Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional regulation of fermentative and respiratory metabolism in Saccharomyces cerevisiae industrial bakers' strains.

Bakers' yeast-producing companies grow cells under respiratory conditions, at a very high growth rate. Some desirable properties of bakers' yeast may be altered if fermentation rather than respiration occurs during biomass production. That is why differences in gene expression patterns that take place when industrial bakers' yeasts are grown under fermentative, rather than respiratory conditions, were examined. Macroarray analysis of V1 strain indicated changes in gene expression similar to those already described in laboratory Saccharomyces cerevisiae strains: repression of most genes related to respiration and oxidative metabolism and derepression of genes related to ribosome biogenesis and stress resistance in fermentation. Under respiratory conditions, genes related to the glyoxylate and Krebs cycles, respiration, gluconeogenesis, and energy production are activated. DOG21 strain, a partly catabolite-derepressed mutant derived from V1, displayed gene expression patterns quite similar to those of V1, although lower levels of gene expression and changes in fewer number of genes as compared to V1 were both detected in all cases. However, under fermentative conditions, DOG21 mutant significantly increased the expression of SNF1 -controlled genes and other genes involved in stress resistance, whereas the expression of the HXK2 gene, involved in catabolite repression, was considerably reduced, according to the pleiotropic stress-resistant phenotype of this mutant. These results also seemed to suggest that stress-resistant genes control desirable bakers' yeast qualities.
Analysis of navigation behaviour of blind users using Browsing Shortcuts

The World Wide Web is today the largest information seeking environment. Millions of people use it to satisfy their information needs. Although it is quite easy for able-bodied users to use it, there are still a lot of problems for people with disabilities. A major group of them are blind users. Blind users navigate the web in a different and less effective and efficient way especially when it comes to information seeking tasks. To ease the problem we introduced the Browsing Shortcuts (BSs) mechanism to enable blind people to move efficiently to various elements of a web page (e.g. functional elements such as forms, navigational aids, etc.), hence operating effectively as an interaction method and a vital counterbalance to low navigability of web pages. Although there are proofs that navigation performance was improved using the BSs mechanism, this effect had never been examined and explained in detail. In this paper, we re-analyse data collected from past experiments and review BSs usage from a navigation behaviour perspective. This is achieved by a new analysis using a visualisation method of “travel graphs” for studying the navigation methods of blind users. We compare behaviours of blind users using the BSs feature to the ones used without it to determine changes in behaviour. The basic aim behind this analysis is to examine how BSs have affected the navigation behaviour of blind users. We wished to determine how non-visual navigation using BSs assists users in parsing a web page into functional or semantic regions. Additionally, we wished to examine if and how these regions are accessed during an information seeking episode with and without the BSs mechanism. Finally, we wished to examine whether these changes are towards more rationalised information seeking behaviour. In overall, this new analysis of the recorded results indicate that the navigation model using BSs signifies more rationalised navigation and significantly change information seeking behaviour improving both navigability and information seeking performance.
Tripartite community structure in social bookmarking data

Community detection is a branch of network analysis concerned with identifying strongly connected subnetworks. Social bookmarking sites aggregate datasets of often hundreds of millions of triples (document, user, and tag), which, when interpreted as edges of a graph, give rise to special networks called 3-partite, 3-uniform hypergraphs. We identify challenges and opportunities of generalizing community detection and in particular modularity optimization to these structures. Two methods for community detection are introduced that preserve the hypergraph's special structure to different degrees. Their performance is compared on synthetic datasets, showing the benefits of structure preservation. Furthermore, a tool for interactive exploration of the community detection results is introduced and applied to examples from real datasets. We find additional evidence for the importance of structure preservation and, more generally, demonstrate how tripartite community detection can help understand the structure of social bookmarking data.
Living Liver Donor Mortality: Where Do We Stand?

