Miracle-dz/UniFAR-FTUs huggingface dataset:
Oleoylethanolamide prevents neuroimmune HMGB1/TLR4/NF‐kB danger signaling in rat frontal cortex and depressive‐like behavior induced by ethanol binge administration

Alcohol abuse is frequently characterized by a specific pattern of intake in binge drinking episodes, inducing neuroinflammation and brain damage. Here, we characterized the temporal profile of neuroinflammation in rats exposed to intragastric binge ethanol administrations (3 times/day × 4 days) and tested the anti‐inflammatory/neuroprotective properties of the satiety factor oleoylethanolamide (OEA). Pre‐treatment with OEA (5 mg/kg, i.p.) previous each alcohol gavage blocked the expression of high mobility group box 1 (HMGB1) danger signal and the innate immunity Toll‐like receptors 4 (TLR4) in frontal cortex, and inhibited the nuclear factor‐kappa B (NF‐kB) proinflammatory cascade induced by alcohol binge administration. OEA reduced the levels of interleukin‐1beta (IL‐1β), the monocyte chemoattractant protein‐1 (MCP‐1), and the enzymes cyclooxygenase‐2 (COX‐2) and inducible nitric oxide synthase (iNOS) in ethanol binged animals. Elevations in plasma tumor necrosis factor alpha (TNF‐α) and IL‐1β after ethanol were also inhibited by OEA. OEA also prevented ethanol‐induced lipid peroxidation, caspase‐8 and pro‐apoptotic caspase‐3 activation in frontal cortex. Additionally, OEA blocked the rise in blood corticosterone levels after ethanol with no alteration in blood ethanol levels and may affect ethanol‐induced gut permeability for endotoxin. Finally, OEA, administered as a pre‐treatment during the ethanol binge, exerted antidepressant‐like effects during acute withdrawal. Altogether, results highlight a beneficial profile of OEA as a potent anti‐inflammatory, antioxidant, neuroprotective and antidepressant‐like compound to treat alcohol abuse.
Angle of Arrival Estimation using WiFi and Smartphones

In this paper we present our experimental results of angle of arrival (AoA) estimation towards smartphones. There have been several approaches that use WiFi access points (APs), equipped with commercial of the shelf WiFi hardware, to estimate the AoA. One of the most interesting application of these methods is tracking the location of a user with a smartphone. Different carrying positions and the signal attenuation of the human body might affect the results. We experimentally evaluate these effects.
Influence of oxygen on the quality of the PZT thin films prepared by IBS

Pb(Zr,Ti)O3 (PZT) is a ferroelectric material interesting for its high dielectric constant and piezoelectric response. PZT thin films can be prepared by various methods, e.g. pulsed laser deposition, chemical vapor deposition, sol-gel and, most frequently, sputtering. Though the magnetron sputtering is used more frequently, PZT thin films can be prepared also by ion-beam sputtering (IBS). In this paper we study the deposition process of PZT thin films in our IBS system with a possibility of ion-beam assisted deposition (IBAD), which has the advantage that more energy can be added to the growing layer. We show how in our system the resulting layers, mainly their quality, the Pb content, which is important for the creation of the perovskite crystal structure, and the resulting crystal structure are influenced by the oxygen flux during the deposition for the samples grown on the silicon substrate with and without an intermediate Ti seeding layer.
Glutathione Limits Ero1-dependent Oxidation in the Endoplasmic Reticulum*

Many proteins of the secretory pathway contain disulfide bonds that are essential for structure and function. In the endoplasmic reticulum (ER), Ero1α and Ero1β oxidize protein disulfide isomerase (PDI), which in turn transfers oxidative equivalents to newly synthesized cargo proteins. However, oxidation must be limited, as some reduced PDI is necessary for disulfide isomerization and ER-associated degradation. Here we show that in semipermeable cells, PDI is more oxidized, disulfide bonds are formed faster, and high molecular mass covalent protein aggregates accumulate in the absence of cytosol. Addition of reduced glutathione (GSH) reduces PDI and restores normal disulfide formation rates. A higher GSH concentration is needed to balance oxidative folding in semipermeable cells overexpressing Ero1α, indicating that cytosolic GSH and lumenal Ero1α play antagonistic roles in controlling the ER redox. Moreover, the overexpression of Ero1α significantly increases the GSH content in HeLa cells. Our data demonstrate tight connections between ER and cytosol to guarantee redox exchange across compartments: a reducing cytosol is important to ensure disulfide isomerization in secretory proteins.
Host behaviour and nest-site characteristics affect the likelihood of brood parasitism by shiny cowbirds on chalk-browed mockingbirds

