Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatic mRNAs up‐regulated by starvation: an expression profile determined by suppression subtractive hybridization

Delineating the molecular basis for the metabolic switch from the well‐fed state to starvation is crucial to understanding nutritionally regulated metabolic abnormalities. We have examined the molecular events associated with nutrient deprivation, using suppression subtractive hybridization to define the transcriptional programs up‐regulated in rat liver by starvation. Of the genes that displayed significant increases in their hepatic mRNA levels following 48‐h starvation, most could be assigned to one of five major functional classes. We found up‐regulation of genes involved in energy and protein metabolism, genes that respond to stress, and genes encoding nutrient transporters or signaling transducers. The genes with functions in energy and protein metabolism have roles in initiating gluconeogenesis, switching fuel sources from carbohydrates to fatty acids, and protein turnover. A variety of stress response genes, including acute‐phase reactants, exhibited a marked increased in expression, indicating an attempt to restore homeostasis. The expression of several integrated membrane nutrient transporters that supply essential metabolic substrates was increased dramatically. Some known cytosolic signal transducers, likely involved in the metabolic shift from an anabolic to a catabolic state and in the stress response, were significantly enhanced as well. We also observed increased expression of a variety of other known and novel genes. Collectively, our findings indicate that starvation stimulates multiple signaling pathways, which likely lead to extensive metabolic alterations in the liver. These data should serve to enhance our understanding of the molecular mechanisms underlying energy and nitrogen expenditure in the starved state.
Variable effects of nicotine, anabasine, and their interactions on parasitized bumble bees

Secondary metabolites in floral nectar have been shown to reduce parasite load in two common bumble bee species. Previous studies on the effects of nectar secondary metabolites on parasitized bees have focused on single compounds in isolation; however, in nature, bees are simultaneously exposed to multiple compounds. We tested for interactions between the effects of two alkaloids found in the nectar of Nicotiana spp. plants, nicotine and anabasine, on parasite load and mortality in bumble bees ( Bombus impatiens) infected with the intestinal parasite Crithidia bombi. Adult worker bees inoculated with C. bombi were fed nicotine and anabasine diet treatments in a factorial design, resulting in four nectar treatment combinations: 2 ppm nicotine, 5 ppm anabasine, 2ppm nicotine and 5 ppm anabasine together, or a control alkaloid-free solution. We conducted the experiment twice: first, with bees incubated under variable environmental conditions (‘Variable’; temperatures varied from 10-35°C with ambient lighting); and second, under carefully controlled environmental conditions (‘Stable’; 27°C incubator, constant darkness). In ‘Variable’, each alkaloid alone significantly decreased parasite loads, but this effect was not realized with the alkaloids in combination, suggesting an antagonistic interaction. Nicotine but not anabasine significantly increased mortality, and the two compounds had no interactive effects on mortality. In ‘Stable’, nicotine significantly increased parasite loads, the opposite of its effect in ‘Variable’. While not significant, the relationship between anabasine and parasite loads was also positive. Interactive effects between the two alkaloids on parasite load were non-significant, but the pattern of antagonistic interaction was similar to that in the variable experiment. Neither alkaloid, nor their interaction, significantly affected mortality under controlled conditions. Our results do not indicate synergy between Nicotiana nectar alkaloids; however, they do suggest a complex interaction between secondary metabolites, parasites, and environmental variables, in which secondary metabolites can be either toxic or medicinal depending on context.
Automatic Clock Abstraction from Sequential Circuits

Our goal is to transform a low-level circuit design into a more abstract representation. A pre-existing tool, Tranalyze [4], takes a switch-level circuit and generates a functionally equivalent gatelevel representation. This work focuses on taking that gate-level sequential circuit and performing a temporal analysis which abstracts the clocks from the circuit. The analysis generates a cycle-level gate model with the detailed timing abstracted from the original circuit. Unlike other possible approaches, our analysis does not require the user to identify state elements or give the timings of internal state signals. The temporal analysis process has applications in simulation, formal verification, and reverse engineering of existing circuits. Experimental results show a 40%-70% reduction in the size of the circuit and a 3X-150X speedup in simulation time.
Whole-Genome Sequencing of Theileria parva Strains Provides Insight into Parasite Migration and Diversification in the African Continent

