bluuebunny/crossref_metadata_2025 huggingface dataset:
Disinfection of Multidrug Resistant Escherichia coli by Solar-Photocatalysis using Fe-doped ZnO Nanoparticles
Authors: Das Sourav , Sinha Sayantan , Das Bhaskar , Jayabalan R. , Suar Mrutyunjay , Mishra Amrita , Tamhankar Ashok J. , Stålsby Lundborg Cecilia , Tripathy Suraj K.
Published: March 2017

Spread of antibiotic resistant bacteria through water, is a threat to global public health. Here, we report Fe-doped ZnO nanoparticles (Fe/ZnO NPs) based solar-photocatalytic disinfection (PCD) of multidrug resistant Escherichia coli (MDR E. coli). Fe/ZnO NPs were synthesized by chemical precipitation technique, and when used as photocatalyst for disinfection, proved to be more effective (time for complete disinfection = 90 min) than ZnO (150 min) and TiO2 (180 min). Lipid peroxidation and potassium (K+) ion leakage studies indicated compromisation of bacterial cell membrane and electron microscopy and live-dead staining confirmed the detrimental effects on membrane integrity. Investigations indicated that H2O2 was the key species involved in solar-PCD of MDR E. coli by Fe/ZnO NPs. X-ray diffraction and atomic absorption spectroscopy studies showed that the Fe/ZnO NPs system remained stable during the photocatalytic process. The Fe/ZnO NPs based solar-PCD process proved successful in the disinfection of MDR E. coli in real water samples collected from river, pond and municipal tap. The Fe/ZnO NPs catalyst made from low cost materials and with high efficacy under solar light may have potential for real world applications, to help reduce the spread of resistant bacteria.
Image-based siRNA screen to identify kinases regulating Weibel-Palade body size control using electroporation
Authors: Ketteler Robin , Freeman Jamie , Stevenson Nicola , Ferraro Francesco , Bata Nicole , Cutler Dan F. , Kriston-Vizi Janos
Published: March 2017

High-content screening of kinase inhibitors is important in order to identify biogenesis and function mechanisms of subcellular organelles. Here, we present a human kinome siRNA high-content screen on primary human umbilical vein endothelial cells, that were transfected by electroporation. The data descriptor contains a confocal fluorescence, microscopic image dataset. We also describe an open source, automated image analysis workflow that can be reused to perform high-content analysis of other organelles. This dataset is suitable for analysis of morphological parameters that are linked to human umbilical vein endothelial cell (HUVEC) biology.
Genome-wide siRNA screen of genes regulating the LPS-induced TNF-α response in human macrophages
Authors: Sun Jing , Katz Samuel , Dutta Bhaskar , Wang Ze , Fraser Iain D.C.
Published: March 2017

The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the human macrophage TNF-α response to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. Tertiary screening with multiple TLR ligands and a microbial extract demonstrate that novel screen hits have broad effects on the innate inflammatory response to microbial stimuli. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory cytokine expression in human macrophages.
Genome-wide siRNA screen of genes regulating the LPS-induced NF-κB and TNF-α responses in mouse macrophages
Authors: Li Ning , Katz Samuel , Dutta Bhaskar , Benet Zachary L. , Sun Jing , Fraser Iain D.C.
Published: March 2017

The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the mouse macrophage TNF-α and NF-κB responses to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory signaling and cytokine expression in mouse macrophages.
Systems Biology Approaches in Pharmacology and Toxicology
Authors: Johnson Dale E.
Published: March 2017

The on-going integration of systems biology functionalities into all aspects of pharmacology and toxicology has resulted in a more network-based focus, which continues to enhance the understanding of therapeutic efficacious and adverse events both at the early and late stages of research and development. These advances have been coupled with the public availability of large datasets of information and new modeling approaches that have enhanced the ability to understand toxicological events and effects at multiple biological levels. Systems toxicology approaches are also being used in the safer design of chemicals and identification of safer alternatives, which are major parts of global green chemistry initiatives. In environmental toxicology, a major advance associated with these new efforts has been the establishment of the adverse outcome pathway concept and modeling approaches used for the identification of hazards and defining risk assessments for the large number of environmental chemicals, most with very few supporting data.
Tools for Green Molecular Design to Reduce Toxicological Risk
Authors: Faulkner David , Rubin Shen Leah K. , De La Rosa Vanessa Y. , Johnson Dale E. , Hemingway Rachel , Williams Richard V. , Judson Philip N. , Arnold John , Vulpe Chris D.
Published: March 2017

Making “greener” chemicals involves maximizing resource efficiency and eliminating or reducing hazards to human health and environmental systems. This chapter presents a review of various tools used in chemical design and predictive toxicology as a practical guide for chemists early in the molecular design process to deal with potential concerns on the front end of synthesis or development. A summary of concepts that can be applied in engineering chemicals that are less likely to be absorbed or biologically active is discussed along with the current milieu of software tools used for toxicity prediction. In this context, the challenges that remain in greener molecular design related to computational toxicology are highlighted. Based on these analyses, a proposed ideal green molecular design tool is outlined.
In silico Toxicology: An Overview of Toxicity Databases, Prediction Methodologies, and Expert Review
Authors: Bower D. , Cross K. P. , Escher S. , Myatt G. J. , Quigley D. P.
Published: March 2017

