Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing the flavanone core toward new selective nitrogen-containing modulators of ABC transporters.

AIM Naringenin (1), isolated in large amount from the aerial parts of Euphorbia pedroi, was chemically derivatized to yield 18 imine derivatives (2-19) and three alkylated derivatives through a Mannich-type reaction (20-22) that were tested as multidrug resistance (MDR) reversers in cancer cells. Results/methodology: While hydrazone (2-4) and azine (5-13) derivatives showed an improvement in their MDR reversal activities against the breast cancer resistance protein, carbohydrazides 14-19 revealed an enhancement in MDR reversal activity toward the multidrug resistance protein 1. CONCLUSION The observed activities, together with pharmacophoric analysis and molecular docking studies, identified the spatial orientation of the substituents as a key structural feature toward a possible mechanism by which naringenin derivatives may reverse MDR in cancer.
Measuring Crowd Collectiveness

Collective motions are common in crowd systems and have attracted a great deal of attention in a variety of multidisciplinary fields. Collectiveness, which indicates the degree of individuals acting as a union in collective motion, is a fundamental and universal measurement for various crowd systems. By integrating path similarities among crowds on collective manifold, this paper proposes a descriptor of collectiveness and an efficient computation for the crowd and its constituent individuals. The algorithm of the Collective Merging is then proposed to detect collective motions from random motions. We validate the effectiveness and robustness of the proposed collectiveness descriptor on the system of self-driven particles. We then compare the collectiveness descriptor to human perception for collective motion and show high consistency. Our experiments regarding the detection of collective motions and the measurement of collectiveness in videos of pedestrian crowds and bacteria colony demonstrate a wide range of applications of the collectiveness descriptor.
Angelica sinensis polysaccharide inhibits proliferation, migration, and invasion by downregulating microRNA‐675 in human neuroblastoma cell line SH‐SY5Y

Neuroblastoma is the most common tumor diagnosed in children and infants, with high recurrence and poor prognosis. Angelica sinensis polysaccharide (AP) whose average molecular weight is 72,900 Da possesses various bioactivities. We aimed to explore the effects of AP on neuroblastoma SH‐SY5Y cells as well as the underlying mechanisms. Effects of AP on cell viability, proliferation, apoptosis, migration, invasion, and expressions of long noncoding RNA H19 (lncRNA‐H19), microRNA (miR)‐675, and CD44 were assessed. Then, effects of miR‐675 overexpression on AP‐treated cells were analyzed. Next, expression of key kinases in the PI3K/AKT and JAK/ STAT pathways was detected. The possible target gene of miR‐675 was finally explored. Cell viability was reduced by 200–500 µg/mL AP. Meanwhile, AP repressed cell proliferation, migration, and invasion, but induced apoptosis. Expressions of lncRNA‐H19 and miR‐675 were upregulated in neuroblastoma cells, and were downregulated by AP. AP was also identified to upregulate CD44. We next found AP affected SH‐SY5Y cells through downregulating miR‐675. Key kinases in the PI3K/AKT and JAK/STAT pathways were downregulated by AP stimulation, while these downregulations were abrogated by miR‐675 overexpression. KIF1B isoform β (KIF1Bβ) is proved to be a target of miR‐675. In conclusion, AP was first identified to inhibit proliferation, migration, and invasion but induce apoptosis. Furthermore, AP might repress tumorigenesis of SH‐SY5Y cells through miR‐675‐mediated inactivation of the PI3K/AKT and JAK/STAT pathways. Besides, KIF1Bβ might be a target of miR‐675.
White matter abnormalities and cognition in patients with conflicting diagnoses and CSF profiles

