Fluid model for a network operating under a fair bandwidth-sharing policy

We consider a model of Internet congestion control that represents the randomly varying number of flows present in a network where bandwidth is shared fairly between document transfers. We study critical fluid models obtained as formal limits under law of large numbers scalings when the average load on at least one resource is equal to its capacity. We establish convergence to equilibria for fluid models and identify the invariant manifold. The form of the invariant manifold gives insight into the phenomenon of entrainment whereby congestion at some resources may prevent other resources from working at their full capacity

State space collapse and diffusion approximation for a network operating under a fair bandwidth sharing policy

We consider a connection-level model of Internet congestion control, introduced by Massouli\'{e} and Roberts [Telecommunication Systems 15 (2000) 185--201], that represents the randomly varying number of flows present in a network. Here, bandwidth is shared fairly among elastic document transfers according to a weighted $\alpha$-fair bandwidth sharing policy introduced by Mo and Walrand [IEEE/ACM Transactions on Networking 8 (2000) 556--567] [$\alpha\in (0,\infty)$]. Assuming Poisson arrivals and exponentially distributed document sizes, we focus on the heavy traffic regime in which the average load placed on each resource is approximately equal to its capacity. A fluid model (or functional law of large numbers approximation) for this stochastic model was derived and analyzed in a prior work [Ann. Appl. Probab. 14 (2004) 1055--1083] by two of the authors. Here, we use the long-time behavior of the solutions of the fluid model established in that paper to derive a property called multiplicative state space collapse, which, loosely speaking, shows that in diffusion scale, the flow count process for the stochastic model can be approximately recovered as a continuous lifting of the workload process.Comment: Published in at http://dx.doi.org/10.1214/08-AAP591 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

No filters, no fridges: a method for preservation of water samples for eDNA analysis

Background: Advancements in the detection of environmental DNA (eDNA) for detecting species of interest will likely allow for expanded use of these techniques in the field. One obstacle that continues to hinder applications in the field is the requirement of a cold chain of storage for water samples containing eDNA. While eDNA has been successfully preserved using Longmire’s lysis buffer applied to filters, it has yet to be tried with freshwater samples collected for eDNA detection of an invasive species. We tested the utility of Longmire’s solution (100 mM Tris, 100 mM EDTA, 10 mM NaCl, 0.5 % SDS, 0.2 % sodium azide) as an additive to freshwater samples for preservation of eDNA. Results: Environmental DNA was effectively preserved in 15 mL water samples with Longmire’s solution added; eDNA positive detection was comparable to freezing the samples at −80 °C and occurred out to 56 days at the highest concentration (5 mL Longmire’s solution: 15 mL sample water). Medium and low concentrations of Longmire’s solution added to 15 mL of sample water generally preserved eDNA out to 56 days but not as well as did freezing or application of the highest concentration of Longmire’s lysis buffer. Treatment and degradation time had a significant effect on average DNA concentration of samples, although not the interaction of treatment and time. Perfect detection occurred out to 56 days with the high Longmire’s treatment group but DNA concentration was significantly lower at this time point compared to 28 days. Conclusion: We conclude that Longmire’s lysis buffer is a viable alternative to cold chain storage that can simplify the collection of eDNA by eliminating the need for filtering and allow more time for sample collection when added at our highest concentration (1 part Longmire’s:3 parts water sample), which could translate to an increase in the chances of detecting a rare or elusive species

EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract)

Multiple sequence alignment (MSA) is a crucial precursor to many downstream biological analyses, such as phylogeny estimation [Morrison, 2006], RNA structure prediction [Shapiro et al., 2007], protein structure prediction [Jumper et al., 2021], etc. Obtaining an accurate MSA can be challenging, especially when the dataset is large (i.e., more than 1000 sequences). A key technique for large-scale MSA estimation is to add sequences into an existing alignment. For example, biological knowledge can be used to form a reference alignment on a subset of the sequences, and then the remaining sequences can be added to the reference alignment. Another case where adding sequences into an existing alignment occurs is when new sequences or genomes are added to databases, leading to the opportunity to add the new sequences for each gene in the genome into a growing alignment. A third case is for de novo multiple sequence alignment, where a subset of the sequences is selected and aligned, and then the remaining sequences are added into this "backbone alignment" [Nguyen et al., 2015; Park et al., 2023; Shen et al., 2022; Liu and Warnow, 2023; Park and Warnow, 2023; Yamada et al., 2016]. Thus, adding sequences into existing alignments is a natural problem with multiple applications to biological sequence analysis. A few methods have been developed to add sequences into an existing alignment, with MAFFT--add [Katoh and Frith, 2012] perhaps the most well-known. However, several multiple sequence alignment methods that operate in two steps (first extract and align the backbone sequences and then add the remaining sequences into this backbone alignment) also provide utilities for adding sequences into a user-provided alignment. We present EMMA, a new approach for adding "query" sequences into an existing "constraint" alignment. By construction, EMMA never changes the constraint alignment, except through the introduction of additional sites to represent homologies between the query sequences. EMMA uses a divide-and-conquer technique combined with MAFFT--add (using the most accurate setting, MAFFT-linsi--add) to add sequences into a user-provided alignment. We evaluate EMMA by comparing it to MAFFT-linsi--add, MAFFT--add (the default setting), and WITCH-ng-add. We include a range of biological and simulated datasets (nucleotides and proteins) ranging in size from 1000 to almost 200,000 sequences and evaluate alignment accuracy and scalability. MAFFT-linsi--add was the slowest and least scalable method, only able to run on datasets with at most 1000 sequences in this study, but had excellent accuracy (often the best) on those datasets. We also see that EMMA has better recall than WITCH-ng-add and MAFFT--add on large datasets, especially when the backbone alignment is small or clade-based

