Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Antigenic Properties of Mammalian Cell-Expressed Theileria parva Antigen Tp9

East Coast Fever (ECF), caused by the tick-borne apicomplexan parasite Theileria parva, is a leading cause of morbidity and mortality in cattle of sub-Saharan Africa. The infection and treatment method (ITM) is currently the only vaccine available to control T. parva. Although ITM elicits levels of protection, its widespread adoption is limited by costs, laborious production process, and antibiotic co-treatment requirement, necessitating the development of a more sustainable vaccine. To this end, efforts have been concentrated in the identification of new T. parva vaccine antigens and in the development of suitable platforms for antigen expression. In this study, we investigated the molecular and antigenic properties of T. parva antigen Tp9 expressed by mammalian cells. Data indicate that Tp9 contains a signal peptide that is weakly functional in mammalian cells. Thus, Tp9 secretion from mammalian cells increased 10-fold after the native signal peptide was replaced with the human tissue plasminogen activator signal peptide (tPA). Sera from all T. parva-immune cattle recognized this recombinant, secreted Tp9. Additionally, PBMC from ITM-immunized cattle produced significant (p < 0.05) amounts of IFNγ following ex vivo exposure to Tp9, but this response varied between cattle of different MHC class I and class II genotypes. In addition, depletion experiments demonstrated that IFNγ to Tp9 was primarily produced by CD4+ T cells. Molecular analysis demonstrated that Tp9 presents a signal peptide that is weakly functional in mammalian cells, suggesting that it remains within lymphocytes during infection. Tp9 secretion from mammalian cells was substantially increased when the tPA secretion signal sequence was substituted for the native secretion signal sequence. Using full-length, recombinant Tp9 secreted from mammalian cells, we demonstrated that T. parva-immune cattle develop both humoral and cellular immune responses to this antigen. Collectively, these results provide rationale for further evaluation of Tp9 as a component of a T. parva subunit vaccine.
Detection of Antibiotic Resistant Staphylococcus aureus from Milk: A Public Health Implication

The aim of this study was to investigate the occurrence, antibiotic susceptibility profiles, and virulence genes determinants of S. aureus isolated from milk obtained from retail outlets of the North-West Province, South Africa. To achieve this, 200 samples of raw, bulk and pasteurised milk were obtained randomly from supermarkets, shops and some farms in the North-West Province between May 2012 and April 2013. S. aureus was isolated and positively identified using morphological (Gram staining), biochemical (DNase, catalase, haemolysis and rapid slide agglutination) tests, protein profile analysis (MALDI-TOF mass spectrometry) and molecular (nuc specific PCR) methods. The antimicrobial resistance profiles of the isolates were determined using the phenotypic agar diffusion method. Genes encoding enterotoxins, exfoliative toxins and collagen adhesins were also screened using PCR. Among all the samples examined, 30 of 40 raw milk samples (75%), 25 of 85 bulk milk samples (29%) and 10 of 75 pasteurised milk samples (13%) were positive for S. aureus. One hundred and fifty-six PCR-confirmed S. aureus isolates were obtained from 75 contaminated milk samples. A large proportion (60%–100%) of the isolates was resistant to penicillin G, ampicillin, oxacillin, vancomycin, teicoplanin and erythromycin. On the contrary, low level resistance (8.3%–40%) was observed for gentamicin, kanamycin and sulphamethoxazole. Methicillin resistance was detected in 59% of the multidrug resistant isolates and this was a cause for concern. However, only a small proportion (20.6%) of these isolates possessed PBP2a which codes for Methicillin resistance in S. aureus. In addition, 32.7% of isolates possessed the sec gene whereas the sea, seb sed, see, cna, eta, etb genes were not detected. The findings of this study showed that raw, bulk and pasteurised milk in the North-West Province is contaminated with toxigenic and multi-drug resistant S. aureus strains. There is a need to implement appropriate control measures to reduce contamination as well as the spread of virulent S. aureus strains and the burden of disease in humans.
Bmc Plant Biology Saccharomyces Cerevisiae Fkbp12 Binds Arabidopsis Thaliana Tor and Its Expression in Plants Leads to Rapamycin Susceptibility

