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Missing hypothesis

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https://www.readbyqxmd.com/read/27913251/unmapped-reads-from-cattle-rnaseq-data-a-source-for-missing-and-misassembled-sequences-in-the-reference-assemblies-and-for-detection-of-pathogens-in-the-host
#1
Tahir Usman, Frieder Hadlich, Wiebke Demasius, Rosemarie Weikard, Christa Kühn
Usually, reads from transcriptome sequencing data unmapped to the target species reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27912000/green-wave-tracking-by-large-herbivores-an-experimental-approach
#2
Inger Maren Rivrud, Marco Heurich, Philipp Krupczynski, Jörg Müller, Atle Mysterud
The forage maturation hypothesis (FMH) states that herbivores should follow the onset of growth in spring to obtain access to forage of higher quality and quantity, the so-called "green wave surfing." Several studies have found correlative evidence in support of this by associating animal movement with plant phenology. However, experimental manipulation of vast natural systems determining causes of large herbivore movement is usually beyond reach. The unique management system involving winter enclosures for wild red deer (Cervus elaphus) in Germany facilitated an opportunity for an experimental approach...
December 2016: Ecology
https://www.readbyqxmd.com/read/27908413/trace-element-and-cytokine-concentrations-in-patients-with-fibrodysplasia-ossificans-progressiva-fop-a-case-control-study
#3
Laura Hildebrand, Timo Gaber, Peter Kühnen, Rolf Morhart, Heinz Unterbörsch, Lutz Schomburg, Petra Seemann
Fibrodysplasia Ossificans Progressiva (FOP) is a rare inherited disease characterized by progressive heterotopic ossification. Disease onset, severity and symptoms vary between FOP patients, as does the frequency and activity of so-called flare-ups, during which tendons, ligaments, muscle and soft tissue are replaced by bone. Traumata, infections or other stressors are known inducers of flare-ups, and the hormone Activin A may be involved in disease activity; however, reliable biomarkers for FOP activity are missing, and the basal trace element and inflammatory state of patients are unknown...
January 2017: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/27896934/increased-identification-of-novel-variants-in-type-2-diabetes-birth-weight-and-their-pleiotropic-loci
#4
Chun-Ping Zeng, Yuan-Cheng Chen, Xu Lin, Jonathan Greenbaum, You-Ping Chen, Cheng Peng, Xia-Fang Wang, Rou Zhou, Wei-Min Deng, Jie Shen, Hong-Wen Deng
BACKGROUND: Clinical and epidemiological findings point to an association between type 2 diabetes (T2D) and low birth weight (BW). However, the nature underlying their relationship is largely unknown. Here, we aim to identify novel single-nucleotide polymorphisms (SNPs) in T2D, BW and their pleiotropic loci. METHODS: We applied a pleiotropy-informed conditional false discovery rate (cFDR) method to two independent GWAS summary statistics of T2D (n = 149,821) and BW (n = 26,836)...
November 29, 2016: Journal of Diabetes
https://www.readbyqxmd.com/read/27886106/multi-target-tracking-using-an-improved-gaussian-mixture-cphd-filter
#5
Weijian Si, Liwei Wang, Zhiyu Qu
The cardinalized probability hypothesis density (CPHD) filter is an alternative approximation to the full multi-target Bayesian filter for tracking multiple targets. However, although the joint propagation of the posterior intensity and cardinality distribution in its recursion allows more reliable estimates of the target number than the PHD filter, the CPHD filter suffers from the spooky effect where there exists arbitrary PHD mass shifting in the presence of missed detections. To address this issue in the Gaussian mixture (GM) implementation of the CPHD filter, this paper presents an improved GM-CPHD filter, which incorporates a weight redistribution scheme into the filtering process to modify the updated weights of the Gaussian components when missed detections occur...
