Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of abscisic acid in grape berry development.

Hormones control plant development by coordinating changes in the expression of numerous genes at crucial times in a tissue and organ-specific manner. They have been implicated in controlling various aspects of grape berry development, in particular, the important process of ripening and are used in some crops to control growth and ripening. Abscisic acid (ABA), is associated in grapevine with the response to water stress but may also have a role in berry ripening. We have shown over three seasons that ABA levels in Cabernet Sauvignon berries increase dramatically at veraison, consistent with it being involved either as a trigger for ripening or as a response to the increase in sugars that occurs at this time. Net ABA accumulation doesn’t occur until veraison, the decrease in ABA concentration in the first phase of berry development being due to berry expansion. The decrease in ABA that occurs later in development is likely to be due to a combination of catabolism and sequestration into the bound form. The genes crucial to ABA synthesis, 9-cisepoxycarotenoid dioxygenase (NCED) and zeaxanthin epoxidase (ZEP), were expressed throughout berry development and no clear correlation was found between their levels and that of ABA. Laboratory studies have shown that isolated berries respond to the presence of sucrose through an increase in ABA biosynthesis pathway gene expression (NCED and ZEP). This resulted in de novo synthesis of ABA as inhibition of the carotenoid synthesis pathway by a phytoene desaturase inhibitor prevented ABA accumulation. Replicated field trials clearly showed that ABA treatments can be effective in significantly enhancing ripening when applied in at or near the end of the first period of berry expansion. Colour accumulation in the skins commenced earlier in ABA-treated fruit as did the increase in sugar levels. ABA treatment also advanced the timing of the second phase of berry expansion as it appeared to eliminate the lag phase of berry growth. Taken together these data demonstrate that ABA is likely to play some part in the control of berry ripening and can be used to advance the timing of ripening. Further investigation into the characteristics of ABA-treated fruit will be needed to investigate the compositional
A Real Scale Prototype to Smooth Short-Time Power Fluctuations of Marine Renewable Energy Sources -Uliss.EMR Project-

This paper presents research and development of an industrial project which aims to propose a realistic solution to smooth short time power fluctuations for marine renewable energy sources. This project, funded by the European Community and Brittany Region (FEDER funding), associates SABELLA and Entech Smart Energies with the French Naval Academy research laboratory. The main objective is to design and test a preindustrial prototype of a controlled Energy Storage System (ESS) based on a supercapacitor bench, which can be associated with marine energy devices. The project includes realistic scale (several hundred kW rated power) design and test of this prototype in a dedicated emulation test bench. This paper details the project context, the test bench and prototype design and configuration.
Glutamate release is inhibitory and unnecessary for the long-term potentiation of presynaptic function

Long-term potentiation (LTP) and long-term depression (LTD) of transmitter release probability (Pr) are thought to be triggered by the activation of glutamate receptors. Here, we demonstrate that glutamate release at CA3-CA1 synapses is in fact inhibitory and unnecessary for increases in Pr. Instead, at active presynaptic terminals, postsynaptic depolarization alone can increase Pr by promoting the release of nitric oxide from neuronal dendrites in a manner dependent on L-type voltage-gated Ca2+ channels. The release of glutamate, in contrast, decreases Pr by activating presynaptic NMDA receptors (NMDAR). Thus, net changes in Pr are determined by the combined effect of both LTP-promoting and LTD-promoting processes, that is, by the amount of glutamate release and postsynaptic depolarization that accompany presynaptic activity, respectively. Neither of these processes directly depends on the activation of postsynaptic NMDARs. We further show that presynaptic changes can be captured by a simple mathematical framework, in which the role of presynaptic plasticity is to ensure that the ability for a presynaptic terminal to release glutamate is matched with its ability to predict postsynaptic spiking.
Cancer Autoantibody Biomarker Discovery and Validation Using Nucleic Acid Programmable Protein Array

