Developing a multi-metric habitat index for wadeable streams in Illinois (T-25-P-001), annual segment report to the Illinois Department of Natural Resources.

USFWS through IDNR State Wildlife Grant Grant/Contract No: T-25-P-001INHS Technical Report Prepared for USFWS through IDNR State Wildlife Gran

OSL Characterisation of Two Fluvial Sequences of the River Usmacinta in its Middle Catchment (SE Mexico)

The report summarizes luminescence profiling, initially using a SUERC PPSL system in Mexico, and laboratory analysis at SUERC, used to characterise the stratigraphy and interpret sedimentary processes in terrace deposits of the Usumacinta River, SE Mexico. This was then followed, by quantitative quartz OSL SAR dating of five sediment samples, aimed at defining the chronologicalframework of two sedimentary sequences, USU13-1 and USU13-2. In the wider region, the middle catchment of the Usumacinta River, contains numerous archaeological sites dating to the Maya Classic Period, including Bonampak, Yaxchilan and Piedras Negras. The broader aim of the investigation is to assess whether the two fluvial sequences contain a proxy record of environmental change through the archaeological period of interest. Initial luminescence profiling revealed that the stratigraphy in each profile was complex, reflecting multiple cycles of deposition, with signal maxima, followed by tails to lower intensities, possibly indicating deposition during extreme flood events, interleaved with periods of slower sedimentation, and potentially better luminescence resetting. Laboratory profiling reproduced the apparent maxima/trends in the field profiling dataset, confirming that both sections record complex depositional histories. Furthermore, the variations in stored dose estimates, and luminescence sensitivities with depth, confirm that the sections do not record simple age-depth progressions. Quantitative quartz OSL SAR dating was undertaken on five sediment samples. Given the information obtained from the field- and laboratory-profiles it is not surprising that the equivalent dose distributions for each sample showed considerable scatter, particularly so for the second section, USU13-2. Nevertheless, throughstatistical analysis, individual quartz OSL SAR ages were obtained for each sample. Individual dates fall into the Mayan Post-Classical Period to early modern Period, with statistical combinations pointing to a late 15th century accumulation of USU13-1, and the 18th century accumulation of the sediment within USU13-2. Interestingly, the three samples from section USU13-2, all show some aliquots which tail to higher equivalent doses; furthermore, in each sample, the mean value determined for this component is similar, suggesting that the sediment sampled in USU13-2, may be sourced from a 15th century or older accumulation upstream

Developing a multi-metric habitat index for wadeable streams in Illinois (T-25-P-001). Annual Segment Report to the Illinois Department of Natural Resources.

Illinois Department of Natural Resources Grant/Contract No: (T-25-P-001)This project was initiated to describe key aquatic habitat characteristics and their association to anthropogenic disturbance by developing a field based, rapid assessment method for qualitatively monitoring instream conditions using a multi-metric habitat index. We have developed and applied a method for rating disturbance in wadeable streams throughout Illinois and collected information on physical habitat at 299 sites to date. Index development is in the preliminary stages with field work to continue during the summer of 2008. This report summarizes work performed for the period ending April 30, 2008 (Appendix A contains Eastern Illinois University subcontract annual report).INHS Technical Report Prepared for Illinois Department of Natural Resource

Nivat's conjecture holds for sums of two periodic configurations

Nivat's conjecture is a long-standing open combinatorial problem. It concerns two-dimensional configurations, that is, maps $\mathbb Z^2 \rightarrow \mathcal A$ where $\mathcal A$ is a finite set of symbols. Such configurations are often understood as colorings of a two-dimensional square grid. Let $P_c(m,n)$ denote the number of distinct $m \times n$ block patterns occurring in a configuration $c$. Configurations satisfying $P_c(m,n) \leq mn$ for some $m,n \in \mathbb N$ are said to have low rectangular complexity. Nivat conjectured that such configurations are necessarily periodic. Recently, Kari and the author showed that low complexity configurations can be decomposed into a sum of periodic configurations. In this paper we show that if there are at most two components, Nivat's conjecture holds. As a corollary we obtain an alternative proof of a result of Cyr and Kra: If there exist $m,n \in \mathbb N$ such that $P_c(m,n) \leq mn/2$, then $c$ is periodic. The technique used in this paper combines the algebraic approach of Kari and the author with balanced sets of Cyr and Kra.Comment: Accepted for SOFSEM 2018. This version includes an appendix with proofs. 12 pages + references + appendi

