Miracle-dz/UniFAR-FTUs huggingface dataset:
When Does Stress Help or Harm? The Effects of Stress Controllability and Subjective Stress Response on Stroop Performance

The ability to engage in goal-directed behavior despite exposure to stress is critical to resilience. Questions of how stress can impair or improve behavioral functioning are important in diverse settings, from athletic competitions to academic testing. Previous research suggests that controllability is a key factor in the impact of stress on behavior: learning how to control stressors buffers people from the negative effects of stress on subsequent cognitively demanding tasks. In addition, research suggests that the impact of stress on cognitive functioning depends on an individual’s response to stressors: moderate responses to stress can lead to improved performance while extreme (high or low) responses can lead to impaired performance. The present studies tested the hypothesis that (1) learning to behaviorally control stressors leads to improved performance on a test of general executive functioning, the color-word Stroop, and that (2) this improvement emerges specifically for people who report moderate (subjective) responses to stress. Experiment 1: Stroop performance, measured before and after a stress manipulation, was compared across groups of undergraduate participants (n = 109). People who learned to control a noise stressor and received accurate performance feedback demonstrated reduced Stroop interference compared with people exposed to uncontrollable noise stress and feedback indicating an exaggerated rate of failure. In the group who learned behavioral control, those who reported moderate levels of stress showed the greatest reduction in Stroop interference. In contrast, in the group exposed to uncontrollable events, self-reported stress failed to predict performance. Experiment 2: In a second sample (n = 90), we specifically investigated the role of controllability by keeping the rate of failure feedback constant across groups. In the group who learned behavioral control, those who reported moderate levels of stress showed the greatest Stroop improvement. Once again, this pattern was not demonstrated in the group exposed to uncontrollable events. These results suggest that stress controllability and subjective response interact to affect high-level cognitive abilities. Specifically, exposure to moderate, controllable stress benefits performance, but exposure to uncontrollable stress or having a more extreme response to stress tends to harm performance. These findings may provide insights on how to leverage the beneficial effects of stress in a range of settings.
A Combination of Flaxseed Oil and Astaxanthin Improves Hepatic Lipid Accumulation and Reduces Oxidative Stress in High Fat-Diet Fed Rats

Hepatic lipid accumulation and oxidative stress are crucial pathophysiological mechanisms for non-alcoholic fatty liver disease (NAFLD). Thus, we examined the effect of a combination of flaxseed oil (FO) and astaxanthin (ASX) on hepatic lipid accumulation and oxidative stress in rats fed a high-fat diet. ASX was dissolved in flaxseed oil (1 g/kg; FO + ASX). Animals were fed diets containing 20% fat, where the source was lard, or 75% lard and 25% FO + ASX, or 50% lard and 50% FO + ASX, or FO + ASX, for 10 weeks. Substitution of lard with FO + ASX reduced steatosis and reduced hepatic triacylglycerol and cholesterol. The combination of FO and ASX significantly decreased hepatic sterol regulatory element-binding transcription factor 1 and 3-hydroxy-3-methylglutaryl-CoA reductase but increased peroxisome proliferator activated receptor expression. FO + ASX significantly suppressed fatty acid synthase and acetyl CoA carboxylase but induced carnitine palmitoyl transferase-1 and acyl CoA oxidase expression. FO + ASX also significantly elevated hepatic SOD, CAT and GPx activity and GSH, and markedly reduced hepatic lipid peroxidation. Thus, FO and ASX may reduce NAFLD by reversing hepatic steatosis and reducing lipid accumulation and oxidative stress.
NUTRIENT COMPOSTION AND USES OF BAMBARA GROUNDNUT ( VIGNIA SUBSTERRANEA (L.) VERDCOURT)

