Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past.

Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non- or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment-based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi-gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).
Vegetation response to a short interval between high‐severity wildfires in a mixed‐evergreen forest

1 Variations in disturbance regime strongly influence ecosystem structure and function. A prominent form of such variation is when multiple high‐severity wildfires occur in rapid succession (i.e. short‐interval (SI) severe fires, or ‘re‐burns’). These events have been proposed as key mechanisms altering successional rates and pathways. 2 We utilized a natural experiment afforded by two overlapping wildfires occurring within a 15‐year interval in forests of the Klamath–Siskiyou Mountains, Oregon (USA). We tested for unique effects of a SI fire (15‐year interval before 2002 fire) by comparing vegetation communities 2 years post‐fire to those following a long‐interval (LI) fire (> 100‐year interval before 2002 fire) and in mature/old‐growth (M/OG) stands (no high‐severity fire in > 100‐year). 3 Nearly all species found in M/OG stands were present at similar relative abundance in both the LI and SI burns, indicating high community persistence through multiple high‐severity fires. However, the SI burn had the highest species richness and total plant cover with additions of disturbance‐associated forbs and low shrubs, likely due to a propagule bank of early seral species that developed between fires. Persistence of flora was driven by vegetative sprouting, on‐site seed banks, and dispersal from off‐site seed sources. Several broadly generalizable plant functional traits (e.g. rapid maturation, long‐lived seed banks) were strongly associated with the SI burn. 4 Sprouting capacity of hardwoods and shrubs was unaltered by recurrent fire, but hardwood/shrub biomass was lower in the SI burn because individuals were smaller before the second fire. Conifer regeneration densities were high in both the SI and LI burns (range = 298–6086 and 406–2349 trees ha−1, respectively), reflecting similar availability of seed source and germination substrates. 5 Synthesis. SI severe fires are typically expected to be deleterious to forest flora and development; however, these results indicate that in systems characterized by highly variable natural disturbances (e.g. mixed‐severity fire regime), native biota possess functional traits lending resilience to recurrent severe fire. Compound disturbance resulted in a distinct early seral assemblage (i.e. interval‐dependent fire effects), thus contributing to the landscape heterogeneity inherent to mixed‐severity fire regimes. Process‐oriented ecosystem management incorporating variable natural disturbances, including ‘extreme’ events such as SI severe fires, would likely perpetuate a diversity of habitats and successional pathways on the landscape.
SsrA‐mediated peptide tagging caused by rare codons and tRNA scarcity

SsrA RNA mediates the addition of a C‐terminal peptide tag (AANDENYALAA) to bacterial proteins translated from mRNAs without in‐frame stop codons. This process involves both tRNA‐ and mRNA‐like functions of SsrA and targets the tagged proteins for degradation. By designing an SsrA variant that adds a peptide tag (AANDENYALDD) that does not result in rapid degradation, we show that tagging of a model protein synthesized from an mRNA without stop codons can be detected both in vivo and in vitro. We also use this assay to demonstrate that ribosome stalling at clusters of rare arginine codons in mRNA is sufficient to recruit and activate the SsrA peptide tagging system. An essential requirement for tagging at rare AGA codons is a scarcity of the cognate tRNA; supplemental tRNAAGA suppresses tagging, and depleting the available pool of tRNAAGA enhances tagging and reveals tagging caused by single rare AGA codons. Protein tagging at sites corresponding to rare codons appears to involve SsrA action at an internal mRNA site rather than at the 3′ end of a cleaved mRNA.
The relationship between body mass index and periodontitis in the Copenhagen City Heart Study.