November 23, 2016: Sensors
https://www.readbyqxmd.com/read/27875982/comparative-genomics-to-explore-phylogenetic-relationship-cryptic-sexual-potential-and-host-specificity-of-rhynchosporium-species-on-grasses
#6
Daniel Penselin, Martin Münsterkötter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H Paskiewicz, Richard J Harrison, David J Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Wöltje, Kevin M King, Bruce D L Fitt, Ulrich Güldener, Anna Avrova, Wolfgang Knogge
BACKGROUND: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27869159/fundamental-scaling-laws-in-nanophotonics
#7
Ke Liu, Shuai Sun, Arka Majumdar, Volker J Sorger
The success of information technology has clearly demonstrated that miniaturization often leads to unprecedented performance, and unanticipated applications. This hypothesis of "smaller-is-better" has motivated optical engineers to build various nanophotonic devices, although an understanding leading to fundamental scaling behavior for this new class of devices is missing. Here we analyze scaling laws for optoelectronic devices operating at micro and nanometer length-scale. We show that optoelectronic device performance scales non-monotonically with device length due to the various device tradeoffs, and analyze how both optical and electrical constrains influence device power consumption and operating speed...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27867079/variability-in-diagnostic-error-rates-of-ten-mri-centers-performing-lumbar-spine-mri-exams-on-the-same-patient-within-a-three-week-period
#8
Richard Herzog, Daniel R Elgort, Adam E Flanders, Peter J Moley
BACKGROUND CONTEXT: In today's healthcare climate, Magnetic Resonance Imaging (MRI) is often perceived as a commodity - a service where there are no meaningful differences in quality and thus an area in which patients can be advised to select a provider based on price and convenience alone. If this prevailing view is correct, then a patient should expect to receive the same radiological diagnosis regardless of which imaging center he or she visits or which radiologist reviews the examination...
November 17, 2016: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/27866307/explicating-the-conditions-under-which-multilevel-multiple-imputation-mitigates-bias-resulting-from-random-coefficient-dependent-missing-longitudinal-data
#9
Nisha C Gottfredson, Sonya K Sterba, Kristina M Jackson
Random coefficient-dependent (RCD) missingness is a non-ignorable mechanism through which missing data can arise in longitudinal designs. RCD, for which we cannot test, is a problematic form of missingness that occurs if subject-specific random effects correlate with propensity for missingness or dropout. Particularly when covariate missingness is a problem, investigators typically handle missing longitudinal data by using single-level multiple imputation procedures implemented with long-format data, which ignores within-person dependency entirely, or implemented with wide-format (i...
November 19, 2016: Prevention Science: the Official Journal of the Society for Prevention Research
https://www.readbyqxmd.com/read/27860510/the-case-of-the-missing-ancient-fungal-polyploids
#10
Matthew A Campbell, Austen R D Ganley, Toni Gabaldón, Murray P Cox
Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events...
December 2016: American Naturalist
https://www.readbyqxmd.com/read/27857709/genotyping-by-pcr-and-high-throughput-sequencing-of-commercial-probiotic-products-reveals-composition-biases
#11
Wesley Morovic, Ashley A Hibberd, Bryan Zabel, Rodolphe Barrangou, Buffy Stahl
Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation "well defined strains," encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27856741/universal-screening-increases-the-representation-of-low-income-and-minority-students-in-gifted-education
#12
David Card, Laura Giuliano
Low-income and minority students are substantially underrepresented in gifted education programs. The disparities persist despite efforts by many states and school districts to broaden participation through changes in their eligibility criteria. One explanation for the persistent gap is that standard processes for identifying gifted students, which are based largely on the referrals of parents and teachers, tend to miss qualified students from underrepresented groups. We study this hypothesis using the experiences of a large urban school district following the introduction of a universal screening program for second graders...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27856446/improving-estimates-of-numbers-of-children-with-severe-acute-malnutrition-using-cohort-and-survey-data
#13
Sheila Isanaka, Ellen O'Neal Boundy, Rebecca F Grais, Mark Myatt, André Briend
Severe acute malnutrition (SAM) is reported to affect 19 million children worldwide. However, this estimate is based on prevalence data from cross-sectional surveys and can be expected to miss some children affected by an acute condition such as SAM. The burden of acute conditions is more appropriately represented by cumulative incidence data. In the absence of incidence data, a method for burden estimation has been proposed that corrects available prevalence estimates to account for incident cases using an "incidence correction factor...
November 17, 2016: American Journal of Epidemiology
https://www.readbyqxmd.com/read/27826276/low-arousing-positive-affect-broadens-visual-attention-and-alters-the-thought-action-repertoire-while-broadened-visual-attention-does-not
#14
Daniel T Jäger, Jascha Rüsseler
The Broaden-and-Build Theory states that positive emotions broaden cognition and therefore build personal resources. However, missing theoretical precision regarding the interaction of the cognitive processes involved offers a variety of possible explanations for the mechanisms of broadening and building. In Experiment 1 we tested the causality assumption which states that positive emotions first broaden visual attention which in turn leads to broadened cognition. We examined the effects of a broadened, narrowed or neutral attentional scope of 72 subjects (30 men) on their momentary thought-action repertoire...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27798129/magnetic-fields-modulate-blue-light-dependent-regulation-of-neuronal-firing-by-cryptochrome
#15
Carlo N G Giachello, Nigel S Scrutton, Alex R Jones, Richard A Baines
: Many animals are able to sense the Earth's geomagnetic field to enable behaviors such as migration. It is proposed that the magnitude and direction of the geomagnetic field modulates the activity of cryptochrome (CRY) by influencing photochemical radical pair intermediates within the protein. However, this proposal will remain theoretical until a CRY-dependent effect on a receptor neuron is shown to be modified by an external magnetic field (MF). It is established that blue-light (BL) photoactivation of CRY is sufficient to depolarize and activate Drosophila neurons...
