Miracle-dz/UniFAR-FTUs huggingface dataset:
Single‐breath CO2 analysis as a predictor of lung volume change in a model of acute lung injury

Objective: To examine the utility of single‐breath CO2 analysis as a measure of lung volume change in a model of acute lung injury. Setting: Animal laboratory in a university‐affiliated medical center. Design: Prospective, animal cohort study comparing 21 variables derived from single‐breath CO2 analysis with lung volume measurements determined by nitrogen washout. Subjects: Seven lambs with saline lavage‐induced acute lung injury. Methods: Animals were treated with repetitive saline lavage to achieve a uniform degree of acute lung injury (PaO2 < 100 torr [13.32 kPa] on FIO2 of 1.0). Twenty‐one derived components of the CO2 expirogram were evaluated as predictors of lung volume change. Lung volume was manipulated by 3‐cm H2O incremental increases in positive end‐expiratory pressure from 0 to 21 cm H2O and ranged between 90 and 765 mL. Measurements and Main Results: Fifty‐five measurements of lung volume were available for comparison with derived variables from the CO2 expirogram. Stepwise linear regression identified five variables that were most predictive of lung volume change: a) dynamic lung compliance; b) the slope of phase III; c) the slope of phase II divided by the mixed expired CO2 concentration; d) airway deadspace; and e) PaO2/FIO2 ratio. The multivariate equation was highly statistically significant and explained 94% of the variance (adjusted r2 = .94, p < .0001). The bias and precision of the calculated lung volume were 10.9 and 55.9, respectively. The mean percentage difference for the lung volume estimate derived from the single‐breath CO2 analysis station was 3.3%. Conclusions: Our data indicate that analysis of the CO2 expirogram can yield accurate information about lung volume in animals with saline lavage‐induced acute lung injury. Specifically, five variables derived from a plot of expired CO2 concentration vs. expired volume predict changes in lung volume in healthy lambs with an adjusted coefficient of determination of 0.94. We hope to further define the utility of this technique by prospective application of this methodology in the clinical setting.
Accurate analysis of temperature effects in I/SUB c/V/SUB BE/ characteristics with application to bandgap reference sources

The inaccuracy of the analyses commonly used for predicting the temperature behavior of the I/SUB C/-V/SUB BE/ characteristics of transistors and the output of bandgap reference sources is pointed out. The problem is traced to a basic assumption implicit in such analyses, namely that the variation of the bandgap voltage of silicon with temperature is linear; this assumption is shown to be of poor accuracy. By taking into account the nonlinearity in this variation, new accurate formulas are derived. Both the previous analyses and the proposed analysis are compared to experiment; a valuable improvement is demonstrated. Equations which should prove to value in the design of bandgap reference sources and bipolar transistor temperatures transducers are given. Higher order effects are discussed.
Communication Optimization on GPU: A Case Study of Sequence Alignment Algorithms

Data movement is increasingly becoming the bottleneck of both performance and energy efficiency in modern computation. Until recently, it was the case that there is limited freedom for communication optimization on GPUs, as conventional GPUs only provide two types of methods for inter-thread communication: using shared memory or global memory. However, a new warp shuffle instruction has been introduced since the Kepler architecture on Nvidia GPUs, which enables threads within the same warp to directly exchange data in registers. This brought new performance optimization opportunities for algorithms with intensive inter-thread communication. In this work, we deploy register shuffle in the application domain of sequence alignment (or similarly, string matching), and conduct a quantitative analysis of the opportunities and limitations of using register shuffle. We select two sequence alignment algorithms, Smith-Waterman (SW) and Pairwise-Hidden-Markov-Model (PairHMM), from the widely used Genome Analysis Toolkit (GATK) as case studies. Compared to implementations using shared memory, we obtain a significant speed-up of 1.2× and 2.1× by using shuffle instructions for SW and PairHMM. Furthermore, we develop a performance model for analyzing the kernel performance based on the measured shuffle latency from a suite of microbenchmarks. Our model provides valuable insights for CUDA programmers into how to best use shuffle instructions for performance optimization.
Output-Based Performance Measures for the North Carolina Alliance for Competitive Technologies

