Miracle-dz/UniFAR-FTUs huggingface dataset:
The Anatomy of the Grid: Enabling Scalable Virtual Organizations

“Grid” computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high performance orientation. In this article, the authors define this new field. First, they review the “Grid problem,” which is defined as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources—what is referred to as virtual organizations. In such settings, unique authentication, authorization, resource access, resource discovery, and other challenges are encountered. It is this class of problem that is addressed by Grid technologies. Next, the authors present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. The authors describe requirements that they believe any such mechanisms must satisfy and discuss the importance of defining a compact set of intergrid protocols to enable interoperability among different Grid systems. Finally, the authors discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. They maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.
Plasmodium falciparum Variant Surface Antigen Expression Patterns during Malaria

The variant surface antigens expressed on Plasmodium falciparum–infected erythrocytes are potentially important targets of immunity to malaria and are encoded, at least in part, by a family of var genes, about 60 of which are present within every parasite genome. Here we use semi-conserved regions within short var gene sequence “tags” to make direct comparisons of var gene expression in 12 clinical parasite isolates from Kenyan children. A total of 1,746 var clones were sequenced from genomic and cDNA and assigned to one of six sequence groups using specific sequence features. The results show the following. (1) The relative numbers of genomic clones falling in each of the sequence groups was similar between parasite isolates and corresponded well with the numbers of genes found in the genome of a single, fully sequenced parasite isolate. In contrast, the relative numbers of cDNA clones falling in each group varied considerably between isolates. (2) Expression of sequences belonging to a relatively conserved group was negatively associated with the repertoire of variant surface antigen antibodies carried by the infected child at the time of disease, whereas expression of sequences belonging to another group was associated with the parasite “rosetting” phenotype, a well established virulence determinant. Our results suggest that information on the state of the host–parasite relationship in vivo can be provided by measurements of the differential expression of different var groups, and need only be defined by short stretches of sequence data.
A quasi-random sampling approach to image retrieval

In this paper, we present a novel approach to contents-based image retrieval. The method hinges in the use of quasi-random sampling to retrieve those images in a database which are related to a query image provided by the user. Departing from random sampling theory, we make use of the EM algorithm so as to organize the images in the database into compact clusters that can then be used for stratified random sampling. For the purposes of retrieval, we use the similarity between the query and the clustered images to govern the sampling process within clusters. In this way, the sampling can be viewed as a stratified sampling one which is random at the cluster level and takes into account the intra-cluster structure of the dataset. This approach leads to a measure of statistical confidence that relates to the theoretical hard-limit of the retrieval performance. We show results on the Oxford Flowers dataset.
Two-phase approach for deblurring images corrupted by impulse plus gaussian noise

The restoration of blurred images corrupted with impulse noise is a difficult problem which has been considered in a series of recent papers. These papers tackle the problem by using variational methods involving an L1-shaped data-fidelity term. Because of this term, the relevant methods exhibit systematic errors at the corrupted pixel locations and require a cumbersome optimization stage. In this work we propose and justify a much simpler alternative approach which overcomes the above-mentioned systematic errors and leads to much better results. Following a theoretical derivation based on a simple model, we decouple the problem into two phases. First, we identify the outlier candidates---the pixels that are likely to be corrupted by the impulse noise, and we remove them from our data set. In a second phase, the image is deblurred and denoised simultaneously using essentially the outlier-free data. The resultant optimization stage is much simpler in comparison with the current full variational methods and the outlier contamination is more accurately corrected. The experiments show that we obtain a 2 to 6 dB improvement in PSNR. We emphasize that our method can be adapted to deblur images corrupted with mixed impulse plus Gaussian noise, and hence it can address a much wider class of practical problems.
Interpreting exposure ages from ice‐cored moraines: a Neoglacial case study on Baffin Island, Arctic Canada

