Miracle-dz/UniFAR-FTUs huggingface dataset:
Caractérisation des éléments intégratifs conjugatifs de la famille ICESt3 et des facteurs influençant leur mobilité

Les elements integratifs conjugatifs (ICE) sont des elements genetiques mobiles se transferant horizontalement d’une bacterie a une autre. Les ICE sont porteurs de genes adaptatifs pouvant significativement ameliorer le fitness de la bacterie hote et permettre son adaptation a de nouvelles niches ecologiques. Lors de ces travaux, des ICE apparentes a ICESt3 ont ete retrouves chez la bacterie commensale et pathogene opportuniste Streptococcus salivarius. Les analyses in silico realisees ont demontre la diversite des ICE de cette famille, notamment au niveau de leurs modules de recombinaison, de regulation mais aussi de leurs genes adaptatifs potentiellement mis a disposition de la communaute microbienne orale et digestive de l’Homme. La fonctionnalite de deux de ces ICE a ete mise en evidence experimentalement a travers l’evaluation de la capacite de ces elements a se transferer intra- et inter-specifiquement. Ces travaux ont egalement permis l’identification de facteurs d’hote influencant la mobilite d’ICESt3, revelant ainsi l’importance, pour le transfert et l’acquisition de cet ICE, des molecules de surface telles que les lipoproteines, les acides teichoiques et les exopolysaccharides. En conclusion, il a ete demontre que les elements de la famille ICESt3 participent a l’evolution du genome chez differentes especes de streptocoques et aux echanges genetiques entre bacteries issues de l’alimentation et bacteries de la flore digestive humaine. Enfin, ces travaux ont contribue a une meilleure comprehension des mecanismes et des facteurs d’hote influencant la mobilite de ces elements genetiques mobiles
Studies on fruit drop in mango varieties

Studies on fruit set and fruit drop were carried out in Kerala Agricultural University on six varieties of mango during 2000-2001. The season of flowering in majority of the varieties was during December–January months except in Neelum in which it was during April-May. The number of inflorescence per square metre ranged from 23.6 to 7.0 and was the maximum in Prior and minimum in Alphonso and Neelum. In the case of percentage of bisexual flowers Alphonso had the maximum (44.39%)bisexual flowers and Muvandan had the minimum. Variation in length, breadth, colour and density of inflorescence was noticed among the varieties. Initial fruit set ranged from 5.39 to 8.45 fruits per inflorescence. Drop occurred to the tune of 50% during the initial 15 days and continued for 45 days. Maximum drop was noted in Alphonso (89.93%) and the minimum in H-151 (79.6%).
METHOD TO EVALUATE THE FIXATION OF IMPLANT COATINGS

The aim of this paper is to present this method as a means of evaluating initial implant fixation by reporting a time zero comparative study of a sintered asymmetric titanium (Ti) particle coating and a conventional sintered spherical Ti bead coating. Since the asymmetric particle coating has been shown to have a higher interfacial friction against bone [2], it is expected that the initial push-out strenth for this coating will be significantly greater than the bead coating.
Catnip essential oil: There is more to it than making your cat go crazy

Catnip (Nepeta cataria) essential oil shows a wide range of biological activities, not only cat stimulation, but also relaxant, antispasmodic, insect repellent, and allelopathic activities. The essential oil is generally dominated by nepetalactone isomers, but the compositions have shown wide variation depending on phenological cycle and geographical location. Numerous other Nepeta species are known and many of those have been characterized in terms of essential oil compositions and biological activities. This review presents an overview of the volatile phytochemistry of catnip (Nepeta cataria), its biological activities, and a survey of recent reports on Nepeta essential oils.
Histologic characterization of stem cells in mammary epithelium and stroma

