Miracle-dz/UniFAR-FTUs huggingface dataset:
Exposition and Analysis of a Suffix Sorting Algorithm

This paper focuses on the suffix sorting algorithm of Maniscalco [10], which at the time of writing is available only as C++ source code on the Internet. We will refer to the program as MSufSort. MSufSort computes the Inverse Suffix Array (ISA) of an input string, which is equivalent to computing the Suffix Array (converting one to the other is discussed in section 8). Recall that for i ∈ [0.n − 1], ISA[i] gives the lexicographic rank of the suffix x[i.n − 1] amongst all the other suffixes of the string x[0.n − 1]. Experiments summarized in [10] suggest that MSufSort outperforms the fastest known suffix sorting programs, while using little extra space aside from the 4n bytes to hold the suffix array and the n bytes for the input string (in the terms of [11] it would be lightweight). It is also purported to perform well on periodic strings, which are known to be catastrophic worst cases for some algorithms. This paper addresses the need for a more formal examination of what appears to be a very robust suffix sorter. We examine and describe the inner workings of the algorithm, and try to explain why MSufSort performs well by analyzing its asymptotic behavior. As published in [10], the MSufSort source code crosses several classes and files and is not easy absorb in a single sitting. The code presented in this paper constitutes a complete rewrite of the original as just a few C functions, and is included not as an optimization, but rather to aid explanation of the approach. After introducing some notation in Section 2, the basic algorithm is described in Section 3 before two powerful heuristics are introduced in Sections 4 and 5. Sections 6 and 7 consider time and space usage. Section 8 discusses ISA to SA transformation. In Section 9 we extensively test MSufSort and compare its performance to that of other leading suffix sorters. Possible areas for future work are outlined in Sections 10 and 11, and brief conclusions are offered in Section 12. It is assumed the reader is familiar with the concept of suffix sorting and its applications, particularly the Burrows-Wheeler Transformation (BWT).
Stressful life events and leukocyte telomere attrition in adulthood: a prospective population-based cohort study

Background. Telomere attrition might be one of the mechanisms through which psychosocial stress leads to somatic disease. To date it is unknown if exposure to adverse life events in adulthood is associated with telomere shortening prospectively. In the current study we investigated whether life events are associated with shortening of telomere length (TL). Method. Participants were 1094 adults (mean age 53.1, range 33–79 years) from the PREVEND cohort. Data were collected at baseline (T1) and at two follow-up visits after 4 years (T2) and 6 years (T3). Life events were assessed with an adjusted version of the List of Threatening Events (LTE). TL was measured by monochrome multiplex quantitative PCR at T1, T2, and T3. A linear mixed model was used to assess the effect of recent life events on TL prospectively. Multivariable regression analyses were performed to assess whether the lifetime life events score or the score of life events experienced before the age of 12 predicted TL cross-sectionally. All final models were adjusted for age, sex, body mass index, presence of chronic diseases, frequency of sports, smoking status, and level of education. Results. Recent life events significantly predicted telomere attrition prospectively (B = −0.031, p = 0.007). We were not able to demonstrate a significant cross-sectional relationship between the lifetime LTE score and TL. Nor did we find exposure to adverse life events before the age of 12 to be associated with TL in adulthood. Conclusions. Exposure to recent adverse life events in adulthood is associated with telomere attrition prospectively.
Health and Quality of Life Outcomes

