Miracle-dz/UniFAR-FTUs huggingface dataset:
Circadian rhythm and cell population growth June 17 , 2010

Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood levels) and cell proliferation. It has been observed in tumor-bearing laboratory rodents that a severe disruption of these physiological rhythms results in accelerated tumor growth. The question of accurately representing the control exerted by circadian clocks on healthy and tumour tissue proliferation to explain this phenomenon has given rise to mathematical developments, which we review. The main goal of these previous works was to examine the influence of a periodic control on the cell division cycle in physiologically structured cell populations, comparing the effects of periodic control with no control, and of different periodic controls between them. We state here a general convexity result that may give a theoretical justification to the concept of cancer chronotherapeutics. Our result also leads us to hypothesize that the above mentioned effect of disruption of circadian rhythms on tumor growth enhancement is indirect, that, is this enhancement is likely to result from the weakening of healthy tissue that are at work fighting tumor growth. keywords : mathematical biology, partial differential equations, physiologically structured models, growth processes, eigenvalues , circadian rhythms, cancer INRIA, projet BANG, Domaine de Voluceau, BP 105, 78156 Le Chesnay Cedex France INSERM U 776, Hôpital Paul-Brousse, 14, Av. Paul-Vaillant-Couturier F94807 Villejuif cedex INRIA Saclay – Île-de-France, projet MAXPLUS CMAP, Ecole Polytechnique, 91128 Palaiseau Cedex, France UPMC Univ Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France.
Ebolavirus Requires Acid Sphingomyelinase Activity and Plasma Membrane Sphingomyelin for Infection

ABSTRACT Acid sphingomyelinase (ASMase) converts the lipid sphingomyelin (SM) to phosphocholine and ceramide and has optimum activity at acidic pH. Normally, ASMase is located in lysosomes and endosomes, but membrane damage or the interaction with some bacterial and viral pathogens can trigger its recruitment to the plasma membrane. Rhinovirus and measles viruses each require ASMase activity during early stages of infection. Both sphingomyelin and ceramide are important components of lipid rafts and are potent signaling molecules. Each plays roles in mediating macropinocytosis, which has been shown to be important for ebolavirus (EBOV) infection. Here, we investigated the role of ASMase and its substrate, SM, in EBOV infection. The work was performed at biosafety level 4 with wild-type virus with specificity and mechanistic analysis performed using virus pseudotypes and virus-like particles. We found that virus particles strongly associate with the SM-rich regions of the cell membrane and depletion of SM reduces EBOV infection. ASM-specific drugs and multiple small interfering RNAs strongly inhibit the infection by EBOV and EBOV glycoprotein pseudotyped viruses but not by the pseudotypes bearing the glycoprotein of vesicular stomatitis virus. Interestingly, the binding of virus-like particles to cells is strongly associated with surface-localized ASMase as well as SM-enriched sites. Our work suggests that ASMase activity and SM presence are necessary for efficient infection of cells by EBOV. The inhibition of this pathway may provide new avenues for drug treatment.
Introduction to Plasmid Biology

An array of issues pertaining to plasmid biology are presented in this unit. Topics include replicators, an explanation of the mechanism of replication and copy‐number control, plasmid incompatibility, selectable markers, cloning sites, and factors to consider when choosing a plasmid vector, whether it be for production of ssDNA, cloning of large inserts, or expression of large quantities of recombinant proteins. Considerations are discussed for the use of plasmids in yeast, cultured mammalian cells and non‐E. coli bacteria. Finally, maps of many common useful plasmids are presented. This unit has recently been updated and extensively revised to include some of the latest developments in plasmid construction and experimental use.
Actinobacillus pleuropneumoniae RTX-toxins: uniform designation of haemolysins, cytolysins, pleurotoxin and their genes.

