Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Protein Structure Prediction

Functional characterization of a protein sequence is one of the most frequent problems in biology. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3‐D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. Comparative modeling remains the only method to reliably predict the 3‐D structure of a protein with an accuracy comparable to a low‐resolution experimentally determined structure. This overview unit describes generic considerations for all four steps of comparative modeling, typical modeling errors, and applications of comparative protein structure models.
A weather-based yield-forcasting model for sugar beet.

A simple model to predict seasonal growth in sugar beet yield is presented. Time from sowing to the so called 'growth point date' (the date on which a plant contains 4 g sugar) is character­ ized by a temperature sum. The increase in sugar yield after this date is calculated from in­ coming solar radiation using an average radiation use efficiency. Temperature sums and radi­ ation use efficiencies were estimated for each of the 11 Dutch sugar beet regions.
The sodium pump

The sodium pump (Na+/K+-ATPase; sodium- and potassium-activated adenosine 5′-triphosphatase; EC 3.6.1.37) has been under investigation for more than four decades. During this time, the knowledge about the structure and properties of the enzyme has increased to such an extent that specialized groups have formed within this field that focus on specific aspects of the active ion transport catalyzed by this enzyme. Taking this into account, this review, while somewhat speculative, is an attempt to summarize the information regarding the enzymology of the sodium pump with the hope of providing to interested readers from outside the field a concentrated overview and to readers from related fields a guide in their search for gathering specific information concerning the structure, function, and enzymology of this enzyme.
Movements of intercolony natal dispersers in the Columbian ground squirrel

Eight yearling male Columbian ground squirrels (Spermophilus columbianus) were radio-collared in an attempt to document emigration from an isolated montane meadow in southwestern Alberta. Six of the eight squirrels emigrated from the meadow over a 14-day period. All six dispersers departed during the first half of the day, before 13:30. Four of the squirrels were known to have travelled briefly in and out of the forest habitat bordering the meadow before emigrating, possibly searching for exit routes. During emigration, squirrels moved quickly (up to 4.0 km/h) over relatively long distances, stopping occasionally for extended periods of time . Emigrating squirrels followed cutbanks along natural drainages, roads, and game trails; routes tended to interconnect patches of suitable ground squirrel habitat. While dispersing, five of the six emigrants were known to have encountered such patches within 10 km of the natal colony. None of the squirrels died while being tracked and four squirrels were known to hav.
Angioimmunoblastic T-cell lymphoma: a tumor of follicular helper T cells derivation with clinical and pathological relevance

Malignancies derived from mature (post-thymic) T cells and NK cells, collectively referred to as peripheral T-cell lymphomas (PTCLs), are a heterogeneous group of diseases, altogether accounting for about 10-15% of all non-Hodgkin lymphomas in most western countries, with a great geographic variation. Irrespective of their pathobiological heterogeneity, PTCLs are, with few exceptions, aggressive diseases with poor prognosis.
Alpha and beta diversity of bees and their pollination role on Cucurbita pepo L. (Cucurbitaceae) in the Guatemalan cloud forest

Abstract. Cucurbita pepo L. (Cucurbitaceae) was an integral component of the diet of Pre-Columbian Mesoamerican cultures and is an important cash crop with high cultural value in contemporaneous indigenous populations of Guatemala. Despite the increasing attention to native bees as pollinators of cucurbit crops, little is known about the diversity of bees that visit or pollinate these crops in many regions. Based on collections from 11 observational plots of C. pepo established in five localities and maintained by the local community across the Cloud Forest Corridor in Guatemala, we documented 27 bee species belonging to 14 genera in Apidae and Halictidae as floral visitors. Species composition was significantly different among plots and among localities; however, honey bees (Apis mellifera Linnaeus, 1758) (Apidae: Apini) and the stingless bee Partamona bilineata (Say, 1837) (Apidae: Meliponini) were the most abundant flower visitors in all plots and localities, accounting up to 80% of the total number of visits. Two species of squash bees were recorded, Peponapis apiculata (Cresson, 1878) and P. limitaris (Cockerell, 1906) (Apidae: Eucerini), but they were rare (3.4% of total number of specimens) across all plots and localities. Based on pollinator exclusion experiments as well as comparisons of fruit weight and seed number and weight, we confirmed the dependence of this crop on insect pollination and the role of honey bees and P. bilineata as main pollinators in the observational plots. Surveys of bees in the surrounding vegetation of the plots indicated a higher diversity (36 species of 28 genera) than in the plots; about 40% of these species are also common visitors of flowers of C. pepo.
BILL LENGTH VARIABILITY IN BIRDS OF THE TRES MARÍAS ISLANDS, MEXICO

