Miracle-dz/UniFAR-FTUs huggingface dataset:
cGMP-Dependent Protein Kinase Type I Is Implicated in the Regulation of the Timing and Quality of Sleep and Wakefulness

Many effects of nitric oxide (NO) are mediated by the activation of guanylyl cyclases and subsequent production of the second messenger cyclic guanosine-3′,5′-monophosphate (cGMP). cGMP activates cGMP-dependent protein kinases (PRKGs), which can therefore be considered downstream effectors of NO signaling. Since NO is thought to be involved in the regulation of both sleep and circadian rhythms, we analyzed these two processes in mice deficient for cGMP-dependent protein kinase type I (PRKG1) in the brain. Prkg1 mutant mice showed a strikingly altered distribution of sleep and wakefulness over the 24 hours of a day as well as reductions in rapid-eye-movement sleep (REMS) duration and in non-REM sleep (NREMS) consolidation, and their ability to sustain waking episodes was compromised. Furthermore, they displayed a drastic decrease in electroencephalogram (EEG) power in the delta frequency range (1–4 Hz) under baseline conditions, which could be normalized after sleep deprivation. In line with the re-distribution of sleep and wakefulness, the analysis of wheel-running and drinking activity revealed more rest bouts during the activity phase and a higher percentage of daytime activity in mutant animals. No changes were observed in internal period length and phase-shifting properties of the circadian clock while chi-squared periodogram amplitude was significantly reduced, hinting at a less robust oscillator. These results indicate that PRKG1 might be involved in the stabilization and output strength of the circadian oscillator in mice. Moreover, PRKG1 deficiency results in an aberrant pattern, and consequently a reduced quality, of sleep and wakefulness, possibly due to a decreased wake-promoting output of the circadian system impinging upon sleep.
The Abundant Larval Transcript-1 and -2 Genes ofBrugia malayi Encode Stage-Specific Candidate Vaccine Antigens for Filariasis

ABSTRACT Lymphatic filariasis is a major tropical disease caused by the mosquito-borne nematodes Brugia and Wuchereria. About 120 million people are infected and at risk of lymphatic pathology such as acute lymphangitis and elephantiasis. Vaccines against filariasis must generate immunity to the infective mosquito-derived third-stage larva (L3) without accentuating immunopathogenic responses to lymphatic-dwelling adult parasites. We have identified two highly expressed genes, designated abundant larval transcript-1 and -2 (alt-1 and alt-2), from each of which mRNAs account for >1% of L3 cDNAs. ALT-1 and ALT-2 share 79% amino acid identity across 125 residues, including a putative signal sequence and a prominent acidic tract. Expression ofalt-1 and alt-2 is initiated midway through development in the mosquito, peaking in the infective larva and declining sharply following entry into the host. Humans exposed toBrugia malayi show a high frequency of immunoglobulin G1 (IgG1) and IgG3 antibodies to ALT-1 and -2, distinguishing them from adult-stage antigens, which are targeted by the IgG4 isotype. Immunization of susceptible rodents (jirds) with ALT-1 elicited a 76% reduction in parasite survival, the highest reported for a single antigen from any filarial parasite. ALT-1 and the closely related ALT-2 are therefore strong candidates for a future vaccine against human filariasis.
Adaptive layout template for effective web content presentation in large-screen contexts

Despite the fact that average screen size and resolution have dramatically increased, many of today's web sites still do not scale well in larger viewing contexts. The upcoming HTML5 and CSS3 standards propose features that can be used to build more flexible web page layouts, but their potential to accommodate a wider range of display environments is currently relatively unexplored. We examine the proposed standards to identify the most promising features and report on experiments with a number of adaptive layout mechanisms that support the required forms of adaptation to take advantage of greater screen real estates, such as automated scaling of text and media. Special attention is given to the effective use of multi-column layout, a brand new feature for web design that contributes to optimising the space occupied by text, but at the same time still poses problems in predominantly continuous vertical-scrolling browsing behaviours. The proposed solutions were integrated in a flexible layout template that was then applied to an existing news web site and tested on users to identify the adaptive features that best support reading comfort and efficiency.
The effects of pilates exercise on lipid metabolism and inflammatory cytokines mRNA expression in female undergraduates

