Miracle-dz/UniFAR-FTUs huggingface dataset:
Recruitment of AP-1 clathrin adaptors to liposomal membranes

Protein and membrane traffic between organelles within the endocytic and exocytic pathway is mediated most prominently by coated vesicles. These vesicles are formed by the assembly of cytosolic coat proteins onto the donor membrane, which deform it into a bud so that vesicles can pinch off. Clathrin with its associated adaptors, COPI and COPII are the three major coats. Various in vitro studies allowed insight into the mechanism of coat formation. COPI and COPII vesicle budding from chemically defined liposomes has been reconstituted in vitro, using pure coat compounds. Further, it has been demonstrated that cargo is sorted into these vesicles. The mechanism of clathrin-coated vesicle formation appears to be more complicated. The AP-1 clathrin adaptor is involved in vesicle formation at the transGolgi network and endosomes. This work presents an in vitro assay where AP-1 is recruited to peptidoliposomes, presenting covalently linked peptides corresponding to sorting signals. In this system, AP-1 recruitment depends on myristyolated ADP-ribosylation factor(ARF1), GTP or GMP-PNP, tyrosine signals and a small amount of phosphoinositides, most prominently phosphatidyl inositol 4,5bisphosphate. In such a minimal system AP-1 is recruited as a highmolecular weight complex indicating the formation of a precoat in the absence of clathrin. GTP hydrolysis, induced by ARF GTPase-activating protein(ARFGAP1), disassembled this complex. Further, AP-1 is able to enhance the GAP activity of ARFGAP1 on myristoylated ARF1, suggesting a regulatory function of GTP hydrolysis in early steps of coat recruitment. This work provides insights into the mechanism of AP-1 clathrin coat formation which might also be used to investigate the recruitment of other coats.
Detection of epistasis and gene effects for quality and yield traits in rice

Scaling test and generation mean analysis were employed to detect epistatasis and gene actions in four crosses of rice for six yield and quality traits. Dominant gene effect was more important than additive in the inheritance of number of effective tillers per plant, alkali digestion value and volume expansion. Number of grains panicle1 and water uptake number were mostly controlled by additive gene effect epistatic gene effects namely, additive x additive (j) and dominance x dominance (l) were more pronounced for most of the characters except number of effective tillers plant−1. Heterosis for yield plant−1 and number of grains panicle−1 were considerably high. It was 71 per cent for grain in the cross MPR 71 x IT 1443. The cross Pusa Basmati 1 x NDR 359 exhibited highest heterosis (79%) for number of grains panicle−1 with low inbreeding depression. In general inbreeding depression in four crosses over the traits ranged from -23.58 to 14.28 per cent for number of grains panicle−1 and alkali digestion value, respectively.
Effect of land configuration and irrigation on sole and linseed (Linum usitatissimum) intercropped chickpea (Cicer arietinum)

pulse crop of India occupying 6.93 million (m) ha with an annual production of 5.6 million tonnes (FAO 2006). It is predominantly grown on residual soil moisture as is evident from the fact that of the total area in the country, only 1.96 million ha (28.3%) is irrigated (FAI 2005). The moisture stress at some of the critical stages of growth often leads to its lower productivity. Further, high incidence of pests, especially pod borer (Helicoverpa armigera Hubner) has rendered the chickpea cultivation uneconomical. Farmers have shifted to its intercropping with linseed (Linum usitatissimum L.) in Bundelkhand region of Uttar Pradesh (GOI 2000), and chickpea + linseed replacement series intercropping (2–3: 1 row ratio) has been found promising (Ahlawat et al. 2005 a). This practice may not only ensure protein nutritional security of the country, but also improves total productivity and profitability of farming. Modified land configurations, such as furrow irrigated raised bed (FIRB) has shown good promise in enhancing chickpea performance (Jat et al. 2005) and water productivity. The information on effect of land configuration in association with irrigation is lacking for chickpea-based intercropping systems in general and chickpea + linseed in particular. In view of the above, the present investigation was undertaken to find out the impact of land configuration in relation to moisture regime in chickpea-based cropping system to maximize the total productivity and profitability. A field experiment was conducted during winter seasons of 2003–05 at the Indian Agricultural Research Institute, New Delhi. The soil was sandy loam containing 0.36% organic carbon, 14 kg/ha of available P and 165 kg/ha of available K with pH 7.8. The field capacity and permanent wilting point values of the soil were 17.3 and 7.5%, respectively, with a bulk density of 1.57 g/cm3 in the top 90 cm soil. The
Predicting the effectiveness of Test of Infant Motor Performance as an early marker of motor development delay in preterm infants

