Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic importance of pulmonary interleukin-1β and interleukin-8 in ventilator-associated pneumonia

Background Ventilator-associated pneumonia (VAP) is the most commonly fatal nosocomial infection. Clinical diagnosis of VAP remains notoriously inaccurate. The hypothesis was tested that significantly augmented inflammatory markers distinguish VAP from conditions closely mimicking VAP. Methods A prospective, observational cohort study was carried out in two university hospital intensive care units recruiting 73 patients with clinically suspected VAP, and a semi-urban primary care practice recruiting a reference group of 21 age- and sex-matched volunteers. Growth of pathogens at >104 colony-forming units (cfu)/ml of bronchoalveolar lavage fluid (BALF) distinguished VAP from “non-VAP”. Inflammatory mediators were quantified in BALF and serum. Mediators showing significant differences between patients with and without VAP were analysed for diagnostic utility by receiver operator characteristic (ROC) curves. Results Seventy-two patients had recoverable lavage—24% had VAP. BALF interleukin-1β (IL-1β), IL-8, granulocyte colony-stimulating factor and macrophage inflammatory protein-1α were significantly higher in the VAP group (all p<0.005). Using a cut-off of 10 pg/ml, BALF IL-1β generated negative likelihood ratios for VAP of 0.09. In patients with BALF IL-1β <10 pg/ml the post-test probability of VAP was 2.8%. Using a cut-off value for IL-8 of 2 ng/ml, the positive likelihood ratio was 5.03. There was no difference in cytokine levels between patients with sterile BALF and those with growth of <104 cfu/ml. Conclusions BALF IL-1β and IL-8 are amongst the strongest markers yet identified for accurately demarcating VAP within the larger population of patients with suspected VAP. These findings have potential implications for reduction in unnecessary antibiotic use but require further validation in larger populations.
Characterizing discourse deficits following penetrating head injury: a preliminary model.

PURPOSE Discourse analyses have demonstrated utility for delineating subtle communication deficits following closed head injuries (CHIs). The present investigation examined the discourse performance of a large group of individuals with penetrating head injury (PHI). Performance was also compared across 6 subgroups of PHI based on lesion locale. A preliminary model of discourse production following PHI was proposed and tested. METHOD Story narratives were elicited from 2 groups of participants, 167 with PHI and 46 non brain-injured (NBI). Micro- and macrostructural components of each story were analyzed. Measures of memory, executive functions, and intelligence were also administered. All measures were compared across groups and PHI subgroups. The proposed model of discourse production was tested with a structural equation modeling procedure. RESULTS No differences for the discourse measures were noted across the six PHI subgroups. Three measures distinguished the PHI and NBI groups: narrative length, story grammar, and completeness. The proposed model of discourse production had an adequate-to-good fit with the cognitive and discourse data. CONCLUSION In spite of differing mechanisms of injury, the PHI group's discourse performance was consistent with what has been reported for individuals with CHI. The model tested represents a preliminary step toward understanding discourse production following traumatic brain injury.
Where Do You Feel Safest? Demographic Factors and Place of Birth

Introduction: The vast majority of planned out‐of‐hospital births in the United States occur among white women; no study has addressed whether black women prefer out‐of‐hospital birth less or whether this racial disparity is due to other causes such as constrained access. This study sought to answer the question of whether white and black women feel safest giving birth in out‐of‐hospital settings at different rates and whether this answer is associated with other socioeconomic indicators. Methods: An interview of 634 nulliparous women during the third trimester of their pregnancy in Michigan provided data regarding where women felt safest giving birth. Feeling safest giving birth out‐of‐hospital was examined in relation to socioeconomic factors including race, age, household income, education, residence in a high‐crime neighborhood, partnered status, and type of insurance. Results: This study found that black and white women say they feel safest giving birth in out‐of‐hospital settings at similar rates (11.5% and 13.1%, respectively). Logistic regression results showed that poverty and having education beyond high school were the only sociodemographic indicators significantly associated with feeling safest giving birth out‐of‐hospital. Discussion: Disparities evident in planned home birth and birth center rates cannot be explained by racial differences in feelings toward out‐of‐hospital birth and should be addressed more specifically in public policy and future studies.
Protein Kinase C Enables the Regulatory Circuit That Connects Membrane Synthesis to Ribosome Synthesis in Saccharomyces cerevisiae *

