Miracle-dz/UniFAR-FTUs huggingface dataset:
Double-rowed Organization of Inner Dynein Arms in Chlamydomonas Flagella Revealed by Tilt-Series Thin-Section Electron Microscopy

The in situ organization of the inner dynein arms of Chlamydomonas axonemes was investigated by analyzing a number of tilt-series thin-section electron micrographs taken with improved fixation and staining protocols. The use of mutant axonemes lacking the outer dynein arms and the radial spokes enabled us to detect a novel feature: inner-arm projections arranged in two rows. The arrangement of projections within each row was deduced by making a model that fitted both tilt-series longitudinal thin-section images and cross-section images. The model suggested that, within a repeating unit of 96 nm, one of the two rows, positioned more centrifugally, consists of four discrete domains and the other, positioned more centripetally, consists of three pairs of globular structures. Whereas the centripetal row resembles the inner-arm arrangement reported previously, the centrifugal row appears to have been identified for the first time in this study. These findings make necessary the re-examination of the arrangement of various inner-arm subspecies within the axoneme.
Standardization of production technology for hybrid coloured capsicum (Capsicum annuum var grossum) based on yield and economic benefit under different protected structures in plains of India

The present experiment was conducted to evaluate the yield and economic gain in cultivation of coloured capsicum (Capsicum annuum var grossum (L.) Sendt) hybrids in different protected structures. Six hybrids of coloured capsicum, i.e. Indra, Natasha, Bomby in red coloured group and Orobelle, Swarna, Kanchan in yellow coloured group were tried in 3 different types of protected structures compared to open field (OF) conditions. It was found that protected technology significantly enhanced crop duration (300) days in fan-pad cum force ventilated polyhouse (FFVP), 265 days in naturally ventilated polyhouse (NVP),250 days in insect proof net house (IPNH) as compared to 200 days in open fields. FFVP technology registered maximum fruit weight and yield (1.98 kg/plant, 11.83 kg/m2) followed by NVP(1.75 kg/plant, 10.42 kg/m2), IPNH(1.11kg/plant, 6.68 kg/m2) and OF (0.33 kg/plant, 1.98 kg/m2), respectively. Economic analysis of different protected structures exhibited considerably higher net returns of Rupees 247.33/m2 in FFVP, Rupees 309.67/m2 in NVP,Â Rupees 86.43/m2 in IPNH andÂ Rupees 14.75/m2 in OF condition. The benefit cost ratio was calculated as 1.73in FFVP, 2.47 in NVP, 1.48 in IPNH while the lowest value of 1.32 in OF condition. Disease incidence cum mortality of plant (2.43%) was minimum in all capsicum varieties grown under FFVP, while it was higher in NVP (6.52%) followed by IPNH (9.75%) with maximum in OF (43.65%). Whereas blossom end rot of fruits was minimum in FFVP (2.98%) followed by OF (3.28%). It is evident from the results that protected structures enhanced the production of coloured capsicum as compared to open field condition particularly during off-season in plains. Further, among different hybrid varieties evaluated, Indra in red group and Orobelle in yellow group are found more suitable for growing in these conditions while Bomby and Swarna were also performed at par under protected structure.
Etude biométrique des genres Dephomys et Stochomys avec quelques notes taxonomiques (Mammalia, Muridae)

Analyse biometrique de ces 2 genres, comparaison avec les genres Hybomys et Typomys. Ces quatre genres sont separes. Le genre Dephomys renferme 2 especes D. defua et D. eburnea tandis que Stochomys montrent 1 espece S. longicaudatus avec 2 sous-especes: longicaudatus et ituricus
Effects of hail nets on orchard light microclimate, apple tree growth, fruiting and fruit quality.

