Miracle-dz/UniFAR-FTUs huggingface dataset:
Bubbles as tracers of heat input to cooling flows

We examine the distribution of injected energy in three-dimensional, adaptive-grid simulations of the heating of cooling flows. We show that less than 10 percent of the injected energy goes into bubbles. Consequently, the energy input from the nucleus is underestimated by a factor of order 6 when it is taken to be given by PVgamma/(gamma-1), where P and V are the pressure and volume of the bubble, and gamma the ratio of principal specific heats.
Proteogenomics Reveals Enriched Ribosome Assembly and Protein Translation in Pectoralis major of High Feed Efficiency Pedigree Broiler Males

Background: In production animal agriculture, the cost of feed represents 60–70% of the total cost of raising an animal to market weight. Thus, development of viable biomarkers for feed efficiency (FE, g gain/g feed) to assist in genetic selection of breeding stock remains an important goal in commercial breeding programs. Methods: Global gene (cDNA microarray, RNAseq) and protein expression (shotgun proteomics) analyses have been conducted on breast muscle samples obtained from pedigree broiler males (PedM) exhibiting high and low FE phenotypes. Using the entire datasets (i.e., no cutoffs for significance or fold difference in expression) the number of genes or proteins that were expressed numerically higher or lower in the high FE compared to the low FE phenotype for key terms or functions, e.g., ribosomal, mitochondrial ribosomal, tRNA, RNA binding motif, RNA polymerase, small nuclear ribonucleoprotein, and protein tyrosine phosphatase, were determined. Bionomial distribution analysis (exact) was then conducted on these datasets to determine significance between numerically up or down expression. Results: Processes associated with mitochondrial proteome expression (e.g., mitochondrial ribosomal proteins, mitochondrial transcription, mitochondrial tRNA, and translation) were enriched in breast muscle from the high FE compared to the low FE pedigree male broiler phenotype. Furthermore, the high FE phenotype exhibited enrichment of ribosome assembly (e.g., RNA polymerase, mitochondrial and cytosolic ribosomes, small, and heterogeneous nuclear ribonucleoproteins), as well as nuclear transport and protein translation processes compared to the low FE phenotype. Quality control processes (proteosomes and autophagy) were also enriched in the high FE phenotype. In contrast, the low FE phenotype exhibited enrichment of cytoskeletal proteins, protein tyrosine phosphatases, and tyrosine kinases compared to the high FE phenotype. These results suggest that processes of mitochondrial and cytosolic ribosomal construction, activity, and protein translation would be enhanced in high FE breast muscle, and that phosphorylation of tyrosine moieties of proteins could be prolonged in the high compared to low FE phenotype. The results indicate the presence of a proteogenomic architecture that could enhance ribosome construction, protein translation, and quality control processes and contribute to the phenotypic expression of feed efficiency in this PedM broiler model.
Phenotyping for drought tolerance of crops in the genomics era

Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
EXACT: rivastigmine improves the high prevalence of attention deficits and mood and behaviour symptoms in Alzheimer's disease*

The objective of this study was to investigate the impact of rivastigmine therapy on attention, apathy, anxiety and agitation in patients with mild‐to‐moderate Alzheimer's disease (AD) in a real‐world clinical setting. Patients with mild‐to‐moderate AD were enrolled in the study by physicians across Canada. They were treated with open‐label rivastigmine (dose at the discretion of the prescribing physicians) for a period of 6 months. Changes from baseline in attention, apathy, anxiety and agitation were assessed using an abbreviated Clinician's Global Impression of Change at 3‐ and 6‐month visits. The Mini Mental State Examination (MMSE) was also used at these visits. Use and changes in use of psychotropic medications were recorded, as were changes in caregiver burden. Analyses of subgroups (outpatients vs. institutionalised patients) were also performed. A total of 2119 patients were enrolled in the study by 375 physicians. At baseline, 91% had deficits in attention, 85.4% had symptoms of anxiety, 78.5% exhibited apathy and 70.1% showed agitation. At 6 months, 67.5% of evaluable patients had improved on the symptom of attention, while 62.3%, 62.6% and 56.0% had improvements in anxiety, apathy and agitation respectively. The percentages with improvements were higher in the institutional subgroup than among outpatients. There was an overall mean improvement of 1.1 points on the MMSE at 6 months. Approximately four times as many caregivers reported a reduced burden than an increased burden at 6 months (40.3% vs. 10.3%). The majority of patients treated with rivastigmine experienced improvements in attention, anxiety, apathy and agitation. These real‐life findings further demonstrate the proven efficacy of rivastigmine in patients with mild‐to‐moderate AD.
Bootstrap prediction intervals in state–space models

