Miracle-dz/UniFAR-FTUs huggingface dataset:
A new retroelement constituted by a natural alternatively spliced RNA of murine replication‐competent retroviruses

Replication of simple retroviruses depends on the recruitment of a single large primary transcript toward splicing, transport/packaging and translation regulations. In this respect, we studied the novel SD′ 4.4 kb RNA of murine leukemia retroviruses (MLV) which results from alternative splicing of the primary transcript. We showed that SD′ RNA was required for optimal replication since expression of a pre spliced SD′ RNA trans‐complemented the impaired infectivity of a SD′‐defective mutant. We monitored the fate of this novel transcript throughout early and late events of the viral life cycle. SD′ RNA was specifically incorporated into virions demonstrating that the unspliced RNA was not the unique viral RNA present in virions. Furthermore, SD′ RNA was reverse transcribed and its DNA copy integrated into the host genome, thus constituting a new splice donor‐associated retroelement (SDARE) in infected cells. Finally, we showed that SD′ mRNA encoded a 50 kDa polyprotein, and to a lower extent an additional 60 kDa polyprotein, which harbored Gag and integrase domains.
Feature selection and data balancing for activity recognition in smart homes

Activities performed in the same location in a smart home share common features and thus become difficult to classify. We propose an activity recognition approach that identifies key features from the information obtained using the sensors deployed in multiple locations and objects. Key features increase the separability between the classes, making the approach suitable for overlapping activities. For fewer number of activity instances in a class, we apply an oversampling approach for data balancing. The classification is performed using a learning method Evidence Theoretic K-Nearest Neighbors (ET-KNN), which performs better in uncertain conditions. Evaluation of the proposed approach using three publicly available smart home datasets demonstrates better recognition performance compared to the existing methods.
Methyldibromoglutaronitrile is an important contact allergen in The Netherlands

From 15 May to 15 December 1994, 2943 patients sunspected of having contact dermatitis(1955 women, 988 men) were patch tested with methyldibromoglutarorutrile 0.3%, 0.1% and 0.05% pet. 119 patients (4.0%: women 4.1%, men 3.8%) proved to be allergic, 71% of the reactions were considered to be relevant. In 2/3 of the patients, causative products were cosmetics, in 1/3 moistened toilet tissues. Testing with methyldibromoghitaronitrile at lower concentrations (0.05% and 0.1%) commercial allergens (Euxyl® K 400 and methyldibromoglutaronitrile, both containing methyldibromoglutaronitrile 0.1%). resulted in a number of falsc‐negative reactions. All preservatives in the European standard series had lower scores than the 4% positive reactions to methyldibromoglutaronitrile (formaldehyde 2.0% MCI/MI (Kathon® CG) 3.2% parabens 1.0% quaternium‐15 1.3%). It is concluded that methyldibromoglutaronitrile (present in the commercial preservative Euxyl® K 400) is an important contact allergen in the Netherlands in cosmetics and moistened toilet tissues. It should be added to cosmetics series and to proctological series. The optimal test concentration is unknown, but may be 0.3% pet. The concentration of 0.1% methyldibromoglutaronitrile in the currenttly available commercial allergens appears to be too low. resulting in a number of false‐negative reactions.
Activation of Phosphorylase by Cyclic AMP without Augmentation of Contractility in the Perfused Guinea Pig Heart

This study was designed to determine whether intracellular cyclic AMP augments myocardial contractility directly. Isolated guinea pig hearts were perfused with media containing cyclic AMP and other adcninc nucleotides with or without 3% dimethylsulfoxide (DMSO) to facilitate myocardial uptake. Phosphorylase b to a transformation, detennined fluorometrically, was used as an index of increased intracellular cyclic AMP. Heart rate, left ventricular pressure and dP/dt were assessed in isovolumic preparations. DMSO, 3%, did not significantly affect myocardial performance or mask increased contractility produced by epinephrine. Cyclic AMP, 10−4M, with or without DMSO depressed left ventricular pressure and dP/dt modestly, even when heart rate was maintained constant by pacing. Phosphorylase activation increased from a control value of 16.5±1.44% (mean±SE, N=12) to 40.0±3.1% (N=19) following perfusion with 10−4M cyclic AMP with 3% DMSO; DMSO alone increased phosphorylase much less. 5′-AMP with DMSO compared to DMSO alone did not activate phosphorylase. The results indicate that increased intracellular cyclic AMP, achieved in the absence of adrenergic stimulation, does not increase myocardial contractility. Thus, they support the view that the positive inotropic effect produced by catecholamines is not mediated by a direct action of cyclic AMP on the contractile apparatus.
Mutual Dependence of Candida albicans Est1p and Est3p in Telomerase Assembly and Activation

