Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical incident reporting in the intensive care unit

Critical incident reporting was introduced into the intensive care unit (ICU) as part of the development of a quality assurance programme within our department. Over a 3‐year period 281 critical incidents were reported. Factors relating to causation, detection and prevention of critical incidents were sought. Detection of a critical incident in over 50% of cases resulted from direct observation of the patient while monitoring systems accounted for a further 27%. No physiological changes were observed in 54% of critical incidents. The most common incidents reported concerned airway management and invasive lines, tubes and drains. Human error was a factor in 55% of incidents while violations of standard practice contributed to 28%. Critical incident reporting was effective in revealing latent errors in our ‘system’ and clarifying the role of human error in the generation of incidents. It has proven to be a useful technique to highlight problems previously undetected in our quality assurance programme. Improvements in quality of care following implementation of preventative strategies await further assessment.
MEMS piezoelectric energy harvester to power wireless sensor nodes for machine monitoring application

Piezoelectric vibration energy harvesters find an important application in powering the wireless sensor nodes used to monitor the condition, wear and tear of AC machines which vibrate at twice the line frequency i.e., 100 Hz. The challenge in the design is to make the resonant frequency of the energy harvester equal to 100 Hz keeping the size less and to obtain the maximum possible output voltage. In this paper various geometries of cantilever beams of a constant length 5 mm have been investigated to get significant reduction in the resonant frequency and to achieve nearly 100 Hz. A new Perforated Tapered shaped cantilever beam has been proposed. The achieved resonant frequency of the final proposed perforated Tapered structure with proof mass is 101 Hz, which is 27.5% lower than that of the commonly used rectangular structure with proof mass of same dimensions. The peak voltage output of the proposed structure is 7.5 V. The proposed structure can be used to generate voltage from the vibration of the AC machines and can provide a long-life solution to the need of powering the batteries in wireless sensor nodes.
Advances and challenges in hereditary cancer pharmacogenetics

ABSTRACT Introduction: Cancer pharmacogenetics usually considers tumor-specific targets. However, hereditary genetic variants may interfere with the pharmacokinetics of antimetabolites and other anti-cancer drugs, which may lead to severe adverse events. Areas covered: Here, the impact of hereditary genes considered in drug labels such as thiopurine S-methyltransferase (TPMT), UDP-glucuronosyltransferase 1A1 (UTG1A1) and dihydropyrimidine dehydrogenase (DPYD) are discussed with respect to guidelines of the Clinical Pharmacogenetics Implementation Consortium (CPIC). Moreover, the association between genetic variants of drug transporters with the clinical outcome is comprehensively discussed. Expert opinion: Precision therapy in the field of oncology is developing tremendously. There are a number of somatic tumor genetic markers that are indicative for treatment with anti-cancer drugs. By contrast, for some hereditary variants, recommendations have been developed. Although we have vast knowledge on the association between drug transporter variants and clinical outcome, the overall data is inconsistent and the predictability of the related phenotype is low. Further developments in research may lead to the discovery of rare, but functionally relevant single nucleotide polymorphisms and a better understanding of multiple genomic, epigenomic as well as phenotypic factors, contributing to drug response in malignancies.
Hyperpolarized magnetic resonance spectroscopy for assessing tumor hypoxia

ABSTRACT Introduction. Hypoxic tumor cells are radioresistant, therefore, identification of hypoxia is crucial. Hyperpolarized magnetic resonance spectroscopy (HPMRS) allows real time measurements of the conversion of pyruvate to lactate, the final step of anaerobic energy production, and may thus allow non-invasive identification of hypoxia or treatment-induced changes in oxygenation. The aim of the study was to investigate the usefulness of HPMRS as a means to assess tumor hypoxia and its dynamics during intervention. Material and methods. C3H mammary carcinomas grown in CDF1 mice were used. To manipulate with tumor oxygenation, non-anaesthetized mice were gassed with air, 10% or 100% oxygen prior to administration of hyperpolarized [1-¹³C]pyruvate and HPMRS analysis. A direct assessment of tumor oxygen partial pressure (pO2) distributions were made using the Eppendorf oxygen electrode in a separate, but similarly treated, group of mice. Results. Even though breathing 100% oxygen improved tumor oxygenation as evidenced by pO2 measurements, the mean (with 1 S.E.) [1-¹³C]lactate/[1-¹³C]pyruvate ratio was unaffected by this intervention, being 34 (30–37) in mice breathing air and 37 (33–42) in mice breathing 100% oxygen. In contrast, and in accordance with pO2 measurements, a significant increase in the [1-¹³C]lactate/[1-¹³C]pyruvate ratio was seen in 10% oxygen-breathing mice with a ratio of 46 (42–50). Conclusions. Although, no metabolic change was observed during 100% O2 breathing using HPMRS, the significant increase in the [1-¹³C]lactate/[1-¹³C]pyruvate ratio during 10% oxygen breathing suggests, that HPMRS can detect hypoxia-driven changes in the metabolic fate of pyruvate. To what extent and for what purposes HPMRS may best supplement or complement established techniques like hypoxia PET needs to be unraveled in future research.
Development of Agricultural Trade of Visegrad Group Countries in Relation to EU and Third Countries