Modelling the Risks Remotely Piloted Aircraft Pose to People on the Ground

Worldwide there is much e ort being directed towards the development of a framework of air- worthiness regulations for remotely piloted aircraft systems (RPAS). It is now broadly accepted that regulations should have a strong foundation in, and traceability to, the management of the safety risks. Existing risk models for RPAS operations do not provide a simple means for incorporating the wide range of technical and operational controls into the risk analysis and evaluation processes. This paper describes a new approach for modelling and evaluating the risks associated with RPAS operations near populous areas based on the barrier bow tie (BBT) model. A BBT model is used to structure the underlying risk management problem. The model focuses risk analysis, evaluation, and decision making activities on the devices, people, and processes that can be employed to reduce risk. The BBT model and a comprehensive set of example risk controls are presented. The general model can be applied to any RPAS operation. The foundations for quantitative and qualitative assessments using a BBT model are also presented. The modelling and evaluation framework is illustrated through its application to a case-study rotary wing RPAS for two operational scenarios. The model can be used as a basis for determining airworthiness certification requirements for RPAS

Psychometric Properties of the PSVT:R Outcome Measure: A Preliminary Study of Introductory Engineering Design Graphics

The Purdue Spatial Visualization Tests: Visualization of Rotations (PVST:R)is among the most commonly used measurement instruments to assess spatial ability. This paper presents the preliminary findings of a factor analysis of the PSVT:R given to 335 introductory engineering design graphics students. Psychometric analysis of the student sample data indicated alternate loading patterns, divergent from a single factor solution

A Comparison of Arch Height Index Measures Between Collegiate Basketball and National Basketball Association Players

The rate of game related basketball injuries is 2xs greater in professionals than collegiate players and the most common injuries occur in the lower extremity. Arch mechanics are often cited as a related factor and the Arch Height Index Measurement System (AHIMS) is a reliable and valid system for quantifying mobility. However, normative or comparative values for basketball athletes have not been reported.https://ecommons.udayton.edu/dpt_symposium/1028/thumbnail.jp

Job Satisfaction and Burnout Among VA and Community Mental Health Workers

Building on two independent studies, we compared burnout and job satisfaction of 66 VA staff and 86 community mental health center staff in the same city. VA staff reported significantly greater job satisfaction and accomplishment, less emotional exhaustion and lower likelihood of leaving their job. Sources of work satisfaction were similar (primarily working with clients, helping/witnessing change). VA staff reported fewer challenges with job-related aspects (e.g. flexibility, pay) but more challenges with administration. Community mental health administrators and policymakers may need to address job-related concerns (e.g. pay) whereas VA administrators may focus on reducing, and helping workers navigate, administrative policies

CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are overlapping, fatal neurodegenerative disorders in which the molecular and pathogenic basis remains poorly understood. Ubiquitinated protein aggregates, of which TDP-43 is a major component, are a characteristic pathological feature of most ALS and FTD patients. Here we use genome-wide linkage analysis in a large ALS/FTD kindred to identify a novel disease locus on chromosome 16p13.3. Whole-exome sequencing identified a CCNF missense mutation at this locus. Interrogation of international cohorts identified additional novel CCNF variants in familial and sporadic ALS and FTD. Enrichment of rare protein-altering CCNF variants was evident in a large sporadic ALS replication cohort. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase complex (SCF(Cyclin F)). Expression of mutant CCNF in neuronal cells caused abnormal ubiquitination and accumulation of ubiquitinated proteins, including TDP-43 and a SCF(Cyclin F) substrate. This implicates common mechanisms, linked to protein homeostasis, underlying neuronal degeneration