Understanding chemical toxicity is a necessary part of the R&D and regulatory approval process across many industries (e.g. pharmaceuticals, cosmetics, and pesticides). Toxicologists have an increasingly rich set of in vivo and in vitro methods to assess hazard and risk, which are being progressively supplemented with newer in silico approaches. The advantages and disadvantages of in silico methods are described alongside in vivo and in vitro tests. This chapter reviews a series of in silico methodologies for predicting toxicity and underpinning all in silico methodologies is the necessity to access high-quality and up-to-date toxicity study data from a variety of sources. Methods for organizing toxicity data in a harmonized manner (such as ToxML) are discussed to support combining toxicology data from different sources along with a number of commonly used toxicology databases. The three most commonly used methodologies for predicting toxicity—expert alerts, QSAR models and read-across—are reviewed. These complementary approaches provide different viewpoints concerning the structural and mechanistic basis for any prediction, alongside an analysis and rationale for supporting analog data. How this information can be then assimilated within an expert review to generate a final conclusion is discussed.
A lysosome targetable fluorescent probe for endogenous imaging of hydrogen peroxide in living cells
Authors: Reja Shahi Imam , Gupta Muskan , Gupta Neha , Bhalla Vandana , Ohri Puja , Kaur Gurcharan , Kumar Manoj
Published: March 2017

A lysosome targetable naphthalimide based fluorescent probe has been designed and synthesized for selective imaging of H2O2 in different cells, tissues and in vivo models.
I2-Promoted formal [3+2] cycloaddition of α-methylenyl isocyanides with methyl ketones: a route to 2,5-disubstituted oxazoles
Authors: Wu Xia , Geng Xiao , Zhao Peng , Zhang Jingjing , Wu Yan-dong , Wu An-xin
Published: March 2017

An I2-promoted formal [3+2] cycloaddition for access to oxazoles has been demonstrated. The salient feature of this approach is unconventional 2,5-disubstituted oxazole formation from isocyanides and ketones rather than 4,5-substituted oxazoline.
Vibronic spectra of protonated hydroxypyridines: contributions of prefulvenic and planar structures
Authors: Garcia R. Lozada , Nieuwjaer N. , Desfrançois C. , Lecomte F. , Leite S. D. , Manil B. , Broquier M. , Grégoire G.
Published: March 2017

The UV photofragmentation spectra of cold protonated hydroxypyridines display well resolved vibrational structures, interpreted with calculations at the CC2 level.
Strategies for stable water splitting via protected photoelectrodes
Authors: Bae Dowon , Seger Brian , Vesborg Peter C. K. , Hansen Ole , Chorkendorff Ib
Published: March 2017

This review provides a comprehensive overview of the key aspects of protection strategies for achieving stable solid/liquid interfaces for photoelectrodes.
Biosynthesis of CdSe nanoparticles by anaerobic granular sludge
Authors: Mal Joyabrata , Nancharaiah Yarlagadda V. , Bera Santanu , Maheshwari Neeraj , van Hullebusch Eric D. , Lens Piet N. L.
Published: March 2017

Simultaneous removal of selenite and cadmium by combining bioremediation of environmentally toxic selenium-rich wastewater with biorecovery of Se as CdSe nanoparticles.
Facile fabrication of CuO/Cu2O composites with high catalytic performances
Authors: Choi Dayeon , Jang Du-Jeon
Published: March 2017

CuO/Cu2O composites having good catalytic properties for the reduction of 4-nitrophenol have been prepared facilely for wastewater treatment.
Rhenium dichalcogenides (ReX2, X = S or Se): an emerging class of TMDs family
Authors: Hafeez Muhammad , Gan Lin , Saleem Bhatti Arshad , Zhai Tianyou
Published: March 2017

ReX2can have wide applications in (opto-)electronics due to an unusual distorted octahedral (1T) crystal structure in which each monolayer contains diamond-shaped chains.
Asperspiropene A, a novel fungal metabolite as an inhibitor of cancer-associated mutant isocitrate dehydrogenase 1
Authors: He Yan , Zheng Mengzhu , Li Qin , Hu Zhengxi , Zhu Hucheng , Liu Junjun , Wang Jianping , Xue Yongbo , Li Hua , Zhang Yonghui
Published: March 2017

In silico screening of an in-house natural product database and confirmatory bioassays led to the identification of asperspiropene A (1) as an inhibitor of cancer-associated mutant IDH1.
Pseudorotaxane capped mesoporous silica nanoparticles for 3,4-methylenedioxymethamphetamine (MDMA) detection in water
Authors: Lozano-Torres Beatriz , Pascual Lluís , Bernardos Andrea , Marcos María D. , Jeppesen Jan O. , Salinas Yolanda , Martínez-Máñez Ramón , Sancenón Félix
Published: March 2017

MDMA, a principal ecstasy component, is detected by using pseudorotaxane-capped mesoporous silica nanoparticles.
Nucleation-dependant chemical bonding paradigm: the effect of rare earth ions on the nucleation of urea in aqueous solution
Authors: Chen Xiaoyan , Sun Congting , Wu Sixin , Xue Dongfeng
Published: March 2017

