Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Current State of Open MPI on Cray Systems

Open MPI provides an implementation of the MPI standard supporting native communication over a range of high-performance network interfaces. Los Alamos National Laboratory (LANL) and Oak Ridge National Laboratory (ORNL) collaborated on creating a port for Cray XE and XK systems. That work has continued and with the release of version 1.8 Open MPI now conforms to MPI-2.2 and MPI-3.0 on Cray XE, XK, and XC systems. The features introduced with this work include dynamic process support (MPI_Comm_spawn()), important for implementing faulttolerant MPI systems; improved collective operations required for scalability and performance of applications; and Aries support to enable running Open MPI on Cray XC systems. In this paper, we present an update on the design and implementation of Open MPI for Cray systems and evaluate the performance and scaling characteristics on both Gemini and Aries networks. Keywords-Open MPI; Cray; Gemini; Aries; uGNI; Generic Network Interface; XPMEM
Does reduced heterozygosity influence dispersal? A test using spatially structured populations in an alpine ungulate

Despite having a profound effect on population dynamics, the reasons that animals disperse are poorly understood. Evolutionary explanations have focused on inbreeding and competition, where the potential cost of philopatry is negated through dispersal. Such scenarios lead to the prediction that less successful individuals preferentially disperse, termed ‘fitness-associated dispersal’. Since heterozygosity is associated with fitness, we assessed whether dispersed animals had less observed heterozygosity (HO) than residents. We tested this prediction using both genetic and population-monitoring data of mountain goats (Oreamnos americanus). Individuals classified as dispersers through cross-assignment had the lowest mean HO, followed by residents, and then admixed individuals. Dispersed individuals had 6.3 per cent less HO than their subpopulation of origin. In the long-term study of the mountain goat herd at Caw Ridge, Alberta, immigrants had the lowest HO; however, the opposite pattern was seen in emigrants, which may be related to density dependence. This study is the first to provide empirical evidence that heterozygosity is associated with dispersal.
Monitoring peanut allergen in food products by measuring Ara h 1.

BACKGROUND Peanut allergy is an important health problem in the United States, affecting approximately 0.6% of children. Inadvertent exposure to peanut is a risk factor for life-threatening food-induced anaphylaxis. OBJECTIVE The purpose of this investigation was to develop an immunoassay for a major peanut allergen, Ara h 1, to detect peanut allergen in foods so that the risk of inadvertent exposure can be reduced. METHODS A specific 2-site monoclonal antibody-based ELISA was developed to measure Ara h 1 in foods. The sensitivity of the assay was 30 ng/mL. Ara h 1 was measured in foods (n = 83) with or without peanut and in experiments to optimize allergen yield and to determine peanut contamination in spiked foods. RESULTS Ara h 1 levels in food products ranged from less than 0.1 microg/g to 500 microg/g. Ara h 1 measured in ng/mL was transformed to microg/g for food products. Peanut butter contained the highest amounts of Ara h 1. Peanut extracts contained from 0.5 to 15 mg Ara h 1/g of peanut depending on the extraction conditions. Optimal extraction of Ara h 1 was obtained by using phosphate buffer with 1 mol/L NaCl and Tween at 60 degrees C. Ara h 1 was not always detected in presence of chocolate under the extraction conditions tested. Spiking experiments showed that the assay could detect approximately 0.1% Ara h 1 contamination of food with ground peanut. There was an excellent correlation between Ara h 1 levels and peanut content measured by using a commercial polyclonal antibody-based ELISA (r = 93, n = 31, P <.001). CONCLUSION A new sensitive and specific monoclonal antibody-based ELISA was used to monitor Ara h 1 content in food products. This assay should be useful for monitoring peanut contamination in the food manufacturing and processing industry and in developing thresholds for sensitization or allergic reaction in persons with peanut allergy.
Media Now: A Historical Review of a Media Literacy Curriculum.