The three different pore-forming RTX-toxins of Actinobacillus pleuropneumoniae are reviewed, and new and uniform designations for these toxins and their genes are proposed. The designation ApxI (for Actinobacillus pleuropneumoniae RTX-toxin I) is proposed for the RTX-toxin produced by the reference strains for serotypes 1, 5a, 5b, 9, 10 and 11, which was previously named haemolysin I (HlyI) or cytolysin I (ClyI). This protein is strongly haemolytic and shows strong cytotoxic activity towards pig alveolar macrophages and neutrophils; it has an apparent molecular mass in the range 105 to 110 kDa. The genes of the apxI operon will have the designations apxIC, apxIA, apxIB, and apxID for the activator, the structural gene and the two secretion genes respectively. The designation ApxII is proposed for the RTX-toxin which is produced by all serotype reference strains except serotype 10 and which was previously named App, HlyII, ClyII or Cyt. This protein is weakly haemolytic and moderately cytotoxic and has an apparent molecular mass between 103 and 105 kDa. The genes of the apxII operon will have the designations apxIIC for the activator gene and apxIIA for the structural toxin gene. In the apxII operon, no genes for secretion proteins have been found. Secretion of ApxII seems to occur via the products of the secretion genes apxIB and apxID of the apxI operon. The designation ApxIII is proposed for the nonhaemolytic RTX-toxin of the reference strains for serotypes 2, 3, 4, 6 and 8, which was previously named cytolysin III (ClyIII), pleurotoxin (Ptx), or macrophage toxin (Mat). (ABSTRACT TRUNCATED AT 250 WORDS)
On the Performance of Alamouti Scheme in Gamma-Gamma Fading FSO Links With Pointing Errors

The error performance of the free space optical (FSO) link suffers from the atmospheric turbulence. By employing an additional transmit aperture at the transmitter along with Alamouti code, the error rate of the FSO communication system can be significantly improved. However, the pointing errors, generated because of the building sway, has the potential to eradicate the benefits of the Alamouti scheme. Therefore, for a general and realistic study of the FSO based Alamouti scheme, the effect of pointing errors in the Gamma-Gamma fading atmospheric fluctuations is considered in this paper. Specifically, we derive the symbol error rate and the average capacity of the Alamouti scheme over the Gamma-Gamma fading FSO links with pointing errors. The moment generating function (MGF) of the scheme is derived in terms of the Meijer-G function. An MGF based approach is used to derive the ergodic capacity of the scheme. The effect of pointing errors over the performance of the scheme is analyzed under different scenarios and it is observed that the pointing errors significantly degrade the diversity of the considered FSO system.
Tuning the electron energy by controlling the density perturbation position in laser plasma accelerators

A density perturbation in an underdense plasma was used to improve the quality of electron bunches produced in the laser-plasma wakefield acceleration scheme. Quasi-monoenergetic electrons were generated by controlled injection in the longitudinal density gradients of the density perturbation. By tuning the position of the density perturbation along the laser propagation axis, a fine control of the electron energy from a mean value of 60 MeV to 120 MeV has been demonstrated with a relative energy-spread of 15 ± 3.6%, divergence of 4 ± 0.8 mrad, and charge of 6 ± 1.8 pC.
A proposal for robust temperature compensation of circadian rhythms

The internal circadian rhythms of cells and organisms coordinate their physiological properties to the prevailing 24-h cycle of light and dark on earth. The mechanisms generating circadian rhythms have four defining characteristics: they oscillate endogenously with period close to 24 h, entrain to external signals, suffer phase shifts by aberrant pulses of light or temperature, and compensate for changes in temperature over a range of 10°C or more. Most theoretical descriptions of circadian rhythms propose that the underlying mechanism generates a stable limit cycle oscillation (in constant darkness or dim light), because limit cycles quite naturally possess the first three defining properties of circadian rhythms. On the other hand, the period of a limit cycle oscillator is typically very sensitive to kinetic rate constants, which increase markedly with temperature. Temperature compensation is therefore not a general property of limit cycle oscillations but must be imposed by some delicate balance of temperature dependent effects. However, “delicate balances” are unlikely to be robust to mutations. On the other hand, if circadian rhythms arise from a mechanism that concentrates sensitivity into a few rate constants, then the “balancing act” is likely to be more robust and evolvable. We propose a switch-like mechanism for circadian rhythms that concentrates period sensitivity in just two parameters, by forcing the system to alternate between a stable steady state and a stable limit cycle.
Assessment of Chemical Disinfectants Efficacy against Escherichia coli Biofilm Developed on Glass and Wood at Refrigeration and Room Temperatures.

