Miracle-dz/UniFAR-FTUs huggingface dataset:
Continuum limits of particles interacting via diffusion

We consider a two-phase system mainly in three dimensions and we examine the coarsening of the spatial distribution, driven by the reduction of interface energy and limited by diffusion as described by the quasistatic Stefan free boundary problem. Under the appropriate scaling we pass rigorously to the limit by taking into account the motion of the centers and the deformation of the spherical shape. We distinguish between two different cases and we derive the classical mean-field model and another continuum limit corresponding to critical density which can be related to a continuity equation obtained recently by Niethammer andOtto. So, the theory of Lifshitz, Slyozov, and Wagner is improved by taking into account the geometry of the spatial distribution.
Development of an imaging system dedicated to the acquisition analysis and multispectral characterisation of skin lesion. (Développement d'un outil d'imagerie dédié à l'acquisition, à l'analyse et à la caractérisation multispectrale des lésions dermatologiques)

Visual evaluation of cutaneous lesions is the analysis the most commonly performedby dermatologists. This diagnostic is mainly done by naked eye and is based on criterionsuch as the size, shape, symmetry but principally on colour of the lesions. However, thisanalysis is subjective because it depends on the practician experience and the acquisitionconditions. We propose in this dissertation (1) the development of a multispectralcamera specifically dedicated for dermatological use. This device is based on a filterwheel composed of interferential filters and a neural network-based algorithm, generatinga hyperspectral cube of cutaneous data. This setting combines advantage of both spectrophotometer(spectral information) and digital camera (spatial information). Its maininterest is also to provide reproducible information which is independent of the acquisitionconditions. The setting-up of an acquisition protocol of healthy skin data from five of thesix exisiting skin phototypes allows the validation of our system by comparing spectragenerated by our system and theoretical spectra acquired by professional spectrophotometer. (2) Skin spectral reflectance provides precious information because it is directly linkedto the skin chromophore composition. Quantitative measure of cutaneous tissue opticalproperties can be based on the modelisation of light propagation in skin. For this purpose,we based our method on Kubelka-Munk model with which we associated an optimizationmethod based on evolutionary algorithm. This method helps for the model inversion.Using this approach, quantification of diverse parameters of skin can be obtained such asmelanin and haemoglobin. (3) The validation of this model is performed on disease skindata (vitiligo and melasma) and allows to quantify difference between healthy and affectedskin area within a single image.
Centromeric alphoid DNA heteromorphisms of chromosome 22 revealed by FISH‐technique

To the Editor: We read with interest the article of Verma et al. (1) regarding heteromorphisms of the centromeric alphoid DNA of chromosome 21. They pointed out, that the size of this region can vary between absent, small, medium, large and very large. The two groups with small and absent signals, respectively, present in about 25% of the studied chromosome 21 cases, are of special interest for the interpretation of interphase cytogenetics results. However, it would be of importance to know if this size variation can be observed exclusively in chromosome 21, or in other chromosomes, too. We performed a comparable investigation with the fluorescence in situ hybridization (FISH) techniqiue using the commercially available biotin-labeled alpha satellite DNA probe specific for D22Z1 and D14Z1 (Oncor) of chromosomes 22 and 14. It seems to exist a similar range of chromosomes 22 presenting with small to (nearly) absent alphoid regions as it has been proven by Verma et al. (1) for chromosome 21. We studied in summary ten cases with different chromosome 22 marker chromosomes. Five cases of Philadelphia chromosome positive chronic myeloic leukemias (CML) (2, 3) and five cases of patients suffering from cat eye syndrome (CES) (4). In each CML case two different alphoid regions of chromosome 22 could be analyzed, in the CES cases three different ones, due to the dicentric marker chromosome 22. For one of five cases each, a polymorphism of one chromosome 22, with small to almost absent alphoid region was identified (Fig. 1). In summary, two of 25 studied alphoid regions of chromosome 22 (8%) presented with almost undetectable alphoid regions in the metaphase and were completely undetectable in the interphase nuclei. Thus, the interpretation of results in interphase cytogenetic studies using alphoid DNA-probes must be done very carefully, especially, using the probes for chromosomes 13/21 and 14/22. Interestingly, neither Verma and colleagues reported comparable size variations in the alphoid region of chromosome 13, nor were variations found in the alphoid regions of chromosome 14. Nevertheless more data, particularly on the range of polymorphisms with absent and small aiphoid regions for all the other human chromosomes would be desirable.
Electropharmacologic Effects of a New Phosphodiesterase III Inhibitor, Toborinone (OPC‐18790), Assessed in an In Vivo Canine Model