BACKGROUND Obesity is hypothesized to involve immunoinflammatory alterations, and the condition has been related to increased susceptibility to periodontitis. The present study analyzed the association between overweight/obesity and periodontitis assessed as clinical attachment loss (AL) and bleeding on probing (BOP) in a cross-sectional design. METHODS Participants included 878 women and 719 men aged 20 to 95 years (participation rate 54%) who underwent an oral examination, including full-mouth recording of clinical AL and BOP. Overweight and obesity were assessed by body mass index (BMI) using the World Health Organization criteria. BMI was related to clinical AL (defined as mean > or =3 mm) and BOP (defined as > or =25%) by multivariable logistic regression in the total population and in subjects stratified by gender and smoking habits. RESULTS Obese participants had a lower odds ratio (OR) for clinical AL compared to participants with normal weight (OR: 0.60; 95% confidence interval [CI]: 0.36 to 0.99). The same tendency was observed in subjects stratified by smoking habit. Obese never-smokers had a lower OR for clinical AL compared to never-smoking participants with normal weight (OR: 0.32; 95% CI: 0.11 to 0.91). Overweight participants had a higher OR for BOP compared to subjects with normal weight (OR: 1.36; 95% CI: 1.04 to 1.78). In addition, overweight never-smokers had a higher OR for BOP compared to normal weight never-smokers (OR: 1.63; 95% CI: 1.03 to 2.59). CONCLUSION BMI may be inversely associated with clinical AL but positively related to BOP.
Intraoperative transfusion practices in Europe

Background. Transfusion of allogeneic blood influences outcome after surgery. Despite widespread availability of transfusion guidelines, transfusion practices might vary among physicians, departments, hospitals and countries. Our aim was to determine the amount of packed red blood cells (pRBC) and blood products transfused intraoperatively, and to describe factors determining transfusion throughout Europe. Methods. We did a prospective observational cohort study enrolling 5803 patients in 126 European centres that received at least one pRBC unit intraoperatively, during a continuous three month period in 2013. Results. The overall intraoperative transfusion rate was 1.8%; 59% of transfusions were at least partially initiated as a result of a physiological transfusion trigger- mostly because of hypotension (55.4%) and/or tachycardia (30.7%). Haemoglobin (Hb)- based transfusion trigger alone initiated only 8.5% of transfusions. The Hb concentration [mean (sd)] just before transfusion was 8.1 (1.7) g dl−1 and increased to 9.8 (1.8) g dl−1 after transfusion. The mean number of intraoperatively transfused pRBC units was 2.5 (2.7) units (median 2). Conclusion. Although European Society of Anaesthesiology transfusion guidelines are moderately implemented in Europe with respect to Hb threshold for transfusion (7–9 g dl−1), there is still an urgent need for further educational efforts that focus on the number of pRBC units to be transfused at this threshold. Clinical trial registration. NCT 01604083.
Subcutaneous fat changes in low-income lactating mothers and growth of breast-fed infants.

OBJECTIVE We studied changes in body fat of lactating mothers and its relationship to milk fat and growth of exclusively breast-fed infants during the first 3 months of life. METHOD Changes in body fat measured by body mass index (BMI) and skinfold thickness (triceps, suprailiac, subscapular, pectoral) of 39 low socioeconomic status women were measured every 15 days during the first 3 months postpartum. Milk fat concentrations and growth of exclusively breast-fed infants were followed at the same intervals. Attained growth (ponderal and linear) of infants was analyzed through multivariate analyses against changes in maternal adiposity (BMI and sum of skinfolds), weight, and milk fat concentrations. RESULTS There was a decrease in maternal skinfold thickness from the 15th day postpartum. Milk fat concentrations decreased significantly only at the second month of lactation. CONCLUSION Statistical model adjustments for duration of study, milk fat concentration, and birth weight of infants explained 88% of variance in infant growth (r2 = 0.886, p = 0.0001).
Field Evaluation of Willow Under Short Rotation Coppice for Phytomanagement of Metal-Polluted Agricultural Soils

Short rotation coppice (SRC) of willow and poplar might be a promising phytoremediation option since it uses fast growing, high biomass producing tree species with often a sufficient metal uptake. This study evaluates growth, metal uptake and extraction potentials of eight willow clones (Belders, Belgisch Rood, Christina, Inger, Jorr, Loden, Tora and Zwarte Driebast) on a metal-contaminated agricultural soil, with total cadmium (Cd) and zinc (Zn) concentrations of 6.5 ± 0.8 and 377 ± 69 mg kg−1 soil, respectively. Although, during the first cycle, on average generally low productivity levels (3.7 ton DM (dry matter) ha−1 y−1) were obtained on this sandy soil, certain clones exhibited quite acceptable productivity levels (e.g. Zwarte Driebast 12.5 ton DM ha−1 y−1). Even at low biomass productivity levels, SRC of willow showed promising removal potentials of 72 g Cd and 2.0 kg Zn ha−1 y−1, which is much higher than e.g. energy maize or rapeseed grown on the same soil. Cd and Zn removal can be increased by 40% if leaves are harvested as well. Nevertheless, nowadays the wood price remains the most critical factor in order to implement SRC as an acceptable, economically feasible alternative crop on metal-contaminated agricultural soils.
Cardiac function at rest and with exercise in the chronic fatigue syndrome.