Variability of bill length was compared between populations of species present on the Tres Marias Islands and appropriate nearby mainland. Four species were significantly less variable on the islands, one species was significantly more variable, and 11 species were not significantly different in the two regions. Explanations are offered in terms of available food supply: availability may be influenced by competitors. Data from other islands are consistent with this interpretation. However, no clear trend towards greater or less variability on islands has so far been revealed.
Mapping of Quantitative Trait Loci for Milk Yield Traits on Bovine Chromosome 5 in the Fleckvieh Cattle

52 Background 54 Materials and Methods 56 Animals and phenotypes 56 DNA preparation and microsatellite marker selection and genotyping. 56 SNP selection, genotyping and haplotyping 57 Linkage map construction 58 QTL fine mapping 59 Multiple-QTL analysis using linkage disequilibrium and linkage analysis (LDLA) method 60 Estimation of model parameters and test statistics 61
Kinetic Study on Transfructosylation by b-Fructofuranosidase from Aspergillus niger ATCC 20611 and Availability of a Membrane Reactor for Fructooligosaccharide Production

Transfructosylation catalyzed by fructooligosaccharide-producing b-fructofuranosidase from Aspergillus niger ATCC 20611 was kinetically studied and a reaction model of transfructosylation was proposed. Kinetic parameters (Vm, Km, and Ki) were determined from experimental data on the transfructosylation rates at various substrate concentrations with and without addition of glucose. Transfructosylation reaction was found to be inhibited non-competitively (Ki=0.12 mol l−1) by glucose. Simulation results in sugar composition due to the action of a β-fructofuranosidase were in good agreement with the experimental data. In order to get higher reaction conversion with a simultaneous removal of glucose, a membrane reactor system was developed using nano-filtration membrane, through which glucose permeated but sucrose and fructooligosaccharides did not permeate. Fructooligosaccharide percentage of the reaction product was increased to above 90%, which was much higher than that of the batch reaction product (55–60%) and comparable to that of the chromatography processed product. The membrane reactor system will be applicable for production of fructooligosaccharides.
Role of insulin-like growth factor (IGF) axis in the development of tamoxifen resistance in breast cancer epithelial cells

The development of tamoxifen resistance (TamR) in oestrogen receptor positive (ER+) breast cancer is a major therapeutic challenge. Mechanisms suggested to ac-count for this have mainly focussed on the activation of alternative growth factor pathways. The insulin-like growth factor (IGF) axis is a prime candidate for investiga-tion in this area and the use of anti-IGF strategies in the clinical setting of tamoxifen resistance is under investigation. However such strategies, usually targeted to block the IGF-1 receptor (IGF-1R) have proved disappointing. The IGF axis is a multicom-ponent molecular system and the activity of IGF is modulated by the presence of six soluble high affinity IGF binding proteins (IGFBP 1-6). Given the potential role of the IGF axis in the development of tamoxifen resistance it is important to investigate whether the IGFBP family may play a role in this process opening up a route for alter-native anti-IGF based therapies. Using the ER+ MCF-7 cell line we demonstrated that five IGF axis genes (IGF-IR, IGF-2R, IGFBP-2, IGFBP-4 and IGFBP-5) were ex-pressed by both parental wt and tamoxifen resistant (TamR) MCF-7 cells with the re-maining genes (IGF-1, IGF-2, IGFBP-1, IGFBP-3 and IGFBP-6) either not expressed or expressed only at a very low level. IGFBP-5 expression was down-regulated by approximately 7-fold while IGFBP-2 was up-regulated by approximately 2-fold in TamR versus wt cells. These alterations in IGFBP-2 and IGFBP-5 gene expression were mirrored in protein levels measured in a conditioned medium by ELISA, Western and Ligand blot. Significantly, a knockdown of IGFBP-2 in TamR cells restored sensi-tivity to 4-hydroxytamoxifen (4-HT), reduced ERα expression to 45 ± 11.9% and en-hanced cell migration. Knock down of IGFBP-5 in wt cells had no effect on sensitivity to 4-HT but enhanced cell migration. Exogenous IGFBP-2 had no effect on tamoxifen sensitivity which may suggest an intracellular mechanism of action for IGFBP-2. Im-munohistochemical analysis of breast cancer tissue microarrays (TMAs) indicated that expression of IGFBP-2 was significantly associated with survival advantage in tamoxifen resistant patients.
Identification of QTLs for seed dormancy in rice (Oryza sativa L.)