The disease caused by the apicomplexan protozoan parasite Theileria parva, known as East Coast fever or Corridor disease, is one of the most serious cattle diseases in Eastern, Central, and Southern Africa. We performed whole-genome sequencing of nine T. parva strains, including one of the vaccine strains (Kiambu 5), field isolates from Zambia, Uganda, Tanzania, or Rwanda, and two buffalo-derived strains. Comparison with the reference Muguga genome sequence revealed 34 814–121 545 single nucleotide polymorphisms (SNPs) that were more abundant in buffalo-derived strains. High-resolution phylogenetic trees were constructed with selected informative SNPs that allowed the investigation of possible complex recombination events among ancestors of the extant strains. We further analysed the dN/dS ratio (non-synonymous substitutions per non-synonymous site divided by synonymous substitutions per synonymous site) for 4011 coding genes to estimate potential selective pressure. Genes under possible positive selection were identified that may, in turn, assist in the identification of immunogenic proteins or vaccine candidates. This study elucidated the phylogeny of T. parva strains based on genome-wide SNPs analysis with prediction of possible past recombination events, providing insight into the migration, diversification, and evolution of this parasite species in the African continent.
ECG Quantification of Myocardial Scar in Cardiomyopathy Patients With or Without Conduction Defects: Correlation With Cardiac Magnetic Resonance and Arrhythmogenesis

Background—Myocardial scarring from infarction or nonischemic fibrosis forms an arrhythmogenic substrate. The Selvester QRS score has been extensively validated for estimating myocardial infarction scar size in the absence of ECG confounders, but has not been tested to quantify scar in patients with hypertrophy, bundle branch/fascicular blocks, or nonischemic cardiomyopathy. We assessed the hypotheses that (1) QRS scores (modified for each ECG confounder) correctly identify and quantify scar in ischemic and nonischemic patients when compared with the reference standard of cardiac magnetic resonance using late-gadolinium enhancement, and (2) QRS-estimated scar size predicts inducible sustained monomorphic ventricular tachycardia during electrophysiological testing. Methods and Results—One hundred sixty-two patients with left ventricular ejection fraction ≤35% (95 ischemic, 67 nonischemic) received 12-lead ECG and cardiac magnetic resonance using late-gadolinium enhancement before implantable cardioverter defibrillator placement for primary prevention of sudden cardiac death. QRS scores correctly diagnosed cardiovascular magnetic resonance scar presence with receiver operating characteristics area under the curve of 0.91 and correlation for scar quantification of r=0.74 (P<0.0001) for all patients. Performance within hypertrophy, conduction defect, and nonischemic subgroups ranged from area under the curve of 0.81 to 0.94 and r=0.60 to 0.80 (P<0.001 for all). Among the 137 patients undergoing electrophysiological or device testing, each 3-point QRS-score increase (9% left ventricular scarring) was associated with an odds ratio for inducing monomorphic ventricular tachycardia of 2.2 (95% CI, 1.5 to 3.2; P<0.001) for all patients, 1.7 (1.0 to 2.7, P=0.04) for ischemics, and 2.2 (1.0 to 5.0, P=0.05) for nonischemics. Conclusions—QRS scores identify and quantify scar in ischemic and nonischemic cardiomyopathy patients despite ECG confounders. Higher QRS-estimated scar size is associated with increased arrhythmogenesis and warrants further study as a risk-stratifying tool.
Peanut Sensitization Profiles in Italian Children and Adolescents with Specific IgE to Peanuts

