bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of CID versus ETD‐based MS/MS fragmentation for the analysis of doubly derivatized steroids
Authors: Juang Yu‐Min , She Tzu‐Fang , Chen Hui‐Yi , Lai Chien‐Chen
Published: December 2013

Electrospray ionization coupled with collision‐induced dissociation (CID) and tandem mass spectrometry (MS/MS) is a commonly used technique to analyze the chemical composition of steroids. However, steroids are structurally similar compounds, making it difficult to interpret their product‐ion spectra. Electron transfer dissociation (ETD), a relatively new technique for protein and peptide fragmentation, has been shown to provide more detailed structural information. In this study, we compared the ability of CID with that of ETD to differentiate between eight 3,20‐dioxosteroids that had been derivatizated with a quaternary ammonium salt, Girard reagent P (GirP), at room temperature or after exposure to microwave irradiation to generate doubly charged ions. We found that the derivatization of steroid with GirP hydrazine occurred in less than 10 min when the reaction was carried out in the presence of microwave irradiation compared to 30 min when the reaction was carried out at room temperature. According to the MS/MS spectra, CID provided rich, structurally informative ions; however, the spectra were complex, thereby complicating the peak assignment. In contrast, ETD generated simpler spectra, making it easier to recognize individual peaks. Remarkably, both CID and ETD were allowed to differentiate of steroid isomers, 17α‐hydroxyprogesterone (17OHP) and deoxycorticosterone (DOC), but the signature ions obtained from CID were less intense than those generated by ETD, which generated much clearer spectra. These results indicate that ETD in conjunction with CID can provide more structural information for precise characterization of steroids. Copyright © 2013 John Wiley & Sons, Ltd.
Metabolic activity measured on PET/CT correlates with clinical outcomes in patients with limb and girdle sarcomas
Authors: Skamene Sonia R. , Rakheja Rajan , Dalhstrom Kristina R. , Roberge David , Nahal Ayoub , Charest Mathieu , Turcotte Robert , Hickeson Marc , Freeman Carolyn
Published: December 2013

Objective

To explore the relationship between metabolic activity and outcome in patients with extremity sarcomas.

Methods

Between June 2004 and December 2011, 120 patients with newly diagnosed limb and girdle sarcomas underwent FDG‐PET/CT for disease staging prior to curative intent treatment. The maximum standardized uptake value (SUVmax) was measured for each primary tumor and correlated with outcome. Progression‐free survival and overall survival (OS) were analyzed using the Kaplan–Meier method.

Results

Soft‐tissue sarcomas were more frequent (68%) than bone (27%) or cartilage (5%) tumors. Median follow‐up was 33.2 months. 51% of patients progressed during the follow‐up interval and 38% died. SUVmax was dichotomized with a cut‐point of 10.3. Patients with SUVmax < 10.3 had better DFS and OS compared with patients with SUVmax ≥ 10.3 (P < 0.001 and P < 0.001, respectively [log‐rank test]). Multivariate analysis confirmed that even after adjusting for age, sex, site, tumor type (bone vs. soft‐tissue), grade, and stage; an SUVmax ≥ 10.3 correlated with a twofold risk of progression and 2.4 times greater risk of death (hazard ratio [HR] 2.0, 95% CI, 1.1–3.7, and HR, 2.4, 95% CI, 1.1–4.9).

Conclusion

SUVmax is an independent adverse prognostic factor for both progression and OS in patients with extremity sarcomas. J. Surg. Oncol. 2014 109:410–414. © 2013 Wiley Periodicals, Inc.
Axillary reverse mapping using fluorescence imaging is useful for identifying the risk group of postoperative lymphedema in breast cancer patients undergoing sentinel node biopsies
Authors: Sakurai Takashi , Endo Mariko , Shimizu Ken , Yoshimizu Nobunari , Nakajima Kenichirou , Nosaka Kaori , Dai Yuuko , Iwao Akiko , Jinnai Yuki
Published: December 2013

Background

Axillary reverse mapping (ARM) is a novel technique for preserving the upper extremity lymphatic pathways during axillary lymph node surgery. However, there is no evidence of the usefulness of ARM for patients undergoing sentinel lymph node biopsy (SNB).

Methods

Between August 2009 and July 2012, 372 patients who underwent the SNB procedure for breast cancer were enrolled in this study. Using the indocyanine green fluorescence technique and indigocarmine blue dye method, we studied the relationship between the upper extremity lymphatic flow and breast sentinel node (SN). Our aim of this study was the probability of postoperative lymphedema with respect to whether the upper extremity lymphatics corresponded to the breast SN.

Results

Among the 327 patients who underwent the SNB procedure, the upper extremity lymphatics drainage into the breast SN in 76 (23.2%; corresponding group), and only 5 patients in this group developed lymphedema. In contrast, none of the patients in the noncorresponding group developed lymphedema.