The nucleation-dependant chemical bonding paradigm of urea in the presence of rare earth ions in aqueous solution has been identified.
The effect of Sr(OH)2 on the hydrogen storage properties of the Mg(NH2)2–2LiH system
Authors: Cao Hujun , Wang Han , Pistidda Claudio , Milanese Chiara , Zhang Weijin , Chaudhary Anna-Lisa , Santoru Antonio , Garroni Sebastiano , Bednarcik Jozef , Liermann Hanns-Peter , Chen Ping , Klassen Thomas , Dornheim Martin
Published: March 2017

Sr(OH)2 influences both the thermodynamics and kinetics of the Mg(NH2)2–2LiH system, lowering the dehydrogenation onset and peak temperatures by ca. 70 °C and 13 °C.
Structural characterization and photoluminescence in the rare earth-free oxy-fluoride anti-perovskites Sr3−xBi2x/3AlO4F and Sr3−xBi2x/3GaO4F
Authors: Quilty Calvin D. , Avdeev Maxim , Driskell Jeremy D. , Sullivan Eirin
Published: March 2017

The oxy-fluoride anti-perovskites Sr3−xBi2x/3AlO4F and Sr3−xBi2x/3GaO4F form rare earth-free phosphors where Bi3+ions preferentially occupy the ten coordinate Sr(1) site.
1,8-Bis(silylamido)naphthalene complexes of magnesium and zinc synthesised through alkane elimination reactions
Authors: Bradley Mark A. , Birchall Chris , Blake Alexander J. , Lewis William , Moxey Graeme J. , Kays Deborah L.
Published: March 2017

Alkane elimination reactions afford magnesium and zinc 1,8-bis(triorganosilyl)diamidonaphthalene complexes, where the tuning of the reaction conditions and steric bulk allows manipulation of the coordination environment.
Thermo-acoustofluidic separation of vesicles based on cholesterol content
Authors: Dolatmoradi Ata , Mirtaheri Elnaz , El-Zahab Bilal
Published: March 2017

Vesicles with various membrane stiffness values depending on their cholesterol content were separated using a thermo-acoustofluidic technique.
Evaluation of subcutaneous infiltration of autologous platelet-rich plasma on skin-wound healing in dogs
Authors: Farghali Haithem A. , AbdElKader Naglaa A. , Khattab Marwa S. , AbuBakr Huda O.
Published: March 2017

Platelet-rich plasma (PRP) is known to be rich in growth factors and cytokines, which are crucial to the healing process. This study investigate the effect of subcutaneous (S/C) infiltration of autologous PRP at the wound boundaries on wound epithelization and contraction. Five adult male mongrel dogs were used. Bilateral acute full thickness skin wounds (3 cm diameter) were created on the thorax symmetrically. Right side wounds were subcutaneously infiltrated with activated PRP at day 0 and then every week for three consecutive weeks. The left wound was left as control. Wound contraction and epithelization were clinically evaluated. Expression of collagen type I (COLI) A2, (COLIA2),histopathology and immunohistochemical (IHC) staining of COLI α1 (COLIA1) were performed on skin biopsies at first, second and third weeks. The catalase activity, malondialdehyde (MDA) concentration and matrix metalloproteinase (MMP) 9 (MMP-9) activity were assessed in wound fluid samples. All data were analysed statistically. The epithelization percent significantly increased in the PRP-treated wound at week 3. Collagen was well organized in the PRP-treated wounds compared with control wounds at week 3. The COLIA2 expression and intensity of COLIA1 significantly increased in PRP-treated wounds. MDA concentration was significantly decreased in PRP-treated wound at week 3. The catalase activity exhibited no difference between PRP treated and untreated wounds. The activity of MMP-9 reached its peak at the second week and was significantly high in the PRP-treated group. S/C infiltration of autologous PRP at the wound margins enhances the wound epithelization and reduces the scar tissue formation.
Association of A1538G and C2437T single nucleotide polymorphisms in heat shock protein-70 genes with diabetic nephropathy among South Indian population
Authors: Dhamodharan Umapathy , Ezhilarasi Krishnamoorthy , Ponjayanthi Balashanmugam , Sireesh Dornadula , Ramkumar Kunka Mohanram , Viswanathan Vijay
Published: March 2017

Diabetic Nephropathy (DN) is the leading cause of end-stage renal disease, characterized by progressive albuminuria and conferring additional risk of cardiovascular disease (CVD) and mortality. The crucial role of heat-shock proteins (HSPs) on renal function in patients with DN has been well documented. The present study was aimed to understand the association of HSP-70 gene variants on the susceptibility of Type 2 Diabetes Mellitus (T2DM) and DN. A total of 946 subjects (549 Males; 397 Females) were recruited and divided into four groups according to the levels of urinary albumin excretion (UAE): those with normoalbuminuria (UAE <30 mg/24 h; n=230), those with microalbuminuria (30≤ UAE ≤300 mg/24 h; n=230), and those with macroalbuminuria (UAE> 300 mg/24 h; n=230). The control group randomly enrolled a consecutive population of 256 healthy subjects who had a routine medical check-up in our hospital. Those subjects had no history or clinical symptoms of diabetes. Subjects were genotyped for HSP70-2 (+1538 A/G; rs2763979) and HSP70-hom (+2437 C/T; rs2227956) by PCR-restriction fragment length polymorphism (RFLP). The ‘G’ allele of HSP70-2 (+1538 A/G) single nucleotide polymorphism (SNP) showed relative risk for normoalbuminuria, microalbuminuria and macroalbuminuria subjects whereas the ‘T’ allele of HSP70-hom (+2437 C/T) SNP showed significant protection against macroalbuminuria subjects. In conclusion, our results indicate that the HSP70-2 (+1538 A/G) and HSP70-hom (+2437 C/T) SNPs are highly associated with renal complications in T2DM among the South Indian population.
The Impact of Clinical History on the Threshold Estimation of Auditory Brainstem Response Results for Infants
Authors: Zaitoun Maha , Cumming Steven , Purcell Alison , O'Brien Katie
Published: March 2017

