Availability of coal resources for mining in Illinois : Newton and Princeville quadrangles, Jasper, Peoria, and Stark Counties

U.S. Geological Survey under assistance award No. 1434-94-A-1266Ope

The impact of targeting all elderly persons in England and Wales for yearly influenza vaccination: excess mortality due to pneumonia or influenza and time trend study.

OBJECTIVE: To investigate the impact on mortality due to pneumonia or influenza of the change from risk-based to age group-based targeting of the elderly for yearly influenza vaccination in England and Wales. DESIGN: Excess mortality estimated using time series of deaths registered to pneumonia or influenza, accounting for seasonality, trend and artefacts. Non-excess mortality plotted as proxy for long-term trend in mortality. SETTING: England and Wales. PARTICIPANTS: Persons aged 65-74 and 75+ years whose deaths were registered to underlying pneumonia or influenza between 1975/1976 and 2004/2005. OUTCOME MEASURES: Multiplicative effect on average excess pneumonia and influenza deaths each winter in the 4-6 winters since age group-based targeting of vaccination was introduced (in persons aged 75+ years from 1998/1999; in persons aged 65+ years from 2000/2001), estimated using multivariable regression adjusted for temperature, antigenic drift and vaccine mismatch, and stratified by dominant circulating influenza subtype. Trend in baseline weekly pneumonia and influenza death rates. RESULTS: There is a suggestion of lower average excess mortality in the six winters after age group-based targeting began compared to before, but the CI for the 65-74 years age group includes no difference. Trend in baseline pneumonia and influenza mortality shows an apparent downward turning point around 2000 for the 65-74 years age group and from the mid-1990s in the 75+ years age group. CONCLUSIONS: There is weakly supportive evidence that the marked increases in vaccine coverage accompanying the switch from risk-based to age group-based targeting of the elderly for yearly influenza vaccination in England and Wales were associated with lower levels of pneumonia and influenza mortality in older people in the first 6 years after age group-based targeting began. The possible impact of these policy changes is observed as weak evidence for lower average excess mortality as well as a turning point in baseline mortality coincident with the changes

AMAnD: an automated metagenome anomaly detection methodology utilizing DeepSVDD neural networks

The composition of metagenomic communities within the human body often reflects localized medical conditions such as upper respiratory diseases and gastrointestinal diseases. Fast and accurate computational tools to flag anomalous metagenomic samples from typical samples are desirable to understand different phenotypes, especially in contexts where repeated, long-duration temporal sampling is done. Here, we present Automated Metagenome Anomaly Detection (AMAnD), which utilizes two types of Deep Support Vector Data Description (DeepSVDD) models; one trained on taxonomic feature space output by the Pan-Genomics for Infectious Agents (PanGIA) taxonomy classifier and one trained on kmer frequency counts. AMAnD's semi-supervised one-class approach makes no assumptions about what an anomaly may look like, allowing the flagging of potentially novel anomaly types. Three diverse datasets are profiled. The first dataset is hosted on the National Center for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) and contains nasopharyngeal swabs from healthy and COVID-19-positive patients. The second dataset is also hosted on SRA and contains gut microbiome samples from normal controls and from patients with slow transit constipation (STC). AMAnD can learn a typical healthy nasopharyngeal or gut microbiome profile and reliably flag the anomalous COVID+ or STC samples in both feature spaces. The final dataset is a synthetic metagenome created by the Critical Assessment of Metagenome Annotation Simulator (CAMISIM). A control dataset of 50 well-characterized organisms was submitted to CAMISIM to generate 100 synthetic control class samples. The experimental conditions included 12 different spiked-in contaminants that are taxonomically similar to organisms present in the laboratory blank sample ranging from one strain tree branch taxonomic distance away to one family tree branch taxonomic distance away. This experiment was repeated in triplicate at three different coverage levels to probe the dependence on sample coverage. AMAnD was again able to flag the contaminant inserts as anomalous. AMAnD's assumption-free flagging of metagenomic anomalies, the real-time model training update potential of the deep learning approach, and the strong performance even with lightweight models of low sample cardinality would make AMAnD well-suited to a wide array of applied metagenomics biosurveillance use-cases, from environmental to clinical utility

Order in de Broglie - Bohm quantum mechanics

A usual assumption in the so-called {\it de Broglie - Bohm} approach to quantum dynamics is that the quantum trajectories subject to typical `guiding' wavefunctions turn to be quite irregular, i.e. {\it chaotic} (in the dynamical systems' sense). In the present paper, we consider mainly cases in which the quantum trajectories are {\it ordered}, i.e. they have zero Lyapunov characteristic numbers. We use perturbative methods to establish the existence of such trajectories from a theoretical point of view, while we analyze their properties via numerical experiments. Using a 2D harmonic oscillator system, we first establish conditions under which a trajectory can be shown to avoid close encounters with a moving nodal point, thus avoiding the source of chaos in this system. We then consider series expansions for trajectories both in the interior and the exterior of the domain covered by nodal lines, probing the domain of convergence as well as how successful the series are in comparison with numerical computations or regular trajectories. We then examine a H\'{e}non - Heiles system possessing regular trajectories, thus generalizing previous results. Finally, we explore a key issue of physical interest in the context of the de Broglie - Bohm formalism, namely the influence of order in the so-called {\it quantum relaxation} effect. We show that the existence of regular trajectories poses restrictions to the quantum relaxation process, and we give examples in which the relaxation is suppressed even when we consider initial ensembles of only chaotic trajectories, provided, however, that the system as a whole is characterized by a certain degree of order.Comment: 25 pages, 12 figure

Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data

The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar. The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We are most grateful to the Ahmanson Foundation, the Theodore F. and Claire M. Hubbard Family Foundation, the Primate Action Fund / Conservation International, the Margot Marsh Biodiversity Foundation, and the National Geographic Society, for financial assistance