SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree, a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons

An Experimental Study of the Effect of Shared Information on Pilot/Controller Re-Route Negotiation

Air–ground data link systems are being developed to enable pilots and air traffic controllers to share information more fully. The sharing of information is generally expected to enhance their shared situation awareness and foster more collaborative decision making. An exploratory, part-task simulator experiment is described which evaluates the extent to which shared information may lead pilots and controllers to cooperate or compete when negotiating route amendments. The results indicate an improvement in situation awareness for pilots and controllers and a willingness to work cooperatively. Independent of data link considerations, the experiment also demonstrates the value of providing controllers with a good-quality weather representation on their plan view displays. Observed improvements in situation awareness and separation assurance are discussed. It is argued that deployment of this relatively simple, low-risk addition to the plan view displays be accelerated.the National Aeronautics and Space Administration Ames Research Center under grant NAG 2-716 and by The Analytical Sciences Corporation (TASC) as part of the FAA Center of Excellence in Operations Research

Work hour restrictions: impact on neurosurgical resident training at the University of Utah

Journal ArticleResident work hour restrictions imposed by the Accreditation Council for Graduate Medical Education became effective on July 1, 2003. To evaluate the effect of these regulations on resident operative experience, we reviewed and compared the surgical experience of junior and senior neurosurgical residents four years before and one year after the ACGME restrictions were implemented. Resident work hours since May 2003 and operative caseload during the study period were recorded in commercially available data systems. The mean number of hours worked per week by junior and chief residents decreased f r om 104 and 110 hours before the ACGME work hour restrictions to 81 and 84 hours afterward, respectively. During the four academic years before the work hour limitations took effect, the mean number of major cases performed each year was 802.5 for the chief residents and 849.3 for t he junior residents. Following the restrictions, little changed for t he chief residents. However, the junior residents averaged only 467 cases, a 45 percent decrease f r om t he previous years studied. The mean number of cases covered by each junior resident per month decreased by 30.5 percent after the work hour restrictions were instituted, and the mean number of cases covered per post-call junior resident in one month declined 47.8 percent, from 23 to 12. At our institution, the ACGME work hour restrictions have resulted in decreased resident work hours for all residents at t he expense of the operative experience for junior residents. The operative caseload for chief residents has not been affected

A review of the genus Agapetus Curtis (Trichoptera: Glossosomatidae) in eastern and central North America, with description of 12 new species

Twenty-nine species of caddisflies in the genus Agapetus Curtis in eastern and central North America are reviewed. Twelve are described as new species: Agapetus aphallus (known only from females); Agapetus baueri, Agapetus flinti, Agapetus harrisi, Agapetus hesperus, Agapetus ibis, Agapetus kirchneri, Agapetus meridionalis, Agapetus pegram, Agapetus ruiteri, Agapetus stylifer, and Agapetus tricornutus. Agapetus rossi Denning 1941 is recognized as a junior subjective synonym of Agapetus walkeri (Betten and Mosely 1940), new synonym. A key to males is provided, and species’ distributions are mapped

Sporadic osteochondroma of the cervical spine

Journal ArticleOsteochondroma is the most common benign tumor of bone, but axial skeleton involvement is uncommon and usually indicates a hereditary cause such as osteochondromatosis (hereditary multiple exostosis). 1 Approximately 7% of hereditary osteochondromas occur along the vertebral column, which is double the rate of vertebral column occurrences among sporadic cases.4 We present a rare pediatric case of a large sporadic osteochondroma arising from the C-3 lamina. A previously healthy 13-year-old girl with no family history of osteochondroma noticed a posterior neck mass that continued to enlarge over the following year. On examination, the mass was readily visible and nontender to palpation. The patient denied clumsiness of the hands or feet, paresthesias, or neck pain. No motor weakness, sensory disturbance, or hyperreflexia was noted. A lateral plain radiograph demonstrated a calcified mass arising dorsally from the posterior elements of the cervical spine between C-2 and C-4 (Fig. 1). Computerized tomography (CT) scans revealed that the mass was arising from the lamina of C-3 with bone remodeling of the C-2 and C-4 laminae (Fig. 2). Magnetic resonance imaging demonstrated a large multilobulated, cystic, and irregularly enhancing mass with calcified components, measuring 5.8 3 5.5 3 8.7 cm and causing mild cord compression at C3?4 (Fig. 2). The differential diagnosis for this rapidly growing spinal bone lesion included osteochondroma, osteoblastoma, osteosarcoma, and chondrosarcoma. The patient underwent a complete resection via a posterior midline cervical incision. At surgery, the tumor appeared lobulated, well-circumscribed, firm, and calcified (Fig. 3). The tumor and the C-3 lamina were removed. The results of a pathological examination were consistent with an osteochondroma. The postoperative CT scan demonstrated a gross-total resection with stable sagittal alignment

An approach to verification and validation of a reliable multicasting protocol: Extended Abstract

This paper describes the process of implementing a complex communications protocol that provides reliable delivery of data in multicast-capable, packet-switching telecommunication networks. The protocol, called the Reliable Multicasting Protocol (RMP), was developed incrementally using a combination of formal and informal techniques in an attempt to ensure the correctness of its implementation. Our development process involved three concurrent activities: (1) the initial construction and incremental enhancement of a formal state model of the protocol machine; (2) the initial coding and incremental enhancement of the implementation; and (3) model-based testing of iterative implementations of the protocol. These activities were carried out by two separate teams: a design team and a V&V team. The design team built the first version of RMP with limited functionality to handle only nominal requirements of data delivery. This initial version did not handle off-nominal cases such as network partitions or site failures. Meanwhile, the V&V team concurrently developed a formal model of the requirements using a variant of SCR-based state tables. Based on these requirements tables, the V&V team developed test cases to exercise the implementation. In a series of iterative steps, the design team added new functionality to the implementation while the V&V team kept the state model in fidelity with the implementation. This was done by generating test cases based on suspected errant or off-nominal behaviors predicted by the current model. If the execution of a test in the model and implementation agreed, then the test either found a potential problem or verified a required behavior. However, if the execution of a test was different in the model and implementation, then the differences helped identify inconsistencies between the model and implementation. In either case, the dialogue between both teams drove the co-evolution of the model and implementation. We have found that this interactive, iterative approach to development allows software designers to focus on delivery of nominal functionality while the V&V team can focus on analysis of off nominal cases. Testing serves as the vehicle for keeping the model and implementation in fidelity with each other. This paper describes (1) our experiences in developing our process model; and (2) three example problems found during the development of RMP. Although RMP has provided our research effort with a rich set of test cases, it also has practical applications within NASA. For example, RMP is being considered for use in the NASA EOSDIS project due to its significant performance benefits in applications that need to replicate large amounts of data to many network sites