Purpose

This study assesses the impact of patient clinical history on audiologists' performance when interpreting auditory brainstem response (ABR) results.

Method

Fourteen audiologists' accuracy in estimating hearing threshold for 16 infants through interpretation of ABR traces was compared on 2 occasions at least 5 months apart. On the 1st occasion, ABR traces were presented to the audiologists with no clinical information except for the age of the child. On the 2nd occasion, audiologists were given a full clinical history for the ABR cases.

Results

The addition of clinical history information had no statistically significant impact on sensitivity, specificity, or accuracy of diagnosis. Although the mean numbers of true-negative and true-positive diagnoses were higher when audiologists were given clinical information, the difference was again not statistically significant.

Conclusion

This study suggests that if there are circumstances in which case material is incomplete or unavailable, audiologists have no cause for concern regarding the accuracy of their interpretation of ABR traces. In a clinical manner, this may help audiologists with large caseloads or audiologists who need to provide a diagnosis of hearing loss in a short time by allowing them to focus on conducting ABR without the need for case history information.
Exploring Use of the Coordinate Response Measure in a Multitalker Babble Paradigm
Authors: Humes Larry E. , Kidd Gary R. , Fogerty Daniel
Published: March 2017

Purpose

Three experiments examined the use of competing coordinate response measure (CRM) sentences as a multitalker babble.

Method

In Experiment I, young adults with normal hearing listened to a CRM target sentence in the presence of 2, 4, or 6 competing CRM sentences with synchronous or asynchronous onsets. In Experiment II, the condition with 6 competing sentences was explored further. Three stimulus conditions (6 talkers saying same sentence, 1 talker producing 6 different sentences, and 6 talkers each saying a different sentence) were evaluated with different methods of presentation. Experiment III examined the performance of older adults with hearing impairment in a subset of conditions from Experiment II.

Results

In Experiment I, performance declined with increasing numbers of talkers and improved with asynchronous sentence onsets. Experiment II identified conditions under which an increase in the number of talkers led to better performance. In Experiment III, the relative effects of the number of talkers, messages, and onset asynchrony were the same for young and older listeners.

Conclusions

Multitalker babble composed of CRM sentences has masking properties similar to other types of multitalker babble. However, when the number of different talkers and messages are varied independently, performance is best with more talkers and fewer messages.
Secrecy performance of threshold‐based decode‐and‐forward cooperative cognitive radio network
Authors: Chopra Khyati , Bose Ranjan , Joshi Anupam
Published: March 2017

This study evaluates the intercept and outage probability of a decode‐and‐forward (DF) underlay cognitive radio network. The secondary users are subject to interference limitations from the primary network, with an eavesdropper tapping the second hop of cognitive network, when all the links undergo Rayleigh fading. For this threshold‐based system, without assuming that the DF relays can always decode the message correctly, here the authors consider that only a set of relays whose SNR satisfies a predetermined threshold can decode the message successfully. The authors have obtained asymptotic analysis for both cases, when average SNRs of secondary source‐relay and relay‐destination links are balanced or unbalanced. The authors have shown that the desired secrecy rate, predetermined threshold, eavesdropper channel quality and interference power limitations significantly affects the secrecy performance of the cognitive radio system. They have investigated the outage and intercept probability of relay selection scheme, when either full instantaneous channel state information or statistical channel state information of all the links is available. They have shown that the optimal relay selection improves the performance of the multi‐relay cognitive system, when the number of relays is increased.
Social‐spider optimised particle filtering for tracking of targets with discontinuous measurement data
Authors: Ahmadi Kaveh , Salari Ezzatollah
Published: March 2017

The particle filter (PF), a non‐parametric implementation of the Bayes filter, is commonly used to estimate the state of a dynamic non‐linear non‐Gaussian system. The key idea is to construct a posterior probability satisfying a set of hypotheses representing a potential state of the system. Despite PF's successful applications, it suffers from sample impoverishment in real‐world applications. Most of the recent PF‐based techniques attempt to improve the functionality of the PF through evolutionary algorithms in the cases of unexpected changes in the system states. However, they have not addressed the discontinuity of observations which is unpreventable in the real world. This study incorporates a recently developed social‐spider optimisation technique into PF to overcome the drawback of previous methods in these cases. To avoid premature degeneracy, evolutionary search extends the particle search space when observation is unavailable. The social‐spider inspired proposal distribution and the corresponding particle weights are derived to approximate real model states. The experimental results show that the proposed method has superior performance in relation to other evolutionary PF in cases of large changes or discontinuous observations.
Optimal transmission access for generators in wind‐integrated power systems: stochastic and robust programming approaches
Authors: Uzuncan Ezgi , Hesamzadeh Mohammad Reza , Balkwill Andy
Published: March 2017