Objective To determine whether white matter changes influence progression of cognitive decline in individuals with clinically diagnosed Alzheimer disease (AD) and differing biomarker profiles. Methods Two hundred thirty-six individuals from the Alzheimer's Disease Neuroimaging Initiative database with clinical diagnoses of cognitively normal older adult (older controls [OCs]), mild cognitive impairment, and AD were studied. Support vector machine experiments were first performed to determine the utility of various biomarkers for classifying individuals by clinical diagnosis. General linear models were implemented to assess the relationships between CSF measures of β-amyloid 1–42, phosphorylated tau181p, and MRI-based white matter signal abnormality (WMSA) volumes and cognitive decline. Analyses were performed across all patients as well as within subgroups of individuals that were defined by clinical cutoff points for both CSF measures. Results CSF biomarkers alone classified individuals with AD vs OCs with 82% accuracy, and the addition of WMSA did not enhance this. Both CSF biomarkers as well as WMSA volume significantly contributed to predicting cognitive decline in executive and memory domains when assessed across all 236 individuals. In individuals with pathologic levels of both CSF biomarkers, WMSA only significantly contributed to models of future executive function decline. In individuals with subpathologic CSF biomarker levels (levels similar to those in OC individuals), WMSA significantly contributed to prediction of memory decline and were the sole significant predictor of executive function decline. Conclusions WMSA hold additional predictive power regarding cognitive progression in older individuals and are most effective as biomarkers in individuals who are cognitively impaired but do not fit the expected CSF biomarker profile of AD.
A Pharmacodynamic Study of Docetaxel in Combination with the P-glycoprotein Antagonist Tariquidar (XR9576) in Patients with Lung, Ovarian, and Cervical Cancer

Purpose: P-glycoprotein (Pgp) antagonists have been difficult to develop because of complex pharmacokinetic interactions and a failure to show meaningful results. Here we report the results of a pharmacokinetic and pharmacodynamic trial using a third-generation, potent, noncompetitive inhibitor of Pgp, tariquidar (XR9576), in combination with docetaxel. Experimental Design: In the first treatment cycle, the pharmacokinetics of docetaxel (40 mg/m2) were evaluated after day 1 and day 8 doses, which were administered with or without tariquidar (150 mg). 99mTc-sestamibi scanning and CD56+ mononuclear cell rhodamine efflux assays were conducted to assess Pgp inhibition. In subsequent cycles, 75 mg/m2 docetaxel was administered with 150 mg tariquidar every 3 weeks. Results: Forty-eight patients were enrolled onto the trial. Nonhematologic grade 3/4 toxicities in 235 cycles were minimal. Tariquidar inhibited Pgp-mediated rhodamine efflux from CD56+ cells and reduced 99mTc-sestamibi clearance from the liver. There was striking variability in basal sestamibi uptake; a 12% to 24% increase in visible lesions was noted in 8 of 10 patients with lung cancer. No significant difference in docetaxel disposition was observed in pairwise comparison with and without tariquidar. Four partial responses (PR) were seen (4/48); 3 in the non–small cell lung cancer (NSCLC) cohort, measuring 40%, 57%, and 67% by RECIST, and 1 PR in a patient with ovarian cancer. Conclusions: Tariquidar is well tolerated, with less observed systemic pharmacokinetic interaction than previous Pgp antagonists. Variable effects of tariquidar on retention of sestamibi in imageable lung cancers suggest that follow-up studies assessing tumor drug uptake in this patient population would be worthwhile. Clin Cancer Res; 17(3); 569–80. ©2010 AACR.
Distribution of calcium and phosphorus in leaves of the proteaceae

The overall aim of our research program is to discover the physiological basis of calcium toxicity in Proteaceae plant species that typically inhabit low-phosphorus, acidic soils and avoid calcareous (alkaline) soils. The phenomenon of Ca toxicity has been known for decades, but so far no clear mechanistic explanation is available. We propose that Ca toxicity in P-efficient Proteaceae is the result of a shift in cell type where P accumulates, from epidermal cells as seen in dicots generally to mesophyll cells in P-efficient Proteaceae species [1]. Conversely, we hypothesise that Ca toxicity is avoided in the few Proteaceae species that inhabit calcareous soils by shifting the accumulation of Ca from mesophyll cells, where dicots generally accumulate Ca, to epidermal cells so as to prevent interference with efficient P utilisation.
Deflection of Steel Dendrite Growing in the Fluid Flow Driven by Electromagnetic Stirrer

Synopsis : In order to evaluate the flow velocity of molten steel driven by electromagnetic stirrer in the mold, not only deflection mechanism of dendrite due to fluid flow but also fluid dynamics promoted by Lorentz force have been taken into account. Deflection angle of dendrite in cross section have been analysed in various steels which have been cast with various width and promotive forces. The relation between deflection angle and promotive force is not well correlated (correlation factor: 0.63). It is found from the numerical analysis of fluid dynamics that the flow velocity increases with increasing width of stab, at a constant promotive force. Thus, promotive forces are normarized with respect to width. Since the deflection angle of steel dendrite is affected by carbon content, experimental data on deflection angle are also modified by carbon content. The relation between normarized promotive force and modified deflection angles is then quite well correlated (correlation factor: 0.97). Since the Lorentz force is a body one, the flow velocity (Us) can be simply derived. The ratio between flow velocity calculated from modified deflection angle and Us is approximately 0.4, which may be constant with usual casting condition of slab. This indicates that 60% of imposed electromagnetic force disappears due to the interaction of 3D flow, due to the interference between submerged entry nozzle etc. To estimate the flow velocity, it is important to take the effect of carbon content on deflection angle into consideration.
Effect of Chitosan Coating Enriched with Cinnamon Oil (Cinnamomum zeylanicum) on Storage Stability of Refrigerated Chicken Meat Nuggets

