on Experimental Empyema by Pseudomonas aeruginosa

Background:Pseudomonas aeruginosa is a cause of infections of the lower respiratory tract among patients with chronic lung disorders. It is questionable whether virulence of this species may be influenced by multidrug resistance (MDR). Objectives: To define the impact of MDR in experimental lung infection. Methods: Experimental empyema was induced in rabbits by MDR (group A, n = 16) and by susceptible isolates (group B, n = 10). Pleural fluid was sampled for quantitative culture and estimation of cell apoptosis and of tumor necrosis factor-alpha (TNFα) and malondialdehyde (MDA). Survival was recorded. Cytokine production was stimulated in U937 monocytes by samples of pleural fluid. Whole blood of rabbits was incubated with the isolates; induction of apoptosis was assessed. Results: Survival of group A was prolonged compared to group B. This was accompanied by lower bacterial counts of the inoculated pathogens in pleural fluid and in the lungs of group A compared with group B. Early apoptosis of neutrophils of pleural fluid of group A was lower compared with group B. Pleural fluid concentrations of TNFα and MDA did not differ between the groups. Cytokine production by U937 monocytes after stimulation with pleural fluid was greater in group B than in group A. The susceptible isolate induced apoptosis of neutrophils in vitro at a greater rate than the MDR isolate. Conclusions: Experimental empyema by susceptible P. aeruginosa is accompanied by greater mortality compared with MDR P. aeruginosa. This phenomenon may be attributed to the different growth pattern of the pathogens or to their interaction with the innate immune system.
Prophylactic Low Dose Ketamine and Ondansetron for Prevention of Shivering During Spinal Anaesthesia

Background: Perioperative shivering is a common problem during anaesthesia. Apart from physical warming many drugs have also been used for prevention of shivering. Ketamine has been used for preventing shivering during anaesthesia in doses of 0.5 to 0.75mg kg-1, but even these doses causes too much sedation and hallucination. Ondansetron (8 mg) has been recently evaluated for its perioperative antishivering effect in patients under anaethesia. Present study was conducted to evaluate the efficacy and safety of low dose Ketamine (0.25mg kg-1) and Ondansetron (4 mg) for prevention of shivering during spinal anaesthesia. Patients & Methods: Total 120 patients undergoing lower abdominal surgery under spinal anaesthesia were included. 3ml of hyperbaric bupivacaine 0.5% was used for spinal anaesthesia. After intrathecal injection, the patients were randomly divided in 3 groups of 40 each who received Ketamine 0.25mg kg-1or Ondansetron 4mg IV or Saline. Vitals, temperature and shivering scores were recorded every 5 minutes. Side effects i.e. hypotension, nausea and vomiting, sedation and hallucinations were also recorded. Results: Fall in temperature was more significant in saline and ondansetron group (gp) than in ketamine group at all time interval. Out of 40 patients, shivering was maximum & seen in 17 patients (42.50%) in saline gp, 4 patients (10%) in ondansetron gp and in only 1patient (2.5%) in ketamine gp. Odd ratio of ketamine, ondansetron and saline are 1, 4.33 and 28.33 respectively which means that shivering in saline gp was 28.83 times higher than ketamine gp and 6.65 times higher than in ondansetron . Shivering rate was 4.33 times higher in ondansetron gp than in ketamine gp. Hypotension was lowest in ketamine gp (10%) in comparison to ondansetron gp (22.5%) and saline gp. (20%). Mild sedation was seen in almost all (95%) patients in ketamine gp, Conclusion: Prophylactic low dose ketamine (0.25mg kg-1) and Ondansetron (4mg) significantly decreased shivering in patients undergoing spinal anaesthesia without significant side effects.