Hail nets are necessary protection in some fruit growing regions. Several trials showed that the net color may influence tree growth and fruiting. The influence of hail nets on orchard light microclimate, growth, flowering and fruiting of apple trees was examined in field experiment in the years 2004–2010. ‘Šampion’ and ‘Rubinstar’ apple trees grafted on M.9, were planted in spring 2004. After planting, half of the experimental plot was covered with three kinds of hail nets: white, gray and black. The other half was kept uncovered as the control. Tree growth, fruit bud formation, fruiting and fruit quality were recorded. Solar radiation was measured above and below the nets and within tree canopy. Black and gray nets stimulated tree growth and yield of ‘Šampion’ tree, but had no positive influence on ‘Rubinstar’ trees. Covering the trees with gray and black nets caused poor red blush development and reduced soluble solids content in apples of both cultivars. Fruit firmness was unaffected by netting.
Geomorphic control of rain-forest floristic composition in French Guiana: more than a soil filtering effect?

Abstract: The influence of geomorphological features on rain-forest diversity has been reported in different Amazonian regions. Soil filtering is often assumed to underlie the observed geomorphic control on the floristic composition but other hypotheses related to biogeography or long-term forest dynamics are also possible. We tested relationships between geomorphology, soil properties and forest composition in French Guiana rain forest using a recent geomorphological map and a large dataset comprising 3132 0.2-ha plots and 421 soil cores. Soil properties were characterized by laboratory analyses and by field descriptions indicating drainage capacity and classification according to the World Reference Base (WRB). The influence of soils and geomorphology on beta-diversity was tested using variance partitioning and ANOVA-like tests. Our results confirm the hypothesis of a strong relationship between geomorphological landscapes and soil properties. Soil filtering significantly influenced the abundance of more than 40 species or groups of species. However geomorphic control of forest composition involves much more than the effects of the soil, which only explain a minor part of the broad-scale patterns of forest diversity related to geomorphological landscapes. These results reinforce the alternative hypotheses linking geomorphological landscapes to long-term forest change under the control of historical processes that shaped forest diversity.
Rennet coagulation properties of UHT‐treated phosphocasein dispersions as a function of casein and NaCl concentrations

The renneting properties of whey protein-free, UHT-heated (140 °C/10 s) casein dispersions were investigated as a function of casein and NaCl concentration. It was found that the rennet coagulation time and gel firmness can be optimised when the whey protein-free casein concentration is increased, while the added NaCl concentration is kept low. The strongest gel firmness occurs at 0.05 and 0.08 m NaCl addition and at a micellar casein concentration between 6.0 and 6.6 g/100 mL. Weak rennet gels were formed at 3.0--3.6 g/100 mL casein at all NaCl concentrations tested.
Cryopreservation of Alpine Bucks Semen

The aim of this study was to evaluate the comparative efficacy of two semen cryopreservation techniques for the preservations of 6 bucks of Alpine breed semen. In Protocol first 18 ejaculates were frozen in the standard extender that contains fructose, tris and natrium citrate using two steps method. While in the protocol II, total 10 subsequent ejaculations were frozen in glucose, tris and natrium citrate using one step methodology. The qualitative results of the fresh and frozen semen were evaluated by CASA and results of study revealed that mean motility score of the fresh semen were 8.66±0.13 while this mean mortality was reported 4.33±0.25 and 2.95±0.17 (P>0.05**) for the frozen semen by protocol I and protocol II respectively. The mean value of VAP, VCL and VSL was reported 9.83±1.61, 4.12±0.72, 12.61±1.15 μm/s and 4.55±0.74, 2.23±0.32, 5.43±0.67 μm/s (P>0.05***) for the protocol I and II respectively. Further, good motility and velocities for fertilization rate was reported for the protocol I freezing while for the protocol II appropriate results of survival rate was not reported for the frozen-thawed semen. Myagmarsuren P * , Baatar A and Batsukh T
Prevalence of Porphyromonas gingivalis and its relationship with herpesvirus in Indian subjects with chronic periodontitis: A cross-sectional study

