Miracle-dz/UniFAR-FTUs huggingface dataset:
Acetylation of Stat1 modulates NF-B activity

Acetylation of signaling molecules can lead to apoptosis or differentiation of carcinoma cells. The molecular mechanisms underlying these processes and the biological role of enzymes mediating the transfer or removal of an acetyl-group are currently under intense investigation. Our study shows that Stat1 is an acetylated protein. Stat1 acetylation depends on the balance between Stat1-associated histone deacetylases (HDACs) and histone acetyltransferases (HATs) such as CBP. Remarkably both inhibitors of HDACs and the cytokine interferon α alter this equilibrium and induce Stat1 acetylation. The analysis of Stat1 mutants reveals Lys 410 and Lys 413 as acetylation sites. Experiments with Stat1 mutants mimicking either constitutively acetylated or nonacetylated states show that only acetylated Stat1 is able to interact with NF-κB p65. As a consequence, p65 DNA binding, nuclear localization, and expression of anti-apoptotic NF-κB target genes decrease. These findings show how the acetylation of Stat1 regulates NF-κB activity and thus ultimately apoptosis.
Modelling cadmium accumulation by benthic invertebrates in situ: The relative contributions of sediment and overlying water reservoirs to organism cadmium concentrations

An in situ experiment was designed (1) to determine the relative importance of Cd in the sediment versus Cd in the overlying water for its accumulation in benthic animals and (2) to test in situ the acid volatile sulfide (AVS) model. Sediments of a low‐Cd shield lake were artificially contaminated with various amounts of Cd and placed at a littoral site in open plastic containers in the lake bottom for 11 months to allow colonization by indigenous lake bcnthos. Gradients in sedimentary and interstitial water Cd concentrations were, thus, created in situ, although Cd concentrations in the overlying water remained low. Accumulation of Cd by benthic invertebrates was significantly and linearly correlated with sediment Cd concentrations across treatment levels for most taxa. The magnitude of the response to the sediment Cd gradient was taxon specific and consistent with differences in animal ecology. Despite the high Cd contamination levels attained in the experiment, the population densities of most taxa appear to have been unaffected by the presence of Cd. We used the results from the experimental containers to predict the sources of Cd for benthic animals in the environs. For almost all of the taxa studied, individuals living in the low‐Cd sediments outside the experimental containers accumulated their Cd almost exclusively from the overlying water; only the burrowing, sediment‐feeding taxa Chironomus stuegeri and members of the Tubificidae obtained substantial Cd from the sediment. Cadmium activities in the pore waters of the containers were in agreement with the AVS model, but the Cd concentrations found in the benlhic organisms did not. Our results from this shield lake suggest that predictions of Cd concentrations in most benthic animals would be more accurate if they were based on water column rather than on sedimentary Cd concentrations.
Plantain-derived Diploid Hybrids (TMP2x) with Black Sigatoka Resistance

Plantain (Musa spp., AAB group), a triploid (2n = 3x = 33) giant perennial herb of the tropics, is a natural interspecific hybrid between the two wild banana species M. acuminata Colla. and M. balbisiana Colla. These diploid species contributed the A and B genomes, respectively (Simmonds, 1962). Triploidy makes plantain crossbreeding difficult but not impossible (Swennen and Vuylsteke, 1993). As such, plantain progenies were obtained when triploid plantains were crossed with diploid M. acuminata clones (Vuylsteke et al., 1993c). Genetic improvement of plantain is required because its sustainable production is threatened by increasing disease and pest pressure (Vuylsteke et al., 1993b). One of the major constraints is the black sigatoka leaf spot disease (Mycosphaerella fijiensis Morelet), which causes yield losses of at least 33% (Mobambo et al., 1993). Production and cultivation of resistant cultivars are generally considered the most appropriate means to control the disease. The International Institute of Tropical Agriculture (IITA) targets the development of improved plantain germplasm. So far, 14 improved plantain-derived tetraploid (4x) hybrids with black sigatoka resistance have been selected for multilocational testing and further cultivar release by national agricultural research programs (Vuylsteke et al., 1993d). In addition to the tetraploid hybrids, progenies with other ploidies were also recovered from the 3x x 2x crosses, diploids (2x) being most numerous (Vuylsteke et al., 1993c). Plantainderived diploids play an important role in
A Recommender System Based on Cohorts' Similarity

Aiming to better understand the genetic and environmental associations of Alzheimer's disease, many clinical trials and scientific studies have been conducted. However, these studies are often based on a small number of participants. To address this limitation, there is an increasing demand of multi-cohorts studies, which can provide higher statistical power and clinical evidence. However, this data integration implies dealing with the diversity of cohorts structures and the wide variability of concepts. Moreover, discovering similar cohorts to extend a running study is typically a demanding task. In this paper, we present a recommendation system to allow finding similar cohorts based on profile interests. The method uses collaborative filtering mixed with context-based retrieval techniques to find relevant cohorts on scientific literature about Alzheimer's diseases. The method was validated in a set of 62 cohorts.
Early detection of skeletal muscle bioenergetic deficit by magnetic resonance spectroscopy in cigarette smoke-exposed mice

Skeletal muscle dysfunction is a common complication and an important prognostic factor in patients with chronic obstructive pulmonary disease (COPD). It is associated with intrinsic muscular abnormalities of the lower extremities, but it is not known whether there is an easy way to predict its presence. Using a mouse model of chronic cigarette smoke exposure, we tested the hypothesis that magnetic resonance spectroscopy allows us to detect muscle bioenergetic deficit in early stages of lung disease. We employed this technique to evaluate the synthesis rate of adenosine triphosphate (ATP) and characterize concomitant mitochondrial dynamics patterns in the gastrocnemius muscle of emphysematous mice. The fibers type composition and citrate synthase (CtS) and cytochrome c oxidase subunit IV (COX4) enzymatic activities were evaluated. We found that the rate of ATP synthesis was reduced in the distal skeletal muscle of mice exposed to cigarette smoke. Emphysematous mice showed a significant reduction in body weight gain, in the cross-sectional area of the total fiber and in the COX4 to CtS activity ratio, due to a significant increase in CtS activity of the gastrocnemius muscle. Taken together, these data support the hypothesis that in the early stage of lung disease, we can detect a decrease in ATP synthesis in skeletal muscle, partly caused by high oxidative mitochondrial enzyme activity. These findings may be relevant to predict the presence of skeletal bioenergetic deficit in the early stage of lung disease besides placing the mitochondria as a potential therapeutic target for the treatment of COPD comorbidities.
Too Cute to Kill? The Need for Objective Measurements of Quality of Life

Simple Summary Animal welfare is affected by how people think we should treat animals, and what people think is important affects the way they treat animals. The way people think about their animals is affected by how cute they perceive them to be. Animal welfare affects quality of life, which is about how sentient animals experience their lives, and understanding this requires animal welfare science. Ethics weighs that scientific knowledge with human desires (e.g., to earn a living by farming, to keep an animal as a companion, to clear land and build houses), so we decide how we should treat animals. The decisions that society has reached using science and ethical reasoning about how we ought to treat animals are reflected in animal welfare law. However, animal welfare law may often set a low standard of care, as there is little public money to enforce higher standards or the public is not aware of the welfare problems. The first step in ensuring a good quality of life is to measure welfare and then take action to improve it. Abstract The recognition of animal suffering is influenced by cultural and societal prejudices and the cuteness of an animal leads to bias in the way it is treated. It is important to consider the animal’s behaviour and its environment—not just its physical condition—when assessing its quality of life. The Animal Welfare Assessment Grid (AWAG) is a useful tool for this purpose. The AWAG offers an evidence-based tool for continual welfare assessment, using technology where appropriate, such as digital activity recording, to facilitate decision-making and lead to improvements in the animals’ quality of life. It is highly adaptable to any species by assessing the four parameters of physical health, psychological wellbeing, environmental quality, and clinical and management procedural events. The outcome of assessing welfare should be action to improve it. Societal ethics and policy-making lead to legislation balancing the values we hold for different species. Influencing policy development in such matters as animal welfare, ecological conservation, and risks to humans requires a focus on public attitudes to, and understanding of, science, as well as consideration of potential unforeseen consequences of the social/environmental/economic impacts of policies.
The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa

Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We investigated the characteristics of P. aeruginosa clinical strains naturally resistant to phages and compared them to highly susceptible strains. The phage-resistant strains were defective in lipopolysaccharide (LPS) biosynthesis, were nonmotile and displayed an important degree of autolysis, releasing phages and pyocins. Complete genome sequencing of three resistant strains showed the existence of a large accessory genome made of multiple insertion elements, genomic islands, pyocins and prophages, including two phages performing lateral transduction. Mutations were found in genes responsible for the synthesis of LPS and/or type IV pilus, the major receptors for most phages. CRISPR-Cas systems appeared to be absent or inactive in phage-resistant strains, confirming that they do not play a role in the resistance to lytic phages but control the insertion of exogenous sequences. We show that, despite their apparent weakness, the multiphage-resistant strains described in this study displayed selective advantages through the possession of various functions, including weapons to eliminate other strains of the same or closely related species.
Ribosomal internal transcribed spacer regions are not suitable for intra- or inter-specific phylogeny reconstruction in haplosclerid sponges (Porifera: Demospongiae)

Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equivalent, and sequences from multiple clones from a number of individuals of a single species could not be separated on phylogenetic trees. As a result, the ITS regions are not suitable markers for population level studies in marine haplosclerids. Sequences of these regions were highly species specific, and large differences were found between species. ITS sequences from three Callyspongia and three Haliclona species could not be aligned successfully and therefore this locus could not be used to investigate relationships between these putative close relatives. However, ITS sequences retrieved from one H. cinerea were very different from sequences generated from other H. cinerea individuals indicating that this species comprises more than one taxon.
Propofol improves intestinal ischemia-reperfusion injury in rats through NF-κB pathway.

OBJECTIVE The aim of this study was to investigate the effects of propofol on intestinal ischemia-reperfusion injury in rats through the nuclear factor-kappa B (NF-κB) pathway. MATERIALS AND METHODS A total of 24 Sprague-Dawley rats were selected and randomly divided into three groups, including sham operation group, ischemia group and propofol group. Rats in sham operation group were only treated with isolation of superior mesenteric artery, which was clipped for 1 h and reperfused for 2 h in ischemia group. Meanwhile, propofol (60 mg/kg) was injected into the femoral vein 1 h before ischemia in propofol group. TUNEL assay was performed to detect cell apoptosis of intestinal tissues. Real-time quantitative polymerase chain reaction (RT-qPCR) was conducted to measure the expression levels of malondialdehyde (MDA), superoxide dismutase (SOD), myeloperoxidase (MPO), caspase-3 and B-cell lymphoma-2 (Bcl-2) in rats of each group. Western blotting was utilized to detect the protein expression levels of NF-κB pathway related molecules, such as myeloid differential protein-88 (MyD88), v-rel avian reticuloendotheliosis viral oncogene homolog A (RelA) and NF-κB. Furthermore, changes in plasma cytokine levels were determined via enzyme-linked immunosorbent assay (ELISA). RESULTS The number of apoptotic cells in ischemia group was remarkably higher than that in sham operation group (p<0.05). However, it decreased notably in propofol group compared with ischemia group (p<0.05). In comparison with sham operation group, significantly up-regulated expression of caspase-3 and down-regulated expression of Bcl-2 were observed in the intestinal tissues of rats in ischemia group (p<0.05). Caspase-3 was lowly expressed, while Bcl-2 was highly expressed in the intestinal tissues of rats in propofol group compared with ischemia group (p<0.05). In addition, no statistically significant differences were observed in the expression level of SOD among sham operation group, ischemia group and propofol group (p>0.05). The expression levels of MDA and MPO were overtly higher in the intestinal tissues of rats in ischemia group than those in sham operation group and propofol group (p<0.05). Besides, the protein expression levels of MyD88, RelA and NF-κB in the intestinal tissues of rats in ischemia group were remarkably higher than those in sham operation group and propofol group (p<0.05). The activity of the NF-κB pathway in the intestinal tissues of rats in propofol group significantly declined compared with ischemia group (p<0.05). Moreover, compared with sham operation group, plasma levels of TNF-α, interleukin (IL)-2, IL-6 and IL-4 increased significantly in rats of ischemia group (p<0.05). However, they were markedly lower in propofol group than those in ischemia group (p<0.05). CONCLUSIONS Propofol protects rats from intestinal ischemia-reperfusion injury through the NF-κB pathway.
Impact of fire on Picea mariana and Pinus banksiana seedlings in subarctic lichen woodlands

The demography of Picea mariana (black spruce) and Pinus banksiana (jack pine) seedlings was monitored through five censuses over 13 months in four different seed bed types after fire of four severity levels in lichen woodland. Most seeds germinated just before early frost in late summer 1990 or immediately after snow thaw in early spring 1991; the germination rate subsequently decreased. For both species, germination rate decreased along a gradient of fire severity. The proportion of Pinus seeds that produced a seedling surviving 13 months after sowing was 4.3 % and 0.4 % respectively in the intact lichen mat and in the mineral soil seed bed type. For Picea these values are 3.2 % and 0.2 % respectively. The low germination rate in a severely burned seed bed type appeared to be associated with the formation of a water-repellent crust at the soil surface following the fire. Seedlings were contagiously distributed and were more frequent in flat and hollow microsites, where there is probably more water available than on bumps or among pebbles. Properties of experimentally burned seed bed types may differ from those under natural fires where regeneration by seed generally occurs following dispersal. However, the high germination rate observed in the intact lichen mat suggests that scattered lichen woodland patches may respond to increased seed input by a higher frequency of seedling establishment.
Attitude and Barriers in Palliative Care and Advance Care Planning in Nonmalignant Chronic Lung Disease: Results From a Danish National Survey

Introduction: Patients with chronic obstructive pulmonary disease and interstitial lung disease have a significant burden of symptoms. Many are not offered palliative care (PC). Our aim was to investigate the attitudes to and barriers for PC among physicians. Method: A web-based survey was conducted among members of the Danish Respiratory Society. The questionnaire included contextual (gender, age, clinical experience, type of center, patient caseload) and outcome questions (knowledge and use of statements for PC and advance care planning [ACP], practice of communication about end-of-life decisions, practice for referral to PC, barriers regarding structural surroundings, clinical skills, and organization). Results: One hundred fifty-six (45%) physicians responded. Median age was 40 - 49 years and 55% were female. Fifty-two percent were specialists; 71% worked at a university hospital. The majority of physicians (60%) reported barriers for discussions about PC and ACP; 63% reported lack of time, 52% lack of multidisciplinary staff settings, 63% reported the unpredictability of the prognosis, and 20% insufficient awareness of patient’s culture, religion, or spirituality. Fewer specialists than nonspecialists reported barriers toward ACP. The majority had knowledge of guidelines in PC and ACP, but only a minority used these in daily clinical practice. Conclusion: The attitude toward PC and ACP conversations was positive and implementation was regarded as important, but only a minority performed these conversations in practice. Main barriers were lack of time and staff. Palliative care guidelines were known but only scarcely used. Structural changes at the organizational level to improve access to palliation for patients with nonmalignant chronic lung diseases are needed.
On the use of connectivity measures in spatial ecology

P 0 I I Opinion is intended to facilitate communication between reader and author and reader and reader. Comments, viewpoints or suggestions arising from published papers are welcome. N Discussion and debate about important issues in ecology, e.g. theory or terminology, may I I also be included. Contributions should be as precise as possible and references should be P 0 kept to a minimum. A summary is not required. O N
Relationships between daily, morning, evening and peak yield and persistency in Turkish Saanen goats

A matrix of persistency values is given instead of one value of persistency or persistency values based on succeeding test days. Overall, the persistency matrix of morning milk had higher values than the persistency matrix of evening milk. As the distance between the test days increased, the correlations dramatically decreased. The effects of morning milk yield b = 0.23 (P < 0.01) on standard deviation of morning and evening milk yield and on peak the milk yield was higher compared to the evening daily milk yield b = 0.03 (P = 0.05) and the total daily milk yield 0.10 (P < 0.01). Increased persistency means that the lactation curve may be flatter. Since the peak value of morning milk (1597 mL) was lower than evening milk (1799 mL), and morning milk was more persistent than evening milk, morning milk can be said to contribute more to the flatness of the lactation curve. Overall, the morning milk volume (938 mL) was larger than the evening milk volume (835 mL). A 3D plot of peak milk versus morning and evening milk yield indicated that increasing the evening milk yield increases the peak yield while the morning milk yield holds the peak value lower and the curve stable.
Positive indicators of cattle welfare and their applicability to on-farm protocols

Abstract Most of the research on animal welfare has focused on the negative aspects of the matter including an array of stress categories, whereas little has been done about the positive states of well being. The present study aims to describe indicators of positive animal welfare suitable for on-farm assessment. Appropriate environmental stimulation favours good welfare and, in an adequately enriched environment, positive indicators of welfare such as play behaviour tend to be more common. In addition, animals are motivated to perform these behaviours only if their primary needs are satisfied. In cattle, beneficial effects of social licking have been observed with positive correlation between being licked vs. milk production and weight gain, respectively. Ruminants are gregarious and a high degree of synchronisation within the herd may indicate a positive welfare state, in particular for subordinate animals. They may be able to meet their basic feeding and resting requirements performing these behaviours when the competition for a particular resource is low, however their welfare state would be improved if they could choose when and where (i.e. along with the other members of the group) to perform such behaviours. Due to the reduced applicability (mainly young animals), low feasibility (time consuming) and lack of research on reliability, play behaviour, albeit of proven validity, does not appear to be suitable for a rapid implementation in a welfare assessment scheme. Social licking is rarely expressed and its detection may be time consuming and scarcely feasible. Although validity and reliability need more studies, behaviour synchrony seems to be a promising positive welfare indicator as the instantaneous scan sampling technique makes this indicator easily applicable. Recently, a new methodology called “qualitative assessment of animal behaviour” has been developed. The method relies on a number of terms which are freely generated by observers. Thus, when positive aspects are observed they can be rated on a quantitative scale. Because of its high inter- and intra-observer reliability, this method appears to be the most promising.
Fungal Endophytes in Stems and Leaves: From Latent Pathogen to Mutualistic Symbiont

Endophytes are fungi that form inapparent infections within leaves and stems of healthy plants. Closely related to virulent pathogens but with limited, if any, pathogenic effects themselves, many endophytes protect host plants from natural enemies. Animal herbivores and, in some cases, pathogenic microbes are poisoned by the mycotoxins produced by endophytes. "Constitutive mutualism" is the relatively faithful association, usually with grasses, of endophytes that infect host ovules and are propagated in host seed; substantial fungal biomass with probable high metabolic cost develops throughout the aerial parts of the host plant. "Inducible mutualist" endophytes are not involved with host seed and disseminate independently through air or in water. Infecting only vegetative parts of the host and remaining metabolically inactive for long periods with relatively little fungal biomass, inducible mutualists grow rapidly and produce toxins against herbivores when damaged host tissues provide new sites for infection. I surmise that endophytes may be as common among plants as are mycorrhyzae.