UCHIME improves sensitivity and speed of chimera detection

Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments

Field Test of Two Energetic Models for Yellow Perch

Field data from a population of yellow perch Perca flavescens in Saginaw Bay, Lake Huron, were used to evaluate the ability of two energetic models to predict consumption by yellow perch. Field estimates of daily ration for age‐1–4 fish during May through October 1987 and 1988 were compared with independent predictions made by the Wisconsin energetic model and an energetic model developed by Karås and Thoresson. Predictions of daily ration using the Wisconsin model were lower than daily rations estimated from field data for all ages, primarily due to poor model–field agreement at temperatures above 22°C. This caused estimates of cumulative consumption from the Wisconsin model to be 25–50% lower than field estimates. Predictions of daily ration by the Karås–Thoresson model agreed with field estimates over a temperature range of 10–26°C for age‐1–3 yellow perch but not for older fish. Despite improvement, model predictions of cumulative consumption were 2–35% lower than field estimates. Although these tests of predicted and estimated rations may provide insight into which model produced more accurate results, it must be emphasized that field measures of daily ration are also estimates and may be in error, particularly at temperatures above 22°C where gastric evacuation rates were estimated. The Karås–Thoresson modification of the Wisconsin energetic model produced better fits to field ration data and is recommended for model applications.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142095/1/tafs0414.pd

The Antiferromagnetic Band Structure of La2CuO4 Revisited

Using the Becke-3-LYP functional, we have performed band structure calculations on the high temperature superconductor parent compound, La2CuO4. Under the restricted spin formalism (rho(alpha) equal to rho(beta)), the R-B3LYP band structure agrees well with the standard LDA band structure. It is metallic with a single Cu x2-y2/O p(sigma) band crossing the Fermi level. Under the unrestricted spin formalism (rho(alpha) not equal to rho(beta)), the UB3LYP band structure has a spin polarized antiferromagnetic solution with a band gap of 2.0 eV, agreeing well with experiment. This state is 1.0 eV (per formula unit) lower than that calculated from the R-B3LYP. The apparent high energy of the spin restricted state is attributed to an overestimate of on-site Coulomb repulsion which is corrected in the unrestricted spin calculations. The stabilization of the total energy with spin polarization arises primarily from the stabilization of the x2-y2 band, such that the character of the eigenstates at the top of the valence band in the antiferromagnetic state becomes a strong mixture of Cu x2-y2/O p(sigma) and Cu z2/O' p(z). Since the Hohenberg-Kohn theorem requires the spin restricted and spin unrestricted calculations give exactly the same ground state energy and total density for the exact functionals, this large disparity in energy reflects the inadequacy of current functionals for describing the cuprates. This calls into question the use of band structures based on current restricted spin density functionals (including LDA) as a basis for single band theories of superconductivity in these materials.Comment: 13 pages, 8 figures, to appear in Phys. Rev. B, for more information see http://www.firstprinciples.co

Ten Year Real World Experience with Ultrafiltration for the Management of Acute Decompensated Heart Failure

Background: Randomized controlled trials (RCT) of ultrafiltration (UF) have demonstrated conflicting results regarding its efficacy and safety. Objective: We reviewed 10 years of data for adjustable UF during heart failure hospitalizations in a real world cohort. Methods: We performed a retrospective, single center analysis of 335 consecutive patients treated with adjustable rate UF using the CHF Solutions Aquadex Flex Flo System from 2009 to 2019. Results: Compared to previous RCTs investigating UF, our cohort was older, with worse renal impairment and more antecedent HF hospitalizations in the year preceding therapy. Mean fluid removal with UF was 14.6 l. Mean weight loss with UF was 15.6 lbs (range 0.2–57 lbs) and was sustained at 1–2 week follow-up. Mean creatinine change upon stopping UF, at discharge and follow-up (mean 30 days) was +0.11 mg/dl, +0.07 mg/dl and +0.11 mg/dl, respectively. HF rehospitalizations at 30 days, 90 days and 1 year were 12.4 %, 14.9 % and 27.3 % respectively. On average patients had 1.74 fewer hospitalizations for HF in the year following UF when compared to 12 months preceding UF. Major bleeding defined as requiring discontinuation of anticoagulation occurred in 3.6 % of patients. Conclusions: Compared with previous UF trials, our study demonstrates that UF compares favorably for HF rehospitalizations, renal function response, and weight/volume loss. Importantly, our real world experience allowed for the adjustment of UF rate during therapy and we believe this is a major contributor to our favorable outcomes. In clinical practice, UF can be a safe and effective strategy for decongestion

Proper Motions of the Jets in the Region of HH 30 and HL/XZ Tau. Evidence for a Binary Exciting Source of the HH 30 Jet

We present [SII] images of the HH 30 and HL/XZ Tau region obtained at two epochs, as well as long-slit optical spectroscopy of the HH 30 jet. We measured proper motions of about 100-300 km/s for the HH 30 jet and counterjet, and of about 120 km/s for the HL Tau jet. Inclination angles with respect to the plane of the sky are 0-40 deg for the HH 30 jet and 60 deg for the HL Tau jet. Comparison with previous observations suggests that most of the jet knots consist of persisting structures. Also, we corroborate that the HH 30-N knots correspond to the head of the HH 30 jet. The overall HH 30 jet structure can be well described by a wiggling ballistic jet, arising either by the orbital motion of the jet source around a primary or by precession of the jet axis because of the tidal effects of a companion. In the first scenario, the orbital period would be 53 yr and the total mass 0.25-2 solar masses. In the precession scenario, the mass of the jet source would be 0.1-1 solar masses, the orbital period <1 yr, and the mass of the companion less than a few times 0.01 solar masses, thus being a substellar object or a giant exoplanet. In both scenarios a binary system with a separation <18 AU (<0.13 arcsec) is required. Since the radius of the flared disk observed with the HST is about 250 AU, we conclude that this disk appears to be circumbinary rather than circumstellar, suggesting that the search for the collimating agent of the HH 30 jet should be carried out at much smaller scales.Comment: 42 pages, 7 figures, 5 tables. To Appear in The Astronomical Journal, Vol. 133 No. 6 (June 2007

