Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection, Characterization, and Biological Effect of Quorum-Sensing Signaling Molecules in Peanut-Nodulating Bradyrhizobia

Bacteria of the genus Bradyrhizobium are able to establish a symbiotic relationship with peanut (Arachis hypogaea) root cells and to fix atmospheric nitrogen by converting it to nitrogenous compounds. Quorum sensing (QS) is a cell-cell communication mechanism employed by a variety of bacterial species to coordinate behavior at a community level through regulation of gene expression. The QS process depends on bacterial production of various signaling molecules, among which the N-acylhomoserine lactones (AHLs) are most commonly used by Gram-negative bacteria. Some previous reports have shown the production of QS signaling molecules by various rhizobia, but little is known regarding mechanisms of communication among peanut-nodulating strains. The aims of this study were to identify and characterize QS signals produced by peanut-nodulating bradyrhizobial strains and to evaluate their effects on processes related to cell interaction. Detection of AHLs in 53 rhizobial strains was performed using the biosensor strains Agrobacterium tumefaciens NTL4 (pZLR4) and Chromobacterium violaceum CV026 for AHLs with long and short acyl chains, respectively. None of the strains screened were found to produce AHLs with short acyl chains, but 14 strains produced AHLs with long acyl chains. These 14 AHL-producing strains were further studied by quantification of β-galactosidase activity levels (AHL-like inducer activity) in NTL4 (pZLR4). Strains displaying moderate to high levels of AHL-like inducer activity were subjected to chemical identification of signaling molecules by high-performance liquid chromatography coupled to mass spectrometry (LC-MS/MS). For each AHL-producing strain, we found at least four different AHLs, corresponding to N-hexanoyl-dl-homoserine lactone (C6), N-(3-oxodecanoyl)-l-homoserine lactone (3OC10), N-(3-oxododecanoyl)-l-homoserine lactone (3OC12), and N-(3-oxotetradecanoyl)-l-homoserine lactone (3OC14). Biological roles of 3OC10, 3OC12, and 3OC14 AHLs were evaluated in both AHL-producing and -non-producing peanut-nodulating strains. Bacterial processes related to survival and nodulation, including motility, biofilm formation, and cell aggregation, were affected or modified by the exogenous addition of increasing concentrations of synthetic AHLs. Our results clearly demonstrate the existence of cell communication mechanisms among bradyrhizobial strains symbiotic of peanut. AHLs with long acyl chains appear to be signaling molecules regulating important QS physiological processes in these bacteria.
Distance Education in 2001

There are significant personnel shortages in education and rehabilitation in the field of blindness and visual impairment. Some university-based programs that prepare teachers, orientation and mobility specialists, rehabilitation teachers and counselors, and low vision specialists to serve individuals with visual impairments strive to increase the number of service providers and assist professionals in maintaining skills and best practices in many ways. This article provides a brief overview of one approach—distance education.
Power conscious fixed priority scheduling for hard real-time systems

Power efficient design of real-time systems based on programmable processors becomes more important as system functionality is increasingly realized through software. This paper presents a power efficient version of a widely used fixed priority scheduling method. The method yields a power reduction by exploiting slack times, both those inherent in the system schedule and those arising from variations of execution times. The proposed run-time mechanism is simple enough to be implemented in most kernels. Experimental results show that the proposed scheduling method obtains a significant power reduction across several kinds of applications.
GPU‐UPGMA: high‐performance computing for UPGMA algorithm based on graphics processing units

Constructing phylogenetic trees is of priority concern in computational biology, especially for developing biological taxonomies. As a conventional means of constructing phylogenetic trees, unweighted pair group method with arithmetic (UPGMA) is also an extensively adopted heuristic algorithm for constructing ultrametric trees (UT). Although the UT constructed by UPGMA is often not a true tree unless the molecular clock assumption holds, UT is still useful for the clocklike data. Moreover, UT has been successfully adopted in other problems, including orthologous‐domain classification and multiple sequence alignment. However, previous implementations of the UPGMA method have a limited ability to handle large taxa sets efficiently. This work describes a novel graphics processing unit (GPU)‐UPGMA approach, capable of providing rapid construction of extremely large datasets for biologists. Experimental results indicate that the proposed GPU‐UPGMA approach achieves an approximately 95× speedup ratio on NVIDIA Tesla C2050 GPU over the implementation with 2.13 GHz CPU. The developed techniques in GPU‐UPGMA also can be applied to solve the classification problem for large data set with more than tens of thousands items in the future.Copyright © 2014 John Wiley & Sons, Ltd.
Participatory Bean Breeding with Women and Small Holder Farmers in Eastern Ethiopia

