Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Gene Expression during Adaptation of Listeria monocytogenes to the Soil Environment

Listeria monocytogenes is a ubiquitous opportunistic pathogen responsible for listeriosis. In order to study the processes underlying its ability to adapt to the soil environment, whole-genome arrays were used to analyse transcriptome modifications 15 minutes, 30 minutes and 18 h after inoculation of L. monocytogenes EGD-e in soil extracts. Growth was observed within the first day of incubation and large numbers were still detected in soil extract and soil microcosms one year after the start of the experiment. Major transcriptional reprofiling was observed. Nutrient acquisition mechanisms (phosphoenolpyruvate-dependent phosphotransferase systems and ABC transporters) and enzymes involved in catabolism of specific carbohydrates (β-glucosidases; chitinases) were prevalent. This is consistent with the overrepresentation of the CodY regulon that suggests that in a nutrient depleted environment, L. monocytogenes recruits its extensive repertoire of transporters to acquire a range of substrates for energy production.
Systematic review and meta‐analysis of the diagnostic accuracy of low‐dose computed tomography of the kidneys, ureters and bladder for urolithiasis

Renal colic is a common clinical condition which is often investigated with a CT of the kidneys, ureters and bladder (CTKUB). Recent technological improvements have allowed a reduction in dose with the emergence of low‐dose CTKUB (LD‐CTKUB) techniques. The present meta‐analysis aims to determine the diagnostic accuracy of LD‐CTKUB in the diagnosis of clinically significant uroliths. A systematic review was performed using nine electronic databases from their dates of inception to May 2016. Inclusion criteria included studies reporting comparative outcomes using LD‐CTKUB with a dose less than 3 millisieverts compared to an imaging gold standard or clinical and surgical evaluation. The primary endpoint was detection of a urolith ≥3 mm where specified and any urolith when size was unspecified. Twelve studies were identified according to selection criteria, involving 1250 patients. LD‐CTKUB demonstrated a pooled sensitivity of 93.1% (95%CI 91.5–94.4), specificity of 96.6% (95%CI 95.1–97.7%), positive likelihood ratio of 19.9 (95%CI 12.7–31.2), negative likelihood ratio of 0.05 (95%CI 0.02–0.10) and AUC of 0.9877 in the detection of clinically significant uroliths. Although 86 alternative diagnoses were noted across seven studies, none assessed the accuracy of LD‐CTKUB in their detection. The majority of newer studies report an average radiation dose from 1 to 1.5 millisieverts. This study demonstrates a high sensitivity, specificity and positive predictive value in the detection of uroliths, however, its accuracy in the detection of alternative diagnoses is unknown. Therefore, we recommend using LD‐CTKUB when the pre‐test probability of stone disease is significantly higher than the pre‐test probability of alternative diagnoses, such as follow‐up of known calculi. We suggest caution when the pre‐test probability of alternative diagnoses is high, such as the initial presentation of renal colic.
Prevalence and Risk Factors for Vitamin C Deficiency in North and South India: A Two Centre Population Based Study in People Aged 60 Years and Over

Background Studies from the UK and North America have reported vitamin C deficiency in around 1 in 5 men and 1 in 9 women in low income groups. There are few data on vitamin C deficiency in resource poor countries. Objectives To investigate the prevalence of vitamin C deficiency in India. Design We carried out a population-based cross-sectional survey in two areas of north and south India. Randomly sampled clusters were enumerated to identify people aged 60 and over. Participants (75% response rate) were interviewed for tobacco, alcohol, cooking fuel use, 24 hour diet recall and underwent anthropometry and blood collection. Vitamin C was measured using an enzyme-based assay in plasma stabilized with metaphosphoric acid. We categorised vitamin C status as deficient (<11 µmol/L), sub-optimal (11–28 µmol/L) and adequate (>28 µmol/L). We investigated factors associated with vitamin C deficiency using multivariable Poisson regression. Results The age, sex and season standardized prevalence of vitamin C deficiency was 73.9% (95% confidence Interval, CI 70.4,77.5) in 2668 people in north India and 45.7% (95% CI 42.5,48.9) in 2970 from south India. Only 10.8% in the north and 25.9% in the south met the criteria for adequate levels. Vitamin C deficiency varied by season, and was more prevalent in men, with increasing age, users of tobacco and biomass fuels, in those with anthropometric indicators of poor nutrition and with lower intakes of dietary vitamin C. Conclusions In poor communities, such as in our study, consideration needs to be given to measures to improve the consumption of vitamin C rich foods and to discourage the use of tobacco.
Isolation, Purification, and Characterization of Five Active Diketopiperazine Derivatives from Endophytic Streptomyces SUK 25 with Antimicrobial and Cytotoxic Activities.