It is unknown whether native cells in benign breast tissue mediate risk of cancer.We therefore aimed to identify cell types in benign human mammary tissueimmunohistologically using markers of stemness and differentiation, and toinvestigate their possible associations with clinical risk factors for breast cancer.We found that cells that are integrated in benign epithelium and areimmunoreactive for the stem cell marker ALDH1 are negative for markers ofglandular differentiation, proliferation, and estrogen receptor. High numbers ofthese cells were associated with the risk factors family history of breast cancer,BRCA1/2 carrier status, low parity, and hormone use.Stromal ALDH1+ cells are either spindle-shaped/polygonal (s/p) or round/oval(r/o), and the latter are positive for the contractile protein marker SMMHC.ALDH1+ s/p cells are positive for the stellate cell marker vinculin. Low numbersof these cells were associated with family history, and when negative for the stemcell marker CD44 they were associated with nulliparity. Low numbers ofALDH1+ CD44+ CD24– r/o cells were associated with family history. ALDH1+r/o cells were positively or negatively associated with low parity depending on thepatients' BRCA1/2 status.High numbers of r/o cells that are positive for the mesenchymal stem cellmarker SSEA3 were associated with low parity, family history, and hormone useafter menopause.This study describes novel stromal cells in breast that were associated with riskfactors for breast cancer. If confirmed in independent cohorts, they may be usedfor stratification of women with regard to risk of breast cancer.
A Pre-Training Technique to Localize Medical BERT and to Enhance Biomedical BERT

Background: Pre-training large-scale neural language models on raw texts has been shown to make a significant contribution to a strategy for transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as Bidirectional Encoder Representations from Transformers (BERT), the performance of information extraction from free text by NLP has significantly improved for both the general domain and the medical domain; however, it is difficult for languages in which there are few publicly available medical databases with a high quality and a large size to train medical BERT models that perform well.Method: We introduce a method to train a BERT model using a small medical corpus both in English and in Japanese. Our proposed method consists of two interventions: simultaneous pre-training, which is intended to encourage masked language modeling and next-sentence prediction on the small medical corpus, and amplified vocabulary, which helps with suiting the small corpus when building the customized corpus by byte-pair encoding. Moreover, we used whole PubMed abstracts and developed a high-performance BERT model, Bidirectional Encoder Representations from Transformers for Biomedical Text Mining by Osaka University (ouBioBERT), in English via our method. We then evaluated the performance of our BERT models and publicly available baselines and compared them.Results: We confirmed that our Japanese medical BERT outperforms conventional baselines and the other BERT models in terms of the medical-document classification task and that our English BERT pre-trained using both the general and medical domain corpora performs sufficiently for practical use in terms of the biomedical language understanding evaluation (BLUE) benchmark. Moreover, ouBioBERT shows that the total score of the BLUE benchmark is 1.1 points above that of BioBERT and 0.3 points above that of the ablation model trained without our proposed method.Conclusions: Our proposed method makes it feasible to construct a practical medical BERT model in both Japanese and English, and it has a potential to produce higher performing models for biomedical shared tasks.
A new species of Lepanthes (Orchidaceae: Pleurothallidinae) from northwestern Ecuador

A new species of Lepanthes form Ecuador, Lepanthes kayii , is described, illustrated and compared with other similar species. L. kayii is compared to the similar species L. saltatrix and is the latest discovered species from a group of species of this genus which share several unique features in flower and plant morphologies.
Uji Efektivitas Berbagai Konsentrasi Pestisida Nabati Bintaro (Cerbera manghas) terhadap Hama Ulat Grayak (Spodoptera litura) pada Tanaman Kedelai

Spodoptera litura is a major pest in soybean cultivation causing damage by 80%. One of control is done by using bintaro plants ( Cerbera manghas ) potential as a botanical pesticide (insecticide). This study aims to determine the effectiveness of botanical pesticide from bintaro extract and get the precise extract concentration of fruit, young leaves, and old leaves of bintaro to control Spodoptera litura on soybean plants, and its influence to the growth of soybean plants. This study used an experimental method that is designed in a single factor completely randomized design using pesticides Bintaro (young leaves, old leaves, and fruit), which consists of three concentrations (100 g / l, 200 g / l, and 300 g / l), add two treatments, namely, sprayed with water and a synthetic pesticides as a control. Result showed the leaves and fruit of Bintaro at concentrations of 100 g/ l to 300 g/ l by solvent extraction has not been effectively used as botanical pesticide to control Spodoptera litura on soybean plants. Old leaf Bintaro extract (100 g/ l) produces highest pest mortality value and rate of 40.00% and 2.00. The use of botanical pesticide from extract bintaro (fruit and leaf) is not inhibit the growth of soybean plants.
Characterization of the Role of Ubiquitin Protein Ligase E3 Component N-recognin 4 (UBR4) in the Murine Circadian Clock

