Bond-orientational ordering and shear rigidity in modulated colloidal liquids

From Landau-Alexander-McTague theory and Monte-Carlo simulation results we show that the modulated liquid obtained by subjecting a colloidal system to a periodic laser modulation has long range bond-orientational order and non-zero shear rigidity. From infinite field simulation results we show that in the modulated liquid phase, the translational order parameter correlation function decays to zero exponentially while the correlation function for the bond-orientational order saturates to a finite value at large distances.Comment: 8 pages, elsart documentclass, to be published in Physica A as part of proceedings for Stat-Phys 3, Calcutt

Insights on heterogeneity in blinking mechanisms and non-ergodicity using sub-ensemble statistical analysis of single quantum-dots

Photo-luminescence intermittency (blinking) in semiconductor nanocrystals (NCs), a phenomenon ubiquitous to single-emitters, is generally considered to be temporally random intensity fluctuations between bright (On) and dark (Off) states. However, individual quantum-dots (QDs) rarely exhibit such telegraphic signal, and yet, the vast majority of single-NC blinking data are analyzed using a single fixed threshold, which generates binary trajectories. Further, blinking dynamics can vary dramatically over NCs in the ensemble, and it is unclear whether the exponents (m) of single-particle On-/Off-time distributions (P(t)-On/Off), which are used to validate mechanistic models of blinking, are narrowly distributed or not. Here, we sub-classify an ensemble based on the emissivity of QDs, and subsequently compare the (sub)ensemble behaviors. To achieve this, we analyzed a large number (>1000) of intensity trajectories for a model system, Mn+2 doped ZnCdS QDs, which exhibits diverse blinking dynamics. An intensity histogram dependent thresholding method allowed us to construct distributions of relevant blinking parameters (such as m). Interestingly, we find that single QD P(t)-On/Off s follow either truncated power law or power law, and their relative proportion vary over sub-populations. Our results reveal a remarkable variation in m(On/Off) amongst as well as within sub-ensembles, which implies multiple blinking mechanisms being operational among various QDs. We further show that the m(On/Off) obtained via cumulative single-particle P(t)-On/Off is clearly distinct from the weighted mean value of all single-particle m(On/Off), an evidence for the lack of ergodicity. Thus, investigation and analyses of a large number of QDs, albeit for a limited time-span of few decades, is crucial to characterize possible blinking mechanisms and heterogeneity thereinComment: 29 pages including supporting information (single file), 7 main figures, 10 supporting figures and table

A potent betulinic acid analogue ascertains an antagonistic mechanism between autophagy and proteasomal degradation pathway in HT-29 cells

Betulinic acid (BA), a member of pentacyclic triterpenes has shown important biological activities like anti-bacterial, anti-malarial, anti-inflammatory and most interestingly anticancer property. To overcome its poor aqueous solubility and low bioavailability, structural modifications of its functional groups are made to generate novel lead(s) having better efficacy and less toxicity than the parent compound. BA analogue, 2c was found most potent inhibitor of colon cancer cell line, HT-29 cells with IC50 value 14.9 μM which is significantly lower than standard drug 5-fluorouracil as well as parent compound, Betulinic acid. We have studied another mode of PCD, autophagy which is one of the important constituent of cellular catabolic system as well as we also studied proteasomal degradation pathway to investigate whole catabolic pathway after exploration of 2c on HT-29 cells. Mechanism of autophagic cell death was studied using fluorescent dye like acridine orange (AO) and monodansylcadaverin (MDC) staining by using fluorescence microscopy. Various autophagic protein expression levels were determined by Western Blotting, qRT-PCR and Immunostaining. Confocal Laser Scanning Microscopy (CLSM) was used to study the colocalization of various autophagic proteins. These were accompanied by formation of autophagic vacuoles as revealed by FACS and transmission electron microscopy (TEM). Proteasomal degradation pathway was studied by proteasome-Glo™ assay systems using luminometer.The formation of autophagic vacuoles in HT-29 cells after 2c treatment was determined by fluorescence staining – confirming the occurrence of autophagy. In addition, 2c was found to alter expression levels of different autophagic proteins like Beclin-1, Atg 5, Atg 7, Atg 5-Atg 12, LC3B and autophagic adapter protein, p62. Furthermore we found the formation of autophagolysosome by colocalization of LAMP-1 with LC3B, LC3B with Lysosome, p62 with lysosome. Finally, as proteasomal degradation pathway downregulated after 2c treatment colocalization of ubiquitin with lysosome and LC3B with p62 was studied to confirm that protein degradation in autophagy induced HT-29 cells follows autolysosomal pathway. In summary, betulinic acid analogue, 2c was able to induce autophagy in HT-29 cells and as proteasomal degradation pathway downregulated after 2c treatment so protein degradation in autophagy induced HT-29 cell