Proximate and amino acid compositions of raw and roasted bambara groundnut seeds were determined. The dry matter values ranged from 95.24 - 96.36%; crude protein 20.05 -22.54%; crude fat 7.15 - 8.31% and ash 3.40 - 3.48% for the raw and roasted seeds respectively. The crude fibre had values ranging from 4.88 to 5.48% and nitrogen free extract values ranged from 57.15 to 59.16% for the roasted and raw seeds respectively. Results on the amino acid profiles of raw and roasted bambara groundnut seeds showed that the concentrations of some amino acids like histidine, aspartic acid, proline, cystine, valine, methionine, isoleucine, tyrosine, and phenylalanine decreased due to heat processing. However, some amino acids like lysine, threonine, serine, glutamic acid, glycine, alanine and leucine had their concentrations increased with heat processing. The amino acid with the highest concentration in bambara groundnut was glutamic acid with 15.76g/16gN in the raw seeds and 15.91g/16gN in the roasted seeds. Sulphur-containing amino acids were found to be the most limiting. The concentrations of methionine were 1.04g/16gN and 0.97g/16gN while the concentrations of cystine were 1.25g/16gN and 0.71g/16gN for the raw and roasted seeds respectively. The essential amino acid, leucine had the highest value of 7.76g/16gN for the raw seeds and 7.99g/16gN for the roasted seeds of bambara groundnut. Bambara groundnut is used in several ways, which includes soup making, porridge, seeds grilled as snacks, in cake and bread, preparation of milk, fortification of baby food, seeds canned in gravy, in the preparation of various fried, or steamed products, such as “akara” (bean cake) and “moin-moin” and “okpa” (beans pudding) and as livestock feedstuff. essential amino acid in bambara groundnut. The values obtained for leucine was closely followed by arginine with the value of 6.41g/16gN for both raw and roasted seeds. The lysine values of 5.93g/16gN for raw bambara groundnut and 6.22g/16g/N for the roasted seeds obtained in this study are within the range of 6.63 to 6.97g/16gN reported by Doku et al . (1978). Sulphur-containing amino acids were found to be the most limiting. Methionine values were 1.04g/16gN and 0.97g/16gN while cystine had values of 1.25g/16gN and 0.71g/16gN for the raw and roasted seeds respectively. These values were also close to those reported by Doku et al . (1978) but much lower than those Onwudike and Eguakun (1994). Variations in the amino acid concentrations between this study and those other authors might be due some factors like; the effect to significant influence the composition amino acids plant Other factors include; effect on and acid digestion method in preparing the samples for amino acid analysis 1999; Hassan Umar, 2005).
MUSCLE FIBERS CHARACTERIZATION AND GROWTH DYNAMICSIN GASTROCNEMIUS MUSCLE OF DEVELOPING WHITE LEGHORN CHICKIN RELATION TO SOMATIC GROWTH

Present communication reports the fiber identification, fiber orientation in relation to functional activity and the fiber growth dynamics in relation to the somatic growth rate of the Gastrocnemius muscle of developing male white Leghorn chick. The study tested three hypotheses; a) muscle fibers typing on the basis of histochemical nature are similar in the muscle mass, b) distribution pattern of different muscle fibers in muscle mass are in relation to the functional activities of that particular species, c) fiber growth dynamics are related to the somatic growth rate of that species. Results of the histochemical studies revealed presence of all three basic fiber types i.e. red, pink and white which confirms the first hypothesis. Results also showed that the growth of all three fiber types occurred by hypertrophy exclusively. True hyperplasia did not evidentin any age group; it was possibly seized in the late embryonic stage. Splitting of large fibers into smaller fibers was evident in some cases of pink and white fibers only. Observed results showed that all three basic fiber types grew by hypertrophy almost exclusively irrespective of their location and functional activities. Muscle fiber growth in this muscle mass was definitely in relation to the somatic growth rate of the chick.
Ischemia-Induced Coronary Collateral Growth Is Dependent on Vascular Endothelial Growth Factor and Nitric Oxide

