Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptosporidium Pathogenicity and Virulence

SUMMARY Cryptosporidium is a protozoan parasite of medical and veterinary importance that causes gastroenteritis in a variety of vertebrate hosts. Several studies have reported different degrees of pathogenicity and virulence among Cryptosporidium species and isolates of the same species as well as evidence of variation in host susceptibility to infection. The identification and validation of Cryptosporidium virulence factors have been hindered by the renowned difficulties pertaining to the in vitro culture and genetic manipulation of this parasite. Nevertheless, substantial progress has been made in identifying putative virulence factors for Cryptosporidium. This progress has been accelerated since the publication of the Cryptosporidium parvum and C. hominis genomes, with the characterization of over 25 putative virulence factors identified by using a variety of immunological and molecular techniques and which are proposed to be involved in aspects of host-pathogen interactions from adhesion and locomotion to invasion and proliferation. Progress has also been made in the contribution of host factors that are associated with variations in both the severity and risk of infection. Here we provide a review comprised of the current state of knowledge on Cryptosporidium infectivity, pathogenesis, and transmissibility in light of our contemporary understanding of microbial virulence.
Fuzzy logic and local features based medical image segmentation

A fuzzy logic based active contour model for medical image segmentation is proposed. Image local features are incorporated in active contour model. Fuzzy logic is used to assign weights to pixels. Higher weights are assigned to pixels having less entropy and local variance whereas Lower weights are assigned to pixels having high entropy and local variance. Simulation results show the improvement in segmentation results in terms of efficiency and accuracy.
Introduction: How Languages Fit Together in Codemixing

In virtually all bilingual corpora empirically studied, mixed discourse is ovenvhelmingly constituted of lone elements, usually major-class content words, of one language embedded in the syntax of another (Berk-Seligson,l986; Nortier, 1989; Poplack, Sankoff, & Miller, 1988; Treffers-Daller, 1994; to name but a few). The status of these items is notoriously ambiguous. They may be codeswitches or borrowings or yet another type of language mixture. They are at the heart of a fundamental disagreement among rcscarcliers about data, not so much how they should be gathered (although this too is contentious), but rather how types of language mixture should be classified. Are these lone items iritegrnted into the grammatical system in which they are embedded (i.e., borrolved) or conditioned by some interaction between grammars (codeswitches)? Empirical study has confirmed early claims (e.g., Haugen, 1950) that major-class content words such as nouns, verbs, and adjectives are the most likely to be borrowed (e.g., Poplack, et al., 1988; van Hout & Muysken, 1994). The papers in this issue ofthe hirer-iinfionnl J O Z W I ~ ~ ofEilirigzinlisrii are consecrated to the study of the behavior of such items in bilingual discourse. Though other linguistic elements are also borrowed occasionally (e.g., tags, discourse markers, or grammatical function ivords), these generally are instantiations of other products of language contact (e.g., de Rooij, 1995; Poplack 1980). The conclusions of the papers assembled here thus apply only to lone other-language content lvords. Classic indications of loanword integration have had mediocre results in disambiguating the status of lone content items because different measures produce conflicting results. While these items are usually syntactically positioned according to the language in which they are embedded, they often appear to retain the phonetic properties of the donor language and sometimes appear to conserve donor-language morphology. Disagreement over the appropriate classification of lone items has resulted in a range of codeswitching theories. At one end of the spectrum, where lone items are defined as codeswitches, researchers tend to consider the relationship betiveen languages in bilingual discourse asymmetrical, with one grammar clearly predominating (e.g., Joshi, 1985;
Labor Market Outcomes under Search , Matching , and Endogenous Contact Rates 1

