149 research outputs found
Standardization of Monofilament use in a Resident-Run Clinic
Study Aim:
The aim of this study was to improve incidence of regular foot exams among clinic diabetic patients.https://jdc.jefferson.edu/patientsafetyposters/1040/thumbnail.jp
Maintaining Continuity in a resident run clinic-Impact of the 6+2 Scheduling.
Objective:
The aim of this study was to evaluate the continuity of care with regards to follow up with the same team (and optimally same resident) 1 year prior to implementing the 6+2 scheduling block and 1 year post schedule block change.https://jdc.jefferson.edu/patientsafetyposters/1039/thumbnail.jp
Population Health and Complexity Science: A Leadership Primer
Objectives
1) Describe the current state of health outcomes2) Define complexity science3) Describe healthcare as a complex adaptive system4) Introduce implementation science5) Describe the Cynefin framework for decision makin
Survival Probability for the Stadium Billiard
We consider the open stadium billiard, consisting of two semicircles joined
by parallel straight sides with one hole situated somewhere on one of the
sides. Due to the hyperbolic nature of the stadium billiard, the initial decay
of trajectories, due to loss through the hole, appears exponential. However,
some trajectories (bouncing ball orbits) persist and survive for long times and
therefore form the main contribution to the survival probability function at
long times. Using both numerical and analytical methods, we concur with
previous studies that the long-time survival probability for a reasonably small
hole drops like Constant/time; here we obtain an explicit expression for the
Constant.Comment: 13 pages, 6 figure
Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes
Empirical substitution matrices represent the average tendencies of
substitutions over various protein families by sacrificing gene-level
resolution. We develop a codon-based model, in which mutational tendencies of
codon, a genetic code, and the strength of selective constraints against amino
acid replacements can be tailored to a given gene. First, selective constraints
averaged over proteins are estimated by maximizing the likelihood of each 1-PAM
matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution
matrices. Then, selective constraints specific to given proteins are
approximated as a linear function of those estimated from the empirical
substitution matrices.
Akaike information criterion (AIC) values indicate that a model allowing
multiple nucleotide changes fits the empirical substitution matrices
significantly better. Also, the ML estimates of transition-transversion bias
obtained from these empirical matrices are not so large as previously
estimated. The selective constraints are characteristic of proteins rather than
species. However, their relative strengths among amino acid pairs can be
approximated not to depend very much on protein families but amino acid pairs,
because the present model, in which selective constraints are approximated to
be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can
provide a good fit to other empirical substitution matrices including cpREV for
chloroplast proteins and mtREV for vertebrate mitochondrial proteins.
The present codon-based model with the ML estimates of selective constraints
and with adjustable mutation rates of nucleotide would be useful as a simple
substitution model in ML and Bayesian inferences of molecular phylogenetic
trees, and enables us to obtain biologically meaningful information at both
nucleotide and amino acid levels from codon and protein sequences.Comment: Table 9 in this article includes corrections for errata in the Table
9 published in 10.1371/journal.pone.0017244. Supporting information is
attached at the end of the article, and a computer-readable dataset of the ML
estimates of selective constraints is available from
10.1371/journal.pone.001724
Mass and Hot Baryons in Massive Galaxy Clusters from Subaru Weak Lensing and AMiBA SZE Observations
We present a multiwavelength analysis of a sample of four hot (T_X>8keV)
X-ray galaxy clusters (A1689, A2261, A2142, and A2390) using joint AMiBA
Sunyaev-Zel'dovich effect (SZE) and Subaru weak lensing observations, combined
with published X-ray temperatures, to examine the distribution of mass and the
intracluster medium (ICM) in massive cluster environments. Our observations
show that A2261 is very similar to A1689 in terms of lensing properties. Many
tangential arcs are visible around A2261, with an effective Einstein radius
\sim 40 arcsec (at z \sim 1.5), which when combined with our weak lensing
measurements implies a mass profile well fitted by an NFW model with a high
concentration c_{vir} \sim 10, similar to A1689 and to other massive clusters.