[Purpose] The purpose of the study was to verify the effects of Pilates exercise by observing the impact of 8 weeks of Pilates exercise on lipid metabolism and inflammatory cytokine mRNA expression in female undergraduates in their 20s who had no prior experience in Pilates exercise and had not exercised in the previous 6 months. [Methods] There were 18 subjects with no prior experience in Pilates exercise. The subjects were separated into the Pilates exercise group (n = 9) and the non-exercise control group (n = 9). The former performed Pilates exercise for 60-70 minutes over 8 weeks with a gradual strength increase of 9-16 in the Rating of Perceived Exercise (RPE). The body composition, creatine kinase in the bloodstream and lipid metabolism (TC, LDL-C, HDL-C, TG) were measured before and after the experiment and Real-Time PCR was used to investigate the mRNA expression of the inflammatory cytokines IL-6 and TNF-⍺. [Results] The creatine kinase (CK) in the blood had significant differences between the groups. The test group showed significant increase compared to the control group after 8 weeks of Pilates exercise (p = 0.007). Lipid analysis showed that the level of high-density lipoprotein cholesterol (HDL-C) was significantly different in the two groups (p = 0.049), with the Pilates exercise group exhibiting significantly higher levels compared to the control group. No significant differences were observed in the levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG). IL-6 mRNA expression did not show significant differences between the groups either. Timing and TNF-α mRNA expression showed significant effect in both the exercise and the control groups (p = 0.013) but no correlation. [Conclusion] It was found from the study that Pilates exercise for 8 weeks affected CK expression (the muscle damage marker) and induced positive changes in the levels of high-density lipoprotein.
Erosion Phenomenon Caused by Water Droplet Impingement and Life Prediction of Industrial Materials : Part 1 - Investigation of Droplet Impingement Factors and Erosion Testing Methods

発電所などに設置されている低圧蒸気タービンブレー ドや配管に,液滴の衝突によるエロージョンが発生する ことがある1), 2). さらに,発電効率を向上させるために 低圧最終段ブレード翼を長くする傾向があり,液滴衝突 エロージョンが加速されるので材料にとってはより過酷 な条件といえる3). 液滴衝突エロージョンの発生は,装 置の性能や安全性の低下につながるため,用いられる材 料の耐エロージョン性をあらかじめ充分に評価していな ければならない. また使用材料の寿命予測は重要な課題 である. ところが,液滴衝突エロージョンに関する研究 では,液滴速度を上昇させる目的で装置が大がかりにな るため汎用的な試験装置は少ない4). そこで,著者らは 過去に液滴衝突エロージョンと損傷機構的に類似性のあ るキャビテーションエロージョン現象を利用して材料の 評価を行った5)-7). しかし,この試験環境でキャビテー ションによる材料への攻撃性が液滴衝突と比してどれ程 のものか分からないために,材料優劣の評価にとどまっ た. また,実機の損傷データがなければエロージョン量 の推算は不可能であった7). そこで,本研究の第 1 報では,比較的容易に高速ジェ ットが得られるウォータージェット法を試験装置に用 い,まず本試験法における液滴の衝突速度や衝突頻度な どを把握した. 次に,比較的軟らかい材料を用いて, 様々な液滴の衝突条件下でのエロージョン試験およびキ ャビテーションエロージョン試験を行い,両者の相違か らエロージョン量の評価法の有効性について検討した. さらに,液滴衝突エロージョン量推算の基礎式を提案し た.
Proceedings of the Rank Forum on Vitamin D

