Miracle-dz/UniFAR-FTUs huggingface dataset:
On Drawings and Decompositions of 1-Planar Graphs

A graph is called 1-planar if it can be drawn in the plane so that each of its edges is crossed by at most one other edge. We show that every 1-planar drawing of any 1-planar graph on $n$ vertices has at most $n-2$ crossings; moreover, this bound is tight. By this novel necessary condition for 1-planarity, we characterize the 1-planarity of Cartesian product $K_m\times P_n$. Based on this condition, we also derive an upper bound on the number of edges of bipartite 1-planar graphs, and we show that each subgraph of an optimal 1-planar graph (i.e., a 1-planar graph with $n$ vertices and $4n-8$ edges) can be decomposed into a planar graph and a forest.
Effects of amino acids on expression of enterococcal vancomycin resistance

The effects of various amino acids on vancomycin MICs obtained with resistant enterococci was investigated by using broth dilution testing. For both the type A (i.e., possessing transferable resistance to teicoplanin and vancomycin) and the type B (i.e., possessing teicoplanin susceptibility and nontransferable vancomycin resistance) resistant strains, vancomycin MICs in the presence of glycine were substantially lower than those in unsupplemented broth (range of MIC decrease, 8- to 128-fold). No such effect was seen with Enterococcus gallinarum AIB-39 or with the susceptible control Enterococcus faecalis ATCC 29212. Further testing of two type B strains (E. faecalis V583 and V583-2) showed that certain other amino acids (i.e., D-methionine, D-serine, D-alanine, and D-phenylalanine) had effects similar to that of glycine. Results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis with membrane preparations from these strains revealed the production of vancomycin-inducible proteins of sizes comparable to those describe for other enterococcal isolates that exhibit acquired vancomycin resistance. Even in the presence of 0.2 M glycine, the inducible proteins were produced. These results indicate that certain amino acids specifically interfere with the mechanism(s) of acquired vancomycin resistance in enterococci and that the nature of interference probably involves inhibition or circumvention of the inducible proteins' functions.
Cefoxitin resistance as a surrogate marker for the detection of methicillin-resistant Staphylococcus aureus.

OBJECTIVES To evaluate the usefulness of cefoxitin when used as a surrogate marker for the detection of methicillin resistance. PATIENTS AND METHODS Eight hundred and seventy-one strains of Staphylococcus aureus, collected from eight tertiary referral centres serving diverse socio-economic populations, were included in the study using NCCLS disc diffusion and the agar dilution methods. RESULTS Using cefoxitin and NCCLS criteria for disc diffusion, the sensitivity and specificity for recognizing methicillin resistance were both 100%. Similar results were obtained when the strains were tested by the agar dilution method. The cefoxitin MICs for methicillin-susceptible strains were < or = 4 mg/L. CONCLUSIONS Testing with cefoxitin as a surrogate marker for the detection of methicillin resistance was very accurate with both disc diffusion and agar dilution methods. Such testing clearly distinguished methicillin-resistant strains of S. aureus from methicillin-susceptible strains.
h-Caldesmon, a Useful Positive Marker in the Diagnosis of Pleural Malignant Mesothelioma, Epithelioid Type

Although a large number of immunohistochemical markers that can facilitate the differential diagnosis between epithelioid pleural mesothelioma and lung adenocarcinoma involving the pleura have proven to be valuable, no single antibody has demonstrated absolute sensitivity and/or specificity in making this distinction. Using immunohistochemical analysis with h-caldesmon, a specific marker for smooth muscle tumors, we examined 70 cases of epithelial mesotheliomas and 70 cases of lung adenocarcinomas. In addition, immunohistochemistry for muscle markers, such as desmin, alpha-smooth-muscle actin, muscle-specific actin, myoglobin, myogenin, myosin, and MyoD-1, was performed on all mesothelioma cases. Reactivity for h-caldesmon was obtained in 68 (97%) of the 70 epithelial mesotheliomas, but in none of the adenocarcinoma cases. All mesothelioma cases were found to be negative for the other muscle markers examined. We conclude that h-caldesmon is a highly sensitive and specific marker and suggest its inclusion in the immunohistochemical panel for the differential diagnosis of epithelioid mesothelioma versus lung adenocarcinoma.
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis

The immense volume of data resulting from DNA microarray experiments, accompanied by an increase in the number of publications discussing gene-related discoveries, presents a major data analysis challenge. Current methods for genome-wide analysis of expression data typically rely on cluster analysis of gene expression patterns. Clustering indeed reveals potentially meaningful relationships among genes, but can not explain the underlying biological mechanisms. In an attempt to address this problem, we have developed a new approach for utilizing the literature in order to establish functional relationships among genes on a genome-wide scale. Our method is based on revealing coherent themes within the literature, using a similarity-based search in document space. Content-based relationships among abstracts are then translated into functional connections among genes. We describe preliminary experiments applying our algorithm to a database of documents discussing yeast genes. A comparison of the produced results with well-established yeast gene functions demonstrates the effectiveness of our approach.
The fascinating and secret wild life of the budding yeast S. cerevisiae