Currently in the US, many patients with cancer do not benefit from the population-based screening, due to challenges associated with the existing cancer screening scheme. Blood-based diagnostic assays have the potential to detect diseases in a non-invasive way. Proteins released from small early tumors may only be present intermittently and get diluted to tiny concentrations in the blood, making them difficult to use as biomarkers. However, they can induce autoantibody (AAb) responses, which can amplify the signal and persist in the blood even if the antigen is gone. Circulating autoantibodies is a promising class of molecules that have potential to serve as early detection biomarkers for cancers. This Ph.D thesis aims to screen for autoantibody biomarkers for the early detection of two deadly cancer, basal-like breast cancer and lung adenocarcinoma. First, a method was developed to display proteins in both native and denatured conformation on protein array. This method adopted a novel protein tag technology, called HaloTag, to covalently immobilize proteins on glass slide surface. The covalent attachment allowed these proteins to endure harsh treatment without getting dissociated from slide surface, which enabled the profiling of antibody responses against both conformational and linear epitopes. Next, a plasma screening protocol was optimized to significantly increase signal to noise ratio of protein array based AAb detection. Following this, the AAb responses in basal-like breast cancer were explored using nucleic acid programmable protein arrays (NAPPA) containing 10,000 full-length human proteins in 45 cases and 45 controls. After verification in a large sample set (145 basal-like breast cancer cases / 145 controls / 70 non-basal breast cancer) by ELISA, a 13-AAb classifier was developed to differentiate patients from controls with a sensitivity i of 33% at 98% specificity. Similar approach was also applied to the lung cancer study to identify AAbs that distinguished lung cancer patients from computed-tomography positive benign pulmonary nodules (137 lung cancer cases, 127 smoker controls, 170 benign controls). In this study, two panels of AAbs were discovered that showed promising sensitivity and specificity. Six out of eight AAb targets were also found to have elevated mRNA level in lung adenocarcinoma patients using TCGA data. These projects as a whole provide novel insights on the association between AAbs and cancer, as well as general B cell antigenicity against self-proteins.
Annual variation of oilseed rape habitat quality and role of grassy field margins for seed eating carabids in arable mosaics

Promoting the weed seed predation service by carabids requires an understanding of the spatio‐temporal distribution of carabid species during the cropping season. In the present study, we analyzed the spatio‐temporal dynamics of three abundant seed‐eating carabid species in oilseed rape (OSR) and its adjacent habitat (cereal crop or grassy field margin) with four indicators: activity density, nutritional state, the use of the interface with the adjacent habitat, and the proportion of carabids leaving OSR. The activity density and nutritional state of Poecilus cupreus decreased after harvest, comprising a period related to a decrease of resource availability and the end of life cycle. We detected a tendency of movement from OSR to the adjacent habitat after harvest for Amara similata, although this was not as strong as expected. The presence of grassy field margins influenced the spatio‐temporal dynamics of Pseudoophonus rufipes and A. similata, suggesting that spillover processes exist for these two species but not for P. cupreus. Monitoring four complementary indicators gave a more thorough understanding of the perception of local and adjacent habitats by carabids, which is a prerequisite for the identification of landscape configurations that enhance the activity density of these natural enemies within crops.
Lactic acid bacteria as bio-preservatives in bakery : role of sourdough systems in the quality, safety and shelf life of bread