Ubiquitination is an important post-translational modification in the molecular clock that regulates degradation of clock proteins through ubiquitin ligases. However, no ubiquitin ligase has been implicated in the photic entrainment pathways in mammals thus far. In this thesis, I characterized the physiological and molecular phenotype of a new ubiquitin ligase named UBR4 in the murine circadian clock. UBR4 is expressed throughout the suprachiasmatic nucleus in a time-of-day-dependent fashion and is light-inducible in the early subjective night. Homozygous ubr4 knockout are embryonic lethal, therefore heterozygous ubr4 mice (ubr4 +/) were used to study its physiological role in the circadian clock. I found that mice with reduced expression of UBR4 show differential phenotype in circadian paradigms that involve chronic light disturbances. Furthermore, preliminary data suggest that casein kinase 2 beta subunit is a potential substrate of UBR4, affecting molecular clock component PER in vivo and in vitro.
Effects of different levels of Aloe Vera gel on some of hematological, biochemical and immunological parameters in the chicken model.

Introduction: The present study was conducted to investigate the effects of subchronic administration of different levels of Aloe Vera gel on some biochemical and immunological factors in the chicken model. Material and Methods: Two hundred and forty-one-day old Ross 308 (male and female) broilers were used on a completely randomized design in 5 groups with 4 replicates, and each replicate was consisting of 12 broilers. The groups included one control group (basal diet) and four experimental groups with basal diet mixed with different levels of Aloe Vera gel (1%, 2% and 3%) plus virginiamycin antibiotic. Results: No significant difference between experimental groups was observed in serum albumin level and ALP activity on days 14, 28 and 42. On the day 14, the variation of albumin and total protein levels were significant. In the days 28 and 42, the level of blood glucose in the group receiving 3% Aloe Vera and in the group receiving 1% Aloe Vera on the day 28 was decreased significantly. On the day 28, the count of lymphocytes was raised significantly in the group receiving 3% Aloe Vera. Also in this day, the most count of heterophils was found in the control and virginiamycin groups. On the day 42, the significant rise of lymphocyte count was observed in all groups receiving Aloe Vera gel. On the day 28, the level of antibody titers against sheep red blood cell was raised significantly. Conclusion: Daily supplementation with 1% Aloe Vera gel markedly potentiates cellular and humeral immunity in chickens and can be used as a food additive in order to prevent infections.
Modeling the consequences of heterogeneity in microbial population dynamics

Chapter 1 The rate at which unicellular micro-organisms progress through the cell cycle is a major component of their evolutionary fitness. Measuring fitness phenotypes in a given environment or genetic background forms the basis of most quantitative assays of drug sensitivity or genetic interaction, including genome-wide assays. Growth rate is typically measured in bulk cell populations, inoculated with anything from hundreds to millions of cells sampled from purified, isogenic colonies. High-throughput microscopy reveals that striking levels of growth rate heterogeneity arise between isogenic cell lineages (Levy et al., 2012). Using published Saccharomyces cerevisiae data, I examine the implications for interpreting bulk, population scale growth rate observations, given observed levels of growth rate heterogeneity at the lineage level. I demonstrate that selection between cell lineages with a range of growth rates can give rise to an apparent lag phase at the population level, even in the absence of evidence for a lag phase at the lineage level. My simulations further predict that, given observed levels of heterogeneity, final populations should be dominated by one or a few lineages. Chapter 2 In order to validate and further explore the conclusions from Chapter 1, I re-analyzed high-throughput microscopy experiments carried out on Quantitative Fitness Analysis (QFA) S. cerevisiae cultures (Addinall et al., 2011), an approach referred to as μQFA. To allow for precise observation of purely clonal lineages including very fast-growing lineages and non-dividing cells, I re-designed an existing image analysis tool for μQFA, now available as an open source Python package. Fast-growing outliers in particular influence the extent of the lag phase apparent at the population level, making the precision of growth rate estimation a key ingredient for successfully simulating population observations. μ QFA data include population observations which I used to validate the population simulations generated from individual lineage data. I explored various options for modeling lineage growth curves and for carrying out growth rate parameter inference, and included the full workflow in an open source R package. Contact helena.herrmann@postgrad.manchester. ac.uk
RESPONSE OF MAIZE (Zea mays L.) TO DIFFERENT TILLAGE REGIMES AND NITROGEN TIMINGS UNDER SEMI-ARID IRRIGATED CONDITIONS

