Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate method for analysis of a packet-speech multiplexer with limited delay

In a packet-speech multiplexer with limited delay, packets arriving once the queue has reached a certain limit are either discarded, or if embedded encoding has been used, shortened. The uniform arrival and service model, which assumes that the information flow in and out of the multiplexer is uniform rather than in discrete packets, is used to analyze such a multiplexer. The equilibrium queue distribution is described by a set of differential equations that can be solved, together with a set of boundary equations describing the queue behavior at its limits, to yield equilibrium distributions of delay and packet loss. Comparisons to simulations using data collected from real conversations show that the packet loss can be determined accurately if the delay limit is less than 400 ms and more than half the packet length. >
Individual peak gamma frequency predicts switch rate in perceptual rivalry

Perceptual rivalry—the experience of alternation between two mutually exclusive interpretations of an ambiguous image—provides powerful opportunities to study conscious awareness. It is known that individual subjects experience perceptual alternations for various types of bistable stimuli at distinct rates, and this a stable, heritable trait. Also stable and heritable is the peak frequency of induced gamma‐band (30–100 Hz) oscillation of a population‐level response in occipital cortex to simple visual patterns, which has been established as a neural correlate of conscious processing. Interestingly, models for rivalry alternation rate and for the frequency of population‐level oscillation have both cited inhibitory connections in cortex as crucial determinants of individual differences, and yet the relationship between these two variables has not yet been investigated. Here, we used magnetoencephalography to compare differences in alternation rate for binocular and monocular types of perceptual rivalry to differences in evoked and induced gamma‐band frequency of neuromagnetic brain responses to simple nonrivalrous grating stimuli. For both types of bistable images, alternation rate was inversely correlated with the peak frequency of late evoked gamma activity in primary visual cortex (200–400 ms latency). Our results advance models of inhibition that account for subtle variation in normal visual cortex, and shed light on how small differences in anatomy and physiology relate to individual cognition and performance. Hum Brain Mapp 36:566–576, 2015. © 2014 Wiley Periodicals, Inc.
HEMOLYSIS OF RABBIT ERYTHROCYTES BY PURIFIED STAPHYLOCOCCAL ALPHA-TOXIN III

Madoff, Morton A. (New England Center Hospital, Boston, Mass.), Louis Z. Cooper, and Louis Weinstein. Hemolysis of rabbit erythrocytes by purified staphylococcal alpha-toxin. III. Potassium release. J. Bacteriol. 87:145–149. 1964. —The reaction between staphylococcal alpha-toxin and erythrocytes was characterized by rapid release of K+ from the cells, early in the prelytic period; 50 to 75% of this loss occurred before leakage of hemoglobin was detectable. The addition of specific antitoxin early enough in the reaction to inhibit gross hemolysis also inhibited cation release. The presence of sucrose or polyethylene glycol prevented hemoglobin release, but was without effect on K+ leak. These observations suggest that K+ loss is a more specific indication of the progress of the reaction between alpha-toxin and erythrocytes than is the release of hemoglobin.
Winnowing sequences from a database search

In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy. " An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.
Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies

Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees, inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: Empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple evolutionary model that is both biologically plausible and produces the imbalance seen in empirical trees is a challenging problem, to which none of the existing models provide a satisfying answer. Here we propose a simple, biologically plausible macroevolutionary model in which the rate of speciation decreases with species age, whereas extinction rates can vary quite generally. We show that this model provides a remarkable fit to the thousands of trees stored in the online database TreeBase. The biological motivation for the identified age-dependent speciation process may be that recently evolved taxa often colonize new regions or niches and may initially experience little competition. These new taxa are thus more likely to give rise to further new taxa than a taxon that has remained largely unchanged and is, therefore, well adapted to its niche. We show that age-dependent speciation may also be the result of different within-species populations following the same laws of lineage splitting to produce new species. As the fit of our model to the tree database shows, this simple biological motivation provides an explanation for a long standing problem in macroevolution.
Community-Based School Feeding during Indonesia'S Economic Crisis: Implementation, Benefits, and Sustainability

The Indonesian Government initiated a community-based national school-feeding program in 1996. Implementation was decentralized and involved multiple participants. In 1998 we evaluated the implementation of the program and the perceived benefits for community stakeholders using a survey of principals in 143 randomly selected schools and follow-up with in-depth interviews and observations in a subsample of 16 communities. The evaluation covered the period of the 1998 Asian economic crisis, affording the opportunity to assess its impact on the program. The program was implemented in all targeted schools, with excellent community participation. Feeding was sustained through the crisis, in spite of a dramatic escalation in food costs. The families of schoolchildren, farmers, and those who prepared food received economic benefits. The snacks replaced those sold at schools and were of better nutritional value. The children benefited because the snacks compensated for losses in the home diet resulting from the economic crisis. Characteristics of the program that may be important in explaining its success include the involvement of a range of community stakeholders, engagement with existing village administrative structures, scope for local community adaptation and innovation, and the use of local foods that dispersed benefits and ensured sustained implementation during the crisis.
Exploring Local Knowledge and Capacities to Address Climate Risk and Adaptation Along the North Shore of Minnesota.