We investigated the association between brood parasitism by shiny cowbirds ( Molothrus bonariensis ), and behaviour and nest-site characteristics of chalk-browed mockingbirds ( Mimus saturninus ). This host builds nests on trees, it is aggressive against intruders and it is larger than shiny cowbirds. We conducted focal observations of mockingbird nests, and registered mockingbird activity and attentiveness around the nest. To characterize nest sites, we measured nest cover, nest height, and distance from the nest to the closest perch, and included host laying date and year as additional predictor variables. We also evaluated experimentally host agonistic behaviours directed towards a female cowbird and a control model, and the association between aggressive behaviour and parasitism. Nest attentiveness, nest cover and laying date were associated with parasitism. These results contradict the host-activity hypothesis, because more attentive pairs were less parasitized, and the nest-exposure hypothesis, because more concealed nests were more parasitized. Experiments showed that unparasitized pairs were more aggressive against cowbird models than were parasitized ones. Our findings indicate that shiny cowbirds prefer to parasitize more concealed nests, where they could lay undetected by the host, and that mockingbird nest attentiveness and aggression towards cowbirds are effective first lines of defence against brood parasitism.
Urinary thiobarbituric acid-reacting substances as potential biomarkers of intrauterine hypoxia.

BACKGROUND Currently available clinical tools cannot accurately identify the extent of perinatal hypoxic injuries. During hypoxia, reactive oxygen species cause lipid peroxidation of cell membranes, yielding oxidation products that constitute thiobarbituric acid-reacting substances (TBARS). OBJECTIVE To see if the concentrations of TBARS excreted in urine would be elevated during the first day of life in term and preterm infants following chronic hypoxia or acute asphyxia. DESIGN Thiobarbituric acid-reacting substances levels were measured by a spectrophotometric assay in urine samples collected from term and near-term (>/= 34 weeks gestation, n = 22), and preterm (<34 weeks gestation, n = 52) infants on the first day of life. PATIENTS Infants were admitted to the St Peter's University Hospital (New Brunswick, NJ) neonatal intensive care unit from July 1997 to January 1999. Acute asphyxia was defined as umbilical cord blood pH values less than 7.05, or Apgar scores of less than 5 at 5 minutes. Chronic hypoxia was defined as intrauterine growth retardation or low birth weight (small for gestational age) associated with pregnancy-induced hypertension or reversal of umbilical arterial blood flow. RESULTS Among term infants, urinary TBARS levels were significantly increased following acute asphyxia (P =.02). Levels of TBARS also tended to be elevated following chronic hypoxia. Urinary TBARS levels in term infants tended to be increased in those requiring mechanical ventilation (P =.05) or delivery room resuscitation (P =.15), as well as in those passing intrauterine meconium (P =.13) or having clinical evidence of hypoxic-ischemic encephalopathy (P =.24). CONCLUSIONS The results show a correlation between elevated urinary TBARS levels in term and near-term infants, and perinatal hypoxia (as determined by low Apgar scores or umbilical cord blood acidosis). We speculate that TBARS concentrations may be useful as a biomarker for perinatal hypoxic injury in newborns. Further studies are needed to determine whether elevations in TBARS levels are better predictors of the extent of hypoxic injury than existing markers.
Pragmatic Forces in Conceptual Integration : How Blend Recruitment is Used to Make Metaphors More Compelling

Metaphor and analogy are cognitive tools which, in serving specific communicative goals and descriptive needs, are subject to a host of pragmatic pressures. Knowing that these pressures will shape the interpretation of a given metaphor, an effective communicator will exploit them to structure the conceptual content of the metaphor in such a way as to maximise its perceived aptness and argumentative force to the recipient. This paper considers the form that such pressures can take, and the computational strategies that a communicator can employ to maximise the effectiveness of a given metaphor. This consideration will address not only computational models of structured metaphor/analogy and conceptual blending, but computational accounts of the role, and importance, of similarity in metaphor. We choose as our domain of discourse a collection of visual metaphors which highlights the effect of pragmatic strategies on metaphoric communication.
A Commensal Bifidobacterium longum Strain Prevents Gluten-Related Immunopathology in Mice through Expression of a Serine Protease Inhibitor

