Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining the Effect of Pterostilbene on Insulin Secretion Using Chemoproteomics

Pterostilbene, the 3,5-dimethoxy derivative of resveratrol, is a well-known polyphenolic compound, mainly found in blueberries, grapevines, and Pterocarpus marsupium heartwood, which has recently attracted a great deal of attention due to its wide bio-pharmacological profile. Moreover, pterostilbene is more lipophilic than resveratrol, with a consequently better bioavailability and a more interesting therapeutic potential. In this work, a chemoproteomic approach, based on affinity chromatography, was applied on pterostilbene in the attempt to identify the biological targets responsible for its bioactivity. On this basis, syntaxins, a group of proteins involved in the formation of SNARE complexes mediating vesicles exocytosis, were selected among the most interesting pterostilbene interactors. In vitro and in cell assays gave evidence of the pterostilbene ability to reduce insulin secretion on glucose-stimulated pancreatic beta cells, opening the way to potential applications of pterostilbene as a supplement in the care of insulin-dependent metabolic disorders.
AN IMPROVED USER-INDEPENDED ALGORITHM FOR ROOM ACOUSTIC PARAMETERS CALCULATION

We present a novel algorithm for room acoustic parameters calculation which addresses one of the major uncertainties in room acoustics prediction, that of user defined termination criteria. One of the uncertainties in room acoustics predictions that take place using geometrical acoustics methods is the user defined termination criteria. Ray tracing algorithms require maximum length and number of rays to be send. Image source algorithms require maximum reflection orders and/or maximum sound attenuation. Our algorithm adjusts progressively its termination criteria until a correct result is approximated, based on an intelligent guessing, therefore removing this burden and risk from the user. We explain the algorithm’s termination procedure and we compare with typical implementations. We show that the results approximate measurements equally well or better, having the benefit that the user does not need to worry anymore about these settings.
An Algorithm to Design Redundant Manipulators of Optimally Fault-Tolerant Kinematic Structure

One measure of the global fault tolerance of a redundant robot is the size of its self-motion manifold. If this size is defined as the range of its joint angles, then the optimal self-motion manifold size for an <inline-formula><tex-math notation="LaTeX">$n$</tex-math></inline-formula>-degree-of-freedom (DoF) robot is <inline-formula><tex-math notation="LaTeX">$n\times 2\pi$</tex-math></inline-formula>, which is not typical for existing robot designs. This letter presents a novel two-step algorithm to optimize the kinematic structure of a redundant manipulator to have an optimal self-motion manifold size. The algorithm exploits the fact that singularities occur on large self-motion manifolds by optimizing the robots kinematic parameters around a singularity. Because a gradient for the self-motion manifold size does not exist, the kinematic parameter optimization uses a coordinate descent procedure. The algorithm was used to design 4-DoF, 7-DoF, and 8-DoF manipulators to illustrate its efficacy at generating optimally fault-tolerant robots of any kinematic structure.
Sampling effort and fish species richness in small terra firme forest streams of central Amazonia, Brazil

Small streams are important components of the landscape in terra firme forests in central Amazonia and harbor a large number of fish species. Nevertheless, the lack of a common sampling protocol in studies of this ichthyofauna hinders comparisons among available results. This study evaluates how the length of stream reach sampled affects estimates of local fish species density in 1st, 2nd, and 3rd order streams, and proposes a mean minimum sampling length that best approximates the absolute number of species in a given stream segment. We sampled three streams in the Biological Dynamics of Forest Fragments Project's study sites, between May and August 2004. At each stream, one 1st order, one 2nd order, and one 3rd order segment was sampled. We sampled five 20-m reaches in each stream segment. Three to four people collected along each reach for 45 to 60 minutes. We used Jaccard's coefficient to estimate the similarity of species composition among stream reaches and segments. Estimates of species richness were obtained with Jackknife 1 and Bootstrap algorithms and species accumulation curves. We used simple linear regressions to look for relationships between species density and fish abundance and between species density and the volume of 100-m stream segments. Species density in 1st order stream reaches was slightly higher than in 2nd and 3rd order stream reaches, whereas fish abundance was apparently higher in 3rd order reaches. Similarity in fish species composition between 20-m reaches was low for all studied streams. Species density values in pooled 100-m stream segments represented 71.4% to 94.1% of the estimated values for these streams. Species density showed a direct relationship both with volume of the sampled stream segment and fish abundance. It seems plausible that larger streams contain a higher number of microhabitat types, which allow for the presence of more fish species per stream length. Based on the values of asymptotes and equations for species accumulation curves, the mean minimum sampling length that best estimates the absolute number of species in a stream segment is 180 m ± 20 sd for 1st order segments; 213 m ± 23 sd for 2nd order segments, and 253 m ± 30 sd for 3rd order stream segments.
Wind erosion in the Sahelian zone of Niger : processes, models, and control techniques

