Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorus and Biomass Distribution, and P-efficiency by Diverse Brassica Cultivars Exposed to Adequate and P-stress Environment

To acclimate under orthophosphate (Pi) starved environment, plant species and cultivars display an elegant myriad of Pi-adaptive and rescue responses via reprioritizing internal Pi use and maximizing external Pi acquisition by reprogramming metabolism and restructuring root system architecture.Exploitation of considerable genetic diversity both between and within crop species and harnessing of these genetic variations can lead us to develop smart plants with improved P-acquisition, growth and yield under P-deprivation. To elucidate the effect of P-stress on plant growth, and P-efficiency under Pstarvation, 14 diverse Brassica cultivars were grown hydroponically in a climatically controlled chamber using sufficient (200 and 400 μM) and stress (10 and 20 μM) P-levels using ammonium phosphate (NH4H2PO4) as a P source. Cultivars showed differential growth behaviour in terms of biomass accumulation (shoot and root dry matter partitioning), percent distribution of Pi-concentration ([P]) and P-contents in plant parts (roots and shoots), and P-efficiency ratio (% PER)(relative shoot growth) indicating considerable genetic diversity among the tested Brassica cultivars. PER and the proportional increases in shoot dry matter (SDM) accumulation (SDMmax/SDMmin) in response to the P levels assisted in categorizing the cultivars into efficient and inefficient utilizers of the absorbed P from an ambient environment. Cultivars were classified into efficient responsive (ER), efficient non-responsive (ENR), non-efficient responsive (NER) and non-efficient non-responsive (NENR) by plotting ordination plots between PER and SDMmax/SDMmin under P-stress environment. Differential PER values at stress P levels corresponds to high P levels suggest that P efficiency mechanisms can be different from one cultivar to another within a give plant species and cultivars exhibiting high PER values are better choice to thrive under P-starvation.
Inbreeding adjustments and effect on genetic trend estimates

Inbreeding affects both phenotypic means and genetic variances within populations and limits genetic progress even in very large populations (Goddard and Smith, 1990). As average inbreeding increases, routine evaluations may need to model the effects on both the means and the variances. Some national genetic evaluations have included non-additive genetic effects, such as heterosis and recombination between breeds or between North American Holsteins and European Friesians, but few have included inbreeding depression except in research studies (Interbull, 2005).
Protective role of Centella asiatica (L.) Urban extract against methylmethanesulphonate and cyclophosphamide induced genotoxic damage in cultured human lymphocytes.

Plants are used as a good source of medicines by the pharmaceutical industry. In the present study the action of Centella asiatica (L.) extract on chromosomal aberrations (CAs), mitotic index (MI), sister chromatid exchanges (SCEs) and replication index (RI) induced by methylmethane sulphonate (MMS) and cyclophosphamide (CP) was assessed in human lymphocytes in vitro. The study was performed both in the absence as well as presence of metabolic activation (S9 mix). The extract at the dosages of 1.075 × 10-4, 2.127 × 10-4 and 3.15 × 10-4 g/ml of culture medium was given separately, along with 60 μM of MMS and 0.16 μg/ml of CP, respectively. The used dosages of plant infusion did not induced CAs and SCEs significantly nor affect RI and MI both in the absence as well as presence of metabolic activation (S9 mix). A dose dependent significant decrease in the genotoxic damage was observed at all the tested dosages of plant extract when given along with 60 μM of MMS (without S9 mix) and 0.16 μg/ml of CP (with S9 mix). The results indicate that the plant extract per se do not have genotoxic activity but can modulate the genotoxic activity of MMS and CP in human lymphocytes in vitro. 1. Section of Genetics, Department of Zoology, Faculty of Life sciences, Aligarh Muslim University, Aligarh-202 002, India. 2. Forest Entomology Division, Forest Research Institute, Dehradun 248 006, India. * Corresponding author: E-mail: yasir_hasansiddique@rediffmail.com PDF created with pdfFactory trial version www.pdffactory. com 370 RPMP Vol. 19 – Phytopharmacology & Therapeutic Values I
Early interactions of non-typhoidal Salmonellawith human epithelium

