Miracle-dz/UniFAR-FTUs huggingface dataset:
WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these datasets. Here, we compare and analyze four recent approaches based on the Wright-Fisher model for inferring selection coefficients (s) given effective population size (Ne), with simulated temporal datasets. Furthermore, we demonstrate the advantage of a recently proposed ABC-based method that is able to correctly infer genome-wide average Ne from time-serial data, which is then set as a prior for inferring per-site selection coefficients accurately and precisely. We implement this ABC method in a new software and apply it to a classical time-serial dataset of the medionigra genotype in the moth Panaxia dominula. We show that a recessive lethal model is the best explanation for the observed variation in allele frequency by implementing an estimator of the dominance ratio (h).
CDC 02-REG 1097 Optimal Filtering for Denial of Service Mitigation

An optimal approach to mitigation of flooding denial of service attacks is presented. The objective is to minimize effect of the mitigation while protecting the server. The approach relies on routers filtering enough packets so that the server is not overwhelmed while ensuring that as little filtering is performed as possible. The optimal solution is to filter packets at routers through which the “attack packets” are passing. The identification of which router the packets are passing is carried out by routers filtering a small but time varying fraction of the packets. The arrival of packets at the server is correlated to router filtering providing an indication through which routers the attack packets are passing. Once sufficient confidence in the identification is achieved, the routers that forward more attack packets filter more packets than router that forward less attack packets.
Bandwidth selection: classical or plug-in?

Bandwidth selection for procedures such as kernel density estimation and local regression have been widely studied over the past decade. Substantial evidence has been collected to establish superior performance of modern plug-in methods in comparison to methods such as cross validation ; this has ranged from detailed analysis of rates of convergence, to simulations, to superior performance on real datasets. In this work we take a detailed look at some of this evidence, looking into the sources of differences. Our findings challenge the claimed superiority of plug-in methods on several fronts. First, plug-in methods are heavily dependent on arbitrary specification of pilot bandwidths and fail when this specification is wrong. Second, the often-quoted variability and undersmoothing of cross validation simply reflects the uncertainty of bandwidth selection; plug-in methods reflect this uncertainty by oversmoothing and missing important features when given difficult problems. Third, we look at asymptotic theory. Plug-in methods use available curvature information in an inefficient manner, resulting in inefficient estimates. Previous comparisons with classical approaches penalized the classical approaches for this inefficiency. Asymptotically, the plug-in based estimates are beaten by their own pilot estimates.
Lyrics-Based Music Genre Classification Using a Hierarchical Attention Network

Music genre classification, especially using lyrics alone, remains a challenging topic in Music Information Retrieval. In this study we apply recurrent neural network models to classify a large dataset of intact song lyrics. As lyrics exhibit a hierarchical layer structure - in which words combine to form lines, lines form segments, and segments form a complete song - we adapt a hierarchical attention network (HAN) to exploit these layers and in addition learn the importance of the words, lines, and segments. We test the model over a 117-genre dataset and a reduced 20-genre dataset. Experimental results show that the HAN outperforms both non-neural models and simpler neural models, whilst also classifying over a higher number of genres than previous research. Through the learning process we can also visualise which words or lines in a song the model believes are important to classifying the genre. As a result the HAN provides insights, from a computational perspective, into lyrical structure and language features that differentiate musical genres.
Rift Valley Fever Virus among Wild Ruminants, Etosha National Park, Namibia, 2011

After a May 2011 outbreak of Rift Valley fever among livestock northeast of Etosha National Park, Namibia, wild ruminants in the park were tested for the virus. Antibodies were detected in springbok, wildebeest, and black-faced impala, and viral RNA was detected in springbok. Seroprevalence was high, and immune response was long lasting.
Glucose Driven Changes in Beta Cell Identity Are Important for Function and Possibly Autoimmune Vulnerability during the Progression of Type 1 Diabetes