Summary: Electropharmacologic effects of a new phosphodiesterase (PDE) III inhibitor toborinone (OPC‐18790) were assessed in a halothaneanesthetized, closed‐chest canine model. Toborinone, 0.03 mg/kg, increased ventricular contractility, decreased total peripheral resistance, and inhibited intraventricular conduction without changing other cardiovascular parameters. A clinically relevant dose of 0.3 mg/kg increased heart rate, systolic blood pressure, and cardiac output, decreased preload to the left ventricle, enhanced atrioventricular nodal conduction, and shortened repolarization and the vulnerable period of the ventricle, in addition to enhancing the effects observed after the low dose. A high dose of 3 mg/kg of toborinone decreased systolic, mean, and diastolic pressures and prolonged the effective refractory period (ERP) in addition to the effects observed after the middle dose. No further change was detected in ventricular repolarization. Most of the cardiohemodynamic effects can be explained by the PDE III inhibition by toborinone. With regard to electrophysiologic properties, the prolongation of intraventricular conduction time and ERP by toborinone suggests sodium channel inhibition. The lack of the prolongation of ventricular repolarization suggests that previously demonstrated inhibition of IKr and IK1 and increased ICa‐L by toborinone might be counteracted by factors such as the cyclic AMP‐dependent outward currents, IKs and ICl.
The Circadian Clock of the Unicellular Eukaryotic Model Organism Chlamydomonas reinhardtii

Abstract The green unicellular alga Chlamydomonas reinhardtii, also called 'green yeast', emerged in the past years as a model organism for specific scientific questions such as chloroplast biogenesis and function, the composition of the flagella including its basal apparatus, or the mechanism of the circadian clock. Sequencing of its chloroplast and mitochondrial genomes have already been completed and a first draft of its nuclear genome has also been released recently. In C. reinhardtii several circadian rhythms are physiologically well characterized, and one of them has even been shown to operate in outer space. Circadian expression patterns of nuclear and plastid genes have been studied. The mode of regulation of these genes occurs at the transcriptional level, although there is also evidence for posttranscriptional control. A clock-controlled, phylogenetically conserved RNA-binding protein was characterized in this alga, which interacts with several mRNAs that all contain a common cis-acting motif. Its function within the circadian system is currently under investigation. This review summarizes the current state of the knowledge about the circadian system in C. reinhardtii and points out its potential for future studies.
Specific features of telomerase RNA from Hansenula polymorpha

Smekalova et al. report the identification of telomerase RNA (TER) from a thermotolerant yeast, Hansenula polymorpha. Conserved RNA structural elements were modeled in comparison to TERs from other budding yeast species. Unexpectedly, telomerase holoenzyme copied one nucleotide past the predicted template 5′ boundary to add a nontelomeric nucleotide in vitro. The extra thymidine added in vitro was shown to be added in vivo at the extreme chromosome 3′ end. TER mutagenesis and in vivo reconstitution suggest that addition of the extra thymidine functions to limit telomere elongation, revealing a new mechanism of telomerase regulation at the telomere.
The A Adenosine Receptor Mediates cAMP Responses to Adenosine Receptor Agonists in Human Intestinal Epithelia (*)