Objectives: The purpose of this study was to determine the effectiveness of Test of Infant Motor Performance (TIMP) in detecting motor developmental delay in preterm infants.Material and methods: The present study was conducted on 30 infants born preterm with corrected age of 2 months and follow up of TIMP at 4 months corrected age and Alberta Infant Motor Scale (AIMS) at 2, 4 and 6 months corrected age. Study period was January 2012 to December 2015.Results: Pearson product moment correlation coefficient used to assess the relationship between the raw scores of TIMP and AIMS percentile rank at corrected age of 2 and 4 months, was 0.757 (p<0.0001) and 0.874 (p<0.0001) respectively. An analysis of the sensitivity, specificity, positive predictive value and negative predictive value of various TIMP cutoff scores for comparison with AIMS scores above and below the 10 percentile revealed the best TIMP score with a cutoff of -1 standard deviation below the mean. The results for comparison of 2, 4, 6 months corrected age AIMS data using Pearson chi square test was highly significant with p 0.001 at 2months CA AIMS data with 4 months CA AIMS data.Conclusion and Interpretation:TIMP and AIMS are equally useful in the assessment of infant motor performance at 4 months of corrected age. A cutoff score of -1 SD from the mean on TIMP was a better predictor of developmental outcome in this study.
Association in horses of orosensory characteristics of foods with their post-ingestive consequences

In the domestic environment, horses are often presented with foods to which they are not evolutionarily adapted, such as low fibre pellets. Horses may not have the ability to learn the consequences of consuming unnatural foodstuffs and adapt their selection accordingly. This study aimed to investigate the horse’s feeding preferences when presented with concentrate pellets differing in nutrient content. Using a choice test, the relative preferences of 12 horses for mint and garlic, in iso-caloric diets, was first assessed over 29 meals. A mint preference, calculated as the proportion of mint in the total food intake, was shown by 11 horses. The horses were then divided into two groups, approximately balanced on the basis of mint preference. Group A was exposed to a choice of a mintflavoured lower energy food or a garlic-flavoured higher energy food, while group B was exposed to mint-flavoured higher energy food and garlic-flavoured lower energy food for 29 meals. Next the flavours were presented in isocaloric foods, initially for 10 meals, then a further 40, before the flavour-energy pairings were reversed for 30 meals. A final iso-caloric test was carried out for 30 meals. Both groups showed a preference for mint in the initial iso-caloric choice test but no such preference was shown in later iso-caloric tests. Both groups showed a higher preference for mint when paired with higher energy (proportion of mint intake to total intake was 0·75 (s.e. 0·02) and 0·73 (s.e. 0·02) for A and B respectively). Group B also showed a preference for garlic when paired with higher energy (proportion of mint intake : 0·32, s.e. 0·02) whilst group A showed a significant decrease in preference for mint when paired with lower energy (by 0·21 (s.e. 0·03), T = 6·88, P < 0·01). The results suggest that horses can select a higher energy diet over a lower energy one and that horses can form associations between foods and their nutritional composition, even if they do not resemble those found in their natural environment.
In vitro Regeneration and Acclimatization Protocols of Selected Ornamental Plants (Agapanthus praecox, Justicia betonica and Celosia cristata) (Protokol Regenerasi Secara In vitro dan Aklimatasi Tumbuhan Hiasan Terpilih (Agapanthus praecox, Justicia betonica dan Celosia cristata))