OBJECTIVE:To explore the use of medical journals, lay media, registries, and transplant center websites to discuss living liver donor mortality.METHODS:To study the incidence of and circumstances relating to living liver donor death, medical journals and lay print media were searched to create a case summary of worldwide living liver donor deaths. The United Network for Organ Sharing (UNOS) and European Liver Transplant Registry (ELTR) were also queried for information regarding living liver donor deaths. Lastly, the Websites of United States transplant centers offering living liver donation were reviewed to identify whether or not death was stated as a donor risk.RESULTS:Literature review revealed 14 living liver donor deaths. One of the five deaths occurring in the United States had been reported to UNOS. One of the 14 cases had been reported only in lay literature, and another only in the ELTR. In at least five cases, surgical complications were not the cause of donor death. Among the 62 transplant center Websites, only 12 centers (19%) specifically mentioned death as a donation risk. Eight of these 12 centers (67%) mentioned death in terms of percent mortality risk; however, risk rates spanned a 10-fold range from 0.2% to 2%. CONCLUSION:Potential living liver donors are best served by accurate information about donor mortality. Access to such data is difficult and these individuals would benefit by a worldwide living liver donor registry and peer-reviewed publication of donor mortality.
Illicit drug use and experience of harm in the night-time economy

Abstract The study investigates illicit drug use in the night-time economy and its association with intoxication, harm and violence experienced by licensed venue patrons. Five-minute structured interviews measuring event-level data were conducted over a 15-month period (March 2010–June 2011) between 9 pm and 1 am. A total of 3949 patrons were interviewed in Newcastle and Geelong, Australian regional cities close to capital cities. Mean age was 24.3 years old (SD=5.8) and 54.4% were male. Six percent of the sample self-reported consuming illicit substances at the time of interview; 7.3% at nightclub venues, 11.8% in the street, 5.5% in pubs and 2.8% in bars. Amphetamines, methamphetamines and ecstasy accounted for two-thirds of substance use. Patrons who reported consuming illicit drugs were 1.90 times as likely to be involved in a prior violent incident (OR 1.35–2.70 95% CI, p < 0.001). Participants who reported illicit drug use at the time of interview were likely to be 0.89 (p < 0.001) points higher on self-reported intoxication scale (0–10), and were more likely to have engaged in high risk alcohol consumption χ2 (1, n = 3396) = 9.63, p < 0.01) than those who did not report using drugs. Illicit drug use contributes significantly to the burden of harm and intoxication in night-time environments, despite being a minority behavior.
Heart rate variability and arrhythmias evaluated with Holter in dogs with degenerative mitral valve disease.

As cardiopatias cursam com alteracoes do controle autonomico do coracao, resultando em taquicardia e consequente diminuicao na variabilidade da frequencia cardiaca (VFC). O objetivo deste estudo foi avaliar se o desenvolvimento de insuficiencia cardiaca secundaria a degeneracao valvar mitral (DVM) leva a alteracoes no controle autonomico do coracao, as quais podem ser determinadas pela eletrocardiografia continua (Holter). Caes foram distribuidos em grupos experimentais apos avaliacao clinica e ecocardiografica da seguinte maneira: controle (saudaveis; n=6), DVM sem insuficiencia cardiaca (n=8) e DVM com insuficiencia cardiaca (n=13). Arritmias e VFC foram determinadas pelo Holter. Animais portadores de DVM, quando comparados ao controle, apresentaram diminuicao significativa da potencia total, a qual e representativa de toda a VFC. Somente caes doentes e com insuficiencia cardiaca apresentaram incidencia elevada de arritmias supraventriculares, frequencia cardiaca aumentada, pequena quantidade de pausas superiores a 2,0s entre batimentos consecutivos, permanencia por mais tempo em taquicardia do que em bradicardia, diminuido indice de alta frequencia (indicativo de controle parassimpatico) e elevado indice de baixa frequencia (indicativo de controle simpatico e parassimpatico), quando comparados ao controle (p<0,05). Assim, conclui-se que, em caes portadores de DVM, as variaveis obtidas com o Holter apresentam-se alteradas devido ao desenvolvimento de insuficiencia cardiaca.
Decoding Tumor Phenotypes for ALK, ROS1, and RET Fusions in Lung Adenocarcinoma Using a Radiomics Approach