Sleep During Pregnancy: The nuMoM2b Pregnancy and Sleep Duration and Continuity Study

Study Objectives: To characterize sleep duration, timing and continuity measures in pregnancy and their association with key demographic variables. Methods: Multisite prospective cohort study. Women enrolled in the nuMoM2b study (nulliparous women with a singleton gestation) were recruited at the second study visit (16-21 weeks of gestation) to participate in the Sleep Duration and Continuity substudy. Women <18 years of age or with pregestational diabetes or chronic hypertension were excluded from participation. Women wore a wrist activity monitor and completed a sleep log for 7 consecutive days. Time in bed, sleep duration, fragmentation index, sleep efficiency, wake after sleep onset, and sleep midpoint were averaged across valid primary sleep periods for each participant. Results: Valid data were available from 782 women with mean age of 27.3 (5.5) years. Median sleep duration was 7.4 hours. Approximately 27.9% of women had a sleep duration of 9 hours. In multivariable models including age, race/ethnicity, body mass index, insurance status, and recent smoking history, sleep duration was significantly associated with race/ethnicity and insurance status, while time in bed was only associated with insurance status. Sleep continuity measures and sleep midpoint were significantly associated with all covariates in the model, with the exception of age for fragmentation index and smoking for wake after sleep onset. Conclusions: Our results demonstrate the relationship between sleep and important demographic characteristics during pregnancy

Conservation of grassland birds in North America: understanding ecological processes in different regions

Many species of birds that depend on grassland or savanna habitats have shown substantial overall population declines in North America. To understand the causes of these declines, we examined the habitat requirements of birds in six types of grassland in different regions of the continent. Open habitats were originally maintained by ecological drivers (continual and pervasive ecological processes) such as drought, grazing, and fire in tallgrass prairie, mixed-grass prairie, shortgrass prairie, desert grassland, and longleaf pine savanna. By contrast, grasslands were created by occasional disturbances (e.g., fires or beaver [Castor canadensis] activity) in much of northeastern North America. The relative importance of particular drivers or disturbances differed among regions. Keystone mammal species grazers such as prairie-dogs (Cynomys spp.) and bison (Bison bison) in western prairies, and dam-building beavers in eastern regions of the continent. Deciduous forests played a crucial, and frequently unappreciated, role in maintaining many grassland systems. Although fire was important in preventing invasion of woody plants in the tallgrass and moist mixed prairies, grazing played a more important role in maintaining the typical grassland vegetation of shortgrass prairies and desert grasslands. Heavy grazing by prairiedogs or bison created a low \u27grazing lawn\u27 that is the preferred habitat for many grassland bird species that are restricted to the shortgrass prairie and desert grasslands. Ultimately, many species of grassland birds are vulnerable because people destroyed their breeding, migratory, and wintering habitat, either directly by converting it to farmland and building lots, or indirectly by modifying grazing patterns, suppressing fires, or interfering with other ecological processes that originally sustained open grassland. Understanding the ecological processes that originally maintained grassland systems is critically important for efforts to improve, restore, or create habitat for grassland birds and other grassland organisms. Consequently, preservation of large areas of natural or seminatural grassland, where these processes can be studied and core populations of grassland birds can flourish, should be a high priority. However, some grassland birds now primarily depend on artificial habitats that are managed to maximize production of livestock, timber, or other products. With a sound understanding of the habitat requirements of grassland birds and the processes that originally shaped their habitats, it should be possible to manage populations sustainably on \u27working land\u27 such as cattle ranches, farms, and pine plantations. Proper management of private land will be critical for preserving adequate breeding, migratory, and winter habitat for grassland and savanna species

Testing and Modeling Ethernet Switches and Networks for Use in ATLAS High-level Triggers

The ATLAS second level trigger will use a multi-layered LAN network to transfer 5 Gbyte/s detector data from ~1500 buffers to a few hundred processors. A model of the network has been constructed to evaluate its performance. A key component of the network model is a model of an individual switch, reproducing the behavior measured in real devices. A small number of measurable parameters are used to model a variety of commercial Ethernet switches. Using parameters measured on real devices, the impact on the overall network performance is modeled. In the Atlas context, both 100 Mbit and Gigabit Ethernet links are required. A system is described which is capable of characterizing the behavior of commercial switches with the required number of nodes under traffic conditions resembling those to be encountered in the Atlas experiment. Fast Ethernet traffic is provided by a high density, custom built tester based on FPGAs, programmed in Handel-C and VHDL, while the Gigabit Ethernet traffic is generated using Alteon NICs with custom firmware. The system is currently being deployed with 32 100Mbit ports and 16 Gigabit ports, and will be expanded to ~256 nodes of 100 Mbit and ~50 GBE nodes