BITSURA-MESZAROS, KARLY AMANDA. Exploring Local Knowledge and Capacities to Address Climate Risk and Adaptation along the North Shore of Minnesota. (Under the direction of Dr. Jordan W. Smith and Dr. Myron F. Floyd). Global increases in greenhouse gas concentrations over the past half-century have dramatically altered Earth’s climate. A one-size-fits-all solution does not exist for climate change adaptation however, as regional impacts are mitigated (or exacerbated) by human socioeconomic systems that are more (or less) capable of successfully adapting. Small communities, like those along the North Shore of Lake Superior, are especially vulnerable to the effects of climate change given their economies are heavily dependent upon nature-based tourism and outdoor recreation. This research, presented in two complimentary chapters, utilizes multiple methods to assess the vulnerability and adaptive capacity of natural and human systems along Minnesota’s North Shore. First, a climate change adaptation plan evaluation tool was modified and applied to existing resource management plans across the North Shore. The modified management plan evaluation tool can be used to assess other nature-based tourism and outdoor recreation dependent communities’ current capacity to adapt to climate change. Second, North Shore stakeholders were engaged in a climate change risk assessment process utilizing participatory GIS. Findings from the risk assessment process reveal important insights into understanding how local community members and resource managers think about climate and its effects on local resource conditions. Collectively, the findings of this research highlight how existing management plans as well as the knowledge and perceptions of local stakeholders can be leveraged and utilized in future regional adaptation efforts. © Copyright 2015 by Karly Bitsura-Meszaros All Rights Reserved Exploring Local Knowledge and Capacities to Address Climate Risk and Adaptation Along The North Shore of Minnesota
Ensuring Rapid Mixing and Low Bias for Asynchronous Gibbs Sampling

Gibbs sampling is a Markov chain Monte Carlo technique commonly used for estimating marginal distributions. To speed up Gibbs sampling, there has recently been interest in parallelizing it by executing asynchronously. While empirical results suggest that many models can be efficiently sampled asynchronously, traditional Markov chain analysis does not apply to the asynchronous case, and thus asynchronous Gibbs sampling is poorly understood. In this paper, we derive a better understanding of the two main challenges of asynchronous Gibbs: bias and mixing time. We show experimentally that our theoretical results match practical outcomes.
Traffic incident detection using particle swarm optimization

This paper proposes a new approach to automatic incident detection on traffic highways using particle swarm optimization (PSO). The rampant growth in traffic incidents, which is high cost incurring, has led to significant interest in the development of effective incident detection techniques in recent years. Various techniques have been proposed to effectively address this problem, the most promising of which are artificial neural networks (ANN) based methods. Backpropagation (BP) has proven to be one of the best methods to train weights of ANN for incident detection. However it has several limitations including slow convergence, heuristic determination of parameters and possibility of getting stuck in a local minima. This paper overcomes these problems by using particle swarm optimization to train a neural network in place of BP. Actual data from a highway was used for training and testing of this method. Simulation results show that PSO performed better than the backpropagation algorithm.
Constraints on belief functions imposed by fuzzy random variables

Dempster's upper and lower probabilities occur when dealing with multivalued mappings and qualify as Shafer's belief and plausibility measures. In this paper we generalize the notion of upper and lower probabilities while maintaining their properties as belief and plausibility measures, and subsequently apply this concept on Kwakernaak's fuzzy random variables. It is shown how fuzzy random variables induce belief and plausibility functions and it is pointed out what relations exist between fuzzy probabilities and degrees of belief and plausibility. Finally we focus on empirical fuzzy random variables and investigate their asymptotic behavior in terms of belief and plausibility constraints and gain a framework for nonparametric statistical reasoning on the basis of uncertain evidences. >
Ichthyofauna checklist (Chordata: Actinopterygii) for indicating water quality in Kampar River catchment, Malaysia