Non-typhoidal Salmonella is an important bacterial pathogen causing worldwide morbidity and mortality. Early interactions between Salmonella Typhimurium and intestinal epithelium have been demonstrated in animal models, but little is known in humans. The aims of this thesis were to a) establish in vitro and ex vivo models to study such interactions, b) seek evidence of Salmonella invasion in human tissues in vivo, and c) identify virulence genes responsible for Salmonella adherence, invasiveness, and intracellular growth using a high throughput screening model based on transposon mediated differential hybridisation (TMDH). HEp-2 cell cultures were validated as a reproducible in vitro model at different early stages and for investigating host cell cytokine responses and signalling pathways. The model discriminated between different wild-type and characterised mutant strains; it also demonstrated the ability of probiotic lactobacilli to inhibit IL-8 expression in IL- 1β-pretreated and Salmonella-co-treated cells. This was not via IκBα degradation, phosphorylation of NF-κB p65 or its nuclear translocation. Lactobacilli did not postinfectiously affect intracellular Salmonella proliferation or IL-8 production. Polarised Caco-2 cells were employed to investigate host responses to various bacterial pathogen associated molecular patterns (PAMPs). Exposure to Salmonella Typhimurium DNA triggered IL-8/hBD-2 mRNA expression and infection with its FliC-deficient mutant ΔfliM stimulated IL-8 mRNA expression. Thus, both flagellin and bacterial DNA could elicit pro-inflammatory responses. Histology and immunohistochemistry of in vivo and ex vivo human tissues showed bacterial/Salmonella invasion in epithelial cells, macrophages, and neutrophils. After HEp-2 cell infection and extraction of genomic DNA using 1,440 transposon mutants of Salmonella Typhimurium, Transposon Directed Insertion-site Sequencing (TraDIS) identified 47 genes responsible for bacterial colonisation, among which 5 genes (intergenic sucD-cydA, glyA, yqiC, wzxE, and rfaI) account for bacteria-cell association. Furthermore, we discovered that speG is responsible for intracellular replication. Selected mutants will be re-characterised for pathophysiology investigations and prospective adaptation to prevention/treatment in non-typhoidal salmonellosis.
Folding of the N-terminal, ligand-binding region of integrin α-subunits into a β-propeller domain

The N-terminal ≈440 aa of integrin α subunits contain seven sequence repeats. These are predicted here to fold into a β-propeller domain. A homologous domain from the enzyme phosphatidylinositol phospholipase D is predicted to have the same fold. The domains contain seven four-stranded β-sheets arranged in a torus around a pseudosymmetry axis. The trimeric G-protein β subunit (G beta) appears to be the most closely related β-propeller. Integrin ligands and a putative Mg 2+ ion are predicted to bind to the upper face of the β-propeller. This face binds substrates in β-propeller enzymes and is used by the G protein β subunit to bind the G protein α subunit. The integrin α subunit I domain, which is structurally homologous to the G protein α subunit, is tethered to the top of the β-propeller domain by a hinge that may allow movement of the domains relative to one another. The Ca 2+ -binding motifs in integrin α subunits are on the lower face of the β-propeller.
A genome-wide association study of resistance to the yellow rust pathogen (Puccinia striiformis f. sp. tritici) in elite UK wheat germplasm

ABSTRACT Pauline G. M. Bansept-Basler, 2013 A genome wide association study of resistance to the yellow rust pathogen (Puccinia striiformis f. sp. tritici) in elite UK wheat germplasm Identification of marker-trait associations (MTA) in germplasm relevant to breeding program via association mapping (AM) can be an effective way to identify loci useful for selection. This approach does not require the generation of specific mapping populations and takes advantage of historical phenotypic data. In the present study, an association panel of 327 bread wheat varieties have been assembled and genotyped with 1806 DArT markers. Genetic structure analysis revealed a low stratification of the panel based on geographical origin (UK versus mixed European varieties) and a close relatedness between lines, which is confirmed by pedigree information. Historical evaluations against the yellow rust pathogen (Puccinia striiformis f.sp. tritici (Pst)) carried in the United Kingdom between 1990 and 2009, as well as de novo evaluations against recent Pst races have been collected and analysed for MTAs. Association scans considering historical data focused on specific Pst pathotypes and de novo seedling tests identified markers linked to known racespecific Yr genes Yr6, Yr7, Yr9, Yr17 and Yr32. When evaluated against current Pst races in the field, 35% of the lines from the panel presented repeatedly a high level of resistance (Area Under the Disease Progress Curve relative<0.2) which is due to the presence of seedling resistances as well as adult plant resistances within the lines. AM with de novo phenotypes revealed 23 MTA groups pointing to potential resistance loci, 14 of them were also identified with historical data and six seemed to point to adult plant resistance loci on chromosomes 2A, 2B, 3A, 6A, 6B and 7A. These results confirm the value of AM using historical data for QTL discovery and suggest the availability of diverse sources of yellow rust resistances within wheat elite UK germplasm.
Micropropagación de tres especies de heliconia de interés comercial en México vía organogénesis directa