The Ethiopian national bean program traditionally followed conventional approaches in bean improvement for smallholder farmers. The relative effectiveness and efficiency of Participatory Plant Breeding (PPB) compared to conventional approaches is not fully understood. The study was initiated to evaluate participatory plant breeding in bean improvement to disseminate more acceptable and productive bean varieties for poor farmers. The study was conducted in eastern Ethiopia. Breeders and farmer selectors evaluated and then selected lines on-station from a diverse germplasm pool. The breeders followed a conventional approach, while farmers evaluated their selected lines on their farm. The germplasms included bush and climbing beans in its selections. The selection demonstrated that farmers were capable of making significant contributions in identification of superior cultivars within a relatively short period. They effectively evaluated and selected from large numbers of fixed lines. They applied up to 40 distinct selection criteria indicating the complexity of the user needs and production conditions. However, yield tolerance to biotic and abiotic stresses, drought, earliness, marketability, cooking characteristics, seed colour and size and growth habit were considered key criteria. Involving farmers in the selection process had several impacts, not only on farmer perceptions and skill building but also on the formal breeding process, farmer acceptance, farmer production and income, farmer-held diversity, farmer breeding and seed processes, farmer empowerment and costs. A new formal-led breeding scheme incorporating farmer participation is also developed. Lack of an effective seed delivery system and supporting policy is likely to constrain release and rapid dissemination of PPB varieties.
Dressed to Influence: The Effects of Experimenter Dress on Participant Compliance

Some psychologists believe that, in addition to any independent variable being tested, the characteristics of the experimenter who is conducting the study can influence how participants will perform during experiments, a phenomenon sometimes referred to as experimenter bias. Participants in this experiment consisted of 67 California State University, Northridge students. In this double-blind procedure, participants were randomly assigned to follow directions from either a casually or professionally-dressed experimenter. The authors predicted that participants in the professionally dressed condition would follow directions more accurately, but results indicated that participants who received directions from a casual experimenter were more compliant. It may be that students follow directions more accurately when those directions are given by someone who is dressed more similar to themselves.
Rendering of Eyes for Eye-Shape Registration and Gaze Estimation

Images of the eye are key in several computer vision problems, such as shape registration and gaze estimation. Recent large-scale supervised methods for these problems require time-consuming data collection and manual annotation, which can be unreliable. We propose synthesizing perfectly labelled photo-realistic training data in a fraction of the time. We used computer graphics techniquesto build a collection of dynamic eye-region models from head scan geometry. These were randomly posed to synthesize close-up eye images for a wide range of head poses, gaze directions, and illumination conditions. We used our model's controllability to verify the importance of realistic illumination and shape variations in eye-region training data. Finally, we demonstrate the benefits of our synthesized training data (SynthesEyes) by out-performing state-of-the-art methods for eye-shape registration as well as cross-dataset appearance-based gaze estimation in the wild.
An overview of assessment of prognostic and predictive factors in breast cancer needle core biopsy specimens

Needle core biopsy (NCB), as part of triple assessment for preoperative evaluation and diagnosis of breast cancer, is now considered as an established, highly accurate method for diagnosing breast cancer that has replaced either fine needle aspiration cytology or excisional biopsy as the initial diagnostic biopsy procedures in many institutions. In addition to its primary role in establishing an accurate histological diagnosis, NCB can potentially provide important additional pathological prognostic information which may be of direct clinical value in certain situations, such as patients being considered for preoperative (neoadjuvant) therapy. With this background in mind we briefly review the current role of NCB in breast cancer diagnosis and then concentrate this review on the usefulness and issues relating to use of this technique in providing accurate, reliable and clinically relevant preoperative prognostic and predictive information in patients with breast cancer.
Analysis of Transgenic Tobacco with Overexpression of Arabidopsis WUSCHEL Gene

The Arabidopsis WUSCHEL (WUS) gene plays a key role in the specification of the stem cells in the shoot apical meristem (SAM). A cDNA of WUS has been amplified with the RT-PCR approach from Arabidopsis. The plant overexpression vector was constructed. It was driven by a dual enhanced CaMV35S promoter. The construct was transformed into tobacco (Nicotiana tabacum L.) via Agrobacterium mediation. Dramatic phenotypic changes appeared in the WUS overexpression transgenic plants. Aberrant cell divisions and ectopic organogenesis could be found in almost every aerial parts of the transgenic tobacco except the meristems and the inner two floral whorls. The data showed a highly conserved function of WUS in tobacco, and suggested that WUS is involved in organogenesis. The leaves were malformed, which strongly matched those only described previously for plants grown in the presence of polar auxin transport inhibitors. It suggested a possible function of WUS in leaf development. These results provide useful information for functional analysis of WUS and important biotechnological implication as well.
Modeling Higher-Order Correlations within Cortical Microcolumns