The Rank Forum on Vitamin D was held on 2nd and 3rd July 2009 at the University of Surrey, Guildford, UK. The workshop consisted of a series of scene-setting presentations to address the current issues and challenges concerning vitamin D and health, and included an open discussion focusing on the identification of the concentrations of serum 25-hydroxyvitamin D (25(OH)D) (a marker of vitamin D status) that may be regarded as optimal, and the implications this process may have in the setting of future dietary reference values for vitamin D in the UK. The Forum was in agreement with the fact that it is desirable for all of the population to have a serum 25(OH)D concentration above 25 nmol/l, but it discussed some uncertainty about the strength of evidence for the need to aim for substantially higher concentrations (25(OH)D concentrations>75 nmol/l). Any discussion of ‘optimal’ concentration of serum 25(OH)D needs to define ‘optimal’ with care since it is important to consider the normal distribution of requirements and the vitamin D needs for a wide range of outcomes. Current UK reference values concentrate on the requirements of particular subgroups of the population; this differs from the approaches used in other European countries where a wider range of age groups tend to be covered. With the re-emergence of rickets and the public health burden of low vitamin D status being already apparent, there is a need for urgent action from policy makers and risk managers. The Forum highlighted concerns regarding the failure of implementation of existing strategies in the UK for achieving current vitamin D recommendations.
Performance and reliability of the Enzygnost measles enzyme-linked immuno-sorbent assay for detection of measles virus-specific immunoglobulin M antibody during a large measles epidemic

Evaluation of the Enzygnost Measles Enzyme-Linked Immuno-Sorbent Assay kit (Behring) performance to detect specific immunoglobulin M (IgM) was carried out with 3,297 single serum samples and 898 paired serum samples collected during a measles epidemic (10,184 reported cases) in Quebec, Canada. Anti-measles IgM and IgG were detected by using the Enzygnost kit with the appropriate conjugates. Complement-fixing (CF) antibody (Ab) titers were assessed by the laboratory branch complement fixation micromethod. The Centers for Disease Control's clinical measles case definition was used. A modification of the manufacturer's optical density interpretation algorithm was introduced to allow for equivocal results, in addition to positive and negative ones. These three categories differed as to their association with a significant increase in CF Ab titer and the time between the onset of symptoms and phlebotomy. The IgM positivity rate for complement fixation-confirmed measles cases was 96.6% for vaccinated subjects and 100% for nonvaccinated subjects. The daily percentage of IgM seropositivity that was detected for subjects who became IgM positive within 30 days increased gradually from 40 to 90% for sera taken 1 to 7 days after the onset of symptoms, and it plateaued at 100% for sera taken 16 to 30 days after the onset of symptoms. IgM seropositivity was strongly associated with IgG seroconversion, CF Ab titer increase, and clinical measles (P less than 0.0001). Reproducibility was 100% for nonreactive sera and 99.1% for reactive sera. In conclusion, the Enzygnost Measles Enzyme-Linked Immuno-Sorbent Assay kit performed adequately to confirm measles virus infection during this epidemic. A second serum sample should be tested when an early-acute-phase serum sample is IgM negative.
CORBA: integrating diverse applications within distributed heterogeneous environments

Large computer networks such as corporate intranets and the Internet are inherently heterogeneous due to such factors as increasingly rapid technological change, engineering trade-offs, accumulation of legacy systems over time, and varying system costs. Unfortunately, such heterogeneity makes the development and maintenance of applications that make the best use of such networks difficult. The Common Object Request Broker Architecture specification created by the Object Management Group provides a stable model for distributed object-oriented systems that helps developers cope with heterogeneity and inevitable change. Applications written to the CORBA standard are abstracted away from underlying networking protocols and transports, instead relying on object request brokers to provide a fast and flexible communication and object activation substrated. The abstractions provided by CORBA ORBs are currently serving as the basis for applications in a wide variety of problem domains, including telecommunications, finance, medicine, and manufacturing, running on platforms ranging from mainframes down to test and measurement equipment. This article first provides an overview of the Object Management Architecture, then describes in detail the CORBA component of that architecture, and concludes with a description of the OMG organization along with some of its current and future work.
The FGF Receptor–1 Tyrosine Kinase Domain Regulates Myogenesis but Is Not Sufficient to Stimulate Proliferation

