Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential In Vitro Cytokine Induction by the Species of Cryptococcus gattii Complex

ABSTRACT Cryptococcal species vary in capsule and cell size, thermotolerance, geographic distribution, and affected populations. Cryptococcus gattii sensu stricto and C. deuterogattii affect mainly immunocompetent hosts; however, C. bacillisporus, C. decagattii, and C. tetragattii cause infections mainly in immunocompromised hosts. This study aimed to compare the capacities of different species of the C. gattii species complex to induce cytokines and antimicrobial molecules in human peripheral blood mononuclear cells (PBMCs). Cryptococcus bacillisporus and C. deuterogattii induced the lowest levels of tumor necrosis factor alpha (TNF-α), interleukin-1β (IL-1β), and IL-6 among the five species of the C. gattii complex. Cryptococcus deuterogattii induced higher levels of IL-22 than those induced by C. tetragattii and the environmental species C. flavescens. In addition, C. bacillisporus and C. gattii sensu stricto proliferated inside human monocyte-derived macrophages after 24 h of infection. All Cryptococcus species were able to generate reactive oxygen species (ROS) in human PBMCs, with C. bacillisporus and C. deuterogattii being more efficient than the other species. In conclusion, C. bacillisporus and C. deuterogattii induce lower levels of the proinflammatory cytokines TNF-α, IL-1β, and IL-6 and higher ROS levels than those induced by the other species. Species of the Cryptococcus gattii complex have different abilities to induce cytokine and ROS production by human PBMCs.
Influence on the Physical Properties of Wheat Straw via Hydrothermal and Chemical Treatments

The physical properties of wheat straw treated with hydrothermal and chemical treatments were investigated using an electronic universal testing machine, Fourier transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM). The thermal stability of the wheat straw was also investigated using thermogravimetric analysis (TGA). The experimental results showed that the chemical treatment was a main factor governing the enzymatic saccharification of wheat straw. Different treatments of wheat straw had the same mass loss trend. The maximum mass loss occurred in the range between 250 and 400 °C for all straw samples. In this range, the wheat straw treated with NaOH showed an exothermic peak, while samples treated with the other treatments showed an endothermic peak. Chemical treatments disrupted the silicified waxy surface and destroyed the C-O bond. The internal structure of wheat straw treated with NaOH became porous and loose and exposed more accessible surface area of the cellulose to cellulase.
A short course of metformin does not reduce OHSS in a GnRH antagonist cycle for women with PCOS undergoing IVF: a randomised placebo-controlled trial.