Building upon a continuous-time model of search with Nash bargaining in a stationary environment, we analyze the effect of changes in minimum wages on labor market outcomes and welfare. While minimum wage increases may or may not lead to increases in unemployment in our model, they can be welfare-improving to labor market participants on both the supply and demand sides of the labor market. Key determinants of the welfare impact of a minimum wage increase is the Nash bargaining power parameter and the matching function. We discuss identification of this model using Current Population Survey data on accepted wages and unemployment durations, and demonstrate that the bargaining power parameter is not identified when the distribution of match values belongs to a location-scale family. By incorporating a limited amount of information from the demand side of the market, we are able to obtain credible and precise estimates of all primitive parameters, including bargaining power and estimable parameters characterizing the matching function. We show that an efficient level of the minimum wage in September 1996 would have been approximately twice its then current level of $4.25. When we allow for endogenous contact rates, the efficient minimum wage would have been $3.36. However, we find no empirical evidence to support the hypothesis that contact rates were impacted by minimum wage changes observed over this period, casting some doubt on the advisability of reductions in the minimum wage.
Order-Preserving Moves for Graph-Cut-Based Optimization

In the last decade, graph-cut optimization has been popular for a variety of labeling problems. Typically, graph-cut methods are used to incorporate smoothness constraints on a labeling, encouraging most nearby pixels to have equal or similar labels. In addition to smoothness, ordering constraints on labels are also useful. For example, in object segmentation, a pixel with a “car wheel” label may be prohibited above a pixel with a “car roof” label. We observe that the commonly used graph-cut \alpha-expansion move algorithm is more likely to get stuck in a local minimum when ordering constraints are used. For a certain model with ordering constraints, we develop new graph-cut moves which we call order-preserving. The advantage of order-preserving moves is that they act on all labels simultaneously, unlike \alpha-expansion. More importantly, for most labels \alpha, the set of \alpha-expansion moves is strictly smaller than the set of order-preserving moves. This helps to explain why in practice optimization with order-preserving moves performs significantly better than \alpha-expansion in the presence of ordering constraints. We evaluate order-preserving moves for the geometric class scene labeling (introduced by Hoiem et al.) where the goal is to assign each pixel a label such as “sky,” “ground,” etc., so ordering constraints arise naturally. In addition, we use order-preserving moves for certain simple shape priors in graph-cut segmentation, which is a novel contribution in itself.
Recognition memory and synaptic plasticity in the perirhinal and prefrontal cortices

Work is reviewed that relates recognition memory to studies of synaptic plasticity mechanisms in perirhinal and prefrontal cortices. The aim is to consider evidence that perirhinal cortex and medial prefrontal cortex store rather than merely transmit information necessary for recognition memory and, if so, to consider what mechanisms are potentially available within these cortices for producing such storage through synaptic change. Interventions with known actions on plasticity mechanisms are reviewed in relation to their effects on recognition memory processes. These interventions importantly include those involving antagonism of glutamatergic and cholinergic receptors but also inhibition of plasticity consolidation and expression mechanisms. It is concluded that there is strong evidence that perirhinal cortex is involved in information storage necessary for object recognition memory and, moreover, that such storage involves synaptic weakening mechanisms including the removal of AMPA glutamate receptors from synapses. There is good evidence that medial prefrontal cortex is necessary for associative and temporal order recognition memory and that this cortex expresses plasticity mechanisms that potentially allow the storage of information. However, the case for medial prefrontal cortex acting as a store requires further support. © 2012 Wiley Periodicals, Inc.
Global, synchronous oscillations in cytosolic calcium and adherence in bradykinin-stimulated Madin-Darby canine kidney cells.

