Miracle-dz/UniFAR-FTUs huggingface dataset:
Abstract 2445: Pan-cancer analysis of tumor microenvironment using deep learning-based cancer stroma and immune profiling in H&E images

Introduction: Tumor purity and deconvolution of cell subsets in tumor environments has been developed based on DNA sequencing data or gene expression profiles. We have developed the artificial intelligence named Lunit SCOPE, identifying and quantifying various histologic components using deep learning from HE 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2445.
S07.3 Challenges in defining Chemsex. Answers for surveillance from EMIS-2017

Sexualised drug use (SDU), the use of drugs in a sexual context, has emerged as a marker of sexual activity with high risk for transmission of HIV and other STIs, and for poor sexual health, particularly among men who have sex with men (MSM). However, there are no robust estimates of the prevalence of SDU. Using data from the 2010 European MSM Internet Survey (EMIS-2010) we have compared illicit drug use from 44 cities and found substantial variance across Europe. In a repeat of EMIS in 2017, we replicated the questions on illicit drug use, and added questions on injecting drugs and combining sex and drugs. EMIS-2017 was online and collecting data in 33 languages across 50 countries from 10/2017 to 01/2018. In this talk, I will give an overview on the prevalence of sexualised drug use in Europe and Canada, based on data collected in EMIS-2017. I will compare the four different ways EMIS-2017 queried SDU, and demonstrate how SDU differs accross 15 selected cities: Amsterdam, Barcelona, Berlin, Brussels, Istanbul, London, Moscow, Paris, Prague, Stockholm, Tel Aviv, Toronto, Vancouver, Warsaw, and Zurich.
Yield Gap Analysis between Dry and Wet Season Rice Crop Grown under High‐Yielding Management Conditions

Rice (Oryza sativa L.) grain yield highly varies depending on cropping seasons under the tropical irrigated conditions. This study aimed to (i) compare the grain yield of rice in dry season (DS) and wet season (WS) and (ii) determine climatic and physiological factors critical to the yield gap between DS and WS. Six genotypes, two each for indica inbred, indica/indica F 1 hybrid, and the second-generation new plant type, were grown in DS and WS of 2003 and 2004. Significantly higher grain yields were achieved in DS than in WS by 94% for 2003 and 35% for 2004. Mean daily radiation was higher in DS than WS, particularly during grain filling stage than before flowering. The greater radiation during ripening in DS contributed to the higher grain yield. Major difference in biomass production between DS and WS occurred after flowering. Greater biomass accumulation from flowering to physiological maturity was associated with higher grain yield in DS than in WS, but not translocation of biomass accumulated before flowering to grains. Higher grain yield in DS was partly the result of greater spikelets due to higher spikelet production efficiency per unit biomass at flowering. Aboveground total biomass at physiological maturity was a crucial physiological factor to the yield gap between DS and WS. Daily mean radiation and biomass accumulation during ripening, and sink production efficiency per unit biomass were critical factors to the yield gap of rice between DS and WS under the high-yielding tropical irrigated conditions.
Characterization of 28 microsatellite loci for the butterfly Bicyclus anynana

We present 28 polymorphic microsatellite loci, including a sex-linked W-chromosome marker, for the Afrotropical butterfly, Bicyclus anynana. Our primary motivation to develop these markers was to apply them in quantitative trait loci (QTL) mapping studies. A technique is also proposed that may be useful in avoiding redundant sequences which are common in lepidopteran-enriched libraries. Pedigree analysis was performed to test Mendelian segregation of the markers and to address the issue of null alleles.
Enhancement of pyrene mineralization in soil by wood‐decaying fungi

The mineralization of [14C]pyrene in sterilized and non-sterile soil was investigated using the wood-decaying fungi Kuehneromyces mutabilis and Agrocybe aegerita in a period of 63 days. In sterilized soil 5.1% and 1.5% of the pyrene was mineralized to 14CO2 by K. mutabilis and by A. aegerita, respectively. In non-sterile soil, 27.3% of pyrene was mineralized by indigenous soil microflora including a Mycobacterium gilvum strain. During soil inoculation with fungi the mineralization was higher (47.7% for K. mutabilis and 38.5% for A. aegerita). For a mass balance analysis the soil was extracted with toluene and methanolic KOH (humic acid extraction). Considering the sum of mineralization and formation of bound residues (non-extractable radioactivity), about 50% (sterilized soil) and 75% (non-sterile soil) of pyrene were eliminated by K. mutabilis. In comparison with indigenous soil microflora, K. mutabilis enhanced pyrene elimination up to 42%.
A simple laboratory class using a Pseudomonas aeruginosa auxotroph to illustrate UV-mutagenic killing, DNA photorepair and mutagenic DNA repair

