Miracle-dz/UniFAR-FTUs huggingface dataset:
Succession of the turkey gastrointestinal bacterial microbiome related to weight gain

Because of concerns related to the use of antibiotics in animal agriculture, antibiotic-free alternatives are greatly needed to prevent disease and promote animal growth. One of the current challenges facing commercial turkey production in Minnesota is difficulty obtaining flock average weights typical of the industry standard, and this condition has been coined “Light Turkey Syndrome” or LTS. This condition has been identified in Minnesota turkey flocks for at least five years, and it has been observed that average flock body weights never approach their genetic potential. However, a single causative agent responsible for these weight reductions has not been identified despite numerous efforts to do so. The purpose of this study was to identify the bacterial community composition within the small intestines of heavy and light turkey flocks using 16S rRNA sequencing, and to identify possible correlations between microbiome and average flock weight. This study also sought to define the temporal succession of bacteria occurring in the turkey ileum. Based upon 2.7 million sequences across nine different turkey flocks, dominant operational taxonomic units (OTUs) were identified and compared between the flocks studied. OTUs that were associated with heavier weight flocks included those with similarity to Candidatus division Arthromitus and Clostridium bartlettii, while these flocks had decreased counts of several Lactobacillus species compared to lighter weight flocks. The core bacterial microbiome succession in commercial turkeys was also defined. Several defining markers of microbiome succession were identified, including the presence or abundance of Candidatus division Arthromitus, Lactobacillus aviarius, Lactobacillus ingluviei, Lactobacillus salivarius, and Clostridium bartlettii. Overall, the succession of the ileum bacterial microbiome in commercial turkeys proceeds in a predictable manner. Efforts to prevent disease and promote growth in the absence of antibiotics could involve target dominant bacteria identified in the turkey ileum that are associated with increased weight gain.
The Intracellular Site of Calcium Activation of Contraction in Frog Skeletal Muscle

Radioautography has been used to localize 45Ca in isotopically labeled frog skeletal muscle fibers which had been quickly frozen during a maintained tetanus, a declining tetanus, or during the period immediately following a tetanus or a contracture. During a tetanus almost all of the myofibrillar 45Ca is localized in the region of the sarcomere occupied by the thin filaments. The amount varies with the tension being developed by the muscle. The movement of calcium within the reticulum from the tubular portion to the terminal cisternae during the posttetanic period has a half-time of about 9 sec at room temperature and a Q 10 of about 1.7. Repolarization is not necessary for this movement. Evidence is given to support the notion that most calcium efflux from the cell occurs from the terminal cisternae into the transverse tubules.
Biochar application in Malaysian sandy and acid sulfate soils: soil amelioration effects and improved crop production over two cropping seasons

The use of biochar as an agricultural soil improvement was tested in acid sulfate and sandy soils from Malaysia, cropped with rice and corn. Malaysia has an abundance of waste rice husks that could be used to produce biochar. Rice husk biochar was produced in a gasifier at a local mill in Kelantan as well as in the laboratory using a controlled, specially designed, top lift up draft system (Belonio unit). Rice husk biochar was applied once to both soils at two doses (2% and 5%), in a pot set up that was carried out for two cropping seasons. Positive and significant crop yield effects were observed for both soils, biochars and crops. The yield effects varied with biochar type and dosage, with soil type and over the cropping seasons. The yield increases observed for the sandy soil were tentatively attributed to significant increases in plant-available water contents (from 4%–5% to 7%–8%). The yield effects in the acid sulfate soil were likely a consequence of a combination of (i) alleviation of plant root stress by aluminum (Ca/Al molar ratios significantly increased, from around 1 to 3–5) and (ii) increases in CEC. The agricultural benefits of rice husk biochar application to Malaysian soils holds promise for its future use.
Shifting Gears in Hippocampus: Temporal Dissociation between Familiarity and Novelty Signatures in a Single Event