To evaluate a possible cardiac pathophysiology of the chronic fatigue syndrome, we compared the resting cardiac function and exercise performance of 41 patients to those of an age-matched and sex-matched normal control group. Persistent fatigue following an acute apparently viral illness was the major complaint of all patients; none had specific cardiac symptoms nor abnormal physical findings. Electrocardiographic spatial patterns were normal in the patients, and there were no differences in the body surface sum of positive T-wave integrals between the patients (240 microV.x 10(2) +/- 107 microV.s x10(2)) and control (244 microV.x 10(2) +/- 108 microV.s x 10(2) subjects. Twenty-four hour ambulatory ECGs revealed no differences in sinus rates and incidences of ventricular dysrhythmias in the two populations. Left ventricular dimensions and systolic fractional shortening values were also similar in both groups; moreover none of the patients had segmental wall motion abnormalities. On graded exercise testing, 20 of 32 normal subjects achieved target (85 percent of age-maximum) heart rates, compared to four of 31 patients (p less than 0.001). The duration of exercise averaged 12 +/- 4 minutes for the normal subjects and 9+/- 4 minutes for the patients (p less than 0.01). The temporal profile of exercise heart rates was dissimilar in the two groups, with patients' rates consistently and progressively less than those of normal subjects. Peak heart rate averaged 152 +/- 16 beats per minute for the normal group vs 124 +/- 19 beats per minute for the patients (p less than 0.0001); in age-related terms, respectively, 82 +/- 6 percent of the maximum heart rate vs 66 +/- 10 percent (p less than 0.0001). Thus, patients with chronic fatigue syndrome have normal resting cardiac function but a markedly abbreviated exercise capacity characterized by slow acceleration of heart rate and fatigue of exercising muscles long before peak heart rate is achieved. (ABSTRACT TRUNCATED AT 250 WORDS)
Spatial Thinking in Undergraduate Science Education

Abstract: Spatial thinking is central to many scientific domains and professions spatial ability predicts success and participation in science. However spatial thinking is not is not emphasized in our educational system. This paper presents a selective review of four types of studies regarding spatial thinking in undergraduate science curricula; (1) correlational studies examining the relations between measures of spatial ability and performance in science disciplines, (2) studies that attempt to train aspects of spatial thinking, (3) studies of how students understand specific spatial representations in sciences (4) studies that use dynamic spatial representations to promote scientific understanding. For each type of study, the evidence is critically evaluated and conclusions are drawn about how to nurture spatial thinking in science.
Tropospheric Comparisons of Vaisala Radiosondes and Balloon-Borne Frost-Point and Lyman-α Hygrometers during the LAUTLOS-WAVVAP Experiment

Abstract The accuracy of all types of Vaisala radiosondes and two types of Snow White chilled-mirror hygrosondes was assessed in an intensive in situ comparison with reference hygrometers. Fourteen nighttime reference comparisons were performed to determine a working reference for the radiosonde comparisons. These showed that the night version of the Snow White agreed best with the references [i.e., the NOAA frost-point hygrometer (FPH) and University of Colorado cryogenic frost-point hygrometer (CFH)], but that the daytime version had severe problems with contamination in the humid upper troposphere. Since the RS92 performance was superior to the other radiosondes and to the day version of the Snow White, it was selected to be the working reference. According to the reference comparison, the RS92 has no bias in the mid- and lower troposphere, with deviations <±5% in relative humidity (RH). In the upper troposphere, the RS92 has a ∼5% RH wet bias, which is partly due to the RS92 time lag error and the ter.
Nicotine-induced grooming: a possible dopaminergic and/or cholinergic mechanism