The purpose of this paper was to evaluate the shelf-life of chitosan and cinnamon oil coated chicken meat nuggets under refrigeration conditions. Three types of coated nuggets were developed viz., Meat coated with Chitosan (1%) and Cinnamon oil (0.05%) (T1), direct addition of Chitosan and Cinnamon oil in emulsion (T2) and nuggets dipped in Chitosan and Cinnamon oil (T3) and were aerobically packaged in low-density polyethylene pouches and assessed for various storage quality parameters under refrigerated (4±1°C) conditions during 28 days of storage. T2 had slightly higher emulsion stability and yield although no significant difference (P>0.05) in between samples. T1 exhibited better storage stability as indicated by lower lipid oxidation than other treatments and the control. Texture profile studies indicated that T2 sample had higher hardness value than other samples. SPC significantly (P<0.05) increased in all the samples with control having the highest value followed by T1, T3 and T2 throughout the storage period. T2 sample exhibited lowest sensory scores and were not accepted by sensory panellist while T1 and T3 samples had better acceptability. It was concluded that chitosan in combination with cinnamon oil had synergistic effect to extend the shelf-life of products (T1 and T3)
Are web-based questionnaires accepted in patients attending rehabilitation?

Abstract Purpose: The aim of the present paper was to study preferences for web based self-administered questionnaires (web SAQs) vs. paper-based self-administered questionnaires (paper SAQs) and to evaluate the feasibility of using web SAQs in patients referred to cardiac, lung, occupational and cancer rehabilitation programs. Methods: The patients were approached by mail and given the choice to answer the compulsory SAQs either on paper or on a web-based platform. Results: Hundred and twenty seven out of 183 eligible patients (69.3%) were willing to participate and 126 completed the study. Web SAQs were preferred by 77.7%, and these patients were significantly younger, more often cohabiting and tended to have higher level of education than paper SAQ users. Mean number of data missing per patient was less among the web SAQ users than the paper SAQ users (0.55 vs. 2.15, p < 0.001). Costs related to human resources were estimated to be 60% lower with web SAQs compared to paper SAQs. Conclusions: Web SAQs were well accepted among the patients scheduled for rehabilitation, led to less missing data and considerable cost savings related to human resources. Patients referred to rehabilitation should be offered the choice to complete self-administered questionnaires on internet platforms when internet access is common and available. Implications for Rehabilitation The high acceptability of web-based self-administered questionnaires among rehabilitation patients suggests that internet platforms are suitable tools to collect patient information for rehabilitation units. Web-based modes of patient data collection demonstrate low number of missing data and can therefore improve the quality of data collection from rehabilitation patients. Use of web-based questionnaires considerably reduces administrative costs of data collection in rehabilitation settings compared to traditional pen and paper methods.
FEASIBILITY OF SUB-MICRON XRF COMBINED TO SCANNING PROBE MICROSCOPY

In-lab high lateral resolution XRF tools are needed, mainly in the field of microelectronics and solar cell industries, as non destructive in-depth chemical analysis equipments. In the present work we have used capillary optics for both illumination and fluorescence signal collection. The primary beam provided by a rotating anode (CuKα line) is focused on the sample using a capillary lens (Xray spot diameter 20 µm), while the EDX detector is equipped with a cylindrical capillary. System modelling and simulation are carried out to estimate the ultimate lateral resolution we could reach in chemical analysis using such equipment. The dependence of the fluorescence signal as a function of detection capillary diameter is simulated. The good agreement with the experimental data validates the model. It is demonstrated here that using an elliptical capillary approached in near field mechanical interaction with the surface would obtain a sub micron lateral resolution in XRF analysis, combined with simultaneous sample topography data acquisition.
Random field topic model for semantic region analysis in crowded scenes from tracklets