We statistically characterize the population spiking activity obtained from simultaneous recordings of neurons across all layers of a cortical microcolumn. Three types of models are compared: an Ising model which captures pairwise correlations between units, a Restricted Boltzmann Machine (RBM) which allows for modeling of higher-order correlations, and a semi-Restricted Boltzmann Machine which is a combination of Ising and RBM models. Model parameters were estimated in a fast and efficient manner using minimum probability flow, and log likelihoods were compared using annealed importance sampling. The higher-order models reveal localized activity patterns which reflect the laminar organization of neurons within a cortical column. The higher-order models also outperformed the Ising model in log-likelihood: On populations of 20 cells, the RBM had 10% higher log-likelihood (relative to an independent model) than a pairwise model, increasing to 45% gain in a larger network with 100 spatiotemporal elements, consisting of 10 neurons over 10 time steps. We further removed the need to model stimulus-induced correlations by incorporating a peri-stimulus time histogram term, in which case the higher order models continued to perform best. These results demonstrate the importance of higher-order interactions to describe the structure of correlated activity in cortical networks. Boltzmann Machines with hidden units provide a succinct and effective way to capture these dependencies without increasing the difficulty of model estimation and evaluation.
Cross-Species Analyses of the Cortical GABAergic and Subplate Neural Populations

Cortical GABAergic (γ-aminobutyric acidergic) neurons include a recently identified subset whose projections extend over relatively long distances in adult rodents and primates. A number of these inhibitory projection neurons are located in and above the conventionally identified white matter, suggesting their persistence from, or a correspondence with, the developmental subplate. GABAergic and subplate neurons share some unique properties unlike those of the more prevalent pyramidal neurons. To better understand the GABAergic and subplate populations, we constructed a database of neural developmental events common to the three species most frequently used in experimental studies: rat, mouse, and macaque, using data from the online database www.translatingtime. net as well as GABAergic and subplate developmental data from the empirical literature. We used a general linear model to test for similarities and differences, a valid approach because the sequence of most neurodevelopmental events is remarkably conserved across mammalian species. Similarities between the two rodent populations are striking, permitting us to identify developmental dates for GABAergic and subplate neural events in rats that were previously identified only in mice, as well as the timing in mouse development for events previously identified in rats. Primate comparative data are also compelling, although slight variability in statistical error measurement indicates differences in primate GABAergic and subplate events when compared to rodents. Although human extrapolations are challenging because fewer empirical data points are available, and because human data display more variability, we also produce estimates of dates for GABAergic and subplate neural events that have not yet been, or cannot be, determined empirically in humans.
Session Perceived Exertion Following Traditional and Circuit Resistance Exercise Methods in Older Hypertensive Women

This study compared session ratings of perceived exertion (SRPE) between traditional multiple-set (TR) and circuit (CI) resistance exercise methods in treated hypertensive women. Fourteen volunteers (69.9 ± 5.6 years) performed two training sessions (TR and CI) in a random order, with the same number of sets, exercises, and loads. SRPE was obtained 30 minutes following each session using Foster’s scale. OMNI-resistance exercise scale (OMNI-RES) measures were subsequently taken. Foster’s SRPE was not significantly different between sessions (3.8 ± 0.9 TR vs. 3.4 ± 1.0 CI; p = .125), but OMNI-RES values were significantly higher following TR than following CI (5.2 ± 1.3 vs. 4.6 ± 1.5; p = .033). Total session duration was longer for TR (29.3 ± 1.2 vs. 20.0 ± 0.9 minutes; p < .001). Using moderate loads, the CI method did not elicit higher SRPE when compared with TR. Conversely, significantly lower OMNI-RES values follow CI. These results will be useful for prescribing exercise regimens for older hypertensive women.
Improved Visual Cognition through Stroboscopic Training

Humans have a remarkable capacity to learn and adapt, but surprisingly little research has demonstrated generalized learning in which new skills and strategies can be used flexibly across a range of tasks and contexts. In the present work we examined whether generalized learning could result from visual–motor training under stroboscopic visual conditions. Individuals were assigned to either an experimental condition that trained with stroboscopic eyewear or to a control condition that underwent identical training with non-stroboscopic eyewear. The training consisted of multiple sessions of athletic activities during which participants performed simple drills such as throwing and catching. To determine if training led to generalized benefits, we used computerized measures to assess perceptual and cognitive abilities on a variety of tasks before and after training. Computer-based assessments included measures of visual sensitivity (central and peripheral motion coherence thresholds), transient spatial attention (a useful field of view – dual task paradigm), and sustained attention (multiple-object tracking). Results revealed that stroboscopic training led to significantly greater re-test improvement in central visual field motion sensitivity and transient attention abilities. No training benefits were observed for peripheral motion sensitivity or peripheral transient attention abilities, nor were benefits seen for sustained attention during multiple-object tracking. These findings suggest that stroboscopic training can effectively improve some, but not all aspects of visual perception and attention.
Sp1 and Sp3 regulate basal transcription of the human APOBEC3G gene