The hippocampus is known to be involved in encoding and retrieval of episodes. However, real-life experiences are expected to involve both encoding and retrieval, and it is unclear how the human hippocampus subserves both functions in the course of a single event. We presented participants with brief movie clips multiple times and examined the effect of familiarity on the hippocampal response at event onset versus event offset. Increased familiarity resulted in a decreased offset response, indicating that the offset response is a novelty-related signature. The magnitude of this offset response was correlated, across hippocampal voxels, with an independent measure of successful encoding, based on nonrepeated clips. This suggests that the attenuated offset response to familiar clips reflects reduced encoding. In addition, the posterior hippocampus exhibited an increased onset response to familiar events, switching from an online familiarity signal to an offline novelty signal during a single event. Moreover, participants with stronger memory exhibited increased reactivation of online activity during familiar events, in line with a retrieval signature. Our results reveal a spatiotemporal dissociation between novelty/encoding and familiarity/retrieval signatures, assumed to reflect different computational modes, in response to the same stimulus.
DAISEE: Dataset for Affective States in E-Learning Environments

Extracting and understanding a ective states of subjects through analysis of face videos is of high consequence to advance the levels of interaction in human-computer interfaces. This paper aims to highlight vision-related tasks focused on understanding \reactions" of subjects to presented content which has not been largely studied by the vision community in comparison to other emotions. To facilitate future study in this eld, we present an e ort in collecting DAiSEE, a free to use large-scale dataset using crowd annotation, that not only simulates a real world setting for e-learning environments, but also captures the interpretability issues of such a ective states by human annotators. In addition to the dataset, we present benchmark results based on stan- dard baseline methods and vote aggregation strategies, thus providing a springboard for further research.
Pathways to relapse: factors controlling the reinitiation of drug seeking after abstinence.

Although considerable knowledge has accumulated over the past 50 years concerning the systems of the brain that support the reinforcing effects of drug of abuse, this knowledge has not been easily translated into effective treatment. The primary problem for treatment of drug abuse remains the reinitiation of drug craving and seeking after abstinence (relapse). It is not understood why, for example, when drugs are unavailable for long periods of time or when users are successful in curbing their own drug use for extended periods, individuals remain vulnerable to relapse. Studies carried out in rats over the last several years have demonstrated clearly that reinitiation of drug seeking can be induced by re-exposure to cues previously associated with drug exposure, by re-exposure to the drug, itself, and by acute exposure to certain stressors. Thus, when rats are trained to self-administer drugs such as cocaine or heroin, and are then subjected to a period of extinction training, the presentation of cues that have been explicitly paired with drug delivery, an experimenter delivered injection of the drug, or acute exposure to footshock stress all result in an increase in pressing on lever previously associated with drug delivery; the amount of responding during the period of extinction and during the test for relapse can be considered to reflect the magnitude of drug seeking or the level of motivation to obtain the drug. Studies carried out in a number of laboratories have provided evidence that the brain systems mediating the effects of conditioned stimuli, priming injections of drugs and stress on the reinitiation of drug seeking are to some degree dissociable (Erb, Shaham, & Stewart, 2001b; McFarland & Kalivas, 2001; Shaham, Erb, & Stewart, 2000a; Shalev, Grimm, & Shaham, 2002; Stewart, 2000). Nonetheless, new evidence is beginning to emerge suggesting that the motivation underlying drug seeking induced by all of these manipulations is influenced by two factors, the duration and intensity of pre-exposure to a drug, and the time since withdrawal of the drug. In this paper I will discuss how these two factors could act to increase the motivation to take drugs that is observed in the experienced drug user even after long periods of abstinence. Before doing this, however, I will review the evidence showing that repeated exposure to some drugs of abuse does induce changes in the circuitry relevant for reinstatement of drug seeking and will discuss possible mechanisms for the induction of these changes. I will then review evidence showing that pre-exposure to stimulant and opioid drugs affects both appetitive and aversive motivational processes.
The bistatic electromagnetic signature of heterogeneous sea surface: Study of the hydrodynamic phenomena