AbstractQuantitative imaging using radiomics can capture distinct phenotypic differences between tumors and may have predictive power for certain phenotypes according to specific genetic mutations. We aimed to identify the clinicoradiologic predictors of tumors with ALK (anaplastic lymphoma kinase), ROS1 (c-ros oncogene 1), or RET (rearranged during transfection) fusions in patients with lung adenocarcinoma.A total of 539 pathologically confirmed lung adenocarcinomas were included in this retrospective study. The baseline clinicopathologic characteristics were retrieved from the patients’ medical records and the ALK/ROS1/RET fusion status was reviewed. Quantitative computed tomography (CT) and positron emission tomography imaging characteristics were evaluated using a radiomics approach. Significant features for the fusion-positive tumor prediction model were extracted from all of the clinicoradiologic features, and were used to calculate diagnostic performance for predicting 3 fusions’ positivity. The clinicoradiologic features were compared between ALK versus ROS1/RET fusion-positive tumors to identify the clinicoradiologic similarity between the 2 groups.The fusion-positive tumor prediction model was a combination of younger age, advanced tumor stage, solid tumor on CT, higher values for SUVmax and tumor mass, lower values for kurtosis and inverse variance on 3-voxel distance than those of fusion-negative tumors (sensitivity and specificity, 0.73 and 0.70, respectively). ALK fusion-positive tumors were significantly different in tumor stage, central location, SUVmax, homogeneity on 1-, 2-, and 3-voxel distances, and sum mean on 2-voxel distance compared with ROS1/RET fusion-positive tumors.ALK/ROS1/RET fusion-positive lung adenocarcinomas possess certain clinical and imaging features that enable good discrimination of fusion-positive from fusion-negative lung adenocarcinomas.
The Effects of a Worksite On-line Health Education Program on Metabolic Syndrome Risk Factors and Nutrient Intakes of Male Workers

Worksite health promotion programs have been associated with reductions in health risks but are labor-intensive and costly to implement. Therefore, innovative strategies to provide a cost-effective approach to health education program are needed. The purpose of this study was to investigate the effects of a worksite on-line health education program by email on metabolic syndrome risk factors and dietary intakes in male workers with metabolic syndrome. Anthropometric and biochemical parameters were measured and the nutrient intakes were assessed through FFQ. The diagnosis of metabolic syndrome was adapted from NCEP-ATP Ⅲ with blood pressure, fasting blood glucose, triglyceride, HDL cholesterol, and Asia-Pacific definition with waist circumference. The education group consisted of 212 male workers and the non-education group of 236 age-matched male workers. The on-line health education program provided 10 sessions by e-mail. After a worksite on-line health education program, systolic blood pressure (p < 0.001), diastolic blood pressure (p < 0.001) and fasting blood glucose (p < 0.001) were significantly decreased and HDL cholesterol (p < 0.001) was significantly increased in the education group. Intakes of total energy (p < 0.05), carbohydrate (p < 0.05), sodium (p < 0.05) were significantly decreased in the education group, but there were no significant differences in dietary intakes in the non-education group after a worksite on-line health education program. The results indicate that online health education program by e-mail is effective for improving metabolic syndrome risk factors and dietary intakes in male workers and show potential for use in the working setting.
Estrogen/hormone replacement therapy present and past