In the Sahelian zone of Niger, severe wind erosion occurs mainly in the first half of the rainy season (May - July), when violent winds preceding thunderstorms result in intense sediment transport. Quantification of this wind erosion is difficult due to a high degree of temporal and spatial variability in wind-blown particle mass fluxes. Using improved techniques to collect field data in Niger and developed models revealed that a single wind erosion event may result in severe losses of soil particles and nutrients from unprotected fields. The many technical measures available to reduce wind erosion do not always fit into the Sahelian farming systems. A survey revealed that mulching with crop residues is the main control technique applied by Nigerien farmers, but the quantity of crop residues available for soil conservation is limited, as stover has also other important uses. Field tests with flat pearl millet stalks showed that small quantities can significantly reduce sediment transport during moderate storms. However, sediment transport may actually be intensified by small quantities of mulch during severe storms, because of increased turbulence around the stalks.
Upotreba koncentrata dušika iz krumpira u proizvodnji α-amilaze s pomoću plijesni Aspergillus oryzae

Summary The influence of various nitrogen sources and media supplements on a-amylase (EC 3.2.1.1) formation by Aspergillus oryzae ATCC 1011 was investigated in shake flask experiments and batch fermentations. Both inorganic and organic nitrogen-containing supplements have been applied, while corn starch and ammonium sulphate were used as the major source of carbon and nitrogen, respectively. Shake flask experiments revealed that potato nitrogen concentrate (PNC) is almost equivalent to corn steep liquor (CSL) in supporting amylase formation. A pretreatment step consisting of clarification of the turbid material did not show any significant effect. The replacement of the inorganic nitrogen source by sodium nitrate led to lower enzyme yields. Other complex supplements may reduce the enzyme level formed, e.g. casein hydrolysate, or increase the amylase titre slightly, e.g. yeast extract or malt extract. Cultivations in instrumented bench top reactors on media supplemented with PNC led to higher cell growth rates and yields of a-amylase in comparison with the medium without any supplement. Replacement of PNC by CSL revealed a slightly increased enzyme level, which is in the range of 9–17 % after 100 h of cultivation. Only minor differences were revealed in the growth kinetics and enzyme formation when PNC was used as the sole nitrogen source, replacing a mixture of soybean meal, yeast extract, malt extract and casein hydrolysate in bioreactor cultivations with lactose as the carbon source. However, metabolic differences as seen from the course of dissolved oxygen tension (DOT), a-amino nitrogen concentration and the amount of acid needed to maintain a constant pH were observed.
A floristic analysis of the vegetation of Platberg, eastern Free State, South Africa

A checklist of vascular plants of Platberg was compiled to determine species richness, rarity and endemism. The floristic analysis is part of the Department of Economic, Tourism and Environmental Affairs Free State biodiversity assessment programme and conservation management plan for Platberg. The analysis identified a total of 669 species belonging to 304 genera and 95 families, with 214 species belonging to the Monocotyledoneae and 438 species to the Dicotyledoneae. The largest family is Asteraceae with 126 species, followed by Poaceae with 73 species, Cyperaceae with 39 species, Fabaceae with 33 species, and Scrophulariaceae with 27 species. Various fynbos species were found, as well as 26 endemic/near-endemic species belonging to the Drakensberg Alpine Centre or Eastern Mountain Region. The results of this study revealed that Platberg shares inselberg floral richness and endemism that can be tracked via the Afromontane archipelago-like string of inselbergs and mountains, which stretch north through the Chimanimani Mountains, into Malawi, the Eastern Arc Mountains via Tanzania and north through Ethiopia, into Eurasia. Conservation implications: Platberg, as an inselberg, is a site of significant biological diversity, with high species richness, vegetation selection and ecosystem complexity. It shares floral richness and endemism via inselbergs and mountains throughout Africa. The high species richness, Red Data species and ecosystems make this area an important conservation site that should be legislated and protected.
Occurrence of Pierce's disease of grapevines and its control strategies in Taiwan.