Background: The Health of the Nation Outcome Scales was developed to routinely measure outcomes for adults with mental illness. Comparable instruments were also developed for children and adolescents (the Health of the Nation Outcome Scales for Children and Adolescents) and older people (the Health of the Nation Outcome Scales 65+). All three are being widely used as outcome measures in the United Kingdom, Australia and New Zealand. There is, however, no comprehensive review of these instruments. This paper fills this gap by reviewing the psychometric properties of each. Method: Articles and reports relating to the instruments were retrieved, and their findings synthesised to assess the instruments' validity (content, construct, concurrent, predictive), reliability (test-retest, inter-rater), sensitivity to change, and feasibility/utility. Results: Mostly, the instruments perform adequately or better on most dimensions, although some of their psychometric properties warrant closer examination. Conclusion: Collectively, the Health of the Nation Outcome Scales family of measures can assess outcomes for different groups on a range of mental health-related constructs, and can be regarded as appropriate for routinely monitoring outcomes. The Health of the Nation Outcome Scales (HoNOS) arose out of the UK's Health of the Nation Strategy, and was created by Wing and colleagues as an instrument that could be routinely used to measure outcomes for adults with mental illness [1,2]. Comparable measures for children and adolescents (HoNOSCA) and older people (HoNOS65+) were later developed by Gowers and colleagues [3,4] and Burns et al [5], respectively. All three instruments measure mental health and social/ behavioural functioning (see Table 1), and are being used increasingly as routine clinical outcome measures against Published: 28 November 2005 Health and Quality of Life Outcomes 2005, 3:76 doi:10.1186/1477-7525-3-76 Received: 04 November 2005 Accepted: 28 November 2005 This article is available from: http://www.hqlo. com/content/3/1/76 © 2005 Pirkis et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Kin selection in Columbian ground squirrels (Urocitellus columbianus): littermate kin provide individual fitness benefits

Since W. D. Hamilton's seminal work on the evolution of sociality, a large body of research has accumulated on how kin selection might explain the evolution of cooperation in many group-living species. Our study examined the evolutionary basis of philopatry and cooperation; specifically, whether individuals benefit from the presence of close kin. We applied an individual fitness approach to a 16-year study of Columbian ground squirrels (Urocitellus columbianus) to investigate potential causal paths by which the presence of kin might act on individual fitness. Our results indicate that individual fitness benefits resulted from associations of philopatric female kin, and support the hypothesis that increased tolerance of proximity of kin is a proximate mechanism for these benefits. The major life-history influence of kin on individual fitness was through improved reproductive success, and this benefit may have been owing to philopatric settlement of kin that were recognized through familiarization in the natal burrow. Thus, we demonstrated an evolutionary basis necessary for ongoing kin-selected cooperation in Columbian ground squirrels, though the mechanism of familiarity may determine which kin individuals benefit from cooperative behaviours.
Adiabatic shear of titanium and polymethylmethacrylate

Abstract Polymethylmethacrylate specimens are loaded by a flat-ended punch, both by impact and using an Instron machine. The deformation is compared with that produced in similarly loaded titanium and copper specimens and with related work by other researchers. It is found in these experiments that deformation occurs in localized bands; it is argued that these arise because of thermal softening effects.
Stochastic Resonance within the Somatosensory System: Effects of Noise on Evoked Field Potentials Elicited by Tactile Stimuli

Stochastic resonance (SR) is commonly understood to be the enhancement, by noise, of the response of a system to a weak input signal. The aim of this study was to demonstrate the occurrence of SR in spinal and cortical evoked field potentials (EFPs) elicited by periodic tactile stimuli in the anesthetized cat. The electrodes were positioned in spinal and cortical somatosensory regions in which the largest negative EFPs were detected. The periodic tactile stimuli consisted of local skin displacements on the central pad of the hindpaw. Two series of experiments were performed. First, periodic tactile stimuli and the noisy tactile stimuli were applied with the same indenter. Second, noisy tactile stimuli were applied with an additional indenter placed on the glabrous skin of the third hindpaw digit. This last protocol ensured that the signal and noise were mixed not in the skin but in the somatosensory regions of the CNS. All cats showed distinct SR behavior at the spinal and cortical stages of the sensory encoding. Such SR was abolished in the cortical but not in the spinal recording after sectioning of the dorsal columns and the ipsilateral dorsolateral funiculus. This suggests that the spinal neurons may also contribute to the SR observed at the cortical level. To the best of our knowledge, this is the first documented evidence that such a remarkable phenomenon embodies electrical processes of the spinocortical somatosensory system itself.
I/O Scheduling Service for Multi-Application Clusters