Despite the continually growing value of agricultural trade of the Czech Republic, Hungary, Slovakia and Poland, agricultural trade in the case of all of the countries of the Visegrad group represents only a marginal part of the total merchandise trade. The agricultural trade of the individual analyzed countries is, both in terms of the commodity structure as well as the territorial structure, very distinctly concentrated. The overwhelming majority of agricultural trade – export as well as import – je conducted in relation to EU countries. These countries participate in agricultural trade of individual countries of the V4 group with a share of over 80%. If we focus on the actual objective of the article, which was to identify the comparative advantages of agricultural trade of the V4 countries in the area of commodity structure and territorial structure, both in relation to the global market, as well as in relation to EU27, the following may be stated. The agricultural trade of the Czech Republic, Slovakia and Hungary as a whole does not have comparative advantages either on the global market or on the internal market of the EU countries. However, Poland as the only representative of the V4 countries has comparative advantages in the field of agricultural trade, in relation to both the internal market of the EU countries, as well as in relation to the global market (to the market of third countries). If we focus on the territory of the EU27 countries, which represents the main trading partner of all of the analyzed countries, both in terms of exports as well as in terms of imports, it may be stated that despite the fact that the Czech Republic, Slovakia and Hungary do not have comparative advantages in the area of agricultural trade in regard to the EU as a whole, they are able to achieve comparative advantages at the level of bilateral relationships with individual member countries of the EU. This paper is part of a research project carried out within the framework of the grant no. 6046070906, funded by the Ministry of Education, Youth and Sports of the Czech Republic.
The Effect of Disordered Microscale Holes in the Front Dielectric Layer of AC Plasma Display Panels

Using polymethyl methacrylate (PMMA) beads, disordered microscale holes were fabricated in the front dielectric layer of ac plasma display panels. The density of the disordered microscale holes was easily controlled by varying the weight percentage of the PMMA beads. As their density increased, the voltage of self-erasing discharge and the minimum sustain voltage decreased. In addition, the sustain discharge time lag was improved according to the measurement results of the response time and spatiotemporal infrared emission from an intensified charge-coupled device camera. The wall voltage at the state of sustain discharge was investigated by measuring the threshold voltage using wall voltage measurement system. In the test panel of the front dielectric layer with disordered microscale holes, the wall voltage increased. In addition, the increase in the wall voltage at the state of sustain discharge was improved as the density of the disordered microscale holes increased. The decrease in the self-erasing discharge and minimum sustain voltage and the improvement of the sustain discharge time lag resulted from a strong electric field that originated in the increase in the wall voltage.
Cytoskeleton interactions in the ascus development and sporulation of Sordaria macrospora

The organization of actin during meiosis and sporulation in the ascus of the filamentous ascomycete Sordaria macrospora was determined by immunofluorescence without removal of the cell wall. Actin is present as a dense cortical network of microfilaments (MF) and plaques, a perinuclear shell of actin in prophase I of meiosis, and a complex array of MF involved in alignment of prespore nuclei and closure of spore cell membranes. The relationship of actin to the previously examined microtubule system of the ascus was determined by double-label immunofluorescence. The cytoskeletal inhibitors nocodazole, cytochalasin D and 2,3-butanedione monoxime were used to examine the roles of actin and myosin in ascus development. Microfilament and microtubule arrays are interdependant; disruption of one network results in abnormalities in the other. Both microfilaments and actin-myosin interaction are required for separation and migration of duplicated spindle pole bodies, septation and sporulation
Sexually dimorphic expression of hypothalamic estrogen receptors α and β and kiss1 in neonatal male and female rats