Ng CKC, Ooi PAC, Wong WL, Khoo G. 2018. Ichthyofauna checklist (Chordata: Actinopterygii) for indicating water quality in Kampar River catchment, Malaysia. Biodiversitas 19: 2252-2274. The limnological habitats are receptors of pollution, thus local fish species richness is a plausible biological indicator to reflect the quality of a particular water body. However, database on species occurrence that corresponds with the water physico-chemistry constituents is often not available. The problem is compounded by the lack of species identification description to assist those working on river and freshwater resource conservation projects. This paper attempts to fill the gaps in the context of Kampar River drainage. Based on sampling exercises conducted from October 2015 to March 2017, an annotated list with visual data for 56 species belonging to 44 genera and 23 families is presented. The water physico-chemistry data is also summarized with the corresponding visual data of limnological zones studied. The species diversity results are further compared with other local drainages and the correlation between area size and their relationship is expressed by y = 17.627e0. 0601x. This paper provides species-level identification information for front line practice and demonstrates how the fish taxonomy discipline can be adapted for practical application in freshwater resource monitoring and management.
Potential role of inorganic polyphosphate in the cycling of phosphorus within the hypoxic water column of Effingham Inlet, British Columbia

The upper basin of Effingham Inlet possesses permanently anoxic bottom waters, with a water column redox transition zone typically occurring at least 40 m above the sediment‐water interface. During our sampling campaign in April and July 2007, this redox transition zone was associated with sharp peaks in a variety of parameters, including soluble reactive phosphorus (SRP) and total particulate phosphorus (TPP). Based on sequential extraction results, TPP maxima exhibited preferential accumulation of an operationally defined class of loosely adsorbed organic phosphorus (P), which may contain a substantial fraction of polyphosphate (poly‐P). This poly‐P may furthermore be involved in the redox‐dependent remobilization of SRP. For example, direct fluorometric analysis of poly‐P content revealed that particulate inorganic poly‐P was present at concentrations ranging from 1 to 9 nM P within and several meters above the TPP maximum. Below the depth of 1% oxygen saturation, however, particulate inorganic poly‐P was undetectable (<0.8 nM in situ). Assuming this concentration profile reflects the remineralization of inorganic poly‐P to SRP across the redox transition, inorganic poly‐P degradation accounted for as much as 4 ± 3% (average ± standard deviation) to 9 ± 8% of the vertical turbulent diffusive SRP flux. This finding is a conservative estimate due in part to sample storage effects associated with our analysis of poly‐P content. By comparison, iron‐linked P cycling accounted for at most 65 ± 33% of the diffusive SRP flux, leaving ∼25% unaccounted for. Thus, while redox‐sensitive poly‐P remineralization in Effingham Inlet appears modest based on our direct conservative estimate, it may be higher from a mass balance viewpoint. Poly‐P cycling may therefore be an overlooked mechanism for the redox‐sensitive cycling of P in some hypoxic/anoxic boundaries, especially iron‐poor marine oxygen minimum zones.
Antibiotic Metabolites from a Marine Pseudomonad

An antibiotic-producing pseudomonad was isolated from a seawater sample from a La Jolla, Calif. , tidepool. The pseudomonad produces two novel antibacterial compounds, 2-n-pentyl-4-quinolinol and 2-n-heptyl-4-quinolinol. It also synthesizes indole-3-carboxaldehyde, 6-bromoindole-3-carboxaldehyde, and the known antibiotic p-hydroxybenzaldehyde. Each of these compounds was identified by analysis of spectral data, and the structures were confirmed by synthesis or comparison with authentic samples.
Distribution of Environmentally Regulated Genes of Streptococcus suis Serotype 2 among S. suis Serotypes and Other Organisms

ABSTRACT The occurrence of 36 environmentally regulated genes of Streptococcus suis strain 10 among all 35 S. suis serotypes was determined by using hybridization with the amplified genes as probes. In addition, the distribution of these genes among the virulence phenotypes of serotypes 1 and 2 was assessed. Hybridization was also performed with various other streptococcal species and nonstreptococcal bacterial species which may be present in pigs. Interestingly, probe ivs-25/iri-1, similar to agrA and sapR, hybridized only with S. suis serotype 1 and 2 strains with virulent phenotypes and is therefore suitable as a diagnostic parameter. Only one probe was specific for S. suis. This probe's sequence was identical to the epf gene, a putative virulence factor of S. suis. Probe ivs-31 was similar to a virulence factor of S. suis, namely, a gene encoding a fibronectin- and fibrinogen-binding protein. This probe hybridized only with oral streptococci. Nearly half of the probes (45%) hybridized with the oral streptococci (S. oralis, S. milleri, S. sanguis, S. gordonii, and S. mitis) and with Streptococcus pneumoniae. This indicates a close relationship between S. suis, the oral streptococci, and S. pneumoniae with respect to the selected environmentally regulated genes. One probe only hybridized with gram-negative species and therefore seems to be obtained by S. suis from a gram-negative organism by horizontal transfer.
Composition and in vitro Anticancer Activities of the Leaf Essential Oil of Neolitsea variabillima from Taiwan