Article history: Received on: 04/10/2015 Revised on: 07/11/2015 Accepted on: 26/11/2015 Available online: 27/12/2015 Objectives: The aim of this work was to study the formation of biofilm on glass and wood coupons at refrigeration and room temperatures, different incubation periods and to assess the efficacy of hydrogen peroxide (HP), Para Acetic Acid (PAA), Sodium hypochlorite (SH) and mixture of PAA + SH against the biofilm. Method: 200 μL of 10 8 suspension E. coli ATCC 29922 was inoculated on the coupons inside petri dishes containing 20 ml of tryptic soy broth, incubated at 10 and 27 0 C for 24, 48, 72 and 168 hours. Biofilm developed at each hour above was quantified by bead-vortex followed by agar plating. The action of disinfectants was tested on 168 hours biofilm. The surfaces were exposed to the disinfectants and incubated at 27 °C for 10 minutes, followed by deactivation for 5 minutes. Cells that resisted disinfectants effect were vortexed and enumerated by agar plating. Results: The results showed that E. coli can develop high biofilm on wood apart from glass. After disinfection treatment, HP had the highest efficacy at 27°C followed by PAA then SH, whilst PAA + SH had the least. Conclusion: It can be concluded that HP and PAA can be good disinfectants agents against E. coli biofilm.
In reply: distraction, compression, and extension reduction of basilar invagination and atlantoaxial dislocation.

1. Chandra PS, Kumar A, Chauhan A, Ansari A, Mishra NK, Sharma BS. Distraction, compression, and extension reduction of basilar invagination and atlantoaxial dislocation: a novel pilot technique. Neurosurgery. 2013;72(6):1040-1053. 2. Yin YH, Yu XG, Zhou DB, et al. Three-dimensional Configuration and Morphometric Analysis of the lateral atlantoaxial Articulation in Congenital Anomaly with Occipitalization of the atlas. Spine (Phila Pa 1976). 2012;37(3):E170-E173. 3. Goel A. Goel's classification of atlantoaxial “facetal” dislocation. J Craniovert Jun Spine. 2014;5:3-8.
Title A mindfulness-based stress management program and treatment with omega-3 fatty acids to maintain a healthy mental state in hospital nurses ( Happy Nurse Project ) : Study protocol for a randomized controlled trial

Background: It is reported that nursing is one of the most vulnerable jobs for developing depression. While they may not be clinically diagnosed as depressed, nurses often suffer from depression and anxiety symptoms, which can lead to a low level of patient care. However, there is no rigorous evidence base for determining an effective prevention strategy for these symptoms in nurses. After reviewing previous literature, we chose a strategy of treatment with omega-3 fatty acids and a mindfulness-based stress management program for this purpose. We aim to explore the effectiveness of these intervention options for junior nurses working in hospital wards in Japan. Methods/Design: A factorial-design multi-center randomized trial is currently being conducted. A total of 120 nurses without a managerial position, who work for general hospitals and gave informed consent, have been randomly allocated to a stress management program or psychoeducation using a leaflet, and to omega-3 fatty acids or identical placebo pills. The stress management program has been developed according to mindfulness cognitive therapy and consists of four 30-minute individual sessions conducted using a detailed manual. These sessions are conducted by nurses with a managerial position. Participants allocated to the omega-3 fatty acid groups are provided with 1,200 mg/day of eicosapentaenoic acid and 600 mg/day of docosahexaenoic acid for 90 days. The primary outcome is the change in the total score of the Hospital Anxiety and Depression Scale (HADS), determined by a blinded rater via the telephone at week 26. Secondary outcomes include the change in HADS score at 13 and 52 weeks; presence of a major depressive episode; severity of depression, anxiety, insomnia, burnout, and presenteeism; utility scores and adverse events at 13, 26 and 52 weeks. Discussion: An effective preventive intervention may not only lead to the maintenance of a healthy mental state in nurses, but also to better quality of care for inpatients. This paper outlines the background and methods of a randomized trial that evaluates the possible additive value of omega-3 fatty acids and a mindfulness-based stress management program for reducing depression in nurses. Trial registration: Clinicaltrials.gov: NCT02151162 (registered on 27 May 2014).
Transformerless Dynamic Voltage Restorer for voltage sag mitigation