One hundred and fifty years ago, the pharmacist Ernst Schering founded the ‘green pharmacy’ in the center of Berlin. He generated the basis for the Schering company of today. The first product ‘Piperazin’ which was promoted as a ‘fountain of youth for the male’ was unsuccessful. Years later, however, this drug proved itself to be effective in the treatment of gout and arthritis. Around 1925, Schering started to work in the field of sex hormones, and, in 1928, the first climacteric estrogenic product Progynon was developed, followed by Proluton in 1933, the first progestogenic compound. Another area of research was the development of male androgens, Proviron in 1934 and Testoviron in 1937. One of the milestones within this history of inventions was the synthesis of ethinylestradiol, the orally effective estrogen component in the contraceptive ‘pill’. The earliest modern investigations into the endocrine function of the female gonads can probably be traced back to Vienna. Three gynecologists, Rudolf Chrobak, Emil Knauer and Josef Halban, were protagonists in the treatment of climacteric symptoms. They also believed in the possibility that a substance in the ovary stimulates the uterus and other genital organs. Progress was made when Edgar Allen, together with Dr Doisy, developed a semi-quantitative assay for the determination of the estrus response. Selmar Aschheim and Bernhard Zondek from the Berlin-Charité Hospital demonstrated that this estrus-producing compound is contained in the urine of pregnant women. Hormone research at Schering was initiated by Walter Schoeller as early as 1923. Schoeller, in successful collaboration with the chemist Adolf Butenandt (University of Göttingen), developed the first estrogenic preparation Progynon for climacteric symptoms. The material source was primarily from animal placentas and later from female urine.
Constitutive activation of Bruton's tyrosine kinase induces the formation of autoreactive IgM plasma cells

B‐cell receptor (BCR)‐mediated signals provide the basis for B‐cell differentiation in the BM and subsequently into follicular, marginal zone, or B‐1 B‐cell subsets. We have previously shown that B‐cell‐specific expression of the constitutive active E41K mutant of the BCR‐associated molecule Bruton's tyrosine kinase (Btk) leads to an almost complete deletion of immature B cells in the BM. Here, we report that low‐level expression of the E41K or E41K‐Y223F Btk mutants was associated with reduced follicular B‐cell numbers and significantly increased proportions of B‐1 cells in the spleen. Crosses with 3‐83μδ and VH81X BCR Tg mice showed that constitutive active Btk expression did not change follicular, marginal zone, or B‐1 B‐cell fate choice, but resulted in selective expansion or survival of B‐1 cells. Residual B cells were hyperresponsive and manifested sustained Ca2+ mobilization. They were spontaneously driven into germinal center‐independent plasma cell differentiation, as evidenced by increased numbers of IgM+ plasma cells in spleen and BM and significantly elevated serum IgM. Because anti‐nucleosome autoantibodies and glomerular IgM deposition were present, we conclude that constitutive Btk activation causes defective B‐cell tolerance, emphasizing that Btk signals are essential for appropriate regulation of B‐cell activation.
Computer-assisted diagnosis in CT angiography of abdominal aortic aneurysms

The purpose of this study was to develop methods for automatic 3D-segmentation and automatic quantification of vascular structures in CT angiographic studies, e.g., abdominal aortic aneurysms. Methods for segmentation were developed based on thresholding, maximum gradient, and second derivative techniques. All parameters for the segmentation are generated automatically, i.e. no user interaction is necessary for this process. Median filtering of all images is initially performed to reduce the image noise. The algorithm then automatically identifies the starting point inside the aorta for the volume growing. The segmentation of the vascular tree is achieved in two steps. First, only the aorta and small parts of branch vessels are segmented by using strong restrictions in the parameters for threshold and gradient. A description of the aorta is generated by fitting the detected outer border of the aorta with an ellipse. This description includes centerline, direction, contour, eccentricity, and area. In the second step, segmentation parameters are changed automatically for segmentation of branch vessels. A shaded surface display of the segmented structures is then generated. The segmentation of the aorta appears accurate, is fast, and the 3D display can be manipulated in real time. The quantitative description of the aorta is reliable giving reproducible information. Total CPU time for the segmentation and description is less than five minutes on a standard workstation. Time-consuming manual segmentation and parameterization of vascular structures are obviated, with 3D visualization and quantitative results available in minutes instead of hours. This technique for segmentation and description of the aorta and renal arteries shows the feasibility of computer assisted diagnosis in CT angiographic studies without user interaction. Besides the description, a rapid 3D view of the vessels is generated, often needed by the physician and normally only achievable by time consuming manual segmentation.
In vitro investigations of the effect of probiotics and prebiotics on selected human intestinal pathogens.