This paper discussed on the effectiveness of BAP and NAA growth hormones on establishment of plant regeneration for selected ornamentals; Agapanthus praecox, Justicia betonica and Celosia cristata. Various explants (leaf, stem, shoot tip and bulb) derived from one-month-old aseptic seedlings of A. praecox and C. cristata, as well as explants from intact plants of J. betonica were utilized to achieve complete plant regeneration of these species. MS medium supplemented with various hormones, with an emphasis on BAP and NAA was tested to obtain direct and indirect regeneration. Both A. praecox (bulbs) and C. cristata (shoots) formed complete plantlets on MS added with 0.5-2.0 mg/L BAP and NAA, while direct regeneration was achieved for J. betonica on MS media containing BAP. Several methods were attempted to acclimatize the regenerants, with A. praecox gave the highest percentage of survival rates (96.67%), followed by J. betonica (80.00%) and C. cristata (75.00%).
Mortality of different developmental stages of Callosobruchus maculatus F. and Callosobruchus subinnotatus Pic. (Coleoptera: Bruchidae) in bambara groundnut Vigna subterranea (L.) Verdc. seeds exposed to simulated solar heat

The susceptibility of Callosobruchus maculatus F. and Callosobruchus subinnotatus Pic. eggs, first and late instar larvae as well as adults to the lethal effect of solar heat of a temperature of 50 °C simulated in an incubator was evaluated. Development of adult progeny was completely suppressed in both species in bambara groundnut seeds bearing 1-day-old eggs or harboring first instar larvae exposed for 4 or 6 h to this temperature. Suppression of adult progeny development was due to the fact that this level of heat caused 100 % mortality of these developmental stages of the bruchids. In C. maculatus, 100 % mortality occurred in first instar larvae exposed for 2 h while in C. subinnotatus, 100% mortality occurred in eggs and first instar larvae exposed for a similar duration. In addition, adults of both species that were exposed for 25 min, and in the case of C. maculatus, adults exposed for 20 min as well, sustained 100 % mortality. On average, C. maculatus adults with a mortality figure of 50.7 % were more susceptible to the lethal effect of this level of heat than C. subinnotatus adults with a mortality figure of 37.0 %. Solar heat could be used as an inexpensive method for control of these pest species in developing countries.
Leaf breakdown in an Atlantic Rain Forest stream

The hypothesis of this study was that colonizers in decaying leaf litter prefer native species (Erythrina verna) to exotic ones (Eucalyptus camaldulensis and Protium heptaphyllum). Therefore, native species are expected to show higher breakdown rates, increased biomass, richness and density of invertebrate species, and increased biomass of decomposer fungi. Breakdown of leaf litter from these three species was assessed in an Atlantic Rain Forest stream. Four samples were collected during a period of 90 days and washed on a sieve to separate the invertebrates. Then, a series of leaf disks were cut to determine ash-free dry mass and fungal biomass, and the remaining material was oven-dried to determine the dry weight. Eucalyptus camaldulensis and E. verna showed higher breakdown rates than P. heptaphyllum, due to differences in leaf physical and chemical characteristics. The harder detritus (P. heptaphyllum) broke down more slowly than detritus with high concentrations of labile compounds (E. camaldulensis). The density of the invertebrates associated with detritus increased with time. There were no differences in density, taxonomic richness or biomass of invertebrates among the leaf types, which indicated that the invertebrates did not distinguish between exotic and native detritus. Fungal colonization varied among samples; E. camaldulensis showed the lowest ergosterol concentrations, mainly due to a high concentration of total phenolics. The detritus with the highest hardness value was colonized most slowly by fungi. These results showed that leaf breakdown in Atlantic Rain Forest streams could be affected either by changes in riparian vegetation, or by becoming more savanna-like process due to climate change.
Variable domain orientations in antigen receptors

