Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical significance of small pulmonary nodules with little or no 18F-FDG uptake on PET/CT images of patients with nonthoracic malignancies.

UNLABELLED Small pulmonary nodules with little or no perceptible (18)F-FDG uptake are relatively common findings on combined PET/CT images of patients with nonthoracic malignancies. Interpreting such nodules is often a diagnostic challenge, and this study aimed to evaluate the clinical significance of the nodules. METHODS Patients with pulmonary nodules < or =1 cm in diameter showing no (18)F-FDG uptake or uptake less than the mediastinal background were included. Nodules with clearly benign or metastatic findings on CT were excluded. One hundred twenty-one patients had either tissue confirmation or clinical follow-up with additional chest images. The subjects were studied by 3 variables: (i) solitary versus multiple nodules, (ii) presence of accompanying benign lung lesion versus absence, and (iii) imperceptible (18)F-FDG uptake versus faint (18)F-FDG uptake. The malignancy rates were calculated for each variable. RESULTS Of the 121 patients, 24 had malignancy, with a strong possibility of pulmonary metastasis (19.8%). Six of the 44 patients with solitary nodules (13.6%) and 18 of the 77 patients with multiple nodules (23.4%) had malignancies, though there was no statistically significant difference in the incidences of malignancy between the solitary and multiple groups. On the other hand, there was a statistically significant difference (P = 0.040) between the accompanying lung lesion present (8.3%) and absent (24.7%) groups. No statistically significant difference was noted between the (18)F-FDG uptake imperceptible group and faint (18)F-FDG uptake group (20.7% vs. 17.2%). CONCLUSION For patients with incidental lung nodules of indeterminate nature with no (18)F-FDG uptake or uptake less than that of the mediastinum on PET/CT images, >19% of the cases turned out to be malignant. The nodule was more likely to be malignant when no other benign pulmonary lesions could be identified elsewhere in the lung field. Thus, regardless of the number of nodules and (18)F-FDG uptake, tissue confirmation or close imaging follow-up is necessary when small nodules with imperceptible or faint (18)F-FDG activity are present on the PET/CT images, especially in the absence of accompanying benign lung lesions.
Preliminary study with SprayShield™ Adhesion Barrier System in the prevention of abdominal adhesions

Introduction Peritoneal adhesions, the fibrotic bands that form between the surfaces in the peritoneal cavity following surgery, still pose a difficult clinical challenge. Aim To evaluate the SprayShield™ Adhesion Barrier System (PEG ester amine solution and a buffer solution) in reducing post-operative adhesion formation. Material and methods This was a prospective, multi-center, randomized, single blind study. A total of 11 subjects diagnosed with ulcerative colitis (UC) or familial adenomatous polyposis (FAP) were randomized: 8 to the SprayShield™ arm and 3 to the control arm. SprayShield™ was applied on the viscera directly under the midline peritoneal incision and at the site of ileostomy. During the follow-up surgery, the incidence, extent, and severity of post-operative adhesion formation were evaluated, as well as the time required to mobilize the ileal loop. Results In patients who received SprayShield™ the time required to mobilize the ileal loop at the ileostomy closure was slightly shorter and the incidence and severity of adhesions were somewhat lower vs. control subjects (NS). Conclusions SprayShield™ was found to be easy to use, safe, and quick to apply, and performed well in adherence and conformity. The incidence and severity of adhesions were lower for SprayShield™ subjects vs. control subjects, but due to the limited number of patients there are not enough data to confirm the effectiveness of the SprayShield™ Adhesion Barrier System in prevention of adhesions.
Exploring NoC mapping strategies: an energy and timing aware technique

Complex applications implemented as systems on chip (SoC) demand extensive use of system level modeling and validation. Their implementation gathers a large number of complex IP cores and advanced interconnection schemes, such as hierarchical bus architectures or networks on chip (NoC). Modeling applications involves capturing its computation and communication characteristics. Previously proposed communication weighted models (CWM) consider only the application communication aspects. This work proposes a communication dependence and computation model (CDCM) that can simultaneously consider both aspects of an application. It presents a solution to the problem of mapping applications on regular NoC while considering execution time and energy consumption. The use of CDCM is shown to provide estimated average reductions of 40% in execution time, and 20% in energy consumption, for current technologies.
High-Strength Composites Based on Tung Oil Polyurethane and Wood Flour : Effect of the Filler Concentration on the Mechanical Properties