AIMS AND METHODS Intercellular Ca2+ oscillations are a universal mode of signalling in both excitable and non-excitable cells. Here, we study the relationship between Ca2+ signalling and coherent changes in adhesion properties by measuring the transepithelial impedance across bradykinin-stimulated Madin-Darby canine kidney (MDCK) cell layers grown on a microelectrode. During hormone stimulation, the impedance is found to oscillate, reflecting that the cells undergo morphological/adhesive alterations with high spatio-temporal organization. The experiments are supplemented with parallel, digital imaging fluorescence microscopy of bradykinin-induced single-cell Ca2+ oscillations. RESULTS In agreement with previous experiments, MDCK cells are found to elicit synchronous, multicellular Ca2+ oscillations in response to hormone stimulus. The periods of the Ca2+ oscillations and the electrical fluctuations are found to coincide. Further, blocking of gap junctions by 18alpha-glycyrrhetinic acid causes a loss of synchrony in Ca2+ signals and inhibition of impedance oscillations, emphasizing the importance of gap junctions in the signal transduction process. CONCLUSION Based on these observations it is concluded that the co-ordinated adhesive changes in MDCK cells are a direct consequence of synchronized Ca2+ oscillations. Calcium signalling represents an efficient way of organizing physiological responses in a tissue. A possible functional implication of the structural changes might be to modulate transportation of various substances across the cell sheet.
Development and evolution of melanophore patterns in fishes of the genus Danio (Teleostei: Cyprinidae)

Pigmentation patterns in vertebrates have become an important model for those interested in mechanisms of pattern determination. I present detailed information on the development of melanophore patterns in the zebrafish, Danio rerio, five close relatives of that species, and an outgroup. The comparison of the ontogeny of melanophore patterns in this group is an important first step towards understanding the developmental basis of the interspecific variation. Pigment patterns in this group range from no distinct patterning at all to stripes of differing numbers and widths to reticulated stripes. Species examined form identical larval patterns and follow a common sequence of events from which different elements are eliminated or altered to produce the variety of patterns seen in the group. As flexion is completed, melanophores move from larval positions onto the flanks of the fish. In D. rerio, D. rerio ‘leo,’ D. kerri, and D. malabaricus, xanthophores become established on the body of the fish as the melanophores move; erythrophores become established on the flanks of D. albolineatus and D. sp. cf. aequipinnatus. An increase in melanophore number, begun at this time, continues at a higher rate in D. rerio, D. kerri, D. sp. cf. aequipinnatus and Tanichthys albonubes than in the other three species. This results in a greater number of melanophores on adults in those species with a higher rate of melanophore increase. No distinct pattern forms, except on the caudal peduncle, in D. albolineatus. In all other Danio species, melanophore stripes form first below then above the horizontal myoseptum. Additional stripes are added first below then above these initial two stripes. D. kerri develops fewer, wider melanophore stripes than D. rerio. After initial stripe formation, D. malabaricus and D. sp. cf. aequipinnatus both developed vertical pattern elements and reticulations in the melanophore pattern. Differences in patterns between species are similar in several cases to described mutants of the zebrafish, suggesting that some aspects of interspecific pigmentation pattern variation may be under relatively simple genetic control. J. Morphol. 241:83–105, 1999. © 1999 Wiley‐Liss, Inc.
NaCl does not affect hypothalamic noradrenergic input in deoxycorticosterone acetate/NaCl and Dahl salt-sensitive rats.

Previous studies from our laboratories demonstrated that dietary NaCl supplementation in NaCl-sensitive spontaneously hypertensive rats elevates blood pressure, increases peripheral sympathetic nervous system activity, and depresses endogenous norepinephrine stores and turnover in the anterior hypothalamus. These findings suggest that reduced noradrenergic input to sympathoinhibitory neurons in anterior hypothalamus contributes to NaCl-sensitive hypertension in spontaneously hypertensive rats. The current study tested the hypothesis that dietary NaCl supplementation depresses endogenous norepinephrine stores and turnover in anterior hypothalamus of two other NaCl-sensitive models of hypertension, the Dahl salt-sensitive rat and the deoxycorticosterone acetate/NaCl hypertensive rat, thus increasing blood pressure by reducing noradrenergic input to the anterior hypothalamus. Dahl salt-sensitive rats were fed a high (8%) NaCl diet, and deoxycorticosterone acetate/NaCl rats rats drank 1% NaCl solution ad libitum for 2 or 4 weeks. Age-matched Dahl salt-sensitive rats fed a basal 1% NaCl diet and uninephrectomized Sprague-Dawley rats drinking tap water were controls. Regional brain catecholamines were determined by high-performance liquid chromatography with electrochemical detection. Norepinephrine turnover in hypothalamus (anterior, posterior, and ventral regions) and brain stem (pons and medulla) was assessed using the dopamine beta-hydroxylase inhibitor 1-cyclohexyl-2-mercapto-imidazole. High NaCl treatment caused significant elevations in blood pressure in Dahl salt-sensitive and deoxycorticosterone acetate/NaCl rats, but endogenous norepinephrine levels and turnover rates were not significantly different in anterior hypothalamus or any other brain region studied between the NaCl-supplemented and control groups. (ABSTRACT TRUNCATED AT 250 WORDS)
Grounded theory: the missing methodology on the interpretivist agenda