PD of grapes caused by Xylella fastidiosa, a xylem-limited bacterium, has been listed as one of the international quarantine plant diseases. From 2002, the Bureau of Animal and Plant Health Inspection and Quarantine launched a survey project to detect PD in Taiwan. So far, a total of 13,666 grapevines were confirmed to be infected by X. fastidiosa via direct isolations and PCR protocols. Other than grapes, the following four plants were confirmed to be the alternative hosts of PD in Taiwan: Diplocyclos palmatus (L.) C. Jeffrey, Ampelopsis brevipedunculata (Maxim.) Trautv var. hancei (Planch.) Rehder. , Humulus scandens (Lour.) Merr. , and Mallotus paniculatus (Lam.) Muell. -Arg. The 16S rRNA sequences of PD strains isolated from tissues of grapevines exhibiting PD symptoms collected from 5 counties and 4 alternative hosts were compared with X. fastidiosa from other hosts. The phylogenetic trees constructed with neighbour-joining method revealed that X. fastidiosa strains from different hosts could be divided into five subgroups and the PD strains from Taiwan were grouped with grapevine and mulberry strains from the Americas. The control strategies recommended for limiting the spread of PD are as follows: (1) to plant the healthy seedlings and eradicate the PD-like grapevines immediately (2) to eradicate the alternative hosts and the weeds that insect vectors favor (3) to control the population of indigenous insect vectors and avoid the invasion of foreign insect vectors. The occurrence of Pierce’s disease of grapevines and its control strategies in Taiwan 146
Statistical Applications in Genetics and Molecular Biology

Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall the Griffiths-Tavare and Stephens-Donnelly proposals and emphasize the relation between the latter proposal and exact sampling from the infinite alleles model. We also introduce a new proposal that takes knowledge of the ancestral state into account. The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavare (1994).
The influence of osmotic concentration of media on the growth of Sago Palm (Metroxylon sagu Rottb.) in vitro.

This study investigated the role of osmotic potential of media on the early growth stages of sago palm in vitro. There were significant effects on the growth rate of explants after four weeks of culture under different sucrose and D-sorbitol combinations. A modified Murashige and Skoog (MS) medium supplied with 22.5 g sucrose and 7.5 g sorbitol which created a low osmotic potential environment (-0.457 MPa) had significant effects on the increase in weight of explants. This osmotic potential was found optimal for the initial growth of sago palm explants in vitro. In contrast, explants cultured in intermediate osmotic potential media (-0.380 MPa) obtained little increase in weight. Results suggested that owing to the sago palm's ecology where it is highly adapted to flooding even by saline water, explants likewise prefer a low osmotic potential in in vitro culture.
Effects of water deficit on growth, nodulation and physiological and biochemical processes in Medicago sativa-rhizobia symbiotic association

ABSTRACT The effects of water deficit on growth, nodulation, and several physiological and biochemical processes in six symbiotic combinations involving three Moroccan alfalfa (Medicago sativa L.) populations (Tafilalet1, Adis-Tata and Demnate2), an American Moapa variety and two rhizobial strains (RhL9 and RhL10) were studied. The experiment was conducted under greenhouse conditions. Seedlings were separately inoculated with the suspension of two rhizobial strains and grown under two irrigation regimes: 80% of field capacity (optimal irrigation) and 40% of field capacity (water deficit). The water stress was applied for five weeks and the agro-physiological and biochemical parameters related to water deficit tolerance were assessed. The results showed that the water deficit had significantly reduced the height of the plants, the dry biomass and nodulation. This constraint also negatively affected the relative water content of leaves, the membrane permeability, the stomatal conductance, the maximum quantum yield of photosystem II, the time to reach maximum fluorescence, the total chlorophyll content and the total nitrogen content. Comparison among the tested symbiotic combinations showed that their behaviors were significantly different. Under drought, oasis populations Ad and Ta maintained high PS II efficiency, membrane stability, relative water content, chlorophyll and nitrogen content in comparison to the mountain one Dm2 and the American Moapa variety. These parameters were maintained at adequate levels in the plants inoculated with the rhizobial strain RhL9 that showed a tolerance to water deficit conditions.
Minerva

Should doctors wear white coats? Most patients, especially older ones, would apparently rather see doctors wear white coats as a way of identifying who they are. Most doctors, on the other hand, perceive them as an infection risk and find them uncomfortable (Postgraduate Medical Journal 2004;80: 284-6). Minerva wonders if the infection risk would seem as great if coats were exchanged for clean ones every day.
Evaluation of Antioxidant Activity of Selected Indian Mushrooms

Cellular damage caused by reactive oxygen species (ROS) has been implicated in several diseases, and hence antioxidants have significant importance in human health. In this study, five methods were used to test and compare the antioxidant activity at different levels involving formation and scavenging of free radicals by the extracts of four mushrooms that have medicinal values. The results were expressed as Trolox equivalent antioxidant capacity (TEAC) and ascorbic acid equivalent antioxidant capacity (AEAC). In the DPPH (1,1-diphenyl 2-picryl hydrazyl) assay, the ethyl acetate extract of Phellinus rimosus showed more potent activity than the methanolic extracts of Pleurotus florida, Pleurotus sajour-caju, and Ganoderma lucidum. The ethyl acetate extract of P. rimosus at a concentration of 0.1% showed a high TEAC value (12.488). In the ABTS (2,2-azobis-3-ethylbenzthiazoline-6-sulfonic acid) spectrophotometric assay, it possessed the most effective antioxidant activity (TEAC 4.84) compared to methanolic extracts of P. florida, P. sajour-caju, and G. lucidum. The extract of P. rimosus also possessed higher activity compared to other extracts in the ferric-reducing antioxidant power (FRAP) assay. In the pulse radiolysis studies and the ORAC (oxygen radical absorbance capacity) assay also, these mushrooms showed significant activities. Results of the DPPH, ABTS, FRAP, and ORAC assays indicate that all the four mushrooms examined showed significant antioxidant activities. Among these, P. rimosus extract seems to be the more effective antioxidant.
Long-Term Sensitization of a Defensive Withdrawal Reflex in Aplysia