The budding yeast Saccharomyces cerevisiae has been used in laboratory experiments for over a century and has been instrumental in understanding virtually every aspect of molecular biology and genetics. However, it wasn't until a decade ago that the scientific community started to realise how little was known about this yeast's ecology and natural history, and how this information was vitally important for interpreting its biology. Recent large-scale population genomics studies coupled with intensive field surveys have revealed a previously unappreciated wild lifestyle of S. cerevisiae outside the restrictions of human environments and laboratories. The recent discovery that Chinese isolates harbour almost twice as much genetic variation as isolates from the rest of the world combined suggests that Asia is the likely origin of the modern budding yeast. DOI: http://dx.doi. org/10.7554/eLife.05835. 001
Highly Reliable Heterologous System for Evaluating Resistance of Clinical Herpes Simplex Virus Isolates to Nucleoside Analogues

ABSTRACT Clinical resistance of herpes simplex virus (HSV) types 1 and 2 to acyclovir (ACV) is usually caused by the presence of point mutations within the coding region of the viral thymidine kinase (TK) gene. The distinction between viral TK mutations involved in ACV resistance or part of viral polymorphism can be difficult to evaluate with current methodologies based on transfection and homologous recombination. We have developed and validated a new heterologous system based on the expression of the viral TK gene by the protozoan parasiteLeishmania, normally devoid of TK activity. The viral TK genes from 5 ACV-susceptible and 13 ACV-resistant clinical HSV isolates and from the reference strains MS2 (type 2) and KOS (type 1) were transfected as part of an episomal expression vector inLeishmania. The susceptibility of TK-recombinant parasites to ganciclovir (GCV), a closely related nucleoside analogue, was evaluated by a simple measurement of the absorbance ofLeishmania cultures grown in the presence of the drug. Expression of the TK gene from ACV-susceptible clinical isolates resulted in Leishmania susceptibility to GCV, whereas expression of a TK gene with frameshift mutations or nucleotide substitutions from ACV-resistant isolates gave rise to parasites with high levels of GCV resistance. The expression of the HSV TK gene inLeishmania provides an easy, reliable, and sensitive assay for evaluating HSV susceptibility to nucleoside analogues and for assessing the role of specific viral TK mutations.
Use of the doubly-labeled water method to assess energy expenditure in free living cats and dogs.

The doubly-labeled water method uses naturally occurring stable isotopes of water (H2 18O and D2O) to assess energy expenditure, body composition and water flux in animals and humans. The technique is relatively noninvasive (a few blood or urine samples over 2 wk) and is performed in free living conditions during a period of between 5 and 20 d. This is the first report of the use of the method in three cats and two dogs. The measured energy expenditure during 11 d was 207 +/- 12 and 263 kJ.kg-1.d-1 for cats and dogs, respectively. These values were 30 and 10% lower, respectively, than NRC recommendations for energy requirement (NRC 1985, NRC 1986). The percentage body fat was 23 +/- 5% in the three cats and 35% in the two dogs used in this study. The water output (urine + breath) was 36 +/- 4 ml.kg-1.d-1 for the cats and 60 ml.kg-1.d-1 for the dogs. Of the water output, 23% (cats) and 17% (dogs) was lost as insensible water loss. The precision and accuracy of the method are discussed in relation to the assumptions made with this technique and by comparison with published values.
Quenching of the Radio Jet during the X-Ray High State of GX 339–4

We have observed the black hole candidate X-ray binary GX 339-4 at radio wavelengths before, during, and after the 1998 high/soft X-ray state transition. We find that the radio emission from the system is strongly correlated with the hard X-ray emission and is reduced by a factor of ≥25 during the high/soft state compared with the more usual low/hard state. At the points of state transition, we note brief periods of unusually optically thin radio emission that may correspond to discrete ejection events. We propose that in the low/hard state, black hole X-ray binaries produce a quasi-continuous outflow, that in the high/soft state, this outflow is suppressed, and that state transitions often result in one or more discrete ejection events. Future models for low/hard states, such as advection-dominated solutions, need to take into account the strong outflow of relativistic electrons from the system. We propose that the inferred Comptonizing corona and the base of the jetlike outflow are the same thing, based on the strong correlation between radio and hard X-ray emission in GX 339-4 and other X-ray binaries and on the similarity in inferred location and composition of these two components.
Studies on megakaryopoiesis in patients with myelodysplasia and idiopathic thrombocytopenic purpura