Conclusions

ARM during SN biopsy can identify the group of patients who are at high risk for developing lymphedema. More risk‐focused guidance should be used for these patients. J. Surg. Oncol. 2014 109:612–615. © 2013 The Authors. Surgical Oncology Published by Wiley Periodicals, Inc.
Solid‐phase microextraction with a graphene‐composite‐coated fiber coupled with GC for the determination of some halogenated aromatic hydrocarbons in water samples
Authors: Zhang Guijiang , Li Zhi , Zang Xiaohuan , Wang Chun , Wang Zhi
Published: December 2013

In this work, a graphene composite was coated onto etched stainless‐steel wire through a sol–gel technique and it was used as a solid‐phase microextraction (SPME) fiber. The prepared fiber was characterized by SEM, which revealed that the fiber had a highly porous structure. The application of the fiber was evaluated through the headspace SPME of five halogenated aromatic hydrocarbons (chlorobenzene, bromobenzene, 1,3‐dichlorobenzene, 1,2‐dichlorobenzene, and 1,2,4‐trichlorobenzene) in water samples followed by GC with flame ionization detection. The main factors influencing the extraction efficiency, including headspace volume, extraction time, extraction temperature, stirring rate, ionic strength of sample solution, and desorption conditions, were studied and optimized. Under the optimum conditions, the linearity of the method ranged from 2.5 to 800.0 μg/L for 1,2,4‐trichlorobenzene and from 2.5 to 500.0 μg/L for chlorobenzene, bromobenzene, 1,3‐dichlorobenzene, and 1,2‐dichlorobenzene, with the correlation coefficients (r) ranging from 0.9962 to 0.9980, respectively. The LODs (S/N = 3) of the method for the analytes were in the range between 0.5 and 1.0 μg/L. The recoveries of the method for the analytes obtained for the spiked water samples at 50.0 and 250.0 μg/L were from 76.0 to 104.0%.
Direct Pyrolysis ‐ Mass Spectrometry Analysis of Thermal Degradation of Thio‐Click‐Modified Poly(2‐oxazoline)
Authors: Atilkan Nurcan , Schlaad Helmut , Nur Yusuf , Hacaloglu Jale
Published: December 2013

Poly(2‐(3‐butenyl)‐2‐oxazoline)s (PBOX) with glucose‐S‐butyl (Glc) and perfluoroalkyl‐S‐butyl (F) side chains (three samples: Glc/F = 100/0, 0/100, and 88/12) are synthesized by ring‐opening polymerization of 2‐butenyl‐2‐oxazoline and thiol‐ene click photochemistry, and their thermal properties are analyzed by direct‐pyrolysis mass spectrometry. Significant changes in the thermal stability and thermal‐degradation products are observed depending on the structure of the side chain. The thermal degradation of PBOX‐Glc and PBOX‐F homopolymers starts with loss of side chains at relatively low temperatures and successive cleavage along the side and main chains follows. The stability of the glucose units of the PBOX‐Glc/F copolymer is significantly increased by the presence of perfluoroalkyl groups, attributable to OH···F hydrogen bonding interactions during pyrolysis.

image
A discrete Gould transform data hiding scheme
Authors: Varsaki E.E. , Fotopoulos V. , Skodras A.N.
Published: December 2013

Discrete Gould transform has been recently introduced in image processing. This paper proposes a data hiding scheme that uses the discrete Gould transform in order to invisibly embed a secret message. The Gould coefficients represent the differences between neighboring pixels. Small changes of the coefficients generate even smaller changes to the pixels. By this, a high capacity fragile steganographic technique is achieved. The message is easily destroyed after any manipulation, and therefore, its absence can prove that the image has been altered in some way. Because of this property, the proposed technique finds application in image authentication and tamper proofing. Copyright © 2013 John Wiley & Sons, Ltd.
Variational multiscale proper orthogonal decomposition: Navier‐stokes equations
Authors: Iliescu Traian , Wang Zhu
Published: December 2013

We develop a variational multiscale proper orthogonal decomposition (POD) reduced‐order model (ROM) for turbulent incompressible Navier‐Stokes equations. Under two assumptions on the underlying finite element approximation and the generation of the POD basis, the error analysis of the full discretization of the ROM is presented. All error contributions are considered: the spatial discretization error (due to the finite element discretization), the temporal discretization error (due to the backward Euler method), and the POD truncation error. Numerical tests for a three‐dimensional turbulent flow past a cylinder at Reynolds number show the improved physical accuracy of the new model over the standard Galerkin and mixing‐length POD ROMs. The high computational efficiency of the new model is also showcased. Finally, the theoretical error estimates are confirmed by numerical simulations of a two‐dimensional Navier‐Stokes problem. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 641–663, 2014
Fabrication of continuous nanofiber yarn using novel multi‐nozzle bubble electrospinning
Authors: He Jian‐Xin , Qi Kun , Zhou Yu‐Man , Cui Shi‐Zhong
Published: December 2013