ABSTRACT Telomerase is an RNA-protein complex responsible for extending one strand of the telomere terminal repeats. Analysis of the telomerase complex in budding yeasts has revealed the presence of one catalytic protein subunit (Est2p/TERT) and at least two noncatalytic components (Est1p and Est3p). The TERT subunit is essential for telomerase catalysis, while the functions of Est1p and Est3p have not been precisely elucidated. In an earlier study, we showed that telomerase derived from a Candida est1-null mutant is defective in primer utilization in vitro; it exhibits reduced initiation and processivity on primers that terminate in two regions of the telomere repeat. Here we show that telomerase derived from a Candida est3-null mutant has nearly identical defects in primer utilization and processivity. Further analysis revealed an unexpected mutual dependence of Est1p and Est3p in their assembly into the full telomerase complex, which accounts for the similarity between the mutant enzymes. We also developed an affinity isolation and an in vitro reconstitution protocol for the telomerase complex that will facilitate future mechanistic studies.
DNA barcoding reveals polymorphism in the pygmy grasshopper Tetrix bolivari (Orthoptera, Tetrigidae)

Abstract Many pygmy grasshopper species exhibit colour-marking polymorphism. However, this polymorphism in some species, such as Tetrix bolivari, is almost unknown. The aim of this work is to identify using DNA barcoding the colour-marking polymorphic morphs of this pygmy grasshopper species collected from both grass and sand microhabitats. Analysis by NJ clustering and pairwise distances indicated that all specimens collected showing colour-marking polymorphism are species of Tetrix bolivari. Haplotype network construction showed ten different haplotypes from a total of 57 Tetrix bolivari individuals with H1(82.5%) being the most common type and it also displayed low divergence within Tetrix bolivari population. The haplotype analyses were consistent with the NJ clustering. Our field census showed the frequency of Tetrix bolivari morphs differed significantly, with the rank order of morphs (from high to low) typeA1, type B1, type A2, type A3, type A4, type A5, type A6, type A7, type B2, type B3, and type B4. The most common type A morphs were without contrasting markings, while the rarer type B morphs have contrasting white markings. We suggest that type B morphs have greater camouflage effects against natural backgrounds such as grass or sand than type A morphs. Both our field census and haplotype analysis revealed that type A has higher frequency and more haplotypes than type B.
Identification of Tumor‐Related Proteins by Proteomic Analysis of Cerebrospinal Fluid from Patients with Primary Brain Tumors

Cerebrospinal fluid (CSF) has been rediscovered in the post-genomic era as a great source of potential protein biomarkers for various diseases. The source allows rapid screening, low sample consumption, and accurate protein identification by proteomic technology. In the present study, we identified 2 candidate tumor-related proteins, N-myc oncoprotein and low-molecular weight caldesmon (l-CaD), in CSF samples of patients with primary brain tumors by using 2-dimensional polyacrylamide gel electrophoresis (2D PAGE), followed by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis. N-myc and l-CaD were related to tumor cell nuclei and blood vessels, respectively, in tissue sections of the tumor biopsies taken from the same patients from whom CSF was processed. N-myc oncoprotein and l-CaD have not been detected in CSF before. The practical value of these proteins as possible tumor markers, prognosticators, or their utility in monitoring response to chemotherapy is currently a subject of investigation. It is concluded that the combination of 2D PAGE and MALDI-TOF-MS is successful as an unbiased global screening tool for CSF.
Association of polymorphisms in pulmonary surfactant protein A1 and A2 genes with high-altitude pulmonary edema.