In our search for new sources of bioactive secondary metabolites from Streptomyces sp. , the ethyl acetate extracts from endophytic Streptomyces SUK 25 afforded five active diketopiperazine (DKP) compounds. The aim of this study was to characterize the bioactive compounds isolated from endophytic Streptomyces SUK 25 and evaluate their bioactivity against multiple drug resistance (MDR) bacteria such as Enterococcus raffinosus, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter spp. , and their cytotoxic activities against the human hepatoma (HepaRG) cell line. The production of secondary metabolites by this strain was optimized through Thornton's medium. Isolation, purification, and identification of the bioactive compounds were carried out using high-performance liquid chromatography, high-resolution mass liquid chromatography-mass spectrometry, Fourier transform infrared spectroscopy, and nuclear magnetic resonance, and cryopreserved HepaRG cells were selected to test the cytotoxicity. The results showed that endophytic Streptomyces SUK 25 produces four active DKP compounds and an acetamide derivative, which were elucidated as cyclo-(L-Val-L-Pro), cyclo-(L-Leu-L-Pro), cyclo-(L-Phe-L-Pro), cyclo-(L-Val-L-Phe), and N-(7-hydroxy-6-methyl-octyl)-acetamide. These active compounds exhibited activity against methicillin-resistant S. aureus ATCC 43300 and Enterococcus raffinosus, with low toxicity against human hepatoma HepaRG cells. Endophytic Streptomyces SUK 25 has the ability to produce DKP derivatives biologically active against some MDR bacteria with relatively low toxicity against HepaRG cells line.
Growth Strategies of Tropical Tree Species: Disentangling Light and Size Effects

An understanding of the drivers of tree growth at the species level is required to predict likely changes of carbon stocks and biodiversity when environmental conditions change. Especially in species-rich tropical forests, it is largely unknown how species differ in their response of growth to resource availability and individual size. We use a hierarchical Bayesian approach to quantify the impact of light availability and tree diameter on growth of 274 woody species in a 50-ha long-term forest census plot in Barro Colorado Island, Panama. Light reaching each individual tree was estimated from yearly vertical censuses of canopy density. The hierarchical Bayesian approach allowed accounting for different sources of error, such as negative growth observations, and including rare species correctly weighted by their abundance. All species grew faster at higher light. Exponents of a power function relating growth to light were mostly between 0 and 1. This indicates that nearly all species exhibit a decelerating increase of growth with light. In contrast, estimated growth rates at standardized conditions (5 cm dbh, 5% light) varied over a 9-fold range and reflect strong growth-strategy differentiation between the species. As a consequence, growth rankings of the species at low (2%) and high light (20%) were highly correlated. Rare species tended to grow faster and showed a greater sensitivity to light than abundant species. Overall, tree size was less important for growth than light and about half the species were predicted to grow faster in diameter when bigger or smaller, respectively. Together light availability and tree diameter only explained on average 12% of the variation in growth rates. Thus, other factors such as soil characteristics, herbivory, or pathogens may contribute considerably to shaping tree growth in the tropics.
Functional ability and nutritional status of free-living elderly people