Microbial contamination and survival during storage of bread are a cause of both health concerns and economic losses. Traditional fermentation systems were studied as sources of lactic acid bacteria (LAB) with antagonistic potential against foodborne pathogens and spoilage organisms, with the aim to improve the safety and shelf life of bakery products. The antagonistic activity of four types of buttermilk (BM) products fermented with Lactococcus lactis subsp. lactis was evaluated against a number of pathogenic bacteria to select the best fermented-BM for application as bio-preservatives in bread crumpets, showing up to 9 μg/ml of nisin equivalent antimicrobial activity. These food ingredients could be suitable to be used in crumpet formulations, BM fermented with Lc. lactis subsp. lactis and nisin influenced the quality and shelf life of crumpets; the pH value and firmness of products with fermented BM was lower and the acidity and springiness was higher than for unfermented BM treatment and control withouth additive. The nisin and fermented BM treatment had beneficial effects on the pore size and colour in comparison with the control, and improved microbial shelf life by 2 days. Commercial and traditional sourdough and bread samples (n=18) were collected to assess the diversity of LAB strains and potential properties when applied to dough and bread. DGGE followed by sequencing showed that Lactobacillus was the predominant genus in the studied sourdoughs. Lb. plantarum and Lb. brevis strains accounted for 69% of the 32 isolates, out of which 10 were amylolytic and 12 had proteolytic activity. Most were also good acid producers after 24 h at 30°C. Some LAB strains presented a strong in vitro inhibitory activity against five indicator strains, showing potential as starter cultures to ferment sourdough. In subsequent experiments, the properties of 24 sourdoughs were evaluated, and one of them, fermented with Lb. plantarum (SIN3) yielded low pH value, high lactic acid production, and suitable microbial growth, and was selected for further bread making performance trials. The bread with fast fermentation and high sourdough concentration (FFHSD) had a lower pH, higher acidity and increased the quality attributes with significantly better shelf life comparing to the other treatments during the storage period. Sensory evaluation demonstrated that fast-fermented breads were more acceptable than the slow-fermented counterparts. Bread prepared with high level (18%) of sourdough fast-fermented with the selected culture (SIN3) had a good eating quality and shelf life. The approach of this study is likely to yield feasible improvements of the current methods of preparation of baking goods.
AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome

Metatranscriptome has become increasingly important along with the application of next generation sequencing in the studies of microbial functional gene activity in environmental samples. However, the quantification of target active gene is hindered by the current relative quantification methods, especially when tracking the sharp environmental change. Great needs are here for an easy-to-perform method to obtain the absolute quantification. By borrowing information from the parallel metagenome, an absolute quantification method for both metagenomic and metatranscriptomic data to per gene/cell/volume/gram level was developed. The effectiveness of AQMM was validated by simulated experiments and was demonstrated with a real experimental design of comparing activated sludge with and without foaming. Our method provides a novel bioinformatic approach to fast and accurately conduct absolute quantification of metagenome and metatranscriptome in environmental samples. The AQMM can be accessed from https://github.com/biofuture/aqmm.
Dietary calcium salts of fatty acids and soybean oil effects on mid-lactation dairy cows performance

This study aimed to evaluate the effects fat supplementation with soybean oil (SO) and calcium salts of fatty acids (CSFA) on mid-lactation dairy cows on feed intake and nutrients digestibility, ruminal fermentation, milk yield and composition, and nitrogen balance. Sixteen multiparous Holstein cows (638 ± 73 kg of body weight and 116 ± 26 days in milk) were used in a 4 × 4 Latin square design for evaluate following diets: CONT) control, without additional fat source; SO) 30 g/kg of soybean oil; CSFA1) inclusion of 30 g/kg of calcium salts of long-chain fatty acids (MEGALAC-E®); and CSFA2) inclusion of 30 g/kg of calcium salts of long-chain fatty acids (LACTOPLUS®) on dry matter basis. Both evaluated CSFA were manufactured using soybean oil. Fat sources addition decreased dry matter intake (23.2 vs 21.7 kg/d) and increased (P<0.001) ether extract intake and digestibility (P<0.001). Ruminal pH, NH3-N, total volatile fatty acid, acetate, propionate and butyrate production were similar among treatments (P≥0.121). Fat supplementation had no effect on milk yield (32.0 kg/d) and composition. However, soybean oil decreased milk fat yield compared to CSFA diets. Dietary addition of fat sources decreased N intake (P < 0.001) without affect on N balance. Inclusion of fat source in the diet, either as free or rumen-protected decreased dry matter intake without affect the ruminal fermentation and performance of mid-lactation dairy cows.
Standard operating procedure for somatic variant refinement of tumor sequencing data