10Be dating of moraines has greatly improved our ability to constrain the timing of past glaciations and thus past cold events. However, the spread in ages from a single moraine is often greater than would be expected from measurement uncertainty, making paleoclimatic interpretations equivocal. Here we present 28 new 10Be ages from ice‐cored Neoglacial moraines on Baffin Island, Arctic Canada, and explore the processes at play in moraine formation and evolution through field observations and a numerical debris‐covered glacier model. The insulating effect of debris cover modifies glacier lengths and results in the development of ice‐cored moraines over multiple advances and thousands of years. Although ice cores can persist for several millennia, spatially variable ice core melt‐out contributes to moraine degradation and boulder destabilization, making it likely that the 10Be clock is reset on moraine boulders in these settings. Thus, exposure ages from ice‐cored moraines must be interpreted with caution. The oldest ages, after excluding samples with inheritance, provide the best estimates of initial moraine formation. Three Baffin Island moraines yield 10Be ages suggesting formation at 5.2, 4.6 and 3.5 ka, respectively, adding to a growing body of evidence for significant summer cooling millennia before the Little Ice Age.
Uptake of Kynurenine into Rat Brain Slices

Abstract: The transport of [3H]kynurenine ([3H]KYN) into slices from rat tissue was examined in vitro. Brain accumulated KYN seven to eight times more effectively than any of several peripheral organs. Of all the organs tested, only the brain exhibited a sodium‐dependent component of the uptake process. After an incubation period of 1 h, sodium‐dependent transport amounted to 60% of total uptake. Both processes were abolished by prior sonication of the tissue and significantly inhibited by inclusion of metabolic blockers in the incubation medium. Time resolution showed that the sodium‐independent uptake occurred rapidly and reached saturation within 30 min. In contrast, sodium‐dependent transport was linear for at least 2 h of incubation. Brain regional analysis revealed a sevenfold difference between the areas of highest (cortex) and lowest (cerebellum) uptake. With the exception of cerebellar tissue, the ratio between sodium‐dependent and sodium‐independent processes was consistent among brain regions. Kinetic analyses were performed on striatal slices and revealed a Km of 927 μM and a Vmax of 18 nmol/h/mg of protein for the sodium‐dependent process, and a Km of 3.8 mM and a Vmax of 38 nmol/10 min/mg of protein for the sodium‐independent transport. The transporters were equally amenable to inhibition by KYN and tryptophan, indicating that KYN entry into the cell may be mediated by neutral amino acid uptake sites. No strict stereoselectivity existed, but L enantiomers were clearly more active than the D forms. Studies in ibotenate‐lesioned striata showed a 70%decrease in the sodium‐dependent process and a concomitant 60%increase in the sodium‐independent transport, suggesting differential cellular associations of the two uptake sites. Cellular uptake of KYN may constitute a critical step in the disposition of KYN metabolites such as quinolinic acid and kynurenic acid in the brain.
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Seroprevalence of HTLV‐1 and HTLV‐2 amongst mothers and children in Malawi within the context of a systematic review and meta‐analysis of HTLV seroprevalence in Africa

Human T‐lymphotropic virus (HTLV)‐1 causes T‐cell leukaemia and myelopathy. Together with HTLV‐2, it is endemic in some African nations. Seroprevalence data from Malawi are scarce, with no reports on associated disease incidence. HTLV seroprevalence and type were tested in 418 healthy mothers from Malawi. In addition, we tested the sera of 534 children to investigate mother‐to‐child transmission. To provide context, we conducted a systematic review and meta‐analysis of HTLV seroprevalence in African women and children.
Adenomatoid tumors: A light microscopic, histochemical, and ultrastructural study

The histogenesis of the adenomatoid tumor has been controversial. The clinical, light microscopic, and histochemical features of six cases, with electron microscopy of three cases is presented and compared to previous studies. The histologic diagnosis rests upon recognition of one of three distinctive patterns: plexiform, tubular, or canalicular, or their various admixtures. There is a similarity of these areas with foci of malignant mesotheliomas. Acid mucopolysaccharide (AMPS), a product of both normal and neoplastic mesothelium, was histochemically present in all six cases and in the reported results of five previous studies. This material was at least partially digested by hyaluronidase. Electron microscopic features include microvilli, desmosomes, tonofilaments and tonofilament‐like structures, and dilated intercellular spaces. This agrees with previous studies, which compared normal mesothelium and mesotheliomas with adenomatoid tumors, and gives further support to a mesothelial origin of these tumors.
Orexin A/Hypocretin-1 Selectively Promotes Motivation for Positive Reinforcers