Distributed applications, especially the ones being I/O intensive, often access the storage subsystem in a nonsequential way (stride requests). Since such behaviours lower the overall system performance, many applications use parallel I/O libraries such as ROMIO to gather and reorder requests. In the meantime, as cluster usage grows, several applications are often executed concurrently, competing for access to storage subsystems and, thus, potentially canceling optimisations brought by parallel I/O libraries. The aIOLi project aims at optimising the I/O accesses within the cluster and providing a simple POSIX API. This article presents an extension of aIOLi to address the issue of disjoint accesses generated by different concurrent applications in a cluster. In such a context, good trade-off has to be assessed between performance, fairness and response time. To achieve this, an I/O scheduling algorithm together with a "requests aggregator" that considers both application access patterns and global system load, have been designed and merged into aIOLi This improvement led to the implementation of a new generic framework pluggable into any I/O file system layer. A test composed of two concurrent IOR benchmarks has shown improvements on read accesses by a factor ranging from 3.5 to 35 with POSIX calls and from 3.3 to 5 with ROMIO, both reference benchmarks have been executed on a traditional NFS server without any additional optimisations
Motion Similarity Analysis and Evaluation of Motion Capture Data

Motion similarity analysis is a critical stage for the successful reuse of motion capture data. Some previous works use one or multiple motion features, such as the difference between joint positions, joint angles, joint velocities and accelerations to capture the similarity information between two frames of different or the same motion streams. In this paper, two typical motion similarity approaches are reviewed and related problems are identified. To address the problems, a novel motion similarity method is proposed and two different features are used to measure the similarity between two motion frames: the curvature of space curve and the difference between joint relative positions. Additionally, we also propose a new general criterion to evaluate and to compare the performance of different motion similarity techniques. The experimental results demonstrate that our new motion similarity method can automatically generate visually acceptable results efficiently and that the other methods can be
Semi-Blind Channel Estimation Relying on Optimum Pilots Designed for Multi-Cell Large-Scale MIMO Systems

Channel estimation in the presence of pilot contamination-induced inter-cell interference (ICI) is a major challenge in large-scale multiple-input multiple-output (LS-MIMO) systems. In this paper, a subspace-based semi-blind channel estimator (SBCE) relying on an optimum pilot design (in the sense of minimizing the channel estimation error covariance) is proposed for LS-MIMO systems. The proposed SBCE is capable of exploiting the asymptotic orthogonality of the channel vectors encountered in LS-MIMO systems, while taking advantage of both the optimized pilots and the data symbols. In order to ensure the best-possible performance of the proposed SBCE, we analyze the properties to be satisfied by the optimal pilots and then design these pilots relying on Zadoff-Chu sequences. As a beneficial result, the intra-cell interference is completely eliminated, and the ICI is substantially reduced. Our analytical and numerical results confirm that the performance of the proposed SBCE is superior to that of the representative state-of-the-art channel estimators in practical LS-MIMO systems, which have a finite number of base station antennas and data symbols available to be capitalized on for channel estimation.
Is there an influence of relative age on participation in non-physical sports activities? The example of shooting sports

Abstract The aims of this study were to test for the presence of a relative age effect among male (n = 119,715) and female (n = 12,823) members of the shooting sports federation, and to determine whether any such effect has an impact on dropout from the sport. For the boys and girls, the results show a uniform distribution of dropout. A relative age effect was not found for the girls, showing that in female shooting sports there is no such effect. For the males, a significant statistical relative age effect was not detected in the 18–20 and 13–14 year categories. However, a relative age effect was found among adults and the 11–12 and under 11 year categories. A significant “inverse” relative age effect was found for the 15–17 year group. Further qualitative research is needed to clarify which factors contribute to this asymmetric distribution of birth dates in French male shooting sports.
Exploring the relationship between tourism and offshore finance in small island economies: lessons from Jersey