Las heliconias son ornamentales tropicales cultivadas principalmente como flor de corte; su cultivo en Mexico ha experimentado un crecimiento limitado por algunos problemas que incluyen la disponibilidad de material vegetativo de alta calidad fitosanitaria. En esta investigacion se desarrollo un protocolo de micropropagacion de Heliconia collinsiana , H. nickeriensis y cv. Golden Torch via organogenesis. Las yemas laterales se desinfectaron con detergente comercial, hipoclorito de sodio (30% v/v) y Tween® 20. Se evaluaron concentraciones de bencilaminopurina (4.4-17.8 µM) para inducir y multiplicar brotes asi como auxinas para promover el enraizamiento. En H. collinsiana la induccion de 4.8 brotes por explante se logro en medio de cultivo MS adicionado con 13.3 µM de bencilaminopurina, mientras que en H. nickeriensis y cv. Golden Torch la induccion de 3.0 y 2.1 brotes se obtuvo con 11.1 µM de bencilaminopurina, respectivamente. Los brotes se originaron en la base del explante y en las axilas de las hojas. La multiplicacion de brotes se obtuvo con 11.1 µM de bencilaminopurina combinado con 1 µM de acido indolacetico en las tres especies; 6.9 brotes por explante en H. collinsiana, 4.1 brotes en cv. Golden Torch y 3.6 en H. nickeriensis . El enraizamiento se indujo con 1 µM de acido naftalenacetico y la aclimatacion de las plantas se logro en mezcla de turba y perlita con riegos de 50% de solucion nutritiva Steiner despues de 55 dias del trasplante.
Growth Analysis of Dry Bean (Phaseolus vulgaris L.) in Different Weed Interference Situations

In production agriculture, weed plants play an important role in yield reduction. Analysis of crop growth can reveal underlying processes of yield loss under weed interference conditions. Therefore, an experiment was conducted in 2011 in order to assess the effect of weed competition on different aspects of dry bean growth. The experiment was a randomized complete block design with 3 replications. Treatments included weed-infested and weed-free periods until 0, 10, 20, 30, 40 and 50 days after crop emergence. Aboveground dry matter and leaf area were measured every two weeks. The functional approach to growth analysis was used to examine temporal patterns in crop growth in weed interference conditions. A negative relationship between weed biomass and dry bean growth indexes was observed. In all treatments, crop biomass had a similar trend and progressively increased over the crop cycle, then after reaching the maximum amount, gradually decreased. The lowest crop biomass (676.60 g m-2) was observed in season-long weed-infested treatment, while the maximum one (1238.82 g m-2) was recorded in season-long weed-free treatment. Relative growth rate (RGR) and net assimilation rate (NAR) had a declining trend during the growing season. Increase in weed-infested periods intensified decrease of them. Effect of weed competition on crop growth was trifle at the early of growing season. Since NAR and RGR represent photosynthesis potential and dry matter accumulation of the crop, their reduction can be the main cause of yield loss.
Flow-Guided Neural Prediction for Sketch-Based Freeform Surface Modeling”

Our training dataset is automatically generated through non-photo-realistic rendering (NPR) of 3D models [Rusinkiewicz and DeCarlo, 2013], which makes it possible to build a very large and diverse dataset with ground truth signals. Each sample of the training data contains a pair of input data and ground truth output data. The input consists of the line sketch rendered by NPR, silhouette mask, optional depth samples and curvature hints. The output data contains the projected surface curvature directions for training DFNet, and the depth and normal maps of the rendered surface for training GeomNet. The overall guidelines for data generation are:
Effect of levels and mode of phosphorus and biofertilizers on chickpea (Cicer arietinum) under dryland conditions

A field experiment was conducted.during the winter seasons of 2000 2001 and 2001 2002, to study the ef fect of levels and mode of phosphorus, and biofertilizers [vesicular arbuscular mycorrhiza (VAM) and phosphate solubilizing bacteria (PSB)] on yield attributes and yield of chickpea (Cicer arietinum L.). Inoculation of biofertilizers significantly increased yield attributes of podslplant and seedslplant and yield of chickpea. Among biofertilizers, dual inoculation of PSB VAM markedly enhanced these yield attributes and yield compared with PSB or VAM alone. Application of phosphorus from 0 to 60 kg P,OJha resulted in linear increase in yield at tributes and yield. Aqua placement of phosphorus significantly increased grain yield in first year only.
PREMATÜRE RETİNOPATİSİ MUAYENESİ’NDE AĞRI YÖNETİMİ

Premature Retinopatisi (ROP), dusuk dogum agirlikli (<1500 gr) ve preterm yenidoganlarda (<32 hafta) gorulen, gozde retinal damarlarin anormal gelisimine bagli olusan bir hastaliktir. Gozde miyopi, retina dekolmani, ambliyopi, strabismus, makula ektopisi, pupilla blogu ve tam korluk gibi cesitli komplikasyonlara neden olan ROP, yapilan goz muayeneleriyle erken donemde belirlenip tedavi edilebilmektedir. ROP muayenesi topikal anestezik damlalar kullanilarak uygulansa da yapilan calismalar islem sirasinda yenidoganlarin yuksek agri cektiklerini bildirmektedir. Agrinin en az duzeye indirilmesi ya da giderilmesi her yenidoganin en dogal hakkidir ve multidisipliner bir ekip yaklasimi gerektirir. Yenidoganin agrisinin azaltilmasi ya da giderilmesinde cesitli farmakolojik ve nonfarmakolojik yontemler kullanilabilir. Bu calismada ROP muayenesi yapilan preterm yenidoganlarda agri yonetiminde kullanilan farmakolojik ve nonfarmakolojik yontemler tartisilmistir. Bu dogrultuda saglik profesyonelleri bu yontemlerden etkinligi kanitlanmis olanlari uygulamali ve yenidoganda agriyi azaltmada kanita dayali uygulamalara ve uygulamalarin etkinligini degerlendiren calismalara yer vermelidirler
The accuracy of plant assemblage prediction from species distribution models varies along environmental gradients

Aim Climatic niche modelling of species and community distributions implicitly assumes strong and constant climatic determinism across geographical space. We tested this assumption by assessing how stacked-species distribution models (S-SDMs) perform for predicting plant species assemblages along elevation gradients. Location The western Swiss Alps. Methods Using robust presence–absence data, we first assessed the ability of topo-climatic S-SDMs to predict plant assemblages in a study area encompassing a 2800-m wide elevation gradient. We then assessed the relationships among several evaluation metrics and trait-based tests of community assembly rules. Results The standard errors of individual SDMs decreased significantly towards higher elevations. Overall, the S-SDM overpredicted far more than they underpredicted richness and could not reproduce the humpback curve along elevation. Overprediction was greater at low and mid-range elevations in absolute values but greater at high elevations when standardized by the actual richness. Looking at species composition, overall prediction success, kappa and specificity increased with increasing elevation, while the Jaccard index and sensitivity decreased. The best overall evaluation – as driven by specificity – occurred at high elevation where species assemblages were shown to be subject to significant environmental filtering of small plants. In contrast, the decreased overall accuracy in the lowlands was associated with functional patterns representing any type of assembly rule (environmental filtering, limiting similarity or null assembly). Main conclusions We provide a thorough evaluation of S-SDM emphasizing the need to carefully interpret standard evaluation metrics, which reflect different aspects of assemblage predictions. We further reported interesting patterns of change in S-SDM errors with changes in assembly rules along elevation. Yet, significant levels of assemblage prediction errors occurred throughout the gradient, calling for further improvement of SDMs, e.g. by adding key environmental filters that act at fine scales and developing approaches to account for variations in the influence of predictors along environmental gradients.
Uma abordagem linguística para sistemas de Perguntas e Respostas Curtas