STUDY QUESTION Does 'metformin' reduce the incidence of ovarian hyperstimulation syndrome (OHSS) for women with polycystic ovary syndrome (PCOS) undergoing a GnRH antagonist assisted conception treatment cycle? SUMMARY ANSWER A short course of metformin does not reduce the incidence of OHSS for women with PCOS undergoing a GnRH antagonist treatment cycle. WHAT IS KNOWN ALREADY Metformin does reduce the incidence of OHSS in a GnRH-agonist treatment cycle. STUDY DESIGN, SIZE, DURATION A randomised placebo-controlled trial (RCT) using metformin or placebo. Randomisation was blinded to both patient and investigator, using a random permuted blocks method with a 50:50 allocation ratio. The study was completed over 5 years (2009-2014) with 153 randomised patients. A sample size calculation based on the incidence of OHSS was completed prospectively suggesting a minimum of 146 recruits was required for the trial with a power of 80% and a type 1 error of 0.05. PARTICIPANTS/MATERIALS, SETTING, METHODS All patients met the Rotterdam criteria for PCOS and were treated with a standard GnRH antagonist IVF/ICSI treatment cycle in a tertiary infertility clinic. The study medication was started prior to stimulation and continued to oocyte retrieval. Of the 153 patients, 77 received metformin and 76 placebo. MAIN RESULTS AND THE ROLE OF CHANCE There was no reduction in the incidence of moderate-severe OHSS (Placebo (PLA) 12.2%, metformin (MET) = 16%, 95% CI -0.08-0.16, P = 0.66). There was no difference in total gonadotrophin dose (PLA = 1200, MET = 1200, 95% CI -118.67-118.67, P = 0.75), oocytes retrieved (PLA = 15, MET = 14, 95% CI -2.37-4.37, P = 0.66) or fertilisation rate (PLA = 60.7%, MET = 53.3%, 95% CI -0.96-14.94, P = 0.07). However, using metformin resulted in a reduced clinical pregnancy rate (CPR) per cycle started (PLA = 48.7%, MET = 28.6%, 95% CI 0.04-0.35, P = 0.02) and live birth rate (PLA = 51.6%, MET = 27.6%, 95% CI 0.05-0.40, P = 0.02). Furthermore, when ethnicity was taken into account there was a significant reduction in pregnancy outcome for the South Asian population irrespective of metformin or placebo use (CPR per cycle started, White Caucasian = 44.4%, South Asian = 19.4%; 95% CI 0.06-0.39, P = 0.01). LIMITATIONS, REASONS FOR CAUTION This study was only undertaken on an infertility population with PCOS with a limited duration of study medication use. WIDER IMPLICATIONS OF THE FINDINGS This is the first adequately powered RCT to assess the impact of metformin on OHSS in a high-risk group (women with PCOS) undergoing a GnRH antagonist cycle. It does not support the empirical prescribing of metformin as an adjunct to a GnRH antagonist treatment cycle. STUDY FUNDING/COMPETING INTERESTS None. TRIAL REGISTRATION NUMBER EudraCT number 2009-010952-81. TRIAL REGISTRATION DATE 21 September 2009. DATE OF FIRST PATIENT'S ENROLMENT 30 October 2009.
Interactive comment on “ Impacts of aerosol direct effects on tropospheric ozone through changes in atmospheric dynamics and photolysis rates ” by Jia

[Comment]: it appears that the authors did not examine (or mention, unless I missed it) the aerosol effect on ozone through heterogeneous chemistry but I would expect this effect to be at least as large as the effects from dynamics and photolysis. Not accounting for the effect of aerosols on heterogeneous chemistry (for example through N2O5 hydrolysis) compromises in my opinion the policy-relevant conclusions about the sensitivity of ozone to aerosol reductions.
The five factor model of personality and individualism/collectivism in South Africa: an exploratory study

The Five-Factor Model (FFM) of personality is one of the prominent models in contemporary psychology and defines personality in terms of five broad factors, namely, Neuroticism, Extraversion, Openness to Experience, Agreeableness, and Conscientiousness. Recent research, however, questions the comprehensiveness of the FFM with evidence indicating the presence of other factors not addressed in the FFM most notably Individualism/Collectivism. Therefore, this study investigated the relationship of the FFM of personality to Individualism/Collectivism in a sample of 176 students from the University of the Witwatersrand using the Basic Traits Inventory and the Individualism/Collectivism scale. Results indicate that there were no significant relationships between the five factors and Individualism/Collectivism. In addition no significant difference was found between race and the five factors and Individualism/Collectivism. There were also no significant differences between home language and the five factors and Individualism/Collectivism.
Sunspot series prediction using adaptive identification

In this paper a parallel and adaptive methodology for optimizing the time series prediction using System Identification is shown. In order to validate this methodology, a set of time series based on the sun activity measured during the 20th century have been used. The prediction precision for short and long term improves with this technique when it is compared with the found results using System Identification with classical values for the main parameters.
Antifungal activity of stigmasterol, sitosterol and ergosterol from Bulbine natalensis Baker (Asphodelaceae)