Ligand-stimulated activation of FGF receptors (FGFRs) in skeletal muscle cells represses terminal myogenic differentiation. Skeletal muscle cell lines and subsets of primary cells are dependent on FGFs to repress myogenesis and maintain growth. To understand the intracellular events that transduce these signals, MM14 skeletal muscle cells were transfected with expression vectors encoding chimeric receptors. The chimeras are comprised of the PDGF β receptor (PDGFβR) extracellular domain, the FGFR-1 intracellular domain, and either the PDGFβR or FGFR-1 transmembrane domain. The chimeric receptors were autophosphorylated upon PDGF-BB stimulation and are capable of stimulating mitogen-activated protein kinase activity. Activation of the tyrosine kinase domain of either chimera repressed myogenesis, suggesting intracellular responses regulating skeletal muscle differentiation are transduced by activation of the FGFR-1 tyrosine kinase. Unexpectedly, we found that activation of either chimeric receptor failed to stimulate cellular proliferation. Thus, it appears that regulation of skeletal muscle differentiation by FGFs requires only activation of the FGFR tyrosine kinase. In contrast, stimulation of proliferation may require additional, as yet unidentified, signals involving the receptor ectodomain, the FGF ligand, and heparan sulfate either alone, or in combination.
Novel search method for the discovery of functional relationships

Motivation: Numerous annotations are available that functionally characterize genes and proteins with regard to molecular process, cellular localization, tissue expression, protein domain composition, protein interaction, disease association and other properties. Searching this steadily growing amount of information can lead to the discovery of new biological relationships between genes and proteins. To facilitate the searches, methods are required that measure the annotation similarity of genes and proteins. However, most current similarity methods are focused only on annotations from the Gene Ontology (GO) and do not take other annotation sources into account. Results: We introduce the new method BioSim that incorporates multiple sources of annotations to quantify the functional similarity of genes and proteins. We compared the performance of our method with four other well-known methods adapted to use multiple annotation sources. We evaluated the methods by searching for known functional relationships using annotations based only on GO or on our large data warehouse BioMyn. This warehouse integrates many diverse annotation sources of human genes and proteins. We observed that the search performance improved substantially for almost all methods when multiple annotation sources were included. In particular, our method outperformed the other methods in terms of recall and average precision. Contact: mario.albrecht@mpi-inf.mpg. de Supplementary Information: Supplementary data are available at Bioinformatics online.
Using performance maps to understand the behavior of Web caching policies

One of the most important differences between traditional caching and Web caching is the high variability of the size of Web objects. As a consequence of that variability, we use two metrics to assess performance of Web caching replacement policies: hit ratio (HR) and byte hit ratio (BHR). The paper presents an analytical model relating these two performance metrics. We show that the relation between hit ratio and byte hit ratio is a function of the mean size of the Web cache server responses and of the mean size of the hit responses. Based on the analytical relationship, we introduce the concept of performance map for a given workload. Performance maps are useful tools for designing and comparing the performance of different replacement policies that deal with objects of variable size, such as the Web caches. Performance maps are applied to some actual workloads that have been used as de-facto standards for comparing the performance of Web caching management algorithms.
Chemical modifier screen identifies HDAC inhibitors as suppressors of PKD models

Polycystic kidney disease (PKD) is a common human genetic disease with severe medical consequences. Although it is appreciated that the cilium plays a central role in PKD, the underlying mechanism for PKD remains poorly understood and no effective treatment is available. In zebrafish, kidney cyst formation is closely associated with laterality defects and body curvature. To discover potential drug candidates and dissect signaling pathways that interact with ciliary signals, we performed a chemical modifier screen for the two phenotypes using zebrafish pkd2hi4166 and ift172hi2211 models. pkd2 is a causal gene for autosomal dominant PKD and ift172 is essential for building and maintaining the cilium. We identified trichostatin A (TSA), a pan-HDAC (histone deacetylase) inhibitor, as a compound that affected both body curvature and laterality. Further analysis verified that TSA inhibited cyst formation in pkd2 knockdown animals. Moreover, we demonstrated that inhibiting class I HDACs, either by valproic acid (VPA), a class I specific HDAC inhibitor structurally unrelated to TSA, or by knocking down hdac1, suppressed kidney cyst formation and body curvature caused by pkd2 deficiency. Finally, we show that VPA was able to reduce the progression of cyst formation and slow the decline of kidney function in a mouse ADPKD model. Together, these data suggest body curvature may be used as a surrogate marker for kidney cyst formation in large-scale high-throughput screens in zebrafish. More importantly, our results also reveal a critical role for HDACs in PKD pathogenesis and point to HDAC inhibitors as drug candidates for PKD treatment.
Mechanical Properties of Skin in Ehlers‐Danlos Syndrome, Types I, II, and III