In this article, we carried out a preliminary study on the hydrodynamic effect (non-linear) produced by the breaking of a coastal wave on the scattering coefficient (in horizontal and vertical polarization) in the bi-static configuration (forward propagation). We calculated in X-band (10 GHz) σ<inf>HH</inf> and σ<inf>VV</inf> of a series of oceanic surfaces (different phases of construction of a breaking wave (θ<inf>i</inf> = −20°) then we studied the different characteristics for each scattering coefficients. In this first study we considered that the maritime surface is the perfect conductor.
Genomic Classification of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP53-Mutant Tumors and Identifies NRAS as an Oncogenic Driver

Purpose: Low-grade serous ovarian carcinomas (LGSC) are Ras pathway-mutated, TP53 wild-type, and frequently associated with borderline tumors. Patients with LGSCs respond poorly to platinum-based chemotherapy and may benefit from pathway-targeted agents. High-grade serous carcinomas (HGSC) are TP53-mutated and are thought to be rarely associated with borderline tumors. We sought to determine whether borderline histology associated with grade 2 or 3 carcinoma was an indicator of Ras mutation, and we explored the molecular relationship between coexisting invasive and borderline histologies. Experimental Design: We reviewed >1,200 patients and identified 102 serous carcinomas with adjacent borderline regions for analyses, including candidate mutation screening, copy number, and gene expression profiling. Results: We found a similar frequency of low, moderate, and high-grade carcinomas with coexisting borderline histology. BRAF/KRAS alterations were common in LGSC; however, we also found recurrent NRAS mutations. Whereas borderline tumors harbored BRAF/KRAS mutations, NRAS mutations were restricted to carcinomas, representing the first example of a Ras oncogene with an obligatory association with invasive serous cancer. Coexisting borderline and invasive components showed nearly identical genomic profiles. Grade 2 cases with coexisting borderline included tumors with molecular features of LGSC, whereas others were typical of HGSC. However, all grade 3 carcinomas with coexisting borderline histology were molecularly indistinguishable from typical HGSC. Conclusion: Our findings suggest that NRAS is an oncogenic driver in serous ovarian tumors. We demonstrate that borderline histology is an unreliable predictor of Ras pathway aberration and underscore an important role for molecular classification in identifying patients that may benefit from targeted agents. Clin Cancer Res; 20(24); 6618–30. ©2014 AACR.
Motor Cortex Maturation Is Associated with Reductions in Recurrent Connectivity among Functional Subpopulations and Increases in Intrinsic Excitability

Behavior is derived from the configuration of synaptic connectivity among functionally diverse neurons. Fine motor behavior is absent at birth in most mammals but gradually emerges during subsequent postnatal corticospinal system maturation; the nature of circuit development and reorganization during this period has been largely unexplored. We investigated connectivity and synaptic signaling among functionally distinct corticospinal populations in Fischer 344 rats from postnatal day 18 through 75 using retrograde tracer injections into specific spinal cord segments associated with distinct aspects of forelimb function. Primary motor cortex slices were prepared enabling simultaneous patch-clamp recordings of up to four labeled corticospinal neurons and testing of 3489 potential synaptic connections. We find that, in immature animals, local connectivity is biased toward corticospinal neurons projecting to the same spinal cord segment; this within-population connectivity significantly decreases through maturation until connection frequency is similar between neurons projecting to the same (within-population) or different (across-population) spinal segments. Concomitantly, postnatal maturation is associated with a significant reduction in synaptic efficacy over time and an increase in intrinsic neuronal excitability, altering how excitation is effectively transmitted across recurrent corticospinal networks. Collectively, the postnatal emergence of fine motor control is associated with a relative broadening of connectivity between functionally diverse cortical motor neurons and changes in synaptic properties that could enable the emergence of smaller independent networks, enabling fine motor movement. These changes in synaptic patterning and physiological function provide a basis for the increased capabilities of the mature versus developing brain.
Effect of cAMP signaling on expression of glucocorticoid receptor, Bim and Bad in glucocorticoid-sensitive and resistant leukemic and multiple myeloma cells