Bulbine natalensis Baker. (Asphodelaceae) is indigenous to only southern Africa and is widely used as a skin remedy. B. natalensis contain secondary metabolites that have antibacterial properties. Phytosterols are a group of steroid alcohols and phytochemicals that occur naturally in plants. Aspergillus, Penicillium and Fusarium species are considered to be the most toxigenic fungi. They produce a large consortium of mycotoxins that include aflatoxins B1, B2, G1, G2, fumonisin B1 and ochratoxins. They are found in foodstuffs and are not destroyed by normal industrial processing or cooking since they are heat-stable. The purpose of the project was to extract and quantify phytosterols, such as ergosterol, stigmasterol and sitosterol from B. natalensis using phytochemical methods such as thin layer chromatography and high performance liquid chromatography. The extract was tested against Aspergillus flavus, Penicillium digitatum and Fusarium verticilloides for antifungal activities. 1 ml of saponified extract contained 0.07 µg of sitosterol, 0.16 µg of stigmasterol and 0.37 µg of ergosterol. Saponifiable, unsaponifiable and crude extracts showed minimal activity against F. verticilloides, whereas potent activity was exhibited against A. flavus.
Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form

Large-scale forward genetic screens have been instrumental for identifying genes that regulate development, homeostasis, and regeneration, as well as the mechanisms of disease. The zebrafish, Danio rerio, is an established genetic and developmental model used in genetic screens to uncover genes necessary for early development. However, the regulation of postembryonic development has received less attention as these screens are more labor intensive and require extensive resources. The lack of systematic interrogation of late development leaves large aspects of the genetic regulation of adult form and physiology unresolved. To understand the genetic control of postembryonic development, we performed a dominant screen for phenotypes affecting the adult zebrafish. In our screen, we identified 72 adult viable mutants showing changes in the shape of the skeleton as well as defects in pigmentation. For efficient mapping of these mutants and mutation identification, we devised a new mapping strategy based on identification of mutant-specific haplotypes. Using this method in combination with a candidate gene approach, we were able to identify linked mutations for 22 out of 25 mutants analyzed. Broadly, our mutational analysis suggests that there are key genes and pathways associated with late development. Many of these pathways are shared with humans and are affected in various disease conditions, suggesting constraint in the genetic pathways that can lead to change in adult form. Taken together, these results show that dominant screens are a feasible and productive means to identify mutations that can further our understanding of gene function during postembryonic development and in disease.
Distinct and Cooperative Roles of amh and dmrt1 in Self-Renewal and Differentiation of Male Germ Cells in Zebrafish

Spermatogenesis is a fundamental process in male reproductive biology and depends on precise balance between self-renewal and differentiation of male germ cells. However, the regulative factors for controlling the balance are poorly understood. In this study, we examined the roles of amh and dmrt1 in male germ cell development by generating their mutants with Crispr/Cas9 technology in zebrafish. Amh mutant zebrafish displayed a female-biased sex ratio, and both male and female amh mutants developed hypertrophic gonads due to uncontrolled proliferation and impaired differentiation of germ cells. A large number of proliferating spermatogonium-like cells were observed within testicular lobules of the amh-mutated testes, and they were demonstrated to be both Vasa- and PH3-positive. Moreover, the average number of Sycp3- and Vasa-positive cells in the amh mutants was significantly lower than in wild-type testes, suggesting a severely impaired differentiation of male germ cells. Conversely, all the dmrt1-mutated testes displayed severe testicular developmental defects and gradual loss of all Vasa-positive germ cells by inhibiting their self-renewal and inducing apoptosis. In addition, several germ cell and Sertoli cell marker genes were significantly downregulated, whereas a prominent increase of Insl3-positive Leydig cells was revealed by immunohistochemical analysis in the disorganized dmrt1-mutated testes. Our data suggest that amh might act as a guardian to control the balance between proliferation and differentiation of male germ cells, whereas dmrt1 might be required for the maintenance, self-renewal, and differentiation of male germ cells. Significantly, this study unravels novel functions of amh gene in fish.
Streptococcus pneumoniae PspC Subgroup Prevalence in Invasive Disease and Differences in Contribution to Complement Evasion