October 19, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27793347/the-mammalian-skeletal-muscle-dhpr-has-larger-ca-2-conductance-and-is-phylogenetically-ancient-to-the-early-ray-finned-fish-sterlet-acipenser-ruthenus
#16
Kai Schrötter, Anamika Dayal, Manfred Grabner
The L-type Ca(2+) channel or dihydropyridine receptor (DHPR) in vertebrate skeletal muscle is responsible for sensing sarcolemmal depolarizations and transducing this signal to the sarcoplasmic Ca(2+) release channel RyR1 via conformational coupling to initiate muscle contraction. During this excitation-contraction (EC) coupling process there is a slow Ca(2+) current through the mammalian DHPR which is fully missing in euteleost fishes. In contrast to ancestral evolutionary stages where skeletal muscle EC coupling is still depended on Ca(2+)-induced Ca(2+)-release (CICR), it is possible that the DHPR Ca(2+) conductivity during mammalian (conformational) EC coupling was retained as an evolutionary remnant (vestigiality)...
October 23, 2016: Cell Calcium
https://www.readbyqxmd.com/read/27789325/timing-and-host-plant-associations-in-the-evolution-of-the-weevil-tribe-apionini-apioninae-brentidae-curculionoidea-coleoptera-indicate-an-ancient-co-diversification-pattern-of-beetles-and-flowering-plants
#17
Sven Winter, Ariel L L Friedman, Jonas J Astrin, Brigitte Gottsberger, Harald Letsch
Host plant shifts of insects can lead to a burst of diversification driven by their arrival in a new adaptive zone. In this context, our study aims to explore timing and patterns in the evolution of the weevil tribe Apionini (Brentidae, Curculionoidea, Coleoptera), particularly in relation to affiliations with their host plants. The classification of Apionini is difficult because of their relatively uniform appearance. Most taxa live mono- or oligophagously on members of Asteraceae or Fabaceae, but many are associated with other plant families, like Lamiaceae, Malvaceae and Polygonaceae...
October 24, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27788953/prospective-validation-of-a-high-dimensional-shape-model-for-organ-motion-in-intact-cervical-cancer
#18
Casey W Williamson, Garrett Green, Sonal S Noticewala, Nan Li, Hanjie Shen, Florin Vaida, Loren K Mell
PURPOSE: Validated models are needed to justify strategies to define planning target volumes (PTVs) for intact cervical cancer used in clinical practice. Our objective was to independently validate a previously published shape model, using data collected prospectively from clinical trials. METHODS AND MATERIALS: We analyzed 42 patients with intact cervical cancer treated with daily fractionated pelvic intensity modulated radiation therapy and concurrent chemotherapy in one of 2 prospective clinical trials...
November 15, 2016: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/27777086/interdomain-interactions-rearrangements-control-the-reaction-steps-of-a-thermostable-dna-alkyltransferase
#19
Castrese Morrone, Riccardo Miggiano, Mario Serpe, Alberto Massarotti, Anna Valenti, Giovanni Del Monaco, Mosè Rossi, Franca Rossi, Menico Rizzi, Giuseppe Perugino, Maria Ciaramella
BACKGROUND: Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs...
October 22, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27774567/mice-haploinsufficient-for-map2k7-a-gene-involved-in-neurodevelopment-and-risk-for-schizophrenia-show-impaired-attention-a-vigilance-decrement-deficit-and-unstable-cognitive-processing-in-an-attentional-task-impact-of-minocycline
#20
R L Openshaw, D M Thomson, J M Penninger, J A Pratt, B J Morris
RATIONALE: Members of the c-Jun N-terminal kinase (JNK) family of mitogen-activated protein (MAP) kinases, and the upstream kinase MKK7, have all been strongly linked with synaptic plasticity and with the development of the neocortex. However, the impact of disruption of this pathway on cognitive function is unclear. OBJECTIVE: In the current study, we test the hypothesis that reduced MKK7 expression is sufficient to cause cognitive impairment. METHODS: Attentional function in mice haploinsufficient for Map2k7 (Map2k7 (+/-) mice) was investigated using the five-choice serial reaction time task (5-CSRTT)...
October 24, 2016: Psychopharmacology
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