Miracle-dz/UniFAR-FTUs huggingface dataset:
PII: S1366-5545(02)00006-6

This paper studies the influencing factors on entry (certification) of new airlines into the US airline industry over 21 years (1979–1999). These rates exhibit considerable fluctuations over the observed period. We analyze the US airline industry for a period of 21 years to determine the relationship of the observed fluctuations in the entry rates with political and extraordinary events, economic conditions and several industry specific variables. We present maximum likelihood estimates of an entry model on the negative Binomial distribution. This methodology reflects the discrete nature of the dependent variable. The results support the notions of positive macro-economic and industry specific developments on the entry opportunities of new airline companies. 2002 Elsevier Science Ltd. All rights reserved.
Impediments affecting entrepreneurial intent in South African MBA graduates

ii DECLARATION . iii CONTENTS . iv LIST OF TABLES . viii LIST OF ACRONYMS AND ABBREVIATIONS . viii 1. CHAPTER 1: DEFINITION OF PROBLEM AND PURPOSE . 1 1.1. Background to the research problem . 1 1.2. Business and Academic Rationale for Research and Purpose . 3 2. Chapter 2: Literature Review . 4 2.
Corrosion behaviours of B + F dual-phase X80 pipeline steel in simulated near neutral and acidic soil solution

Slow strain rate tensile corrosion (SSRT), immersion corrosion and polarisation behaviours of B + F dual-phase X80 pipeline steel in simulated near-neutral and acidic soil solutions were compared. The stress corrosion of X80 steel in acidic soil solution is more sensitive, whose mechanism is intergranular fracture induced by pitting. Crack nucleates at the bottom of corrosion pit and propagates along the weak path–grain boundary. In near-neutral soil solution, the crack is originated from a corrosion pit and propagated mainly transgranular. The parabolic velocity constant in immersion test and corrosion current of X80 steel in acidic soil solution is much higher, 40 and 2.7 times of those in near-neutral soil solution respectively. Dual-phase X80 steel has poor corrosion resistance in acidic soil solution. X80 steel in near-neutral soil solution corrodes in the form of an irregular corrosion pit at the bainite area, or a round corrosion pit near inclusions.
Experimental investigations on regeneration energy and energy management strategy in series hydraulic/electric synergy system

ABSTRACT This research work draws an insight into the experimental investigations on a series hydraulic/electric synergy system—a green transportation system. An experimental test rig of the system with all necessary sensors and instrumentation has been developed to study the energy saving through hydraulic regenerative braking. The effect of various system parameters, such as braking time, maximum accumulator pressure, pre-charge pressure of hydro-pneumatic accumulator, volumetric displacement of the hydraulic master pump, and hydraulic regeneration pump on the quantum of regeneration energy, was analyzed. In addition, an AMESim model of the real-time experimental test rig has been developed and validated with experimental results. A set of five different experimental designs (parameter variations) of the system is defined with the available standard component sizes. The best design is selected of the available experimental designs based on the maximum hydraulic regeneration energy and regeneration efficiency. It was observed that the selected design has an energy efficiency of 13.3% and a regeneration efficiency of 43.8%. An accumulator-centric control strategy for energy management is developed and implemented on the experimental test rig configured with the selected design. The effectiveness of the control strategy is tested through experiments and simulation on the developed test rig.
SLQAL at the NTCIR-13 QA Lab-3 Task

The SLQAL team participated in Phase-1, Phase-2 and Research run of the NTCIR-13 QA Lab-3 Japanese subtask(National Center Tests(Multiple-Choice type questions)) [2]. This paper describes our approraches and results in Phase-1 and Phase-2.
Covering Points by Hyperplanes and Related Problems

For a set P of n points in R, for any d ≥ 2, a hyperplane h is called k-rich with respect to P if it contains at least k points of P . Answering and generalizing a question asked by Peyman Afshani, we show that if the number of k-rich hyperplanes in R, d ≥ 3, is at least Ω(n/k + n/k), with a sufficiently large constant of proportionality and with d ≤ α < 2d − 1, then there exists a (d − 2)-flat that contains Ω(k(2d−1−α)/(d−1)) points of P . We also present upper bound constructions that give instances in which the above lower bound is tight. An extension of our analysis yields similar lower bounds for k-rich spheres. 2012 ACM Subject Classification Theory of computation → Computational geometry
Sweepstakes reproductive success via pervasive and recurrent selective sweeps

Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.
Topological defects govern mesenchymal condensations, offering a morphology-based tool to predict cartilage differentiation

A critical initial stage of skeletal morphogenesis involves formation of highly compact aggregates of mesenchymal cells, known as mesenchymal condensations, appearing as regularly-spaced pattern of spots. Conventional computational models to understand their patterning have been based on chemotaxis, haptotaxis, and reaction-diffusion equations. In this work, we investigate the mesenchymal condensations from a different perspective, namely topological defects within liquid crystal-like pattern. Using bone marrow-derived mesenchymal stromal cells (bm-MSCs), we observed emergence of cellular swirls in confluent in-vitro cultures, followed by appearance of mesenchymal condensations at the centers of the selfassembled swirls. Specifically, the condensations appeared at the ‘comet-like’ (+1/2) and ‘spiral-shaped’ (+1) topological defect sites within the swirl pattern. Next, with the rationale that cellular swirls precede skeletal morphogenesis, and supported with the qualitative observation that swirl pattern-features are donor-specific, we probed the correlation between swirl pattern and the chondrogenic differentiation outcome of bm-MSCs. Towards this, we first generated and imaged cellular swirls systematically across 5 donors by controlling seeding density, culture vessel geometry, and culture duration. We observed that the swirl pattern features quantified as variance of coherency correlated strongly with the cartilage matrix proteins, sulfated glycosaminoglycan and collagen-II, quantified from the standard in-vitro chondrogenic differentiation assay. Our work shows that swirl-pattern quantification provides a novel and powerful tool to predict efficacy of bm-MSCs for in-vitro cartilage regeneration. Significance Statement Mesenchymal condensation is a critical stage in the formation of bone and cartilage, where the mesenchymal cells form high density cell clusters that are regularly spaced. In this work, we inspect the patterning of these condensations in-vitro from a novel perspective. We first show that at high density, bone-marrow-derived mesenchymal stromal cells (bm-MSCs) self-assemble to form cellular swirls resembling the vortices in a turbulent flow. This is followed by cell aggregations at the centers of the vortices, which show correspondence to mesenchymal condensations. Interestingly, we observed that the swirl pattern made by bm-MSCs isolated from human donors, varies from individual to individual and correlates with their propensity to differentiate into cartilage. This suggests that swirl pattern quantification via image analysis can be used to predict differentiation outcome, in context of regenerative cell therapy.
Global statistical models of protein coevolution reveal higher-order sectors beyond those obtained from structure alone

Recent methods have shown promise in using pairwise sequence coevolution predictions to illuminate physical interactions and functional relationships between pairs of protein residues. As a result, there has been an increased interest in identifying higher-order correlations between sequence positions in an effort to further understand how the multiple sequence alignment (MSA) encodes the conserved biological properties of a protein family. To this end, we propose a robust and generalizable spectral clustering model that can extract interconnected networks of coevolving residues – termed “protein sectors” – using pairwise sequence coevolution predicted by a global statistical model. We assess the statistical and evolutionary origins for protein sectors extracted from the MSA for 120 protein families. We show that protein sectors are extracted from a subset of densely connected components in the sequence coevolution matrix, many of which are not present in the pairwise residue contact graph that is constructed from the protein crystal structure, revealing the existence of networks of paired residues that are not necessarily in direct physical contact but are nonetheless evolutionarily coupled. We found that protein sectors form structurally connected entities in three-dimensional space, despite sector identification being independent of protein crystal structure. Interestingly, protein families with high structural similarity do not share similar protein sectors, suggesting that nuances in the sequence coevolution matrix can differentiate between the evolutionary histories of structurally-related protein families.
Response of sleep slow oscillations to acoustic stimulation is evidenced by distinctive synchronization processes