Separation Assurance and Scheduling Coordination in the Arrival Environment

Separation assurance (SA) automation has been proposed as either a ground-based or airborne paradigm. The arrival environment is complex because aircraft are being sequenced and spaced to the arrival fix. This paper examines the effect of the allocation of the SA and scheduling functions on the performance of the system. Two coordination configurations between an SA and an arrival management system are tested using both ground and airborne implementations. All configurations have a conflict detection and resolution (CD&R) system and either an integrated or separated scheduler. Performance metrics are presented for the ground and airborne systems based on arrival traffic headed to Dallas/ Fort Worth International airport. The total delay, time-spacing conformance, and schedule conformance are used to measure efficiency. The goal of the analysis is to use the metrics to identify performance differences between the configurations that are based on different function allocations. A surveillance range limitation of 100 nmi and a time delay for sharing updated trajectory intent of 30 seconds were implemented for the airborne system. Overall, these results indicate that the surveillance range and the sharing of trajectories and aircraft schedules are important factors in determining the efficiency of an airborne arrival management system. These parameters are not relevant to the ground-based system as modeled for this study because it has instantaneous access to all aircraft trajectories and intent. Creating a schedule external to the CD&R and the scheduling conformance system was seen to reduce total delays for the airborne system, and had a minor effect on the ground-based system. The effect of an external scheduler on other metrics was mixed

Community-based therapy for multidrug-resistant tuberculosis in Lima, Peru.

BACKGROUND: Despite the prevalence of multidrug-resistant tuberculosis in nearly all low-income countries surveyed, effective therapy has been deemed too expensive and considered not to be feasible outside referral centers. We evaluated the results of community-based therapy for multidrug-resistant tuberculosis in a poor section of Lima, Peru. METHODS: We describe the first 75 patients to receive ambulatory treatment with individualized regimens for chronic multidrug-resistant tuberculosis in northern Lima. We conducted a retrospective review of the charts of all patients enrolled in the program between August 1, 1996, and February 1, 1999, and identified predictors of poor outcomes. RESULTS: The infecting strains of Mycobacterium tuberculosis were resistant to a median of six drugs. Among the 66 patients who completed four or more months of therapy, 83 percent (55) were probably cured at the completion of treatment. Five of these 66 patients (8 percent) died while receiving therapy. Only one patient continued to have positive cultures after six months of treatment. All patients in whom treatment failed or who died had extensive bilateral pulmonary disease. In a multiple Cox proportional-hazards regression model, the predictors of the time to treatment failure or death were a low hematocrit (hazard ratio, 4.09; 95 percent confidence interval, 1.35 to 12.36) and a low body-mass index (hazard ratio, 3.23; 95 percent confidence interval, 0.90 to 11.53). Inclusion of pyrazinamide and ethambutol in the regimen (when susceptibility was confirmed) was associated with a favorable outcome (hazard ratio for treatment failure or death, 0.30; 95 percent confidence interval, 0.11 to 0.83). CONCLUSIONS: Community-based outpatient treatment of multidrug-resistant tuberculosis can yield high cure rates even in resource-poor settings. Early initiation of appropriate therapy can preserve susceptibility to first-line drugs and improve treatment outcomes

Time to Culture Conversion and Regimen Composition in Multidrug-Resistant Tuberculosis Treatment

Sputum cultures are an important tool in monitoring the response to tuberculosis treatment, especially in multidrug-resistant tuberculosis. There has, however, been little study of the effect of treatment regimen composition on culture conversion. Well-designed clinical trials of new anti-tuberculosis drugs require this information to establish optimized background regimens for comparison. We conducted a retrospective cohort study to assess whether the use of an aggressive multidrug-resistant tuberculosis regimen was associated with more rapid sputum culture conversion. We conducted Cox proportional-hazards analyses to examine the relationship between receipt of an aggressive regimen for the 14 prior consecutive days and sputum culture conversion. Sputum culture conversion was achieved in 519 (87.7%) of the 592 patients studied. Among patients who had sputum culture conversion, the median time to conversion was 59 days (IQR: 31–92). In 480 patients (92.5% of those with conversion), conversion occurred within the first six months of treatment. Exposure to an aggressive regimen was independently associated with sputum culture conversion during the first six months of treatment (HR: 1.36; 95% CI: 1.10, 1.69). Infection with human immunodeficiency virus (HR 3.36; 95% CI: 1.47, 7.72) and receiving less exposure to tuberculosis treatment prior to the individualized multidrug-resistant tuberculosis regimen (HR: 1.58; 95% CI: 1.28, 1.95) were also independently positively associated with conversion. Tachycardia (HR: 0.77; 95% CI: 0.61, 0.98) and respiratory difficulty (HR: 0.78; 95% CI: 0.62, 0.97) were independently associated with a lower rate of conversion. This study is the first demonstrating that the composition of the multidrug-resistant tuberculosis treatment regimen influences the time to culture conversion. These results support the use of an aggressive regimen as the optimized background regimen in trials of new anti-TB drugs