Release of gonadotropins in adult rodents is sex specific and dependent upon kisspeptin (Kiss1) neurons. This crucial pathway within the hypothalamic‐pituitary‐gonadal (HPG) axis is profoundly influenced by neonatal estrogens, which induce a male‐like phenotype. Classically, estrogen activity is mediated via the estrogen receptors α and β (ERα and ERβ), but the relative roles each plays in organizing the sex‐specific ontogeny of kisspeptin signaling pathways remain unresolved. Thus, the present study used in situ hybridization histochemistry (ISHH) to map the temporal and sexually dimorphic neonatal mRNA expression profiles of ERα, ERβ, and Kiss1 in the anterioventral periventricular nucleus (AVPV), medial preoptic area (MPOA), ventromedial nucleus (VMN), and arcuate nucleus (ARC), all regions critical for kisspeptin regulation of gonadotropin secretion. In general, females had higher levels of ERα, in all regions examined, a sex difference that persisted until postnatal day (PND) 19 except in the ARC. Males had significantly more ERβ expression in the AVPV at birth, but this sex difference was lost and then re‐emerged on PND 19, with females having more than males. VMN ERβ levels were higher in females until PND 19. Kiss1 was not detectable until PND 11 in the anterior hypothalamus, but expression levels were equivalent at birth in the ARC. By PND 2, ARC ERα and Kiss1 levels were abundant, sexually dimorphic (higher in females), and, respectively, showed a U‐ and a bell‐shaped pattern with age. Sex differences in ARC Kiss1 expression provide evidence that Kiss1 may play a role in the sexual dimorphic organization of the neonatal brain. These detailed profiles of neonatal Kiss1 and ERs mRNA levels will help elucidate the relative roles each plays in the sex‐specific, estrogen‐dependent organization of gonadotropin signaling pathways. J. Comp. Neurol. 519:2954–2977, 2011. © 2011 Wiley‐Liss, Inc.
A novel D104G mutation in the adenine nucleotide translocator 1 gene in autosomal dominant progressive external ophthalmoplegia patients with mitochondrial DNA with multiple deletions

Autosomal dominant progressive external ophthalmoplegia is a mitochondrial disorder characterized by multiple large deletions of mitochondrial DNA. A recent study showed pathogenic heterozygous missense mutations in the heart/skeletal muscle isoform of the adenine nucleotide translocator 1 gene in autosomal dominant progressive external ophthalmoplegia patients. In one Japanese autosomal dominant progressive external ophthalmoplegia family, we found a novel A‐to‐G heterozygous mutation at nucleotide 311 of the adenine nucleotide translocator 1 gene, which segregated with affected individuals and could not be detected in the genomic DNA sequence of 120 normal controls. This mutation converted a highly conserved aspartic acid into a glycine at codon 104. Polymerase chain reaction analysis of single muscle fibers showed the presence of one type of deletion in each fiber, suggesting clonal expansion of mitochondrial DNA with deletions. These findings support the pathogenesis of the adenine nucleotide translocator 1 gene mutation in human disease.
Synthesis and Structure−Activity Relationship of (Lactamylvinyl)cephalosporins Exhibiting Activity against Staphylococci, Pneumococci, and Enterococci

The synthesis and structure−activity relationships of a new class of vinylcephalosporins substituted with a lactamyl residue (1) are described. These compounds show excellent activity against enterococci and retain the broad spectrum activity of third-generation cephalosporins such as ceftriaxone.
Bacteria and asthma: more there than we thought

Evaluation of: Huang YJ, Nelson CE, Brodie EL et al. Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J. Allergy Clin. Immunol. 127(2), 372–381, e371–e373 (2011). In a recently performed case–control study, characteristics of the airway microbiota in suboptimally controlled adult asthmatics were compared with those of healthy, nonasthmatic adult subjects. Bacterial burden was significantly greater in asthmatic subjects. Further, increased airway microbiota variability and diversity were correlated with increased bronchial hyper-responsiveness. Although several limitations are present, this study provides an intriguing initial insight into the possible relationship between the airway microbiota and asthma pathogenesis.
Potential for improvement of population diet through reformulation of commonly eaten foods

Abstract Food reformulation Reformulation of foods is considered one of the key options to achieve population nutrient goals. The compositions of many foods are modified to assist the consumer bring his or her daily diet more in line with dietary recommendations. Initiatives on food reformulation Over the past few years the number of reformulated foods introduced on the European market has increased enormously and it is expected that this trend will continue for the coming years. Limits to food reformulation Limitations to food reformulation in terms of choice of foods appropriate for reformulation and level of feasible reformulation relate mainly to consumer acceptance, safety aspects, technological challenges and food legislation. Impact on key nutrient intake and health The potential impact of reformulated foods on key nutrient intake and health is obvious. Evaluation of the actual impact requires not only regular food consumption surveys, but also regular updates of the food composition table including the compositions of newly launched reformulated foods.
Reducing execution profiles: techniques and benefits