Closed loop acoustic stimulation (CLAS) during sleep has shown to boost slow wave (SW) amplitude and spindle power. Moreover, sleep SW are suggested to be classified based on different processes of neuronal synchronization. Following this, different types of SW events may have distinct functional roles and be differentially affected by external stimuli. However, the SW synchronization processes affected by CLAS are not well understood. Here, we studied the effect of CLAS on the dissociation of SW events based on two features of neuronal synchronization in the EEG (topological spread and wave slope). We evaluated and classified individual SW events of fourteen healthy subjects during a CLAS stimulated (STM) and a control night (CNT). Three main categories of SW events were found denoting (C1) steep-slope SW with global spread, (C2) flat-slope waves with localized spread and homeostatic regulation, and (C3) multipeaked flat-slope events with global spread. Comparing between conditions, we found a consistent increase of event proportion and trough amplitudes for C1 events during the time of stimulation. Furthermore, we found similar increases in post-stimulus spectral power in θ, β and σ frequencies for CNT vs STIM condition independently of sleep stage or SW categories. However, topological analysis showed differentiated spatial dynamics in N2 and N3 for SW categories and the co-occurrence with spindle events. Our findings reveal the nature of post-stimulus SW and suggest that CLAS boosts SW amplitudes by increasing neuronal synchronization of wave troughs, leading thus the post-stimulus SW-spindle co-occurrence.
Molecular phylogeny of human adenovirus type 41 lineages

Type 41 of human adenovirus species F (HAdV-F41) is a frequent aetiology of gastroenteritis in children, and nosocomial as well as kindergarten outbreaks have been frequently described. In contrast to other HAdV types, HAdV-F41 was not associated with life-threatening disseminated disease in allogeneic haematopoietic stem cell transplant (HSCT) recipients or any severe organ infections so far. Due to the limited clinical significance, the evolution of HAdV-F41 has not been studied in detail. Recently, HAdV-F41 has been associated with severe hepatitis in young children, and interest in HAdV-F41 has skyrocketed, although the aetiology of the hepatitis has not been resolved. Complete genomic HAdV-F41 sequences from 32 diagnostic specimens of the past 11 years (2011–2022) were generated, all originating from gastroenteritis patients. Additionally, 33 complete HAdV-F41 genomes from GenBank were added to our phylogenetic analysis. Phylogenetic analysis of 65 genomes indicated that HAdV-F41 evolved with three lineages co-circulating. Lineage 1 included the prototype ‘Tak’ from 1973 and six isolates from 2007 to 2017 with an average nucleotide identity of 99.3 %. Lineage 2 included 53 isolates from 2000 to 2022, had an average nucleotide identity of 99.8 %, and split into two sublineages. Lineage 3, probably described for the first time in 2009, had a 45nt deletion in the long fiber gene and had evolved significantly in the short fiber and E3 region. Moreover, a recent lineage 3 isolate from 2022 had a recombinant phylogeny of the short fiber gene. Fibers interact with cellular receptors and determine cellular tropism, whereas E3 gene products interfere with the immune recognition of HAdV infected cells. This in-depth study on the phylogeny of HAdV-F41 discovered significant evolution of recently described lineage 3 of HAdV-F41, possibly resulting in altered cellular tropism, virulence and pathophysiology.
Monocyte-derived macrophages aggravate pulmonary vasculitis via cGAS/STING/IFN-mediated nucleic acid sensing

Autoimmune vasculitis is a group of life-threatening diseases, whose underlying pathogenic mechanisms are incompletely understood, hampering development of targeted therapies. Here, we demonstrate that patients suffering from anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV) showed increased activity of the DNA sensor cGAS and enhanced IFN-I signature. To identify potential therapeutic targets, we developed a mouse model for pulmonary AAV that mimics severe disease in patients. Immunogenic DNA accumulated during disease onset, triggering cGAS/STING/IRF3-dependent IFN-I release that promoted endothelial damage, pulmonary hemorrhages, and lung dysfunction. Macrophage subsets played dichotomic roles in disease. While recruited monocyte-derived macrophages were major disease drivers by producing most IFN-β, resident alveolar macrophages contributed to tissue homeostasis by clearing red blood cells and limiting infiltration of IFN-β-producing macrophages. Moreover, pharmacological inhibition of STING, IFNAR-I or its downstream JAK/STAT signaling reduced disease severity and accelerated recovery. Our study unveils the importance of STING/IFN-I axis in promoting pulmonary AAV progression and identifies cellular and molecular targets to ameliorate disease outcome. Graphical abstract Summary Kessler et al. identify aberrant DNA recognition by cGAS/STING axis and IFN-I production by inflammatory macrophages as a major driver of severe ANCA-associated vasculitis (AAV). Pharmacological interventions blocking this pathway ameliorate disease and accelerate recovery, identifying potential targets for therapeutic intervention in patients.
sMAP: An interactive microarray data analysis tool for early-stage researchers