Purpose: Manual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors. Methods: Open source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review. Results: We present a standard operating procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewer’s confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection. Conclusion: Standardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.
Contrasting species responses to continued nitrogen and phosphorus addition in tropical montane forest tree seedlings

Global changes in nutrient deposition rates are likely to have profound effects on plant communities, particularly in the nutrient‐limited systems of the tropics. We studied the effects of increased nutrient availability on the seedlings of six tree species in montane forests of southern Ecuador in situ. After five years of continued N, P, or N+P addition, naturally grown seedlings of each of the two most common species at each elevation (1000, 2000, and 3000 m asl) were harvested for analyses of leaf morphology, nutrient content, herbivory, and tissue biomass allocation. Most species showed increased foliar N and P concentrations after addition of each respective element. Leaf tissue N:P ratios of >20 in the control plants of all species suggest that P is more growth‐limiting in these forests than N. Leaf morphological responses to nutrient addition were species and nutrient specific, with some species (Hedyosmum purparescens, Graffenrieda emarginata) exhibiting increased specific leaf area (SLA), and others (Graffenrieda harlingii) increased leaf area ratios (LAR). Pouteria torta (1000 m) had lower SLA and LAR after P addition. Increased herbivory was only evident in G. emarginata (after N and N+P addition). Only the species from 3000 m asl modified biomass allocation after nutrient addition. In general, N and N+P addition more strongly affected the species studied at the upper elevations, whereas P addition had a similar range of effects on the species at all elevations. We conclude that the responses of the studied tropical montane forest tree seedlings to chronic N and P addition are highly species‐specific and that successful adaptation to increased nutrient availability will depend on species‐specific morphological and physiological plasticity.
Regulation of eIF4F complex by the peptidyl prolyl isomerase FKBP7 in taxane-resistant prostate cancer

Targeted therapies that exploit the signaling pathways involved in prostate cancer are required to overcome chemoresistance and improve treatment outcomes for men. Molecular chaperones play a key role in the regulation of protein homeostasis and are potential targets to alleviate chemoresistance. Using image-based high content siRNA functional screening based on a gene expression signature, we identified FKBP7, a molecular chaperone overexpressed in docetaxel-resistant and in cabazitaxel-resistant prostate cancer cells. FKBP7 was upregulated in human prostate cancers and correlated with the recurrence in patients receiving Docetaxel. FKBP7 silencing showed that FKBP7 is required to maintain the growth of chemoresistant cell lines and of chemoresistant tumors in mice. Mass spectrometry analysis revealed that FKBP7 interacts with the eIF4G component of the eIF4F translation initiation complex to mediate survival of chemoresistant cells. Using small molecule inhibitors of eIF4A, the RNA helicase component of eIF4F, we were able to overcome docetaxel and cabazitaxel resistance.
The unique role of the non-lemniscal pathway on stimulus-specific adaptation (SSA) in the auditory system

Stimulus-specific adaptation (SSA) is a special type of adaptation that allows neurons to cease responding only to repetitive, background stimuli, while preserving its responsiveness for other, new upcoming deviant stimuli. It emerges subcortically in non-lemniscal neurons of the inferior colliculi, propagating and evolving throughout the auditory pathway, until reaching its uppermost manifestation in the non-lemniscal areas of the auditory cortex. In this review, we will discuss the fundamental role of the non-lemniscal pathway in the generation of SSA, which is usually disregarded in cortical SSA research, despite being a major anatomical source of the mismatch negativity (MMN).
Characterisation and diversity of Indian isolates of Ralstonia solanacearum causing bacterial wilt of Capsicum annuum L.