Dynamic Voltage Restorers are identified to be cost effective solution for protecting sensitive loads from voltage related power quality issues. The extension of cost reduction and efficiency can be improved by eliminating the injection transformer. This paper discusses a transformer-less dynamic voltage restorer based on three-single phase Voltage Source Inverters(VSI). Since the DVR does not have an injection transformer, it has lower loss, lower cost and it is less bulky. The DVR control is implemented using Synchronous Reference Frame(SRF)theory. Estimation of the reference load voltage is carried out using unit vectors. The simulation results carried out in MATLAB shows the effectiveness of the DVR in compensating the voltage sag.
Fitzpatrick skin typing: applications in dermatology.

Fitzpatrick skin phototypes were developed by Thomas B. Fitzpatrick in 1975 based on a persons skin color and responses to sun exposure in terms of degree of burning and tanning. Though subjective, Fitzpatrick skin typing has a proven diagnostic and therapeutic value. It has been most commonly used to analyze the sun sensitivity in population-based and case-control studies related to cause of skin cancer, exposure to UV radiation, tanning, and protective behaviors. [1,2] The Fitzpatrick scale has been applied as a standard for self-assessment of sun sensitivity in self-administered questionnaires and has been shown to correlate well for white skin as compared to brown skin. [3] Skin phototype typing is widely used for estimating UV, PUVA, and laser treatment doses.
Enhancing an event-based OO framework for distributed programming

The paper discusses an asynchronous event based object oriented framework, OVOPS, employing the usage of design patterns to incorporate and interwork with a CORBA enabled environment. Distributed programming is constantly evolving into a very realistic technology which enhances systems integration through interoperability, adaptability and flexibility. However such advantages, coupled with performance, can only be gained by the proper analysis and design of the systems or frameworks in question. A critical examination would reveal that such a framework can be made realistically possible through the usage of object oriented methods combined with the elegance of design patterns and the advances made in CORBA technology. The described environment will ensure consistent creation of protocols and other such similar services through reusable object oriented components communicating over a heterogeneous network while addressing certain shortcomings, such as ensuring asynchronous communication remaining guaranteed and providing native event and message based features without resorting to CORBA based messaging and event services. It also attempts to shield the developer from network specific issues by providing a more generic but very consistent technique to interface to the underlying services. Two areas in which such a framework can be employed are described within the Intelligent Networks realm to illustrate the available methods and practices.
Cytomegalovirus and Mucoepidermoid carcinoma: A possible causal relationship? A pilot study

Background: Human cytomegalovirus (CMV) infection has tropism for salivary gland ductal epithelium and establishes a persistent and lifelong infection. Mucoepidermoid carcinoma (MEC) is the most common salivary gland tumor. Recent studies have established that mouse CMV-induced tumorigenesis displays histologic and molecular characteristics similar to human MEC. We wished to explore further down the lane by analyzing the expression of pp65 and the key oncogenic signaling pathway in cases of MEC and their etiological relevance in the Indian scenario as a pilot study. Materials and Methods: Histopathologically confirmed cases of MEC (n = 4) and normal salivary gland tissue (n = 4) were subjected to immunohistochemical analysis using the markers pp65 and epidermal growth factor receptor (EGFR). Results: The pp65 antigen expression was found to be negative in all the studied cases and one case of high-grade MEC showed EGFR expression. Conclusion: The purpose of the study was to explore the role of CMV in the development of MEC, as it might help to exploit this etiological agent as a therapeutic target. Similar to human papillomavirus (HPV), these might identify a subset of neoplasms with a varied biological behavior and alternative therapies. However, this vision is obscured by contradicting evidence in the literature. As of today, surgery remains the only best possible management for these patients unless proven otherwise.
Gammacoronavirus and Deltacoronavirus in Quail

