Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analysis of Herpes Simplex Virus Type 1 Transcription Using an Oligonucleotide-Based DNA Microarray

ABSTRACT More than 100 transcripts of various abundances and kinetic classes are expressed during phases of productive and latent infections by herpes simplex virus (HSV) type 1. To carry out rapid global analysis of variations in such patterns as a function of perturbation of viral regulatory genes and cell differentiation, we have made DNA microchips containing sets of 75-mer oligonucleotides specific for individual viral transcripts. About half of these are unique for single transcripts, while others function for overlapping ones. We have also included probes for 57 human genes known to be involved in some aspect of stress response. The chips efficiently detect all viral transcripts, and analysis of those abundant under various conditions of infection demonstrates excellent correlation with known kinetics of mRNA accumulation. Further, quantitative sensitivity is high. We have further applied global analysis of transcription to an investigation of mRNA populations in cells infected with a mutant virus in which the essential immediate-early α27 (UL54) gene has been functionally deleted. Transcripts expressed at 6 h following infection with this mutant can be classified into three groups: those whose abundance is augmented (mainly immediate-early transcripts) or unaltered, those whose abundance is somewhat reduced, and those where there is a significant reduction in transcript levels. These do not conform to any particular kinetic class. Interestingly, levels of many cellular transcripts surveyed are increased. The high proportion of such transcripts suggests that the α27 gene plays a major role in the early decline in cellular gene expression so characteristic of HSV infection.
Approach to a theory of software evolution

Summary form only given. The paper briefly refers to a number of the, by now well known, results of the author's studies of software evolution since they provide a basis and framework for the development of a theory of the phenomenon. The author then summarises his most recent results outlining a proof that every E-type program reflects an unbounded number of assumptions about the application implemented, supported or modelled by the program. He shows that the presence of such assumptions is inevitable and that some of these become invalid over time as a consequence of changes in the dynamic real world. Some of the finite set of known assumptions reflected in the program is also become invalid. Together the resultant ever extending invalidity causes the software to require continuing change or to become ever more unsatisfactory or even invalid. This phenomenon provides the underlying and unavoidable cause of the universal experience that E-type software must be continually evolved to remain satisfactory and suggests that its further study and the development of methods and tools to reduce its considerable impact, economic and social cost, must form an important part of future software engineering R & D.
Animal models of asthma: potential usefulness for studying health effects of inhaled particles.

Asthma is now recognized to be a chronic inflammatory disease that affects the whole lung. Incidence appears to be increasing despite improved treatment regimens. There is substantial epidemiological evidence suggesting a relationship between the incidence and severity of asthma (e.g., hospitalizations) and exposure to increased levels of air pollution, especially fine and ultrafine particulate material, in susceptible individuals. There have been a few studies in animal models that support this concept, but additional animal studies to test this hypothesis are needed. However, such studies must be performed with awareness of the strengths and weaknesses of the currently available animal models. For studies in mice, the most commonly used animal, a broad spectrum of molecular and immunological tools is available, particularly to study the balance between Th1 and Th2 responses, and inbred strains may be useful for genetic dissection of susceptibility to the disease. However, the mouse is a poor model for bronchoconstriction or localized immune responses that characterize the human disease. In contrast, allergic lung diseases in dogs and cats may more accurately model the human condition, but fewer tools are available for characterization of the mechanisms. Finally, economic issues as well as reagent availability limit the utility of horses, sheep, and primates.
Internet-delivered indicated prevention for anxiety disorders: Six-month follow-up

This project aims to conduct a medium-term follow-up to assess the efficacy of a preventive cognitive behavioural intervention delivered via the Internet to individuals at risk of developing anxiety disorders. Previous work on immediate outcome indicated that the program was effective in reducing depression and anxiety-related cognitions. Forty-two university students with elevated anxiety sensitivity who were randomised either to an Internet-based program over a period of 6 weeks or a waiting list control were followed up at 6 months after intervention. As with the outcome immediately after intervention, significant treatment effects were found for anxiety-related cognitions and symptoms of depression. Long-term outcomes were related to program component satisfaction.
Limits to the precision of gradient sensing with spatial communication and temporal integration

