The relationship between species detection probability and local extinction probability.

In community-level ecological studies, generally not all species present in sampled areas are detected. Many authors have proposed the use of estimation methods that allow detection probabilities that are <1 and that are heterogeneous among species. These methods can also be used to estimate community-dynamic parameters such as species local extinction probability and turnover rates (Nichols et al. Ecol Appl 8:1213–1225; Conserv Biol 12:1390–1398). Here, we present an ad hoc approach to estimating community-level vital rates in the presence of joint heterogeneity of detection probabilities and vital rates. The method consists of partitioning the number of species into two groups using the detection frequencies and then estimating vital rates (e.g., local extinction probabilities) for each group. Estimators from each group are combined in a weighted estimator of vital rates that accounts for the effect of heterogeneity. Using data from the North American Breeding Bird Survey, we computed such estimates and tested the hypothesis that detection probabilities and local extinction probabilities were negatively related. Our analyses support the hypothesis that species detection probability covaries negatively with local probability of extinction and turnover rates. A simulation study was conducted to assess the performance of vital parameter estimators as well as other estimators relevant to questions about heterogeneity, such as coefficient of variation of detection probabilities and proportion of species in each group. Both the weighted estimator suggested in this paper and the original unweighted estimator for local extinction probability performed fairly well and provided no basis for preferring one to the other

Development of a high-resolution NGS-based HLA-typing and analysis pipeline

The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions

Spin-dependent cross sections from the three-body photodisintegration of He 3 at incident energies of 12.8 and 14.7 MeV

The first measurement of the three-body photodisintegration of polarized 3He using a circularly polarized photon beam has been performed at incident energies of 12.8 and 14.7 MeV. This measurement was carried out at the high-intensity γ-ray source located at Triangle Universities Nuclear Laboratory. A high-pressure 3He target, polarized via spin exchange optical pumping with alkali metals, was used in the experiment. The spin-dependent double- and single-differential cross sections from 3He(γ,n)pp for laboratory angles varying from 30° to 165° are presented and compared with state-of-the-art three-body calculations. The data reveal the importance of including the Coulomb interaction between protons in the three-body calculations

Using microphone arrays to investigate microhabitat selection by declining breeding birds

Understanding the microhabitat preferences of animals can help managers to develop better conservation and recovery strategies but this is challenging. Traditional methods are limited by cost, accuracy and human resources. In this study, we investigated avian microhabitat preferences using microphone arrays that are capable of accurately locating vocalizing birds. Our objective was to identify the microhabitat associations of two common species in steep population decline, the Boreal Chickadee Poecile hudsonicus and the Cape May Warbler Setophaga tigrina. We deployed 68 eight‐channel arrays at random locations in Labrador, Canada, during the 2016 avian breeding season. We returned in 2017 to the 18 array locations where the target species had been detected the previous year and characterized the microhabitat at the exact locations where they had been detected. We also characterized the microhabitat at randomly determined control locations. Results show that Boreal Chickadees select trees with greater diameter‐at‐breast‐height that are surrounded by greater stem density. We did not find evidence that Cape May Warblers exhibit microhabitat selection during song production. The study shows that microphone arrays are an effective tool for identifying preferred microhabitat that could be incorporated into future conservation or recovery strategies

Serologic Reactivity Reflects Clinical Expression of Ulcerative Colitis in Children

Background In contrast to pediatric Crohn's disease (CD), little is known in pediatric ulcerative colitis (UC) about the relationship between disease phenotype and serologic reactivity to microbial and other antigens. Aim The aim of this study was to examine disease phenotype and serology in a well-characterized inception cohort of children newly diagnosed with UC during the PROTECT Study (Predicting Response to Standardized Pediatric Colitis Therapy). Methods Patients were recruited from 29 participating centers. Demographic, clinical, laboratory, and serologic (pANCA, ASCA IgA/IgG, Anti-CBir1, and Anti-OmpC) data were obtained from children 4-17 years old with UC. Results Sixty-five percent of the patients had positive serology for pANCA, with 62% less than 12 years old and 66% 12 years old or older. Perinuclear anti-neutrophil cytoplasmic antibodies did not correspond to a specific phenotype though pANCA ò100, found in 19%, was strongly associated with pancolitis (P = 0.003). Anti-CBir1 was positive in 19% and more common in younger children with 32% less than 12 years old as compared with 14% 12 years old or older (P < 0.001). No association was found in any age group between pANCA and Anti-CBir1. Relative rectal sparing was more common in +CBir1, 16% versus 7% (P = 0.02). Calprotectin was lower in Anti-CBir1+ (Median [IQR] 1495 mcg/g [973-3333] vs 2648 mcg/g [1343-4038]; P = 0.04). Vitamin D 25-OH sufficiency was associated with Anti-CBir1+ (P = 0.0009). Conclusions The frequency of pANCA in children was consistent with adult observations. High titer pANCA was associated with more extensive disease, supporting the idea that the magnitude of immune reactivity may reflect disease severity. Anti-CBir1+ was more common in younger ages, suggesting host-microbial interactions may differ by patient age