A simple and cheap laboratory class is proposed to illustrate the lethal effect of UV radiation on bacteria and the operation of different DNA repair mechanisms. The class is divided into two sessions, an initial 3-hour experimental session and a second 2-hour analytical session. The experimental session involves two separate experiments: one dedicated to illustrating the lethal effect of UV radiation and the protective effect of DNA photorepair; the second to explore the operation of DNA repair mechanisms that prioritise survival but introduce mutations. The procedure makes use of a Pseudomonas aeruginosa double auxotroph, which serves to detect UV-induced back-mutations to prototrophy. The proposed scheme is carried out by undergraduate students of the Bacterial Physiology and Genetics course, as part of our Biotechnology curriculum. We think that it will be a valuable tool for microbiology students to increase their understanding of basic genetic concepts.
Abstract LB-205: A lipoplex-based mRNA nanovaccine for cancer immunotherapy

Intracellular delivery of messenger RNA (mRNA)-based cancer vaccines have shown great potential to activate antitumor immune response for cancer prevention and therapy. In vivo delivery efficiency of mRNA has been greatly improved by various nucleotide chemical modifications and nanovector formulations, but the efficacy of mRNA vaccine remains unsatisfied. Here, we report a lipoplex-based mRNA nanovaccine that can markedly improve mRNA delivery in antigen presenting cells, activate T cell response, and induce robust antitumor immunity. The nanovaccine formulation contains three components: cationic polymer/lipid(poly(amidoamine)/alkylene oxide), DSPE-PEG2000, and epitope-encoding mRNA. With appropriate ratio, the optimized nanovaccine show effective mRNA delivery in dendritic cells, and strongly active antigen-specific immune response in vitro and in vivo. The mRNA@lipoplex nanovaccine enhanced mRNA uptake by dendritic cells, and significantly increased T cell activation reflected by IL-2 and IFN-γsecretion in an in vitro antigen presentation assay. Besides enhancing cross-presentation, nanoparticle itself can promote the expression of inflammatory cytokines such as IL-12 via stimulating NF-κB signal pathway in dendritic cells. In a tumor prevention setting, mRNA@lipoplex nanovaccine produced strong CD8+ T cell activation and great efficacy in preventing tumor development. Furthermore, treatment of established B16 and B16-OVA melanoma and MC38-OVA colon tumors with nanovaccine containing mRNA encoding cancer-associated antigen resulted in great therapeutic efficacy and prolonged survival. Re-challenge of tumor-free mice with MC38-OVA cells led to complete tumor rejection, suggesting long-term antitumor memory. In conclusion, our work presents a new means to deliver mRNA cancer vaccine, which in principle may be applied for immunotherapy for a wide range of tumor types. Citation Format: Zhang Hongxia, You Xinru, Wang Xiaojuan, Wang Zining, Xu Feifei, Wu Jun, Xia Xiaojun. A lipoplex-based mRNA nanovaccine for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-205.
Progress and outlook for the control of nivalenol and deoxynivalenol contamination due to Fusarium head blight in wheat

Use of appropriate fungicides is most effective and reliable practice to control Fusarium head blight (FHB). Therefore, re-evaluation of registered fungicides and screening new candidates for control of mycotoxin contamination are considered mandatory. We found that seven chemicals; metoconazole, tebuconazole, captan, thiofanate-methyl, oxine-copper, copper-hydroxide and phosphorous acid would control deoxynivalenol (DON) and nivalenol (NIV). On the contrary, treatment of azoxystrobin significantly increased the level of DON and NIV compared to the control plots, even though it reduced disease severity of FHB. We propose that new fungicide evaluation system based on efficacy for mycotoxin contamination should be introduced. In order to develop effective strategies for controlling the risk of toxin contamination, we investigated the manner in which toxin accumulation occurs in grain. The results indicated (i) high levels of DON and NIV can be produced beyond 20 days after anthesis (DAA) even by early infection, and (ii) infection at a late stage, at least as late as 20 DAA, can cause grain contamination with these toxins. Thus, developing control strategies that cover the late stage as well as the early stage would be desirable to reduce the risk of toxin contamination in wheat.
Helminth parasites of Clarias gariepinus (Teugels) in Zaria, Nigeria