ABSTRACT Microbiota-modulating strategies, including probiotic administration, have been tested for the treatment of chronic gastrointestinal diseases despite limited information regarding their mechanisms of action. We previously demonstrated that patients with active celiac disease have decreased duodenal expression of elafin, a human serine protease inhibitor, and supplementation of elafin by a recombinant Lactococcus lactis strain prevents gliadin-induced immunopathology in the NOD/DQ8 mouse model of gluten sensitivity. The commensal probiotic strain Bifidobacterium longum NCC2705 produces a serine protease inhibitor (Srp) that exhibits immune-modulating properties. Here, we demonstrate that B. longum NCC2705, but not a srp knockout mutant, attenuates gliadin-induced immunopathology and impacts intestinal microbial composition in NOD/DQ8 mice. Our results highlight the beneficial effects of a serine protease inhibitor produced by commensal B. longum strains. IMPORTANCE Probiotic therapies have been widely used to treat gastrointestinal disorders with variable success and poor mechanistic insight. Delivery of specific anti-inflammatory molecules has been limited to the use of genetically modified organisms, which has raised some public and regulatory concerns. By examining a specific microbial product naturally expressed by a commensal bacterial strain, we provide insight into a mechanistic basis for the use of B. longum NCC2705 to help treat gluten-related disorders.
RASA1 and NF1 are Preferentially Co-Mutated and Define A Distinct Genetic Subset of Smoking-Associated Non–Small Cell Lung Carcinomas Sensitive to MEK Inhibition

Purpose: Ras-GTPase–activating proteins (RasGAP), notably NF1 and RASA1, mediate negative control of the RAS/MAPK pathway. We evaluated clinical and molecular characteristics of non–small cell lung carcinoma (NSCLC) with RASA1 mutations in comparison with NF1-mutated cases. Experimental Design: Large genomic datasets of NSCLC [MSK-IMPACT dataset at MSKCC (n = 2,004), TCGA combined lung cancer dataset (n = 1,144)] were analyzed to define concurrent mutations and clinical features of RASA1-mutated NSCLCs. Functional studies were performed using immortalized human bronchial epithelial cells (HBEC) and NSCLC lines with truncating mutations in RASA1, NF1, or both. Results: Overall, approximately 2% of NSCLCs had RASA1-truncating mutations, and this alteration was statistically, but not completely, mutually exclusive with known activating EGFR (P = 0.02) and KRAS (P = 0.02) mutations. Unexpectedly, RASA1-truncating mutations had a strong tendency to co-occur with NF1-truncating mutations (P < 0.001). Furthermore, all patients (16/16) with concurrent RASA1/NF1-truncating mutations lacked other known lung cancer drivers. Knockdown of RASA1 in HBECs activated signaling downstream of RAS and promoted cell growth. Conversely, restoration of RASA1 expression in RASA1-mutated cells reduced MAPK and PI3K signaling. Although growth of cell lines with inactivation of only one of these two RasGAPs showed moderate and variable sensitivity to inhibitors of MEK or PI3K, cells with concurrent RASA1/NF1 mutations were profoundly more sensitive (IC50: 0.040 μmol/L trametinib). Finally, simultaneous genetic silencing of RASA1 and NF1 sensitized both HBECs and NSCLC cells to MEK inhibition. Conclusions: Cancer genomic and functional data nominate concurrent RASA1/NF1 loss-of-function mutations as a strong mitogenic driver in NSCLC, which may sensitize to trametinib. Clin Cancer Res; 24(6); 1436–47. ©2017 AACR. See related commentary by Kitajima and Barbie, p. 1243
First principle investigation of atomic hydrogen adsorption on Pd-doped MgB 2

tilizing density functional theory calculations, the atomic adsorption of hydrogen on a Pd-doped Mg-terminated MgB 2 (0001) surface was investigated in terms of total energies and structural properties. Pd doping of about 11% Mg surface sites in MgB 2 caused the lattice parameters a and c to be reduced by 1.3% and 1.7%, respectively. The hollow site far from the Pd impurity was found to be the most preferred site for atomic hydrogen adsorption, which can be explained by the availability of additional electrons. The present results provide an initial understanding of the mechanisms for atomic H adsorption on Pd-doped MgB 2 (0001). U
Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