Integrating wind generation in power systems has raised the issue of optimal transmission access for generators. The available transmission capacity for a generator is now subject to the uncertain wind generation. Therefore, the need for a transmission access mechanism has emerged. This study proposes three different optimisation models for calculating transmission access under uncertain wind generation. First, it develops a mathematical model to find the expected transmission access. A chance‐constrained optimisation model is derived to find different levels of access to the transmission network with pre‐specified reliability levels. The chance‐constrained model provides detailed information regarding the available transmission access at different reliability levels. This gives options to a connecting generator regarding its choice of transmission access. Finally, a robust model for transmission access is proposed. The robust model provides the conservative transmission access which is assured against all future realisations of wind generation. The proposed expected, chance‐constrained and robust approaches for optimal transmission access are numerically studied using an illustrative 2‐bus example and the IEEE 30‐bus and IEEE 300‐bus case studies. The moment‐matching technique is used to generate wind and demand scenarios. The numerical results show the utility of three derived models to calculate the optimal transmission access for generators.
Slip Hankel matrix series‐based singular value decomposition and its application for fault feature extraction
Authors: Xu Jian , Tong Shuiguang , Cong Feiyun , Chen Jin
Published: March 2017

The failure of rolling bearings is one of the most important factors for rotating machinery breakdown. The detection of initial fault in rolling bearings is crucial for the further prevention of equipment malfunction and failure. In this study, a new rolling bearing fault diagnosis method based on the singular value decomposition, slip Hankel matrix series construction and maximum singular value energy analysis is proposed. It has been validated that the proposed method has an excellent impulse recognition capacity, which can be further applied to design the optimal band‐pass filter for rolling bearing fault diagnosis. Then, the minimum entropy deconvolution (MED) technique is introduced to improve the fault extraction ability of the proposed method. Simulated signals and artificial fault tests are used to prove the capacity of the new method for rolling bearing fault detection. Furthermore, the result of accelerated life test indicates the initial bearing fault can be recognised by the proposed method, while the envelope spectrum cannot directly distinguish the failure type because of the redundant frequency interference. It can be concluded that the proposed method has the effectiveness of initial fault identification and redundant frequency elimination for rolling bearing fault diagnosis.
OP-Management: Gesundheitsökonomische Effizienz
Authors: Mewis Dirk
Published: March 2017

Sowohl Chirurgen als auch Patienten profitieren von der Digitalisierung des OP. Es werden mehr schonende Eingriffe möglich, die Risiken sinken und die Effizienz steigt. Das ist auch nötig, denn die Zahl der Operationen nimmt zu.
37. Tagung „Technik im Krankenhaus“ – TK 2017: Medizintechnik als ein Schwerpunktthema
Authors: Fouckhardt-Bradt Birgit
Published: March 2017

Die Medizintechnik hat es sich zur Aufgabe gemacht, Verfahren und Geräte zur Diagnostik und Therapie und deren kontinuierliche Überwachung zum Nutzen des Patienten zu entwickeln und weiter zu optimieren. Sie rettet Leben, hilft heilen und verbessert die Lebensqualität. Ihr Innovationspotenzial ist durch die fortschreitende Digitalisierung erheblich – sie steht sogar am Anfang einer Revolution.
Immunohistochemical Expression of the Tumor Suppressor Protein p16INK4a in Cervical Adenocarcinoma
Authors: Lima Thiago Silva , Cunha Maria do Perpétuo Socorro , Cavalcante Diane Isabelle Magno , Silva Angélica Maria Holanda , Eleutério Jr José
Published: March 2017

Objective To evaluate the diagnostic utility of the p16ink4a protein expression as a marker for adenocarcinoma of the cervix.

Methods In a cross-sectional study, p16ink4a expression was evaluated in 30 cervical biopsies from patients diagnosed with invasive adenocarcinoma from 2 reference clinics in Brazil, and compared with 18 biopsies of endocervical polyps (control cases). The performance of the tests for p16ink4a was evaluated using a conventional contingency table, and the Kappa (κ) index was used to evaluate the agreement of the marker with the tissue diagnosis.

Results In total, 66% of the invasive adenocarcinoma cases were positive for p16ink4a. All of the adenomatous polyps cases used as negative controls were shown to be negative for p16ink4a. The marker showed a high sensitivity and a high negative predictive value. The Kappa index was good for p16ink4a (κ = 0.6).

Conclusion Considering the strong association between the p16ink4a marker and the cervical adenocarcinoma, its use represents an important tool for reducing incorrect diagnoses of adenocarcinoma and thereby avoiding overtreatment.
Prevalence of Hypertrophic Cardiomyopathy in Fetuses of Mothers with Gestational Diabetes before Initiating Treatment
Authors: Simões Mona Adalgisa , Silva Jean Carl , Santos Anelise Darabas dos , Silva Mariana Ribeiro e , Ferreira Bruna , Palmieri Carolina Rossi
Published: March 2017

Objective To evaluate the prevalence of hypertrophic cardiomyopathy (HCM) in fetuses of pregnant women with gestational diabetes mellitus (GDM) in the beginning of the treatment.