In this paper, a Random Field Topic (RFT) model is proposed for semantic region analysis from motions of objects in crowded scenes. Different from existing approaches of learning semantic regions either from optical flows or from complete trajectories, our model assumes that fragments of trajectories (called tracklets) are observed in crowded scenes. It advances the existing Latent Dirichlet Allocation topic model, by integrating the Markov random fields (MR-F) as prior to enforce the spatial and temporal coherence between tracklets during the learning process. Two kinds of MRF, pairwise MRF and the forest of randomly spanning trees, are defined. Another contribution of this model is to include sources and sinks as high-level semantic prior, which effectively improves the learning of semantic regions and the clustering of tracklets. Experiments on a large scale data set, which includes 40, 000+ tracklets collected from the crowded New York Grand Central station, show that our model outperforms state-of-the-art methods both on qualitative results of learning semantic regions and on quantitative results of clustering tracklets.
A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis

BRCA1/2 screening in Hereditary Breast and Ovarian Syndrome (HBOC) is an essential step for effective patients’ management. Next-Generation Sequencing (NGS) can rapidly provide high throughput and reliable information about the qualitative and quantitative status of tumor-associated genes. Straightforwardly, bioinformatics methods play a key role in molecular diagnostics pipelines. BRCA1/2 genes were evaluated with our NGS workflow, coupled with Multiplex Amplicon Quantification (MAQ) and Multiplex Ligation-dependent Probe Amplification (MLPA) assays. Variant calling was performed on Amplicon Suite, while Copy Number Variant (CNV) prediction by in house and commercial CNV tools, before confirmatory MAQ/MLPA testing. The germline profile of BRCA genes revealed a unique HBOC pattern. Although variant calling analysis pinpointed heterozygote and homozygote polymorphisms on BRCA1 and BRCA2, respectively, the CNV predicted by our script suggested two conflicting interpretations: BRCA1 duplication and/or BRCA2 deletion. Our commercial software reported a BRCA1 duplication, in contrast with variant calling results. Finally, the MAQ/MLPA assays assessed a whole BRCA2 copy loss. In silico CNV analysis is a time and cost-saving procedure to powerfully identify possible Large Rearrangements using robust and efficient NGS pipelines. Our layout shows as bioinformatics algorithms alone cannot completely and correctly identify whole BRCA1/2 deletions/duplications. In particular, the complete deletion of an entire gene, like in our case, cannot be solved without alternative strategies as MLPA/MAQ. These findings support the crucial role of bioinformatics in deciphering pitfalls within NGS data analysis.
Kull , M . , & Flach , P . A . ( 2014 ) . Reliability Maps : A Tool to Enhance

Probability Estimates and Improve Classification Accuracy (Best paper award). In T. Calders, F. Esposito, E. Hullermeier, & R. Meo (Eds.), Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2014, Nancy, France, September 15-19, 2014. Proceedings, Part II (pp. 18-33). (Lecture Notes in Artificial Intelligence; Vol. 8725). Springer Berlin Heidelberg, 2010. DOI: 10.1007/978-3-66244851-9_2
Calcium sensitive ring-like oligomers formed by synaptotagmin

Significance Synaptotagmin-1 is the calcium sensor for synchronous neurotransmitter release. It couples calcium influx to the soluble N-ethylmaleimide–sensitive factor activating protein receptor (SNARE)-catalyzed fusion, but how this coupling happens is unknown. Here, using electron microscopy, we report that the cytosolic domain of synaptotagmin can assemble into ring-like oligomers under calcium-free conditions, and these rings disassemble rapidly upon calcium binding. This process suggests a novel but speculative mechanism to explain calcium coupling, in which the synaptotagmin rings separate the vesicle and plasma membranes and prevent the completion of SNARE complex assembly until the influx of calcium. The synaptic vesicle protein synaptotagmin-1 (SYT) is required to couple calcium influx to the membrane fusion machinery. However, the structural mechanism underlying this process is unclear. Here we report an unexpected circular arrangement (ring) of SYT’s cytosolic domain (C2AB) formed on lipid monolayers in the absence of free calcium ions as revealed by electron microscopy. Rings vary in diameter from 18–43 nm, corresponding to 11–26 molecules of SYT. Continuous stacking of the SYT rings occasionally converts both lipid monolayers and bilayers into protein-coated tubes. Helical reconstruction of the SYT tubes shows that one of the C2 domains (most likely C2B, based on its biochemical properties) interacts with the membrane and is involved in ring formation, and the other C2 domain points radially outward. SYT rings are disrupted rapidly by physiological concentrations of free calcium but not by magnesium. Assuming that calcium-free SYT rings are physiologically relevant, these results suggest a simple and novel mechanism by which SYT regulates neurotransmitter release: The ring acts as a spacer to prevent the completion of the soluble N-ethylmaleimide–sensitive factor activating protein receptor (SNARE) complex assembly, thereby clamping fusion in the absence of calcium. When the ring disassembles in the presence of calcium, fusion proceeds unimpeded.
Functional Magnetic Mesoporous Silica Microparticles Capped with an Azo-Derivative: A Promising Colon Drug Delivery Device