The modern Western diet is rich in advanced glycation end products (AGEs). We have previously shown an association between dietary AGEs and markers of inflammation and oxidative stress in a population of end stage renal disease (ESRD) patients undergoing peritoneal dialysis (PD). In the current pilot study we explored the effects of dietary AGEs on the gut bacterial microbiota composition in similar patients. AGEs play an important role in the development and progression of cardiovascular (CVD) disease. Plasma concentrations of different bacterial products have been shown to predict the risk of incident major adverse CVD events independently of traditional CVD risk factors, and experimental animal models indicates a possible role AGEs might have on the gut microbiota population. In this pilot randomized open label controlled trial, twenty PD patients habitually consuming a high AGE diet were recruited and randomized into either continuing the same diet (HAGE, n = 10) or a one-month dietary AGE restriction (LAGE, n = 10). Blood and stool samples were collected at baseline and after intervention. Variable regions V3-V4 of 16s rDNA were sequenced and taxa was identified on the phyla, genus, and species levels. Dietary AGE restriction resulted in a significant decrease in serum Nε-(carboxymethyl) lysine (CML) and methylglyoxal-derivatives (MG). At baseline, our total cohort exhibited a lower relative abundance of Bacteroides and Alistipes genus and a higher abundance of Prevotella genus when compared to the published data of healthy population. Dietary AGE restriction altered the bacterial gut microbiota with a significant reduction in Prevotella copri and Bifidobacterium animalis relative abundance and increased Alistipes indistinctus, Clostridium citroniae, Clostridium hathewayi, and Ruminococcus gauvreauii relative abundance. We show in this pilot study significant microbiota differences in peritoneal dialysis patients’ population, as well as the effects of dietary AGEs on gut microbiota, which might play a role in the increased cardiovascular events in this population and warrants further studies.
Enhanced segmentation and skeletonization for endovascular surgical planning

Endovascular surgery is becoming widely deployed for many critical procedures, replacing invasive medical operations with long recovery times. However, there are still many challenges in improving the efficiency and safety of its usage, and reducing surgery time; namely, regular exposure to radiation, manual navigation of surgical tools, lack of 3D visualization, and lack of intelligent planning and automatic tracking of a surgical end-effector. Thus, our goal is to develop hardware and software components of a tele-operation system to alleviate the abovementioned problems. There are three specific objectives in this project: (i) to reduce the need for a surgeon to be physically next to a patient during endovascular surgery; (ii) to overcome the difficulties encountered in manual navigation; and, (iii) to improve the speed and experience of performing such surgeries. To achieve (i) we will develop an electro-mechanical interface to accurately guide mechanically controlled surgical tools from a close distance, along with a 3D visualization interface; for (ii) we will replace the current surgical tools with an "intelligent wire" controlled by the electro-mechanical system; for (iii) we will segment 3D medical images to extract precise shapes of blood vessels, following which we will perform automatic path planning for a surgical end-effector.
Mer Tyrosine Kinase Regulates Disseminated Prostate Cancer Cellular Dormancy