Peanuts are one of the most relevant foods implicated in IgE-mediated adverse reactions in pediatric population. This study aimed to evaluate the pattern of sensitization towards five peanut allergenic components (rAra h 1, 2, 3, 8 and 9) in a population of Italian children and adolescents with specific IgE (sIgE) to peanut. rAra h 9 was the main allergen implicated in peanut sensitization (58%), followed by rAra h 8 (35%), rAra h 2 (27%), rAra h 3 (23%) and rAra h 1 (12.5%). rAra h 1, 2, and 3 were the main allergenic components in young children: 8/13 (62%) between 2 and 5 years, 8/23 (35%) between 6 and 11 years, and 3/12 (25%) between 1 and 16 years. No differences were found among the levels of sIgE towards rAra h 1, 2, 3, and 9 in the three groups; in contrast, the levels of sIgE against rAra h 8 showed an increasing trend according to age. In conclusion rAra h 1, 2, and 3 were the prevalent sensitizing allergens during the first years of life in Italian patients with sIgE to peanuts (“genuine” allergy); in contrast rAra h 9 and 8 were mainly involved in school-age children and adolescents with pollen allergy (“secondary” sensitization).
Using Visual Information for Grounding and Awareness in Collaborative Tasks

When pairs work together on a physical task, seeing a common workspace facilitates communication and benefits performance. When mediating such activities, however, the choice of technology can transform the visual information in ways that impact critical coordination processes. In this article we examine two coordination processes that are impacted by visual information—situation awareness and conversational grounding—which are theoretically distinct but often confounded in empirical research. We present three empirical studies that demonstrate how shared visual information supports collaboration through these two distinct routes. We also address how particular features of visual information interact with features of the task to influence situation awareness and conversational grounding, and further demonstrate how these features affect conversation and coordination. Experiment 1 manipulates the immediacy of the visual information and shows that immediate visual feedback facilitates collaboration by improving both situation awareness and conversational grounding. In Experiment 2, by misaligning the perspective through which the Worker and Helper see the work area we disrupt the ability of visual feedback to support conversational grounding but not situation awareness. The findings demonstrate that visual information supports the central mechanism of conversational grounding. Experiment 3 disrupts the ability of visual feedback to support situation awareness by reducing the size of the common viewing area. The findings suggest that visual information independently supports both situation awareness and conversational grounding. We conclude with a general discussion of the results and their implications for theory development and the future design of collaborative technologies.
A Survey of Current Datasets for Vision and Language Research

Integrating vision and language has long been a dream in work on artificial intelligence (AI). In the past two years, we have witnessed an explosion of work that brings together vision and language from images to videos and beyond. The available corpora have played a crucial role in advancing this area of research. In this paper, we propose a set of quality metrics for evaluating and analyzing the vision & language datasets and categorize them accordingly. Our analyses show that the most recent datasets have been using more complex language and more abstract concepts, however, there are different strengths and weaknesses in each.
Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.
Real-time observer-based (adaptive) control of a permanent-magnet synchronous motor without mechanical sensors

A theoretical and experimental analysis is presented of a closed-loop adaptive velocity control system for a 200 W permanent magnet synchronous motor. The control system utilities a mechanically sensorless full-state observer for the generation of all controller feedback information. Both the control system and its experimental performance using an implementation based on the Motorola 68020 microprocessor are presented. It is shown that the real-time observer-based adaptive velocity controller is capable of successful operation. <<ETX>>
Real‐time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers

Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf–dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf–dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.
Testing for abuse liability of drugs in humans. Proceedings of a conference. November 5-6, 1988, Princeton, NJ.

In summary, there are a number of factors to be considered in abuse liability testing such as the purpose of the testing and its potential applications that determine which subject population we should employ. Furthermore, we should not expect to see a perfect correlation between abuse liability testing and the actual abuse of these drugs because there are many factors that will modulate or modify whether or not abuse liability becomes activated and the abuse of any specific drug becomes a social problem.
Intestinal Barrier Interactions with Specialized CD8 T Cells

The trillions of microorganisms that reside in the gastrointestinal tract, essential for nutrient absorption, are kept under control by a single cell barrier and large amounts of immune cells. Intestinal epithelial cells (IECs) are critical in establishing an environment supporting microbial colonization and immunological tolerance. A large population of CD8+ T cells is in direct and constant contact with the IECs and the intraepithelial lymphocytes (IELs). Due to their location, at the interphase of the intestinal lumen and external environment and the host tissues, they seem ideally positioned to balance immune tolerance and protection to preserve the fragile intestinal barrier from invasion as well as immunopathology. IELs are a heterogeneous population, with a large innate-like contribution of unknown specificity, intercalated with antigen-specific tissue-resident memory T cells. In this review, we provide a comprehensive overview of IEL physiology and how they interact with the IECs and contribute to immune surveillance to preserve intestinal homeostasis and host-microbial relationships.
Smallholders’ Tree Planting Activity in the Ziro Province, Southern Burkina Faso: Impacts on Livelihood and Policy Implications