The Elizabeth Thoman Archive at the Harrington School of Communication and Media, University of Rhode Island, has the last complete kit of one of the milestones in the early chronology of media literacy, the 1972 Media Now curriculum. This curriculum was the first of its kind, using self-contained lesson modules that were part of a larger series of kits, text references, and accompanying workbook. Its self-directed learning model gave students the opportunity to learn about the media, by doing, responding to, and reflecting on core concepts of media production. Using physical artifacts from the Media Now kit, historical documents, promotional materials, phone interviews with the founders and teachers of the curriculum, the authors were able to trace the development of Media Now from its historical and educational roots of the 1960s, to its full production, distribution, and training out of the facility at the Southwest Iowa Learning Resource Center (SILRC). The historical and educational impetus for creation of what started as a Title III innovation grant of the Elementary and Secondary Educational Act of 1965, matured to be a curriculum that was implemented in 600 schools across the U.S a testament to both its need and its success. However, as times and politics changed, federal and local government cut funding for Media Now. As we reviewed its original approach to curriculum design and pedagogy, we found that the Media Now story calls for a new examination of the creative materials and techniques used in the 1970s, in light of the current need for media literacy education in and outside of the 21st century digital classroom.
Oestrogen receptor co-activator AIB1 is a marker of tamoxifen benefit in postmenopausal breast cancer

Background The oestrogen receptor (ER) co-activator amplified in breast cancer 1 (AIB1) has been suggested as a treatment predictive and prognostic marker in breast cancer. Studies have however not been unanimous. Patients and methods AIB1 protein expression was analysed by immunohistochemistry on tissue micro-arrays with tumour samples from 910 postmenopausal women randomised to tamoxifen treatment or no adjuvant treatment. Associations between AIB1 expression, clinical outcome in the two arms and other clinicopathological variables were examined. Results In patients with ER-positive breast cancer expressing low tumour levels of AIB1 (<75%), we found no significant difference in recurrence-free survival (RFS) or breast cancer-specific survival (BCS) between tamoxifen treated and untreated patients. In patients with high AIB1 expression (>75%), there was a significant decrease in recurrence rate (HR 0.40, 95% CI 0.26–0.61, P < 0.001) and breast cancer mortality rate (HR 0.38, 95% CI 0.21–0.69, P = 0.0015) with tamoxifen treatment. In the untreated arm, we found high expression of AIB1 to be significantly associated with lower RFS (HR 1.74, 95% CI 1.20–2.53, P = 0.0038). Conclusion Our results suggest that high AIB1 is a predictive marker of good response to tamoxifen treatment in postmenopausal women and a prognostic marker of decreased RFS in systemically untreated patients.
Tropical freshwater ecosystems have lower bacterial growth efficiency than temperate ones

Current models and observations indicate that bacterial respiration should increase and growth efficiency (BGE) should decrease with increasing temperatures. However, these models and observations are mostly derived from data collected in temperate regions, and the tropics are under-represented. The aim of this work was to compare bacterial metabolism, namely bacterial production (BP) and respiration (BR), bacterial growth efficiency (BGE) and bacterial carbon demand (BCD) between tropical and temperate ecosystems via a literature review and using unpublished data. We hypothesized that (1) tropical ecosystems have higher metabolism than temperate ones and, (2) that BGE is lower in tropical relative to temperate ecosystems. We collected a total of 498 coupled BP and BR observations (Ntotal = 498; Ntemperate = 301; Ntropical = 197), calculated BGE (BP/(BP+BR)) and BCD (BP+BR) for each case and examined patterns using a model II regression analysis and compared each parameter between the two regions using non-parametric Mann–Whitney U test. We observed a significant positive linear regression between BR and BP for the whole dataset, and also for tropical and temperate data separately. We found that BP, BR and BCD were higher in the tropics, but BGE was lower compared to temperate regions. Also, BR rates per BP unit were at least two fold higher in the tropics than in temperate ecosystems. We argue that higher temperature, nutrient limitation, and light exposure all contribute to lower BGE in the tropics, mediated through effects on thermodynamics, substrate stoichiometry, nutrient availability and interactions with photochemically produced compounds. More efforts are needed in this study area in the tropics, but our work indicates that bottom-up (nutrient availability and resource stoichiometry) and top-down (grazer pressure) processes, coupled with thermodynamic constraints, might contribute to the lower BGE in the tropics relative to temperate regions.
Information processing approaches to emotion