With 3 figures and 3 tables Abstract Preharvest sprouting (PHS) can damage end-use quality in a number of cereal crop species. The trait is closely related to seed dormancy, for which there is known genetic variation in rice and other cereals. A set of 122 back-cross-inbred lines from the cross of ‘N22’ (indica, strongly dormant) and ‘Nanjing 35’ (japonica, no-dormant) were used to identify quantitative trait loci (QTL) for seed dormancy. Three QTL were detected on chromosomes 1, 2 and 3, and the proportion of the phenotypic variance explained by each was 18%, 8% and 7%. At all three loci, the dormancy-increasing allele was inherited from cv. ‘N22’. To map the chromosome 1 locus qSd-1 more precisely, an advanced back-cross (BC6F2) population was developed. The result of this population indicated that qSd-1 is in fact a pair of distinct, linked loci qSd-1-1 and qSd-1-2, which act additively to promote dormancy. Simple Sequence Repeats (SSRs) closely linked to each of the QTL identified should allow for the marker-assisted transfer of the dormancy shown by cv. ‘N22’ for the improvement of the PHS of low dormancy cultivars.
An Analysis of the Romanian E-Commerce Trade Trends in European Perspective

The paper employs regression analysis of relevance to outline significant differences in the perception of Romanian urban customers regarding the evolution of e-commerce, as the most dynamic sales channel, against the background of the econometric analysis of trends in e-commerce across 29 EU countries, based on selected information society macroeconomic indicators. The conclusions of the macroeconomic analysis can be checked for the consumers by an empirical survey, examining the consumer attitudes and preferences about the use of electronic commerce in Romanian urban areas. The analyzed sample comprised 385 young urban consumers, stratified by gender, age, income, employment status and level of education, which were directly interviewed, the questionnaire containing 20 items. Based on the macroeconomic data analysis, the results showed that Romania is occupying one of the last places of the hierarchy of countries according to the number of computers users per 100 inhabitants, due to the lack of computers in the rural areas. The empirical analysis showed that the low usage rate of the e-commerce is due, in the opinion of users, to fear for fraud, the lack of trust in the payment safety on the internet, ineffective web-sites and also due to the low promotion of e-commerce. The main conclusions of the analysis pointed out that, in the near future, new selling technologies are thought to spread globally in each country, company and household.
Frequency of methicillin resistant Staphylococcus aureus in the noses of Malaysian chicken farmers and their chicken.

Summary The prevalence of methicillin resistant Staphylococcus aureus (MRSA) and methicillin sensitive Staphylococcus aureus (MSSA) carriage among poultry and poultry farmers in Malaysia is largely unknown. In the current investigation, chickens and chicken farmers from 30 chicken farms were screened for MRSA and S. aureus carriage. The genetic characteristics of the isolates were determined through multi locus sequence typing (MLST), Staphylococcus protein A (spa) typing and virulent gene profiling. The outcome of the study showed lack of MRSA and extremely low S. aureus prevalence (n=7 of 503, 1.4%) among chicken flocks and the poultry farmers in Malaysia. Staphylococcus aureus isolates belonged to 4 sequence types (ST): ST97 (spa type t359), ST1179 (t359), ST 692 (t2247) and ST188 (t189). It can be concluded that MRSA/MSSA prevalence is very low among chicken and chicken farmers, human and chicken cross transmission of S. aureus does not seem to be a threat in Malaysia.
Lifetime individual plasticity in body condition of a migratory bird

Body condition is an important trait that reflects the capacity of individuals to acquire food or resist disease, eventually allowing successful reproduction and survival. We first quantified the effects of condition on life history and a secondary sexual trait using long-term lifetime data on condition in a migratory bird species, the barn swallow, Hirundo rustica. Second, we quantified sources of individual variation in condition by separating the within-individual from the between-individual components of variation of environmental condition and age on body condition. Therefore, we were able to partition variation as a result of selection and phenotypic plasticity. Within-individual variation in body condition increased in early life until middle age (i.e. 3–4 years of age) in the two sexes followed by only a slight decrease in body condition during senescence in males but not in females. After accounting for age-dependent variation, condition could be partitioned into a within-individual plastic response to environmental conditions during migration and a nonplastic response (i.e. a between-individual difference) to environmental conditions experienced in the African winter quarters. Specifically, there was a within-individual increase in body condition as environmental conditions during migration improved in both males and females, independent of age. There was a between-individual effect of condition found in the winter quarter in body condition of females, but not in males, which was attributed to the disappearance of females in poor body condition from the study population as a result of the higher natal dispersal of low-quality females compared to high-quality ones during years with favourable environmental conditions in the African winter quarters. Males and females also tended to be in better body condition during the warmer springs upon arrival at the breeding grounds. There was a temporal decline in female body condition during 1991–2007, whereas no significant trend was detected in males. Therefore, both intrinsic (e.g. age and sex) and extrinsic factors (e.g. climate) affected body condition. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 420–434.
Plenty more fish in the sea