Sheila A. Martin is a senior economist in the Research Triangle Institute’s Center for Economics Research. She earned a Ph.D. in Economics from Iowa State University in 1992 and holds an M.A. in International Studies from the University of Kentucky. At the Center for Agricultural and Rural Development, she researched industrial and rural development policy issues, including industryand plant-level productivity and efficiency, agglomeration economies, plant location and survival factors, and development policy effectiveness. At RTI, Dr. Martin manages and performs research in science and technology policy, environmental economics, and food safety policy.
Effect of high intensity pulsed electric fields and heat treatments on vitamins of milk

The effects of high intensity pulsed electric field (HIPEF) treatments at room or moderate temperature on water-soluble (thiamine, riboflavin, ascorbic acid) and fat-soluble vitamins (cholecalciferol and tocopherol) were evaluated and compared with conventional thermal treatments. Vitamin retention was determined in two different substrates, milk and simulated skim milk ultrafiltrate (SMUF). Samples were subjected to HIPEF treatments of up to 400 μs at field strengths from 18·3 to 27·1 kV/cm and to heat treatments of up to 60 min at temperatures from 50 to 90 °C. No changes in vitamin content were observed after HIPEF or thermal treatments except for ascorbic acid. Milk retained more ascorbic acid after a 400 μs-treatment at 22·6 kV/cm (93·4%) than after low (63 °C-30 min; 49·7% retained) or high (75 °C-15 s; 86·7% retained) heat pasteurisation treatments. Retention of ascorbic acid fitted a first-order kinetic model for both HIPEF and thermal processes. First-order constant values varied from 1·8×10−4 to 1·27×10−3 μs−1 for the HIPEF treatments (18·3–27·1 kV/cm) and, for thermal processing ranged from 5×10−3 to 8×10−2 min−1 (50–90 °C). No significant differences were found between the results obtained after applying HIPEF treatments at room or moderate temperature. However, results depended on the treatment media. A beneficial effect of natural skim milk components, mainly proteins, was observed on the preservation of ascorbic acid, since skim milk retained more ascorbic acid than SMUF after HIPEF treatments.
Notch signaling controls germline stem cell niche formation in the Drosophila ovary

Stem cells, which can self-renew and generate differentiated cells, have been shown to be controlled by surrounding microenvironments or niches in several adult tissues. However, it remains largely unknown what constitutes a functional niche and how niche formation is controlled. In the Drosophila ovary, germline stem cells (GSCs), which are adjacent to cap cells and two other cell types, have been shown to be maintained in the niche. In this study, we show that Notch signaling controls formation and maintenance of the GSC niche and that cap cells help determine the niche size in the Drosophila ovary. Expanded Notch activation causes the formation of more cap cells and bigger niches, which support more GSCs, whereas compromising Notch signaling during niche formation decreases the cap cell number and niche size and consequently the GSC number. Furthermore, the niches located away from their normal location can still sufficiently sustain GSC self-renewal by maintaining high local BMP signaling and repressing bam as in normal GSCs. Finally, loss of Notch function in adults results in rapid loss of the GSC niche, including cap cells and thus GSCs. Our results indicate that Notch signaling is important for formation and maintenance of the GSC niche, and that cap cells help determine niche size and function.
Semi-Supervised Semantic Role Labeling

Large scale annotated corpora are prerequisite to developing high-performance semantic role labeling systems. Unfortunately, such corpora are expensive to produce, limited in size, and may not be representative. Our work aims to reduce the annotation effort involved in creating resources for semantic role labeling via semi-supervised learning. Our algorithm augments a small number of manually labeled instances with unlabeled examples whose roles are inferred automatically via annotation projection. We formulate the projection task as a generalization of the linear assignment problem. We seek to find a role assignment in the unlabeled data such that the argument similarity between the labeled and unlabeled instances is maximized. Experimental results on semantic role labeling show that the automatic annotations produced by our method improve performance over using hand-labeled instances alone.
Patient-Perceived Quality of Life after Total Hip Arthroplasty: Elective versus Traumatological Surgery