New composite materials with a high percentage of their composition based on renewable resources, matrix and reinforcement, were prepared. The excellent compatibility of the main phases lead to an unusual outstanding composite behavior as follows: higher modulus and strength, but also higher deformability and fracture resistance than the neat polymer. A biobased polyol was obtained by chemical modification of tung oil to be used in the production of polyurethane composites reinforced with pine wood flour (WF). The mechanical behavior as a function of wood flour content was evaluated through tensile and impact tests. Increasing the filler content induced an increase in tensile modulus and strength as well as in impact strength. Composites containing 10 and 15 wt% of wood flour presented higher tensile ultimate strain than that of the unfilled polyurethane. These results were explained by a strong interfacial adhesion (physical and chemical bonding), which was also supported by SEM micrography and strength modeling. POLYM. ENG. SCI., 49:713– 721, 2009. a 2009 Society of Plastics Engineers
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors

MOTIVATION Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored. RESULTS In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial. AVAILABILITY The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.
Retinoids induce lumen morphogenesis in mammary epithelial cells

Lumen formation is a fundamental step in the development of the structural and functional units of glandular organs, such as alveoli and ducts. In an attempt to elucidate the molecular signals that govern this morphogenetic event, we set up an in vitro system in which cloned mammary epithelial cells grown in collagen gels under serum-free conditions form solid, lumen-less colonies. Addition of as little as 0.1% donor calf serum (DCS) was sufficient to induce the formation of a central cavity. Among a number of serum constituents analyzed, retinol was found to mimic the effect of DCS in inducing lumen morphogenesis. Since the biological activities of retinol are largely dependent on its conversion to all-trans-retinoic acid (RA), we examined in more detail the effect of RA on lumen formation. RA induced the formation of lumen-containing colonies (cysts) in a concentration- and time-dependent manner, a half-maximal effect after 9 days of culture being observed with 100 pM RA. The pleiotropic effects of retinoids are mediated by nuclear retinoic acid receptors (RARs; α, β and γ) and retinoid X receptors (RXRs; α, β and γ). To identify the signaling pathway involved in RA-induced lumen formation, we used receptor-specific synthetic retinoids. TTNPB, a selective RAR agonist, promoted lumen morphogenesis, whereas RXR-selective ligands lacked this activity. Lumen formation was also induced at picomolar concentrations by Am-580, a synthetic retinoid that selectively binds the RARα receptor subtype. Moreover, co-addition of Ro 41-5253, an antagonist of RARα, abrogated the lumen-inducing activity of both RA and DCS, indicating that this biological response is mediated through an RARα-dependent signaling pathway. To gain insight into the mechanisms underlying RA-induced lumen formation, we assessed the potential role of matrix metalloproteinases (MMP). Using gelatin zymography, we observed a dose-dependent increase in latent and active forms of gelatinase B (MMP-9) upon RA treatment. In addition, lumen formation was abrogated by addition of the synthetic MMP inhibitor BB94, indicating that this morphogenetic process is likely to require MMP activity. Collectively, our results provide evidence that RA promotes lumen formation by mammary epithelial cells in vitro and suggest that it plays a similar role during mammary gland development in vivo.
Modeling the socio-semantic dynamics of scientific communities. (Modélisation des dynamiques socio-sémantiques dans les communautés scientifiques)

How are the social and semantic structures of a scientific communitydriving future research dynamics? In this thesis we combine naturallanguage processing techniques and network theory methods to analyzeavery large dataset of scientific publications in the field of computationallinguistics,i.e.the ACL Anthology. Ultimately, our goal is to understandthe role of collaborations among researchers in building and shaping thelandscape of scientific knowledge, and, symmetrically, to understand howthe configuration of this landscape influences individual trajectories ofresearchers and their interactions. We use natural language processingtools to extract the terms corresponding to scientific concepts from thetexts of the publications. Then we reconstruct a socio-semantic networkconnecting researchers and scientific concepts, and model the dynamicsof its evolution at different scales. To achieve this, we first build astatistical model, based on multivariate logistic regression, that quantifiesthe role that social and semantic features play in the evolution of thesocio-semantic network, namely in the emergence of new links. Then, wereconstruct the evolution of the field through different visualizations of theknowledge produced therein, and of the flow of researchers across thedifferent subfields of the domain. To summarize, we have shown throughour work that the combination of natural language processing techniqueswith complex network analysis makes it possible to investigate in a novelway the evolution of scientific fields.
Reduced Serum Caeruloplasmin Levels in Non-Wilsonian Movement Disorders