Climate variability and change significantly affect smallholder farmers’ food security and livelihoods in sub-Saharan Africa. Tree planting is one of the measures promoted by development programs to mitigate and adapt to climate change. Tree planting is also believed to positively contribute to livelihoods. This paper examines factors influencing smallholders’ tree planting activities in four villages in the Ziro province, Southern Burkina Faso. Furthermore, it analyses the challenges encountered and willingness to continue tree planting under current tenure arrangements. The data was obtained through key informants, household interviews, focus group discussions, and field observations. Results indicate that the majority of farmers interviewed planted Mangifera indica (50%), Anacardium occidentale (32%) and Moringa oleifera (30%). In a number of trees planted, Eucalyptus camaldulensis, Mangifera indica and Anacardium occidentale dominated. Tree planters were mainly farmers who held large and old farm areas, were literate and relatively wealthy, had favorable attitudes toward tree planting, and with considerable years of participation in a farmers’ group. The main reasons for planting trees included income generation from the sale of tree products, access to markets and local support for tree planting. Preference for agriculture, tenure insecurity and lack of sufficient land were the main reasons cited for not planting trees. Farm households that were relatively poor, had smaller workforces and smaller farm sizes were not willing to continue tree planting. To effectively engage farmers in tree planting and to make it more attractive, policies are needed that address tenure insecurity for migrants, enable better access to markets, and support fair pricing structures for wood and other tree resources.
Multi-field-of-view strategy for image-based outcome prediction of multi-parametric estrogen receptor-positive breast cancer histopathology: Comparison to Oncotype DX

In this paper, we attempt to quantify the prognostic information embedded in multi-parametric histologic biopsy images to predict disease aggressiveness in estrogen receptor-positive (ER+) breast cancers (BCa). The novel methodological contribution is in the use of a multi-field-of-view (multi-FOV) framework for integrating image-based information from differently stained histopathology slides. The multi-FOV approach involves a fixed image resolution while simultaneously integrating image descriptors from many FOVs corresponding to different sizes. For each study, the corresponding risk score (high scores reflecting aggressive disease and vice versa), predicted by a molecular assay (Oncotype DX), is available and serves as the surrogate ground truth for long-term patient outcome. Using the risk scores, a trained classifier is used to identify disease aggressiveness for each FOV size. The predictions for each FOV are then combined to yield the final prediction of disease aggressiveness (good, intermediate, or poor outcome). Independent multi-FOV classifiers are constructed for (1) 50 image features describing the spatial arrangement of cancer nuclei (via Voronoi diagram, Delaunay triangulation, and minimum spanning tree graphs) in H and E stained histopathology and (2) one image feature describing the vascular density in CD34 IHC stained histopathology. In a cohort of 29 patients, the multi-FOV classifiers obtained by combining information from the H and E and CD34 IHC stained channels were able to distinguish low- and high-risk patients with an accuracy of 0.91 ± 0.02 and a positive predictive value of 0.94 ± 0.10, suggesting that a purely image-based assay could potentially replace more expensive molecular assays for making disease prognostic predictions.
Nonlinear Models Using Dirichlet Process Mixtures

We introduce a new nonlinear model for classification, in which we model the joint distribution of response variable, y, and covariates, x, non-parametrically using Dirichlet process mixtures. We keep the relationship between y and x linear within each component of the mixture. The overall relationship becomes nonlinear if the mixture contains more than one component, with different regression coefficients. We use simulated data to compare the performance of this new approach to alternative methods such as multinomial logit (MNL) models, decision trees, and support vector machines. We also evaluate our approach on two classification problems: identifying the folding class of protein sequences and detecting Parkinson's disease. Our model can sometimes improve predictive accuracy. Moreover, by grouping observations into sub-populations (i.e., mixture components), our model can sometimes provide insight into hidden structure in the data.