Significance Knowing which way to move is crucial for many biological processes, from organismal development to migration of cancer cells and from motion of microbes to wound healing. To find their preferred directions, biological systems compare concentrations of a chemical cue at their different edges. The comparison requires information from these different locations to be communicated to the same place. However, all communication is noisy (just think of the childhood game “telephone”). This communication noise, as well as noise in the individual measurements themselves, sets the accuracy of the direction sensing. Here we quantify the importance of the communication noise and propose a mechanism that can improve the accuracy of direction sensing. Gradient sensing requires at least two measurements at different points in space. These measurements must then be communicated to a common location to be compared, which is unavoidably noisy. Although much is known about the limits of measurement precision by cells, the limits placed by the communication are not understood. Motivated by recent experiments, we derive the fundamental limits to the precision of gradient sensing in a multicellular system, accounting for communication and temporal integration. The gradient is estimated by comparing a “local” and a “global” molecular reporter of the external concentration, where the global reporter is exchanged between neighboring cells. Using the fluctuation–dissipation framework, we find, in contrast to the case when communication is ignored, that precision saturates with the number of cells independently of the measurement time duration, because communication establishes a maximum length scale over which sensory information can be reliably conveyed. Surprisingly, we also find that precision is improved if the local reporter is exchanged between cells as well, albeit more slowly than the global reporter. The reason is that whereas exchange of the local reporter weakens the comparison, it decreases the measurement noise. We term such a model “regional excitation–global inhibition. ” Our results demonstrate that fundamental sensing limits are necessarily sharpened when the need to communicate information is taken into account.
Heregulin‐stimulated acetylcholine receptor gene expression in muscle: requirement for MAP kinase and evidence for a parallel inhibitory pathway independent of electrical activity

Binding of heregulin (HRG) to its receptor, ErbB3, results in a dimerization with ErbB2/neu and activation of their intrinsic tyrosine kinases, initiating a cascade of events resulting in the stimulation of acetylcholine receptor (AChR) genes in muscle. Here we have examined the signalling downstream of the HRG receptor. We show that phosphatidylinositol 3′‐kinase (PI3K) and SHC bind to the HRG‐activated ErbB3 in myotubes. Subsequently, p70S6 kinase (p70S6k), and MAP kinase ERK2 and thereby p90rsk are activated. However, inhibition of PI3K and p70S6k by wortmannin and rapamycin, respectively, failed to antagonize AChR α‐subunit gene expression stimulated by HRG, despite the fact that the activities of the kinases were inhibited. In contrast, these inhibitors elevated AChR α‐subunit mRNA levels, by themselves, independently of muscle electrical activity. On the other hand, the 17mer antisense oligonucleotide, EAS1, caused a specific depletion of ERK2 and eliminated the ability of HRG to stimulate AChR α‐subunit gene expression. These results indicate that HRG stimulates expression of AChR genes via ERK2 activation, and provide a physiological example of neurotrophic factor‐associated repression of AChR genes by stimulation of p70S6k activity which may contribute to the expression of adult type AChR genes at the neuromuscular junction.
New Results on Nonlinear Observer Design for Continuous-Time Nonlinear Systems

In this paper, new results have been derived for the existence of local exponential observers for nonlinear control systems. Our main result, viz. necessary condition for local exponential observers for nonlinear control systems can be viewed as a dual result of the famous necessary condition due to R.W. Brockett (1983) for asymptotic stabilization of nonlinear control systems. As an application of our new result, we establish that there do not exist local exponential observers for bifurcating systems in the classical case, where the trivial equilibrium of the state dynamics does not change with the real parametric uncertainty and where the output function is purely a function of the state and independent of the parametric uncertainty.
Contemporary retinal imaging techniques in diabetic retinopathy: a review

Over the last decade, there has been an expansion of imaging modalities available to clinicians to diagnose and monitor the treatment and progression of diabetic retinopathy. Recently, advances in image technologies related to OCT and OCT angiography have enabled improved visualization and understanding of this disease. In this review, we will describe the use of imaging techniques such as colour fundus photography, fundus autofluorescence, fluorescein angiography, infrared reflectance imaging, OCT, OCT‐Angiography and techniques in adaptive optics and hyperspectral imaging in the diagnosis and management of diabetic retinopathy.
Experimental peritonitis induced by oral administration of indomethacin in Mongolian gerbils

The possibility of inducing peritoneal inflammation in three murine species (gerbils, rats and mice) via the oral administration of indomethacin was investigated with the overall aim of developing an experimental animal model for human peritonitis. Gerbils given high doses of indomethacin at a rate of 30 mg and 40 mg/kg body weight showed swelling of the abdomen, depression and dyspnea within 4 days after the treatment. The severity of the clinical symptoms increased with time. The animals were confirmed as having developed peritonitis based on the pathological features including inflammation of the peritoneum, and fibrinous adhesion of the abdominal organs in the abdominal cavity. The severity of peritonitis increased with increasing dose of indomethacin, and was not related to the gender of the animal. On the other hand, peritoneal inflammation did not develop in the rats and mice even at high doses. Therefore, the administration of 30 mg/kg body weight of indomethacin is an effective and simple method of inducing peritonitis in 5-week-old Mongolian gerbils. The animal peritonitis model used in this study can be used as an effective tool for examining potential therapeutic compounds for preventing peritoneal damage during peritonitis, and provide insight into the pathophysiology of peritonitis.
Psychological-level systems theory: The missing link in bridging emotion theory and neurobiology through dynamic systems modeling

Bridging between psychological and neurobiological systems requires that the system components are closely specified at both the psychological and brain levels of analysis. We argue that in developing his dynamic systems theory framework, Lewis has sidestepped the notion of a psychological level systems model altogether, and has taken a partisan approach to his exposition of a brain-level systems model.
Alternative Framework in "Body Coordination" Topic: A Progress Report for Interior of Malaysia.