The cluster A2142 shows complex mass substructure, and displays a shallower
profile (c_{vir} \sim 5), consistent with detailed X-ray observations which
imply recent interaction. The AMiBA map of A2142 exhibits an SZE feature
associated with mass substructure lying ahead of the sharp north-west edge of
the X-ray core suggesting a pressure increase in the ICM. For A2390 we obtain
highly elliptical mass and ICM distributions at all radii, consistent with
other X-ray and strong lensing work. Our cluster gas fraction measurements,
free from the hydrostatic equilibrium assumption, are overall in good agreement
with published X-ray and SZE observations, with the sample-averaged gas
fraction of = 0.133 \pm 0.027, for our sample = (1.2 \pm
0.1) \times 10^{15} M_{sun} h^{-1}. When compared to the cosmic baryon fraction
f_b = \Omega_b/\Omega_m constrained by the WMAP 5-year data, this indicates
/f_b = 0.78 \pm 0.16, i.e., (22 \pm 16)% of the baryons are missing
from the hot phase of clusters.Comment: accepted for publication in ApJ; high resolution figures available at
http://www.asiaa.sinica.edu.tw/~keiichi/upfiles/AMiBA7/ms_highreso.pd
Subthreshold psychosis in 22q11.2 deletion syndrome: multisite naturalistic study
Nearly one-third of individuals with 22q11.2 deletion syndrome (22q11.2DS) develop a psychotic disorder during life, most of them by early adulthood. Importantly, a full-blown psychotic episode is usually preceded by subthreshold symptoms. In the current study, 760 participants (aged 6-55 years) with a confirmed hemizygous 22q11.2 microdeletion have been recruited through 10 medical sites worldwide, as part of an international research consortium. Of them, 692 were nonpsychotic and with complete measurement data. Subthreshold psychotic symptoms were assessed using the Structured Interview for Prodromal Syndromes (SIPS). Nearly one-third of participants met criteria for positive subthreshold psychotic symptoms (32.8%), less than 1% qualified for acute positive subthreshold symptoms, and almost a quarter met criteria for negative/disorganized subthreshold symptoms (21.7%). Adolescents and young adults (13-25 years) showed the highest rates of subthreshold psychotic symptoms. Additionally, higher rates of anxiety disorders and attention deficit/hyperactivity disorder (ADHD) were found among the study participants with subthreshold psychotic symptoms compared to those without. Full-scale IQ, verbal IQ, and global functioning (GAF) scores were negatively associated with participants' subthreshold psychotic symptoms. This study represents the most comprehensive analysis reported to date on subthreshold psychosis in 22q11.2DS. Novel findings include age-related changes in subthreshold psychotic symptoms and evidence that cognitive deficits are associated with subthreshold psychosis in this population. Future studies should longitudinally follow these symptoms to detect whether and how early identification and treatment of these manifestations can improve long-term outcomes in those that eventually develop a psychotic disorder
Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences
A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated.The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that assuming variable mutation rates over sites lead to the overestimation of branch lengths
The Druze: A Population Genetic Refugium of the Near East
BACKGROUND: Phylogenetic mitochondrial DNA haplogroups are highly partitioned across global geographic regions. A unique exception is the X haplogroup, which has a widespread global distribution without major regions of distinct localization. PRINCIPAL FINDINGS: We have examined mitochondrial DNA sequence variation together with Y-chromosome-based haplogroup structure among the Druze, a religious minority with a unique socio-demographic history residing in the Near East. We observed a striking overall pattern of heterogeneous parental origins, consistent with Druze oral tradition, together with both a high frequency and a high diversity of the mitochondrial DNA (mtDNA) X haplogroup within a confined regional subpopulation. Furthermore demographic modeling indicated low migration rates with nearby populations. CONCLUSIONS: These findings were enabled through the use of a paternal kindred based sampling approach, and suggest that the Galilee Druze represent a population isolate, and that the combination of a high frequency and diversity of the mtDNA X haplogroup signifies a phylogenetic refugium, providing a sample snapshot of the genetic landscape of the Near East prior to the modern age
Enhanced Maternal Origin of the 22q11.2 Deletion in Velocardiofacial and DiGeorge Syndromes
Velocardiofacial and DiGeorge syndromes, also known as 22q11.2 deletion syndrome (22q11DS), are congenital-anomaly disorders caused by a de novo hemizygous 22q11.2 deletion mediated by meiotic nonallelic homologous recombination events between low-copy repeats, also known as segmental duplications. Although previous studies exist, each was of small size, and it remains to be determined whether there are parent-of-origin biases for the de novo 22q11.2 deletion. To address this question, we genotyped a total of 389 DNA samples from 22q11DS-affected families. A total of 219 (56%) individuals with 22q11DS had maternal origin and 170 (44%) had paternal origin of the de novo deletion, which represents a statistically significant bias for maternal origin (p = 0.0151). Combined with many smaller, previous studies, 465 (57%) individuals had maternal origin and 345 (43%) had paternal origin, amounting to a ratio of 1.35 or a 35% increase in maternal compared to paternal origin (p = 0.000028). Among 1,892 probands with the de novo 22q11.2 deletion, the average maternal age at time of conception was 29.5, and this is similar to data for the general population in individual countries. Of interest, the female recombination rate in the 22q11.2 region was about 1.6–1.7 times greater than that for males, suggesting that for this region in the genome, enhanced meiotic recombination rates, as well as other as-of-yet undefined 22q11.2-specific features, could be responsible for the observed excess in maternal origin
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