In this thesis mechanisms of thrombocytopenia (a low number of platelets) in patients with myelodysplastic syndromes (MDS) or idiopathic thrombocytopenic purpura (ITP) were investigated. Thrombocytopenia can cause serious bleeding complications and elucidation of the underlying pathophysiology of thrombocytopenia in these disorders may lead to new treatment strategies. MDS are a heterogeneous group of bone marrow disorders, in which abnormalities of hematopoietic stem cells result in a decreased production of blood cells, including platelets. In ITP the thrombocytopenia develops because autoantibodies are formed against antigens on platelets leading to increased platelet destruction. In a large subgroup of ITP patients these antibodies also induce a reduced platelet production. In this thesis we provide evidence that premature cell death of megakaryocytes, the bone marrow cells that produce platelets, contributes to the reduced platelet production in both ITP and MDS. The types of cell death in ITP and MDS megakaryocytes, however, are different. The mechanisms for these forms of cell death are not fully elucidated. We show that in ITP factors which are present in the plasma, most likely the antibodies, can induce cell death in megakaryocytes. In MDS intrinsic abnormalities of megakaryocytes are important. External factors, such as signals from the bone marrow microenvironment, may also affect the cell death process in the hematopoietic precursor cells. This was suggested from our study on MDS erythroblasts (precursor cells of red cells). The level of cell death and presence of other abnormalities in these erythroblasts depended on the presence or absence of the bone marrow microenvironment. Finally, we observed that successful prednisone therapy can reverse the cell death abnormalities in ITP megakaryocytes. In keeping with these findings we also found that ITP patients with a decreased platelet production respond better to prednisone therapy than patients with a normal or increased production.
Real-time characterization of the molecular epidemiology of an influenza pandemic

Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We use Bayesian phylogenetics to simulate real-time estimates of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes and the choice of growth model is important for accurate estimation of r0. This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.
Keyword Generation for Search Engine Advertising

Keyword generation for search engine advertising is an important problem for sponsored search or paid-placement advertising. A recent strategy in this area is bidding on nonobvious yet relevant words, which are economically more viable. Targeting many such nonobvious words lowers the advertising cost, while delivering the same click volume as expensive words. Generating the right nonobvious yet relevant keywords is a challenging task. The challenge lies in not only finding relevant words, but also in finding many such words. In this paper, we present TermsNet, a novel approach to this problem. This approach leverages search engines to determine relevance between terms and captures their semantic relationships as a directed graph. By observing the neighbors of a term in such a graph, we generate the common as well as the nonobvious keywords related to a term
Calcium, Magnesium, Iron, Zinc and Copper, Compositions of Human Milk from Populations with Cereal and ‘Enset’ Based Diets

Background As breast milk is normally the only source of food in the early stages of life, the dietary levels of the essential elements in the milk of lactating mothers are significantly important. Ethiopia is a country of many nations and nationalities with distinct dietary habits. This variation in food habit may result in the variation of the nutritional quality of milk of lactating mothers who live in different part of the country, which in turn may affect the intake of nutrients by breast-fed infants. Therefore, a cross-sectional study of the levels of Ca, Mg, Fe, Zn and Cu in milk of mothers from societies with cereal and ‘enset’ based dietary habits was carried out to assess the influence of maternal diet on the levels of the elements in human milk. Methods Milk samples were collected from 27 voluntary mothers in Jimma and in 18 rural areas of Welkite. Breast milk samples were collected within four days postpartum and the concentrations of the elements were determined by using FAAS. Results Average concentrations (mg/L) of the elements determined in the milk of mothers from Jimma and rural Welkite respectively were: Ca (758 ± 107, 579 ± 168); Mg (22.6 ± 7.87, 30.5 ± 13.4); Fe (0.50 ± 0.08, 0.41 ± 0.17); Zn (2.3 ± 1.2, 2.49 ± 0.88) and Cu (0.28 ± 0.14, 0.16 ± 0.08). Conclusions Milk samples from Jimma were found to have significantly higher levels of Ca and Cu than those of rural Welkite (P < 0.05). Breast milk Ca and Cu levels were thus found to be influenced by dietary intake.
Learning people detection models from few training samples

People detection is an important task for a wide range of applications in computer vision. State-of-the-art methods learn appearance based models requiring tedious collection and annotation of large data corpora. Also, obtaining data sets representing all relevant variations with sufficient accuracy for the intended application domain at hand is often a non-trivial task. Therefore this paper investigates how 3D shape models from computer graphics can be leveraged to ease training data generation. In particular we employ a rendering-based reshaping method in order to generate thousands of synthetic training samples from only a few persons and views. We evaluate our data generation method for two different people detection models. Our experiments on a challenging multi-view dataset indicate that the data from as few as eleven persons suffices to achieve good performance. When we additionally combine our synthetic training samples with real data we even outperform existing state-of-the-art methods.
Assessing Subjective Daytime Sleepiness: An Internal State Versus Behavior Approach

