Fabrication and operation of a two-dimensional ion-trap lattice on a high-voltage microchip

Microfabricated ion traps are a major advancement towards scalable quantum computing with trapped ions. The development of more versatile ion-trap designs, in which tailored arrays of ions are positioned in two dimensions above a microfabricated surface, will lead to applications in fields as varied as quantum simulation, metrology and atom-ion interactions. Current surface ion traps often have low trap depths and high heating rates, because of the size of the voltages that can be applied to them, limiting the fidelity of quantum gates. Here we report on a fabrication process that allows for the application of very high voltages to microfabricated devices in general and use this advance to fabricate a two-dimensional ion-trap lattice on a microchip. Our microfabricated architecture allows for reliable trapping of two-dimensional ion lattices, long ion lifetimes, rudimentary shuttling between lattice sites and the ability to deterministically introduce defects into the ion lattice.

In vitro Antioxidant and Antibacterial Activities of Methanol Extract of Kyllinga nemoralis

The present study was designed to evaluate the antioxidant and antibacterial activity of methanol extract of Kyllinga nemoralis. Six different in vitro antioxidant assays including 2,2-diphenyl-1-picrylhydrazyl, hydroxyl radical, superoxide anion radical, hydrogen peroxide radical, ferric reducing antioxidant power assay and reducing power were carried out to ensure the scavenging effect of the plant on free radicals. In addition, total antioxidant capacity assay, total phenolic contents, tannins, flavonoids and flavonol contents of the plant were also analysed by the standard protocols. Kyllinga nemoralis exhibited high antioxidant activity on 2,2-diphenyl-1-picrylhydrazyl assay (IC50= 90 μg/ml), superoxide radical scavenging assay (IC50= 180 μg/ml) and hydrogen peroxide radical scavenging assay (IC50= 200 μg/ml), compared with standards. These observations provide comprehensible supporting evidence for the antioxidant potential of the plant extract. Reducing power (IC50= 213.16 μg/ml) and hydroxyl radical scavenging activity (IC50= 223 μg/ml) of the plant extract was remarkable. The methanol extract of K. nemoralis exhibited significant antimicrobial activity against Gram-positive human pathogenic bacteria. Standard in vitro antioxidant assays assessed the electron donating ability of the plant extract in scavenging free radicals. The inhibitory effect of the plant extract against bacterial pathogens may be due to the presence of phytochemicals. Thus, the results suggest that Kyllinga nemoralis is a potential source of antioxidants and could serve as the base for drug development.

Prevalence and etiology of subclinical mastitis among buffaloes (Bubalus bubalus) in Namakkal, India

Milk samples from 206 apparently healthy buffaloes of marginal farmers maintained under the prevailing field conditions were screened for Subclinical Mastitis (SCM) to determine its prevalence and etiology by White Side Test (WST), California Mastitis Test (CMT), Somatic Cell Count (SCC) and Bacteriological examination. 26.20% of animals were positive for SCM in SCC and bacteriological examination. Prevalence in graded Murrah buffaloes were found to be higher compared to graded Surti and Non-descript breeds. The prevalence of SCM was highest in above 6th stage of lactation. Single quarter infection (51.85%) was more common compared to multiple quarter infection. Hind (83.34%) and left side (57.41%) quarters were more prone to SCM. The indirect tests such as WST and CMT were found to be closely agreement with SCC and bacteriological examination. Due to their efficacious, easy to perform and interpret, these tests can effectively be employed to detect SCM under field conditions. Somatic cell count of = 3,00,000/mL of milk was regarded as the upper limit for normal buffaloes. The SCC of = 3,00,000/mL of milk with positive bacterial growth were used to diagnose SCM in the present study. Staphylococcus sp. 25 (46.30%) was the most common pathogens isolated from SCM followed by Streptococcus sp. 11 (20.37%) and E. coli 06 (11.11%) of the 54 bacterial isolates. Monobacterial and mixed bacterial infections were observed in 47 (87.04%) and 7 (12.96%) cases respectively.

Investigations on the physico chemical properties of 4-bromochalcone single crystals for nonlinear optical applications

Good quality yellow transparent single crystals of 4-bromochalcone (4BC) crystal have been synthesized and grown by slow evaporation solution growth method. The UV-Vis spectra was recorded for the grown crystal. The thermal behavior of the title crystal was studied. Fourier transform infrared and Raman spectral studies were performed for analyzing and assigning the vibrations and to identify the functional groups. The relative SHG efficiency of the material was investigated to explore the NLO characteristics for the first time in the literature. The SHG efficiency of the material is found to be 1.14 times greater than urea. Hyperpolarizability and HOMO-LUMO analysis of 4-bromochalcone (4BC) were performed with the help of Density Functional Theory (DFT) calculations using Gaussian 03 software.