Purpose. The aim was to evaluate and compare patient's health-related quality of life after THA for osteoarthritis and femoral neck fracture. The postoperative outcome was retrospectively evaluated in patients who underwent THA with an intracapsular femoral neck fracture (Group A) or with an hip osteoarthritis (Group B). Methods. Length discrepancy was measured on postoperative X-rays. Study groups were compared as to age, results of WOMAC and SF-36 tests, limb length discrepancy (LLD) by independent group t-test. Correlations between LLD and results obtained atWOMAC test were performed. 117 patients were enrolled. The 2 groups were similar as to age, type of implanted stem and sex. Mean follow up was 2,4 years for group A and 2,3 years for group B. Results. WOMAC score was found higher in group A in all items examinated. Correlation tests did not indicate a statistically significant linear relationship between LLD and WOMAC score in both groups. Conclusions. Patients who received THA for arthritis have better perception of quality of life than traumatologic patients. Although LLD should always be strongly considered by the surgeons performing a THA, LLD alone can't be considered as an indicator of patient dissatisfaction or clinical bad result after a 2-year followup.
CFHTLenS tomographic weak lensing: quantifying accurate redshift distributions

The Canada–France–Hawaii Telescope Lensing Survey (CFHTLenS) comprises deep multicolour (u^*g′r′i′z′) photometry spanning 154 deg^2, with accurate photometric redshifts and shape measurements. We demonstrate that the redshift probability distribution function summed over galaxies provides an accurate representation of the galaxy redshift distribution accounting for random and catastrophic errors for galaxies with best-fitting photometric redshifts z_p < 1.3. We present cosmological constraints using tomographic weak gravitational lensing by large-scale structure. We use two broad redshift bins 0.5 < z_p ≤ 0.85 and 0.85 < z_p ≤ 1.3 free of intrinsic alignment contamination, and measure the shear correlation function on angular scales in the range ∼1–40 arcmin. We show that the problematic redshift scaling of the shear signal, found in previous Canada–France–Hawaii Telescope Legacy Survey data analyses, does not affect the CFHTLenS data. For a flat Λ cold dark matter model and a fixed matter density Ω_m = 0.27, we find the normalization of the matter power spectrum σ_8 = 0.771 ± 0.041. When combined with cosmic microwave background data (Wilkinson Microwave Anisotropy Probe 7-year results), baryon acoustic oscillation data (BOSS) and a prior on the Hubble constant from the Hubble Space Telescope distance ladder, we find that CFHTLenS improves the precision of the fully marginalized parameter estimates by an average factor of 1.5-2. Combining our results with the above cosmological probes, we find Ω_m = 0.2762 ± 0.0074 and σ_8 = 0.802 ± 0.013.
Moxifloxacin Pharmacokinetic Profile and Efficacy Evaluation in Empiric Treatment of Community-Acquired Pneumonia

ABSTRACT When antimicrobials are used empirically, pathogen MICs equal to clinical breakpoints or epidemiological cutoff values must be considered. This is to ensure that the most resistant pathogen subpopulation is appropriately targeted to prevent emergence of resistance. Accordingly, we determined the pharmacokinetic (PK) profile of moxifloxacin at 400 mg/day in 18 patients treated empirically for community-acquired pneumonia. We developed a population pharmacokinetic model to assess the potential efficacy of moxifloxacin and to simulate the maximal MICs for which recommended pharmacokinetic-pharmacodynamic (PK-PD) estimates are obtained. Moxifloxacin plasma concentrations were determined the day after therapy initiation using ultra-high-performance liquid chromatography. Peak drug concentrations (Cmax) and area under the free drug concentration-time curve from 0 to 24 h (fAUC0–24) values predicted for each patient were evaluated against epidemiological cutoff MIC values for Streptococcus pneumoniae, Haemophilus influenzae, and Legionella pneumophila. PK-PD targets adopted were a Cmax/MIC of ≥12.2 for all pathogens, an fAUC0–24/MIC of >34 for S. pneumoniae, and an fAUC0–24/MIC of >75 for H. influenzae and L. pneumophila. Individual predicted estimates for Cmax/MIC and fAUC0–24/MIC as well as simulated maximal MICs resulting in target attainment for oral and intravenous administration of the drug were suitable for S. pneumoniae and H. influenzae but not for L. pneumophila. These results indicate that caution must be taken when moxifloxacin is used as monotherapy to treat community-acquired pneumonia caused by L. pneumophila. In conclusion, this report reveals key information relevant to the empirical treatment of community-acquired pneumonia while highlighting the robust and flexible nature of this population pharmacokinetic model to predict therapeutic success. (Clinical Trials Registration no. NCT01983839.)
Thoroughly sampling sequence space: Large‐scale protein design of structural ensembles