Adenosine is thought to be a major effector in immunological stimulation of Cl secretion in intestinal epithelia. Previous studies indicate that both apical and basolateral domains of intestinal epithelial cells possess functionally defined adenosine receptors. However, it is unclear whether the same receptor subclass is expressed, what the receptor subclass(es) is, or how the receptors signal the Cl secretory response. We now characterize the intestinal epithelial adenosine receptor subtype using the model epithelium, T84. Both apical and basolateral adenosine receptor agonist response profiles revealed a hierarchy (ED) of 5′-(N-ethylcarboxamido)adenosine > adenosine > CGS-21680. Similarly, inhibition studies revealed identical ID hierarchies for apical and basolateral antagonism by xanthine amine congener > 1,3-diethyl-8-phenylxanthine > aminophylline. Analyses of both agonist and antagonist pharmacological hierarchies in Chinese hamster ovary cells stably expressing the A receptor revealed these same hierarchies. Northern blots performed on RNA extracted from polarized T84 monolayers demonstrated no detectable message for A1 or A adenosine receptor, but strong hybridization was detected for the A adenosine receptor. Subsequent Northern blots of RNA prepared from human alimentary tract revealed that A adenosine receptor message was heavily expressed throughout the colon, in the appendix, and more modestly expressed in the small intestine (ileum). Analyses of cAMP generation in T84 cells in response to adenosine indicated that the basolateral A receptor elicits Cl secretion through this signaling pathway. Stimulation of Cl secretion through the apical A receptor exhibited relatively small but significant increases in cAMP compared with basolateral stimulation. The protein kinase A inhibitor H-89, used at concentrations that did not affect short circuit current responses to the Ca-mediated agonist carbachol, effectively inhibited short circuit current elicited by either apical or basolateral adenosine. These data suggest that the major intestinal epithelial adenosine receptor is the A subclass, which is positively coupled to adenylate cyclase. Such observations have potentially important implications for the treatment of diarrheal diseases.
Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel‐like activity, and the role of the amidated C‐terminus

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C‐terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C‐terminus introduced a negative charge at an all‐positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide's primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel‐like activity on anionic bilayers with a well‐defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans‐negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
The effect of the temperature of incubation on the spread of Herpes simplex virus in an immune environment in cell culture.

The MP variant of Herpes simplex virus was used in experiments designed to determine the relative rates of spread of virus infection from infected to noninfected FL cells incubated at different temperatures in the presence of antibody. Preliminary experiments showed that one infectious particle is sufficient to infect a cell, and that an infected cell will almost invariably produce a macroplaque when deposited on a monolayer culture and incubated at 37°C in the presence of antibody. The conditions required to effect infection of all or most cells in an FL cell culture were also determined. On the basis of these experiments, the mean size of macroplaques formed by infected cells added to the monolayer culture and incubated in the presence of antibody at 30°, 31°, 34°, 37°, and 39.5°C were determined. From these experiments it was learned that the largest macroplaque area is attained after 4 days of incubation at 37°C. Below and above 37°C the mean size of macroplaques after a similar incubation period is progressively reduced. In view of the absence of the cell fluid-cell transmission of infection in the presence of antibody in the fluid phase, the increase in macroplaques may be taken as a measure of the direct cell-cell transmission of the virus from infected to noninfected cells. The significance of the observed rates of spread of infection at different temperatures with respect to a) virus formation at different temperatures, b) virus release from infected cells at different temperatures, and c) recurrent herpetic infections in man were discussed.
Pathophysiological significance of c-jun N-terminal kinase in acetaminophen hepatotoxicity