Methods A cross-sectional study was performed between July 1, 2013, and December 20, 2013, in a public maternity clinic in southern Brazil. The subjects were 63 fetuses of mothers with gestational diabetes, with a single pregnancy and no other associated pathologies. We diagnosed HCM through a fetal echocardiography before treatment and evaluated the maternal and fetal characteristics.

Results The average age of the pregnant women was 32.32 (±6.2) years, and the average gestational age at the time of the evaluation was 30.59 (±2.27) weeks. The interventricular septum thickness showed a standard deviation of more than two in 50.8% of the fetuses (95% confidence interval [95%CI]: 38.1–63.5%). The left ventricular wall thickness showed a standard deviation of more than 2 in 13 (20.6%) fetuses (95%CI: 11.1–30.2%). The HCM was confirmed in 54% of the fetuses (95%CI: 41.3–65.1%). The fetal abdominal circumference was normal in 46 (73%) fetuses, and 50% of these fetuses had HCM.

Conclusion The prevalence of hypertrophic cardiomyopathy in fetuses of pregnant women with GDM before treatment was of 54% (95%CI: 41.3–65.1%).
Recombinant Human Acidic Fibroblast Growth Factor (aFGF) Expressed in Nicotiana benthamiana Potentially Inhibits Skin Photoaging
Authors: Ha Jang-Ho , Kim Ha-Neul , Moon Ki-Beom , Jeon Jae-Heung , Jung Dai-Hyun , Kim Su-Jung , Mason Hugh , Shin Seo-Yeon , Kim Hyun-Soon , Park Kyung-Mok
Published: March 2017

Responding to the need for recombinant acidic fibroblast growth factor in the pharmaceutical and cosmetic industries, we established a scalable expression system for recombinant human aFGF using transient and a DNA replicon vector expression in Nicotiana benthamiana. Recombinant human-acidic fibroblast growth factor was recovered following Agrobacterium infiltration of N. benthamiana. The optimal time point at which to harvest recombinant human acidic fibroblast growth factor expressing leaves was found to be 4 days post-infiltration, before necrosis was evident. Commassie-stained SDS-PAGE gels of His-tag column eluates, concentrated using a 10 000 molecular weight cut-off column, showed an intense band at the expected molecular weight for recombinant human acidic fibroblast growth factor. An immunoblot confirmed that this band was recombinant human acidic fibroblast growth factor. Up to 10 µg recombinant human-acidic fibroblast growth factor/g of fresh leaves were achieved by a simple affinity purification protocol using protein extract from the leaves of agroinfiltrated N. benthamiana. The purified recombinant human acidic fibroblast growth factor improved the survival rate of UVB-irradiated HaCaT and CCD-986sk cells approximately 89 and 81 %, respectively. N. benthamiana-derived recombinant human acidic fibroblast growth factor showed similar effects on skin cell proliferation and UVB protection compared to those of Escherichia coli-derived recombinant human acidic fibroblast growth factor. Additionally, N. benthamiana-derived recombinant human acidic fibroblast growth factor increased type 1 procollagen synthesis up to 30 % as well as reduced UVB-induced intracellular reactive oxygen species generation in fibroblast (CCD-986sk) cells.

UVB is a well-known factor that causes various types of skin damage and premature aging. Therefore, the present study demonstrated that N. benthamiana-derived recombinant human acidic fibroblast growth factor effectively protects skin cell from UVB, suggesting its potential use as a cosmetic or therapeutic agent against skin photoaging.
Our changing view of Mars
Authors: Vasavada Ashwin R.
Published: March 2017

The orbiters, landers, and rovers that have probed the red planet over the past two decades reveal it to be chemically complex, historically watery, and suitable as a home for life.
Singlet Photoreactivity of 3-Methyl-2-phenyl-2H-azirine
Authors: Weragoda Geethika K. , Das Anushree , Sarkar Sujan K. , Sriyarathne H. Dushanee M. , Zhang Xiaoming , Ault Bruce S. , Gudmundsdottir Anna D.
Published: March 2017

Irradiation of 3-methyl-2-phenyl-2H-azirine (1) at 254 nm in argon matrices results in ylide 6. Similarly, laser flash photolysis (λ = 266 nm) of azirine 1 in acetonitrile yields ylide 6, which has a transient absorption with λmax at ~340 nm and a lifetime of 14 μs. Density functional theory calculations were preformed to support the characterisation of ylide 6 in solution and argon matrices. Irradiation of azirine 1 above 300 nm has previously been reported (J. Org. Chem. 2014, 79, 653) to yield triplet vinylnitrene in solution and ketenimine in cryogenic argon matrices. Thus, the photochemistry of azirine 1 is dependent on the irradiation wavelength.
High diversity of powdery mildew resistance in the ICARDA wild barley collection
Authors: Dreiseitl Antonín
Published: March 2017