Background: Porphyromonas gingivalis (P. gingivalis) is a periodontal pathogen that is commonly harbored in the dental plaque of humans. The aim of this study was to look into the prevalence of P. gingivalis and its association with herpesvirus in Indian subjects. This is probably the first study on the association of this bacterium with herpesvirus in Indians. Materials and Methods: This cross-sectional study consists of 200 subjects, with 100 subjects each in the healthy group and the chronic periodontitis (CP) group. Upon plaque collection, one portion of the samples was immediately plated, on culture media that is selective for P. gingivalis. Total colony-forming units (CFU)/mL from each plate was recorded. The remaining plaque sample was subjected to DNA extraction and polymerase chain reaction (PCR) was performed using specific primers for Cytomegalovirus (CMV) and Epstein–Barr virus (EBV). The data are analyzed using the chi-square test, Spearman's rho correlation coefficient, and Mann–Whitney U test. Results: P. gingivalis was detected in 66% of the subjects with CP and in 40% in the healthy group, and this difference was statistically significant (P = 0.00023). The correlation of clinical parameters with P. gingivalis showed a significant positive correlation, indicating that higher levels of clinical parameters were associated with higher CFUs of P. gingivalis in culture. The comparison of the presence of P. gingivalis between herpesvirus-negative and -positive cases showed that CMV-positive cases had significantly higher levels of this bacterium. Conclusions: The results of this study confirmed the earlier finding of P. gingivalis presence in significantly higher levels in CP subjects and in CMV-positive sites. In addition, there was a positive association of the bacterium with clinical parameters.
Resistance of furfurylated wood to termite attack

This paper provides results of a laboratory and field test study that evaluated the termite resistance of furfurylated wood. Sapwood test specimens of three wood species were furfurylated to two or three levels of modification: 15 to 17 percent, 40 to 45 percent, and 99 to 160 percent total weight increase (TWI). The wood species investigated were Scots pine (Pinus sylvestris L.), agathis (Agathis dammara), and sengon (Paraserianthes falcataria). The laboratory test was conducted on the resistance of furfurylated wood to the dry wood termite (Cryptotermes cynocephalus Light). Termite mortality, weight loss, and protection level of each specimen were determined. One-year field testing of two test sites in Java was conducted and the protection level and weight loss of each test specimen caused by Macrotermes gilvus Hagen attack was determined. Results showed that low-furfurylated (15% to 17% TWI) wood was poorly protected against termite attack. In contrast, medium- and high-furfurylated (40% to 45% and 99% to 160% TWI, respectively) specimens were highly resistant to attack by both dry wood and subterranean termites.
Etiologia e perfil de sensibilidade de bactérias aeróbias isoladas de éguas suspeitas de endometrite procedentes do estado de Pernambuco

Objetivou-se com este trabalho determinar a frequencia e o perfil de sensibilidade antimicrobiana dos microrganismos isolados do utero de eguas durante o estro. Foram selecionadas 64 eguas de varias racas, sendo 39 sem suspeita de endometrite e 25 suspeitas, procedentes do Estado de Pernambuco. O material obtido foi semeado em agar base acrescido de 8% (v/v) de sangue ovino desfibrinado e agar levine. Os testes de sensibilidade antimicrobiana in vitro dos isolados foram realizados utilizando-se a tecnica de difusao em agar Mueller Hinton. Observou-se que das 64 eguas analisadas, 41 (64,4%) foram positivas ao exame microbiologico e o microrganismo mais frequente foi a Escherichia coli (20,4%) seguido de Klebsiella sp (10,9%) e Shigella sp (10,9%). O perfil de sensibilidade dos microrganismos isolados demonstrou que a maioria destes foi sensivel a gentamicina (70,0%). Constatou-se ainda que a eritromicina (88,5%), ampicilina (86,5%) e penicilina (83,0%) apresentaram um elevado indice de resistencia. Os resultados obtidos indicam a necessidade de se realizar manobras ginecologicas adequadas com vistas a evitar a contaminacao uterina por agentes ambientais. Alem disso, os resultados dos testes de susceptibilidade aos antimicrobianos ressaltam a importância de se realizar ensaios in vitro para a conducao de uma terapeutica mais eficiente.
An experimental test of sub-hourly changes in macroinvertebrate drift density associated with hydropeaking in a regulated river