Abstract. Prediction intervals in state–space models can be obtained by assuming Gaussian innovations and using the prediction equations of the Kalman filter, with the true parameters substituted by consistent estimates. This approach has two limitations. First, it does not incorporate the uncertainty caused by parameter estimation. Second, the Gaussianity of future innovations assumption may be inaccurate. To overcome these drawbacks, Wall and Stoffer [Journal of Time Series Analysis (2002) Vol. 23, pp. 733–751] propose a bootstrap procedure for evaluating conditional forecast errors that requires the backward representation of the model. Obtaining this representation increases the complexity of the procedure and limits its implementation to models for which it exists. In this article, we propose a bootstrap procedure for constructing prediction intervals directly for the observations, which does not need the backward representation of the model. Consequently, its application is much simpler, without losing the good behaviour of bootstrap prediction intervals. We study its finite‐sample properties and compare them with those of the standard and the Wall and Stoffer procedures for the local level model. Finally, we illustrate the results by implementing the new procedure to obtain prediction intervals for future values of a real time series.
Concomitant Panniculectomy Affects Wound Morbidity but Not Hernia Recurrence Rates in Abdominal Wall Reconstruction: A Propensity Score Analysis

Background: Studies of abdominal wall reconstruction with concurrent panniculectomy have reported contradictory results. The authors hypothesized that patients undergoing abdominal wall reconstruction with concurrent panniculectomy experience more wound healing complications but similar rates of hernia recurrence compared with abdominal wall reconstruction alone. Methods: Of 548 consecutive patients, 305 patients (55.7 percent) underwent abdominal wall reconstruction alone and 243 (44.3 percent) underwent abdominal wall reconstruction with concurrent panniculectomy. Mean follow-up was 30 months. The authors compared these two groups’ postoperative complications and outcomes before and after propensity score analysis. Results: Abdominal wall reconstruction with concurrent panniculectomy patients had a significantly higher overall complication rate (38.3 percent versus 29.2 percent; p = 0.025) and a trend toward a higher surgical-site occurrence rate (27.6 percent versus 20.7 percent; p = 0.06) compared with abdominal wall reconstruction alone. There were significantly higher incidences of skin dehiscence (19.3 percent versus 12.5 percent; p = 0.032), fat necrosis (10.7 percent versus 3.6 percent; p = 0.002), and infection abscess (9.5 percent versus 4.3 percent; p = 0.023) but no significant difference in hernia recurrence (6.9 percent versus 11.5 percent; p = 0.27) at long-term follow-up. Propensity score analysis yielded 188 pairs of matched patients with no significant differences in overall complication and hernia recurrence rates. Significantly higher rates of fat necrosis (9.6 percent versus 4.3 percent; p = 0.041) and abscess (10.1 percent versus 3.2 percent; p = 0.007) were observed in the abdominal wall reconstruction with concurrent panniculectomy group. Conclusions: Abdominal wall reconstruction with concurrent panniculectomy is associated with higher wound morbidity but similar surgical-site occurrence and hernia recurrence rates at long-term follow-up. The authors believe that panniculectomy can be safely performed when indicated.
Adherence and Dosage Contributions to Parenting Program Quality

Objective: The 3 most examined elements of treatment fidelity are adherence, dosage, and quality. The relationships between these fidelity elements are complex, and additional research is needed to provide clarity. Improving clarity may be especially relevant to parenting programs, which tend to include direct explicit instruction (DEI) elements (i.e., instruction, modeling, and practice). The adherence to and dosage of these DEI elements are frequently assumed to improve program quality; however, little information is available to determine if adherence to and dosage of these DEI elements affect program quality. This study examines whether adherence to and dosage of DEI elements predict quality ratings for a widely disseminated, manualized parenting program. Method: Adherence is defined as the percentage of intervention tasks completed for each DEI element. Dosage is defined as the number of minutes and seconds spent in each intervention DEI element. Treatment fidelity is assessed for 36 of 144 sessions across 10 program facilitators. A hierarchical linear regression analysis examines the contributions of adherence and dosage in the prediction of session quality ratings. Results: The analysis indicates that adherence accounts for a significant proportion of the variance (26%), whereas dosage contributes a nonsignificant proportion of variance (11%). Adherence to skill practice was the strongest individual predictor (β = .445, p < .01). Conclusions: Findings suggest that ensuring a high degree of adherence may contribute to quality program delivery. However, more exploration is needed to better understand the ways in which adherence and dosage of DEI elements affect program quality.
Covalent binding of 7,12-dimethylbenz(a)anthracene and 10-fluoro-7,12-dimethylbenz(a)anthracene to mouse epidermal DNA and its relationship to tumor-initiating activity.