APOBEC3G (A3G), a member of the recently discovered family of human cytidine deaminases, is expressed in peripheral blood lymphocytes and has been shown to be active against HIV-1 and other retroviruses. To gain new insights into the transcriptional regulation of this restriction factor, we cloned and characterized the promoter region of A3G. Transcriptional start sites were identified by 5′-rapid amplification of cDNA ends analysis. Luciferase reporter assays demonstrated that a 1025 bp A3G promoter sequence (from −959 to +66 relative to the major transcriptional start site) displayed constitutive promoter activity. In T cells, the A3G promoter was not inducible by mitogenic stimulation, interferon treatment or expression of HIV-1 proteins. Using a series of 5′ deletion promoter constructs in luciferase reporter assays, we identified a 180 bp region that was sufficient for full promoter activity. Transcriptional activity of this A3G core promoter was dependent on a GC-box (located at position −87/−78 relative to the major transcriptional start site) and was abolished after mutation of this DNA element. Electrophoretic mobility shift assays and chromatin immunoprecipitation assays demonstrated that the identified GC-box represented a binding site for the ubiquitous transcription factors specificity protein (Sp) 1 and Sp3.
Optimization of Three-Phase Induction Motor Design. Part II: The Efficiency and Cost of an Optimal Design

With the continuing increase of the cost of electrical energy, motor manufacturers and consumers became increasingly concerned with the energy conservation available from highly efficient electrical motors. Motor cost and efficiency are interrelated; therefore, the effect of motor cost on the maximum obtainable efficiency is of interest both to the motor manufacturer and to the consumer. The relation between the power factor and the maximum efficiency of a motor is another aspect of energy conservation. The optimal motor design, with respect to the maximum efficiency, and with respect to the minimum motor cost (by means of a mathematical optimization method described in Part I), was used in Part II to investigate the above-mentioned motor relations. Three motor-cost functions were investigated: production cost, capitalized cost, and annual cost. The motor that was used in the study was a 100 hp, three-phase, squirrel-cage induction motor.
PLIERS at TREC8

The use of the PLIERS text retrieval system in TREC8 experiments is described. The tracks entered for are: Ad-Hoc, Filtering (Batch and Routing) and the Web Track (Large only). We describe both retrieval efficiency and effectiveness results for all these tracks. We also describe some preliminary experiments with BM_25 tuning constant variation.
Genome Sequence of a Food Spoilage Lactic Acid Bacterium, Leuconostoc gasicomitatum LMG 18811T, in Association with Specific Spoilage Reactions

ABSTRACT Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium causing spoilage of cold-stored, modified-atmosphere-packaged (MAP), nutrient-rich foods. Its role has been verified by challenge tests in gas and slime formation, development of pungent acidic and buttery off odors, and greening of beef. MAP meats have especially been prone to L. gasicomitatum spoilage. In addition, spoilage of vacuum-packaged vegetable sausages and marinated herring has been reported. The genomic sequencing project of L. gasicomitatum LMG 18811T was prompted by a need to understand the growth and spoilage potentials of L. gasicomitatum, to study its phylogeny, and to be able to knock out and overexpress the genes. Comparative genomic analysis was done within L. gasicomitatum LMG 18811T and the three fully assembled Leuconostoc genomes (those of Leuconostoc mesenteroides, Leuconostoc citreum, and Leuconostoc kimchii) available. The genome of L. gasicomitatum LMG 18811T is plasmid-free and contains a 1,954,080-bp circular chromosome with an average GC content of 36.7%. It includes genes for the phosphoketolase pathway and alternative pathways for pyruvate utilization. As interesting features associated with the growth and spoilage potential, LMG 18811T possesses utilization strategies for ribose, external nucleotides, nucleosides, and nucleobases and it has a functional electron transport chain requiring only externally supplied heme for respiration. In respect of the documented specific spoilage reactions, the pathways/genes associated with a buttery off odor, meat greening, and slime formation were recognized. Unexpectedly, genes associated with platelet binding and collagen adhesion were detected, but their functionality and role in food spoilage and processing environment contamination need further study.
Dendritic cells are contained within melanocytic nevus nests in vivo and can alter gene expression of epidermal melanocytes in vitro

To take out a personal subscription, please click here More information about Pigment Cell & Melanoma Research at www.pigment. org Dendritic cells are contained within melanocytic nevus nests in vivo and can alter gene expression of epidermal melanocytes in vitro Nicholas Gulati, Hiroshi Mitsui, Judilyn Fuentes-Duculan, Juana Gonzalez, Claire Q. F. Wang, Kejal R. Shah, Patricia Gilleaudeau, Mary Sullivan-Whalen, Felix Kiecker, Neil S. McNutt, Mayte Suárez-Fariñas and James G. Krueger