Abstract Genetic diversity of 13 isolates of Ralstonia solanacearum causing bacterial wilt in hot pepper and bell pepper (Capsicum annuum L.) from 6 states of India was assessed. All isolates of R. solanacearum belonged to biovar 3, race 1 and phylotype I. These isolates consisted of 4 distinct DNA types at 75% similarity coefficient using ERIC, BOX and REP-PCRs techniques. Multilocus sequence analysis of hrpB, fliC and egl genes of 6 isolates of R. solanacearum along with 2 out group bacteria was done and they showed high level of variability within these three regions of the genome involving in pathogenicity.
Effects of Fire Frequency and Soil Temperature on Soil CO2 Efflux Rates in Old-Field Pine-Grassland Forests

Soil CO2 efflux (Rs) is a significant source of carbon dioxide from soils to the atmosphere and is a critical component of total ecosystem carbon budgets. Prescribed fire is one of the most prevalent forest management tools employed in the southeastern USA. This study investigated the influence of prescribed fire on Rs rates in old-field pine-grassland forests in north Florida, USA, that had been managed with prescribed fire annually and biennially for over 40 years, or left unburned for approximately the same period. Monthly measurements were taken of Rs, soil temperature (Ts), and soil moisture from August 2009 to May 2011. Results showed that sites managed with annual and biennial dormant season prescribed fire had significantly lower monthly mean Rs rates and estimated annual soil carbon fluxes than sites where fire had been excluded. While Ts explained a significant amount of the temporal variations in Rs, it did not explain the differences in Rs among prescribed fire treatments. Our results provide new insight into the effects of prescribed fire and fire exclusion on soil carbon fluxes, and suggest that future methods to model ecosystem carbon budgets should incorporate not only current vegetative conditions, but also prescribed fire management activities.
The first crocodylomorph from the Mesozoic of Turkey (Barremian of Zonguldak) and the dispersal of the eusuchians during the Cretaceous

A new crocodylomorph from the upper Barremian İncigez Formation of Zonguldak (NW Turkey) is described for the first time based on jaw and limb bone elements from the collection of the Istanbul Technical University. The material is attributed to Turcosuchus okani gen. et sp. nov. according to a unique combination of character states, such as a strong heterodonty, composed of non-spatulated teeth, a maximum of 10 teeth posterior to the symphysis, a sigmoidal dorsal margin of the dentary in lateral view, and a splenial excluded from the symphysis. An updated phylogenetic analysis of crocodylomorphs confirms that this new taxon belongs to the Hylaeochampsidae, and that it forms a relatively robust clade with the derived Unasuchus, Acynodon, Iharkutosuchus and Hylaeochampsa. Turcosuchus also presents some anatomical convergence with bernissartids, allodaposuchids, basal globidontans and other crocodylians. Turcosuchus okani is one of the earliest, but not basal hylaeochampsids, and the first known Early Cretaceous eusuchian outside Europe and North America. Our results support the clear geographical segregation between the Late Cretaceous tribodont eusuchians: basal globidontans in North America, and hylaeochampsids in the Tethyan area. http://zoobank.org/urn:lsid:zoobank.org:pub:7071FA88-2C3D-4814-8649-4ADB581E190A
A Brief Overview of Folksonomy and its applications

To express instant gratification, tagging has become easily available tool on social networking sites. Recently, it has gained popularity on the web as it doesn't require any special skill to master the art of tagging. When an individual tags a post or the user meta-data are accumulated together, it forms a collaborative tagging system. These systems allow users to create and share data, generally in the form of sets of at least three elements, namely tags, users and resources. The totality of these sets, accumulated around any resource, results into classification called Folksonomy. The classification that has emerged from Folksonomy considers not only similarity of the posted tags by the users, but also implicit user preferences and interests. This paper explores Folksonomy and its applications.
Nonlinear Absorption Measurements of Aza-Borondipyrromethene Dyes by the Z-Scan Method

We studied the effects of bromine substitution on the nonlinear absorption properties of aza-dipyrromethene dyes. Nonlinear absorption is measured at wavelengths of 1200, 1500, and 1700nm At 1200nm, excited-state absorption due to two-photon excitation appears, and it is more pronounced in the brominated polymethine cyanine.