Abstract: Mechanical properties of skin were evaluated in vivo in 17 children suffering from Ehlers‐Danlos syndrome (EDS) types I, II, and III. These were compared with normal values from 63 healthy children. Non‐invasive measurements were performed under suction of 500 mbar using a Cutometer equipped with a 4‐mm probe. Prominent increases in skin extensibility and elasticity were the most distinctive and diagnostic features of all three EDS types. Differences in the average values of biome‐chanical variables were present among the three types. Patients with EDS‐I were the most affected, whereas those with EDS‐III had virtually normal skin. However, interindividual differences in the severity of rheo‐logical alterations were found within each type, illustrating a continuum in the variation of mechanical properties of EDS skin rather than yielding step differences among the types.
Clinical application of the hemagglutination-inhibition test for West Nile virus antibodies.

This paper reports the utilization in clinical practice of the hemagglutination-inhibition (HAI) technique for the detection and quantitation of antibodies against West Nile virus. The hemagglutinating property of West Nile virus, as well as Japanese B and certain other neurotropic viruses was first demonstrated by Sabin and co-workers.1'2 Further studies by Chanock and others3 and by Casals and co-workers45 established optimal and practicable conditions for the titration of HAI antibodies to West Nile virus. Casals and Brown4
Obese and Nonobese Patients: Complications of Abdominoplasty

We analyzed 80 patients who underwent abdominoplasty at the University of Tor Vergata “Policlinico Casilino”, Rome to determine the effect of obesity on the incidence of complications after this surgery. The study patients were divided into 3 groups, obese, overweight, and normal weight, based on the degree to which their preoperative weights varied from their ideal body weight. A history of previous bariatric surgery was also analyzed to determine what impact that might have on subsequent abdominoplasty. Results showed that the records of 80 patients who underwent an abdominoplasty at University of Tor Vergata Policlinico indicated that 76% of obese patients had complications compared with the overweight and normal-weight patients, who had complication rates of 35% and 33%, respectively. Previous gastric bypass surgery had no significant effect on the incidence of postabdominoplasty complications. Based on these findings, the authors conclude that obesity at the time of abdominoplasty has a profound influence on the wound complication rate following surgery, regardless of any previous weight-reduction surgery.
Halogen Occultation Experiment (HALOE) and balloon-borne in situ measurements of methane in stratosphere and their relation to the quasi-biennial oscillation (QBO)

Abstract. Measurements of methane have been made from various observational platforms in the atmosphere. In this article, we have compared four high precision balloon-borne measurements from Hyderabad (17.5°N), India in the period of 1987 and 1998 with a part of HALOE/UARS global observations available since 1991. All the balloon measurements correspond to boreal spring (March and April) but belong to different years. A comparison shows fairly good agreement with each other. The gradient in CH 4 profiles in the troposphere is controlled by the variation in vertical transport. The strongest effect of dynamical influence on methane vertical profiles is shown to be resulting from the dynamical quasi-biennial oscillation in the stratosphere, and that has been consistently derived from both the measurement techniques and chemistry-transport model simulations. It is observed that the QBO signal in CH 4 anomaly exhibits interhemispheric asymmetry caused by the tropics to midlatitude circulation in the stratosphere. A mechanism is suggested to explain how and to what extent the methane vertical profiles over Hyderabad and higher latitudes could be modulated by the prevailing QBO winds in the tropics. We have also discussed how the same mechanism would affect ozone distribution in the stratosphere quite differently.
A Rule-Based System for Automatic De-identification of Medical Narrative Texts

This paper presents an automatic de-identification system for Serbian, based on the adaptation of the existing rule-based named entity recognition system. Built on a finite-state methodology and lexical resources, the system is designed to detect and replace all the explicit personal protected health information present in the medical narrative texts, while still preserving all the relevant medical concepts. The results of a preliminary evaluation demonstrate the usefulness of this method both in preserving patient privacy and the de-identified document interoperability.