This preliminary study was conducted in interior of Malaysia. The study employed the Body Coordination Two Tier Concept Test to assess students’ understandings of body coordination topic. The test consisted of 14 questions as two tier question style. The students needed to select the answer and write down the justifications of each answer. Interview was conducted with six students to get in-depth opinion about Body Coordination.
Yes-Associated Protein Regulates the Hepatic Response After Bile Duct Ligation

Human chronic cholestatic liver diseases are characterized by cholangiocyte proliferation, hepatocyte injury, and fibrosis. Yes‐associated protein (YAP), the effector of the Hippo tumor‐suppressor pathway, has been shown to play a critical role in promoting cholangiocyte and hepatocyte proliferation and survival during embryonic liver development and hepatocellular carcinogenesis. Therefore, the aim of this study was to examine whether YAP participates in the regenerative response after cholestatic injury. First, we examined human liver tissue from patients with chronic cholestasis. We found more‐active nuclear YAP in the bile ductular reactions of primary sclerosing cholangitis and primary biliary cirrhosis patient liver samples. Next, we used the murine bile duct ligation (BDL) model to induce cholestatic liver injury. We found significant changes in YAP activity after BDL in wild‐type mice. The function of YAP in the hepatic response after BDL was further evaluated with liver‐specific Yap conditional deletion in mice. Ablating Yap in the mouse liver not only compromised bile duct proliferation, but also enhanced hepatocyte necrosis and suppressed hepatocyte proliferation after BDL. Furthermore, primary hepatocytes and cholangiocytes isolated from Yap‐deficient livers showed reduced proliferation in response to epidermal growth factor in vitro. Finally, we demonstrated that YAP likely mediates its biological effects through the modulation of Survivin expression. Conclusion: Our data suggest that YAP promotes cholangiocyte and hepatocyte proliferation and prevents parenchymal damage after cholestatic injury in mice and thus may mediate the response to cholestasis‐induced human liver disease. (HEPATOLOGY 2012;56:1097–1107)
Genetics of the First Seven Proprotein Convertase Enzymes in Health and Disease

Members of the substilisin/kexin like proprotein convertase (PCSK) protease family cleave and convert immature pro-proteins into their biologically active forms. By cleaving for example prohormones, cytokines and cell membrane proteins, PCSKs participate in maintaining the homeostasis in a healthy human body. Conversely, erratic enzymatic function is thought to contribute to the pathogenesis of a wide variety of diseases, including obesity and hypercholestrolemia. The first characterized seven PCSK enzymes (PCSK1-2, FURIN, PCSK4-7) process their substrates at a motif made up of paired basic amino acid residues. This feature results in a variable degree of biochemical redundancy in vitro, and consequently, shared substrate molecules between the different PCSK enzymes. This redundancy has confounded our understanding of the specific biological functions of PCSKs. The physiological roles of these enzymes have been best illustrated by the phenotypes of genetically engineered mice and patients that carry mutations in the PCSK genes. Recent developments in genome-wide methodology have generated a large amount of novel information on the genetics of the first seven proprotein convertases. In this review we summarize the reported genetic alterations and their associated phenotypes.
Making Equal Opportunities Training Effective

During the last five years a group of consultants, who have been working with organisations on programmes to increase equality of opportunity, have been developing a number of new perspectives on the issues that underlie inequality. This has led them to develop new approaches to training, new training designs and new training skills. The most important of these perspectives are laid out, and the implications for training that follow from them are explored. Issues of sex are mainly dealt with, but the principles outlined are as true for work on race or disability.
Clathrin complexes with the inhibitor kappa B kinase signalosome: imaging the interactome

Many receptors involved with innate immunity activate the inhibitor kappa B kinase signalosome (IKK). The active complex appears to be assembled from the two kinase units, IKKα and IKKβ with the regulatory protein NEMO. Because we previously found that RNA silencing of clathrin heavy chains (CHC), in transformed human lung pneumocytes (A549), decreased TNFα‐induced signaling and phosphorylation of inhibitor kappa B (IκB), we hypothesized that CHC forms cytoplasmic complexes with members of the IKK signalosome. Widely available antibodies were used to immunoprecipitate IKKα and NEMO interactomes. Analysis of the affinity interactomes by mass spectrometry detected clathrin with both baits with high confidence. Using the same antibodies for indirect digital immunofluorescence microscopy and FRET, the CHC–IKK complexes were visualized together with NEMO or HSP90. The natural variability of protein amounts in unsynchronized A549 cells was used to obtain statistical correlation for several complexes, at natural levels and without invasive labeling. Analyses of voxel numbers indicated that: (i) CHC–IKK complexes are not part of the IKK signalosome itself but, likely, precursors of IKK–NEMO complexes. (ii) CHC–IKKβ complexes may arise from IKKβ–HSP90 complexes.
Sensor Network Deployment For Agronomical Data Gathering in Semi-Arid Regions