Prediction models of donor arrest and graft utilization in liver transplantation from maastricht-3 donors after circulatory death

Shortage of organs for transplantation has led to the renewed interest in donation after circulatory-determination of death (DCDD). We conducted a retrospective analysis (2001-2009) and a subsequent prospective validation (2010) of liver Maastricht-Category-3-DCDD and donation-after-brain-death (DBD) offers to our program. Accepted and declined offers were compared. Accepted DCDD offers were divided into donors who went on to cardiac arrest and those who did not. Donors who arrested were divided into those producing grafts that were transplanted or remained unused. Descriptive comparisons and regression analyses were performed to assess predictor models of donor cardiac arrest and graft utilization. Variables from the multivariate analysis were prospectively validated. Of 1579 DCDD offers, 621 were accepted, and of these, 400 experienced cardiac arrest after withdrawal of support. Of these, 173 livers were transplanted. In the DCDD group, donor age < 40 years, use of inotropes and absence of gag/cough reflexes were predictors of cardiac arrest. Donor age >50 years, BMI >30, warm ischemia time >25 minutes, ITU stay >7 days and ALT ≥ 4× normal rates were risk factors for not using the graft. These variables had excellent sensitivity and specificity for the prediction of cardiac arrest (AUROC = 0.835) and graft use (AUROC = 0.748) in the 2010 prospective validation. These models can feasibly predict cardiac arrest in potential DCDDs and graft usability, helping to avoid unnecessary recoveries and healthcare expenditure.

Automatic adverse drug events detection using letters to the editor

We present and test the intuition that letters to the editor in journals carry early signals of adverse drug events (ADEs). Surprisingly these letters have not yet been exploited for automatic ADE detection unlike for example, clinical records and PubMed. Part of the challenge is that it is not easy to access the full-text of letters (for the most part these do not appear in PubMed). Also letters are likely underrated in comparison with full articles. Besides demonstrating that this intuition holds we contribute techniques for post market drug surveillance. Specifically, we test an automatic approach for ADE detection from letters using off-the-shelf machine learning tools. We also involve natural language processing for feature definitions. Overall we achieve high accuracy in our experiments and our method also works well on a second new test set. Our results encourage us to further pursue this line of research.

Computational Prediction of Phylogenetically Conserved Sequence Motifs for Five Different Candidate Genes in Type II Diabetic Nephropathy

BACKGROUND

Computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces. Furthermore, they are strongly conserved among orthologs, indicating their evolutionary importance. The study aimed to analyze five candidate genes involved in type II diabetic nephropathy and to predict phylogenetic motifs from their corresponding orthologous protein sequences.

METHODS

AKR1B1, APOE, ENPP1, ELMO1 and IGFBP1 are the genes that have been identified as an important target for type II diabetic nephropathy through experimental studies. Their corresponding protein sequences, structures, orthologous sequences were retrieved from UniprotKB, PDB, and PHOG database respectively. Multiple sequence alignments were constructed using ClustalW and phylogenetic motifs were identified using MINER. The occurrence of amino acids in the obtained phylogenetic motifs was generated using WebLogo and false positive expectations were calculated against phylogenetic similarity.

RESULTS

In total, 17 phylogenetic motifs were identified from the five proteins and the residues such as glycine, leucine, tryptophan, aspartic acid were found in appreciable frequency whereas arginine identified in all the predicted PMs. The result implies that these residues can be important to the functional and structural role of the proteins and calculated false positive expectations implies that they were generally conserved in traditional sense.

CONCLUSION

The prediction of phylogenetic motifs is an accurate method for detecting functionally important conserved residues. The conserved motifs can be used as a potential drug target for type II diabetic nephropathy.

Comparative potential therapeutic effect of sesame oil and peanut oil against acute monocrotaline (Crotalaria) poisoning in a rat model

BACKGROUND

Many Crotalaria plant species contain hepatotoxic pyrrolizidine alkaloids (such as monocrotaline) that can cause acute and chronic poisoning in cattle and other animals.

HYPOTHESIS

Peanut oil, atropine sulfate, and antidiarrheal agents are used to treat acute monocrotaline poisoning. The effect of sesame on acute monocrotaline poisoning has never been investigated.