There has been considerable discussion in recent years over the application of interpretive methodologies such as phenomenology, hermeneutics, and semiotics within the field of marketing research, particularly consumer behaviour. However, while these approaches have inspired a wealth of publications, scant attention has been paid to the potential of grounded theory. This is attributed largely to misconceptions regarding both the principles of the method and the two distinct approaches associated with the original authors, Glaser and Strauss (1967). The paper outlines the development of the method and explicates the philosophy underpinning its procedures. Finally, it suggests that grounded theory if applied in its true sense has scope and potential for the study of consumer behaviour and consumption experiences given its emphasis on context, theoretical emergence, and the social construction of realities.
Network on Chip and Parallel Computing in Embedded Systems

In order to cope with the increasing application requirements, heterogeneous MPSoC are considered as the major solution of future embedded systems thanks to their advantages in performance and low power dissipation. However traditional communication infrastructure such as a bus or a point to point are not scalable and become communication bottleneck for large systems. Network on chip (NoC) architectures have been proposed to handle this communication problem. One of the most critical problem in NoC based heterogeneous MPSoC is how to map an application on this platform. Due to the large solution search space, design of tools that can automate this step is of major importance. In this paper, we present a new tool for mapping applications on NoC based heterogeneous MPSoC. A set of multi-objective optimization algorithms are used to explore the mapping space and to find a set of Pareto optimal solutions.
Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking

The automated docking program AutoDock was used to dock nine phosphatidic acids (PAs), six phosphatidylcholines, five phosphatidylethanolamines, four phosphatidylglycerols, one phosphatidylinositol and two phosphatidylserines, which have two identical saturated fatty acid residues with an even numbers of carbon atoms, onto the active site of Streptomyces sp. PMF phospholipase D (PLD). Two PAs with one double bond on the fatty acid chain linked to the C2 of the glycerol residue were also docked. In general, binding energies become progressively more negative as fatty acid residues become longer. When these residues are of sufficient length, one is coiled against a hydrophobic cliff in a well that also holds the glycerol and phosphate residues and the head group, while the other generally is bound by a hydrophobic surface outside the well. Phosphatidylcholines have the only head group that is firmly bound by the active site, giving a possible structural explanation for the low selectivity of Streptomyces PLD for other phospholipid substrates. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Teaching Management and Finance through Simulation - Choosing the Proper Paradigm

Compared to analytical modelling, simulation has sometimes a greater expressive and computational power, especially for a behavioural study of an activity, system, organisation and other topics from the Social Sciences, which an analytic study cannot adequately achieve. In this paper simulation is discussed as a support for teaching and knowledge transfer: a model can be built and used to dynamically show and explain a particular phenomenon through direct experiments, though contributing to a “maieutical” way of learning by the students (learning by doing). Also team work is triggered by using simulation models as a educational tool. In particular, three simulation paradigms are described, along with their potential applications and points of strength and weakness. Management and Finance are the focus of the work, but the same considerations may be extended to other social disciplines and sciences. Note: Although the article is the result of a joint research project, the paragraphs are divided among the authors as follows: paragraphs 1 and 5 are jointly written and equally divided among all the authors; paragraph 2 is by Nicola Miglietta; paragraph 3 is by Anna Maria Bruno and Marco Remondino; paragraph 4 is by Marco Remondino.
The relation between brain natriuretıc peptide and patent ductus arteriosus in premature infants