Reduction in caeruloplasmin (Cp) levels is sometimes found in other sporadic movement disorders, not limited to Wilson’s disease (WD). Serum levels of Cp, copper, iron and gamma-glutamyl transpeptidase were measured in 71 patients with various diagnoses of movement disorders, including Parkinson’s disease (PD), atypical parkinsonian disorders, tardive dyskinesia, essential tremor, and idiopathic focal dystonia, and compared with those of 26 healthy age- and gender-matched controls. The mean Cp level in the patient group was 20.5 ± 4.2 mg/dl , lower than in controls (23.5 ± 7.2 mg/dl; p = 0.005). In subgroup analysis, mean Cp level of PD patients (19.6 ± 3.0 mg/dl) was lower than that of controls (p = 0.045). In a group analysis as neurodegenerative movement disorders (NDD), their mean Cp level was 19.9 ± 3.0 mg/dl, lower than that of controls (p = 0.019). Linear regression analysis indicated that the presence of NDD was the main factor associated with lower Cp levels. The finding of reduced serum Cp level in non-Wilsonian movement disorders and selective reduction in the neurodegenerative subgroup supports the notion that Cp might be associated with the cascade of neurotoxicity in NDD. The variation in Cp level in other non-WD conditions highlights the fact that Cp level is a poor screening test for WD in the absence of clear clinical suspicion.
Discovery of the Novel mTOR Inhibitor and Its Antitumor Activities In Vitro and In Vivo

The phosphoinositide 3-kinase (PI3-K)/Akt and mTOR signaling pathway plays a critical role in cell survival and proliferation and is often aberrantly activated in many types of cancer. The mTOR kinase protein, one of the key molecules in this pathway, has been shown to be an important target for cancer therapy. In the present study, a ligand docking method was used to screen for novel scaffold mTOR inhibitors. Sixty thousand compounds in the Natural Product Database were screened against the mTOR homologous structure, and 13 commercially available compounds listed in the top-ranked 100 compounds were selected for further examination. Compound [(E)-3-(4-(benzo[d][1,3]dioxol-5-yl)-2-oxobut-3-en-1-yl)- 3-hydroxyindolin-2-one; designated herein as 3HOI-BA-01] was then selected for further study of its antitumor activity. An in vitro study has shown that 3HOI-BA-01 inhibited mTOR kinase activity in a dose-dependent manner by directly binding with mTOR. In a panel of non–small cell lung cancer cells, the compound also attenuated mTOR downstream signaling, including the phosphorylation of p70S6K, S6, and Akt, resulting in G1 cell-cycle arrest and growth inhibition. Results of an in vivo study have shown that intraperitoneal injection of 3HOI-BA-01 in A549 lung tumor–bearing mice effectively suppressed cancer growth without affecting the body weight of the mice. The expression of downstream signaling molecules in the mTOR pathway in tumor tissues was also reduced after 3HOI-BA-01 treatment. Taken together, we identified 3HOI-BA-01 as a novel and effective mTOR inhibitor. Mol Cancer Ther; 12(6); 950–8. ©2013 AACR.
Proteomic investigations on the effect of different membrane materials on blood protein adsorption during haemodialysis.

BACKGROUND During haemodialysis procedure, the contact of blood with the membrane material contained in the hemodialyser results in protein deposition and adsorption, and surface-adsorbed proteins may trigger a variety of biological pathways with potential pathophysiologic consequences. The present work was undertaken to examine for protein adsorption capacity of two membranes used for clinical haemodialysis, namely cellulose triacetate (a derivatized cellulosic membrane) and the synthetic polymer polysulfone-based helixone. MATERIALS AND METHODS We performed a prospective cross-over study in chronic haemodialysis patients, routinely treated with a cellulose triacetate dialyser (n=3) or with a helixone dialyser (n=3). Dialysers from each patient were obtained after dialysis session, and flushed with a litre of saline to remove residual blood. Adsorbed proteins were then eluted by a strong chaotropic buffer. Patients were next switched to the other membrane dialyser for four weeks, at the end of this period protein adsorption being evaluated again. After silver staining, expression profile protein of the two groups was analyzed by 2-DE gels, analyzed and identified by Peptide Mass-finger printing and MALDI-TOF-MS/MS sequency. Moreover nanoLC-MS/MS shotgun profiling was pursued using a semi-quantitative label free approach by emPAI data analysis. RESULTS A total of 54 differentially expressed proteins were identified: 22 proteins more concentrated in helixone membrane (predominantly low abundant plasma proteins) and 32 in cellulose triacetate (most represented by high abundant plasma proteins). The difference proved to be related to membrane material and not to patient's characteristics. DISCUSSION Proteomic techniques represent a useful approach for the investigation of proteins surface-adsorbed onto a haemodialysis membrane, and can also be applied for critical assessment to compare efficiencies of different dialyser membrane materials in the adsorption of plasma proteins.
Synthesis of High-Phase Purity SrTi1–xZrxO3 Ceramics by Sol-Spray Pyrolysis Method