Specific recognition of pathogenic molecules by the immune system is mediated by proteins known as antigen receptors. One such component is the antibody. Binding properties of natural and engineered antibodies can be understood by studying the structure of their variable domains, VH and VL. In this thesis we investigate how the two variable domains orientate with respect to one another and therefore influence the geometry of the antigen binding site which is formed between them. We describe a method which fully characterises the VH-VL orientation in a consistent and absolute sense using five angles and a distance. The ABangle method is used to investigate variable domain orientation in structures collected by our database SAbDab. Using the ABangle method we compare VH-VL orientation to the corresponding property in a different component of the immune system, the T-cell receptor (TCR). Despite having similar individual domain structures the variable domain orientations of antibodies and TCRs are found to be distinct. This is found to affect an antibody’s ability to mimic TCR specificity. ABangle's characterisation is used to find determinants of the VH-VL orientation. We identify sequence and structural properties that influence the variable domain pose. A feature based method for predicting VH-VL orientation is presented and assessed. Future directions of this research and its application to the development of antibody therapeutics are described.
Protoperidinium tricingulatum sp. nov. (Dinophyceae), a new motile form of a round, brown, and spiny dinoflagellate cyst

A small, broadly ovoidal and heterotrophic dinoflagellate containing round, brownish, and spiny cyst was found in the water column of Huibertsplaat in the Wadden Sea off the coast of the Netherlands. This dinoflagellate had these conspicuous morphological characters: a five‐sided first apical plate (1′), only three cingular plates, and an extremely small first antapical plate. Based on these morphological features, Protoperidinium tricingulatum Kawami, vanWezel, Koeman et Matsuoka is described as a new species. The flagellar pore of P. tricingulatum is covered with a small fin, which rises from the left side of the right sulcal plate to the large V‐shaped posterior sulcal plate. This feature suggests that P. tricingulatum is assigned to the Abé's Monovela Group. The cyst stage of P. tricingulatum was positively linked to the vegetative stage by comparison of the ribosomal 5.8S rDNA, internal transcribed spacers (ITS1 and ITS2). Living cysts of P. tricingulatum are round, brownish, and covered with many slender spines bearing capitate or cauliforate distal ends. The cyst also possesses a theropylic archeopyle formed by a slit corresponding to parasutures between three apical and two apical intercaraly plates. These morphological characters indicate that this species is morphologically related to two dinoflagellate cyst‐genera Islandinium and Echinidinium.
FUNCTION AND REGULATION OF MATRIX METALLOPROTEINASE-1 IN GLIOBLASTOMA MULTIFORME

xvii Chapter 1 General Introduction 1.1 Brain Tumors: Overview 2 1.2. Classification of brain tumors 3 1.3. Symptoms and Diagnosis 7 1.4 Treatment 1.4. 1 Surgery 10 1.4. 2 Radiotherapy 12 1.4. 3 Chemotherapy 13 1.5 Glioma Biology 1.5. 1 Glioma biology as basis for therapy 25 1.5. 2 Immunotherapy 29 1.5. 3 Brain tumor stem cells 30 1.6 Invasion 1.6. 1 Invasion in cancer in general 31 vi 1.6. 2 Invasion in GBM 36 1.7 Matrix metalloproteinases 1.7. 1 Nomenclature and Classification 39 1.7. 2 Structure of MMPs 43 1.7. 3 Function of MMPs Functions in normal physiology 47 Functions in pathology 51 1.7. 4 Regulation of MMPs 54 1.8 Matrix metalloproteinase-1 55 1.9 Epidermal growth factor receptor signaling 61 1.9. 1 MAPK pathway 64 1.9. 2 PI3K-AKT pathway 65 1.10 EGFR biology in GBM 66 AIMS 68 2. Matrix metalloproteinase-1 over-expression in human glioblastomas: Implications in glioma cell invasion 2.1 Abstract 70 2.2 Introduction 71 2.3 Materials and Methods 73
A prospective evaluation of blunt trauma abdomen in rural setup