In 1990 almost half a billion people in the world were over 60 years old (World Bank, 1994). In only 40 years time this number will nearly triple. By the end of those same 40 years three-quarters of the world’s elderly population will be living in developing countries (Kinsella & Suzman, 1992). The challenge for the next century is to alter focus accordingly. Living longer comes at a price. Extra years will not necessarily be years of good health. In the complicated context of ageing biology, transitions from disease to disability rather than disease to death take on prime importance for older people. For many chronic diseases that can never be completely cured, delaying the onset of functional decline, or minimizing the impact of lost independent function on daily life, in effect approximates a ‘cure’ of the condition for those concerned (Besdine, 1990). Moreover, the presence of illness as measured by objective clinical data does not necessarily determine the presence or severity of dependency. And of course for many elderly people in developing countries the luxury of access to such knowledge is often unavailable. With risk of death increasingly likely, and both the longand short-term effects of disease, diet and life style hard to disentangle, the traditional health measures of life expectancy and morbidity begin to appear inadequate outcomes against which to measure any health or nutritional indicator in older people, or evaluate preventive strategies. To what then should we turn? The present paper addresses the following questions: Is functional ability an appropriate outcome indicator of health and nutritional status in free-living people in developing countries? What is functional ability and how can it be assessed? Is there any evidence of a relationship between functional ability and nutritional status in free-living elderly people? I will focus on the community as the site in which functional impairment first appears most often and my bias is towards malnutrition in developing countries. At times, I will refer to our own recent fieldwork experience amongst elderly slum dwellers in Bombay, but no data will be presented. The present paper aims to serve as an introduction to a new issue of growing practical importance in both nutritional gerontology and nutrition in the Third World.
Empirical Evaluation of Advanced Ear Biometrics

We present results of the largest experimental investigation of ear biometrics to date. Approaches considered include a PCA ("eigen-ear") approach with 2D intensity images, achieving 63.8% rank-one recognition; a PCA approach with range images, achieving 55.3% Hausdorff matching of edge images from range images, achieving 67.5% and ICP matching of the 3D data, achieving 98.7%. ICP based matching not only achieves the best performance, but also shows good scalability with size of dataset. The data set used represents over 300 persons, each with images acquired on at least two different dates. In addition, the ICP-based approach is further applied on an expanded data set of 404 subjects, and achieves 97.5% rank one recognition rate. In order to test the robustness and variability of ear biometrics, ear symmetry is also investigated. In our experiments around 90% of people’s right ear and left ear are symmetric.
Microgeographic morphological variation across larval wood frog populations associated with environment despite gene flow

Abstract Gene flow has historically been thought to constrain local adaptation; yet, recent research suggests that populations can diverge despite exchanging genes. Here I use a common garden experiment to assess the combined effects of gene flow and natural selection on morphological variation of 16 wood frog (Rana sylvatica) populations, a species known to experience divergent selection pressures in open‐ and closed‐canopy ponds across relatively small geographic scales. Wood frog tadpoles from different ponds showed significant morphological variation associated with canopy type with a trade‐off between tail length and body depth consistent with previous research. In contrast, neutral genetic differentiation of nine microsatellite loci as measured by Jost's D was not associated with canopy type, indicating no pattern of isolation by environment. Genetic structure analyses indicated some substructure across the 16 ponds (K = 4); however, three out of four assigned clusters included both open‐ and closed‐canopy ponds. Together, these results suggest that morphological divergence among these wood frog populations is occurring despite gene flow and that selection within these environments is strong. Furthermore, morphological variation among ponds differed across two sampling periods during larval development, demonstrating the importance of evaluating phenotypic divergence over multiple time periods and at a time relevant to the processes being studied.
Micro-Loans, Insecticide-Treated Bednets and Malaria: Evidence from a Randomized Controlled Trial in Orissa (India)