STUDY OBJECTIVES A potential pathogenetic cofactor for the development of high-altitude pulmonary edema (HAPE) is an increase in capillary permeability, which could occur as a result of an inflammatory reaction and/or free-radical-mediated injury to the lung. Pulmonary surfactant protein A (SP-A), the most abundant surfactant protein, has potent antioxidant properties and protects unsaturated phospholipids and growing cells from oxidative injury. Single-nucleotide polymorphisms (SNPs) in SP-A1 and SP-A2, genes encoding SP-A, have been associated with susceptibility to respiratory distress syndrome, COPD, and pulmonary infections. In view of the protective role of SP-A against inflammatory reactions and oxidative damage, the two underlying mechanisms in development of HAPE, we examined the association of constitutional susceptibility to HAPE with polymorphisms in SP-A1 and SP-A2. DESIGN A cross-sectional case-control study. SETTING Blood samples were collected at an altitude (> or = 3,500 m). PARTICIPANTS Twelve low-altitude native (LAN) subjects with a history of HAPE, 15 healthy LAN sojourners without a history of HAPE (LAN control subjects), and 19 healthy high-altitude natives (HANs) without a history of HAPE (HAN control subjects). MEASUREMENTS The SNPs in four exons and intermediate introns of the SP-A1 and SP-A2 were screened by polymerase chain reaction and sequencing. Biochemical parameters related to oxidative stress (malondialdehyde and reduced glutathione in RBC) and membrane permeability (circulating levels of lactate dehydrogenase) were measured in plasma. RESULTS Allele frequencies of three loci in SP-A1 and one in SP-A2 were significantly different between LAN HAPE patients (SP-A1 C1101T: C allele, 36.4% and T allele, 63.6%; SP-A1 T3192C: T allele, 61.1% and C allele, 38.9%; SP-A1 T3234C: T allele, 61.1% and C allele, 38.9%; and SP-A2 A3265C: A allele, 21.4% and C allele, 78.6%) and LAN control subjects (SP-A1 C1101T: C allele, 8.3% and T allele, 91.7%; SP-A1 T3192C: T allele, 15% and C allele, 85%; SP-A1 T3234C: T allele, 15% and C allele, 85%; and SP-A2 A3265C: A allele, 37.5% and C allele, 62.5%) [C1101T odds ratio [OR], 6.3 with 95% confidence interval (CI), 2.8 to 14.3; T3192C OR, 8.9 with 95% CI, 4.5 to 17.6; T3234C OR, 8.9 with 95% CI, 4.5 to 17.6; and A3265C OR, 2.2 with 95% CI, 1.2 to 4.1 (p < or = 0.01)]. Heterozygous individuals, with respect to SP-A1 C1101T and SP-A2 A3265C, showed less severity in oxidative damage in comparison with homozygous subjects (SP-A1 T1101 and SP-A2 C3265). CONCLUSION The polymorphisms in SP-A1 (C1101T, T3192C, and T3234C) and SP-A2 (A3265C) might be one of the genetic factors contributing to susceptibility to HAPE.
Study of Fitness Cost in Three Rigid Ryegrass Populations Susceptible and Resistant to Acetyl-CoA Carboxylase Inhibiting Herbicides

Evaluation of fitness differences between herbicide-resistant and susceptible weed biotypes, allows a better prediction of further dispersal of herbicide-resistance populations and the design of a management strategy in order to achieve a mitigation of the problem in the absence of herbicide. In this study an evaluation of germination and seedling emergence characteristics of three rigid ryegrass biotypes (one susceptible and two resistant populations with different mutations, namely Ile 1781 Leu and Ile 2041 Asn) and of competition between this weed and wheat using replacement series experiments was conducted. The results showed that when seeds were on the soil surface (0 cm) to depth of 2 cm and again for the depth of 6 cm, there were not any significant differences between the biotypes regarding seed germination percentage. On the contrary, when seeds were sown in 2-4 cm depth, R-1781 consistently displayed lower emergence than the S and R-2041 biotypes. Moreover, when seeds were sown at 8 cm depth, final proportions of emerged seedlings were similar for R-2041 and R-1781, while both populations had significantly higher emergence than the S population. The competitive ability of the three biotypes was similar, as determined by a replacement series experiment with wheat. Our results under competitive conditions revealed that Triticum aestivum was more competitive than Lolium rigidum. Overall, there was no apparent fitness penalty associated to ACCase-inhibitor resistance, while different mutations may impose different competitive ability and therefore require case-specific management strategies.
Effects of sample size on the performance of species distribution models