Introduction: Blunt abdominal trauma accounts for the majority of abdominal injuries seen in the Emergency Department. It is responsible for substantial morbidity and mortality. Selecting appropriate approach has been recently a point of conflict in management of abdominal blunt trauma, and criteria for nonoperative management are being changed frequently. Objective: With aim to identify some of the determining factors of successful non-operative management. Methods: A 2 year tertiary care teaching hospital based longitudinal study was done. Selection criteria were defined and a prestructured proforma was made to assess and note the findings. Results: 34 patients were studied. 29.4% of patients were in the age group of >20-30 years with the mean age 35.29 ± 15.84 years. 79.4% were male. Road traffic accident was responsible for 79.4% of blunt abdominal trauma cases while majority of the patients presented with abdominal pain (91.2%) and abdominal tenderness (91.2%). Associated extra abdominal injuries were found in 10 cases. The common extra abdominal injuries were head injuries (14.7%). 9 patients underwent exploratory laparotomy. 25 were selected for nonoperative management. The most commonly injured organ was spleen (38.9%) followed by liver & stomach. 3 patients died in the present study. The sensitivity and specificity of the Emergency USG findings were 80.9% and 92.3% respectively, and that of the CT findings were 100% and 0% respectively. Conclusion: Non operative management (NOM) was found to be highly successful and safe. Hemodynamic stability along with ultra sound, CT scan and repeated clinical examination were the sheet anchors of NOM
Incorporating harvest rates into the sex-age-kill model for white-tailed deer†

Although monitoring population trends is an essential component of game species manage- ment, wildlife managers rarely have complete counts of abundance. Often, they rely on population models to monitor population trends. As imperfect representations of real-world populations, models must be rigor- ously evaluated to be applied appropriately. Previous research has evaluated population models for white- tailed deer (Odocoileus virginianus); however, the precision and reliability of these models when tested against empirical measures of variability and bias largely is untested. We were able to statistically evaluate the Pennsylvania sex-age-kill (PASAK) population model using realistic error measured using data from 1,131 radiocollared white-tailed deer in Pennsylvania from 2002 to 2008. We used these data and harvest data (number killed, age-sex structure, etc.) to estimate precision of abundance estimates, identify the most efficient harvest data collection with respect to precision of parameter estimates, and evaluate PASAK model robustness to violation of assumptions. Median coefficient of variation (CV) estimates by Wildlife Management Unit, 13.2% in the most recent year, were slightly above benchmarks recommended for managing game species populations. Doubling reporting rates by hunters or doubling the number of deer checked by personnel in the field reduced median CVs to recommended levels. The PASAK model was robust to errors in estimates for adult male harvest rates but was sensitive to errors in subadult male harvest rates, especially in populations with lower harvest rates. In particular, an error in subadult (1.5-yr-old) male harvest rates resulted in the opposite error in subadult male, adult female, and juvenile population estimates. Also, evidence of a greater harvest probability for subadult female deer when compared with adult (� 2.5-yr- old) female deer resulted in a 9.5% underestimate of the population using the PASAK model. Because obtaining appropriate sample sizes, by management unit, to estimate harvest rate parameters each year may be too expensive, assumptions of constant annual harvest rates may be necessary. However, if changes in harvest regulations or hunter behavior influence subadult male harvest rates, the PASAK model could provide an unreliable index to population changes. 2012 The Wildlife Society.
Effect of the cultivation mode on red pigments production from Monascus ruber

Summary In submerged cultures performed in chemically defined fermentation medium containing glucose and glutamate, the growth and production of water-soluble red pigments and citrinin by the filamentous fungus Monascus ruber were studied under various carbon/nitrogen (C/N) ratios. The specific production of the red pigments was optimal at a glucose/glutamate ratio of about 10 and then steadily decreased at higher C/N ratio. In contrast, the production of the mycotoxin increased with increased C/N with an optimum in the range of 30–45. In a fed-batch mode, it was also found that the production of pigments was not favoured in fed-batch mode by feeding the medium with glucose while keeping the C/N ratio lower than 10. This low production likely resulted from concurrent high accumulation of L-malic acid that was reported to inhibit this production. In contrast, this mode of cultivation was rather favourable for the production of the mycotoxin.