Background: The eukaryotic TOR pathway controls translation, growth and the cell cycle in response to environmental signals such as nutrients or growth-stimulating factors. The TOR protein kinase can be inactivated by the antibiotic rapamycin following the formation of a ternary complex between TOR, rapamycin and FKBP12 proteins. The TOR protein is also found in higher plants despite the fact that they are rapamycin insensitive. Previous findings using the yeast two hybrid system suggest that the FKBP12 plant homolog is unable to form a complex with rapamycin and TOR, while the FRB domain of plant TOR is still able to bind to heterologous FKBP12 in the presence of rapamycin. The resistance to rapamycin is therefore limiting the molecular dissection of the TOR pathway in higher plants.
Larval and early juvenile development of Paralomis granulosa reared at different temperatures: tolerance of cold and food limitation in a lithodid crab from high latitudes

Paralomis granulosa Jacquinot is a commercially fished lithodid crab species living in subantarctic and cold-temperate regions of southern South America. Its larval stages (Zoea I, II, Megalopa) are fully lecithotrophic, developing in the complete absence of food from hatching through metamorphosis; first feeding occurs in the first juvenile crab stage. In laboratory rearing experiments conducted at constant 1, 3, 6, 9, 12, and 15°C, we studied rates of larval and early juve- nile survival and development in relation to temperature. At 1°C, many larvae (52%) reached the Megalopa stage almost 2 mo after hatching, but all died subsequently without passing through meta- morphosis. Larval development was successfully completed at all other temperatures, with maximum survival at 6 to 9°C. The time of non-feeding larval development from hatching to metamorphosis lasted, on average, from 24 d (at 15°C) to almost 4 mo (117 d, at 3°C). When the experiment was ter- minated 1 yr after hatching, the 3rd (3°C) to 8th (15°C) juvenile crab instar had been reached. The relationship between the time of development through individual larval or juvenile stages (y) and temperature (T) was described as a power function (y = a × T b , or log(y) = log(a) + b · log(T); the same regression model was also used to describe the temperature-dependence of cumulative periods of development from hatching. The wide thermal tolerance window for successful larval development (at least 3 to 15°C) and the broad geographic range of this species show that the early life-cycle stages of P. granulosa are cold-eurythermal. This physiological trait together with larval independence of food indicate that this lithodid crab species is well adapted to severe conditions of cold in com- bination with the food-limitation in subantarctic regions. Since similar traits have been also observed in other Lithodidae, we suggest that early life-history adaptations to low temperatures and low plank- tonic productivity may explain the high number of lithodid species occurring at high latitudes and in the deep sea, i.e. in conditions under which other Decapoda show strongly reduced diversity.
Assessment of oxidative stress in chronic pancreatitis patients.

AIM To assess the levels of antioxidant capacity and oxidative damage in blood of chronic pancreatitis (CP) patients in comparison with those in healthy control subjects, by using several different analytical techniques. METHODS Thirty-five CP patients and 35 healthy control subjects were investigated prospectively with respect to plasma levels of thiols, ferric reducing ability of plasma (FRAP, i.e. antioxidant capacity), levels of protein carbonyls and thiobarbituric acid reactive substances (TBARS). Additionally, we evaluated the production of reactive oxygen species (ROS) in whole blood. RESULTS The antioxidative thiols including cysteine, cysteinylglycine and glutathione were significantly lower in CP patients. In addition, the non-enzymatic antioxidant capacity was significantly lower in CP patients, which correlated with the amount of oxidative protein (protein carbonyls) and the extent of lipid damage (TBARS), both were significantly higher in CP patients. The ROS production in whole blood after stimulation with phorbol 12-myritate 13-acetaat, demonstrated a strong tendency to produce more ROS in CP patients. CONCLUSION Oxidative stress may contribute to the pathogenesis of chronic pancreatitis by decreasing antioxidant capacity and increasing oxidative damage in CP patients may be a rationale for intervention with antioxidant therapy.
Comparative Biochemical Analysis Suggests That Vinculin and Metavinculin Cooperate in Muscular Adhesion Sites*

Metavinculin, the muscle-specific splice variant of the cell adhesion protein vinculin, is characterized by a 68-amino acid insert within the C-terminal tail domain. The findings that mutations within this region correlate with hereditary idiopathic dilated cardiomyopathy in man suggest a specific contribution of metavinculin to the molecular architecture of muscular actin-membrane attachment sites, the nature of which, however, is still unknown. In mice, metavinculin is expressed in smooth and skeletal muscle, where it co-localizes with vinculin in dense plaques and costameres, respectively, but is of conspicuously low abundance in the heart. Immunoprecipitates suggest that both isoforms are present in the same complex. On the molecular level, both vinculin isoforms are regulated via an intramolecular head-tail interaction, with the metavinculin tail domain having a lower affinity for the head as compared with the vinculin tail. In addition, metavinculin displays impaired binding to acidic phospholipids and reduced homodimerization. Only in the presence of phospholipid-activated vinculin tail, the metavinculin tail domain is readily incorporated into heterodimers. Mutational analysis revealed that the metavinculin insert significantly alters binding of the C-terminal hairpin loop to acidic phospholipids. In summary, our data lead to a model in which unfurling of the metavinculin tail domain is impaired by the negative charges of the 68-amino acid insert, thus requiring vinculin to fully activate the metavinculin molecule. As a consequence, microfilament anchorage may be modulated at muscular adhesion sites through heterodimer formation.
Porting PHYLIP phylogenetic package on the Desktop GRID platform XtremWeb-CH