This study investigated the chemical composition and in vitro anticancer activities of the essential oil isolated from the leaf of Neolitsea variabillima. The essential oil was isolated using hydrodistillation in a Clevenger-type apparatus, and characterized by GC-FID and GC-MS. Sixty-seven compounds were identified, representing 100% of the oil. The main components identified were trans-β-ocimene (13.4%), α-cadinol (10.5%), terpinen-4-ol (9.3%), τ-cadinol (9.2%), β-caryophyllene (8.8%), and sabinene (6.7%). The anticancer activities of oil were evaluated. The results showed that the oil exhibited cytotoxic activity against human oral, liver, lung, colon, melanoma, and leukemic cancer cells. The presence of β-caryophyllene, τ-cadinol, and α-cadinol significantly contributed to the anticancer activities of N. variabillima leaf oil.
Phagosome-lysosome fusion is a calcium-independent event in macrophages

Phagosome-lysosome membrane fusion is a highly regulated event that is essential for intracellular killing of microorganisms. Functionally, it represents a form of polarized regulated secretion, which is classically dependent on increases in intracellular ionized calcium ([Ca2+]i). Indeed, increases in [Ca2+]i are essential for phagosome- granule (lysosome) fusion in neutrophils and for lysosomal fusion events that mediate host cell invasion by Trypanosoma cruzi trypomastigotes. Since several intracellular pathogens survive in macrophage phagosomes that do not fuse with lysosomes, we examined the regulation of phagosome-lysosome fusion in macrophages. Macrophages (M phi) were treated with 12.5 microM bis-(2-amino-S-methylphenoxy) ethane- N,N,N',N',-tetraacetic acid tetraacetoxymethyl ester (MAPT/AM), a cell- permeant calcium chelator which reduced resting cytoplasmic [Ca2+]; from 80 nM to < or = 20 nM and completely blocked increases in [Ca2+]i in response to multiple stimuli, even in the presence of extracellular calcium. Subsequently, M phi phagocytosed serum-opsonized zymosan, staphylococci, or Mycobacterium bovis. Microbes were enumerated by 4',6- diamidino-2-phenylindole, dihydrochloride (DAPI) staining, and phagosome-lysosome fusion was scored using both lysosome-associated membrane protein (LAMP-1) as a membrane marker and rhodamine dextran as a content marker for lysosomes. Confirmation of phagosome-lysosome fusion by electron microscopy validated the fluorescence microscopy findings. We found that phagosome-lysosome fusion in M phi occurs noramlly at very low [Ca2+]i (< or = 20 nM). Kinetic analysis showed that in M phi none of the steps leading from particle binding to eventual phagosome-lysosome fusion are regulated by [Ca2+]i in a rate- limiting way. Furthermore, confocal microscopy revealed no difference in the intensity of LAMP-1 immunofluorescence in phagolysosome membranes in calcium-buffered vs. control macrophages. We conclude that neither membrane recognition nor fusion events in the phagosomal pathway in macrophages are dependent on or regulated by calcium.
Long-term treatment with etanercept significantly reduces the number of proinflammatory cytokine-secreting peripheral blood mononuclear cells in patients with rheumatoid arthritis.

OBJECTIVES To determine the influence of etanercept treatment on the number of peripheral blood mononuclear cells (PBMC) secreting immunoregulatory key cytokines and the correlation of these cell counts with treatment response in patients with rheumatoid arthritis (RA). METHODS Nineteen patients with RA were treated with etanercept as monotherapy. Frequencies of PBMC secreting cytokines were determined by ELISPOT analysis before and after 9 months of therapy and compared with values for healthy controls (HC). The clinical outcome was assessed as defined by the ACR criteria. RESULTS Fifteen patients fulfilled the ACR20, seven patients the ACR50 and two patients the ACR70 criteria. Initially elevated numbers of tumour necrosis factor-alpha- and interleukin (IL)-1beta-secreting PBMC were reduced to HC levels, and normal or low numbers of IL-6- and interferon-gamma (IFN-gamma)-secreting PBMC were reduced below HC levels. The number of IL-10-secreting PBMC did not differ from that in HC and did not change significantly over time. The pretreatment IFN-gamma:IL-10 ratio correlated to reduction in the tender and swollen joint counts. CONCLUSIONS Long-term treatment with etanercept in patients with RA significantly reduces the numbers of proinflammatory cytokine-secreting PBMC, while the number of IL-10-secreting cells is unaffected. Although the changes described did not affect the safety or efficacy of etanercept therapy, these alterations may account for the long-term systemic effects. The pretreatment IFN-gamma:IL-10 ratio may be of prognostic value in predicting the improvement in joint symptoms.