354 research outputs found
miQC : An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a 'low-quality' cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA (mtDNA) encoded genes and (ii) if a small number of genes are detected. Current best practices use these QC metrics independently with either arbitrary, uniform thresholds (e.g. 5%) or biological context-dependent (e.g. species) thresholds, and fail to jointly model these metrics in a data-driven manner. Current practices are often overly stringent and especially untenable on certain types of tissues, such as archived tumor tissues, or tissues associated with mitochondrial function, such as kidney tissue [1]. We propose a data-driven QC metric (miQC) that jointly models both the proportion of reads mapping to mtDNA genes and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses. Our software package is available at https://bioconductor.org/packages/miQC. Author summary We developed the miQC package to predict the low-quality cells in a given scRNA-seq dataset by jointly modeling both the proportion of reads mapping to mitochondrial DNA (mtDNA) genes and the number of detected genes using mixture models in a probabilistic framework. We demonstrate how our QC metric easily adapts to different types of single-cell datasets to remove low-quality cells while preserving high-quality cells that can be used for downstream analyses.Peer reviewe
Loss to follow-up barriers in care for Cornea Ulcers and Glaucoma: A Scoping Review Protocol
To cite data:
Saylor, K., Hicks, PM., Kang, L., Stagg, BC. Newman-Casey, PA., Woodward, MA., Literature search files for Loss to follow-up barriers in care for Cornea Ulcers and Glaucoma: A Scoping Review [Data set]. University of Michigan - Deep Blue.In this scoping review, we sought to understand the barriers, both financial and nonfinancial, to accessing care for treatment of glaucoma and corneal ulcers utilizing Penchansky and Thomas’ five dimensions associated with access to care as a framework. We have chosen both an acute and chronic eye condition to determine if there are barrier differences or similarities between the two conditions. Understanding these barriers can have implications to address these barriers so patients may avoid outcomes of vision-loss and blindness.National Eye Institute (R01EY031033 [MAW]), Research to Prevent Blindness, Career Advancement Award (MAW).The funding sources had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.http://deepblue.lib.umich.edu/bitstream/2027.42/168393/1/LTFCG_Protocol_20210716.pdfDescription of LTFCG_Protocol_20210716.pdf : ProtocolSEL
Measurement of the nuclear multiplicity ratio for hadronization at CLAS
The influence of cold nuclear matter on lepto-production of hadrons in
semi-inclusive deep inelastic scattering is measured using the CLAS detector in
Hall B at Jefferson Lab and a 5.014 GeV electron beam. We report the
multiplicity ratios for targets of C, Fe, and Pb relative to deuterium as a
function of the fractional virtual photon energy transferred to the
and the transverse momentum squared of the . We find that the
multiplicity ratios for are reduced in the nuclear medium at high
and low , with a trend for the transverse momentum to be
broadened in the nucleus for large .Comment: Submitted to Phys. Lett.
Making sense of frailty: An ethnographic study of the experience of older people living with complex health problems
Aim: To explore how older people with complex health problems experience frailty in their daily lives. Background: A better understanding of the personal experience of frailty in the context of fluctuating ill-health has the potential to contribute to the development of personalised approaches to care planning and delivery. Design: An ethnographic study of older people, living at home, receiving support from a community matron service in a large city in the North of England. Methods: Up to six care encounters with each of ten older people, and their community matron, were observed at monthly intervals, over a period of time ranging from four to eleven months. Semi-structured interviews were conducted with the older participants in their own homes. Fieldwork took place over a four-year period. Data analysis was undertaken using the constant comparative method. Findings: The experience of frailty was understood through the construction of four themes: Fluctuating ill-health and the disruption of daily living; Changes to the management of daily living; Frailty as fear, anxiety and uncertainty; Making sense of changes to health and daily living. Conclusions: Older people work hard to shape and maintain daily routines in the context of complicated and enduring transitions in health and illness. However, they experience episodic moments of frailty, often articulated as uncertainty, where daily living becomes precarious and their resilience is threatened. Developing an understanding of the personal experiences of frail older people in the context of transition has the potential to inform nursing practice in person centred care
The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study
The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. A total of 881 women were included (369 breast cancers, 93 nonmalignant cases and 419 population-based controls). The V4 region of the 16S rRNA gene was sequenced from oral and fecal samples. Alpha-diversity (observed amplicon sequence variants [ASVs], Shannon index and Faiths Phylogenetic Diversity) and beta-diversity (Bray-Curtis, Jaccard and weighted and unweighted UniFrac) metrics were computed. MiRKAT and logistic regression models were used to investigate the case-control associations. Oral sample alpha-diversity was inversely associated with breast cancer and nonmalignant breast disease with odds ratios (95% CIs) per every 10 observed ASVs of 0.86 (0.83-0.89) and 0.79 (0.73-0.85), respectively, compared to controls. Beta-diversity was also associated with breast cancer and nonmalignant breast disease compared to controls (P ≤ .001). The relative abundances of Porphyromonas and Fusobacterium were lower for breast cancer cases compared to controls. Alpha-diversity and presence/relative abundance of specific genera from the oral and fecal microbiome were strongly correlated among breast cancer cases, but weakly correlated among controls. Particularly, the relative abundance of oral Porphyromonas was strongly, inversely correlated with fecal Bacteroides among breast cancer cases (r = -.37, P ≤ .001). Many oral microbial metrics were strongly associated with breast cancer and nonmalignant breast disease, and strongly correlated with fecal microbiome among breast cancer cases, but not controls
Chronic non-specific low back pain - sub-groups or a single mechanism?