SUMMARY This paper expands on a previous report about coronaviruses in quail. After surveillance carried out in 2009 and 2010, some farmers started vaccinating quail with the Massachusetts avian infectious bronchitis virus serotype. The samples for this study were collected in 2013 from São Paulo state in southeastern Brazil. Pools of trachea, lungs, reproductive tract, kidneys, and enteric contents from quail and laying hens kept in the same farms and from quail-only farms as well as from both healthy birds and those showing infectious bronchitis–like symptoms were sampled in this study. The samples were screened using nested RT-PCR targeting the 3′-untranslated region of the Gammacoronavirus genus. Based on the DNA sequence for the RNA-dependent RNA polymerase (RdRp) gene, the strains isolated from quail clustered within either the Gammacoronavirus or Deltacoronavirus genus, and sequences from both genera were found in one quail sample. The phylogeny based on the partial S1 subunit sequence showed that the gammacoronaviruses detected in quail and layers belonged to the Brazil type. These results suggest that quail are susceptible to Gammacoronavirus and Deltacoronavirus viruses and indicate that the Massachusetts vaccination was not controlling IBV in quail or chickens.
Experiment evaluation of reliable control using equivalent transfer function for speed feedback loop failure

In this paper, a reliable control method is proposed for a position control system using multiple loops. If a speed feedback loop fails, such as a case of the speed sensor break down, the position control system becomes unstable and has a big fluctuation. To cope with this problem, the proposed method uses an equivalent transfer function (ETF) as an active redundancy compensation after the loop failure. The ETF is designed so that it does not change the transfer function of the whole system before and after the loop failure. Therefore, the stability of the position control system using this proposed system is guaranteed even if the speed feedback loop fails. The effectiveness of this proposed system is confirmed by the experimental results.
Evaluation of an In Vitro Cell Culture Assay for the Potency Assessment of Recombinant Human Erythropoietin

Recombinant human erythropoietin is a sialoglycoprotein that stimulates erythropoiesis. To assess potency of human erythropoietin produced by recombinant technology, we investigated an in vitro TF-1 cell proliferation assay, which was applied in conjunction with a reversed-phase liquid chromatography method for the determination of the content of sialic acids. The results obtained, which were higher than 126.8ng/μg, were compared with those obtained with the in vivo normocythaemic mouse bioassay. The in vitro assay resulted in a non-significant lower mean difference of the estimated potencies (0.61% ± 0.026, p > 0.05). The use of this combination of methods represents an advance toward the establishment of alternative in vitro approaches, in the context of the Three Rs, for the potency assessment of biotechnology-derived medicines.
Protein Sequence Motif Detection using Novel Rough Granular Computing Model

Protein sequence motifs information is essential for the analysis of biologically significant regions. Discovering sequence motifs is a key task to realize the connection of sequences with their structures. Protein sequence motifs have the potential to determine the function and activities of the proteins. Many algorithms or techniques are used to determine motifs which require a predefined fixed window size. Our input dataset is extremely large as a result, an efficient technique is demanded. So we apply three different granular computing models to find protein motif information which transcend protein family boundaries. The constructed segments from 3000 protein sequences are divided into granules using Rough K-Means and then K-Means has been applied on each granule. The highly structured clusters are further considered to find motif patterns. This approach is compared with Adaptive Fuzzy Granular model. The proposed Rough Granular computing model generates more number of highly structured motif patterns. Keywords-Protein Sequence Motifs, DBI, HSSP-BLOSUM62, Granular Computing, K-Means, Adaptive Fuzzy C-Means, Rough K-Means.
Multilayer folded-waveguide dual-band filter

This paper presents a primary investigation into developing a compact dual passband filter using novel folded-waveguide resonators with a multilayer structure. A new coupling scheme for dual-band operation is realized. Both slot and aperture couplings are used for the implementation. For the demonstration, a 4-pole dual-band filter of this type has been designed, fabricated and tested. Simulation and experimental results are presented to validate the design and to show the advantages of this type of filter.