Stimulation of cAMP signaling induces apoptosis in glucocorticoid-sensitive and resistant CEM leukemic and MM.1 multiple myeloma cell lines, and this effect is enhanced by dexamethasone in both glucocorticoid-sensitive cell types and in glucocorticoid-resistant CEM cells. Expression of the mRNA for the glucocorticoid receptor alpha (GR) promoters 1A3, 1B and 1C, expression of mRNA and protein for GR, and the BH3-only proapoptotic proteins, Bim and Bad, and the phosphorylation state of Bad were examined following stimulation of the cAMP and glucocorticoid signaling pathways. Expression levels of GR promoters were increased by cAMP and glucocorticoid signaling, but GR protein expression was little changed in CEM and decreased in MM.1 cells. Stimulation of these two signaling pathways induced Bim in CEM cells, induced Bad in MM.1 cells, and activated Bad, as indicated by its dephosphorylation on ser112, in both cell types. This study shows that leukemic and multiple myeloma cells, including those resistant to glucocorticoids, can be induced to undergo apoptosis by stimulating the cAMP signaling pathway, with enhancement by glucocorticoids, and the mechanism by which this occurs may be related to changes in Bim and Bad expression, and in all cases, to activation of Bad.
The role of thermal contraction crack polygons in cold-desert fluvial systems

Abstract Thermal contraction crack polygons modify the generation, transport, and storage of water in Wright Valley gullies. Water generation is contributed to by trapping of windblown snow in polygon troughs. Water transport is modified by changes to the ice-cement table and active layer topography caused by polygon trough formation. Water storage is modified by sediment grain-size distribution within polygons in gully distal hyporheic zones. Patterned ground morphological variation can serve as an indicator of fluvial modification, ranging from nearly unmodified composite-wedge polygons to polygons forming in association with gully channels. Thermal contraction crack polygons may also constrain the gully formation sequence, suggesting the continuous presence of permafrost beneath the Wright Valley gullies during the entire period of gully emplacement. This analysis provides a framework for understanding the relationships between polygons and gullies observed on Mars. If comparable stratigraphic relationships can be documented, the presence of an analogous impermeable ice-cemented layer beneath the gullies can be inferred, suggesting an atmospheric source for Martian gully-carving fluids.
Subanesthetic Isoflurane Reduces Zymosan-Induced Inflammation in Murine Kupffer Cells by Inhibiting ROS-Activated p38 MAPK/NF-κB Signaling

Volatile anesthetic isoflurane (ISO) has immunomodulatory effects. The fungal component zymosan (ZY) induces inflammation through toll-like receptor 2 or dectin-1 signaling. We investigated the molecular actions of subanesthetic (0.7%) ISO against ZY-induced inflammatory activation in murine Kupffer cells (KCs), which are known as the resident macrophages within the liver. We observed that ISO reduced ZY-induced cyclooxygenase 2 upregulation and prostaglandin E2 release, as determined by western blot and radioimmunoassay, respectively. ISO also reduced the production of tumor necrosis factor-α, interleukin-1β, IL-6, high-mobility group box-1, macrophage inflammatory protein-1α, macrophage inflammatory protein-2, and monocyte chemoattractant protein-1 as assessed by enzyme-linked immunosorbent assays. ISO blocked the ZY-induced nuclear translocation and DNA-binding activity of nuclear factor- (NF)-κB p65. Moreover, ISO attenuated ZY-induced p38 mitogen-activated protein kinase (MAPK) activation partly by scavenging reactive oxygen species (ROS); the interregulation that ROS activated p38 MAPK followed by NF-κB activation was crucial for the ZY-induced inflammatory responses in KCs. An in vivo study by peritoneal injection of ZY into BALB/C mice confirmed the anti-inflammatory properties of 0.7% ISO against ZY in KCs. These results suggest that ISO ameliorates ZY-induced inflammatory responses in murine KCs by inhibiting the interconnected ROS/p38 MAPK/NF-κB signaling pathways.
Multicriteria meta-heuristics for AGV dispatching control based on computational intelligence