A total of 240 Clarias gariepinus (Teugels) were randomly purchased from fish landings in Sabon-gari market, Zaria. The fish were examined parasitologically for gastrointestinal parasites. Five species of helminth parasites comprising 3 cestodes, 1 nematode and 1 acanthocephala were isolated from the fish. The cestodes and their prevalence were Anomotaenia sp. (2.5%), Monobothrium sp. (13.33%) and Polyonchobothrium clariae (1.67%). The nematode, Procamallanus laevionchus and the acanthocephalan, Neoechinorhynchus rutili had a prevalence of 0.83% and 0.83% respectively. Majority of the parasites were found in the intestine. Infection was limited to fish with length ranging from 30.0 – 39.9 cm (prevalence: 15.83%; mean intensity: 3.78) and 40.0 – 49.9 cm (prevalence: 3.33%; mean intensity: 2.5) Fish specimens that were lighter in weight (150.0 – 299.9 g) were free of infection, but those found with parasites weighed between 350.0 – 399.0 g (prevalence, 7.5%) and 450.0 – 500.0 g (prevalence 6.67%). There was no statistically significant difference (P > 0.05) in the infection of the male and female C. gariepinus . The study highlights the importance of changing feeding habit of C. gariepinus with age on the prevalence and intensity of gastrointestinal parasites, and parasitised male fish have lower condition factor than unparasitised ones. Key Words: Helminth, parasites, Clarias gariepinus, Zaria. Journal of Aquatic Sciences Vol.19(2) 2004: 71-76
Can an Ecoregion Serve as a Seed Transfer Zone? Evidence from a Common Garden Study with Five Native Species

Prairie restoration is often limited by the availability of appropriate local plant materials. Use of locally adapted seed is a goal in restoration, yet little information to inform seed transfer guidelines is available for native plant species. We established common gardens of five plants (Eriophyllum lanatum var. leucophyllum, Epilobium densiflorum, Potentilla gracilis var. gracilis, Lupinus polyphyllus var. polyphyllus, and Saxifraga oregana) frequently used in prairie restoration in the Pacific Northwest of North America to determine if populations differed in morphological and phenological traits and whether this variability was structured by geography, climate, or habitat. Ordination techniques were used to summarize the observed variability of multiple traits for each species. Ordination distance was significantly correlated with geographic distance in L. polyphyllus var. polyphyllus, and populations of this species differed significantly among geographic groups within an ecoregion. Little or no spatial structure was detected in the remaining species, despite correlations between ordination scores and monthly temperatures. We suggest that a single seed zone in the Willamette Valley ecoregion may be appropriate for all species examined except L. polyphyllus var. polyphyllus. Ecoregions in general may be useful boundaries for seed transfer zones, especially in regions with relatively little topographical or climatic variation.
Data-Driven Locomotive Strategies of the UVMS Propelled by Undulating Fins

This paper addresses a data-driven locomotive strategy of an underwater vehicle-manipulator system (UVMS). Two modular designed biomimetic underwater propellers are deployed on the UVMS. Each propeller has a ribbon fin that consists of twelve rays linked by a thin latex membrane. Each ray is individually actuated. By distributing all rays in phases of undulating patterns, different form of waves can be generated from the propeller. A measurement platform is constructed to obtain the horizontal and vertical force generated by the waves of the undulating fin. The current in main circuit of the propeller is also measured. The measured data are calculated into five output results. Three types of waves are performed on the platform, including sinusoidal waves, fusiform sinusoidal waves and inward counter-propagating sinusoidal waves. Output results are varied by parameters of undulating patterns. By diversifying parameters of undulating patterns, multiple waves are carried out and their output results are obtained. With these data, a locomotive strategy for the UVMS is established. The strategy is to select the output results of the two propellers by optimization methods to meet the requirements of the UVMS on standards of driving force, stability and power consumption. With this strategy, two biomimetic propellers can perform suitable undulating patterns when the UVMS is required to implement certain locomotions.
Larval stage controls on Pacific sardine recruitment variability: high zooplankton abundance linked to poor reproductive success