Many islands host tourism and offshore finance but research tends to focus on either industry without examining the nature of the relationship(s) between these two where they co-exist. This paper examines the nature of the relationships using a case study of the British Channel Island of Jersey. Both industries demand labour, land and capital that are frequently scarce in small islands. Given their common characteristics and, drawing lessons from Jersey, the paper then considers the nature and the dynamics of their relationship, and the issue of resource competition between the two sectors. In light of the unusual context of small polities and the political power of external actors, the paper also analyses the dynamics of the central relationship between tourism, offshore finance and the state in islands. Finally, the paper considers the overall impact of the relationship between tourism and offshore finance and how it affects the economic development trajectory of small islands.
Repeated Lake-Stream Divergence in Stickleback Life History within a Central European Lake Basin

Life history divergence between populations inhabiting ecologically distinct habitats might be a potent source of reproductive isolation, but has received little attention in the context of speciation. We here test for life history divergence between threespine stickleback inhabiting Lake Constance (Central Europe) and multiple tributary streams. Otolith analysis shows that lake fish generally reproduce at two years of age, while their conspecifics in all streams have shifted to a primarily annual life cycle. This divergence is paralleled by a striking and consistent reduction in body size and fecundity in stream fish relative to lake fish. Stomach content analysis suggests that life history divergence might reflect a genetic or plastic response to pelagic versus benthic foraging modes in the lake and the streams. Microsatellite and mitochondrial markers further reveal that life history shifts in the different streams have occurred independently following the colonization by Lake Constance stickleback, and indicate the presence of strong barriers to gene flow across at least some of the lake-stream habitat transitions. Given that body size is known to strongly influence stickleback mating behavior, these barriers might well be related to life history divergence.
Expression of the Ganglioside GD3 in Human Meningiomas Is Associated with Monosomy of Chromosome 22

Abstract: The ganglioside composition of 59 meningiomas has been compared with a molecular genetic analysis of chromosome 22 in the same specimens. Major gangliosides were GM3 (II3NeuAc‐LacCer) and/orGD3 [II3(NeuAc)2‐LacCer]. In specimens with no or partial deletions of chromosome 22, the GM3 ganglioside predominated, and the mean value for GM3, 61% of total sialic acid, was around four times higher than that for GD3. A loss of chromosome 22, found in 56% of the specimens, was shown to be associated with an increase in the proportion of ganglioside GD3, with the ratio between mean values of GM3 and GD3 being ∼ 1:1. Logistic regression revealed that the probability of predicting monosomy of chromosome 22 by the GD3 proportion was 66%.
Receptor interacting protein kinase mediates necrotic cone but not rod cell death in a mouse model of inherited degeneration

Retinitis pigmentosa comprises a group of inherited retinal photoreceptor degenerations that lead to progressive loss of vision. Although in most cases rods, but not cones, harbor the deleterious gene mutations, cones do die in this disease, usually after the main phase of rod cell loss. Rod photoreceptor death is characterized by apoptotic features. In contrast, the mechanisms and features of subsequent nonautonomous cone cell death remain largely unknown. In this study, we show that receptor-interacting protein (RIP) kinase mediates necrotic cone cell death in rd10 mice, a mouse model of retinitis pigmentosa caused by a mutation in a rod-specific gene. The expression of RIP3, a key regulator of programmed necrosis, was elevated in rd10 mouse retinas in the phase of cone but not rod degeneration. Although rd10 mice lacking Rip3 developed comparable rod degeneration to control rd10 mice, they displayed a significant preservation of cone cells. Ultrastructural analysis of rd10 mouse retinas revealed that a substantial fraction of dying cones exhibited necrotic morphology, which was rescued by Rip3 deficiency. Additionally, pharmacologic treatment with a RIP kinase inhibitor attenuated histological and functional deficits of cones in rd10 mice. Thus, necrotic mechanisms involving RIP kinase are crucial in cone cell death in inherited retinal degeneration, suggesting the RIP kinase pathway as a potential target to protect cone-mediated central and peripheral vision loss in patients with retinitis pigementosa.
Low expression of MicroRNA‐126 is associated with poor prognosis in colorectal cancer