ANIMALS

Fifty male Sprague-Dawley rats were used for toxicity studies.

METHODS

Experiment 1: Group I, control. Groups II-IV were given monocrotaline (205.2 mg/kg) and euthanized 6, 12, and 24 hours later. Experiment 2: Group I, control. Group II monocrotaline alone (205.2 mg/kg). Groups III-VI were given monocrotaline (205.2 mg/kg) and 1 hour later, Groups III and IV were given sesame oil (1 and 2 mL/kg) and Groups V and VI were given peanut oil (1 and 2 mL/kg).

RESULTS

Monocrotaline significantly decreased (P < .05) serum amylase activity, but, over time, increased (P < .05) pancreatic and lung injury. AST and ALT activity and liver injury peaked at 24 hours. Sesame oil and peanut oil (P < .05) inhibited the changes in all tested parameters in acute monocrotaline poisoning. Although peanut oil inhibited acute monocrotaline poisoning, it induced steatosis, but sesame oil did not.

CONCLUSION AND CLINICAL IMPORTANCE

We hypothesize that early pancreatic and lung injury and late liver injury contribute to acute monocrotaline poisoning and that sesame oil is more efficacious than peanut oil against acute monocrotaline poisoning in rats. However, additional studies are needed to confirm that these oils have the same effects in cattle and other animals.

Structural and functional analysis of KIT gene encoding receptor tyrosine kinase and its interaction with sunitinib and HDAC inhibitors: an in silico approach

KIT is a growth factor receptor, important for normal germ cell migration and development. The malfunction of KIT gene results in constitutive activation of the tyrosine kinase activity of c-KIT which is believed to be the major oncogenic event in stomach, small intestine mastocytosis, acute leukemias, melanomas and colon tumors. The genetics of these diseases could be better understood by knowing the functional relevance of their SNP variation. In this study, a computational analysis to detect the most deleterious nonsynonymous SNPs of KIT gene was performed and investigated its binding affinity to native and predicted mutant protein structure (D816V) with sunitinib and HDAC (Trichostatin A and Panobinostat) inhibitors was investigated. Out of 1,288 SNPs retrieved from dbSNP database against KIT gene, 11 non-synonymous SNPs were detected to be damaging and deleterious by SIFT, PolyPhen and I-Mutant2.0 servers. Further, we modeled the mutant protein based on the deleterious nsSNP (rs121913507) and showed that the mutation from Aspartic acid to Valine at 816 position exhibit greatest impact on stability. The RMSD values of mutant and native structures are found to be 0.40 and 1.9 A, respectively. Furthermore, the binding affinity of sunitinib and HDAC inhibitors were compared with native and mutant protein. In this regard, it was found that trichostatin A has a high binding efficacy towards the mutant protein with a binding energy of -35.274 kcal mol(-1), as compared to the native structure which has a binding energy of -25.996 kcal mol(-1). Also, the FastSNP tool suggested that 3 SNPs found to affect protein splicing site and splicing regulation. From present results, it was clear that the non-synonymous SNP rs121913507 (D816V) could be the most deleterious SNP for KIT gene and HDAC inhibitors can serve as a best drug for the mutant protein.

Preliminary radiological safety assessment for decommissioning of thoria dissolver of the ²³³U pilot plant, Trombay

The thoria dissolver, used for separation of (233)U from reactor-irradiated thorium metal and thorium oxide rods, is no longer operational. It was decided to carry out assessment of the radiological status of the dissolver cell for planning of the future decommissioning/dismantling operations. The dissolver interiors are expected to be contaminated with the dissolution remains of irradiated thorium oxide rods in addition to some of the partially dissolved thoria pellets. Hence, (220)Rn, a daughter product of (228)Th is of major radiological concern. Airborne activity of thoron daughters (212)Pb (Th-B) and (212)Bi (Th-C) was estimated by air sampling followed by high-resolution gamma spectrometry of filter papers. By measuring the full-energy peaks counts in the energy windows of (212)Pb, (212)Bi and (208)Tl, concentrations of thoron progeny in the sampled air were estimated by applying the respective intrinsic peak efficiency factors and suitable correction factors for the equilibration effects of (212)Pb and (212)Bi in the filter paper during the delay between sampling and counting. Then the thoron working level (TWL) was evaluated using the International Commission on Radiological Protection (ICRP) methodology. Finally, the potential effective dose to the workers, due to inhalation of thoron and its progeny during dismantling operations was assessed by using dose conversion factors recommended by ICRP. Analysis of filter papers showed a maximum airborne thoron progeny concentration of 30 TWLs inside the dissolver.