A digital printer has a printhead ( 10 ) for printing on a substrate and an encoder ( 14 ) which emits pulses ( 122 ) to indicate the relative distance moved by the printhead. A timer device for the digital printer emits output print pulses ( 151 ) for effecting printing and a count module ( 130 ) for receiving pulses ( 122 ) from the encoder ( 14 ) and emitting a print signal after a predetermined number of encoder pulses ( 122 ) to effect the emission of the output print pulse. The timer device is adapted to add a delay between the emission of the print signal and the emission of the output print pulse ( 151 ). In examples described, the pitch of the printed droplets can be closely controlled.
How do cancer patients manage unattainable personal goals and regulate their emotions?

OBJECTIVES This article addressed the role of goal adjustment (i.e. disengagement from unattainable goals and reengagement in alternative goals) and cognitive emotion-regulation strategies (i.e. rumination, catastrophizing, positive refocusing) in cancer patients' psychological well-being. We expected that patients who are better able to disengage from unattainable goals, identify alternative goals, and regulate their emotions by positive refocusing and not engaging in rumination and catastrophizing would experience less negative and more positive affect. DESIGN In this cross-sectional study, data were collected using a self-report questionnaire. METHODS Cancer patients (N=108) were recruited on a psychoeducational meeting aimed to inform them about the illness and its consequences. To examine the relationships between goal adjustment, cognitive emotion-regulation strategies, and affect, Pearson correlations were calculated and regression analyses were performed. RESULTS Regression analyses showed that reengaging in meaningful goals and focusing on pleasant issues were significantly associated with more positive affect. Focusing on pleasant issues was also significantly associated with less negative affect, whereas rumination and catastrophizing were significantly associated with more negative affect. CONCLUSIONS Goal reengagement as well as cognitive emotion-regulation strategies seems to play an important role in cancer patients' psychological well-being. Health care professionals may assist patients in paying more attention to positive experiences in their daily life and in finding new meaningful goals. Techniques based on mindfulness may be used to assist cancer patients in decreasing the repetitive negative thinking about causes, meanings, and consequences of the illness and helping them to focus attention on the present moment.
Rejoining of Radiation-Induced DNA Double-Strand Breaks: Pulsed-Field Electrophoresis Analysis of Fragment Size Distributions after Incubation for Repair

Abstract Gauter, B. , Zlobinskaya, O. and Weber, K. J. Rejoining of Radiation-Induced DNA Double-Strand Breaks: Pulsed-Field Electrophoresis Analysis of Fragment Size Distributions after Incubation for Repair. Radiat. Res. 157, 721–733 (2002). The repair of radiation-induced DNA double-strand breaks (DSBs) is frequently investigated by measuring the time-dependent decrease in the fraction of fragmented DNA that is able to enter electrophoresis gels. When transformed into equivalent doses without repair, such measurements are thought to reflect the removal of DSBs, and they typically exhibit a fast initial component and a decreasing rate at longer repair intervals. This formalism, however, assumes that the spatial distribution of unrejoined breakage resembles the pattern of induction of DSBs. While the size distributions for initial fragmentation, such as that resolved by conventional pulsed-field gel electrophoresis (PFGE) (between about 105 and 107 bp), are well known to agree with the prediction of random breakage, no data are available from studies explicitly testing this relationship for residual breakage. Therefore, Chinese hamster V79 cells and MeWo (human melanoma) cells were irradiated with different doses (10–100 Gy) or were incubated for repair for up to 4 h after a single dose of 100 Gy (V79) or 90 Gy (MeWo) before being subjected to PFGE. Fragment size distributions were calculated by convolution of the PFGE profiles with an appropriately generated size calibration function. The results clearly demonstrate an over-representation of smaller fragments (below about 2–3 Mbp) compared to the prediction of randomness for residual breakage. In consequence, the time-dependent decrease of dose-equivalent values calculated from data on the fraction released may not directly reflect DSB rejoining rates. The present findings are compatible with an earlier suggestion of slow rejoining of breaks which have been induced as multiple breaks (two or more) in large chromosomal loops, thus also predicting an increase of the slowly rejoining DSB fraction with increasing dose.
The role of the dynein light intermediate chain in retrograde IFT and flagellar function in Chlamydomonas