When a weak tactile stimulus is applied to the siphon of Aplysia californica, the animal withdraws the siphon between the parapodia. This defensive withdrawal reflex can be facilitated (sensitized) if the animal is previously given 4 days of training, consisting of four brief noxious stimuli each day. The sensitization of this reflex can last for up to 3 weeks after training and is mediated by the abdominal ganglion which also mediates long-term habituation. This preparation may provide a system for analyzing the neural mechanism of long-term behavioral modifications of complexity which is intermediate between habituation and associative learning.
MORPHOLOGICAL FEATURES OF ZOPE, ABRAMIS BALLERUS, FROM THE MIDDLE STRETCH OF THE ODRA RIVER, POLAND

Background. The zope (blue bream), Abramis ballerus (L., 1758), is a cyprinid fish without economic importance, and its morphology has been poorly known. The monophyly of the genus Abramis is still unclear; therefore any new contribution to the knowledge on the morphology of zope could shed a new light on the phylogeny of this group of fishes. The aim of the present study was to learn and describe meristic- and morphometric futures of zope and to compare the results with published data. Material and methods. A total of 40 specimens of the zope, Abramis ballerus, were caught in the middle stretch of the Odra River, near the city of G∏ogow, western Poland, in October 2002. For each fish, 21 biometric features were measured and selected meristic features (external and internal) were determined. Cephalic sensory canals were studied and their pores were counted. Results. The coefficient of variation for the body proportions of zope from the middle stretch of the Odra River ranged from 3.89% to 19.13% and its principal features were as follows: D III 8–10; A III 34–43; P I 14–18; V II 7–9; l.l. 62–75. It had one row of pharyngeal teeth, most frequently, in 5–5 pattern. The total number of vertebrae ranged from 46 to 48, (mean 47.38). The preoperculo-mandibular canal (CPM) and infraorbital canal (CIO) had the highest number of pores. Conclusion. The presently reported study shows that the sample analysed did not differ significantly from the population of the Dniepr River, although it differed significantly (in body proportions) from those of Lake Dabie. The majority of values of meristic features did not differ significantly from those found in literature. However, there is still too little comparative material regarding internal meristic features and especially its osteology.
Characterization of single nucleotide polymorphisms from expressed sequence tags of Chinese mitten crab Eriocheir sinensis

The Chinese mitten crab Eriocheir sinensis is an important aquaculture species in Asia and causes considerable economic and ecological damage as an invasive species in North America and Europe. Until recently, molecular markers available for genetic analysis in this species were lim- ited to a few microsatellite sequences used in population studies. Here we describe the discovery of 3191 single nucleotide polymorphisms (SNPs) from the alignment of expressed sequence tags (ESTs) in E. sinensis. The observed frequency of SNPs was estimated at 0.78 per 100 bp of contig sequences. C/T substitutions were frequent and accounted for 32.2% of all SNPs. A subset of these SNPs (n = 38) was selected for validation by allele-specific PCR with melting temperature (Tm)-shift primers based on their observed frequency in sequence data; 12 (31.6%) of these were polymorphic in a panel of 40 wild-caught crabs. Eight (21.1%) did not amplify any product, and 18 (47.4%) failed due to amplifi- cation failure of 1 allele-specific primer. A table of optimal codons was deduced from the analysis of the E. sinensis EST dataset, and the results implied that the gene expression levels and GC-content might play important roles in codon usage bias. Sixteen codons ending with a G or C base were defined as 'optimal codons,' which may provide useful information for predicting gene expression in crabs. These are the first SNPs developed for the Chinese mitten crab and will provide a useful complement to currently available genetic markers.
THE GENUS MICROASCUS

Descriptions are given of 14 species of Microascus. M. pyramidus Barron and Gilman is described as a new species and M. trigonosporus var. macrosporus Orr as a new variety. The conidial stage and cultural characteristics are described for most of the species. The genus Microascus is separated from Petriella on the basis of the smaller, lighter-colored ascospores as well as the type of conidia. Most of the species have a Scopulariopsis-type of conidial stage. M. variabilis Massee and Salmon is placed in synonomy under M. longirostris Zukal. Microascus stysanophorus (Matt.) comb. nov. is proposed.