We share our experience in planning, designing and deploying a wireless sensor network of one square kilometre area. Environmental data such as soil moisture, temperature, barometric pressure, and relative humidity are collected in this area situated in the semi-arid region of Karnataka, India. It is a hope that information derived from this data will benefit the marginal farmer towards improving his farming practices. Soon after establishing the need for such a project, we begin by showing the big picture of such a data gathering network, the software architecture we have used, the range measurements needed for determining the sensor density, and the packaging issues that seem to play a crucial role in field deployments. Our field deployment experiences include designing with intermittent grid power, enhancing software tools to aid quicker and effective deployment, and flash memory corruption. The first results on data gathering look encouraging.
Foot Morphology and Substrate Adhesion in the Madagascan Hissing Cockroach, Gromphadorhina portentosa

Abstract Insects are successful terrestrial organisms able to locomote over a wide range of obstacles and substrates. This study investigated how foot morphology (tarsal structure) correlates with substrate adhesion and ecological niche in the Madagascan hissing cockroach, Gromphadorhina portentosa Schaum (Blattaria: Blaberidae). Using light and scanning electron microscopy, the morphology of the different structures of the tarsus of G. portentosa was analysed. Using an Instron® universal testing machine, a series of peak force experiments were then conducted to record the force required to lift the cockroaches off different substrates. G. portentosa was pulled off 10 different substrates, which consisted of smooth Perspex; Perspex scored at 1cm intervals; Perspex hatched at 1 cm, 0.5 cm, and 1 mm intervals; Perspex abraded with fine grade sandpaper; Perspex abraded with coarse grade sandpaper; wood; glass; and Teflon. A clear relationship was seen where an increase in scoring on the Perspex caused a decrease in adhesive ability of G. portentosa. This may be due to there being adequate contact area for the attachment of the pads and to allow the claws to engage. The results obtained suggest that to achieve the greatest adhesion to substrates, G. portentosa uses a combined effect of both adhesive pads and pretarsal claws. Adhesion to a wide range of substrates appears to be an adaptation to life as a wingless forest floor dweller.
The Effects of Weather on the Life Time of Wireless Sensor Networks Using FSO/RF Communication

The increased interest in long lasting wireless sensor networks motivates to use Free Space Optics (FSO) link along with radio frequency (RF) link for communication. Earlier results show that RF/FSO wireless sensor networks have life time twice as long as RF only wireless sensor networks. However, for terrestrial applications, the effect of weather conditions such as fog, rain or snow on optical wireless communication link is major concern, that should be taken into account in the performance analysis. In this paper, life time performance of hybrid wireless sensor networks is compared to wireless sensor networks using RF only for terrestrial applications and weather effects of fog, rain and snow. The results show that combined hybrid network with three threshold scheme can provide efficient power consumption of 6548 seconds, 2118 seconds and 360 seconds for measured fog, snow and rain events respectively resulting in approximately twice of the life time with only RF link.
Mental health should have same priority as physical health

Staying mentally well should be given the same priority by NHS policymakers as keeping physically fit, says an independent think tank based in the United kingdom, the Institute for Public Policy Research. In a report published this week, the institute set out its vision of what mental health services should look like in 2025. It suggests that by then, people with mental health problems will have access to local drop-in services and that public stigma around mental health will have declined. In addition, every neighbourhood will have access workers, …
Investigation of Secondary Organic Aerosol Formation in the Hydrocarbon/Da Reaction: Implementation of APCI/MS as an Analytical On-Line Technique A contribution to subprojects CMD and AEROSOL

The atmospheric fate of terpenes is strongly influenced by ozone generated loss processes in the troposphere (Hoffmann et al, 1997). Products formed in the reaction of biogenic volatile organic compounds (VOCs) with ozone are characterised by their low volatility. Therefore, gas-to-particle conversion of these compounds represents an important pathway for the formation of secondary organic aerosol (SOA) (Andreae and Crutzen, 1997; Zhang et al, 1992). A series of investigations are focussed on the determination of the reaction rate constants (Atkinson, 1997). However, the composition of organic aerosols formed in these reactions is poorly understood and reaction mechanisms are far from being elucidated.