10-Fluoro-7,12-dimethylbenz(a)anthracene (10-F-DMBA) is a more potent skin tumor initiator in SENCAR mice when compared with the parent hydrocarbon 7,12-dimethylbenz(a)anthracene (DMBA). To elucidate the mechanism for this difference, the covalent binding of these two hydrocarbons to the DNA of mouse epidermal cells in vivo and in vitro was compared. The quantity of 10-F-DMBA covalently bound to mouse epidermal DNA in vivo was greater than that of DMBA at all doses tested over the range of 4 to 200 nmol/mouse. The magnitude of this binding difference between 10-F-DMBA and DMBA was greater at the higher doses (e.g., 1.5-fold at 4 nmol/mouse versus 3.4-fold at 200 nmol/mouse). These results correlated closely with the dose-response relationships for tumor initiation by the two hydrocarbons. Analysis of the isolated DNA samples by Servacel DHB chromatography revealed the relative proportion of syn-diol-epoxide:DNA adducts derived from DMBA increased dramatically as a function of dose (approximately 30% at 4 nmol/mouse versus approximately 55% at 200 nmol/mouse). Conversely, the relative proportion of syn-diol-epoxide adducts derived from 10-F-DMBA was low and remained essentially constant over the same dose range. High-pressure liquid chromatographic analyses of the DNA adducts derived from DMBA- and 10-F-DMBA-treated mice revealed qualitatively similar profiles. However, as expected, there was a marked reduction in the relative proportion of syn-diol-epoxide:DNA adducts in the profiles of epidermal samples from 10-F-DMBA-treated mice. The major syn-diol-epoxide:deoxy-adenosine adduct was present at a level only 30% that found in high-pressure liquid chromatographic profiles of DMBA samples. Similar results were obtained when primary cultures of mouse epidermal cells were treated with the hydrocarbons. The results suggest that the increased total binding and possibly the decreased proportion of syn-diol-epoxide:DNA adducts confer greater tumor-initiating potency on 10-F-DMBA.
Lamins at the crossroads of mechanosignaling

The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. In this review, Osmanagic-Myers et al. focus on the role of nuclear lamins in mechanosensing and also discuss how disease-linked lamin mutants may impair the response of cells to mechanical stimuli and influence the properties of the extracellular matrix.
Autosomal Minor Histocompatibility Antigens: How Genetic Variants Create Diversity in Immune Targets

Allogeneic stem cell transplantation (alloSCT) can be a curative treatment for hematological malignancies. Unfortunately, the desired anti-tumor or graft-versus-leukemia (GvL) effect is often accompanied with undesired side effects against healthy tissues known as graft-versus-host disease (GvHD). After HLA-matched alloSCT, GvL and GvHD are both mediated by donor-derived T-cells recognizing polymorphic peptides presented by HLA surface molecules on patient cells. These polymorphic peptides or minor histocompatibility antigens (MiHA) are produced by genetic differences between patient and donor. Since polymorphic peptides may be useful targets to manipulate the balance between GvL and GvHD, the dominant repertoire of MiHA needs to be discovered. In this review, the diversity of autosomal MiHA characterized thus far as well as the various molecular mechanisms by which genetic variants create immune targets and the role of cryptic transcripts and proteins as antigen sources are described. The tissue distribution of MiHA as important factor in GvL and GvHD is considered as well as possibilities how hematopoietic MiHA can be used for immunotherapy to augment GvL after alloSCT. Although more MiHA are still needed for comprehensive understanding of the biology of GvL and GvHD and manipulation by immunotherapy, this review shows insight into the composition and kinetics of in vivo immune responses with respect to specificity, diversity, and frequency of specific T-cells and surface expression of HLA–peptide complexes and other (accessory) molecules on the target cell. A complex interplay between these factors and their environment ultimately determines the spectrum of clinical manifestations caused by immune responses after alloSCT.
Impact of Plug-in Hybrid Electric Vehicles (PHEVs) on the French electric grid

Currently the automotive sector is undergoing a major change. During the next years it is expected that there will be a considerable increase in the numbers of Plug-in Hybrid Electric Vehicles (PHEVs). Based on different charging scenarios, this paper investigates the impact of PHEVs on the French electric grid. Solutions are proposed to increase the maximum penetration rate. Hence we estimate that the French electric grid can accommodate 72% of PHEVs in 2015. This makes it possible to reduce oil imports for France by 22.5% and CO2 emissions due to road transport by 18%.
Recent Advances in the Discovery and Development of Marine Microbial Natural Products