This commentary explores the hypothesis that when autoimmunity leads to a fall of beta cell mass during the progression of type 1 diabetes (T1D), rising glucose levels cause major changes in beta cell identity. This then leads to profound changes in secretory function and less well-understood changes in beta cell susceptibility to autoimmune destruction, which may influence of rate of progression of beta cell killing.
Development of an automatic rotational orthosis for walking with arm swing

Interlimb neural coupling is often observed during normal gait and is postulated to be important for gait restoration. In order to provide a testbed for investigation of interlimb neural coupling, we previously developed a rotational orthosis for walking with arm swing (ROWAS). The present study aimed to develop and evaluate the feasibility of a new system, viz. an automatic ROWAS (aROWAS). We developed the mechanical structures of aROWAS in SolidWorks, and implemented the concept in a prototype. Normal gait data from walking at various speeds were used as reference trajectories of the shoulder, hip, knee and ankle joints. The aROWAS prototype was tested in three able-bodied subjects. The prototype could automatically adjust to size and height, and automatically produced adaptable coordinated performance in the upper and lower limbs, with joint profiles similar to those occurring in normal gait. The subjects reported better acceptance in aROWAS than in ROWAS. The aROWAS system was deemed feasible among able-bodied subjects.
Institutional Equivalence: How Industry and Community Peers Influence Corporate Philanthropy

This paper explores how organizations respond to simultaneous institutional influences from two distinct sources: the industry in which they operate and the local geographic community in which they are headquartered. We theorize that the existence of institutional equivalents—other organizations at the same intersection of different fields, such as the same industry and the same community—provides a clear and well defined reference category for firms and thus shapes which subset of peers the focal organization imitates most closely. We develop hypotheses about how the presence or absence of institutional equivalents affects organizations’ responses to behavioral cues from different peer groups, how these effects vary when peers in different fields exhibit inconsistent behaviors, and how organizational characteristics, such as size and performance, strengthen or weaken the influence of institutional equivalents. We test our propositions through a longitudinal analysis of philanthropic contributions by Fort.
A Las Vegas algorithm to solve the elliptic curve discrete logarithm problem

In this paper, we describe a new Las Vegas algorithm to solve the elliptic curve discrete logarithm problem. The algorithm depends on a property of the group of rational points on an elliptic curve and is thus not a generic algorithm. The algorithm that we describe has some similarities with the most powerful index-calculus algorithm for the discrete logarithm problem over a finite field. The algorithm has no restriction on the finite field over which the elliptic curve is defined.
Acetyl-CoA:lyso-platelet-activating factor acetyltransferase activity in neutrophils from asthmatic patients and normal subjects.

1. Platelet-activating factor is a putative mediator of inflammation in asthma and the enzyme acetyl-CoA:lyso-platelet-activating factor acetyltransferase appears to be important in regulating platelet-activating factor production by leucocytes. To determine whether there are differences in acetyltransferase activity between asthmatic patients and normal subjects, enzyme activity was assayed in neutrophil lysates from atopic asthmatic patients (n = 20), aspirin-sensitive asthmatic patients (n = 12) and healthy, non-atopic, non-asthmatic control subjects (n = 20), both basally and after stimulation with the calcium ionophore A23187. 2. For a range of acetyl-CoA concentrations, acetyltransferase activity (nmol of [acetyl-3H]PAF min-1 mg-1 of protein) in unstimulated neutrophils from atopic asthmatic patients was significantly higher than that for normal subjects (P = 0.038) and the mean Vmax. for atopic asthmatic patients [18.4 (SD 6.9) nmol min-1 mg-1 of protein] was significantly greater than that for the control subjects [14.9 (SD 4.6) nmol min-1 mg-1 of protein P < 0.05]. The mean Vmax. for aspirin-sensitive asthmatic patients [15.9 (SD 6.9) nmol min-1 mg-1 of protein] was not significantly different from that for the normal subjects. 3. The mean ratio Vmax. stimulated/Vmax. unstimulated for acetyltransferase from atopic asthmatic patients (1.71, SD 0.45) was significantly less than that for the normal subjects (2.13, SD 0.63, P < 0.05), suggesting that acetyltransferase from atopic asthmatic patients was less sensitive to stimulation with A23187 in vitro. (ABSTRACT TRUNCATED AT 250 WORDS)
Non-uniform ACC Circuit Lower Bounds