Orexin A/hypocretin-1 (oxA/hcrt-1) is known to be a modulator of dopamine-dependent neuronal activity and behaviors. However, the role of this system in driving motivated behaviors remains poorly understood. Here, we show that orexin/hypocretin receptor-1 (ox/hcrt-1R) signaling is important for motivation for highly salient, positive reinforcement. Blockade of ox/hcrt-1R selectively reduced work to self-administer cocaine or high fat food pellets. Moreover, oxA/hcrt-1 strengthened presynaptic glutamatergic inputs to the ventral tegmental area (VTA) only in cocaine or high fat self-administering rats. Finally, oxA/hcrt-1-mediated excitatory synaptic transmission onto VTA neurons was not potentiated following an arousing, aversive stimulus, suggesting that oxA/hcrt-1-mediated glutamatergic synaptic transmission was potentiated selectively with highly salient positive reinforcers. These experiments provide evidence for a selective role of oxA/hcrt-1 signaling in motivation for highly salient reinforcers and may represent a unique opportunity to design novel therapies that selectively reduce excessive drive to consume positive reinforcers of high salience.
Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease

The generation of genome-modified animals is a powerful approach to analyze gene functions. The CAS9/guide RNA (gRNA) system is expected to become widely used for the efficient generation of genome-modified animals, but detailed studies on optimum conditions and availability are limited. In the present study, we attempted to generate large-scale genome-modified mice with an optimized CAS9/gRNA system, and confirmed the transmission of these mutations to the next generations. A comparison of different types of gRNA indicated that the target loci of almost all pups were modified successfully by the use of long-type gRNAs with CAS9. We showed that this system has much higher mutation efficiency and much lower off-target effect compared to zinc-finger nuclease. We propose that most of these off-target effects can be avoided by the careful control of CAS9 mRNA concentration and that the genome-modification efficiency depends rather on the gRNA concentration. Under optimized conditions, large-scale (∼10 kb) genome-modified mice can be efficiently generated by modifying two loci on a single chromosome using two gRNAs at once in mouse zygotes. In addition, the normal transmission of these CAS9/gRNA-induced mutations to the next generation was confirmed. These results indicate that CAS9/gRNA system can become a highly effective tool for the generation of genome-modified animals.
Non-finite-axiomatizability results in algebraic logic

This paper deals with relation, cylindric and polyadic equality algebras. First of all it addresses a problem of B. Jónsson. He asked whether relation set algebras can be expanded by finitely many new operations in a “reasonable” way so that the class of these expansions would possess a finite equational base. The present paper gives a negative answer to this problem: Our main theorem states that whenever Rs+ is a class that consists of expansions of relation set algebras such that each operation of Rs+ is logical in Jónsson's sense, i.e., is the algebraic counterpart of some (derived) connective of first-order logic, then the equational theory of Rs+ has no finite axiom systems. Similar results are stated for the other classes mentioned above. As a corollary to this theorem we can solve a problem of Tarski and Givant [87], Namely, we claim that the valid formulas of certain languages cannot be axiomatized by a finite set of logical axiom schemes. At the same time we give a negative solution for a version of a problem of Henkin and Monk [74] (cf. also Monk [70] and Németi [89]). Throughout we use the terminology, notation and results of Henkin, Monk, Tarski [71] and [85]. We also use results of Maddux [89a]. Notation. RA denotes the class of relation algebras, Rs denotes the class of relation set algebras and RRA is the class of representable relation algebras, i.e. the class of subdirect products of relation set algebras. The symbols RA, Rs and RRA abbreviate also the expressions relation algebra, relation set algebra and representable relation algebra, respectively. For any class C of similar algebras EqC is the set of identities that hold in C, while Eq1C is the set of those identities in EqC that contain at most one variable symbol. (We note that Henkin et al. [85] uses the symbol EqC in another sense.)
Transition Pattern and Mechanism of B-lymphocyte Precursors in Regenerated Mouse Bone Marrow after Subtotal Body Irradiation