Background: Acetaminophen (APAP) overdose is the leading cause of acute liver failure in the US. Although substantial progress regarding the mechanisms of APAP hepatotoxicity has been made in the past several decades, therapeutic options are still limited and novel treatments are clearly needed. c-jun N-terminal Kinase (JNK) has emerged as a promising therapeutic target in recent years. Areas covered: Early studies established the critical role of JNK activation and mitochondrial translocation in APAP hepatotoxicity. However, this concept has also been challenged. Initial studies failed to reproduce the protection of JNK deficiency in APAP toxicity and concerns over off-target effects of JNK inhibitors and even in knock-out mice are increasing. Interestingly, recent studies have even shown that liver injury can be altered with or without effects on JNK activation. The current review addresses these discrepancies and tries to explain or reconcile some of the conflicting results. Expert opinion: JNK is a potential therapeutic target for APAP poisoning. However, controversies still exist regarding its actual role in APAP hepatotoxicity. Future studies are warranted for more in-depth testing of specific inhibitors in well-defined preclinical models and human hepatocytes before JNK can be considered a relevant therapeutic target for APAP poisoning.
High-performance Computational Framework for Phrase Relatedness

TrWP is a text relatedness measure that computes semantic similarity between words and phrases utilizing aggregated statistics from the Google Web 1T 5-gram corpus. The phrase similarity computation in TrWP is costly in terms of both time and space, making the existing implementation of TrWP impractical for real-world usage. In this work, we present an in-memory computational framework for TrWP, which optimizes the corpus search using perfect hashing and minimizes the required memory cost using variable length encoding. Evaluated using the Google Web 1T 5-gram corpus, we demonstrate that the computational speed of our framework outperforms a file-based implementation by several orders of magnitude.
Proliferation of Intrahyphal Hyphae Caused by Disruption ofcsmA, Which Encodes a Class V Chitin Synthase with a Myosin Motor-Like Domain in Aspergillus nidulans

ABSTRACT We have found that the Aspergillus nidulans csmA gene encodes a novel protein which consists of an N-terminal myosin motor-like domain and a C-terminal chitin synthase domain (M. Fujiwara, H. Horiuchi, A. Ohta, and M. Takagi, Biochem. Biophys. Res. Commun. 236:75–78, 1997). To clarify the roles of csmA in fungal morphogenesis, we constructed csmA null mutants. The growth rate of the mutant colonies was almost the same as that of the wild-type strain, but hyphal growth was severely inhibited when a chitin-binding reagent, Calcofluor white or Congo red, was added to the medium. Moreover, morphological abnormalities in tip growth and septum formation were identified microscopically. Proliferation of intracellular new hyphae, called intrahyphal hyphae, which behaved as intrinsic hyphae, was the most striking phenotypic feature among them. These phenotypes were not suppressed when the only chitin synthase domain of csmA was expressed under the control of thealcA promoter, whereas they were suppressed when the intact form of csmA was expressed. Therefore, it was concluded that the product of csmA (CsmA) has important roles in polarized cell wall synthesis and maintenance of cell wall integrity and that the myosin motor-like domain is indispensable for these functions.
Efficient timing analysis with known false paths using biclique covering

We improve the efficiency of static timing analysis when false paths are considered. The efficiency of timing analysis is critical for the performance driven optimization program because timing analysis is invoked heavily in the inner loop. However, when false paths are dealt with in timing analysis, a large number of tags needs to be created and propagated, thus deteriorating efficiency. In this paper, weminimize the number of the tags through a biclique-covering approach, which iteratively removes a tag if the false path information in the tag is covered by the union of other tags.With the produced tags, we remove the false path timing and guarantee to cover the nonfalse path timing. Since the minimum biclique covering of the general bipartite graph is NP complete [Indag. Math., vol. 39, p. 211, 1977], [Discrete Math., vol. 149, no. 1–3, p. 159, 1996], we use a minimal degree ordering approach to perform the biclique-covering minimization. The experimental results show significant reduction on the number of tags.
Kinematic analysis of a Stewart platform manipulator