In Pakistan farmers of irrigated area plough their lands with shallow tillage implements (simple cultivator) due to less energy cost (fuel consumption) than deep tillage implements in addition to non-availability of deep tillage implements. Repetitive use of same implement for tilling the soil creates a hard pan in the subsoil layer. Presence of hard pan leads to poor soil physical properties such as higher soil bulk density and penetration resistance (Raza et al., 2005) consequently leading to lesser crop yield. Subsoil compaction limits the root length of crops due to higher subsoil bulk density (Ishaq et al., 2001) and resulted to reduction in yield (Coelho et al., 2000) due to less absorption of nutrients and water (Motavalli et al., 2003). The most serious cause of subsoil compaction is the continuous cultivation of soil with same tillage implements which affects the soil physical properties (Ahmad et al., 2009) and adversely affect the crop yield (Wasaya et al., 2011). Among various options for managing the remediation of subsoil compaction are crop rotation and subsoiling (Motavalli et al., 2003). Subsoiling improves the NRE (nitrogen recovery efficiency) and greater NRE was observed from plots with subsoiling treatments as compared to compacted plots (Motavalli et al., 2003). Tillage with moldboard plough along with disk harrowing improves wheat root length density and root biomass compared with no-tillage due to more soil penetration resistance in no-till plots in the upper soil layer (Munoz-Romero et al., 2010). Similarly subsoiling improves the crop yield upto 24% compared with other tillage practices (Botta et al., 2006). Yield increment under conventional tillage compared with reduce and zerotillage occurs due to more availability of soil P and K contents in the former tillage system and the others resulted to yield reduction of 11.28% and 6.31% under zero-tillage and reduced tillage respectively (Gangwar et al., 2004). Farmers of irrigated area generally apply nitrogen at crop sowing or with second irrigation in maize which undergoes different losses in the form of volatilization, denitrification and leaching. Reduction of nitrogen losses and enhancing nitrogen use efficiency (NUE) through higher crops yield is the ultimate goal. To increase NUE, time of N application or split application is a vital component. Pre-plant nitrogen application is subjected to more NO3 leaching compared with side dressing. Application of nitrogen in different splits Pak. J. Agri. Sci., Vol. 54(3), 553-560; 2017 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: DOI: 10.21162/PAKJAS/17.1729 http://www.pakjas. com.pk
THE EFFECT OF DIVERGENT SELECTION FOR SHAPE OF GROWTH CURVE IN JAPANESE QUAIL ON EGG QUALITY

The HG (high growth intensity from 11 to 28 d) and LG (low growth intensity form 11 to 28 d) lines of meat-type Japanese quail, divergently selected for relative body weight gain from 11 to 28 d but constant 49 d weight were used in the experiment. Eggs were analyzed six times during laying period, form 11 to 33 weeks of age. In total 488 eggs of HG and 497 eggs of LG were analyzed for weight of eggs, weight and proportion of yolk, eggshell and albumen, and for yolk colour. Except yolk colour the line had significant effect on all observed characteristics (P<0.05). Age of quails also significantly affected all parameters (P<0.05). Egg weight was higher in LG (13.4 vs. 12.6 g) compared with HG (P<0.05) and yolk weigh was 3.9 g for HG and 4.0 g for LG (P<0.05). Except egg and yolk weight and yolk proportion significant interaction between age and line was calculated (P<0.05).
ACOUSTIC EMISSION NDT OF COMPOSITES DAMAGED BY STATIC AND DYNAMIC LOADING IN AQUEOUS ENVIRONMENTS