Many prostate cancer (PCa) recurrences are thought to be due to reactivation of disseminated tumor cells (DTCs). We previously found a role of the TAM family of receptor tyrosine kinases TYRO3, AXL, and MERTK in PCa dormancy regulation. However, the mechanism and contributions of the individual TAM receptors is largely unknown. Knockdown of MERTK, but not AXL or TYRO3 by shRNA in PCa cells induced a decreased ratio of P‐Erk1/2 to P‐p38, increased expression of p27, NR2F1, SOX2, and NANOG, induced higher levels of histone H3K9me3 and H3K27me3, and induced a G1/G0 arrest, all of which are associated with dormancy. Similar effects were also observed with siRNA. Most importantly, knockdown of MERTK in PCa cells increased metastasis free survival in an intra‐cardiac injection mouse xenograft model. MERTK knockdown also failed to inhibit PCa growth in vitro and subcutaneous growth in vivo, which suggests that MERTK has specificity for dormancy regulation or requires a signal from the PCa microenvironment. The effects of MERTK on the cell cycle and histone methylation were reversed by p38 inhibitor SB203580, which indicates the importance of MAP kinases for MERTK dormancy regulation. Overall, this study shows that MERTK stimulates PCa dormancy escape through a MAP kinase dependent mechanism, also involving p27, pluripotency transcription factors, and histone methylation. J. Cell. Biochem. 118: 891–902, 2017. © 2016 Wiley Periodicals, Inc.
On Integrating Constraint Propagation and Linear Programming for Combinatorial Optimization

Linear programming and constraint propagation are complementary techniques with the potential for integration to benefit the solution of combinatorial optimization problems. Attempts to combine them have mainly focused on incorporating either technique into the framework of the other -- traditional models have been left intact. We argue that a rethinking of our modeling traditions is necessary to achieve the greatest benefit of such an integration. We propose a declarative modeling framework in which the structure of the constraints indicates how LP and CP can interact to solve the problem.
Crystal Structure of the Human SUV39H1 Chromodomain and Its Recognition of Histone H3K9me2/3

SUV39H1, the first identified histone lysine methyltransferase in human, is involved in chromatin modification and gene regulation. SUV39H1 contains a chromodomain in its N-terminus, which potentially plays a role in methyl-lysine recognition and SUV39H1 targeting. In this study, the structure of the chromodomain of human SUV39H1 was determined by X-ray crystallography. The SUV39H1 chromodomain displays a generally conserved structure fold compared with other solved chromodomains. However, different from other chromodomains, the SUV39H1 chromodomain possesses a much longer helix at its C-terminus. Furthermore, the SUV39H1 chromodomain was shown to recognize histone H3K9me2/3 specifically.
An Eigenvalue-Moment-Ratio Approach to Blind Spectrum Sensing for Cognitive Radio Under Sample-Starving Environment

Eigenvalue-based methods have been widely investigated for multiantenna blind spectrum sensing in cognitive radio (CR). However, most of them are formulated in the framework of maximum likelihood (ML) estimation, which is optimal only when the number of samples is much larger than the number of antennas. In relatively small-sample scenarios where the number of antennas is comparable in magnitude to the number of samples, their optimality cannot be guaranteed. Based on the random matrix theory (RMT), an eigenvalue moment ratio (EMR) approach is proposed for spectrum sensing. As the distribution of the EMR statistic in the absence of signals can be precisely determined by the RMT, this approach is able to reliably predict the theoretical threshold. Moreover, as the EMR detector is developed from the RMT perspective and utilizes all the signal eigenvalues for detection, it can be superior to state-of-the-art detection algorithms, particularly for relatively small samples. Furthermore, we derive the asymptotic distribution of the EMR statistic in the presence of signals and analyze the theoretical detection probability of the EMR approach. Additionally, the EMR statistic is calculated via the Frobenius inner product and matrix trace operations instead of the eigenvalue decomposition (EVD), which offers computational efficiency. Simulation results are presented to illustrate the superiority of the EMR approach and confirm our theoretical calculation.
PRIMARY SEX-RATIO VARIATION IN TWO BROOD PARASITIC BIRDS: BROWN-HEADED COWBIRD (MOLOTHRUS ATER) AND COMMON CUCKOO (CUCULUS CANORUS)

Abstract We examined primary sex-ratios of two brood parasitic species, Brown-headed Cowbird (Molothrus ater) and the Common Cuckoo (Cuculus canorus), to determine whether there was any evidence of primary sex-ratio manipulation as has been demonstrated in other species of birds. Despite good reasons for why female brood parasites should manipulate the primary sex-ratio of their young, we found a lack of evidence for a bias in the sex-ratio of eggs produced at the population level, with respect to the host species parasitized or time of breeding season, or in terms of the sex ratio of eggs produced by individual females. Thus, this study provides another example in birds of little evidence for sex-ratio variation in relation to environmental factors.