Os agentes de conversacao para interacao de linguagem natural, em geral, enfrentam alguns desafios no fornecimento de conteudo para suportar as respostas solicitadas pelos usuarios. Normalmente, o conteudo das respostas e definido manualmente, o que nao e uma solucao adequada. Este trabalho apresenta uma abordagem para permitir que esses sistemas usem automaticamente os conceitos e relacionamentos armazenados em Bases de Conhecimento. A principal contribuicao da nossa abordagem e a generalizacao do sistema, que pode responder a perguntas relacionadas a multiplos dominios. Isso e realizado com base em informacoes linguisticas como suporte as atividades de compreensao da linguagem natural. Os resultados obtidos na classificacao dos tipos de questoes e na identificacao de complementos nominais sao apresentados e indicam resultados promissores.
Using OpenStudio in STEM learning - final report to eSTEeM, the OU centre for STEM pedagogy

The ‘Using OpenStudio in STEM learning’ project was established to evaluate the use of online studio-based learning in the Open University. Studio-based learning provides a model that can be adapted for online learning. In conventional teaching settings, studio-based learning follows an apprenticeship model where students work independently or in groups, under the guidance of a tutor, using real-world activities. The project consisted of two main phases: a workshop for module team chairs followed by an in- depth study of the use of OpenStudio on two Computing & IT modules. Educators representing distance learning modules from a range of STEM disciplines including Computing and IT, Design, Engineering and Environmental Technology participated in a workshop to share information about the use of OpenStudio on their modules. A simple model of OpenStudio activities was derived from the workshop to illustrate the process of 'showing and sharing', viewing and reviewing', commenting and critiquing', and 'reviewing and reflecting' involved. Two Computing and IT undergraduate modules were then selected for more detailed analysis, one at level 1 (TU100) and another at level 3 (TM354). Both quantitative and qualitative data were gathered from samples of students on these modules and analysed. In addition, tutors from both TU100 and TM354 were invited to participate in focus groups in online forums to provide a fuller picture of the activities. The data suggest that students enjoy the OpenStudio activities, especially the visual nature of artefacts and the idea that shorter comments may be made, rather than longer more discursive pieces of writing. In addition to learning about their subject area, students are also learning how to give feedback to their peers and how to use the feedback they receive, both of which are important skills. Many students are confident in their own ability and are able to evaluate the feedback they receive. However, some students may lack confidence in their own ability to give feedback on the work of their peers, particularly at level 1. Importantly, there needs to be an opportunity to complete the cycle of the experiential learning model in the activity by allowing students to produce another artefact. The experiential nature of the online studio activity presents an opportunity for students to reflect-in-action as well as reflect on their actions (Schon, 1983). Comparisons between the OpenStudio model, the survey findings and Kolb’s Experiential Learning model (1984) revealed the range of student views and the diversity of students’ experiences of the learning activities, and provided some thought-provoking insights into student behaviour in carrying out the OpenStudio activities. The project team was awarded the Project of the Year trophy in the Innovative/Original Approach to Teaching category at the 8th eSTEeM Annual Conference.
Evolução convergente da protease FtsH5 de Arabidopsis thaliana e seu regulador negativo putativo FIP (FtsH5 interacting protein)

13 LISTA DE FIGURAS . 15 LISTA DE TABELAS . 17 1 INTRODUÇÃO . 19 2 REVISÃO BIBLIOGRÁFICA . 23 2.1 – Compartimentalização celular e controle de qualidade de proteínas . 23 2.2 – AAA/FtsH proteases . 24 2.3 – Proteases FtsH plastidiais . 26 2.4 – Regulação da atividade das proteases FtsH . 30 2.5 – FIP (FtsH5 Interacting Protein) . 32 3 MATERIAL E MÉTODOS . 35 3.1 – Análise de expressão . 35 3.1.1 – Expressão tecido-específica e temporal . 35 3.1.2 – Expressão em resposta a estresses abióticos . 35 3.2 – Análises filogenéticas . 36 3.2.1 – Filogenia dos homólogos de FIP e das proteases do complexo FtsH tilacoidal e inferência sobre o processo de coevolução . 36 3.2.1.1 – Identificação e obtenção das sequências para a análise . 36 3.2.1.2 – Alinhamento múltiplo das sequências e modelo de substituição de DNA . 37 3.2.1.3 – Proposição de modelo evolutivo e inferência sobre a coevolução . 38 3.2.2 – Filogenia representativa dos homólogos das FtsH do tipo A . 39 3.3 – Detecção de sítios de pressão de seleção . 40 3.4 – Análise de conservação de sequência e estrutural do complexo FtsH . 42 4 RESULTADOS E DISCUSSÃO . 45