A wide range of modelling algorithms is used by ecologists, conservation practitioners, and others to predict species ranges from point locality data. Unfortunately, the amount of data available is limited for many taxa and regions, making it essential to quantify the sensitivity of these algorithms to sample size. This is the first study to address this need by rigorously evaluating a broad suite of algorithms with independent presence–absence data from multiple species and regions. We evaluated predictions from 12 algorithms for 46 species (from six different regions of the world) at three sample sizes (100, 30, and 10 records). We used data from natural history collections to run the models, and evaluated the quality of model predictions with area under the receiver operating characteristic curve (AUC). With decreasing sample size, model accuracy decreased and variability increased across species and between models. Novel modelling methods that incorporate both interactions between predictor variables and complex response shapes (i.e. GBM, MARS‐INT, BRUTO) performed better than most methods at large sample sizes but not at the smallest sample sizes. Other algorithms were much less sensitive to sample size, including an algorithm based on maximum entropy (MAXENT) that had among the best predictive power across all sample sizes. Relative to other algorithms, a distance metric algorithm (DOMAIN) and a genetic algorithm (OM‐GARP) had intermediate performance at the largest sample size and among the best performance at the lowest sample size. No algorithm predicted consistently well with small sample size (n < 30) and this should encourage highly conservative use of predictions based on small sample size and restrict their use to exploratory modelling.
Perinatal outcome of children born to mothers with thyroid dysfunction or antibodies: a prospective population-based cohort study.

CONTEXT There are only a few large prospective studies involving evaluation of the effect of maternal thyroid dysfunction on offspring and observations are inconsistent. OBJECTIVE The objective of the study was to investigate the effects of thyroid dysfunction or antibody positivity on perinatal outcome. SETTING AND PARTICIPANTS The study included prospective population-based Northern Finland Birth Cohort 1986 including 9247 singleton pregnancies. First-trimester maternal serum samples were analyzed for thyroid hormones [TSH, free T(4) (fT4)] and antibodies [thyroid-peroxidase antibody (TPO-Ab) and thyroglobulin antibody (TG-Ab)]. Mothers were classified by their hormone and antibody status into percentile categories based on laboratory data and compared accordingly. MAIN OUTCOMES Outcomes were perinatal mortality, preterm delivery, absolute and gestational age-adjusted birth weight, and absolute and relative placental weight. RESULTS The offspring of TPO-Ab- and TG-Ab-positive mothers had higher perinatal mortality, which was not affected by thyroid hormone status. Unadjusted and adjusted (for maternal age and parity) risk for increased perinatal mortality was an odds ratio of 3.1 (95% confidence interval 1.4-7.1) and 3.2 (1.4-7.1) in TPO-Ab- and 2.6 (1.1-6.2) and 2.5 (1.1-5.9) in TG-Ab-positive mothers. TPO-Ab-positive mothers had more large-for-gestational age infants (2.4 vs. 0.8%, P = 0.017), as did mothers with low TSH and high fT4 concentrations vs. reference group (6.6 vs. 2.5%, P = 0.045). Significantly higher placental weights were observed among mothers with low TSH and high fT4 or high TSH and low fT4 levels as well as among TPO-Ab-positive mothers. CONCLUSIONS First-trimester antibody positivity is a risk factor for perinatal death but not thyroid hormone status as such. Thyroid dysfunction early in pregnancy seems to affect fetal and placental growth.
Antibiotic prescribing in dental practice in Belgium.

AIM To assess the types and frequency of antibiotic prescriptions by Belgian dentists, the indications for antibiotic prescription, and dentists' knowledge about recommended practice in antibiotic use. METHODOLOGY In this cross-sectional survey, dental practitioners were asked to record information about all antibiotics prescribed to their patients during a 2-week period. The dental practitioners were also asked to complete a self-administered questionnaire regarding demographic data, prescribing practices, and knowledge about antibiotic use. A random sample of 268 Belgian dentists participated in the survey. RESULTS During the 2-week period, 24 421 patient encounters were recorded; 1033 patients were prescribed an antibiotic (4.2%). The median number of prescriptions per dentist for the 2 weeks was 3. Broad spectrum antibiotics were most commonly prescribed: 82% of all prescriptions were for amoxycillin, amoxycillin-clavulanic acid and clindamycin. Antibiotics were often prescribed in the absence of fever (92.2%) and without any local treatment (54.2%). The most frequent diagnosis for which antibiotics were prescribed was periapical abscess (51.9%). Antibiotics were prescribed to 63.3% of patients with periapical abscess and 4.3% of patients with pulpitis. Patterns of prescriptions were confirmed by the data from the self-reported practice. CONCLUSIONS Discrepancies between observed and recommended practice support the need for educational initiatives to promote rational use of antibiotics in dentistry in Belgium.
An auditory interneurone tuned to the male song frequency in the duetting bushcricket Ancistrura nigrovittata (Orthoptera, Phaneropteridae)