The interest in leveraging data mining and statistical techniques to enable dynamic program analysis has increased tremendously in recent years. Researchers have presented numerous techniques that mine and analyze execution profiles to assist software testing and other reliability enhancing approaches. Previous empirical studies have shown that the effectiveness of such techniques is likely to be impacted by the type of profiled program elements. This work further studies the impact of the characteristics of execution profiles by focusing on their size; noting that a typical profile comprises a large number of program elements, in the order of thousands or higher. Specifically, the authors devised six reduction techniques and comparatively evaluated them by measuring the following: (1) reduction rate; (2) information loss; (3) impact on two applications of dynamic program analysis, namely, cluster‐based test suite minimization (App‐I), and profile‐based online failure and intrusion detection (App‐II). The results were promising as the following: (a) the average reduction rate ranged from 92% to 98%; (b) three techniques were lossless and three were slightly lossy; (c) reducing execution profiles exhibited a major positive impact on the effectiveness and efficiency of App‐I; and (d) reduction exhibited a positive impact on the efficiency of App‐II, but a minor negative impact on its effectiveness. Copyright © 2014 John Wiley & Sons, Ltd.
CD44 Associates With EGFR and erbB2 in Metastasizing Mammary Carcinoma Cells

Type I receptor tyrosine kinases, including the epidermal growth factor receptor (EGFR) and erbB2, have been implicated in mammary carcinoma growth and metastasis. Recent evidence suggests that type I receptor signaling may be mediated by the CD44 family of transmembrane glycoproteins that also have been implicated in mammary tumor progression. Here, the authors tested whether CD44, EGFR, and erbB2 interacted and colocalized with one another in four mammary carcinoma cell lines (MCF-7, MDA-MB-231, MDA-MB-435, and MDA-MB-436) and in cytology samples obtained from patients with metastatic breast cancer. CD44 constitutively colocalized and coimmunoprecipitated with erbB2 and EGFR in all four mammary carcinoma cell lines. CD44 also colocalized with erbB2 and EGFR in all cytology samples expressing erbB2. CD44 colocalized with EGFR in cells from only 1 of 16 erbB2-negative cytology samples. These data indicate that CD44-EGFR-erbB2 protein complexes occur in a high proportion of metastatic mammary carcinomas and suggest that CD44-type I receptor colocalization may be a novel prognostic marker for aggressive mammary cancers.
CMPS 242 Final Project Report : GANTOR

Generative Adversarial Networks (GANs) are a very popular deep learning model for image recognition and generation that demonstrated the ability to generate realistic images. They consist of two competing neural networks: the generator and the discriminator. The generator creates samples from the distribution seen in the training data. The discriminator classifies samples to be correct or incorrect. Both are trained simultaneously with the goal to improve the generator’s creations as well as the discriminator in its decisions in order to ultimately generate samples that mimic actual data.
The high tolerance to aluminium in crucian carp (Carassius carassius) is associated with its ability to avoid hypoxia

It is well known that aluminium is the principle toxicant killing fish in acidified freshwater systems, and it has been shown that crucian carp (Carassius carassius) can survive exposures to aqueous aluminium levels toxic to most other freshwater fish species. The crucian carp has a remarkable ability to survive anoxic conditions, and the aim of the present study was to reveal if the tolerance to aluminium can be associated with the ability to survive prolonged anoxia. Crucian carps were exposed to either acidic Al-rich water (pH 5.8; 960 μg Al/l), acidic Al-poor water (pH 5.8; 50 μg Al/l) or untreated control water (pH 6.5; 50 μg Al/l). Blood, muscle and gill samples were collected from exposed fish, and closed respirometry was performed to measure critical O2-tension an normoxic O2-consumption. The results show an increased gill surface area in Al-exposed fish, while the critical O2-tension did not change. The normoxic O2-consumption was lower in Al-exposed fish and might be due to a reduced metabolic rate. The results suggest that crucian carp exposed to aluminium do not become hypoxic, since haematocrit, plasma lactate and blood ethanol did not differ from that of control fish after 14 days of exposure. We also observed an initial loss of plasma chloride and sodium, followed by a stabilisation of these ions at a lower level than in control fish. The decrease in plasma ions caused a transient increase in haematocrit and water content in muscle tissue, returning to control levels when the ion concentrations stabilised, suggesting that the water balance was restored. We conclude that the high tolerance to aluminium in crucian carp is associated with its ability to avoid hypoxia as well as an ability to counteract a continuous loss of plasma ions.
Microbial Community Analysis During Composting of Digested Sludge and Sawdust by Using Quinone Profile and Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis

Microbial community structure during the composting of digested sewage sludge and sawdust was analyzed by a combination of quinone profile and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The change in total quinine content (TQ) indicated that microbial biomass reached a peak followed by a decrease, whereas the divergence of quinine (DQ) showed that the microbial community diversity increased continuously during the composting process. The PCR-DGGE clarified community changes at species level and the differences in the microbial communities were also determined. The combination of culture-independent methods revealed the community enough to evaluate the composting process.
Combinatorics of distance-based tree inference

Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206–13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances.