Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological and Phylogenetic Studies of the Biogeography of Alkaliphilic Heterotrophic Bacteria from Serpentinizing Habitats

PHYSIOLOGICAL AND PHYLOGENETIC STUDIES OF THE BIOGEOGRAPHY OF ALKALIPHILIC HETEROTROPHIC BACTERIA FROM SERPENTINIZING HABITATS Alyssa N. Kloysuntia August 24, 2014 Director: Dr. Jeffrey McKinnon Department: Biology Serpentinization occurs when ultramafic rocks containing the mineral olivine react with water to produce highly reducing conditions, which are commonly coincident with high concentrations of hydrogen. Hydrogen provides an energy source for microbial metabolism and in combination with mineral catalysts can lead to the abiogenic synthesis of small organic compounds, such as methane. Serpentinite habitats contain abundant potential electron donors, but microorganisms presumably have limited accessibility to electron acceptors. A consequence of serpentinization is the production of highly alkaline (pH 10-12), highly reducing fluids. The stress exerted on microorganisms in such ecosystems can make fundamental cellular processes such as maintaining a proton motive force or stabilizing RNA a difficult task and limit microbial diversity in these environments. It is reputed that the microbial communities in these extreme habitats are able to adjust to the ultrabasic conditions through biochemical and metabolic adaptations. However, it remains to be discovered how microorganisms have physiologically adapted to the serpentinite environment.
Carotenoids of Sea Squirts. I. New Marine Carotenoids, Halocynthiaxanthin and Mytiloxanthinone from Halocynthia roretzi

New marine carotenoids, halocynthiaxanthin (4) and mytiloxanthinone (5), were isolated from the sea squirt, Halocynthia roretzi ("Maboya" in Japanese). The structures of 4 and 5 were established to be (3S, 5R, 6S, 3'R)-5, 6-epoxy-3, 3'-dihydroxy-7', 8'-didehydro-5, 6, 7, 8-tetrahydro-β, β-caroten-8-one and 3, 8'-dihydroxy-7, 8-didehydro-β, κ-carotene-3', 6'-dione, respectively.
Cationic Liposomes Extend the Immunostimulatory Effect of CpG ODN against 1

24 Melioidosis is a severe disease caused by the gram-negative bacterium 25 Burkholderia pseudomallei. Previously we showed that pretreatment of mice with CpG 26 ODN 2-10 days prior to B. pseudomallei challenge conferred as high as 90% protection, 27 but this window of protection was rather short. In the present study, we therefore aimed to 28 prolong this protective window and to gain further insight into the mechanisms underlying 29 the protection induced by CpG ODN against B. pseudomallei infection. It was found that 30 the CpG ODN incorporated with cationic liposomes (DOTAP) but not zwitterionic 31 liposomes (DOPC) provided complete protection against bacterial challenge. Although 32 marked elevation of IFN-γ was found in the infected animals 2 days post infection, it was 33 significantly lowered by the DOTAP+CpG ODN pretreatment. When appropriately 34 activated, the phagocytic index and oxidative burst responses of neutrophils appeared not 35 to be elevated. However, macrophages from stimulated mice showed higher levels of 36 nitric oxide production and exhibited higher levels of antimicrobial activities, judging 37 from lower numbers of viable intracellular bacteria. Taken together, our results 38 demonstrate that DOTAP can enhance the protective window period of CpG ODN to at 39 least 30 days and provide 100% protection against B. pseudomallei infection. The 40 protective effect of DOTAP+CpG ODN could provide an alternative approach to 41 preventing this lethal infection, for which no vaccine is yet available. 42
IN VITRO SCREENING OF TRICHODERMA SPECIES AGAINST MACROPHOMINA PHASEOLINA AND FUSARIUM OXYSPORUM F. SP. LYCOPERSICI

In vitro bioassays were carried out to evaluate antagonistic behavior of seven species of Trichoderma namely T. pseudokoningii , T. harzianum, T. reesei, T. koningii, T. hanatus, T. viridi and T. aureoviridi, against two highly problematic soil-borne plant pathogenic fungi viz. Fusarium oxysporum f. sp. lycopersici (Sacc.) Snyder & Hansn and Macrophomina phaseolina (Tassi) Goid . All the Trichoderma species exhibited pronounced antagonistic behavior against the target fungal pathogens in dual cultures resulting in 45–65% and 59–74% reduction in radial growth of M. phaseolina and F. oxysporum f. sp. lycopersici , respectively . T. harzianum was found to be the most effective biocontrol agent against both the fungal pathogens followed by T. aureoviridi and T. hanatus .
Comparative Study Regarding in Vitro Infections with Erwinia Amylovora and Pseudomonas Syringae Pv. Syringae on Pomaceae Species

Abstract The knowledge about pome fruit trees bacterioses and their evolution in orchards is a major objective for plant protection. Erwinia amylovora and Pseudomonas syringae pv. syringae cause on attacked organs of Pomaceae species similar dieback symptoms in vegetative and flowering shoots of quince, pear and apple in spring. Both bacteria can produce disastrous diseases in orchards and are therefore of great economic importance. Biological materials represented by vegetative shoots, leaves and fruits of Pyrus spp. , Malus spp. , Cydonia spp. were used after isolation of different E. amylovora and Ps. syringae pv. syringae strains for in vitro infections. Results presented in this study established that for in vitro inoculation of Pomaceae species similar symptoms in case of leaves and, respectively different symptoms for vegetative shoots and fruits occurred. The occurrence time was the only difference, because Ps. syringae pv. syringae spread faster than E. amylovora. The vegetative shoots inoculated with E. amylovora, in comparison to Ps. syringae pv. syringae, were more damaged and for both bacteria the highest values for attack degree were recorded in case of pear species, followed by quince and apples, respectively.
Pharmacological Prevention of Postoperative Delirium: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

Background The high prevalence of delirium among postoperative patients has increased morbidity and mortality. The kind of drug that can effectively reduce the incidence of delirium has become the focus of discussion in recent years. However, a consensus in this respect has yet to be reached. Methods Randomized controlled trials (RCTs) were retrieved from the PubMed, Cochrane Library, ClinicalTrials.gov, and Embase databases from their inception through October 12, 2018. We included RCTs of pharmacological prevention for postoperative delirium in adults (at least 18 years), and the Cochrane risk of bias tool was used to evaluate the methodological quality of trials. The primary outcomes were the risk ratios (RRs) of incidence of postoperative delirium, and the secondary outcomes were the RRs of mortality and adverse events in the intervention and control groups. Results Thirty-eight trials, which comprised 20302 patients and 18 different drugs, were included in the analysis. Of the 38 studies, 17 were rated as low risk with respect to methodological quality. Dexmedetomidine administration (RR 0.58, 95%CI 0.44-0.76, P<0.01) was associated with a significantly lower incidence of postoperative delirium than the control conditions. However, the findings from the studies with a low risk of bias did not show a significant difference in this beneficial effect (RR 0.64, 95%CI 0.39-1.04, P=0.07). The antipsychotic drugs olanzapine (RR 0.44, 95%CI 0.30- 0.65, P<0.01) and risperidone (RR 0.42, 95%CI 0.19-0.92, P=0.03) had promising effects, but there was a lack of sufficient evidence to obtain a definitive conclusion. The beneficial effect of other drugs, including haloperidol, methylprednisolone, dexamethasone, gabapentin, ketamine, cyproheptadine, donepezil, hypertonic saline, melatonin, nimodipine, ondansetron, pregabalin, rivastigmine, TJ-54, and tryptophan, was not proven on the basis of present evidence. Conclusion Among the pharmacological prophylactic measures for postoperative delirium, dexmedetomidine, olanzapine, and risperidone showed higher efficacy than other drugs. However, more high-quality evidence is needed to confirm these results.
AN ESTIMATION OF THE NUMBER OF FOXES (VULPES VULPES) IN THE CITY OF BRISTOL, AND SOME POSSIBLE FACTORS AFFECTING THEIR DISTRIBUTION

(1) In two areas of Bristol, one 5.5 km2, the other 3.2 kM2, fox litter counts in two consecutive years were used to estimate the number of fox family groups. There were 3.64 family groups/km2 in the larger area, 3.13/km2 in the smaller. In parts of the larger area densities of 4-5 family groups/km2 were recorded. (2) To obtain data on the distribution and relative densities of foxes throughout Bristol, nearly 88 000 school children were asked to record fox sightings for a period of one month. Since the absolute fox densities were known for two areas, the distribution of recorded sightings could then be used to estimate fox densities throughout the city. By this means it was calculated that there were 211 fox family groups in an area of 116 sq km, a mean density of 1.82 fox family groups/km2. (3) Fox distribution in the city was uneven, and fox density was not found to correlate with household density, housing type, age of housing stock, or any other obvious habitat feature. There was a negative correlation (P < 0.001) between the distribution of stray dogs and urban foxes. This was attributed to disturbance of the fox population by stray dogs. It is suggested that disturbance may be particularly important in the breeding season; dogs were the second major cause of mortality in young fox cubs. (4) Based on post-mortem material, it was calculated that the ratio of breeding to non-breeding vixens was 1:0.35, and so the adult fox population consisted of 211 males, 211 breeding females and 74 barren females. Assuming that all fox family groups breed each year, with a mean birth litter size of 4.80 (calculated from placental scars), the annual cub production would be 1013.
ASSOCIATION BETWEEN THE LEVELS OF PHYSICAL ACTIVITY AND CARDIORESPIRATORY FITNESS AMONG SECURITY GUARDS

Background: Physical fitness is important in most high physically demanding jobs especially in the security services. It has to be ensured that the security guards are both physically fit for work, by matching their capabilities with the physical requirement for their job, and physically fit for life. Cardiorespiratory fitness has a strong relationship with physical activity. This study aims to explore the correlation that exists between physical activity and cardiorespiratory fitness among the security guards.
Effects of population density on horn development in bighorn rams

Trophy hunting is a management goal for many populations of ungulates and has important implications for conservation because of the economic value of trophy males. To determine whether population density affected horn growth of males, a marked population of bighorn sheep (Ovis canadensis) in Alberta, Canada, was studied for 27 years. For the first 9 years, population density was kept stable by removing adult females; afterwards, the numbers of ewes and yearlings tripled before beginning to decline. Horns were measured during repeated captures of marked rams. As the number of adult ewes and yearlings increased, ram horns were shorter and thinner because of decreased horn growth before 4 years of age. Some compensatory horn growth may have occurred at 5 years of age. The effects of population density on horn growth ceased when rams left the nursery groups to join all-male groups. Doubling of male numbers had no detectable effect on net annual horn growth of males ≥4 years old. Spring precipitation had no apparent effect on horn growth of males 3-4 years old, and had a minor positive effect on horn base circumference for rams 5-6 years old. The proportion of rams 6-7 years old that attained 4/5 of a curl decreased from 61-73% at low density to 33-35% at high density. When bighorn sheep populations increase to a density where intraspecific competition in nursery herds affects horn development of young rams, limited ewe harvests may prevent a decrease in size of horns of mature males.
Ruminal pH and N-NH3 behavior: a Bayesian approach

In this work, we present the Bayesian approach as an alternative to frequentist analysis regarding correlated data of pH and N-NH3 in the Holstein cow rumen. It was observed that for pH and N-NH3 data, a posteriori estimates of coefficients of the regression models were significant, which was not observed for least-squares estimates. Thus, the Bayesian approach allowed inferences that were directly linked to the sampling of parameters of interest and statistical comparisons of non-linear functions of the estimated parameters.
Amyloid aggregates accumulate in melanoma metastasis modulating YAP activity

Melanoma progression is generally associated with increased transcriptional activity mediated by the Yes‐associated protein (YAP). Mechanical signals from the extracellular matrix are sensed by YAP, which then activates the expression of proliferative genes, promoting melanoma progression and drug resistance. Which extracellular signals induce mechanotransduction, and how this is mediated, is not completely understood. Here, using secretome analyses, we reveal the extracellular accumulation of amyloidogenic proteins, i.e. premelanosome protein (PMEL), in metastatic melanoma, together with proteins that assist amyloid maturation into fibrils. We also confirm the accumulation of amyloid‐like aggregates, similar to those detected in Alzheimer disease, in metastatic cell lines, as well as in human melanoma biopsies. Mechanistically, beta‐secretase 2 (BACE2) regulates the maturation of these aggregates, which in turn induce YAP activity. We also demonstrate that recombinant PMEL fibrils are sufficient to induce mechanotransduction, triggering YAP signaling. Finally, we demonstrate that BACE inhibition affects cell proliferation and increases drug sensitivity, highlighting the importance of amyloids for melanoma survival, and the use of beta‐secretase inhibitors as potential therapeutic approach for metastatic melanoma.
Allelopathic Effects of Palmer Amaranth (Amaranthus palmeri) on Seedling Growth

Palmer amaranth (Amaranthus palmeri S. Wats. # AMAPA) residue was incorporated into soil to determine its allelopathic effects on the seedling growth of grain sorghum (Sorghum bicolor L. Moench.), cabbage (Brassica oleracea, var. capitata L.), carrot (Daucus carota L.), and onion (Allium cepa L.). Root and shoot growths were equally sensitive to the toxic effects of soil-incorporated Palmer amaranth. Growth of ‘Grand Slam’ cultivar of cabbage was 17 to 30% more sensitive than the growth of 'Sanibel’ cabbage. Growth of onion and carrot seedlings was less inhibited than either cabbage or grain sorghum. Growth of grain sorghum root was severely inhibited by 8000 and 16 000 ppm of Palmer amaranth in soil and was not affected by oven dryings other than lyophilization. Seedling growth was more severely inhibited by thyrsus and leaf tissues than by stem and root tissues of Palmer amaranth.
Biochemical characterization of CBF3, an essential DNA-binding component of the yeast kinetochore

The kinetochore is a structure composed of proteins and centromeric DNA that attaches chromosomes to microtubules of the mitotic spindle. Correct assembly of kinetochores is essential for accurate chromosome segregation during mitosis and meiosis. The centromere of Saccharomyces cerevisiae contains 125 base pairs of DNA organized into three conserved regions, CDEI, CDEII, and CDEIII. CDEIII is bound by CBF3, a complex of four essential proteins, p11 0 , p64, p58, and p23. Only p64 has a recognizable DNA-binding motif, a GAL4-like zinc cluster domain. The oligomeric states, approximate shapes, and subunit-subunit interactions among CBF3 proteins have been characterized using gel filtration chromatography and velocity sedimentation. p110 is an elongated homodimer, p64 is a globular homodimer, p23 is monomeric, and p23 and p58 form a stable heterodimer in solution. p58 binds to each of the other CBF3 components individually. While there is no evidence that other CBF3 proteins can interact in the absence of p58, p58 mediates an interaction between p64 and p1 10. These results suggest that p58 plays a central role in the assembly of CBF3 onto centromeric DNA and allow us to build a scale model of the CBF3-DNA complex. Thesis Supervisor: Peter K. Sorger Title: Howard and Linda Stern Assistant Professor of Biology
The progress in ecosystem services mapping: a review

Ecosystem services mapping has been becoming one of the forefronts in the field of ecosystem services researches. Ecosystems deliver bunches of vital services for human society,such as food,water provision and water purification,carbon sequestration,soil protection,and entertainment. The sustainable capability of ecosystems to provide these services is influenced by changes of biophysical condition( e. g. The changes in land use and land cover, biodiversity, atmospheric composition and climate) and human society( e. g. The changes of socio-economic characteristics,demand and consumptive patterns of human beings),which alter the correlation of demand and supply in ecosystem services through impacting the composition,structure,and processes of ecosystems.Ecosystem services mapping is a process that assesses the component,spatial distribution and mutual relationships of ecosystem services in specific spatial-temporal scales by using multiple mapping methods and multi-sources data. These series of spatially explicit maps not only reveal the quantitative characteristics of the current regional ecosystem service,but also exposit the potential changes caused by different environmental scenarios. These visualized mapping result can facilitate decision makers to integrate ecosystem services into environmental protection planning and implementing,and assist them to weigh the pros and cons of the possible environmental variable scenarios and the consequences of likely decisions,in addition,to make an informed decision which benefits the sustainable developmental of natural-human systems. In the past few years,the widespread use of GIS and availability of the high spatial and temporal resolution RS data sets have prominently promoted the capability of ecosystem services mapping. After reviewing the researches published recently,we identified and summarized that ecosystem services mapping is primarily focusing on:( 1) the mapping ofecosystem services supply which refers to the capacity of an given area to provide a specific bundle of ecosystem services within a particular time scale;( 2) the mapping of ecosystem services demand which is the sum of all ecosystem services consumed by people in a particular area and specific time period;( 3) and the mapping of the ecosystem services trade-offs and synergies,the former refers to the increment of one ecosystem service which is at the cost of the other ecosystem service,the latter means the synchronous variations among many different ecosystem services. Although there are lots of practical cases,ecosystem services mapping is still at its early stage. The core of ecosystem services mapping is a process about how to meet the needs of policy makers by using appropriate mapping methods,however,cautions must be mentioned in the broad use of mapping methods or models because they are scale-dependent and context-specific,and the mapping results need to be validated and verified against the observational data.
The Complete Sequence of the Mitochondrial Genome of the Chamberednautilus (Mollusca: Cephalopoda)

Background: Mitochondria contain small genomes that arephysically separate from those of nuclei. Their comparison serves as amodel system for understanding the processes of genome evolution.Although complete mitochondrial genome sequences have been reported formore than 600 animals, the taxonomic sampling is highly biased towardvertebrates and arthropods, leaving much of the diversity yetuncharacterized. Results: The mitochondrial genome of a cephalopodmollusk, the Chambered Nautilus, is 16,258 nts in length and 59.5 percentA+T, both values that are typical of animal mitochondrial genomes. Itcontains the 37 genes that are typical for animal mtDNAs, with 15 on oneDNA strand and 22 on the other. The arrangement of these genes can bederived from that of the distantly related Katharina tunicata (Mollusca:Polyplacophora) by a switch in position of two large blocks of genes andtranspositions of four tRNA genes. There is strong skew in thedistribution of nucleotides between the two strands. There are an unusualnumber of non-coding regions and their function, if any, is not known;however, several of these demark abrupt shifts in nucleotide skew,suggesting that they may play roles in transcription and/or replication.One of the non-coding regions contains multiple repeats of a tRNA-likesequence. Some of the tRNA genes appear to overlap on the same strand,but this could bemore » resolved if the polycistron were cleaved at thebeginning of the downstream gene, followed by polyadenylation of theproduct of the upstream gene to form a fully paired structure.Conclusions: Nautilus sp. mtDNA contains an expected gene content thathas experienced few rearrangements since the evolutionary split betweencephalopods and polyplacophorans. It contains an unusual number ofnon-coding regions, especially considering that these otherwise often aregenerated by the same processes that produce gene rearrangements. Thisappears to be yet another case where polyadenylation of mitochondrialtRNAs restores what would otherwise bean incompletestructure. « less
Seed bank dynamics in tall-tussock grasslands along an altitudinal gradient

Abstract We studied the germinable soil seed bank of tall-tussock grasslands along an altitudinal gradient in the mountains of central Argentina. We selected 10 sampling plots at three altitudinal levels (1200 m, 1600 m and 2200 m). We assessed the composition of the established vegetation and took ten compound soil samples (0 - 5 cm depth) at each plot in autumn and spring. The soil samples were sieved, chilled, and incubated in a glasshouse to assess the composition of the seed bank. The similarity between the composition of the seed bank flora and that of the established vegetation was low throughout the gradient. Most species did not change their seed bank strategy along the gradient. Seed bank richness and density increased with altitude. Most species had a persistent seed bank at all altitudinal levels, and the proportion of such species increased with altitude. These results suggest that a cold climate directly and/or indirectly favours the formation of seed banks and seed persistence in the soil. Nomenclature: Zuloaga et al. (1994); Zuloaga & Morrone (1996, 1999).
Incorporating intrinsic suppression in deep neural networks captures dynamics of adaptation in neurophysiology and perception

Adding a cellular adaptation mechanism to artificial neural networks explains temporal context modulation of biological vision. Adaptation is a fundamental property of sensory systems that can change subjective experiences in the context of recent information. Adaptation has been postulated to arise from recurrent circuit mechanisms or as a consequence of neuronally intrinsic suppression. However, it is unclear whether intrinsic suppression by itself can account for effects beyond reduced responses. Here, we test the hypothesis that complex adaptation phenomena can emerge from intrinsic suppression cascading through a feedforward model of visual processing. A deep convolutional neural network with intrinsic suppression captured neural signatures of adaptation including novelty detection, enhancement, and tuning curve shifts, while producing aftereffects consistent with human perception. When adaptation was trained in a task where repeated input affects recognition performance, an intrinsic mechanism generalized better than a recurrent neural network. Our results demonstrate that feedforward propagation of intrinsic suppression changes the functional state of the network, reproducing key neurophysiological and perceptual properties of adaptation.