Modeling the inherent flexibility of the protein backbone as part of computational protein design is necessary to capture the behavior of real proteins and is a prerequisite for the accurate exploration of protein sequence space. We present the results of a broad exploration of sequence space, with backbone flexibility, through a novel approach: large‐scale protein design to structural ensembles. A distributed computing architecture has allowed us to generate hundreds of thousands of diverse sequences for a set of 253 naturally occurring proteins, allowing exciting insights into the nature of protein sequence space. Designing to a structural ensemble produces a much greater diversity of sequences than previous studies have reported, and homology searches using profiles derived from the designed sequences against the Protein Data Bank show that the relevance and quality of the sequences is not diminished. The designed sequences have greater overall diversity than corresponding natural sequence alignments, and no direct correlations are seen between the diversity of natural sequence alignments and the diversity of the corresponding designed sequences. For structures in the same fold, the sequence entropies of the designed sequences cluster together tightly. This tight clustering of sequence entropies within a fold and the separation of sequence entropy distributions for different folds suggest that the diversity of designed sequences is primarily determined by a structure's overall fold, and that the designability principle postulated from studies of simple models holds in real proteins. This has important implications for experimental protein design and engineering, as well as providing insight into protein evolution.
Epicardial wave mapping in human long-lasting persistent atrial fibrillation: transient rotational circuits, complex wavefronts, and disorganized activity.

OBJECTIVES To characterize the nature of atrial fibrillation (AF) activation in human persistent AF (PerAF) using modern tools including activation, directionality analyses, complex-fractionated electrogram, and spectral information. BACKGROUND The mechanism of PerAF in humans is uncertain. METHODS AND RESULTS High-density epicardial mapping (128 electrodes/6.75 cm(2)) of the posterior LA wall (PLAW), LA and RA appendage (LAA, RAA), and RSPV-LA junction was performed in 18 patients with PerAF undergoing open heart surgery. Continuous 10 s recordings were analysed offline. Activation patterns were characterized into four subtypes (i) wavefronts (broad or multiple), (ii) rotational circuits (≥2 rotations of 360°), (iii) focal sources with centrifugal activation of the entire mapping area, or (iv) disorganized activity [isolated chaotic activation(s) that propagate ≤3 bipoles or activation(s) that occur as isolated beats dissociated from the activation of adjacent bipole sites]. Activation at a total of 36 regions were analysed (14 PLAW, 3 RSPV-LA, 12 LAA, and 7 RAA) creating a database of 2904 activation patterns. In the majority of maps, activation patterns were highly heterogeneous with multiple unstable activation patterns transitioning from one to another during each recording. A mean of 3.8 ± 1.6 activation subtypes was seen per map. The most common patterns seen were multiple wavefronts (56.2 ± 32%) and disorganized activity (24.2 ± 30.3%). Only 2 of 36 maps (5.5%) showed a single stable activation pattern throughout the 10-s period. These were stable planar wavefronts. Three transient rotational circuits were observed. Two of the transient circuits were located in the posterior left atrium, while the third was located on the anterior surface of the LAA. Focal activations accounted for 11.3 ± 14.2% of activations and were all short-lived (≤2 beats), with no site demonstrating sustained focal activity. CONCLUSION Human long-lasting PerAF is characterized by heterogeneous and unstable patterns of activation including wavefronts, transient rotational circuits, and disorganized activity.
R 1 Principles of Ethics