D1bLIC is a subunit of the retrograde IFT motor. Knockdown or knockout of D1bLIC has dose-dependent effects on flagellar assembly, length, motility, and signaling. iTRAQ-based proteomics identifies novel proteins altered in d1blic mutant flagella. TIRF microscopy reveals the kinetics and remodeling of the retrograde motor at the flagellar tip.
Approximate Nearest Subspace Search

Subspaces offer convenient means of representing information in many pattern recognition, machine vision, and statistical learning applications. Contrary to the growing popularity of subspace representations, the problem of efficiently searching through large subspace databases has received little attention in the past. In this paper, we present a general solution to the problem of Approximate Nearest Subspace search. Our solution uniformly handles cases where the queries are points or subspaces, where query and database elements differ in dimensionality, and where the database contains subspaces of different dimensions. To this end, we present a simple mapping from subspaces to points, thus reducing the problem to the well-studied Approximate Nearest Neighbor problem on points. We provide theoretical proofs of correctness and error bounds of our construction and demonstrate its capabilities on synthetic and real data. Our experiments indicate that an approximate nearest subspace can be located significantly faster than the nearest subspace, with little loss of accuracy.
Ralstonia eutropha H16 Encodes Two and Possibly Three Intracellular Poly[d-(−)-3-Hydroxybutyrate] Depolymerase Genes

ABSTRACT Intracellular poly[d-(−)-3-hydroxybutyrate] (PHB) depolymerases degrade PHB granules to oligomers and monomers of 3-hydroxybutyric acid. Recently an intracellular PHB depolymerase gene (phaZ1) from Ralstonia eutropha was identified. We now report identification of candidate PHB depolymerase genes from R. eutropha, namely, phaZ2 and phaZ3, and their characterization in vivo. phaZ1 was used to identify two candidate depolymerase genes in the genome of Ralstonia metallidurans. phaZ1 and these genes were then used to design degenerate primers. These primers and PCR methods on the R. eutropha genome were used to identify two new candidate depolymerase genes in R. eutropha: phaZ2 and phaZ3. Inverse PCR methods were used to obtain the complete sequence of phaZ3, and library screening was used to obtain the complete sequence of phaZ2. PhaZ1, PhaZ2, and PhaZ3 share ∼30% sequence identity. The function of PhaZ2 and PhaZ3 was examined by generating R. eutropha H16 deletion strains (ΔphaZ1, ΔphaZ2, ΔphaZ3, ΔphaZ1ΔphaZ2, ΔphaZ1ΔphaZ3, ΔphaZ2ΔphaZ3, and ΔphaZ1ΔphaZ2ΔphaZ3). These strains were analyzed for PHB production and utilization under two sets of conditions. When cells were grown in rich medium, PhaZ1 was sufficient to account for intracellular PHB degradation. When cells that had accumulated ∼80% (cell dry weight) PHB were subjected to PHB utilization conditions, PhaZ1 and PhaZ2 were sufficient to account for PHB degradation. PhaZ2 is thus suggested to be an intracellular depolymerase. The role of PhaZ3 remains to be established.
Reduction of Crosstalk Pessimism Using Tendency Graph Approach