We describe findings from the first large-scale cluster randomized controlled trial in a developing country that evaluates the uptake of a health-protecting technology, insecticide-treated bednets (ITNs), through micro-consumer loans, as compared to free distribution and control conditions. Despite a relatively high price, 52 percent of sample households purchased ITNs, highlighting the role of liquidity constraints in explaining earlier low adoption rates. We find mixed evidence of improvements in malaria indices. We interpret the results and their implications within the debate about cost sharing, sustainability and liquidity constraints in public health initiatives in developing countries.
Human Preferences for Symmetry: Subjective Experience, Cognitive Conflict and Cortical Brain Activity

This study examines the links between human perceptions, cognitive biases and neural processing of symmetrical stimuli. While preferences for symmetry have largely been examined in the context of disorders such as obsessive-compulsive disorder and autism spectrum disorders, we examine various these phenomena in non-clinical subjects and suggest that such preferences are distributed throughout the typical population as part of our cognitive and neural architecture. In Experiment 1, 82 young adults reported on the frequency of their obsessive-compulsive spectrum behaviors. Subjects also performed an emotional Stroop or variant of an Implicit Association Task (the OC-CIT) developed to assess cognitive biases for symmetry. Data not only reveal that subjects evidence a cognitive conflict when asked to match images of positive affect with asymmetrical stimuli, and disgust with symmetry, but also that their slowed reaction times when asked to do so were predicted by reports of OC behavior, particularly checking behavior. In Experiment 2, 26 participants were administered an oddball Event-Related Potential task specifically designed to assess sensitivity to symmetry as well as the OC-CIT. These data revealed that reaction times on the OC-CIT were strongly predicted by frontal electrode sites indicating faster processing of an asymmetrical stimulus (unparallel lines) relative to a symmetrical stimulus (parallel lines). The results point to an overall cognitive bias linking disgust with asymmetry and suggest that such cognitive biases are reflected in neural responses to symmetrical/asymmetrical stimuli.
Effects of Natural Zeolites on Bioavailability and Leachability of Heavy Metals in the Composting Process of Biodegradable Wastes

The bioavailability and leachability of heavy metals play an important role in the toxicity of heavy metals in the final compost followed by land application. This chapter examines the effects of natural zeolite on bioavailability of heavy metals (Zn, Cu, Mn, Fe, Ni, Pb, Cd, and Cr) in the form of water soluble and diethylenetriaminepentaace‐ tic acid (DTPA) extractable. The toxicity characteristic leaching procedure (TCLP) test was performed to examine the leachability of heavy metals. Water solubility, DTPA extractability, leachability, and most bioavailable fractions were reduced during agitated pile composting (APC) and rotary drum composting (RDC) of water hyacinth with zeolite addition. The addition of the natural zeolite (clinoptilolite) during the composting process led to an increase in Na, Ca, and K concentrations and signifi‐ cantly reduced the water solubility and DTPA and TCLP extractability of heavy metals. The addition of an appropriate amount of natural zeolite during the composting process enhanced the organic matter degradation, thereby increasing the conversion into the most stabilized organic matter and reducing the bioavailability and leachabil‐ ity of heavy metals. for Zn, 52.7% for Mn, 67.0% for Fe, 67.9% for Ni, 71.0% for Cd, and 72.6% for Cr in zeolite treatments. However, the highest reduction in leachability of Cu (73.2%) and Pb (72.4%) was found in the control during the RDC process of water hyacinth [41]. A higher reduction in leachability of metals was observed in zeolite treatments when compared to control in both APC and RDC of water hyacinth [40, 41]. In the RDC process, the highest reduction in leachability of Zn, Mn, Fe, and Ni was observed in 5% zeolite treatment, whereas the reduction of Cd and Cr was observed in 10% zeolite treatment. In the water hyacinth composting with
Antifungal activity of three fern extracts on causative agents of groundnut early leaf spot and rust diseases.