An auditory interneurone (AN1) of the bushcricket Ancistrura nigrovittata is described; it has a soma and dendrites in the prothoracic ganglion, an ascending axon and axon collaterals in the protocerebrum. As judged from morphological and physiological similarity, it is probably homologous to AN1 described in Tettigonia viridissima and to AN1 described in Gryllus bimaculatus. The occurrence and physiology of AN1 are not sex-specific. It receives predominant excitation between 12 and 16 kHz (male song frequency) and inhibition at lower frequencies and more strongly at higher frequencies. It shows optimum-type intensity/response curves. Frequency tuning and intensity-dependence compare well with female behaviour. Lesion experiments demonstrate that AN1 receives excitation and frequency-dependent inhibition from the soma-contralateral ear and inhibition from the soma-ipsilateral ear. The latter contributes to the clear left­right difference in its responses. AN1 does not obviously discriminate between temporal patterns of different behavioural effectivity. Its spiking, however, is coupled to the temporal pattern. It is hypothesized that AN1 may be involved in frequency processing by female A. nigrovittata.
Dipyridamole Plus Aspirin in Cerebrovascular Disease.

Background The second European Stroke Prevention Study (ESPS-2) recently reported a substantial benefit of dipyridamole combined with aspirin over aspirin alone in the prevention of stroke. This appears to be at odds with previous studies suggesting that dipyridamole adds nothing to aspirin alone. Objectives To review and compare the results of ESPS-2 and previous studies of dipyridamole plus aspirin and aggregate them in a meta-analysis. Methods We combined the detailed data provided by the Antiplatelet Trialists' Collaboration on the previous studies of dipyridamole plus aspirin with the results from ESPS-2. The data on the previous trials were listed in the appendix of the 1994 publication of the Antiplatelet Trialists' Collaboration. Results The results of our meta-analysis demonstrate that for the outcome of nonfatal stroke, ESPS-2 overwhelms previous data, which, even in the aggregate, did not include enough patients or outcome events to exclude efficacy for the combination of dipyridamole and aspirin. Differences between ESPS-2 and previous studies, which may have contributed to different results, include the doses and preparations of aspirin and dipyridamole. Conclusions The ESPS-2 showed that dipyridamole alone prevents stroke. More importantly, it showed a substantial benefit for dipyridamole combined with aspirin over aspirin alone. When the ESPS-2 data are aggregated with the 14 previous trials of dipyridamole combined with aspirin over aspirin alone, the combination reduces the risk of stroke by 23% over aspirin alone. Nevertheless, important questions remain unanswered. We conclude that another randomized clinical trial showing a significant benefit of the combination of dipyridamole plus aspirin over aspirin alone may be needed before the addition of dipyridamole to aspirin is widely accepted for prevention of stroke.
2 Chloro 4,4,5,5 tetramethyl 1,3,2 dioxaphospholane, a reagent for the accurate determination of the uncondensed and condensed phenolic moieties in lignins

The use of 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane as a phosphitylation reagent in quantitative 31P NMR analysis of the hydroxyl groups in lignins has been thoroughly examined, and an experimental protocol recommended for spectra acquisition has been developed. Quantitative analysis of six “standard lignins” gave results comparable to those obtained by other methods of analysis. Excellent resolution of the various phenolic hydroxyl environments including those present in condensed moieties was observed. However, this was at the expense of resolution in the aliphatic hydroxyl region, where no distinction between primary, secondary, and the erythro and threo forms of the secondary hydroxyls of the ,l? -0-4 bonds can be made.
The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic

Swine-origin pandemic human influenza A virus (H1N1pdm) has spread rapidly around the world since its initial documentation in April 2009. Here we have updated initial estimates of the rate of molecular evolution and estimates of the time of origin of this virus in the human population using the large number of viral sequences made available as part of the public health response to this global pandemic. Currently sampled H1N1pdm sequences share a most recent common ancestor in the first 7 weeks of 2009 with the implication that the virus was transmitting cryptically for up to 3 months prior to recognition. A phylogenetic reconstruction of the data shows that the virus has been circling the globe extensively with multiple introductions into most geographical areas.