Magnetic micro-sized mesoporous silica particles were used for the preparation of a gated material able to release an entrapped cargo in the presence of an azo-reducing agent and, to some extent, at acidic pH. The magnetic mesoporous microparticles were loaded with safranin O and the external surface was functionalized with an azo derivative 1 (bearing a carbamate linkage) yielding solid S1. Aqueous suspensions of S1 at pH 7.4 showed negligible safranin O release due to the presence of the bulky azo derivative attached onto the external surface of the inorganic scaffold. However, in the presence of sodium dithionite (azoreductive agent), a remarkable safranin O delivery was observed. At acidic pH, a certain safranin O release from S1 was also found. The pH-triggered safranin O delivery was ascribed to the acid-induced hydrolysis of the carbamate moiety that linked the bulky azo derivatives onto the mesoporous inorganic magnetic support. The controlled release behavior of S1 was also tested using a model that simulated the gastro intestinal tract.
UAV-based SLAM and 3D reconstruction system

3D reconstructing a landscape is a prevalent problem that attracts a lot of interest in recent years. This project intended to verify whether the hypothesis of a UAV-based SLAM and 3D reconstruction system is practical. A GPS-Fused SLAM system is built based on ORB-SLAM. Inverse depth is also implemented to make the system suitable for a UAV-based platform. Meanwhile, REMODE is a depth filter and is tested as not being well enough as a dense mapping module. In the end, PMVS is implemented to build a dense map of the environment which produces a reasonable result. The small-scale-scene experiments produce the total error ratio of 5.60% in the x-y plane and 6.59% in the z axis.
Copper(II) bis(4,4,4-trifluoro-1-phenylbutane-1,3-dionate) complexes with pyridin-2-one, 3-hydroxypyridine and 3-hydroxypyridin-2-one ligands: molecular structures and hydrogen-bonded networks.

Copper(II) bis(4,4,4-trifluoro-1-phenylbutane-1,3-dionate) complexes with pyridin-2-one (pyon), 3-hydroxypyridine (hpy) and 3-hydroxypyridin-2-one (hpyon) were prepared and the solid-state structures of (pyridin-2-one-κO)bis(4,4,4-trifluoro-3-oxo-1-phenylbutan-1-olato-κ2O,O')copper(II), [Cu(C10H6F3O2)2(C5H5NO)] or [Cu(tfpb-κ2O,O')2(pyon-κO)], (I), bis(pyridin-3-ol-κO)bis(4,4,4-trifluoro-3-oxo-1-phenylbutan-1-olato-κ2O,O')copper(II), [Cu(C10H6F3O2)2(C5H5NO)2] or [Cu(tfpb-κ2O,O')2(hpy-κO)2], (II), and bis(3-hydroxypyridin-2-one-κO)bis(4,4,4-trifluoro-3-oxo-1-phenylbutan-1-olato-κ2O,O')copper(II), [Cu(C10H6F3O2)2(C5H5NO2)2] or [Cu(tfpb-κ2O,O')2(hpyon-κO)2], (III), were determined by single-crystal X-ray analysis. The coordination of the metal centre is square pyramidal and displays a rare example of a mutual cis arrangement of the β-diketonate ligands in (I) and a trans-octahedral arrangement in (II) and (III). Complex (II) presents the first crystallographic evidence of κO-monodentate hpy ligation to the transition metal enabling the pyridine N atom to participate in a two-dimensional hydrogen-bonded network through O-H.N interactions, forming a graph-set motif R22(7) through a C-H.O interaction. Complex (III) presents the first crystallographic evidence of monodentate coordination of the neutral hpyon ligand to a metal centre and a two-dimensional hydrogen-bonded network is formed through N-H.O interactions facilitated by C-H.O interactions, forming the graph-set motifs R22(8) and R22(7).