What kinds of acts are right in oncology nursing practice? This basic yet complex question is commonly asked by nurses in oncology and other specialties to determine what they should do in a specific case or how the entire profession should act regarding interactions with patients, families, and colleagues. General ethical principles often are used as guides for right action. The first such contemporary example that proposed principles as guides in a health-related area was the Belmont Report (National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research, 1979), which identified the principles of respect for persons, beneficence, and justice in human subjects research. In 1981, Beauchamp and Childress built on this work and applied it to health care in the first edition of their book Principles of Biomedical Ethics, now in its seventh edition (Beauchamp & Childress, 2012). They proposed four key principles: respect for autonomy, beneficence (the obligation to do good), nonmaleficence (the duty not to harm), and justice. Others in bioethics have suggested additional derivative principles, including veracity (the obligation to tell the truth), fidelity (the duty to keep promises), and avoidance of killing (Veatch, Haddad, & English, 2010). Although helpful in illuminating shared values and important ethical norms in health care, the principlist approach to ethics is not without its problems and critics. For example, polarities and problems exist within the principles themselves, such as tensions between present versus future expressions of autonomy (Collopy, 1988) or disagreement regarding who is best suited to determine benefit (Childress, 1982). Conflicts can also arise between principles, such as when one is attempting to fulfill the demands of respect for autonomy, which can run counter to the health professional’s obligation to avoid harm. Additionally, no one principle of the four is given primacy, so determining which principle carries the day in
Evidence for an Aryl Hydrocarbon Receptor-Mediated Cytochrome P450 Autoregulatory Pathway

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor responsible for mediating the cellular response to the toxic compound 2,3,7,8,-tetrachlorodibenzo-p-dioxin. An essential role for the AhR in cellular biology has been established previously, but no high-affinity endogenous ligand has yet been identified. We have confirmed the presence of a putative endogenous ligand(s) in CV-1 cells through transient transfection with various cytochrome P450 isoforms. Expression of cytochromes P450 1A1, 1A2, or 1B1 reduced AhR-mediated luciferase reporter activity, whereas cytochrome P450 2E1 exhibited no significant effect. Studies with 2,4,3′,5′-tetramethoxystilbene, a potent and specific inhibitor of cytochrome P450 1B1, was able to partially block cytochrome P450 1B1-mediated reduction in reporter gene activity. These results provide evidence of the existence of a possible feedback mechanism in which AhR-regulated cytochromes P450 from the CYP1A and CYP1B families are able to metabolically alter putative endogenous ligand(s). Several experiments were performed to provide initial characterization of these putative endogenous ligands, including electrophoretic mobility shift assay analyses, which demonstrated that these ligands directly activate the AhR. Soluble extracts from various C57BL/6J and Ahr-null mouse tissues were also analyzed for the presence of AhR activators. Studies revealed that Ahr-null mouse lung tissue had a 4-fold increase in AhR-mediated reporter activity in cells. Quantitative polymerase chain reaction analysis revealed that lung tissue exhibits relatively high constitutive CYP1A1 mRNA levels. These results suggest that there is an autoregulatory feedback loop between the AhR and cytochrome P450 1A1 in mouse lung.
Beta sheet propensity and the genetic code

So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a different approach hypothesizing that probably we are partially protected (by the genetic code) from amyloid fibrils formation.
Classifiers based on Bernoulli mixture models for text mining and handwriting recognition tasks

In this paper we describe a model for classifying binary data using classifiers based on Bernoulli mixture models. We show how Bernoulli mixtures can be used for feature extraction and dimensionality reduction of raw input data. The extracted features are then used for training a classifier for supervised labeling of individual sample points. We have applied this method to two different types of datasets, i.e., one from the text mining domain and one from the handwriting recognition area. Empirical experiments demonstrate that we can obtain up to 99.9% reduction in the dimensionality of the original feature set for sparse binary features. Classification accuracy also increases considerably when the combined model is used. This paper compares the performance of different classification algorithms when used in conjunction with the new feature set generated by Bernoulli mixtures. Using this hybrid model of learning we have achieved one of the best accuracy rates on the NOVA and GINA datasets of the dasiaagnostic vs. prior knowledgepsila competition held by the International Joint Conference on Neural Networks in 2007.