In many manufacturing environments, automated guided vehicles are used to move the processed materials between various pickup and delivery points. The assignment of vehicles to unit loads is a complex problem that is often solved in real-time with simple dispatching rules. This paper proposes an automated guided vehicles dispatching approach based on computational intelligence. We adopt a fuzzy multicriteria decision strategy to simultaneously take into account multiple aspects in every dispatching decision. Since the typical short-term view of dispatching rules is one of the main limitations of such real-time assignment heuristics, we also incorporate in the multicriteria algorithm a specific heuristic rule that takes into account the empty-vehicle travel on a longer time-horizon. Moreover, we also adopt a genetic algorithm to tune the weights associated to each decision criteria in the global decision algorithm. The proposed approach is validated by means of a comparison with other dispatching rules, and with other recently proposed multicriteria dispatching strategies also based on computational Intelligence. The analysis of the results obtained by the proposed dispatching approach in both nominal and perturbed operating conditions (congestions, faults) confirms its effectiveness.
The Value of Information for Crop Forecasting with Bayesian Speculators: Theory and Empirical Results

This paper develops a model of the way in which information about current conditions is translated by Bayesian speculative inventory holders into forecasts of the flow of harvests, and in turn, into forecasts of prices in a competitive market system. Improvement in the information system (e.g., more accurate observations) affects the commodity price distribution, and this change can be evaluated using Marshallian surplus from consumption. The model is applied empirically to the case of wheat crop forecasting in the United States.
Stock returns and risk: Evidence from quantile regression analysis

ABSTRACT This paper employs weighted least squares to examine the risk-return relation by applying high-frequency data from four major stock indexes in the US market and finds some evidence in favor of a positive relation between the mean of the excess returns and expected risk. However, by using quantile regressions, we find that the risk-return relation moves from negative to positive as the returns’ quantile increases. A positive risk-return relation is valid only in the upper quantiles. The evidence also suggests that intraday skewness plays a dominant role in explaining the variations of excess returns. KEYWORDS : Risk-return tradeoff, Volatility, Intraday skewness, Quantile Regression, High-frequency data JEL CLASSIFICATION : C12, C13, G10, G11 ACKNOWLEDGEMENTS: We have benefited from conversations and comments from Daniel Dorn, Federico Bandi, Eric Ghysels, Kevin Sheppard, Michael J. Gombola, and discussions with participants at the 2008 Society for Financial Econometrics Inaugural Conference. We assume full responsibility for the analysis and the remaining errors. Corresponding author: Thomas C. Chiang, Department of Finance, Drexel University, 33rd and Chestnut Streets, Philadelphia, PA 19104, U.S.A. Tel: 215-895-1745, Fax: 215-895-2955, Email: chiangtc@drexel.edu
Social Conformity and ASD : A child-friendly take on a classic study

Perhaps surprisingly, given the importance of conformity as a theoretical construct in social psychology and the profound implications autism has for social function, little research has been done on whether autism is associated with the propensity to conform to a social majority. The current study is a modern, child-friendly implementation of the classic Asch conformity studies (1952, 1956). The performance of 15 children with autism was compared to that of 15 typically-developing children on a line judgement task. Children were matched for age, gender, and numeracy and literacy ability. In each trial, the child had to say which of three lines a comparison line matched in length. On some trials, children were misled as to what most people thought the answer was. Children with autism were much less likely to conform in the misleading condition than typically-developing children. This finding was replicated using a continuous measure of autism traits, the Autism Quotient questionnaire, which showed that autism traits negatively correlated with likelihood to conform in the typically-developing group. This study demonstrates the resistance of children with autism to social pressure.