Marine microbial natural products (MMNPs) have attracted increasing attention from microbiologists, taxonomists, ecologists, agronomists, chemists and evolutionary biologists during the last few decades. Numerous studies have indicated that diverse marine microbes appear to have the capacity to produce an impressive array of MMNPs exhibiting a wide variety of biological activities such as antimicrobial, anti-tumor, anti-inflammatory and anti-cardiovascular agents. Marine microorganisms represent an underexplored reservoir for the discovery of MMNPs with unique scaffolds and for exploitation in the pharmaceutical and agricultural industries. This review focuses on MMNPs discovery and development over the past decades, including innovative isolation and culture methods, strategies for discovering novel MMNPs via routine screenings, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology. The potential problems and future directions for exploring MMNPs are also discussed.
A novel enteric neuron–glia coculture system reveals the role of glia in neuronal development

Unlike astrocytes in the brain, the potential role of enteric glial cells (EGCs) in the formation of the enteric neuronal circuit is currently unknown. To examine the role of EGCs in the formation of the neuronal network, we developed a novel neuron‐enriched culture model from embryonic rat intestine grown in indirect coculture with EGCs. We found that EGCs shape axonal complexity and synapse density in enteric neurons, through purinergic‐ and glial cell line‐derived neurotrophic factor‐dependent pathways. Using a novel and valuable culture model to study enteric neuron–glia interactions, our study identified EGCs as a key cellular actor regulating neuronal network maturation.
It takes two to tango. A Review of the Empirical Literature on Information Technology Outsourcing Relationship Satisfaction

There is growing recognition that the overall client-vendor relationship, and not only the contract, plays a critical role in Information Technology Outsourcing (ITO) success. However, our understanding of how ITO relationships function is limited. This paper contributes to this understanding by reviewing empirical literature on ITO success in terms of relationship satisfaction. A key finding is that the majority of reviewed studies concentrates on client satisfaction, thus neglecting the vendor perspective. We argue that this raises questions about the construct validity of these studies. Consequently, concerns exist about the validity and reliability of their empirical findings. Some scholars have acknowledged the problem and use a dyadic perspective. However, a review of these studies reveals that the authors have underestimated their contributions and do not explain why there is a problem. Therefore, the purpose of this paper is to highlight their contributions by comparing the findings of the dyadic perspective studies with those of the "client perspective" research. In doing so, we assess whether the dyadic studies produce better explanations for ITO success than the client-oriented studies. We argue that this is indeed the case, by producing a better view on how underlying mechanisms of ITO relationships work.
A Comparative Analysis of the Agile and Traditional Software Development Processes Productivity

Software development processes are essential for an organization to obtain the required levels of productivity and quality. The productivity analysis of agile and traditional development processes is an open and few explored research area, which has attracted the interest of industrial and academic fellows in order to take advantage of the strengths of both approaches. This research aims to investigate good options for agile and traditional integration by defining a hybrid process that takes advantage of both approaches. An empirical study aiming to evaluate the productivity impact of the proposed hybrid process was carried out in a Brazilian CMMI v.1. 1 Maturity Level 2 medium-sized company. Five groups of similar projects were compared with respect to productivity, some of which were developed using the new hybrid process and others were developed using the older RUP-based process. Quantitative results have shown that four out of five project groups showed significant productivity increase in Scrum-RUP projects. The study shows that it is possible to integrate agile practices in the software development process without losing the rigor needed in the desired sub processes and still get real development productivity gain.
The Quiet Transformations of Literary Studies: What Thirteen Thousand Scholars Could Tell Us

We use quantitative methods to analyze a collection of 21,367 scholarly articles in literary studies from 1889–2013. Our approach reveals aspects of our disciplinary history that have been occluded by existing histories’ emphasis on generational and methodological conflict. We demonstrate gradual, unnoted shifts in the themes and vocabularies of scholarship—including the long rise of new subjects (like violence); we show the surprising novelty of central theoretical concepts; and we explore transformations in the shared rationales for literary scholarship that exceed the boundaries of conventional labels like “New Criticism” and “New Historicism. ” Though our method uses computational tools, we not claim to provide a definitive or objective perspective on disciplinary history; instead, our approach, like the related methods of content analysis in the social sciences, allows us to pursue nuanced interpretations of the language of many texts at once.