The balanced growth of a cell requires the integration of major systems such as DNA replication, membrane biosynthesis, and ribosome formation. An example of such integration is evident from our recent finding that, in Saccharomyces cerevisiae, any failure in the secretory pathway leads to severe repression of transcription of both rRNA and ribosomal protein genes. We have attempted to determine the regulatory circuit(s) that connects the secretory pathway with the transcription of ribosomal genes. Experiments show that repression does not occur through the circuit that responds to misfolded proteins in the endoplasmic reticulum, nor does it occur through circuits known to regulate ribosome synthesis,e.g. the stringent response, or the cAMP pathway. Rather, it appears to depend on a stress response at the plasma membrane that is transduced through protein kinase C (PKC). Deletion ofPKC1 relieves the repression of both ribosomal protein and rRNA genes that occurs in response to a defect in the secretory pathway. We propose that failure of the secretory pathway prevents the synthesis of new plasma membrane. As protein synthesis continues, stress develops in the plasma membrane. This stress is monitored by Pkc1p, which initiates a signal transduction pathway that leads to repression of transcription of the rRNA and ribosomal protein genes. The importance of the transcription of the 137 ribosomal protein genes to the economy of the cell is apparent from the existence of at least three distinct pathways that can effect the repression of this set of genes.
The effect of laser treatment on skin to enhance and control transdermal delivery of 5-fluorouracil.

The effect of three lasers (i.e., the ruby, erbium:YAG, and CO2) on the ability to enhance and control skin permeation of 5-fluorouracil (5-FU) was studied in vitro. Light microscopic and ultrastructural (scanning electron microscopic) changes in the nude mouse skin were also compared for these lasers. The histological observations and permeation profiles of each laser differed because the three lasers produce different physical and physiologic effects when striking the skin. The skin permeation of 5-FU could be moderately promoted by a single photomechanical wave generated by the ruby laser (at 4.0 and 7.0 J/cm(2)) without adversely affecting the viability or structure of the skin. The stratum corneum (SC) layer in the skin was partly ablated by an erbium:YAG laser, resulting in a greater enhancement effect on skin permeation of 5-FU. The flux of 5-FU across erbium:YAG laser-treated skin was 53-133-fold higher than that across intact skin. Both SC ablation and a thermal effect may contribute to the effect of the CO2 laser on skin structure. Lower energies of the CO2 laser did not modulate 5-FU permeation. A 36-41-fold increase in 5-FU flux was observed after exposure to higher fluences (4.0 and 7.0 J/cm(2)) of the CO2 laser. Histological changes induced by both the erbium:YAG and CO2 lasers had completely recovered within 4 days.
A strategy for achieving low percolation and high electrical conductivity in melt-blended polycarbonate (PC)/multiwall carbon nanotube (MWCNT) nanocomposites: Electrical and thermo-mechanical properties

In this work, polycarbonate (PC)/multiwall carbon nanotube (MWCNT) nanocomposites were prepared by sim- ple melt mixing at a temperature (~350°C) well above the processing temperature of PC, followed by compression mold- ing, that exhibited percolation threshold as low as of 0.11 wt% and high electrical conductivity of 1.38! 10 -3 S·cm -1 at only 0.5 wt% MWCNT loading. Due to the lower interfacial energy between MWCNT and PC, the carbon nanotubes are excel- lently dispersed and formed continuous conductive network structure throughout the host polymer. AC electrical conductiv- ity and dielectric permittivity of PC/MWCNT nanocomposites were characterized in a broad frequency range, 10 1 -10 7 Hz. Low percolation threshold (pc) of 0.11 wt% and the critical exponent (t) of ~3.38 was resulted from scaling law equation. The linear plot of log! DC vs. p -1/3 supported the presence of tunneling conduction among MWCNTs. The thermal property and storage modulus of PC were increased with the incorporation of little amount of MWCNTs. Transmission electron microscopy (TEM) and field emission scanning electron microscopy (FESEM) confirmed the homogeneous dispersion and distribution of MWCNTs throughout the matrix phase.
Student-Retention and Career-Placement Rates Between Bachelor's and Master's Degree Professional Athletic Training Programs.