Sum mary Aim: To compare brain natriuretic peptide level and some of the echocardiographic parameters of premature infants and to search its value for the diagnosis of patent ductus arteriosus. Material and Method: Fifty infants born before the 34th gestational week in the neonatology clinic of Bakırkoy Obstetrics and Children’s Education Hospital between March 2009 and August 2009 were inspected prospectively. Patients with patent ductus arteriosus constituted Group 1 (n=20) and patients without patent ductus arteriosus constituted Group 2 (n=30). The diagnosis of patent ductus arteriosus was made by M-mode and Doppler echocardiography on the 7th day postnatally. Ductus diameter, left atrium aortic root diameter ratio, left ventricular end diastolic diameter, interventricular septum thickness, left ventricular posterior wall thickness, ejection fraction and fractional shortening were evaluated. The infants with hemodynamically significant patent ductus arteriosus were treated. Brain natriuretic peptide was evaluated on the 1st, 3rd and 7th days of postnatal age in all patients and also on the 3rd day after treatment. For statistical analysis SPSS for Windows 15.0 was used. The study was conducted after obtaining informed consent from the patients and was approved with the decision of the ethics committee (number 231, date 12-6-2009). Results: Sex, gestational age and birth weight were similar in both grups. When brain natriuretic peptide level was compared with ductus diameter, left atrium aortic root diameter ratio and left ventricular end diastolic diameter values, the results were found to be statistically significant (p<0.05). When comparison was made with interventricular septum thickness, left ventricular posterior wall thickness, ejection fraction and fractional shortening values, the results were found to be statistically insignificant (p>0.05). Brain natriuretic peptide level decreased significantly after treatment. Conclusions: Brain natriuretic peptide level was found be higher in infants with patent ductus arteriosus compared to infants without patent ductus arteriosus. It was shown that ductus diameter, left atrium aortic root diameter ratio and left ventricular end diastolic diameter were related with brain natriuretic peptide levels. (Turk Arch Ped 2012; 47: 92-6)
Evidence for two different heat transduction mechanisms in nociceptive primary afferents innervating monkey skin.

1. Mechano‐ and heat‐sensitive A fibre nociceptors (AMHs) and C fibre nociceptors (CMHs) in hairy skin (forty‐six AMHs and twenty‐one CMHs) and in glabrous skin (fifty‐nine AMHs and ten CMHs) of anaesthetized monkeys were tested with a 30 s, 53 degrees C heat stimulus, delivered by a laser thermal stimulator (0.1 s rise time, 7.5 mm diameter). 2. Two types of heat response were observed in hairy skin AMHs. Type I AMHs had a peak discharge towards the end of the stimulus, response latencies to heat of up to several seconds, a median heat threshold greater than 53 degrees C, and a mean conduction velocity of 25 m s‐1 (n = 33). Type II AMHs had a peak discharge within 1‐3 s, a mean response latency of 120 ms, a median heat threshold of 46 degrees C, and a mean conduction velocity of 15 m s‐1 (n = 13). Type I AMH fibres were sensitized to heat, whereas heat responses of type II AMHs were suppressed following the intense heat stimulus. 3. In glabrous skin, only type I AMHs were found. The absence of type II AMHs is consistent with the absence of first pain to heat in glabrous skin. 4. C fibre nociceptors in hairy skin had a peak discharge near stimulus onset, a mean response latency of 100 ms and a median heat threshold of 41 degrees C. Heat responses of CMHs in glabrous skin were not significantly different from those in hairy skin. 5. Only type II AMHs had response latencies that were short enough to explain first pain to heat. Heat thresholds of type II AMHs were significantly higher than those of CMHs. 6. These results suggest two different heat transduction mechanisms in nociceptive afferents. For one, heat energy is quickly transduced into action potentials, and the peak discharge is reached soon after stimulus onset. For the other, the transduction of heat is distinctly slower, and the peak discharge occurs near the end of the stimulus. Chemically mediated sensitization may be involved in the second transduction mechanism.