Miracle-dz/UniFAR-FTUs huggingface dataset:
Endogenous Surfactant Metabolism in Critically Ill Infants Measured with Stable Isotope Labeled Fatty Acids

Little is known about endogenous surfactant metabolism in infants, because radioactive isotopes used for this purpose in animals cannot be used in humans. We developed a novel and safe method to measure the endogenous surfactant kinetics in vivo in humans by using stable isotope labeled fatty acids. We infused albumin-bound [U-13C]palmitic acid (PA) and [U-13C]linoleic acid (LLA) for 24 h in eight critically ill infants (mean ± SD; weight: 3.7 ± 1.3 kg; age: 51.3 ± 61.6 d) who required mechanical ventilation. The 13C enrichment of PA and LLA in surfactant phosphatidylcholine (PC), obtained from tracheal aspirates, was measured by gas chromatography combustion interface-isotope ratio mass spectrometry. We measured a significant incorporation of both 13C-PA and 13C-LLA into surfactant PC. PC-PA and PC-LLA became enriched after 8.7 ± 4.9 h (range: 3.4-17.3) and 10.0 ± 7.2 h (range: 3.0-22.4), respectively; the times at maximum enrichment were 49.2 ± 8.9 and 45.6 ± 19.3 h, respectively. The fractional synthesis rate of surfactant PC-PA ranged from 0.4 to 3.4% per h, whereas the fractional synthesis rate of PC-LLA ranged from 0.5 to 3.8% per h. The surfactant PC-PA and PC-LLA half-lives ranged from 16.8 to 177.7 and 23.8 to 144.4 h, respectively. This method provides new data on surfactant metabolism in infants requiring mechanical ventilation. We found that synthesis of surfactant from plasma PA and LLA is a slow process and that there were marked differences in PC kinetics among infants. This variability could be related to differences in lung disease and could affect the clinical course of the respiratory failure.
Therapeutic potential of protease-activated receptor-1 antagonists

The serine protease thrombin (EC 3.4.21.5) is central to the maintenance of haemostatic balance through its coagulant, anticoagulant and platelet activating properties. In addition, this enzyme affects numerous cellular responses in a wide variety of cells, such as cell proliferation, cytokine and growth factor release, lipid metabolism and tissue remodelling. A family of Gproteincoupled protease-activated receptors (PARs) mediates these cellular actions of thrombin. While thrombin can activate three of the four PAR family members, PAR-1 represents the primary thrombin-responsive receptor in human cells. The expression of PAR-1 in platelets, the vasculature and myocardium, in cells within atherosclerotic plaque and tissues after vascular injury, indicates that this receptor plays an important role during the response to tissue injury and associated inflammatory processes. With the development of PAR-deficient mice and small-molecule antagonists, it is now clear that intervening in processes mediated by PAR-1 presents a new approach to treating a variety of disorders dependent on thrombin generation, including thrombosis and restenosis. The full potential of PAR-1 antagonists has yet to be realised, but the promise of novel therapeutics that modulate receptor function rather than thrombin’s proteolytic activity, provides an alternative and, perhaps, more desirable means to dampen the pathological effects of thrombin.
External cross‐validation for unbiased evaluation of protein family detectors: Application to allergens

Key issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10‐fold cross‐validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held‐out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected. Proteins 2005. © 2005 Wiley‐Liss, Inc.
DNA DAMAGE AND REPAIR FOLLOWING TREATMENT OF V‐79 CELLS WITH SULFONATED PHTHALOCYANINES

Abstract. Two gallium‐phthalocyanines were tested for their effects on cell survival, trypsinization, and DNA strand breaks in intact and permeable cells, measured by alkaline elution. Gallium‐tetrasulfophthalocyanine was not phototoxic to cells and caused no measurable DNA damage in intact cells, while a mixture of less sulfonated gallium‐sulfophthalocyanines, containing an average of 2.7 sulfonates per molecule, was very phototoxic and induced DNA strand breaks and/or alkali‐sensitive sites; however, both drugs were equally effective at inducing DNA strand breaks in permeable cells. The DNA damage was rapidly repaired in intact cells; this process was not inhibited by aphidicolin, an inhibitor of DNA polymerases alpha and delta, under conditions in which DNA replicative synthesis was inhibited by more than 90%.
A Case–Crossover Study of Wintertime Ambient Air Pollution and Infant Bronchiolitis

We examined the association of infant bronchiolitis with acute exposure to ambient air pollutants. Design We employed a time-stratified case–crossover method and based the exposure windows on a priori, biologically based hypotheses. Participants We evaluated effects in 19,901 infants in the South Coast Air Basin of California in 1995–2000 with a hospital discharge record for bronchiolitis in the first year of life (International Classification of Diseases, 9th Revision, CM466.1). Evaluations/Measurements Study subjects’ ZIP code was linked to ambient air pollution monitors to derive exposures. We estimated the risk of bronchiolitis hospitalization associated with increases in wintertime ambient air pollutants using conditional logistic regression. Results We observed no increased risk after acute exposure to particulate matter ≤ 2.5 μm in aerodynamic diameter (PM2.5), carbon monoxide, or nitrogen dioxide. PM2.5 exposure models suggested a 26–41% increased risk in the most premature infants born at gestational ages between 25 and 29 weeks; however, these findings were based on very small numbers. Conclusions We found little support for a link between acute increases in ambient air pollution and infant bronchiolitis except modestly increased risk for PM2.5 exposure among infants born very prematurely. In these infants, the periods of viral acquisition and incubation concurred with the time of increased risk. Relevance to Professional Practice We present novel data for the infant period and the key respiratory disease of infancy, bronchiolitis. Incompletely explained trends in rising bronchiolitis hospitalization rates and increasing number of infants born prematurely underscore the importance of evaluating the impact of ambient air pollution in this age group in other populations and studies.
Increased angiogenesis in papillary thyroid carcinoma but lack of prognostic importance.

Angiogenesis is important for tumor growth and progress, and the intratumor density of microvessels is a significant prognostic factor in many tumor types. The role in thyroid cancer has not been well studied, and we therefore examined a series of 128 papillary carcinomas with respect to microvessel density (MVD) and patient survival. Follow-up was obtained for all cases (median, 145 months). We found a mean MVD of 216 per mm2 (range, 35-751), and there was an average of 3.14 times more vessels in the tumors, when compared with surrounding non-neoplastic thyroid tissue. MVD was inversely related to age, tumor diameter, histological grade, and primary tumor extent. Furthermore, increasing MVD tended to be associated with improved survival (P = .056). In conclusion, our data indicate that angiogenesis is important for the development and maintenance of papillary thyroid carcinomas, although it was not identified as a prognostic factor.
Language Edit Distance and Maximum Likelihood Parsing of Stochastic Grammars: Faster Algorithms and Connection to Fundamental Graph Problems

Given a context free language G over alphabet Σ and a string s ∈ Σ*, the language edit distance problem seeks the minimum number of edits (insertions, deletions and substitutions) required to convert s into a valid member of the language £(G). The well-known dynamic programming algorithm solves this problem in O(n3) time (ignoring grammar size) where n is the string length [Aho, Peterson 1972, Myers 1985]. Despite its numerous applications, to date there exists no algorithm that computes the exact or approximate language edit distance problem in true subcubic time. In this paper we give the first such algorithm that computes language edit distance almost optimally. For any arbitrary ε > 0, our algorithm runs in Õ(nω/poly(∈)) time and returns an estimate within a multiplicative approximation factor of (1 + ∈) with high probability, where w is the exponent of ordinary matrix multiplication of n dimensional square matrices. It also computes the actual edits required. We further solve the local alignment problem; for all substrings of s, we can estimate their language edit distance within (1 ± ε) factor in Õ(nω/poly(∈)) time with high probability. Next, we design the very first subcubic (Õ(nω)) algorithm that given an arbitrary stochastic context free grammar, and a string returns a nearly-optimal maximum likelihood parsing of that string. Stochastic context free grammars significantly generalize hidden Markov models; they lie at the foundation of statistical natural language processing, and have found widespread applications in many other fields. To complement our upper bound result, we show that exact computation of maximum likelihood parsing of stochastic grammars or language edit distance in true subcubic time will imply a truly subcubic algorithm for all-pairs shortest paths, a long-standing open question. This will result in a breakthrough for a large range of problems in graphs and matrices due to subcubic equivalence. By a known lower bound result [Lee 2002], and a recent development [Abboud et al. 2015] even the much simpler problem of parsing a context free grammar requires Ω(nω) time. Therefore any nontrivial multiplicative approximation algorithms for either of the two problems in time o(nω) are unlikely to exist.
Stress wave propagation in adhesively bonded similar and dissimilar circular cylinders

This study addresses the wave propagation in adhesively bonded similar and dissimilar circular cylinders under an axial impulsive load. The four configurations are considered such as adhesively bonded aluminum–aluminum (Al–Al), steel–steel (St–St), aluminum–steel (Al–St), and steel–aluminum (St–Al) joints. The governing equations of the wave propagation are partial differential equations which are not usually amenable for analytical solutions under complex boundary conditions. Therefore, they are solved numerically using the finite difference method for spatial and temporal discretization. Each component of the adhesively bonded circular cylinders exhibits completely different stress and deformation states under an axial impulsive load. The axial displacement and axial stress components were dominant in both upper and lower adherends as well as the adhesive layer. The peak displacement levels became maximal in the bonded Al–Al and Al–St joints, decreased slightly in the bonded St–Al joint, and became minimal in bonded St–St joint. As the adhesively bonded joint becomes stiffer due to a stiffer (St) upper adherend, the bonded St–St and St–Al joints experience higher stress waves in comparison with those in the bonded Al–Al and Al–St joints, respectively. Moreover, the wave travels at a slightly higher speed through the adherend with a stiffer (St) material.
Trade induced technical change? The impact of Chinese imports on innovation, diffusion and productivity

There is a popular belief that Chinese imports have devastated US and European manufacturing and contributed to rising inequality. Somewhat paradoxically, the consensus amongst empirical economists is that trade has not been a major cause of rising wage inequality (although this is largely based on datasets predating China’s rise). We argue that both views have underestimated the positive impact of Chinese trade on technical change. We examine the impact of the growth of Chinese import competition on technical change (as measured by IT, patent counts and citations, TFP and R&D) using a panel of over to 200,000 European firms through 2007. We correct for endogeneity using quasiexperiments such as China’s entry into the World Trade Organization. Chinese import competition led to both within firm technology upgrading and between firm reallocation of employment towards more technologically intensive plants. These effects account for about 15-20% of technology upgrading 2000-2007 and are growing over time. These results suggest that trade with low wage countries appear to have potentially large beneficial impacts on technical change as recent theories suggest. JEL No. O33, F14, L25, L60,
Memorability as a measure of processing: a unit analysis of prose and list learning.

The percentage of subjects recalling each unit in a list or prose passage is considered as a dependent measure. When the same units are recalled in different tasks, processing is assumed to be the same; when different units are recalled, processing is assumed to be different. Two collections of memory tasks are presented, one for lists and one for prose. The relations found in these two collections are supported by an extensive reanalysis of the existing prose memory literature. The same set of words were learned by 13 different groups of subjects under 13 different conditions. Included were intentional free-recall tasks, incidental free recall following lexical decision, and incidental free recall following ratings of orthographic distinctiveness and emotionality. Although the nine free-recall tasks varied widely with regard to the amount of recall, the relative probability of recall for the words was very similar among the tasks. Imagery encoding and recognition produced relative probabilities of recall that were different from each other and from the free-recall tasks. Similar results were obtained with a prose passage. A story was learned by 13 different groups of subjects under 13 different conditions. Eight free-recall tasks, which varied with respect to incidental or intentional learning, retention interval, and the age of the subjects, produced similar relative probabilities of recall, whereas recognition and prompted recall produced relative probabilities of recall that were different from each other and from the free-recall tasks. A review of the prose literature was undertaken to test the generality of these results. Analysis of variance is the most common statistical procedure in this literature. If the relative probability of recall of units varied across conditions, a units by condition interaction would be expected. For the 12 studies that manipulated retention interval, an average of 21% of the variance was accounted for by the main effect of retention interval, 17% by the main effect of units, and only 2% by the retention interval by units interaction. Similarly, for the 12 studies that varied the age of the subjects, 6% of the variance was accounted for by the main effect of age, 32% by the main effect of units, and only 1% by the interaction of age by units. (ABSTRACT TRUNCATED AT 400 WORDS)
Prospective Evaluation of Precision Multimodal Gallbladder Surgery Navigation: Virtual Reality, Near-infrared Fluorescence, and X-ray-based Intraoperative Cholangiography

Objective: We aimed to prospectively evaluate NIR-C, VR-AR, and x-ray intraoperative cholangiography (IOC) during robotic cholecystectomy. Background: Near-infrared cholangiography (NIR-C) provides real-time, radiation-free biliary anatomy enhancement. Three-dimensional virtual reality (VR) biliary anatomy models can be obtained via software manipulation of magnetic resonance cholangiopancreatography, enabling preoperative VR exploration, and intraoperative augmented reality (AR) navigation. Methods: Fifty-eight patients were scheduled for cholecystectomy for gallbladder lithiasis. VR surgical planning was performed on virtual models. At anesthesia induction, indocyanine green was injected intravenously. AR navigation was obtained by overlaying the virtual model onto real-time images. Before and after Calot triangle dissection, NIR-C was obtained by turning the camera to NIR mode. Finally, an IOC was performed. The 3 modality performances were evaluated and image quality was assessed with a Likert-scale questionnaire. Results: The three-dimensional VR planning enabled the identification of 12 anatomical variants in 8 patients, of which only 7 were correctly reported by the radiologists (P = 0.037). A dangerous variant identified at VR induced a “fundus first” approach. The cystic-common bile duct junction was visualized before Calot triangle dissection at VR in 100% of cases, at NIR-C in 98.15%, and in 96.15% at IOC. Mean time to obtain relevant images was shorter with NIR-C versus AR (P = 0.008) and versus IOC (P = 0.00000003). Image quality scores were lower with NIR-C versus AR (P = 0.018) and versus IOC (P < 0.0001). Conclusions: This high-tech protocol illustrates the multimodal imaging of biliary anatomy towards precision cholecystectomy. Those visualization techniques could complement to reduce the likelihood of biliary injuries (NCT01881399).
Multiple model adaptive control with safe switching

The purpose of this paper is to marry the two concepts of multiple model adaptive control and safe adaptive control. In its simplest form, multiple model adaptive control involves a supervisor switching among one of a finite number of controllers as more is learnt about the plant, until one of the controllers is finally selected and remains unchanged. Safe adaptive control is concerned with ensuring that when the controller is changed in an adaptive control algorithm, the frozen plant–controller combination is never (closed‐loop) unstable. This is a non‐trivial task since by definition of an adaptive control problem, the plant is not fully known. The proposed solution method involves a frequency‐dependent performance measure and employs the Vinnicombe metric. The resulting safe switching guarantees depend on the extent to which a closed‐loop transfer function can be accurately identified. Copyright © 2001 John Wiley & Sons, Ltd.
Are there age differences in the accommodative response curve between 3 and 14 years of age?

The monocular ocular accommodative responses of 118 emmetropic children, aged from 3 to 14 years, were measured at five different stimulus distances (0, 1, 2, 3, 4 D) from the principal plane of the eye with a Canon Autoref R‐1. The change in the accommodative response curve in emmetropic children between 3 and 14 years old was found to be negligible.
Tn10 insertions in the pfkB region of Escherichia coli

The locus pfkB is known to determine expression of a minor phosphofructokinase (Pfk-2). Pfk-2 and pfkB seem to be dispensable, since Tn10 insertions in pfkB, as well as deletions from Tn10 nearby, are obtainable. Strains deleted for both pfkA and pgkB are unable to grow at all on sugars whose primary route of metabolism is via fructose 6-phosphate, confirming earlier reports implicating the low Pfk-2 activity, rather than the pentose-phosphate pathway, as needed for the slow growth on sugars of pfkA pfkB+ strains. The pfkB locus probably contains the structural gene for Pfk-2, since a mutation closely linked to pfkB1, which affects growth on glycerol, is found to alter the enzyme. Partial phenotypic suppression of the pfkA mutant phenotype results from Tn10 insertion very close to the pps gene, ca. 0.5 min from pgkB. The insertion does not clearly affect either Pfk-2 or phosphoenolpyruvate synthetase, and the mechanism of suppression is unclear.
Relationship between expression level of hygromycin B‐resistant gene and Agrobacterium tumefaciens‐mediated transformation efficiency in Beauveria bassiana JEF‐007

Agrobacterium tumefaciens‐mediated transformation (AtMT) is an effective method for generation of entomopathogenic Beauveria bassiana transformants. However, some strains grow on the selective medium containing hygromycin B (HygB), which reduces the selection efficiency of the putative transformants. In this work, a relationship between HygB resistance gene promoter and AtMT efficiency was investigated to improve the transformant selection.
Image Categorization by Learning and Reasoning with Regions

Designing computer programs to automatically categorize images using low-level features is a challenging research topic in computer vision. In this paper, we present a new learning technique, which extends Multiple-Instance Learning (MIL), and its application to the problem of region-based image categorization. Images are viewed as bags, each of which contains a number of instances corresponding to regions obtained from image segmentation. The standard MIL problem assumes that a bag is labeled positive if at least one of its instances is positive; otherwise, the bag is negative. In the proposed MIL framework, DD-SVM, a bag label is determined by some number of instances satisfying various properties. DD-SVM first learns a collection of instance prototypes according to a Diverse Density (DD) function. Each instance prototype represents a class of instances that is more likely to appear in bags with the specific label than in the other bags. A nonlinear mapping is then defined using the instance prototypes and maps every bag to a point in a new feature space, named the bag feature space. Finally, standard support vector machines are trained in the bag feature space. We provide experimental results on an image categorization problem and a drug activity prediction problem.
Evaluation of Bioactivities and Phenolic Content of Selected Edible Mushrooms in Malaysia

Purpose: To determine the radical scavenging, metal chelating, antibacterial and cytotoxic activities of five edible mushrooms in Malaysia. Methods: Mushrooms (H. tessulatus, P. eryngii, P. florida, A. polytricha and F. velutipes) were ovendried and extracted with 90 % ethanol. Radical scavenging and metal chelating assays were based on the measurement of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and ferrozine absorbance at 517 and 562 nm, respectively. Mushrooms total phenolic and flavonoid contents were determined by spectrophotometric methods. Antimicrobial activity was measured using Kirby-Bauer Susceptibility Test. Cytotoxicity was assessed using brine shrimp toxicity assay. Results: Total phenolic and flavonoid contents ranged from 0.90 - 6.03 mg GAE per g of dry sample and 0.17 - 6.95 mg QE per g of dry sample, respectively. A. polytricha demonstrated the strongest radical scavenging and metal chelating activities. Moderate antimicrobial activity was found for extracts of both P. florida and A. polytricha. Cytotoxicity LD50 ranged from 46.9 - 115.8 µg/ml. Conclusion: The results suggest that A. polytricha is a suitable candidate for chemoprevention and would safe for use in large doses.