This paper describes the parallelization (gridification) of the phylogenetic package PHYLIP on a desktop GRID platform termed XtremWeb-CH. PHYLIP is a package of programs for inferring phylogenies (evolutionary trees). It is the most widely-distributed phylogeny package. PHYLIP has been used to build the largest number of published trees. It's known that some modules of PHYLIP are CPU time consuming; their sequential version can not be applied to a large number of sequences. XtremWeb-CH (XWCH) is a software system that makes it easier for scientists and industrials to deploy and execute their parallel and distributed applications on a public-resource computing infrastructure. Universities, research centres and private companies can create their own XWCH platform while anonymous PC owners can participate to these platforms. They can specify how and when their resources could be used. The objective of XWCH is to develop a real High Performance Peer-To-Peer platform with a distributed scheduling and communication system. The main idea is to build a completely symmetric model where nodes can be providers and consumers at the same time. In this paper we describe the porting, deployment, and execution of some PHYLIP modules on the XWCH platform. The parallelized version of PHYLIP is used to generate evolutionary tree related to HIV viruses.
Can one predict when ultrasound will be useful with percutaneous liver biopsy?

OBJECTIVE:We previously showed that ultrasound altered position of biopsy in 15% of cases by demonstrating intervening structures. This study was designed to test whether one could predict in which cases ultrasound would be useful.METHODS:A standard percussion technique was used. The site chosen was marked. Criteria were established to indicate whether a move might be predicted to be likely. If 10 or more points were assigned, then it was predicted that ultrasound would change position. A difficult percussion was assigned 10 points; obesity, 5 points; and chest deformity, 5 points. The ultrasound was then applied to the marked spot in every case. If an intervening structure was present within 6 cm, the biopsy site was moved. Otherwise, the biopsy was taken from the marked site.RESULTS:One hundred seventeen consecutive liver biopsies were included between January 1999 and January 2000. The criteria predicted the desirability of nine moves. No moves were made, however, in these cases. In 17 cases (14.5%), moves were made because of intervening structures. None of the cases were predicted. A move was made in 1 of 23 obese patients. There was no statistical difference in moves made between obese and nonobese patients.CONCLUSIONS:Using criteria of difficult percussion, obesity, and unusual chest shape, we could not predict when ultrasound would be useful. This is in contrast to the belief that ultrasound can be applied to selected liver biopsies considered in advance to be more difficult, as in the obese patients, and instead suggests that to avoid intervening structures, one should apply ultrasound to all cases.
Stability of service under time-of-use pricing

We consider time-of-use pricing as a technique for matching supply and demand of temporal resources with the goal of maximizing social welfare. Relevant examples include energy, computing resources on a cloud computing platform, and charging stations for electric vehicles, among many others. A client/job in this setting has a window of time during which he needs service, and a particular value for obtaining it. We assume a stochastic model for demand, where each job materializes with some probability via an independent Bernoulli trial. Given a per-time-unit pricing of resources, any realized job will first try to get served by the cheapest available resource in its window and, failing that, will try to find service at the next cheapest available resource, and so on. Thus, the natural stochastic fluctuations in demand have the potential to lead to cascading overload events. Our main result shows that setting prices so as to optimally handle the expected demand works well: with high probability, when the actual demand is instantiated, the system is stable and the expected value of the jobs served is very close to that of the optimal offline algorithm.
CageR: from 3D performance capture to cage-based representation