A series of tests has been conducted to investigate the effect of sea water absorption on fatigue damage accumulation in a glass fibre reinforced polyester laminate of the type widely used in the marine and offshore industries, using four-point bend flexural loading to ensure peak strain in the outer layers of the material most subject to sea water absorption. Pre-exposure was found to reduce the flexural strength and enhance damage accumulation in fatigue by stimulating matrix cracking, fibre debonding and delamination. Acoustic emission (AE) was used to characterise damage accumulation. These results were found to correlate well with independent measurements of changing bending stiffness and with observations of the damaged sections.
Northern pintail nest site selection, nest success, renesting ecology and survival in the intensively farmed prairies of southern Saskatchewan: an evaluation of the ecological trap hypothesis

Unlike most prairie nesting ducks (Anas spp.), the North American population of northern pintails (A. acuta, hereafter pintails) has failed to respond as expected to improved wetland conditions on the U.S. and Canadian prairies during the mid to late 1990s. My primary objectives were to test the “ecological trap hypothesis” on a landscape level by examining pintail nest site selection and nest success in a highly agricultural environment in southern Saskatchewan. I also used radiotelemetry to estimate renesting and breeding season survival rates of female pintails; two parameters that are important in productivity and life cycle models. Most (51%) pintail nests were found in crop stubble and generally pintails nested in habitats in proportion to their availability on the landscape. In contrast, most (82%) mallard nests were located in edge and grassland habitats. Mallards nested in habitats with dense cover in greater proportion to their availability and avoided crop stubble. Nest success estimates in crop stubble were lower (<1-4% vs. 6-37%) than the surrounding habitats with greater cover. Nest success estimates in crop stubble were abysmal largely due to high rates of nest predation. Only 20-33% of nests in crop stubble failed due to spring cultivation. For 1998, 1999, and 2000, overall renesting rates for females trapped throughout the nesting season were 50%, 71%, and 41%, but were 61%, 90% and 62% when only first nesting females were included. Renesting propensity declined seasonally, but at different rates among years likely due to variation in wetland abundance. Most (58%) females renested, but few (37%) initiated multiple renests. Survival rate for my 75-day interval (April 30 – 14 July) was 0.81 ± 0.05. Cause-specific mortality rates were greater for avian predators (0.14 ± 0.04) than other sources of mortality. The pintail’s high propensity to nest in crop stubble where nest success is low coupled with lower renesting and breeding season survival rates than mallards
Applicability of Coimmobilized Cellulase and Xylanase to Lignocellulose Hydrolysis

Immobilization is a technology for increasing the stability and realizing the reuse of enzymes. In order to clarify the applicability of cellulase and xylanase immobilized simultaneously on the reversibly soluble polymer Eudragit L-100 to lignocellulose hydrolysis, the hydrolysis of pretreated rice straw with the coimmobilized enzymes was analyzed kinetically, and the reusability of the coimmobilized enzymes was investigated. The coimmobilized enzymes were more stable against the changes in pH and temperature than the free enzymes. A holocellulose conversion rate of 61.4 % was obtained in the hydrolysis of pretreated rice straw with both the coimmobilized enzymes and the free enzymes. The maximum reaction rate decreased from 135.1 mmol/(L·min) to 84.7 mmol/(L·min), while the Michaelis–Menten constant increased from 30.6 g/L to 51.7 g/L due to coimmobilization. 54 % of cellulase activity and 46 % of xylanase activity remained after the coimmobilized enzymes were recycled for three times. It is suggested that the coimmobilized enzymes are applicable to lignocellulose hydrolysis, which may lead to an improvement of the efficiency of enzymatic lignocellulose hydrolysis.
Nanostructured Ti thin films by combining GLAD and magnetron sputtering: a joint experimental and modeling study

In this work magnetron sputter deposition and Glancing Angle Deposition are combined to synthesize nanostructured Ti films. Different type of microstructures (tilted columns, straight pillars, chevrons, .) can be obtained by varying the substrate orientation. In order to understand the mechanisms leading to the formation of each structure the NASCAM code was used to simulate the growth of the film. We show that an advanced growth simulator like NASCAM enables quantitative prediction of numerous physical properties, including film density, surface roughness, and column shape asymmetry. The simulator can also be used to understand the effects of different process variables such as gas pressure and substrate rotation rates.