Background—We hypothesized that ischemia-induced expression of vascular endothelial growth factor (VEGF) and the production of NO stimulate coronary collateral growth. Methods and Results—To test this hypothesis, we measured coronary collateral blood flow and VEGF expression in myocardial interstitial fluid in a canine model of repetitive myocardial ischemia under control conditions and during antagonism of NO synthase. Collateralization was induced by multiple (1/h; 8/d), brief (2 minutes) occlusions of the left anterior descending coronary artery for 21 days. In controls, collateral blood flow (microspheres) progressively increased to 89±9 mL · min−1 · 100 g−1 on day 21, which was equivalent to perfusion in the normal zone. Reactive hyperemic responses (a measure of the severity of ischemia) decreased as collateral blood flow increased. In NG-nitro-l-arginine methyl ester (L-NAME)– and L-NAME+nifedipine–treated dogs, to block the production of NO and control hypertension, respectively, collateral blood flow did not increase and reactive hyperemia was robust throughout the occlusion protocol (P <0.01 versus control). VEGF expression (Western analyses of VEGF164 in myocardial interstitial fluid) in controls peaked at day 3 of the repetitive occlusions but waned thereafter. In sham-operated dogs (instrumentation but no occlusions), expression of VEGF was low during the entire protocol. In contrast, VEGF expression was elevated throughout the 21 days of repetitive occlusions after L-NAME. Reverse transcriptase–polymerase chain reaction analyses revealed that the predominant splice variant expressed was VEGF164. Conclusions—NO is an important regulator of coronary collateral growth, and the expression of VEGF is induced by ischemia. Furthermore, the induction of coronary collateralization by VEGF appears to require the production of NO.
Suppression of Myocardial 18F-FDG Uptake Through Prolonged High-Fat, High-Protein, and Very-Low-Carbohydrate Diet Before FDG-PET/CT for Evaluation of Patients With Suspected Cardiac Sarcoidosis

Background A major obstacle in using FDG-PET/CT to diagnose cardiac sarcoidosis (CS) is the unpredictable physiological myocardial FDG uptake. We hypothesized that a prolonged 72-hour pretest high-fat, high-protein, and very-low-carbohydrate (HFHPVLC) diet preparation could suppress physiologic myocardial uptake of FDG and thus help to identify active CS. Methods This retrospective study included 215 FDG-PET/CT tests from 207 patients with biopsy-proven sarcoidosis and clinical suspicion for CS between July 2014 and December 2015. The patients were classified into 2 groups. Group 1 included 12 FDG-PET/CT scans from 12 patients who had 24-hour or less pretest HFHPVLC diet preparation. Group 2 included 203 FDG-PET/CT scans with 72-hour HFHPVLC diet before FDG-PET/CT. Nonadherent patients and patients with cancer were excluded. Cardiac FDG uptake was classified as: “none” and “ringlike diffuse at base” (negative for CS), “focal” (positive for CS), and “diffuse” (indeterminate for CS). FDG uptake in myocardial lesions was measured as SUVmax and compared with SUVmean of mediastinal blood pool. Final diagnoses were made with consensus among physicians in view of all available clinical information including cardiac MRI and echocardiogram results. Results In group 1, there were 1 (1/12, 8.3%) positive, 5 (5/12, 41.7%) indeterminate, and 6 (6/12, 50.0%) negative for CS. In group 2, 10 patients were excluded (6 patients because of noncompliance with diet, 2 patients with concurrent diagnosis of cancers, 2 patients because of insulin and steroid use within 4 hours before PET/CT); the remaining 185 patients had 193 FDG PET/CT tests (8 repeats), of which there were 19 (19/193, 9.8%) positive, 7 indeterminate (7/193, 3.6%), and 167 (167/193, 86.7.%) negative for CS. The SUVmax of PET-positive myocardial lesions ranges from 3.4 to 12.5, whereas mediastinal blood pool SUVmean ranges from 1.1 to 3.6. The indeterminate rate was significantly lower in group 2 compared with group 1 (P < 0.001). Conclusions The prolonged 72-hour HFHPVLC diet preparation protocol successfully suppressed physiological myocardial FDG uptake and may permit a more sensitive and accurate method of diagnosing active CS using FDG PET/CT.
Bone mass increases in less than 4 wk of voluntary exercising in growing rats.