The class ACC consists of circuit families with constant depth over unbounded fan-in AND, OR, NOT, and MOD$m$ gates, where $m > 1$ is an arbitrary constant. We prove:- $NTIME[2^n]$ does not have non-uniform ACC circuits of polynomial size. The size lower bound can be strengthened to quasi-polynomials and other less natural functions. - $E^{NP}$, the class of languages recognized in $2^{O(n)}$ time with an $NP$ oracle, doesn't have non-uniform ACC circuits of $2^{n^{o(1)}}$ size. The lower bound gives a size-depth tradeoff: for every $d$, $m$ there is a $\delta > 0$ such that $E^{NP}$ doesn't have depth-$d$ ACC circuits of size $2^{n^{\delta}}$ with MOD$m$ gates.Previously, it was not known whether $EXP^{NP}$ had depth-3 polynomial size circuits made out of only MOD6 gates. The high-level strategy is to design faster algorithms for the circuit satisfiability problem over ACC circuits, then prove that such algorithms can be applied to obtain the above lower bounds.
Iron and Infection in Hemodialysis Patients

Intravenous iron is an important component of the treatment of anemia of end‐stage renal disease (ESRD), but it is biologically plausible that iron could increase the risk of infection through impairment of neutrophil and T‐cell function and promotion of microbial growth. Any such increase in risk would be particularly important because infection is a significant cause of mortality and morbidity in dialysis patients. The overall evidence favors an association between iron and infection in hemodialysis patients, but the optimal iron management strategy to minimize infection risk has yet to be identified. There is a need for further research on this topic, particularly in light of increased utilization of intravenous iron following implementation of the bundled ESRD reimbursement system.
Phenotypic and molecular marker distance as a tool for prediction of heterosis and F1 performance in sunflower (Helianthus annuus' L.) under well-watered and water-stressed conditions

The aim of this study was to determine phenotypic and genotypic distances in parental lines of diallel population of sunflower, and to identify correlation between both distances with F1 performance, specific combining ability (SCA) and absolutely mid-parent heterosis. The morphological distance (Euclidean distance; EDs) and genetic distance (Jaccard`s distance; JD) among five sunflower parental lines were calculated based on 12 morphological traits and 160 amplified fragment length polymorphism (AFLP) markers in either well-watered and water-stressed conditions. The un-weighted pair-group method using arithmetic average (UPGMA) clustering algorithm, based on Euclidean and Jaccard distances, classified the studied parental lines into 3 groups. In both water treatment conditions, the high values of JD were correlated with high values of ED. Correlation results revealed that both of ED and JD had significant relation with F1 performance, SCA and heterosis for some traits in both water treatment conditions. Therefore, depending upon target trait, ED and JD could effectively be utilized in order to identify heterosis. Among studied genotypes, LR25 will be regard as a permanent parent in all possible pairwise crosses with other genotypes, to achieve optimum yield in both well-watered and water-stressed conditions.
Acute Endotoxemia Inhibits Microvascular Nitric Oxide-Dependent Vasodilation in Humans