CONTEXT The debate over what the entry-level degree should be for athletic training has heightened. A comparison of retention and career-placement rates between bachelor's and master's degree professional athletic training programs may inform the debate. OBJECTIVE To compare the retention rates and career-placement rates of students in bachelor's and master's degree professional programs. DESIGN Cross-sectional study. SETTING Web-based survey. PATIENTS OR OTHER PARTICIPANTS A total of 192 program directors (PDs) from bachelor's degree (n = 177) and master's degree (n = 15) professional programs. INTERVENTION(S) The PDs completed a Web-based survey. MAIN OUTCOME MEASURE(S) We instructed the PDs to provide a retention rate and career-placement rate for the students in the programs they lead for each of the past 5 years. We also asked the PDs if they thought retention of students was a problem currently facing athletic training education. We used independent t tests to compare the responses between bachelor's and master's degree professional programs. RESULTS We found a higher retention rate for professional master's degree students (88.70% ± 9.02%, 95% confidence interval [CI] = 83.71, 93.69) than bachelor's degree students (80.98% ± 17.86%, 95% CI = 78.30, 83.66) (t25 = -2.86, P = .008, d = 0.55). Similarly, PDs from professional master's degree programs reported higher career-placement percentages (88.50% ± 10.68%, 95% CI = 82.33, 94.67) than bachelor's degree professional PDs (71.32% ± 18.47%, 95% CI = 68.54, 74.10) (t20 = -5.40, P < .001, d = 1.14). Finally, we observed no difference between groups regarding whether retention is a problem facing athletic training (χ(2)1 = 0.720, P = . 40, Φ = . 061). CONCLUSIONS Professional master's degree education appears to facilitate higher retention rates and greater career-placement rates in athletic training than bachelor's degree education. Professional socialization, program selectivity, and student commitment and motivation levels may help to explain the differences noted.
Comparative morphology of porpoise (Cetacea: Phocoenidae) pterygoid sinuses: Phylogenetic and functional implications

High‐resolution X‐ray computed tomographic scans were used to examine pterygoid sinus morphology within extant porpoise species and one delphinid (Tursiops truncatus), in order to consider: 1) intraspecific and interspecific variation among the studied species; 2) the most parsimonious sequence of character acquisition; and 3) the potential functional roles of the preorbital lobes of the sinuses in sound reflection. Scans revealed that the pterygoid/palatine regions are mediolaterally broader in the earliest diverging phocoenid (Neophocaena phocaenoides) and Tursiops truncatus than the dorsoventrally elongated sinuses observed in other species. Rostrocaudal lengths of the sphenoidal regions of the sinuses in all individuals studied are proportionally similar, indicating conservatism in this region across species. The neonate Phocoena phocoena has shorter preorbital lobes than adults, but they are still proportionally longer than Neophocaena phocaenoides and Phocoena spinipinnis. The preorbital lobes broaden mediolaterally to varying degrees across species; in particular, Phocoenoides dalli has the largest dorsal and lateral expansion of this region. Assuming the highest pulse frequency produced by porpoises is 150 kHz, all regions of the preorbital lobes are thick enough to reflect the wavelengths produced. In addition, the neonate preorbital lobes are not as elongated as they are in adults, and the dorsal third of this region may not reflect sound to the same extent. This study reinforces the importance of using nondestructive methods to quantify variation in endocranial anatomy and the value of CT data for recovering phylogenetically useful information, as well as functional roles sinuses play in concert with the soft tissue head anatomy for biosonar. J. Morphol. 2013. © 2012 Wiley Periodicals, Inc.
The tilt cursor: enhancing stimulus-response compatibility by providing 3d orientation cue of pen