SrTi1–xZrxO3 (0 ≤ x ≤ 1.0) ceramics were synthesized from powders generated by sol-spray pyrolysis. Crystal symmetry, morphology, and the band gap of the prepared ceramics were investigated as a function of Ti/Zr ratio. Substitution of Zr4+ for Ti4+ in the solid solution markedly effects crystal symmetry and grain growth and results in an increased band gap. Single-phase products with good crystallinity and dense microstructure were obtained after sintering at 1250°C.
Combining Valosin-containing Protein (VCP) Inhibition and Suberanilohydroxamic Acid (SAHA) Treatment Additively Enhances the Folding, Trafficking, and Function of Epilepsy-associated γ-Aminobutyric Acid, Type A (GABAA) Receptors*

Background: The α1 subunit harboring the A322D mutation is subject to excessive ERAD. Results: VCP inhibition using Eeyarestatin I reduces the ERAD of α1(A322D) subunits, and coapplication of SAHA additively enhances their proteostasis. Conclusion: Combining ERAD inhibition and folding enhancement yields significant functional rescue. Significance: This combination represents a new, promising strategy to treat epilepsy resulting from GABAA receptor misfolding. GABAA receptors are the primary inhibitory ion channels in the mammalian central nervous system. The A322D mutation in the α1 subunit results in its excessive endoplasmic reticulum-associated degradation at the expense of plasma membrane trafficking, leading to autosomal dominant juvenile myoclonic epilepsy. Presumably, valosin-containing protein (VCP)/p97 extracts misfolded subunits from the endoplasmic reticulum membrane to the cytosolic proteasome for degradation. Here we showed that inhibiting VCP using Eeyarestatin I reduces the endoplasmic reticulum-associated degradation of the α1(A322D) subunit without an apparent effect on its dynamin-1 dependent endocytosis and that this treatment enhances its trafficking. Furthermore, coapplication of Eeyarestatin I and suberanilohydroxamic acid, a known small molecule that promotes chaperone-assisted folding, yields an additive restoration of surface expression of α1(A322D) subunits in HEK293 cells and neuronal SH-SY5Y cells. Consequently, this combination significantly increases GABA-induced chloride currents in whole-cell patch clamping experiments than either chemical compound alone in HEK293 cells. Our findings suggest that VCP inhibition without stress induction, together with folding enhancement, represents a new strategy to restore proteostasis of misfolding-prone GABAA receptors and, therefore, a potential remedy for idiopathic epilepsy.
Eco‐friendly durable press finishing of cellulose‐containing fabrics

To impart easy-care properties to cellulose-containing fabrics along with avoiding any harmful effects of formaldehyde on both the health and the environment, attempts have been made to use citric acid (CA) as an ester crosslinking agent along with different catalytic systems in the absence and presence of certain additives. Further, fixation conditions, type of crosslinking agent, as well as type of substrate have been studied. Results revealed that the enhancement in carboxyl content, performance properties, and the decrease in tear strength (TS) as well as in whiteness indices (WI) of the finished fabric samples were increased by increasing CA concentration up to 80 g/L and by raising thermofixation temperature from 140 up to 180°C for 90 s. Inclusion of triethanolamine hydrochloride (TEA. HCl), decreased the carboxyl content, TS, color strength K/S, as well as oily stain release rating (SRR) of the finished fabric samples along with an increase in bound nitrogen (%N), wrinkle recovery angle WRA, and an improvement in WI without affecting the durable press rating (DP). Within the range examined (0–30 g/L), increasing PEG-600 concentration improved the wet resiliency, TS, as well as WI properties of the finished samples. Increasing DMDHEU ratio in the CA/DMDHEU crosslinking system gave rise to an increase in %N, WRA (dry and wet), DP, as well as in free CH2O of finished fabrics, along with a slight improvement in WI values. On the other hand, the TS, carboxyl content, K/S, SRR values of the finished fabric samples were lower at a higher DMDHEU ratio. Increase in carboxyl content, %N, WRA (dry and wet), DP and SRR, as well as extent of post dyeing (K/S) of the treated fabric samples upon using different ester crosslinking agents followed the descending order: citric acid > pyromellitic dianhydride. The opposite holds true for the TS, and WI values. Among the esterifying catalysts used, and for a given set of finishing conditions, NaH2PO2 · H2O proved to be the most effective one, and the following order of effectiveness may be drawn: NaH2PO2 · H2O > K2HPO4 > Na3–citrate > Na2–tartrate. Inclusion of silicone softener in the finishing formulation brought about an improvement in softeness degree, WRA, %N, DP, TS as well as K/S values along with a decrease in carboxyl content, SRR, and WI values of the treated fabric samples, regardless of the used silicone softener.The performance properties of the finished fabric samples were determined by the type and nature of the substrate. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 2243–2253, 2002