The ability of nicotine, to induce grooming in rats was studied. Grooming was induced by i.p. injection of different doses (0.0675-0.5 mg/kg) of nicotine to rats. The effect was dose-dependent. However, the response was decreased with increasing doses of the drug from 0.25-0.5 mg/kg. Administration of the dopamine (DA) D 1/D2 receptor agonist apomorphine (0.025-5 mg/kg, i.p.) also caused grooming in a dose-dependent manner. High doses of apomorphine (0.1-0.5 mg/kg, i.p.) also induced a lower degree of response. Combination of a low dose of nicotine (0.0675 mg/kg) with different doses of apomorphine did not show any interaction. However, there was an interaction between a high dose of nicotine and apomorphine. Thus, combination of a higher dose of nicotine (0.125 mg/kg) with apomorphine, reduced apomorphine-induced grooming. The muscarinic receptor antagonist atropine (5 and 10 mg/kg), peripheral nicotinic receptor antagonist hexamethonium (5 and 10 mg/kg), central nicotinic receptor antagonist mecamylamine (1 and 3 mg/kg) and D1 DA receptor antagonist SCH23390 (0.05 and 0.1 mg/kg) all decreased the response to nicotine. Atropine, mecamylamine and SCH23390 by themselves reduced spontaneous grooming. It is concluded that nicotine elicits grooming indirectly through a possible D1 dopaminergic mechanism. However, muscarinic and nicotinic cholinergic mechanism(s) may be involved.
Macrophage Colony-stimulating Factor Promotes Cell Survival through Akt/Protein Kinase B*

The signaling pathways activated by the macrophage colony-stimulating factor (M-CSF) to promote survival of monocyte and macrophage lineage cells are not well established. In an effort to elucidate these pathways, we have used two cell types responsive to M-CSF: NIH 3T3 fibroblasts genetically engineered to express human M-CSF receptors (3T3-FMS cells) and human monocytes. M-CSF treatment induced M-CSF receptor tyrosine phosphorylation and recruitment of the p85 subunit of phosphatidylinositol 3-kinase (PI3K) to these receptors. These M-CSF receptor events correlated with activation of the serine/threonine kinase Akt. To clarify that PI3K products activate Akt in response to M-CSF, NIH 3T3 fibroblasts expressing mutant human M-CSF receptors (3T3-FMS(Y809F)) that fail to activate Ras in response to M-CSF also exhibit increased Akt kinase activity in response to M-CSF challenge. Furthermore, Akt appears to be the primary regulator of survival in 3T3-FMS cells, as transfection of genes encoding dominant-negative Akt isoforms into these fibroblasts blocked M-CSF-induced survival. In normal human monocytes, M-CSF increased the levels of tyrosine-phosphorylated proteins and induced Akt activation in a PI3K-dependent manner. The PI3K inhibitor LY294002 blocked M-CSF-mediated monocyte survival, an effect that was partially restored by caspase-9 inhibitors. These data suggest that M-CSF may induce cell survival through Akt-induced suppression of caspase-9 activation.
The Description of 4D Product Information Model Based on Hypergraph

On the basis of product 3D model which links with the process of design, 4D Information Model as a structured integration of product information need to express all the complicated relationship between product information and keep the consistency of all these relationships in the whole product evolving process. [1]. Based on the analysis of the information character in product design process, the design process information of 4D Product Information Model (4D-PIM) is elaborated by introducing hypergraph theory. The theory basis for establishing 4D-PIM is studied, and a formalized description of 4D information model is carried out. The paper provides a new research method to product design and the process management of it.
novel interpenetrating polymer network mucoadhesive microspheres of locust bean gum and poly(vinyl alcohol) for the delivery of Famotidine