In order to improve stimulus-response compatibility of touchpad in pen-based user interface, we present the tilt cursor, i.e. a cursor dynamically reshapes itself to providing the 3D orientation cue of pen. We also present two experiments that evaluate the tilt cursor's performance in circular menu selection and specific marking menu selection tasks. Results show that in a specific marking menu selection task, the tilt cursor significantly outperforms the shape-fixed arrow cursor and the live cursor [4]. In addition, results show that by using the tilt cursor, the response latencies for adjusting drawing directions are smaller than that by using the other two kinds of cursors.
Distinct Impacts of Eda and Edar Loss of Function on the Mouse Dentition

Background The Eda-A1-Edar signaling pathway is involved in the development of organs with an ectodermal origin, including teeth. In mouse, mutants are known for both the ligand, Eda-A1 (Tabby), and the receptor, Edar (Downless). The adult dentitions of these two mutants have classically been considered to be similar. However, previous studies mentioned differences in embryonic dental development between Eda Ta and Edar dl-J mutants. A detailed study of tooth morphology in mutants bearing losses of functions of these two genes thus appears necessary to test the pattern variability induced by the developmental modifications. Methodology/Principal Findings 3D-reconstructions of the cheek teeth have been performed at the ESRF (Grenoble, France) by X-ray synchrotron microtomography to assess dental morphology. The morphological variability observed in Eda Ta and Edar dl-J mutants have then been compared in detail. Despite patchy similarities, our detailed work on cheek teeth in Eda Ta and Edar dl-J mice show that all dental morphotypes defined in Edar dl-J mice resolutely differ from those of Eda Ta mice. This study reveals that losses of function of Eda and Edar have distinct impacts on the tooth size and morphology, contrary to what has previously been thought. Conclusion/Signifiance The results indicate that unknown mechanisms of the Eda pathway are implicated in tooth morphogenesis. Three hypotheses could explain our results; an unexpected role of the Xedar pathway (which is influenced by the Eda gene product but not that of Edar), a more complex connection than has been appreciated between Edar and another protein, or a ligand-independent activity for Edar. Further work is necessary to test these hypotheses and improve our understanding of the mechanisms of development.
Many-body aspects of approach to equilibrium

Kinetic theory and approach to equilibrium is usually studied in the realm of the Boltzmann equation. With a few notable exceptions not much is known about the solutions of this equation and about its derivation from fundamental principles. In 1956 Mark Kac introduced a probabilistic model ofN interacting particles. The velocity distribution is governed by a Markov semi group and the evolution of its single particle marginals is governed (in the infinite particle limit) by a caricature of the spatially homogeneous Boltzmann equation. In joint work with Eric Carlen and Maria Carvalho we compute the gap of the generator of this Markov semigroup and show that the best possible rate of approach to equilibrium in the Kac model is precisely the one predicted by the linearized Boltzmann equation. Similar, but less precise results hold for Maxwellian molecules.
Automated alphabet reduction method with evolutionary algorithms for protein structure prediction