Only in the last century did humans overwhelmingly accept that fisheries resources are finite. Consequently, ‘there are more fish still in the sea than ever came out of it’ served as a popular metaphor for unbounded expectations for half a millennium, expectations that also extended to use of the planet in general. By reconstructing historical fishing back 1200 years, we identify when this metaphor actually ceased to be true. For some of our most important stocks, it has not been true for centuries, although surprisingly, for fishes globally, it applied until the last century. We demonstrate, however, that there can still be ‘plenty more fish in the sea’ and that with effective management they provide a continuous flow of benefits for our future.
Fator de atrito em tubos de polietileno de pequenos diâmetros

On this paper, the results of an experimental study on the hydraulic friction loss for small-diameter polyethylene pipes are reported. The experiment was carried out using a range of Reynolds number between 6000 to 72000, obtained by varying discharge at 20oC water temperature, with internal pipe diameters of 10.0 mm, 12.9 mm, 16.1 mm, 17.4 mm and 19.7 mm. According to the analysis results and experimental conditions, the friction factor (f) of the Darcy-Weisbach equation can be estimated with c = 0.300 and m = 0.25. The Blasius equation (c = 0.316 and m = 0.25) gives an overestimate of friction loss, although this fact is non-restrictive for micro-irrigation system designs. The analysis shows that both the Blasius and the adjusted equation parameters allow for accurate friction factor estimates, characterized by low mean error (5.1%).
Genetics and Mating Competitiveness of Ceratitis capitata (Diptera: Tephritidae) Strains Carrying the Marker Sergeant, Sr2

Abstract A dominant mutation, Sergeant (Sr2), which affects expression of a third stripe on the abdomen of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), was recently isolated and the results of an extended genetic analysis are reported here. In addition, field cage data are presented on the mating competitiveness of strains carrying this mutation, including a genetic sexing strain (GSS). The incorporation of a phenotypic marker, such as Sr2, in a Mediterranean fruit fly GSS would complement, and could replace, the use of fluorescent dye for monitoring sterile insect technique programs and increase program efficiency by improving sterile and wild fly identification procedures. The mutation is homozygous lethal, and it is located on chromosome 5 at position 78B and 60D on the salivary and trichogen polytene maps, respectively. The development of the Sr2 GSS is described here, together with data on fitness and penetrance of the mutation. The field-cage results demonstrated 1) random mating between males and females of laboratory strains carrying or lacking Sr2, 2) comparable sexual compatibility of Sr2 and non-Sr2 GSS with two wild populations, and 3) comparable mating competitiveness of males from Sr2 and non-Sr2 GSS with wild males. From these results, no significant effects of the mutation on the sexual competitiveness of strains carrying Sr2 were detectable. The findings of this study point to a satisfactory overall genetic as well as mating behavior profile of Mediterranean fruit fly strains carrying the Sr2 mutation and clearly warrant further evaluation of this mutation in Mediterranean fruit fly GSS.
Unraveling the Secrets of Rice Wild Species

The world is facing a new challenge with global population predicted to plateau at nine billion people by the middle of this century (Godfray et al. 2010). Increasing food production to feed the world’s population is an even greater challenge considering that agriculture is experiencing greater competition for land, water and energy, as well as, the effects of substantial climate change and the unintended effects of crop production on the environment. Part of the solution to increasing food production on the same or less cultivated land lies in exploiting the subset of genes lost during the domestication process and subsequent targeted breeding. Currently, these valuable genes are found only in the progenitor species genepool for crop cultivars. Cultivated plants having desirable genes were utilized in intensive breeding projects focused on increasing yield for particular environments and management systems but this process has narrowed the genetic diversity (Rausher 2001). For cultivated plants, this unexploited genetic material includes both landraces and the more exotic wild relatives. Improving our under‐ standing of this tertiary gene pool and exploiting it for crop improvement is paramount to meeting the challenges of feeding the world in this century through the integration of classical genetics and genomics-enabled research paradigms.
Exploring the origin of the latitudinal diversity gradient: Contrasting the sister fern genera Phegopteris and Pseudophegopteris

The origin of the latitudinal biodiversity gradient has been studied using various approaches. Here, we employ a comparative phylogenetic approach to infer evidence for the hypothesis that differences in diversification rates are one of the main factors contributing to the assembly of this gradient. We infer the phylogeny of the two sister genera Phegopteris and Pseudophegopteris. The two genera are distinct in their species richness (4 vs. 20 spp.) and their preferences to temperate to subtropical (Phegopteris) or tropical climates (Pseudophegopteris). Using sequences of three plastid DNA regions, we confirm the monophyly of each genus and infer the inter‐ and intra‐generic phylogenetic differentiation of the sister clades. We recover evidence for distinct net‐diversification rate between the two genera, which may be caused either by a higher extinction risk of temperate Phegopteris or a higher speciation rate of tropical Pseudophegopteris. We discuss our results in the context of our current knowledge on the speciation processes of ferns. We conclude on the crucial influence of other factors such as the rise of the Himalaya on the diversification of these ferns.