Modern performance capture systems [de Aguiar et al. 2008] provide high resolution 3D mesh sequences which are becoming critical components for today's special effects. Unfortunately, such raw sequences have a large memory footprint and are difficult to edit. We propose CageR, a framework based on spatial deformation with cages to construct automatically a compact and editable high level representation of these raw sequences, resulting in high compression factors and allowing easier post processing. In particular, we formulate an automatic cage fitting algorithm embedding a new relaxation strategy based on Maximum Volume and a new regularization method based on sub-spectral analysis. As a result, we use the CageR representation in various applications, including compression, motion transfer and shape space modeling.
Exploiting Conjugate Symmetry of the Short-Time Fourier Spectrum for Speech Enhancement

Typical speech enhancement algorithms operate on the short-time magnitude spectrum, while keeping the short-time phase spectrum unchanged for synthesis. We propose a novel approach where the noisy magnitude spectrum is recombined with a changed phase spectrum to produce a modified complex spectrum. During synthesis, the low energy components of the modified complex spectrum cancel out more than the high energy components, thus reducing background noise. Using objective speech quality measures, informal subjective listening tests and spectrogram analysis, we show that the proposed method results in improved speech quality.
[Self-management in anticoagulation--a meta-analysis].

BACKGROUND The aim of anticoagulation treatment is to reach an optimal international normalised ratio (INR) level in which the risk of thrombosis as well as bleeding is minimal. Recently developed methods that allow self-managed control of anticoagulation make more frequent testing possible and may thus represent a better alternative than conventional control. MATERIAL AND METHODS In this meta-analysis, randomized, controlled trials comparing self-management with conventional control with regard to time in therapeutic range and number of bleedings and thromboses were investigated. Eight clinical trials fulfilled the criteria for inclusion, representing about 870 patient-years and 1300 patients. RESULTS The difference in time in therapeutic range was on average 10% in favour of self-management. The rate of major and fatal bleedings was 3.5% per patient-years with conventional control, 2.4% per patient-years with self-management. The rate of thrombosis was 3.9% per patient-years with conventional control as against 2.7% with self-management. OddsratioMH for major clinical events was 0.62 (95% CI 0.429, 0.895); p < 0.01. INTERPRETATION This meta-analysis shows that self-managed control of anticoagulation improves safety and efficacy and is probably a better alternative than conventional control for selected groups of patients.
Acute nitric oxide synthase inhibition and endothelin-1-dependent arterial pressure elevation

Key evidence that endogenous nitric oxide (NO) inhibits the continuous, endothelin (ET)-1-mediated drive to elevate arterial pressure includes demonstrations that ET-1 mediates a significant component of the pressure elevated by acute exposure to NO synthase (NOS) inhibitors. This review examines the characteristics of this pressure elevation in order to elucidate potential mechanisms associated with the negative regulation of ET-1 by NO and, thereby, provide potential insight into the vascular pathophysiology underlying NO dysregulation. We surmise that the magnitude of the ET-1-dependent component of the NOS inhibitor-elevated pressure is (1) independent of underlying arterial pressure and other pressor pathways activated by the NOS inhibitors and (2) dependent on relatively higher NOS inhibitor dose, release of stored and de novo synthesized ET-1, and ETA receptor-mediated increased vascular resistance. Major implications of these conclusions include: (1) the marked variation of the ET-1-dependent component, i.e., from 0 to 100% of the pressure elevation, reflects the NO-ET-1 regulatory pathway. Thus, NOS inhibitor-mediated, ET-1-dependent pressure elevation in vascular pathophysiologies is an indicator of the level of compromised/enhanced function of this pathway; (2) NO is a more potent inhibitor of ET-1-mediated elevated arterial pressure than other pressor pathways, due in part to inhibition of intravascular pressure-independent release of ET-1. Thus, the ET-1-dependent component of pressure elevation in vascular pathophysiologies associated with NO dysregulation is of greater magnitude at higher levels of compromised NO.
Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus

ABSTRACT While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap.
Malocclusion in the Kwaio, a Melanesian group on Malaita, Solomon Islands.

In the present investigation, a number of occlusal variables which contribute to malocclusion were quantified among the Kwaio people of Malaita, Solomon Islands. Angle classification, overjet, overbite, openbite, crossbite, rotation, crowding, and spacing were assessed from dental casts of 180 persons (94 males, 86 females) who had complete permanent dentitions anterior to the first molar. Males had significantly more overjet and mandibular incisor crowding than females, and significantly less posterior openbite and mandibular canine-premolar spacing. The frequency of openbite, rotation of maxillary teeth, and crowding of anterior teeth increased with advancing age. The frequency of posterior crowding decreased after age 30. Spacing, in general, increased with advancing age. In the distribution of the Angle classes of occlusion, the Kwaio resembled Australian aborigines living in technologically primitive circumstances.