Establishment of air kerma reference standard for low dose rate Cs-137 brachytherapy sources

A guarded cylindrical graphite ionization chamber of nominal volume 1000 cm3 was designed and fabricated for use as a reference standard for low-dose rate 137Cs brachytherapy sources. The air kerma calibration coefficient (N(K)) of this ionization chamber was estimated analytically using Burlin's general cavity theory, as well as by the Monte Carlo simulation and validated experimentally using Amersham CDCS-J-type 137Cs reference source. In the analytical method, the N(K) was calculated for 662 keV gamma rays of 137Cs brachytherapy source. In the Monte Carlo method, the geometry of the measurement setup and physics-related input data of the 137Cs source and the surrounding material were simulated using the Monte Carlo N-Particle code. The photon energy fluence was used to arrive at the reference air kerma rate (RAKR) using mass energy absorption coefficient. The energy deposition rates were used to simulate the value of charge rate in the ionization chamber, and the N(K) was determined. The analytical and Monte Carlo values of N(K) of the cylindrical graphite ionization chamber for 137Cs brachytherapy source are in agreement within 1.07%. The deviation of analytical and Monte Carlo values from experimental values of N(K) is 0.36% and 0.72%, respectively. This agreement validates the analytical value, and establishes this chamber as a reference standard for RAKR or AKS measurement of 137Cs brachytherapy sources.

Sesamol attenuates oxidative stress–mediated experimental acute pancreatitis in rats

Acute pancreatitis is a potentially fatal disease with no known cure. The initial events in acute pancreatitis may occur within the acinar cells. We examined the effect of sesamol on (i) a cerulein-induced pancreatic acinar cancer cell line, AR42J, and (ii) cerulein-induced experimental acute pancreatitis in rats. Sesamol inhibited amylase activity and increased cell survival. It also inhibited medium lipid peroxidation and 8-hydroxydeoxyguanosine in AR42J cells compared with the cerulein-alone groups. In addition, in cerulein-treated rats, sesamol inhibited serum amylase and lipase levels, pancreatic edema, and lipid peroxidation, but it increased pancreatic glutathione and nitric oxide levels. Thus, we hypothesize that sesamol attenuates cerulein-induced experimental acute pancreatitis by inhibiting the pancreatic acinar cell death associated with oxidative stress in rats.

MeSH: a window into full text for document summarization

MOTIVATION

Previous research in the biomedical text-mining domain has historically been limited to titles, abstracts and metadata available in MEDLINE records. Recent research initiatives such as TREC Genomics and BioCreAtIvE strongly point to the merits of moving beyond abstracts and into the realm of full texts. Full texts are, however, more expensive to process not only in terms of resources needed but also in terms of accuracy. Since full texts contain embellishments that elaborate, contextualize, contrast, supplement, etc., there is greater risk for false positives. Motivated by this, we explore an approach that offers a compromise between the extremes of abstracts and full texts. Specifically, we create reduced versions of full text documents that contain only important portions. In the long-term, our goal is to explore the use of such summaries for functions such as document retrieval and information extraction. Here, we focus on designing summarization strategies. In particular, we explore the use of MeSH terms, manually assigned to documents by trained annotators, as clues to select important text segments from the full text documents.

RESULTS

Our experiments confirm the ability of our approach to pick the important text portions. Using the ROUGE measures for evaluation, we were able to achieve maximum ROUGE-1, ROUGE-2 and ROUGE-SU4 F-scores of 0.4150, 0.1435 and 0.1782, respectively, for our MeSH term-based method versus the maximum baseline scores of 0.3815, 0.1353 and 0.1428, respectively. Using a MeSH profile-based strategy, we were able to achieve maximum ROUGE F-scores of 0.4320, 0.1497 and 0.1887, respectively. Human evaluation of the baselines and our proposed strategies further corroborates the ability of our method to select important sentences from the full texts.

CONTACT

sanmitra-bhattacharya@uiowa.edu; padmini-srinivasan@uiowa.edu.

Vibrational spectra and first order hyperpolarizability studies of dimethyl amino pyridinium 4-nitrophenolate 4-nitrophenol

Vibrational spectra of the organic nonlinear optical crystallized dimethyl amino pyridinium 4-nitrophenolate 4-nitrophenol have been recorded and analyzed. The spectral interpretation has been done based on the density functional theory using the standard B3LYP/LANL2DZ basis set. Total energy distribution is calculated using the scaled quantum mechanic program. Natural bond orbital analysis is also used to explain the inter and intra molecular hydrogen bonding. The relative second harmonic efficiency of the compound is found to be 15 times greater than that of KDP. The effect of intermolecular hydrogen bonding between the phenolate ion of 4-nitrophenol with N-atom of pyridine ring is sufficiently more, enhancing the β value which is the required property of a system to be NLO active.