Microarray data enables biologists to extract differentially expressed genes (DEGs) across multiple phenotypes. While several pipelines and tools exist to perform microarray data analysis, they are targeted to users with moderate to advanced computational understanding and lack an easy-to-use, interactive and dynamic methodology to perform analysis assisted with comprehensive learning resources. In this study, we developed an interactive application “sMAP” (Standard Microarray Analysis Pipeline) to make transcriptome microarray data analysis more accessible in learning environments and to enable the identification of significant pathological biomarkers. In a case study of colorectal cancer, we showed that sMAP enabled us to reproduce previous findings and discover relevant pathways. sMAP provides a comprehensive set of tutorials and learning documentation to help early-stage researchers. The latest URLs of sMAP’s hosting, tutorial, and frequently updated documentation can be found at https://github.com/BI-STEM-Away/sMAP.
A Bioinformatics Approach To Reveal Common Genes And Molecular Pathways Shared By Cutaneous Melanoma and Uveal Melanoma

Background Melanomas are highly aggressive in nature and are known for metastasis and death. Melanocytes that give rise to melanomas are neural crest progenitor-cells. Our research is primarily concerned with Uveal Melanoma (UM) and Cutaneous Melanoma (CM). Although they both share same melanocytic origin, but the biology of their respective is different. Aim The aim of our study is to recognize the common differentially expressed genes (DEGs) between UM and CM. Methodology The gene expression profile was downloaded from the GEO and analyzed by GEO2R for identification of DEGs. By applying DAVID, GO and KEGG, pathway enrichment analysis was performed. PPI of these DEGs was analyzed using STRING and visualized through Cytoscape and MCODE. Further, we utilized HPA and GEPIA to obtain Kaplan-Meier Graph for survival analysis in order to assess the prognostic value of hub genes. Results We examined the UM and CM datasets and discovered three common upregulated and eight common downregulated DEGs for both the melanomas based on computational analysis. HMGCS1 and ELOVL5 were shown to be enriched in a variety of altered molecular pathways and pathways in cancer. Overexpression of HMGCS1 and ELOVL5 were linked to poor prognosis in CM. Conclusion On computational evaluation, we found that HMGCS1 and ELOVL5 were upregulated in both of these melanomas. Enrichment analysis showed that these genes are involved in cancer metabolism pathway and associated with poor prognosis in CM. However, the molecular study of these genes in UM is limited. Therefore, a better understanding of the cancer metabolism pathways should be carried to pave the way for clinical benefits.
Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between two backcross families and two developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage-specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane’s rule in terms of hybrid inviability does not hold. Additionally, QTL mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.
Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs

Ecological and evolutionary dynamics are intrinsically entwined. On short time scales, ecological interactions determine the fate of new mutants and changes in the community they induce, while on longer time scales evolution shapes the whole community. How eco-evolutionary dynamics gives rise to the extensive coexisting diversity of strains found in many bacterial species is a major puzzle. In this paper we study the evolution of large numbers of closely related strains with generalized Lotka Volterra interactions but no niche structure. The host-pathogen-like interactions drive the ecological dynamics into a spatiotemporally chaotic state characterized by continual local blooms and busts. Upon the slow serial introduction of new strains, the community is found to diversify indefinitely, accommodating arbitrarily large numbers of strains in the absence of any kind of stabilizing niche interactions. This diversifying phase is robust to changes in evolutionary parameters, and persists even in the presence of a distribution of general, nonspecific fitness differences between individual strains, which explicitly break the assumption of tradeoffs inherent in much previous work. However, gradual increase of the general fitnesses in the ecosystem slows down the diversification. Quantitative analysis of the range of behaviors is carried out by a combination of analytical methods and simulations. Building on a dynamical-mean field-theory understanding of the ecological dynamics, an approximate effective model captures the effects of evolution on the distributions of key properties, such as strain abundances. This work establishes a potential scenario and a theoretical framework for understanding how the interplay between evolution and ecology can give rise to extensive fine-scale diversity. Future avenues for investigation are suggested, including the effects of the build-up of relatedness between strains, how conditioning on the evolutionary history affects the ecological interactions and dynamics, and application to coevolution of the diversity of a bacterial and a phage species.