Abstract The authors purpose in the current study was to apply P. J. Lang's (1968, 1971, 1985) theory of multiple systems of emotional response to the study of subjective sleepiness. A total of 274 participants completed the Stanford Sleepiness Scale (SSS), the Profile of Mood States (POMS), three sleepiness-related Visual Analogue Scales (VAS), and the Epworth Sleepiness Scale (ESS). The authors completed correlations and factor analysis of the 4 sleepiness measures. The SSS, POMS, and VAS measures were better correlated with each other than with the ESS. Similarly, the SSS, POMS, and VAS measures loaded highly onto one factor, whereas the ESS loaded highly onto a separate factor. These results indicated that the ESS measured a different aspect of subjective sleepiness than the SSS, POMS, or VAS. According to Lang's emotional responses theory, the ESS assessed a behavioral component of sleepiness, and the SSS, POMS, and VAS measures assessed an internal state related to sleepiness.
Soluble ST2 Associates with Diabetes but Not Established Cardiovascular Risk Factors: A New Inflammatory Pathway of Relevance to Diabetes?

Preliminary data mostly from animal models suggest the sST2/IL-33 pathway may have causal relevance for vascular disease and diabetes and thus point to a potential novel inflammatory link to cardiometabolic disease. However, the characterisation of sST2 levels in terms of metabolic or vascular risk in man is completely lacking. We sought to address this gap via a comprehensive analysis of risk factor and vascular correlates of sST2 in a cross-sectional study (pSoBid). We measured sST2 in plasma in 639 subjects and comprehensively related it to cardiovascular and diabetes risk factors and imaged atherosclerosis measures. Circulating sST2 levels increased with age, were lower in women and in highest earners. After adjusting for age and gender, sST2 levels associated strongly with markers of diabetes, including triglycerides [effect estimate (EE) per 1 standard deviation increase in sST2∶1.05 [95%CI 1.01,1.10]), liver function (alanine aminotransaminase [ALT] and γ-glutamyl transferase [GGT]: EE 1.05 [1.01,1.09] and 1.13 [1.07,1.19] respectively), glucose (1.02 [1.00,1.03]) and sICAM-1 (1.05 [1.02,1.07]). However, sST2 levels were not related to smoking, cholesterol, blood pressure, or atheroma (carotid intima media thickness, plaque presence). These results suggest that sST2 levels, in individuals largely without vascular disease, are related principally to markers associated with diabetes and ectopic fat and add support for a role of sST2 in diabetes. Further mechanistic studies determining how sST2 is linked to diabetes pathways may offer new insights into the inflammatory paradigm for type 2 diabetes.
Recent Progress in Intermediate Temperature SOFCs (ITSOFCs) Development at DLR

Metal-supported ITSOFCs having NiO or NiO+YDC 15 anode, yttria stabilized ceria electrolyte (YDC 15) and LSCF or LSCF+CGO composite cathodes were fabricated via plasma spraying for operation in the temperature range of 600-700°C. Highest performance was recorded with NiO+YDC 15 / YDC 15 / LSCF+CGO cells. In the next step it is planned to optimize fabrication parameters in order to attain crack free and thinner electrolytes and more porous composite cathode which will lead to double cell performance.
A pilot study utilizing intraoperative lymphoscintigraphy for identification of the sentinel lymph nodes in vulvar cancer.

OBJECTIVE To identify sentinel lymph nodes using intraoperative lymphoscintigraphy. METHODS Technetium-99-labeled sulfur colloid was injected at the site of primary vulvar carcinoma. An intraoperative gamma counter was used to identify one or more sentinel lymph nodes. RESULTS Ten patients underwent bilateral inguinal and femoral lymphadenectomy. The clinical stages are as follows: T1 in 6, T2 in 2, and T3 in 2. A total of four groins (3 patients) were positive for metastases. In one patient only the sentinel node was positive for disease. In a second patient, two unilateral nodes were positive for disease and both were identified with the gamma counter as sentinel nodes. In the third patient, a single sentinel node was positive for malignancy in each groin. Multiple nonsentinel lymph nodes were positive in each groin in this patient. In no case was the sentinel node negative when other nonsentinel nodes were positive. CONCLUSION Intraoperative lymphoscintigraphy quantitatively identifies one or more sentinel lymph nodes. Since sentinel lymph nodes can be localized transcutaneously, this technique may be useful for selective lymphadenectomy. Larger patient accrual is necessary to verify this technique.