Sardines inhabit some of the most highly productive areas of the ocean (upwelling areas). Despite this, those in the eastern Pacific appear to thrive during warm years characterized by low productivity. Among the explanations for the apparent sardine success during warm years are: (1) lowered predation pressure and (2) access to waters with higher food availability. We examine zooplankton abundance in the sardine Sardinops sagax larval habitat off the coast of southern Cali- fornia. According to our results, increased food availability (represented here by zooplankton abun- dance) cannot alone explain successful sardine year classes. It appears that zooplankton abundance may also be an index of predation pressure on larval stages, combining potential effects of (1) direct predation by zooplankton predators and (2) increased attraction of zooplanktivorus nekton. Accord- ingly, decreased predation pressure during warm years may be a major factor allowing bursts in sardine recruitment. These results suggest a need for modification of the traditional rather linear view of food web energy transfers. This view may neglect potential nonlinear feedbacks introduced in the food web by mortalities on the early life stages of higher trophic level organisms inflicted or mediated by lower trophic level organisms.
Changes in the quantity and composition of mammary gland secretion in the dry period between lactations. II. The complete dry period

Summary The changes in yield and composition of mammary gland secretion throughout the whole of the dry period have been investigated in 6 cows. The yields of lactose, potassium, fat and casein decreased to very low values for the greater part of the dry period but then increased slightly just before parturition. Similar trends were observed for sodium and chloride but they were much less marked. During the middle of the dry period the concentrations of sodium, potassium and chloride tended towards those of blood serum while the concentrations of fat and lactose decreased to < 1%.
What is in a “Cup of Joe”? From green beans to spent grounds: a mini-review on coffee composition and health benefits

Coffee is one of the most popular beverages consumed worldwide and is amongst the main dietary sources of bioactive compounds. Recent studies have described a positive association between caffeine ingestion and health, including improvement of exercise performance and enhancement of long-term memories in humans. However, from roasting to extraction, the processing of the coffee beans has a significant impact on the profile of bioactive compounds. For instance, roasting results on the reduction of 5-caffeoylquinic acid and trigonelline, while increases the concentration of melanoidins. Another important component is its lipid fraction (known as coffee oil), which can migrate to the surface of the beans and undergo changes in its composition during roasting. This mini-review presents an overview of the composition of coffee, including changes that occur during processing—from green beans to spent grounds, and recent research on its health benefits, with special focus on their antioxidant properties.
Migratory behaviour of Skeletonema grethae (Bacillariophyceae) in stratified waters

Even though Skeletonema spp. are among the most important primary producers of the world oceans, little is known about their migratory behaviour and buoyancy properties. Here, we present results obtained from experiments on S. grethae in an artificial, salinity-stratified water column. Beforehand, growth experiments were conducted to find out how S. grethae responded to the set of environmental parameters being used in the water column. The highest growth rates were obtained for a salinity range of 25–35 psu, and an irradiance range of 60–330 μ mol quanta m−2 s−1 (1.3–1.9 div d−1). Inoculum populations were introduced in the upper brackish layer in Experiment 1 (E1) and in the bottom layer in Experiment 2 (E2). During the experiments, the cell/colonies assumed different forms; in E1 they became long and thin with short and weakly silicified connecting processes between them, whereas in E2 there were only minor changes in form and cells looked more like the ‘normal type’, shorter with longer, more heavily silicified connecting processes. In addition, with respect to the buoyancy, subgroups developed, part of the population became ‘floaters’ and part became ‘descenders’, whereas others did not move at all. Such flexibility in migratory behaviour could be an advantage for survival and successful expansion into new areas. It also indicates that there is a phenotypic plasticity in Skeletonema morphology that seems to influence the floating properties of the cells. Long cells remained buoyant for ten days and short cells for more than 17 days. The presence of a strong halocline has a great impact on the vertical displacement of cells/colonies, as revealed by a halt in the ascent/descent of cells within or just below it, resulting in biomass accumulation at these sites. Based on our data nitrate availability could also be involved in the buoyancy control of S. grethae.
Daily Dynamics of Nutrients and Chlorophyll a during a Spring Phytoplankton Bloom in Xiangxi Bay of the Three Gorges Reservoir