Novel interpenetrating polymer network (IPN) of locust bean gum (LBG) and poly vinyl alcohol (PVA) were prepared and crosslinked with glutaraldehyde (GA) to form mucoadhesive microspheres by emulsion cross-linking method to deliver model anti-ulcer drug, famotidine. Various formulations were prepared by changing the ratio of LBG: PVA, extent of cross-linking in order to optimize the formulation variables on drug encapsulation efficiency and release rate. FTIR spectroscopy was done to confirm the formation of interpenetrating network and the chemical stability of famotidine after penetration of microspheres. Microspheres formed were spherical with smooth surfaces as revealed by SEM and mean particle size as measured by optical microscopy ranged between 10.83±0. 75μm to 21.13±0. 74μm. Drug entrapment efficiency was ranges between 65.44±2.57% to 84.67±2.58%. Percentage mucoadhesion of the microspheres was found to be in the range between 63.33±2.57% to 86.66±3.65%. Equilibrium and dynamic swelling studies were performed in 0.1N HCl buffer solution of pH 1.2 and diffusion coefficients were calculated by considering the spherical geometry of the matrices. In vitro release studies were performed in pH 1.2 media. Release data indicated that a drug release which depends on the extent of cross-linking and the ratio of LBG: PVA present in the microsphere. The release data were fitted to an empirical equation to estimate the transport parameters, which indicated that the release follows Super Case II transport mechanism. Based on the results of in-vitro studies it was concluded that these IPN mucoadhesive microspheres provided oral controlled release of famotidine.
A new labdane diterpenoid glycoside from Nervilia fordii.

To study the chemical constituents of Nervilia fordii (Hance) Schltr. , various chromatographic methods were used, including D101 macroporous resin, silica gel, ODS and preparative HPLC chromatographic techniques. A new labdane diterpenoid glycoside named as nervilifordoside A was isolated from 60% EtOH extract of Nerviliafordii. The structure of compound 1 was elucidated as 12, 17-epoxy-3-hydroxy-17-methoxy-labdan-13-en-16, 15-olide 3-O-alpha-rhamnopyranosyl-(1 --> 2)-O-beta-glucopyranoside on the basis of HR-MS, 1D and 2D NMR spectroscopic data as well as chemical methods.
Risk Factors and Clinical Outcomes in Patients with IBD with Melanoma

Background: Patients with inflammatory bowel disease (IBD) are at increased risk to develop malignant melanoma and this risk may increase with use of anti-tumor necrosis factor (TNF) therapy. Impaired survival of immunosuppressed melanoma patients is reported in transplant and rheumatology patients. This study aims to (1) identify risk factors for melanoma development in patients with IBD, (2) compare clinical characteristics of melanoma in patients with IBD to the general population, and (3) assess the influence of immunosuppressive medication on survival. Methods: We retrospectively searched the Dutch Pathology Database to identify all Dutch patients with IBD with cutaneous melanoma between January 1991 and December 2011. We then performed 2 case–control studies. To identify risk factors for melanoma development in IBD, we compared patients with IBD with melanoma to the general IBD population. To compare outcome and survival after melanoma diagnosis, we compared cases with non-IBD melanoma patients. Results: We included 304 patients with IBD with melanoma, 1800 IBD controls, and 8177 melanoma controls. IBD cases had more extensive IBD (ulcerative colitis: pancolitis: cases 44.5% versus IBD controls without melanoma 28.1%; P < 0.01; Crohn's disease: ileal and colonic disease: cases 57.9% versus controls 48.9%; P = 0.02). Despite a lower Nodes (N)-stage in patients with IBD (N1+ 8.3% versus 18.2%; P < 0.01) with comparable Tumor (T) and Metastasis (M) stages, survival was similar between groups, regardless of immunosuppressive or anti-TNF therapy. Conclusions: This study showed that IBD extent is a risk factor for melanoma development. Despite the lower N-stage in patients with IBD, we could not confirm impaired survival after melanoma in patients with IBD, regardless of anti-TNF and/or thiopurine use.
Modeling realistic wide-band indoor propagation channels by using an efficient ray-tracing simulator

This paper proposes a novel procedure to extract the wide-band propagation channel parameters, that employs a RT simulation carried out at different frequencies and followed by a proper processing of the simulated data. In particular, a RT-based tool suitable to be used for accurate and reliable site-planning in the framework of wide-band indoor wireless systems has been implemented, which shows an excellent agreement between simulation results and measured data