Nitric oxide (NO) is crucial for the microvascular homeostasis, but its role played in the microvascular alterations during sepsis remains controversial. We investigated NO-dependent vasodilation in the skin microcirculation and plasma levels of asymmetric dimethylarginine (ADMA), a potent endogenous inhibitor of the NO synthases, in a human model of sepsis. In this double-blind, randomized, crossover study, microvascular NO-dependent (local thermal hyperemia) and NO-independent vasodilation (post-occlusive reactive hyperemia) assessed by laser Doppler imaging, plasma levels of ADMA, and l-arginine were measured in seven healthy obese volunteers, immediately before and 4 h after either a i.v. bolus injection of Escherichia coli endotoxin (LPS; 2 ng/kg) or normal saline (placebo) on two different visits at least 2 weeks apart. LPS caused the expected systemic effects, including increases in heart rate (+43%, P < 0.001), cardiac output (+16%, P < 0.01), and rectal temperature (+1.4°C, P < 0.001), without change in arterial blood pressure. LPS affected neither baseline skin blood flow nor post-occlusive reactive hyperemia but decreased the NO-dependent local thermal hyperemia response, l-arginine, and, to a lesser extent, ADMA plasma levels. The changes in NO-dependent vasodilation were not correlated with the corresponding changes in the plasma levels of ADMA, l-arginine, or the l-arginine/ADMA ratio. Our results show for the first time that experimental endotoxemia in humans causes a specific decrease in endothelial NO-dependent vasodilation in the microcirculation, which cannot be explained by a change in ADMA levels. Microvascular NO deficiency might be responsible for the heterogeneity of tissue perfusion observed in sepsis and could be a therapeutic target.
Personality features differentiate late adolescent females and males with chronic bulimic symptoms.

OBJECTIVE The authors examined gender differences in bulimia-related personality variables among late adolescents with chronic bulimic symptoms. METHOD Ninety-seven females and 14 males were included in the study. They participated in surveys in 1982, and again in 1992, and at each session reported elevated bulimic symptoms. Each respondent completed subscales of the Eating Disorders Inventory (Bulimia, Drive for Thinness, Perfectionism, and Interpersonal Distrust). RESULTS Even compared to males with similar levels of chronic bulimic symptoms, females with chronic bulimic symptoms reported more drive for thinness; compared to females with chronic bulimic symptoms, males with chronic bulimic symptoms reported more perfectionism and interpersonal distrust. DISCUSSION Late adolescent males and females with chronic bulimic symptoms can be distinguished on the basis of personality features. These findings have implications for theory, as well as for clinical assessment and therapeutics.
Determinants of Parenting Styles of Japanese Fathers and Mothers with Children Aged 0 to 10: Perceived Parenting During Childhood or Dysphoric Mood?

Purpose: To study the determinants of current parenting styles in Japan. Methods: Fathers (n = 312) and mothers (n = 333) of children aged between 0 and 10 attending a paediatric clinic were evaluated with regards to the following: parental attitudes rated by spouses using the Parental Bonding Instrument, current dysphoric mood assessed with the Hospital Anxiety and Depression Scale, life time history of Major Depressive Episode (MDE), and perceived parenting styles when the parents themselves were children. Results: Path models showed that current parenting styles were predicted by parents perception of maternal rearing during childhood. Moreover, in mothers only, they were predicted by the manner in which the women were raised by their fathers. This prediction was indirect, occurring via lifetime history of MDE and current dysphoric mood. Conclusion: This study suggests that the way in which parents themselves were raised was no less important than how they currently felt in determining how they were raising their child. Current dysphoric mood or lifetime history of MDE mediated such effects only among mothers.
Crib sheets and exam performance in a data structures course

In this paper, we study the relationship between the use of “crib sheets” or “cheat sheets” and performance on in-class exams. Our extensive survey of the existing literature shows that it is not decisive on the questions of when or whether crib sheets actually help students to either perform better on an exam or better learn the material. We report on our own detailed analysis for a body of crib sheets created for the final exam in a junior-level Data Structures and Algorithms course. We wanted to determine whether there is any feature of the crib sheets that correlates to good exam scores. Exam performance was compared against a number of potential indicators for quality in a crib sheet. We have found that students performed significantly better on questions at the comprehension level of Bloom’s taxonomy when their crib sheet contained good information on the topic, while performance on questions at higher levels of the taxonomy did not show correlation to crib sheet contents. We have also seen that students at certain levels of performance on the final exam (specifically, medium-to-high performance) did relatively better on certain questions than other students at that performance level when they had good coverage of that question’s topic on their crib sheet.
Evolutionary Analysis of HA and NS1 Genes of H5N1 Influenza Viruses in 2004–2005 Epidemics