INTRODUCTION Physical exercise is known to augment bone mass, but the specific mechanisms by which physical activity influences skeletal metabolism is still not thoroughly understood. So far, time related events of bone tissue adaptation to physical training have not been investigated. We, therefore, studied the time-course effects of daily spontaneous exercise training on bone metabolism in the rat by biochemical and tissue analyses. METHODS Forty-five 4-wk-old female Dark Agouti rats were used, randomly assigned to voluntary exercising groups of five animals for 1, 2, 3, and 4 wk, or to age-matched sedentary controls. At sacrifice, blood was sampled for determination of parameters of bone and calcium metabolism (osteocalcin, alkaline phosphatases, total and ionized calcium, phosphorus, parathyroid hormone). Right and left tibiae were removed for bone mass (dry and ash mass, mineral content) and histomorphometric analyses. RESULTS We found that the animals performed large amounts of exercise (reaching 50 +/- 8 km x wk(-1)), and that this voluntary physical training induced significant changes in bone metabolism. An increase (approximately 32%) in serum alkaline phosphatase activity was already measurable at the end of the first week of exercising and persisted throughout the experiment, accompanied by a concomitant increase in osteoblastic bone formation (approximately 27%), as evaluated in bone tissue. These changes were associated with consecutive increases in tibial bone mass (approximately 7.6%), mineral content (approximately 7.4%) and metaphyseal bone volume (approximately 17%) measurable 4 wk after the onset of exercise, with interesting positive correlations between tibial bone mass parameters and soleus muscle mass. Conversely, no change was evidenced in biochemical parameters of calcium metabolism, except for an increase in phosphorus serum levels in trained animals. CONCLUSION Daily spontaneous exercise training induced an increase in bone mass and bone volume in less than 4 wk. Further studies are needed to fully investigate these changes during the very first days of exercising.
A cautionary perspective on cross-layer design

Recently, in an effort to improve the performance of wireless networks, there has been increased interest in protocols that rely on interactions between different layers. However, such cross-layer design can run at cross purposes with sound and longer-term architectural principles, and lead to various negative consequences. This motivates us to step back and reexamine holistically the issue of cross-layer design and its architectural ramifications. We contend that a good architectural design leads to proliferation and longevity, and illustrate this with some historical examples. Even though the wireless medium is fundamentally different from the wired one, and can offer undreamt of modalities of cooperation, we show that the conventional layered architecture is a reasonable way to operate wireless networks, and is in fact optimal up to an order. However the temptation and perhaps even the need to optimize by incorporating cross-layer adaptation cannot be ignored, so we examine the issues involved. We show that unintended cross-layer interactions can have undesirable consequences on overall system performance. We illustrate them by certain cross-layer schemes loosely based on recent proposals. We attempt to distill a few general principles for cross-layer design. Moreover, unbridled cross-layer design can lead to spaghetti design, which can stifle further innovation and be difficult to upkeep. At a critical time when wireless networks may be on the cusp of massive proliferation, the architectural considerations may be paramount. We argue that it behooves us to exercise caution while engaging in cross-layer design.
On Weighted Graph Homomorphisms

For given graphs $G$ and $H$, let $|Hom(G,H)|$ denote the set of graph homomorphisms from $G$ to $H$. We show that for any finite, $n$-regular, bipartite graph $G$ and any finite graph $H$ (perhaps with loops), $|Hom(G,H)|$ is maximum when $G$ is a disjoint union of $K_{n,n}$'s. This generalizes a result of J. Kahn on the number of independent sets in a regular bipartite graph. We also give the asymptotics of the logarithm of $|Hom(G,H)|$ in terms of a simply expressed parameter of $H$. We also consider weighted versions of these results which may be viewed as statements about the partition functions of certain models of physical systems with hard constraints.
Kinetic Characterization of the Glycosyltransferase Module of Staphylococcus aureus PBP2

ABSTRACT We report the heterologous overexpression and purification of Staphylococcus aureus PBP2 and demonstrate efficient glycan polymerization from lipid II in vitro. S. aureus PBP2 is the first purified gram-positive class A penicillin-binding protein to show good transglycosylase activity. This enables further studies on this important class of enzymes.
Extracting a Biologically Relevant Latent Space from Cancer Transcriptomes with Variational Autoencoders

The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor’s response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors. Variational autoencoders (VAEs) are a deep neural network approach capable of generating meaningful latent spaces for image and text data. In this work, we sought to determine the extent to which a VAE can be trained to model cancer gene expression, and whether or not such a VAE would capture biologically-relevant features. In the following report, we introduce a VAE trained on TCGA pan-cancer RNA-seq data, identify specific patterns in the VAE encoded features, and discuss potential merits of the approach. We name our method “Tybalt” after an instigative, cat-like character who sets a cascading chain of events in motion in Shakespeare’s “Romeo and Juliet”. From a systems biology perspective, Tybalt could one day aid in cancer stratification or predict specific activated expression patterns that would result from genetic changes or treatment effects.
Identification of a Novel C5L2 Variant (S323I) in a French Canadian Family With Familial Combined Hyperlipemia