Antimycotic activity of three fern extracts from Hemionitis arifolia (Burm.f.) Moore. , Pteridium aquilinum (Linn.) Kuhn. and Christella parasitica (Linn.) H. Lev. were evaluated against groundnut early leaf spot and rust disease causative agents viz., Puccinia arachidis Speg. and Phaeoisariopsis personata (Berk & M.A. Cuortis) Vanarx. , espectively by mycelial dry weight method. Both the fungi were sensitive to all the three fern extracts tested. Among the extracts, chloroform extract of H. arifolia was found to have maximum antifungal activity against both fungi. Between these two fungi, P. personata was found to be more sensitive to the tested plant extracts than P. arachidis. From this study it is concluded that chloroform extract from H. arifolia can be utilized for managing rust and leaf spots diseases on groundnut.
Identity constructions and transition to adulthood for young people with mild intellectual disabilities

This article explores the self-constructions of young adults with mild intellectual disabilities in talk about their everyday living and how parents and professionals construct young adults with disabilities in talk about their involvement in transition processes. The analysis is related to an interpretive tradition and conducted based on individual interviews with four young adults with mild intellectual disability, five parents of young adults with mild intellectual disabilities and five professionals in the adult service system. The findings show that the young adults define themselves as actors in their own lives, while the parents recognize young adults with mild intellectual disabilities as both actors with resources and actors in need of assistance. Professionals in the adult service system, however, appear to rely on an identity perspective that might hamper young adults’ agency positioning and opportunities to define themselves and influence their future lives.
Oxidative stability of canola oil by Biarum bovei bioactive components during storage at ambient temperature

Abstract In this study, antioxidative activities of aqueous extract of Biarum bovei (BBE) in stabilizing of canola oil during storage at 20°C was evaluated. For this purpose, the total phenolic (TP), flavonoids (TFC), and tocopherol content (TTC) of the extract were determined and β‐carotene bleaching system was used to assess the antioxidant efficacy of BBE. The amount of TP, TFC, and TTC in BBE indicated high antioxidant activity. So, different concentrations (0, 200, 800, and 1400 ppm) of BBE and butylatedhydroxyanisole (BHA; 100 ppm), were added to canola oil for 60 days at 20°C. Peroxide value (PV), carbonyl value (CV), Total polar compounds (TPC), acid value (AV), iodine values (IV), and conjugated dienes (CD) were employed to evaluate the BBE effect on canola oil stabilizing. Results indicated that 1,400 ppm of BBE exhibited stronger antioxidant activity in canola oil than BHA.
Characterization of Multiple C2 Domain and Transmembrane Region Proteins in Arabidopsis1[OPEN]

MCTPs exhibit diverse and overlapping patterns of gene expression and protein localization, and might be involved in Arabidopsis development with potential functional divergence or redundancy. Multiple C2 domain and transmembrane region proteins (MCTPs) are evolutionarily conserved in eukaryotic organisms and may function as signaling molecules that mediate trafficking of other regulators. Although there are a large number of MCTPs found in the plant lineage, biological information on most plant MCTPs remains unknown. Here, we report systematic characterization of 16 members in the entire Arabidopsis (Arabidopsis thaliana) MCTP family. Using GUS and GFP reporter assays, we reveal their distinct or overlapping patterns of gene expression and protein localization in developing Arabidopsis plants and Nicotiana benthamiana leaf epidermal cells. We further analyze in vivo effects of three C2 domains on the regulatory role of MCTP1 (FTIP1) in flowering time control in Arabidopsis, demonstrating that these C2 domains may be cooperative to mediate FTIP1 function during the floral transition. Through examining all available T-DNA insertional mutants of Arabidopsis MCTPs, we further reveal that mctp6-1 significantly enhances the late-flowering phenotype of ftip1-1 possibly through affecting FLOWERING LOCUS T in different manners, exemplifying that different MCTPs additively regulate a specific plant developmental process. Taken together, our results suggest functional divergence or redundancy of MCTP members in Arabidopsis and provide a community resource for further understanding various MCTP functions in plant development.