ABSTRACT The pneumococcal capsular serotype is an important determinant of complement resistance and invasive disease potential, but other virulence factors have also been found to contribute. Pneumococcal surface protein C (PspC), a highly variable virulence protein that binds complement factor H to evade C3 opsonization, is divided into two subgroups: choline-bound subgroup I and LPxTG-anchored subgroup II. The prevalence of different PspC subgroups in invasive pneumococcal disease (IPD) and functional differences in complement evasion are unknown. The prevalence of PspC subgroups in IPD isolates was determined in a collection of 349 sequenced strains of Streptococcus pneumoniae isolated from adult patients. pspC deletion mutants and isogenic pspC switch mutants were constructed to study differences in factor H binding and complement evasion in relation to capsule thickness. Subgroup I pspC was far more prevalent in IPD isolates than subgroup II pspC. The presence of capsule was associated with a greater ability of bound factor H to reduce complement opsonization. Pneumococcal subgroup I PspC bound significantly more factor H and showed more effective complement evasion than subgroup II PspC in isogenic encapsulated pneumococci. We conclude that variation in the PspC subgroups, independent of capsule serotypes, affects pneumococcal factor H binding and its ability to evade complement deposition.
A framework for the integration of MOF-compliant analysis methods

With the increasing maturity of model-driven tools and methods, new model-based analysis methods are developed to support specific stakeholder concerns during software lifecycle. This multiplication of models and their related analysis tools calls for solution addressing the integration of MOF-based analysis methods. Current research works on integration of analysis methods have already addressed the extraction of the needed input data as well as the control and the integration of the tools supporting the analysis execution. However, little attention has been paid to the integration of analysis results back into initial model. We propose a MOF-based framework enabling the integration of analysis results that a) defines a meta-model capturing the integration requirements, b) provides a MOF meta-model extension mechanism with support for upward compatibility; and c) automatically generates a model transformation for model integration. We illustrate the use of our framework by integrating a reliability analysis methods and a fault tolerant reconfiguration method on the ABC/ADL Software Architecture. We applied the resulting analysis composition onto the ECPerf JEE system.
Gateway to Tools of the HIV and HCV Databases

Over the years the staff of the HIV Databases have developed Web-based software for working with HIV sequence data. This is a general overview of the tools that are available on the HIV database website. Many of these tools are very simple, and were developed because we wanted to ease a recurrent task for our experimentalist colleagues who use the database. Some tools are tailored for HIV or HCV, and have counterparts developed specifically for the HCV (http://hcv.lanl.gov) and HIV (http://hiv.lanl.gov) databases. Others are general and can be used for analysis of any organism. A fast way to understand what these programs do is to click the “Sample Input” button on the input page. This causes an example input file to be loaded into the input page, so you can run the program to get an idea about what the output looks like. The first part of this publication provides an outline of these programs organized by their functions. A short description of each tool is provided. If a tool can be applied to any sequence, not just HIV or HCV, it is labeled, “General,” while a tool that is applicable only to HIV or HCV sequences is labeled “HIV/HCV. ”
Projected cancer risks from computed tomographic scans performed in the United States in 2007.

BACKGROUND The use of computed tomographic (CT) scans in the United States (US) has increased more than 3-fold since 1993 to approximately 70 million scans annually. Despite the great medical benefits, there is concern about the potential radiation-related cancer risk. We conducted detailed estimates of the future cancer risks from current CT scan use in the US according to age, sex, and scan type. METHODS Risk models based on the National Research Council's "Biological Effects of Ionizing Radiation" report and organ-specific radiation doses derived from a national survey were used to estimate age-specific cancer risks for each scan type. These models were combined with age- and sex-specific scan frequencies for the US in 2007 obtained from survey and insurance claims data. We estimated the mean number of radiation-related incident cancers with 95% uncertainty limits (UL) using Monte Carlo simulations. RESULTS Overall, we estimated that approximately 29 000 (95% UL, 15 000-45 000) future cancers could be related to CT scans performed in the US in 2007. The largest contributions were from scans of the abdomen and pelvis (n = 14 000) (95% UL, 6900-25 000), chest (n = 4100) (95% UL, 1900-8100), and head (n = 4000) (95% UL, 1100-8700), as well as from chest CT angiography (n = 2700) (95% UL, 1300-5000). One-third of the projected cancers were due to scans performed at the ages of 35 to 54 years compared with 15% due to scans performed at ages younger than 18 years, and 66% were in females. CONCLUSIONS These detailed estimates highlight several areas of CT scan use that make large contributions to the total cancer risk, including several scan types and age groups with a high frequency of use or scans involving relatively high doses, in which risk-reduction efforts may be warranted.
Counting Triangles in Massive Graphs with MapReduce