Little is known about the effects of ionizing radiation on the transition and the related signal transduction of progenitor B cells in the bone marrow. Thus, using an NIH Swiss mouse model, we explored the impact of ionizing radiation on the early stage of B-cell development via an examination of the transition of CLP to pro-B to pre-B cells within bone marrow as a function of radiation doses and times. Our results showed that while the total number of bone marrow lymphoid cells at different stages were greatly reduced by subtotal body irradiation (sub-TBI), the surviving cells continued to transition from common lymphoid progenitors to pro-B and then to pre-B in a reproducible temporal pattern. The rearrangement of the immunoglobulin heavy chain increased significantly 1–2 weeks after irradiation, but no change occurred after 3–4 weeks. The rearrangement of the immunoglobulin light chain decreased significantly 1–2 weeks after sub-TBI but increased dramatically after 3–4 weeks. In addition, several key transcription factors and signaling pathways were involved in B-precursor transitions after sub-TBI. The data indicate that week 2 after irradiation is a critical time for the transition from pro-B cells to pre-B cells, reflecting that the functional processes for different B-cell stages are well preserved even after high-dose irradiation.
TECHNICAL NOTE CRIMINALISTICS

Obtaining quality DNA profiles from firearms can be instrumental in assisting criminal investigations. Typically, swabbings of firearms for handler’s DNA are conducted on specific regions of the firearm prior to submission to the laboratory for analysis. This review examines and compares 32 cases whose gun swabbings were either analyzed individually according to the specific region which was swabbed, or analyzed collectively by combining the swabbings from all the individual areas. Those firearms whose swabs were analyzed separately exhibited lower DNA yields and consequently fewer loci exhibiting genotypes. Those cases whose swabs were analyzed collectively exhibited higher DNA yields and consequently greater numbers of loci exhibiting genotypes. These findings demonstrate that collective swabbings result in more complete profiles and lead to the recommendation that a firearm be swabbed in its entirety using no more than two swabs.
Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high‐throughput next‐generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341 045 sequence reads from 12 populations that we were able to assemble into 15 262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non‐model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome‐level φST while appropriately modelling uncertainty in locus‐specific φST. We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome‐level φST were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post‐Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome‐level data to better understand the phylogeographic history of populations.
Mapping the Gnutella Network: Properties of Large-Scale Peer-to-Peer Systems and Implications for System Design

Despite recent excitement generated by the peer-to-peer (P2P) paradigm and the surprisingly rapid deployment of some P2P applications, there are few quantitative evaluations of P2P systems behavior. The open architecture, achieved scale, and self-organizing structure of the Gnutella network make it an interesting P2P architecture to study. Like most other P2P applications, Gnutella builds, at the application level, a virtual network with its own routing mechanisms. The topology of this virtual network and the routing mechanisms used have a significant influence on application properties such as performance, reliability, and scalability. We have built a "crawler" to extract the topology of Gnutella's application level network. In this paper we analyze the topology graph and evaluate generated network traffic. Our two major findings are that: (1) although Gnutella is not a pure power-law network, its current configuration has the benefits and drawbacks of a power-law structure, and (2) the Gnutella virtual network topology does not match well the underlying Internet topology, hence leading to ineffective use of the physical networking infrastructure. These findings guide us to propose changes to the Gnutella protocol and implementations that may bring significant performance and scalability improvements. We believe that our findings as well as our measurement and analysis techniques have broad applicability to P2P systems and provide unique insights into P2P system design tradeoffs.
The Phonetic Context of American English Flapping: Quantitative Evidence

The phonetic context in which word-medial flaps occur (in contrast to [th]) in American English is explored. The analysis focuses on stress placement, following phone, and syllabification. In Experiment 1, subjects provided their preference for [th] or [ ] in bisyllabic nonce words. Consistent with previous studies, flaps were preferred before stressless syllables and [th] before stressed syllables, but the following phone also exerted a small degree of influence. Experiments 2 and 3 tested whether [th ] or [ ] are associated with a particular syllable position in bisyllabic words. They demonstrate that [th] is favored in onsets, while [ ] is not consistently placed in either the onset or coda, nor is it generally ambisyllabic. These findings contradict analyses that posit syllable division as a conditioning factor in the appearance of [th] versus [ ]. Experiment 4 examined the pronunciation of 480 multisyllabic words from the TIMIT corpus. VCV was seen to favor [ ], while VCV favored [th]. In addition, flaps tend to be followed by syllabic sonorants and [th] by tense vowels. Because the following phones that influenced [th] and [ ] in Experiment 4 differ from those that were significant in Experiment 1, more research is necessary into the effect that following phones have on the appearance of [th] and [ ].