The Stewart platform manipulator is a fully parallel kinematic linkage system that has major mechanical differences from typical serial link robots. Its closed kinematic chain and parallel linkage structure give it greatly rigidity and a high force-to-weight ratio. However, due to the lack of efficient algorithms for solving the kinematic equations, its potential application as a robotic manipulator is difficult to realize. A simplified algorithm for solving the forward kinematics of a six-link, six-degrees-of-freedom Stewart platform is proposed. The algorithm involves solving only three nonlinear simultaneous equations. Explicit expressions for some special configurations that can directly give the geometric limitations to motion (such as the highest position, lowest position, most titled position, most twisted position, etc.) in terms of the geometric dimensions of the platforms and the legs are derived. This information is being used to direct the design of an actual Stewart platform. >
Energy efficient stepper drives for CNC machines

The paper demonstrates the results of the energy efficient stepper drive development for the machines with conventional numerical control. The nonlinear positioning was proposed which provided up to the 30 % energy saving comparing to the symmetrical positioning mode. The nonlinear positioning involved the current amplitude modulation of the stepper drive in the positioning cycle. It was proposed to control the current amplitude of the stepper drive through the additional control loop under the tracking mode. It contributed to the increase of the dynamic moment without regard to the stepper drive load. The proposed solutions provide the positioning stability and the lack of the faults under the heavy load imposed on the stepper drive motor.
5-Azacytidine Induces Anoikis, Inhibits Mammosphere Formation and Reduces Metalloproteinase 9 Activity in MCF-7 Human Breast Cancer Cells

Cancer stem cells are a subset of cancer cells that initiate the growth of tumors. Low levels of cancer stem cells also exist in established cancer cell lines, and can be enriched in serum-free tumorsphere cultures. Since cancer stem cells have been reported to be resilient to common chemotherapeutic drugs in comparison to regular cancer cells, screening for compounds selectively targeting cancer stem cells may provide an effective therapeutic strategy. We found that 5-azacytidine (5-AzaC) selectively induced anoikis of MCF-7 in suspension cultures with an EC50 of 8.014 µM, and effectively inhibited tumorsphere formation, as well as the migration and matrix metalloproteinases-9 (MMP-9) activity of MCF-7 cells. Furthermore, 5-AzaC and radiation collaboratively inhibited MCF-7 tumorsphere formation at clinically relevant radiation doses. Investigating the underlying mechanism may provide insight into signaling pathways crucial for cancer stem cell survival and pave the way to novel potential therapeutic targets.
Comparisons of HIV-affected and non-HIV-affected families over time

This study compares HIV-affected families' and their non-HIV-affected neighbors' behavioral health outcomes and family conflict. To compare two groups from the same neighborhoods at four points over 18 months, mothers living with HIV (MLH) (N = 167) and their school-age children (age 6–20) were recruited from clinical care settings in Los Angeles, CA, and neighborhood control mothers (NCM) without HIV (N = 204) were recruited from modal neighborhoods. In addition, children living at home who were 12 years and older were recruited. We assessed parenting behaviors, family conflict, mental health, sexual behavior, substance use, and HIV-related health behaviors over time. MLH perceived greater economic insecurity at baseline, less employment, and involvement in romantic relationships. MLH reported more emotional distress and substance use than NCM. MLH, however, reported lowered HIV transmission risk. The random regressions indicated that MLH exhibited higher levels of risk and became significantly less depressed and less anxious over time than their non-HIV-affected neighbors. MLH also reported less initial family violence and conflict reasoning than NCM; violence decreased and conflict increased over time for MLH relative to NCM. Children of MLH decreased their marijuana use but hard drug users of MLH increased their risk, over time, compared to children of NCM. Moreover, children of MLH reported more internalizing behaviors than children of NCM. Even when compared to other families living in the same economically disadvantaged communities, MLH and their children continue to face challenges surrounding family conflict and key behavioral health outcomes, especially with respect to substance use and mental health outcomes. These families, however, show much resilience, and MLH report lowered levels of HIV transmission risk, their children report no greater levels of HIV transmission risk, and levels of family violence were lower than reported by families in the same neighborhoods.