Abstract H5N1 avian influenza viruses circulating in early 2004 in eastern Asia appeared to be under strong purifying selection, except for the hemagglutinin (HA) and nonstructural 1 (NS1) genes, where few amino acid positions were found under positive selection pressure. To evaluate whether the widespread circulation of the H5N1 viruses in the following years was accompanied by a change in the evolution of the HA and NS1, phylogenetic and positive selection analyses were performed on 89 HA and 57 NS1 sequences. Results showed that the number of HA positively selected sites decreased compared to 2004; no selection pressure for NS1 was found. These findings suggest a possible change in the adaptation of the H5N1 virus to birds.
Roomware: Toward the Next Generation of Human- Computer Interaction Based on an Integrated Design of Real and Virtual Worlds

The next generation of human-computer interaction (HCI) is determined by a number of new contexts and challenges that have evolved during the last five to ten years and will be evolving more rapidly in the next five to ten years. They are rooted in new, emerging technologies as well as in new application areas asking for new approaches and visions of the future beyond the year 2000. It is not the intention of this chapter to give a comprehensive account of all relevant new contexts. We focus on selected areas complementing other contributions in this book. There is no doubt that new developments in the fields of multimedia, hypertext /hypermedia (especially in their popular versions as World Wide Web-applications), three-dimensional representations, and virtual reality technology will have a great impact on the type of issues HCI has to address and on how interfaces will look in the future. Taken those developments as given, we present an approach and a framework that—at least so far—has not become a mainstream orientation for guiding design and development of the next generation of human-computer interaction. We are aware of the fact that there are related attempts, and we describe them. Nevertheless, there is still an indispensable need for a comprehensive framework. According to our view, the following four areas have to be integrated into an “umbrella” framework: 25
Axonal Transport Defects in Neurodegenerative Diseases

Adult-onset neurodegenerative diseases (AONDs) comprise a heterogeneous group of neurological disorders characterized by a progressive, age-dependent decline in neuronal function and loss of selected neuronal populations. Alterations in synaptic function and axonal connectivity represent early and critical pathogenic events in AONDs, but molecular mechanisms underlying these defects remain elusive. The large size and complex subcellular architecture of neurons render them uniquely vulnerable to alterations in axonal transport (AT). Accordingly, deficits in AT have been documented in most AONDs, suggesting a common defect acquired through different pathogenic pathways. These observations suggest that many AONDs can be categorized as dysferopathies, diseases in which alterations in AT represent a critical component in pathogenesis. Topics here address various molecular mechanisms underlying alterations in AT in several AONDs. Illumination of such mechanisms provides a framework for the development of novel therapeutic strategies aimed to prevent axonal and synaptic dysfunction in several major AONDs.
Ubiquitin Proteasome-dependent Degradation of the Transcriptional Coactivator PGC-1α via the N-terminal Pathway*

PGC-1α is a potent, inducible transcriptional coactivator that exerts control on mitochondrial biogenesis and multiple cellular energy metabolic pathways. PGC-1α levels are controlled in a highly dynamic manner reflecting regulation at both transcriptional and post-transcriptional levels. Here, we demonstrate that PGC-1α is rapidly degraded in the nucleus (t½ 0.3 h) via the ubiquitin proteasome system. An N-terminal deletion mutant of 182 residues, PGC182, as well as a lysine-less mutant form, are nuclear and rapidly degraded (t½ 0.5 h), consistent with degradation via the N terminus-dependent ubiquitin subpathway. Both PGC-1α and PGC182 degradation rates are increased in cells under low serum conditions. However, a naturally occurring N-terminal splice variant of 270 residues, NT-PGC-1α is cytoplasmic and stable (t½ >7 h), providing additional evidence that PGC-1α is degraded in the nucleus. These results strongly suggest that the nuclear N terminus-dependent ubiquitin proteasome pathway governs PGC-1α cellular degradation. In contrast, the cellular localization of NT-PCG-1α results in a longer-half-life and possible distinct temporal and potentially biological actions.