ABSTRACT We investigated the response of the invertebrate drift to the regulated peaking Magpie River under experimental sub-hourly changes in flow conditions. Benthic invertebrates were also quantified upstream of invertebrate drift sampling sites in order to examine the propensity of nearby invertebrates to drift under hydropeaking cycles. To provide an understanding of the natural patterns of drift in relation to changes in discharge, the proximate natural Batchawana River was similarly sampled. Increased discharge was associated with higher drift densities and greater particulate organic matter in the Magpie River. At the family level, multiple drift responses were observed suggesting that ecological traits and behaviors drive drift response to changes in discharge. The drift densities of some invertebrates varied in proportion to discharge; whereas, other invertebrates in the drift decreased to pre-peaking levels shortly after peak discharge was reached, with some invertebrates exhibiting a secondary peak in density as discharge returned to pre-peaking levels. Although average drift densities were comparable between the two rivers, drift density on the natural Batchawana River was much more stable than that of the Magpie River. Changes in drift density associated with flow manipulation likely impact feeding patterns and behavior of drift feeding fish.
Targeting and Specificity of RNA-binding Proteins

Targeting and specificity of RNA-binding proteins Kathleen B. Cook Doctor of Philosophy Graduate Department of Molecular Genetics University of Toronto 2015 RNA-binding proteins (RBPs) are critical parts of the gene regulatory framework, but the vast majority have unknown specificity for RNA. In this thesis I undertook three projects aimed at identifying the determinants of RNA specificity. First, I describe the creation of a database of experimental RNA-binding data that catalogues metazoan RBPs and published measurements of RNA binding. This catalogue allowed me to identify that the RNA-binding specificity of only a small fraction of RBPs was known. In collaboration with other members of the Hughes and Morris labs, I employed RNAcompete, an in vitro microarray-based method for determining the sequence specificity of RBPs, to over 200 eukaryotic RBPs. In order to determine the optimal modelling framework, I performed a systematic comparison of motif-finding methods on the RNAcompete data. The resulting motifs capture a wide range of RNA-binding specificities and allow for the inference of motifs for 20% of metazoan RBPs. In the last data chapter I describe a methodology, termed RNAcompete-S, that I developed for experimentally testing and computationally identifying the sequence and secondary structure preferences of RNA-binding proteins. Applying this method to a panel of RBPs with diverse RNA-binding domains and strategies allowed me to identify the known sequence and structural specificities of these proteins. Specifically, I was able to identify de novo an 18-nt motif matching the conserved SLBP binding site. I
Heterosis for early egg production and feed intake in Japanese quail

Early egg production, body weights and feed intake between 34 and 98 days of age have been compared in two lines DD and EE) of japanese quail selected for egg number at 14 weeks of age and in their reciprocal crosses, for three consecutive years. Genetic type, generation and the interaction had a significant effect on body weights. At 5 weeks of age least squares mean of body weight was between 167 g (line DD) and 210 g (line EE). At 14 weeks, corresponding values were 186 and 248 g. Egg production traits were only influenced by the genetic type. Least squares mean for age at first scoring egg was between 39.6 days (cross ED) and 50.2 days (line DD). For number of scoring eggs, it was between 39.3 (line DD) and 51.4 (cross ED). Daily feed intake varied between generations and genetic types, with some interaction, from 23.8 g (line DD) to 33.7 g (line EE). Heterosis was significant in some years for body weights and feed intake, but with variable values, and even different sign for 14 week body weight. On the opposite, heterosis was significant and rather constant for egg production traits, with values ranging from − 3.4 to − 5.1 days for age at first scoring egg, or from 5.7 to 6.0 for number of scoring eggs. Heterosis for daily feed intake was positive but largely not significant. Finally a multiple regression of feed intake on metabolic mean body weight, weight gain and egg mass was adjusted to the data and compared to a homologous equation obtained with poultry
Determinants of Farmers Adaptation to Climate Change. A Case from Nawalparasi District of Nepal