Cold plasma selectivity and the possibility of a paradigm shift in cancer therapy

Background:

Plasma is an ionised gas that is typically generated in high-temperature laboratory conditions. However, recent progress in atmospheric plasmas has led to the creation of cold plasmas with ion temperature close to room temperature.

Methods:

Both in-vitro and in-vivo studies revealed that cold plasmas selectively kill cancer cells.

Results:

We show that: (a) cold plasma application selectively eradicates cancer cells in vitro without damaging normal cells; and (b) significantly reduces tumour size in vivo. It is shown that reactive oxygen species metabolism and oxidative stress responsive genes are deregulated.

Conclusion:

The development of cold plasma tumour ablation has the potential of shifting the current paradigm of cancer treatment and enabling the transformation of cancer treatment technologies by utilisation of another state of matter.

BioCreative III interactive task: an overview

Background

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested.

Results

A User Advisory Group (UAG) actively participated in the IAT design and assessment. The task focused on gene normalization (identifying gene mentions in the article and linking these genes to standard database identifiers), gene ranking based on the overall importance of each gene mentioned in the article, and gene-oriented document retrieval (identifying full text papers relevant to a selected gene). Six systems participated and all processed and displayed the same set of articles. The articles were selected based on content known to be problematic for curation, such as ambiguity of gene names, coverage of multiple genes and species, or introduction of a new gene name. Members of the UAG curated three articles for training and assessment purposes, and each member was assigned a system to review. A questionnaire related to the interface usability and task performance (as measured by precision and recall) was answered after systems were used to curate articles. Although the limited number of articles analyzed and users involved in the IAT experiment precluded rigorous quantitative analysis of the results, a qualitative analysis provided valuable insight into some of the problems encountered by users when using the systems. The overall assessment indicates that the system usability features appealed to most users, but the system performance was suboptimal (mainly due to low accuracy in gene normalization). Some of the issues included failure of species identification and gene name ambiguity in the gene normalization task leading to an extensive list of gene identifiers to review, which, in some cases, did not contain the relevant genes. The document retrieval suffered from the same shortfalls. The UAG favored achieving high performance (measured by precision and recall), but strongly recommended the addition of features that facilitate the identification of correct gene and its identifier, such as contextual information to assist in disambiguation.

Discussion

The IAT was an informative exercise that advanced the dialog between curators and developers and increased the appreciation of challenges faced by each group. A major conclusion was that the intended users should be actively involved in every phase of software development, and this will be strongly encouraged in future tasks. The IAT Task provides the first steps toward the definition of metrics and functional requirements that are necessary for designing a formal evaluation of interactive curation systems in the BioCreative IV challenge.

The gene normalization task in BioCreative III

BACKGROUND

We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k).

RESULTS

We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively.

CONCLUSIONS

By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance.

A simplified analytical approach to estimate the parameters required for strength determination of HDR 192Ir brachytherapy sources using a Farmer-type ionization chamber

Measuring the strength of high dose rate (HDR) (192)Ir brachytherapy sources on receipt from the vendor is an important component of a quality assurance program. Owing to their ready availability in radiotherapy departments, the Farmer-type ionization chambers are also used to determine the strength of HDR (192)Ir brachytherapy sources. The use of a Farmer-type ionization chamber requires the estimation of the scatter correction factor along with positioning error (c) and the constant of proportionality (f) to determine the strength of HDR (192)Ir brachytherapy sources. A simplified approach based on a least squares method was developed for estimating the values of f and M(s). The seven distance method was followed to record the ionization chamber readings for parameterization of f and M(s). Analytically calculated values of M(s) were used to determine the room scatter correction factor (K(sc)). The Monte Carlo simulations were also carried out to calculate f and K(sc) to verify the magnitude of the parameters determined by the proposed analytical approach. The value of f determined using the simplified analytical approach was found to be in excellent agreement with the Monte Carlo simulated value (within 0.7%). Analytically derived values of K(sc) were also found to be in good agreement with the Monte Carlo calculated values (within 1.47%). Being far simpler than the presently available methods of evaluating f, the proposed analytical approach can be adopted for routine use by clinical medical physicists to estimate f by hand calculations.