Copyright 2008 Wand and O'Connell; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Low back pain is a substantial health problem and has subsequently attracted a
considerable amount of research. Clinical trials evaluating the efficacy of a variety of interventions
for chronic non-specific low back pain indicate limited effectiveness for most commonly applied
interventions and approaches.
Discussion: Many clinicians challenge the results of clinical trials as they feel that this lack of
effectiveness is at odds with their clinical experience of managing patients with back pain. A
common explanation for this discrepancy is the perceived heterogeneity of patients with chronic
non-specific low back pain. It is felt that the effects of treatment may be diluted by the application
of a single intervention to a complex, heterogeneous group with diverse treatment needs. This
argument presupposes that current treatment is effective when applied to the correct patient.
An alternative perspective is that the clinical trials are correct and current treatments have limited
efficacy. Preoccupation with sub-grouping may stifle engagement with this view and it is important
that the sub-grouping paradigm is closely examined. This paper argues that there are numerous
problems with the sub-grouping approach and that it may not be an important reason for the
disappointing results of clinical trials. We propose instead that current treatment may be ineffective
because it has been misdirected. Recent evidence that demonstrates changes within the brain in
chronic low back pain sufferers raises the possibility that persistent back pain may be a problem of
cortical reorganisation and degeneration. This perspective offers interesting insights into the
chronic low back pain experience and suggests alternative models of intervention.
Summary: The disappointing results of clinical research are commonly explained by the failure of
researchers to adequately attend to sub-grouping of the chronic non-specific low back pain
population. Alternatively, current approaches may be ineffective and clinicians and researchers may
need to radically rethink the nature of the problem and how it should best be managed
First measurement of direct photoproduction on the proton
We report on the results of the first measurement of exclusive
meson photoproduction on protons for GeV and GeV. Data were collected with the CLAS detector at the Thomas
Jefferson National Accelerator Facility. The resonance was detected via its
decay in the channel by performing a partial wave analysis of the
reaction . Clear evidence of the meson
was found in the interference between and waves at GeV. The -wave differential cross section integrated in the mass range of
the was found to be a factor of 50 smaller than the cross section
for the meson. This is the first time the meson has been
measured in a photoproduction experiment
Photodisintegration of He into p+t
The two-body photodisintegration of He into a proton and a triton has
been studied using the CEBAF Large-Acceptance Spectrometer (CLAS) at Jefferson
Laboratory. Real photons produced with the Hall-B bremsstrahlung-tagging system
in the energy range from 0.35 to 1.55 GeV were incident on a liquid He
target. This is the first measurement of the photodisintegration of He
above 0.4 GeV. The differential cross sections for the He
reaction have been measured as a function of photon-beam energy and
proton-scattering angle, and are compared with the latest model calculations by
J.-M. Laget. At 0.6-1.2 GeV, our data are in good agreement only with the
calculations that include three-body mechanisms, thus confirming their
importance. These results reinforce the conclusion of our previous study of the
three-body breakup of He that demonstrated the great importance of
three-body mechanisms in the energy region 0.5-0.8 GeV .Comment: 13 pages submitted in one tgz file containing 2 tex file and 22
postscrip figure
Light Vector Mesons in the Nuclear Medium
The light vector mesons (, , and ) were produced in
deuterium, carbon, titanium, and iron targets in a search for possible
in-medium modifications to the properties of the meson at normal nuclear
densities and zero temperature. The vector mesons were detected with the CEBAF
Large Acceptance Spectrometer (CLAS) via their decays to . The rare
leptonic decay was chosen to reduce final-state interactions. A combinatorial
background was subtracted from the invariant mass spectra using a
well-established event-mixing technique. The meson mass spectrum was
extracted after the and signals were removed in a nearly
model-independent way. Comparisons were made between the mass spectra
from the heavy targets () with the mass spectrum extracted from the
deuterium target. With respect to the -meson mass, we obtain a small
shift compatible with zero. Also, we measure widths consistent with standard
nuclear many-body effects such as collisional broadening and Fermi motion.Comment: 15 pages, 18 figures, 3 table
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