A field survey was conducted to study the factor that determines farmers’ decisions to adapt to climate change in Deurali and Agyouli V.D. Cs of Nawalparasi District. Altogether 180 household, 90 from each V.D. C were selected randomly for the study. A logit regression model was employed in the study. However, in order to measure the magnitude of the impact of the explanatory variables on the decision of the farmer to adapt to climate change marginal effects were computed. The study uses a binary dependent variable taking the value 1 if the farmer adapted to climate change and 0 otherwise. A farmer is considered to have adapted to climate change if he/she has employed at least one of the adaptation strategies such as early and late planting, use of drought resistant crops, zero tillage operation, crop diversification, use of mulching and composting of weeds to control water loss and conserving moisture in the field. This current research considers the following as potential factors determining farmers’ decisions to adapt to climate change; economically active members, education of the household head, farm size, annual cash earnings, access to credit, training and extension. Findings reveal that these factors influence farmers’ decisions to adapt to climate change in Nawalparasi District and marginal effects computed showed that per unit increase in these variables increased the probability of practicing different adaptation strategies by 4.3%, 31.4%, 3%, 1.5%, 17%, 66% respectively. The log likelihood was computed to be -43.45. Psuedo. R2 was calculated to be 39%.
Competition and protist predation are important regulators of riverine bacterial community composition and size distribution

ABSTRACT Among the bacterivorous protists, heterotrophic nanoflagellates (HNFs) are considered to be the main grazers of bacteria in freshwaters due to their size-selective grazing. In this work, we assessed the change of a riverine bacterial community in controlled incubations, where HNFs’ predation pressure was initially released through filtration. Filtration did not prevent the passage of cysts, which grew in the enrichments afterwards. Data on the composition of the bacterial community were gathered by Catalyzed Reporter Deposition Fluorescent In situ Hybridization (CARD-FISH) using 16S probes targeting phylogenetic groups. Bacterial cell size was also examined using image analysis. Overall, the initial filtration directly (through release of predation pressure) or indirectly (through competition among bacterial groups) affected the bacterial community composition. When nanoflagellate abundance rose, a reduction of bacterial abundance and changes in cell size distribution were observed. Gamma-Proteobacteria and Actinobacteria were the groups showing the greatest reduction in abundance. Beta-Proteobacteria showed a reduction of cell size and were found in aggregates. Alpha-Proteobacteria and Actinobacteria developed two distinct filamentous morphotypes: short, segmented rods and long chains of rods. Our results showed that the release of the predation pressure and the successive rise of the nanoflagellates changed the bacterial community in terms of composition at large phylogenetic scale. HNF grazing is highly group-specific and seems to reconstruct the community based on cell size, and thus, not only drastically changing the bacterial community composition, but also increasing its functional diversity.
Bryozoan fouling of the blue crab Callinectes sapidus at Beaufort, North Carolina

This study examines the prevalence, intensity, abundance, and spatial distribution of fouling bryozoans on 168 blue crabs, Callinectes sapidus, taken from an estuarine environment in the area of Beaufort, North Carolina. Three epizoic bryozoan species were found on the host crabs. These include Alcyonidium albescens Winston and Key, Membranipora arborescens (Canu and Bassler), and Triticella elongata (Osburn). The proportion of blue crabs fouled was 16%. Results indicate female crabs were significantly more fouled than males. This suggests that the prevalence and intensity of bryozoans are dominantly controlled by the migratory habits of the host, since female crabs spend more time in deeper waters of higher salinity where they are more likely to be fouled by bryozoan larvae. The ventral surface was significantly more fouled than the dorsal. The A. albescens colonies were significantly more abundant on the hosts' lateral spines, M. arborescens dominated the subhepatic sector, and T. elongata was most common around the mouth. The costs and benefits of epibiosis are reviewed. The bryozoan/blue crab relationship described here appears to be phoretic. This means there is minimal negative impact on the crab, the relationship is more beneficial to the bryozoans, and there is no special symbiotic relationship between the crab and the bryozoan.