Graphs and networks are used to model interactions in a variety of contexts. There is a growing need to quickly assess the characteristics of a graph in order to understand its underlying structure. Some of the most useful metrics are triangle-based and give a measure of the connectedness of mutual friends. This is often summarized in terms of clustering coefficients, which measure the likelihood that two neighbors of a node are themselves connected. Computing these measures exactly for large-scale networks is prohibitively expensive in both memory and time. However, a recent wedge-sampling algorithm has proved successful in efficiently and accurately estimating clustering coefficients. In this paper, we describe how to implement this approach in MapReduce to deal with massive graphs. We show results on publicly available networks, the largest of which is 132M nodes and 4.7B edges, as well as artificially generated networks (using the Graph500 benchmark), the largest of which has 240M nodes and 8.5B edges.
Learning performance and brain structure of artificially-reared honey bees fed with different quantities of food

Background Artificial rearing of honey bee larvae is an established method which enables to fully standardize the rearing environment and to manipulate the supplied diet to the brood. However, there are no studies which compare learning performance or neuroanatomic differences of artificially-reared (in-lab) bees in comparison with their in-hive reared counterparts. Methods Here we tested how different quantities of food during larval development affect body size, brain morphology and learning ability of adult honey bees. We used in-lab rearing to be able to manipulate the total quantity of food consumed during larval development. After hatching, a subset of the bees was taken for which we made 3D reconstructions of the brains using confocal laser-scanning microscopy. Learning ability and memory formation of the remaining bees was tested in a differential olfactory conditioning experiment. Finally, we evaluated how bees reared with different quantities of artificial diet compared to in-hive reared bees. Results Thorax and head size of in-lab reared honey bees, when fed the standard diet of 160 µl or less, were slightly smaller than hive bees. The brain structure analyses showed that artificially reared bees had smaller mushroom body (MB) lateral calyces than their in-hive counterparts, independently of the quantity of food they received. However, they showed the same total brain size and the same associative learning ability as in-hive reared bees. In terms of mid-term memory, but not early long-term memory, they performed even better than the in-hive control. Discussion We have demonstrated that bees that are reared artificially (according to the Aupinel protocol) and kept in lab-conditions perform the same or even better than their in-hive sisters in an olfactory conditioning experiment even though their lateral calyces were consistently smaller at emergence. The applied combination of experimental manipulation during the larval phase plus subsequent behavioral and neuro-anatomic analyses is a powerful tool for basic and applied honey bee research.
Small, medium, or large?: estimating the user-perceived scale of stroke gestures

We show that large consensus exists among users in the way they articulate stroke gestures at various scales (i.e., small, medium, and large), and formulate a simple rule that estimates the user-intended scale of input gestures with 87% accuracy. Our estimator can enhance current gestural interfaces by leveraging scale as a natural parameter for gesture input, reflective of user perception (i.e., no training required). Gesture scale can simplify gesture set design, improve gesture-to-function mappings, and reduce the need for users to learn and for recognizers to discriminate unnecessary symbols.
Effect of cholesterol reduction on receptor signaling in neurons.

Background: Cholesterol synthesis is decreased in the brain in diabetes. Results: Cholesterol depletion in neuron-derived cells results in impaired insulin/IGF-1 and neurotrophin signaling and altered apoptosis. Conclusion: Reduction of cellular cholesterol in diabetes causes defects in signal transduction and function in neuron-derived cells. Significance: Reduced brain cholesterol could contribute to the higher prevalence of cognitive dysfunction and Alzheimer disease in diabetes.