Accurate estimation of worst-case crosstalk effects is critical for a realistic estimation of the worst-case behavior of deep sub-micron circuits. Crosstalk analysis models usually assume that the worst-case crosstalk occurs with all the aggressors of a victim (net or path) simultaneously inducing crosstalk even though this may not be possible at all. This overestimated crosstalk is called false noise. Logic correlations have been explored to reduce false noise in J.C. Beck, et al., (2004), which also used branch and bound method to solve the problem. In this paper, we propose a novel approach, named tendency graph approach (TGA), which preprocesses the logic constraints of the circuit to drastically speed up the fundamental branch and bound algorithm. The new approach has been implemented in C++ and tested on an industrial circuit in a current 90 nm technology, demonstrating that TGA considerably accelerates the solution to the false noise problem, and makes in many cases branch and bound feasible in the first place.
The Relationships Of Job And Life Satisfaction With Intention To Leave Among Unionized Hotel Employees In Turkey

Turnover becomes a major concern for Turkey’s tourism sector in which the experienced labour shortages is common. Studying intention to leave and predictors of it will be enlighting for the growing sector. Moving from this point, this study first tries to reveal the job and life satisfaction level of unionized hotel employees, and then test these variables’ effect on intention to leave among a selection of unionized hotels in Turkey in an attempt to shed light to an underresearched topic in unionized hotel settings. Respondents (n=1298) are the members of TOLEYIS union dispersed to different touristic regions in Turkey. Employees have moderate level of job satisfaction. Results show that demographic variables and the employing hotel have effects on each satisfaction. The effect of job satisfaction and number of hotel’s stars on intention to leave is significant. Implications of the findings and future research directions are discussed.
Characterization of Escherichia coli thioredoxin variants mimicking the active‐sites of other thiol/disulfide oxidoreductases

Thiol/disulfide oxidoreductases like thioredoxin, glutaredoxin, DsbA, or protein disulfide isomerase (PDI) share the thioredoxin fold and a catalytic disulfide bond with the sequence Cys‐Xaa‐Xaa‐Cys (Xaa corresponds to any amino acid). Despite their structural similarities, the enzymes have very different redox properties, which is reflected by a 100,000‐fold difference in the equilibrium constant (Keq) with glutathione between the most oxidizing member, DsbA, and the most reducing member, thioredoxin. Here we present a systematic study on a series of variants of thioredoxin from Escherichia coli, in which the Xaa‐Xaa dipeptide was exchanged by that of glutaredoxin, PDI, and DsbA. Like the corresponding natural enzymes, all thioredoxin variants proved to be stronger oxidants than the wild‐type, with the order wild‐type < PDI‐type < DsbA‐type < glutaredoxin‐type. The most oxidizing, glutaredoxin‐like variant has a 420‐fold decreased value of Keq, corresponding to an increase in redox potential by 75 mV. While oxidized wild‐type thioredoxin is more stable than the reduced form (ΔΔGox/red = 16.9 kJ/mol), both redox forms have almost the same stability in the variants. The pH‐dependence of the reactivity with the alkylating agent iodoacetamide proved to be the best method to determine the pKa value of thioredoxin's nucleophilic active‐site thiol (Cys32). A pKa of 7.1 was measured for Cys32 in the reduced wild‐type. All variants showed a lowered pKa of Cys32, with the lowest value of 5.9 for the glutaredoxin‐like variant. A correlation of redox potential and the Cys32 pKa value could be established on a quantitative level. However, the predicted correlation between the measured ΔΔGox/red values and Cys32 pKa values was only qualitative.
Dataxformer: Leveraging the Web for Semantic Transformations

Data transformation is a crucial step in data integration. While some transformations, such as liters to gallons, can be easily performed by applying a formula or a program on the input values, others, such as zip code to city, require sifting through a repository containing explicit value mappings. There are already powerful systems that provide formulae and algorithms for transformations. However, the automated identication of reference datasets to support value mapping remains largely unresolved. The Web is home to millions of tables with many containing explicit value mappings. This is in addition to value mappings hidden behind Web forms. In this paper, we present DataXFormer, a transformation engine that leverages Web tables and Web forms to perform transformation tasks. In particular, we describe an inductive, lter-rene approach for identifying explicit transformations in a corpus of Web tables and an approach to dynamically retrieve and wrap Web forms. Experiments show that the combination of both resource types covers more than 80% of transformation queries formulated by real-world users.