MicroRNA‐126 (miR‐126) has been reported to be a tumor suppressor that targets CXCR4 in colorectal cancer (CRC) cells. This study investigated whether miR‐126 has any prognostic impact in patients with CRC. MiR‐126 and CXCR4 mRNA expression in 92 pairs of CRC and adjacent nontumorous tissues was examined using quantitative real‐time PCR, and CXCR4 protein expression was assessed by immunohistochemistry (IHC) and Western blotting. The correlation between miR‐126 and CXCR4 protein expression and clinicopathological features and overall survival rate was determined. MiR‐126 was downregulated in CRC tissues that expressed high levels of CXCR4 mRNA. IHC and Western blotting detected high expression of CXCR4 protein in CRC tissues. An inverse correlation was observed between miR‐126 and CXCR4 protein expression in CRC tissues. Moreover, low miR‐126 and high CXCR4 protein expression was associated with distant metastasis, clinical TNM stage, and poor survival. Multivariate analysis indicated that miR‐126 was an independent prognostic factor for overall survival, suggesting its clinical significance as a prognostic predictor in CRC patients. © 2014 Wiley Periodicals, Inc.
Essential Role of Alveolar Macrophages in Intrapulmonary Activation of NF- κ B

Acute inflammatory injury in rat lung induced by deposition of immunoglobulin G immune complexes requires expression of cytokines and chemokines as well as activation of the transcription factor nuclear factor (NF)-κB. There is little direct evidence regarding the role of alveolar macrophages in these activation events. In the present studies, rat lungs were depleted of alveolar macrophages by airway instillation of liposome-encapsulated dichloromethylene diphosphonate. These procedures, which greatly reduced the number of retrievable alveolar macrophages, suppressed activation of lung NF-κB in the inflammatory model. In addition, bronchoalveolar lavage levels of tumor necrosis factor-α (TNF-α) and the CXC chemokine, macrophage inflammatory protein-2, were substantially reduced. In parallel, upregulation of the lung vascular adhesion molecule, intercellular adhesion molecule-1, was greatly reduced by intrapulmonary instillation of phosphonate-containing liposomes. Neutrophil accumulation and development o.
Serotonin 2 C receptors in the medial prefrontal cortex facilitate cocaine-induced dopamine release in the rat nucleus accumbens

A functional balance between excitatory and inhibitory control over dopamine (DA)-dependent behavioral and neurochemical effects of cocaine is afforded by the serotonin2C receptor (5-HT2CR) located within the ventral tegmental area and the nucleus accumbens (NAc). The 5-HT2CR located in the medial prefrontal cortex (mPFC) has also been shown to inhibit cocaine-induced behaviors perhaps through inhibition of DA function in the NAc. Using in vivo microdialysis in halothane-anesthetized rats, we tested this hypothesis by assessing the influence of mPFC 5-HT2CRs on cocaine-induced DA outflow in the NAc shell. Intra-mPFC injection of the 5-HT2CR agonist Ro 60-0175 at 5 mg/0.2 ml, but not 1 mg/0.2 ml, potentiated the increase in accumbal DA outflow induced by the intraperitoneal administration of 10 mg/kg of cocaine. Conversely, cocaineinduced accumbal DA outflow was significantly reduced by the intra-mPFC injection of the selective 5-HT2CR antagonist SB 242084 (0.5 mg/0.2 ml) or SB 243213 (0.5 and 1 mg/0.2 ml). These results show that mPFC 5-HT2CRs exert a positive control over cocaine-induced accumbal DA outflow. Observations further support the idea that the overall action of central 5-HT2CRs on accumbal DA output is dependent on the functional balance among different 5-HT2CR populations located within the mesocorticoaccumbens system, and that 5-HT2CRs can modulate DA-dependent behaviors independently of changes of accumbal DA release itself. 2008 Elsevier Ltd. All rights reserved.