Objective—A functional acylation stimulating protein (ASP) receptor, C5L2, has been recently identified in ASP-responsive cells. Impaired ASP-mediated triglyceride synthesis has previously been described in a subset of hyperapolipoprotein B/familial combined hyperlipidemia subjects. Methods and Results—DNA sequencing of C5L2 coding region in 61 unrelated probands identified a heterozygous variant (G968→T) in 1 subject, resulting in Ser323→Ile substitution in the carboxyl terminal region. This variant was not detected in 2176 additional chromosomes by restriction fragment length polymorphism or fluorescence polarization genotyping. Eight family members of the proband were identified with one altered (+/−)C5L2 allele. Nine other family members had the wild-type (+/+)C5L2 sequence. The abnormal allele was associated with increased plasma triglyceride, plasma cholesterol, low-density lipoprotein (LDL) cholesterol, apolipoprotein B and ASP. Of 23 subjects tested in cell-based ASP bioactivity assays, those with C5L2(+/−) variant (n=2) had a 50% reduction in ASP-stimulated triglyceride synthesis, glucose transport and marked reduction in maximal binding (Bmax). By contrast, a C5L2(+/+) family member responded normally, as did hyperapolipoprotein B normal ASP subjects compared with C5L2(+/+) controls (n=6). Conclusion—The S323I variant may alter C5L2 function and might be one molecular basis contributing to familial combined hyperlipidemia.
SafeSlice: a model slicing and design safety inspection tool for SysML

Software safety certification involves checking that the software design meets the (software) safety requirements. In practice, inspections are one of the primary vehicles for ensuring that safety requirements are satisfied by the design. Unless the safety-related aspects of the design are clearly delineated, the inspections conducted by safety assessors would have to consider the entire design, although only small fragments of the design may be related to safety. In a model-driven development context, this means that the assessors have to browse through large models, understand them, and identify the safety-related fragments. This is time-consuming and error-prone, specially noting that the assessors are often third-party regulatory bodies who were not involved in the design. To address this problem, we describe in this paper a prototype tool called, SafeSlice, that enables one to automatically extract the safety-related slices (fragments) of design models. The main enabler for our slicing technique is the traceability between the safety requirements and the design, established by following a structured design methodology that we propose. Our work is grounded on SysML, which is being increasingly used for expressing the design of safety-critical systems. We have validated our work through two case studies and a control experiment which we briefly outline in the paper.
Development of a Multi-Step Leukemogenesis Model of MLL-Rearranged Leukemia Using Humanized Mice

Mixed-lineage-leukemia (MLL) fusion oncogenes are intimately involved in acute leukemia and secondary therapy-related acute leukemia. To understand MLL-rearranged leukemia, several murine models for this disease have been established. However, the mouse leukemia derived from mouse hematopoietic stem cells (HSCs) may not be fully comparable with human leukemia. Here we developed a humanized mouse model for human leukemia by transplanting human cord blood-derived HSCs transduced with an MLL-AF10 oncogene into a supra-immunodeficient mouse strain, NOD/Shi-scid, IL-2Rγ−/− (NOG) mice. Injection of the MLL-AF10-transduced HSCs into the liver of NOG mice enhanced multilineage hematopoiesis, but did not induce leukemia. Because active mutations in ras genes are often found in MLL-related leukemia, we next transduced the gene for a constitutively active form of K-ras along with the MLL-AF10 oncogene. Eight weeks after transplantation, all the recipient mice had developed acute monoblastic leukemia (the M5 phenotype in French-American-British classification). We thus successfully established a human MLL-rearranged leukemia that was derived in vivo from human HSCs. In addition, since the enforced expression of the mutant K-ras alone was insufficient to induce leukemia, the present model may also be a useful experimental platform for the multi-step leukemogenesis model of human leukemia.