Powdery mildew caused by the fungus Blumeria graminis f. sp. hordei (Bgh) is a global disease of barley, and the wild subspecies Hordeum vulgare subsp. spontaneum (Hvs) is the closest relative of cultivated barley (H. vulgare subsp. vulgare). The responses to the pathogen of 363 Hvs accessions maintained by the International Center for Agricultural Research in the Dry Areas (ICARDA) gene bank were assessed. Thirty non-Israeli pathogen isolates representing the global pathogenic diversity were used for testing. Because of genetic heterogeneity within 146 accessions, the results from only 217 accessions are presented and discussed. Additional tests on 152 accessions with homogeneous responses in earlier tests were made by using six Israeli pathogen isolates. There were 154 resistance phenotypes among the set, 141 of which involved single accessions. The six most frequent phenotypes were recorded for 62 accessions, with the most frequent phenotype in 26 accessions that were resistant to all 30 non-Israeli Bgh isolates. The second most frequent phenotype, found in 16 accessions, was susceptible to all 30 non-Israeli isolates. The occurrence of specific resistance was high. The occurrence of specific resistance was high and for breeding barley cultivars the effective resistances can be combined with the resistance gene mlo. In such combinations, the mlo gene prevents rapid increase in the pathogen population from overcoming the given specific resistance, whereas the resistance gene will simultaneously prevent erosion of mlo resistance. A more effective method for achieving durable resistance is accumulation minor resistance genes that are also widely distributed in wild barley.
Evidence of male-biased dispersal in eastern grey kangaroos (Macropus giganteus)
Authors: Coghlan Brett A. , Seddon Jennifer M. , Best Emily C. , Thomson Vicki A. , Goldizen Anne W.
Published: March 2017

Dispersal reduces the likelihood of inbreeding and maintains gene flow among populations. Many polygynous mammals exhibit male-biased dispersal with female philopatry. Previous observational studies of eastern grey kangaroos (Macropus giganteus) suggested female philopatry while genetic studies showed weak structuring. We tested for sex-biased dispersal using two Queensland populations of kangaroos: one in Sundown National Park and the second at Elanda Point, Australia. Samples from 25 females and 23 males were collected from Sundown National Park, and analysed for partial mtDNA control region sequences (n = 47) and genotypes based on 12 microsatellite loci (n = 41). Samples from 18 males and 22 females from Elanda Point were genotyped at 8 loci and a subset sequenced for mtDNA (n = 19). Analyses showed higher mtDNA haplotype and nucleotide diversity in males than females within both populations, genetic relatedness based on microsatellite data was significantly higher among females, and microsatellite allelic richness was higher in males, suggesting that females are more likely to be philopatric and males more likely to disperse. These findings reinforce the value of including multiple types of genetic markers in dispersal analyses as mtDNA results showed higher male diversity (suggesting male dispersal) but males also contributed microsatellite alleles to the local population, masking differentiation between the sexes and confounding analyses.
Metabolic origins of spatial organization in the tumor microenvironment
Authors: Carmona-Fontaine Carlos , Deforet Maxime , Akkari Leila , Thompson Craig B. , Joyce Johanna A. , Xavier Joao B.
Published: March 2017

Significance

Cancers appear as disordered mixtures of different cells, which is partly why they are hard to treat. We show here that despite this chaos, tumors show local organization that emerges from cellular processes common to most cancers: the altered metabolism of cancer cells and the interactions with stromal cells in the tumor microenvironment. With a multidisciplinary approach combining experiments and computer simulations we revealed that the metabolic activity of cancer cells produces gradients of nutrients and metabolic waste products that act as signals that cells use to know their position with respect to blood vessels. This positional information orchestrates a modular organization of tumor and stromal cells that resembles embryonic organization, which we could exploit as a therapeutic target.
Differential roles of α-, β-, and γ-actin in axon growth and collateral branch formation in motoneurons
Authors: Moradi Mehri , Sivadasan Rajeeve , Saal Lena , Lüningschrör Patrick , Dombert Benjamin , Rathod Reena Jagdish , Dieterich Daniela C. , Blum Robert , Sendtner Michael
Published: March 2017

Axonal branching and terminal arborization are fundamental events during the establishment of synaptic connectivity. They are triggered by assembly of actin filaments along axon shafts giving rise to filopodia. The specific contribution of the three actin isoforms, Actα, Actβ, and Actγ, to filopodia stability and dynamics during this process is not well understood. Here, we report that Actα, Actβ, and Actγ isoforms are expressed in primary mouse motoneurons and their transcripts are translocated into axons. shRNA-mediated depletion of Actα reduces axonal filopodia dynamics and disturbs collateral branch formation. Knockdown of Actβ reduces dynamic movements of growth cone filopodia and impairs presynaptic differentiation. Ablation of Actβ or Actγ leads to compensatory up-regulation of the two other isoforms, which allows maintenance of total actin levels and preserves F-actin polymerization. Collectively, our data provide evidence for specific roles of different actin isoforms in spatial regulation of actin dynamics and stability in axons of developing motoneurons.
KDM3A coordinates actin dynamics with intraflagellar transport to regulate cilia stability
Authors: Yeyati Patricia L. , Schiller Rachel , Mali Girish , Kasioulis Ioannis , Kawamura Akane , Adams Ian R. , Playfoot Christopher , Gilbert Nick , van Heyningen Veronica , Wills Jimi , von Kriegsheim Alex , Finch Andrew , Sakai Juro , Schofield Christopher J. , Jackson Ian J. , Mill Pleasantine
Published: March 2017