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Facile Synthesis of [1,2,3]-Triazole-Fused Isoindolines, Tetrahydroisoquinolines, Benzoazepines and Benzoazocines by Palladium-Copper Catalysed Heterocyclisation

An elegant method for the synthesis of 1,2,3-triazoles fused with five-, six-, seven- and eight-membered benzoheterocycles, including isoindoline, tetrahydroisoquinoline, benzoazepine and benzoazocine, has been developed via palladium-copper catalysed reactions in one-pot. The broad scope of this reaction was illustrated by effecting bis-heteroannulations, synthesis of uracil derivatives of biological interest, and employment of acetylene gas as an inexpensive substrate. The reactions are experimentally simple and utilise easily accessible substrates of different type

Palladium–copper catalysed heteroannulation of acetylenic compounds: an expeditious synthesis of isoindoline fused with triazoles

A convenient and general method for the synthesis of isoindoline fused with triazoles from ortho-iodobenzyl azide and acetylenes through palladium–copper catalysis is described. � 2005 Elsevier Ltd. All rights reserved

Palladium-Catalyzed Approach for the General Synthesis of (E)-2- Arylmethylidene-N-tosylindolines and (E)-2-Arylmethylidene-N-tosyl/nosyltetrahydroquinolines: Access to 2-Substituted Indoles and Quinolines

A facile and efficient method for the synthesis of (E)-2-arylmethylidene-N-tosylindolines and (E)-2- arylmethylidene-N-tosyl/nosyltetrahydroquinoline variants has been developed through palladium-catalyzed cyclocondensation of aryl iodides with readily available 1-(2-tosylaminophenyl)prop-2-yn-1-ols and their higher homologues, respectively. The proposed reaction mechanism invokes the operation of trans-aminopalladation during cyclization (5/6-exo-dig), which ensures exclusive (E)-stereochemistry in the products. The method is fast, operationally simple, totally regio- and stereoselective, and versatile enough to access a variety of 2-substituted indoles and quinolines. The reactions proceeded efficiently with a wide variety of substrates and afforded the corresponding products in moderate to excellent yields

A Rapid and Facile Method for the General Synthesis of 3-Aryl Substituted 4,5,6,7-Tetrahydro[1,2,3]Triazolo[1,5-a]Pyrazines and their Ring Fused analogues

We report a general and facile method that provides rapid entry into 3-aryl substituted 4,5,6,7-tetrahydro[1,2,3]triazolo[1,5-a]pyrazines and their ring fused analogues in one-pot under palladium–copper catalysis. The methodology utilises simple and easily available substrates of broad range. The applicability of this reaction for the synthesis of optically active products has been demonstrated. A plausible reaction mechanism has also been proposed

Totally Regio- and Stereoselective Synthesis of (E)-3-Arylidene-3,4- Dihydro-2H-1,4-benzoxazines Under Palladium Catalyst

A new, one-pot palladium catalyzed reaction has been developed for the general synthesis of (E)-3-arylidene- 3,4-dihydro-2H-1,4-benzoxazines at room temperature. The reaction procedure tolerates various functional groups. The method is characterized by regio- and stereoselectivity, operational simplicity, mild reaction conditions, and short reaction time