Abstract This study investigated the effects of selected probiotic microorganisms, in combination with prebiotics, on certain human intestinal food-borne pathogens. Probiotics grown with different carbohydrate sources were observed to inhibit growth of Escherichia coli, Campylobacter jejuni and Salmonella enteritidis, with the extent of inhibition varying according to the carbohydrate source provided. Prebiotics identified as being preferentially utilised by the probiotics tested were oligofructose (FOS), inulin, xylo-oligosaccharide (XOS), and mixtures of inulin:FOS (80:20 w/w) and FOS:XOS (50:50 w/w). Two of the probiotics, Lactobacillus plantarum and Bifidobacterium bifidum were selected for further co-culture experiments. Each was combined with the selected prebiotics, and was observed to inhibit pathogen growth strongly. Results suggested that acetate and lactate were directly conferring antagonistic action, which was not necessarily related to a lowering of culture pH.
Amplification of cytokine production through synergistic activation of NFAT and AP‐1 following stimulation of mast cells with antigen and IL‐33

IL‐33 is associated with atopic and autoimmune diseases and, as reported here, it interacts synergistically with Ag to markedly enhance production of inflammatory cytokines in rodent mast cells even in the absence of degranulation. Investigation of the underlying mechanisms revealed that synergy in signaling occurred at the level of TGF‐β‐activated kinase 1, which was then transmitted downstream through JNK, p38 MAP kinase, and AP‐1. Stimulation of the Ca2+/calcineurin/NFAT pathway by Ag, which IL‐33 did not, was critical for the synergy between Ag and IL‐33. For example, selective stimulation of the NFAT pathway by thapsigargin also markedly enhanced responses to IL‐33 in a calcineurin‐dependent manner. As indicated by luciferase‐reporter assays, IL‐33 failed to stimulate the transcriptional activities of NFAT and AP‐1 but augmented the activation of these transcription factors by Ag or thapsigargin. Robust stimulation of NF‐κB transcriptional activity by IL‐33 was also essential for the synergy. These and pharmacologic data suggested that the enhanced production of cytokines resulted in part from amplification of the activation of AP‐1 and NFAT as well as co‐operative interactions among transcription factors. IL‐33 may retune mast cell responses to Ag toward enhanced cytokine production and thus determine the symptoms and severity of Ag‐dependent allergic and autoimmune diseases.
Influence of depth and sampling time on bacterial community structure in an upland grassland soil.

Abstract Temporal and spatial variation of soil bacterial communities was evaluated with both molecular and metabolic profiling techniques. Soil cores (20 cm deep) were taken from an upland grassland in the Scottish Borders (UK) over 3 days in July 1999, and on single days in October 1999, April 2000, and August 2000. Cores were separated into four 5-cm depths to examine vertical spatial distribution. The 0-5-, 5-10- and 10-15-cm samples represented organic horizons whilst the 15-20-cm depths were from a mineral horizon. The potential metabolic activities were analysed using BIOLOG-GN plates, whereas genotypic diversity was evaluated using molecular profiling of amplified 16S rRNA and 16S rDNA gene fragments (denaturing gradient gel electrophoresis (DGGE)). BIOLOG-GN analysis revealed decreased substrate utilisation in the lowest depths, which was coupled with changes in the DNA and RNA DGGE profiles. Seasonal variation was pronounced in the 5-10-cm and 10-15-cm organic horizons for the July samplings whilst the 15-20-cm depths appeared more stable. Potential factors influencing the observed changes in bacterial communities resulting from soil depth and sampling time are discussed.
Flow cytometry discrimination between bacteria and clay-humic acid particles during growth-linked biodegradation of phenanthrene by Pseudomonas aeruginosa 19SJ.

Abstract Methods that quickly assess microbial density and aggregation in soil and sediments are needed in environmental microbiology. We report a flow cytometry method that uses the green and orange emission of the fluorochrome SYTO-13 to discriminate between bacteria and clay-humic acid particles. This approach distinguishes single or clustered bacteria, and clusters of bacteria and abiotic particles during the growth of the biosurfactant-producing strain Pseudomonas aeruginosa 19SJ on solid phenanthrene in the presence of humic acid-clay complexes.