Aggressive Regimens for Multidrug-Resistant Tuberculosis Decrease All-Cause Mortality

Rationale: A better understanding of the composition of optimal treatment regimens for multidrug-resistant tuberculosis (MDR-TB) is essential for expanding universal access to effective treatment and for developing new therapies for MDR-TB. Analysis of observational data may inform the definition of an optimized regimen. Objectives: This study assessed the impact of an aggressive regimen–one containing at least five likely effective drugs, including a fluoroquinolone and injectable–on treatment outcomes in a large MDR-TB patient cohort. Methods: This was a retrospective cohort study of patients treated in a national outpatient program in Peru between 1999 and 2002. We examined the association between receiving an aggressive regimen and the rate of death. Measurements and Main Results: In total, 669 patients were treated with individualized regimens for laboratory-confirmed MDR-TB. Isolates were resistant to a mean of 5.4 (SD 1.7) drugs. Cure or completion was achieved in 66.1% (442) of patients; death occurred in 20.8% (139). Patients who received an aggressive regimen were less likely to die (crude hazard ratio [HR]: 0.62; 95% CI: 0.44,0.89), compared to those who did not receive such a regimen. This association held in analyses adjusted for comorbidities and indicators of severity (adjusted HR: 0.63; 95% CI: 0.43,0.93). Conclusions: The aggressive regimen is a robust predictor of MDR-TB treatment outcome. TB policy makers and program directors should consider this standard as they design and implement regimens for patients with drug-resistant disease. Furthermore, the aggressive regimen should be considered the standard background regimen when designing randomized trials of treatment for drug-resistant TB

Transport and retention of the mitten crab (Eriocheir sinensis) in a Mid-Atlantic estuary: Predictions from a larval transport model

Invasive species cause extensive ecological damage in freshwater and marine habitats and are a threat to biodiversity in aquatic ecosystems world-wide. One such species, the Chinese mitten crab, Eriocheir sinensis, has invasive populations in northern Europe and San Francisco Bay, and there are confirmed reports of breeding female crabs in both the Chesapeake and Delaware Bays. Despite their threat to these ecosystems, there are still large gaps in the current understanding of this species\u27 larval biology that are critical to predicting the potential for large populations to establish in East Coast bays and estuaries. We addressed these issues by using a physical circulation model of Delaware Bay and the adjacent coastal ocean coupled to a modified particle advection scheme. We used this model to examine the effects of different physical mechanisms and larval behavior on transport, retention, and settlement of larvae in the bay. The circulation model produced flow fields using observed winds and river discharge for 2006 as well as systematic variations of river discharge and wind direction. Since little is known regarding mitten crab larval behavior, the larval component was purposefully general and incorporated a suite of behaviors such as tidal, diel, and ontogenetic vertical migration; however, results of this study showed that vertical migration affects the magnitude, but not locations of larval settlement. Simulations revealed that changes in the time and location of spawning can result in large variations in retention and settlement of larvae in Delaware Bay and the coastal ocean, due to seasonal variations of the physical flow field. Overall results of our study showed that the estuarine and coastal circulation typically found along the Middle Atlantic coast of the United States can result in significant retention of new and established E. sinensis populations in large estuaries as well as transport of larvae to new coastal locations

Aviation turbulence: dynamics, forecasting, and response to climate change

Atmospheric turbulence is a major hazard in the aviation industry and can cause injuries to passengers and crew. Understanding the physical and dynamical generation mechanisms of turbulence aids with the development of new forecasting algorithms and, therefore, reduces the impact that it has on the aviation industry. The scope of this paper is to review the dynamics of aviation turbulence, its response to climate change, and current forecasting methods at the cruising altitude of aircraft. Aviation-affecting turbulence comes from three main sources: vertical wind shear instabilities, convection, and mountain waves. Understanding these features helps researchers to develop better turbulence diagnostics. Recent research suggests that turbulence will increase in frequency and strength with climate change, and therefore, turbulence forecasting may become more important in the future. The current methods of forecasting are unable to predict every turbulence event, and research is ongoing to find the best solution to this problem by combining turbulence predictors and using ensemble forecasts to increase skill. The skill of operational turbulence forecasts has increased steadily over recent decades, mirroring improvements in our understanding. However, more work is needed—ideally in collaboration with the aviation industry—to improve observations and increase forecast skill, to help maintain and enhance aviation safety standards in the future