This paper focuses on automated procedures to reduce the dimensionality ofprotein structure prediction datasets by simplifying the way in which the primary sequence of a protein is represented. The potential benefits ofthis procedure are faster and easier learning process as well as the generationof more compact and human-readable classifiers.The dimensionality reduction procedure we propose consists on the reductionof the 20-letter amino acid (AA) alphabet, which is normally used to specify a protein sequence, into a lower cardinality alphabet. This reduction comes about by a clustering of AA types accordingly to their physical and chemical similarity. Our automated reduction procedure is guided by a fitness function based on the Mutual Information between the AA-based input attributes of the dataset and the protein structure featurethat being predicted. To search for the optimal reduction, the Extended Compact Genetic Algorithm (ECGA) was used, and afterwards the results of this process were fed into (and validated by) BioHEL, a genetics-based machine learningtechnique. BioHEL used the reduced alphabet to induce rules forprotein structure prediction features. BioHEL results are compared to two standard machine learning systems. Our results show that it is possible to reduce the size of the alphabet used for prediction fromtwenty to just three letters resulting in more compact, i.e. interpretable,rules. Also, a protein-wise accuracy performance measure suggests that the loss of accuracy acrued by this substantial alphabet reduction is not statistically significant when compared to the full alphabet.
The Potential Role of Metalloproteinases in Neurogenesis in the Gerbil Hippocampus Following Global Forebrain Ischemia

Background Matrix metalloproteinases (MMPs) have recently been considered to be involved in the neurogenic response of adult neural stem/progenitor cells. However, there is a lack of information showing direct association between the activation of MMPs and the development of neuronal progenitor cells involving proliferation and/or further differentiation in vulnerable (Cornus Ammoni-CA1) and resistant (dentate gyrus-DG) to ischemic injury areas of the brain hippocampus. Principal Findings We showed that dynamics of MMPs activation in the dentate gyrus correlated closely with the rate of proliferation and differentiation of progenitor cells into mature neurons. In contrast, in the damaged CA1 pyramidal cells layer, despite the fact that some proliferating cells exhibited antigen specific characteristic of newborn neuronal cells, these did not attain maturity. This coincides with the low, near control-level, activity of MMPs. The above results are supported by our in vitro study showing that MMP inhibitors interfered with both the proliferation and differentiation of the human neural stem cell line derived from umbilical cord blood (HUCB-NSCs) toward the neuronal lineage. Conclusion Taken together, the spatial and temporal profiles of MMPs activity suggest that these proteinases could be an important component in neurogenesis-associated processes in post-ischemic brain hippocampus.
Design Exploration and Analysis of Carbon-Infiltrated Carbon Nanotube Vascular Stents

Design Exploration and Analysis of Carbon-Infiltrated Carbon Nanotube Vascular Stents Darrell J. Skousen Department of Mechanical Engineering, BYU Master of Science The purpose of this research was to design, develop, and test coronary stent designs composed of carbon-infiltrated carbon nanotubes (CI-CNTs). Coronary stents currently have two major complications: restenosis and thrombosis. CI-CNT stents have potential to address both of these issues, and therefore may provide improved clinical outcomes. CI-CNT stent geometry is patterned using high-resolution photolithography that provide advantages in design possibilities. To develop a coronary stent, a standard design process was followed including: background, design specifications, concept generation, development, analysis, and testing. Background research was first completed and general design specifications for coronary stent performance were compiled. Multiple design concepts were generated, evaluated, and finally a design was selected. This stent design was further developed and optimized using analytical tools along with finite element analysis. This stent design used tapered struts in repeating segments to reduce stress and improve radial force. The design was modeled and analyzed as both a flat geometry as well as in a cylindrical configuration. Mechanics of materials equations and geometry specific finite element analysis were used to guide the final coronary stent design. The stent design was tested mechanically, and additional tests were performed to verify the blood compatibility of the CI-CNT material. The flat version of the stent design was manufactured and mechanically tested to verify performance. The performance of the cylindrical stent configuration was analyzed using an FE model of an atherosclerotic artery. This arterial FE model was created and validated by analyzing balloon angioplasty of a common stainless steel stent. The biocompatibility of CI-CNTs was explored and studied. Blood compatibility testing of CI-CNT samples was performed with results comparable in performance to stainless steel. A method of stent deployment was planned, and several other stent design concepts were analyzed. This research demonstrates that a functioning coronary stent can be manufactured from CICNTs. The optimized design has potential to address problems currently associated with stents. However, a major challenge for CI-CNT stent designs is meeting the design requirement of sufficient radial force. CI-CNT stents also need to have excellent blood compatibility to justify being used in stent applications.