ABSTRACT We studied the daily dynamics of nutrients (total phosphorus [TP], total nitrogen [TN], and dissolved silicate [SiO2]) and chlorophyll a (chl a) during a spring bloom in Xiangxi Bay of the Three Gorges Reservoir in year 2005. According to the daily dynamics of chl a, the bloom occurred in two stages (23 February–25 March and 26 March–28 April). The concentration of SiO2 decreased at different layers of the water column with the development of the bloom. However, the decrease of SiO2 in the layers with high concentration of chl a was more dramatic than in the layers with low concentration of chl a. The concentration of TP was lowest value a few days after the peak of chl a during the first bloom period, and the lowest value of TN was found a few days after the peak of chl a during the second bloom period. Correlative analyses indicated that SiO2 and TP were limiting factors in the first bloom period, and SiO2 and TN were limiting factors in the second bloom period.
Some Toxic Constituents of Chlorination-Stage Effluents from Bleached Kraft Pulp Mills

Constituents responsible for the toxicity of a sample of bleached kraft chlorination-stage effluent to juvenile rainbow trout (Salmo gairdneri) were investigated. Tetrachlorocatechol, 3,4,5-trichlorocatechol, and 2,6-dichlorohydroquinone were identified and evidence was obtained for the presence of other chlorodihydroxybenzenes in toxic acidic fractions of the sample. Concentrations of 0.46 mg/L 3,4,5-trichloro- and 0.74 mg/L tetrachloro-catechol were estimated in the sample by analytical gas chromatography. Toxic materials in the nonacidic fraction were not identified although the nontoxic dichloromethyl methyl sulfone was isolated.Key words: chlorination-stage effluent, toxicity, pulp mill, chlorocatechols, chlorodihydroxybenzenes
Substantial differences in littoral fish community structure and dynamics in subtropical and temperate shallow lakes

Summary 1. Fish play a key role in the functioning of temperate shallow lakes by affecting nutrient exchange among habitats as well as lake trophic structure and dynamics. These processes are, in turn, strongly influenced by the abundance of submerged macrophytes, because piscivorous fish are often abundant at high macrophyte density. Whether this applies to warmer climates as well is virtually unknown. 2. To compare fish community structure and dynamics in plant beds between subtropical and temperate shallow lakes we conducted experiments with artificial submerged and free-floating plant beds in a set of 10 shallow lakes in Uruguay (30°–35°S) and Denmark (55°–57°N), paired along a gradient of limnological characteristics. 3. The differences between regions were more pronounced than differences attributable to trophic state. The subtropical littoral fish communities were characterised by higher species richness, higher densities, higher biomass, higher trophic diversity (with predominance of omnivores and lack of true piscivores) and smaller body size than in the comparable temperate lakes. On average, fish densities were 93 ind. m−2 (±10 SE) in the subtropical and 10 ind. m−2 (±2 SE) in the temperate lakes. We found a twofold higher total fish biomass per unit of total phosphorus in the subtropical than in the temperate lakes, and as fish size is smaller in the former, the implication is that more energy reaches the littoral zone fish community of the warmer lakes. 4. Plant architecture affected the spatial distribution of fish within each climate zone. Thus, in the temperate zone fish exhibited higher densities among the artificial free-floating plants while subtropical fish were denser in the artificial submerged plant beds. These patterns appeared in most lakes, regardless of water turbidity or trophic state. 5. The subtropical littoral fish communities resembled the fish communities typically occurring in temperate eutrophic and hypertrophic lakes. Our results add to the growing evidence that climate warming may lead to more complex and omnivory-dominated food webs and higher density and dominance of smaller-sized fish. This type of community structure may lead to a weakening of the trophic cascading effects commonly observed in temperate shallow lakes and a higher risk of eutrophication.