Cilia assembly and disassembly are coupled to actin dynamics, ensuring a coherent cellular response during environmental change. How these processes are integrated remains undefined. The histone lysine demethylase KDM3A plays important roles in organismal homeostasis. Loss-of-function mouse models of Kdm3a phenocopy features associated with human ciliopathies, whereas human somatic mutations correlate with poor cancer prognosis. We demonstrate that absence of KDM3A facilitates ciliogenesis, but these resulting cilia have an abnormally wide range of axonemal lengths, delaying disassembly and accumulating intraflagellar transport (IFT) proteins. KDM3A plays a dual role by regulating actin gene expression and binding to the actin cytoskeleton, creating a responsive “actin gate” that involves ARP2/3 activity and IFT. Promoting actin filament formation rescues KDM3A mutant ciliary defects. Conversely, the simultaneous depolymerization of actin networks and IFT overexpression mimics the abnormal ciliary traits of KDM3A mutants. KDM3A is thus a negative regulator of ciliogenesis required for the controlled recruitment of IFT proteins into cilia through the modulation of actin dynamics.
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy
Authors: Megjhani Murad , Correa de Sampaio Pedro , Leigh Carstens Julienne , Kalluri Raghu , Roysam Badrinath
Published: March 2017

Motivation

Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context.

Results

The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm. The method was evaluated on multi-spectral images of multiplex-labeled pancreatic ductal adenocarcinoma (PDAC) tissue samples. The former constraint ensures that neighbouring pixels correspond to morphologically similar structures, and the latter constraint ensures that neighbouring pixels have similar spectral signatures. The average Mean Squared Error (MSE) and Signal Reconstruction Error (SRE) ratio of the proposed method was 39.6% less and 8% more, respectively, compared to the best of all other algorithms that do not exploit these spatial constraints.

Availability and Implementation

Open source software (MATLAB).

Supplementary information

Supplementary data are available at Bioinformatics online.
ctsGE—clustering subgroups of expression data
Authors: Sharabi-Schwager Michal , Or Etti , Ophir Ron
Published: March 2017

A pre-requisite to clustering noisy data, such as gene-expression data, is the filtering step. As an alternative to this step, the ctsGE R-package applies a sorting step in which all of the data are divided into small groups. The groups are divided according to how the time points are related to the time-series median. Then clustering is performed separately on each group. Thus, the clustering is done in two steps. First, an expression index (i.e. a sequence of 1, −1 and 0) is defined and genes with the same index are grouped together, and then each group of genes is clustered by k-means to create subgroups. The ctsGE package also provides an interactive tool to visualize and explore the gene-expression patterns and their subclusters. ctsGE proposes a way of organizing and exploring expression data without eliminating valuable information.

Availability and Implementation

Freely available as part of the Bioconductor project at https://bioconductor.org/packages/ctsGE/.

Supplementary information

Supplementary data are available at Bioinformatics online.
PeptideMapper: efficient and versatile amino acid sequence and tag mapping
Authors: Kopczynski Dominik , Barsnes Harald , Njølstad Pål R , Sickmann Albert , Vaudel Marc , Ahrends Robert
Published: March 2017

The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i.e. up to 1000× faster than state-of-the-art software) in terms of memory footprint and execution speed, with regards to both the indexing and the querying of protein sequence databases.

Availability and Implementation

PeptideMapper is implemented in the open source Java CompOmics framework under the permissive Apache 2.0 license https://github.com/compomics/compomics-utilities.

Supplementary information

Supplementary data are available at Bioinformatics online.
Proton tomography through deeply virtual Compton scattering
Authors: Ji Xiangdong
Published: March 2017

In this prize talk, I recall some of the history surrounding the discovery of deeply virtual Compton scattering, and explain why it is an exciting experimental tool to obtain novel tomographic pictures of the nucleons at Jefferson Lab 12 GeV facility and the planned Electron-Ion Collider in the USA. It is certainly a great honor to have received the 2016 Herman Feshbach Prize in theoretical nuclear physics by the American Physical Society. I sincerely thank my colleagues in the Division of Nuclear Physics to recognize the importance of some of the theoretical works I have done in the past, particularly their relevance to the experimental programs around the world.
Organizational Barriers to Technology Adoption: Evidence from Soccer-Ball Producers in Pakistan*
Authors: Atkin David , Chaudhry Azam , Chaudry Shamyla , Khandelwal Amit K. , Verhoogen Eric
Published: March 2017

This article studies technology adoption in a cluster of soccer-ball producers in Sialkot, Pakistan. We invented a new cutting technology that reduces waste of the primary raw material and gave the technology to a random subset of producers. Despite the clear net benefits for nearly all firms, after 15 months take-up remained puzzlingly low. We hypothesize that an important reason for the lack of adoption is a misalignment of incentives within firms: the key employees (cutters and printers) are typically paid piece rates, with no incentive to reduce waste, and the new technology slows them down, at least initially. Fearing reductions in their effective wage, employees resist adoption in various ways, including by misinforming owners about the value of the technology. To investigate this hypothesis, we implemented a second experiment among the firms that originally received the technology: we offered one cutter and one printer per firm a lump-sum payment, approximately a month’s earnings, conditional on demonstrating competence in using the technology in the presence of the owner. This incentive payment, small from the point of view of the firm, had a significant positive effect on adoption. The results suggest that misalignment of incentives within firms is an important barrier to technology adoption in our setting.