A novel multi‐nozzle bubble electrospinning apparatus, including spinning unit, metering pump, constant flow pump, metal funnel and yarn winder, was designed for the preparation of continuous twisted polyacrylonitrile nanofiber yarns, and the principle of nanofiber yarn spinning was studied. An innovative spinning unit consisting of nozzle and air chamber was used to improve the production of nanofibers. Double conjugate electrospinning was developed using two pairs of oppositely charged spinning units to neutralize the charges. The effects of applied voltage, air flow rate, overall solution flow rate and funnel rotary speed on the fiber diameter, production rate and mechanical properties of the nanofiber yarns were analyzed. Nanofibers could be aggregated stably and bundled continuously, then twisted into nanofiber yarns uniformly at an applied voltage of 34 kV, air flow rate of 1200 mL min−1 and overall solution flow rate of 32 mL h−1. With an increase in the funnel rotary speed, the twist angle of the nanofiber yarns gradually increased when the take‐up speed was constant. The yarn tensile strength and elongation at break showed an increasing trend with increasing twist angle. Nanofiber yarns obtained using this novel method could be produced at a rate from 2.189 to 3.227 g h−1 with yarn diameters ranging from 200 to 386 µm. Nanofiber yarns with a twist angle of 49.7° showed a tensile strength of 0.592 cN dtex−1 and an elongation at break of 65.7%. © 2013 Society of Chemical Industry
Evaluation and prognostic significance of ACAT1 as a marker of prostate cancer progression
Authors: Saraon Punit , Trudel Dominique , Kron Ken , Dmitromanolakis Apostolos , Trachtenberg John , Bapat Bharati , van der Kwast Theodorus , Jarvi Keith A. , Diamandis Eleftherios P.
Published: December 2013

INTRODUCTION

Prostate cancer is the second leading cause of cancer‐related death among men in North America. While a majority of prostate cancer cases remain indolent, subsets of patients develop aggressive cancers, which may lead to death. The current methods of detection include digital rectal examination and the serum PSA test. However, due to lack of specificity, neither of these approaches is able to accurately discriminate between indolent and aggressive cancer, which is why there is a need for additional prognostic factors. Previously, we identified enzymes of the ketogenic pathway, particularly ACAT1, to be elevated in aggressive prostate cancer.

METHODS

In the current study, we assessed the diagnostic and prognostic potential of ACAT1 by analyzing its expression using immunohistochemistry on a tissue microarray consisting of 251 clinically localized prostate cancer patients who have undergone radical prostatectomy.

RESULTS

Using quantitative digital imaging software, we found that ACAT1 expression was significantly greater in cancerous cores compared to adjacent benign cores (P < 0.0001), in Gleason score (GS) ≥8 cancers versus GS≤6 cancers (P < 0.0001), GS≥8 cancers versus GS7 cancers (P = 0.001), as well as pT3/pT4 versus pT2 cancers (P = 0.001). In addition, ACAT1 predicted biochemical recurrence in univariate (HR, 1.81, CI = 1.13–2.9, P = 0.0128), and multivariate models (HR, 1.69, CI = 1.01–2.81, P = 0.0431) including pre‐operative PSA level, Gleason score and pathological stage. In univariate time‐to‐recurrence analysis, ACAT1 expression predicted recurrence in ERG negative cases (P = 0.0025), whereas ERG positive cases did not display any differences.

DISCUSSION

Taken together, these findings indicate that ACAT1 expression could serve as a potential prognostic marker in prostate cancer, specifically in differentiating indolent and aggressive forms of cancer. Prostate 74:372–380, 2014. © 2013 Wiley Periodicals, Inc.
Modern and future nuclear fuel cycles and the relationship with nuclear waste management
Authors: Hannum William H.
Published: December 2013

Discussions of nuclear fuel cycles and nuclear waste typically focus on very long‐term radiological hazards and on concerns over proliferation of nuclear weapons. While there are technical solutions to address the radiological hazards for any of the various feasible fuel cycles, there are substantial practical differences that may influence both the cost and political acceptability of waste disposal options. Only full recycle reduces the actual long‐term hazard in a major way. Efficient use of the energy content of uranium will eventually require some form of recycle of used nuclear fuel, but with known recoverable uranium resources, this is not an urgent concern. Proliferation concerns differ among the various fuel cycles and each presents its own challenges, but ultimately, the differences in proliferation risks are more political than technical. At this point, the actual cost of any of the options for closing the fuel cycle is not adequately known to provide guidance. WIREs Energy Environ 2014, 3:323–329. doi: 10.1002/wene.99

This article is categorized under:

Nuclear Power > Science and Materials
Prevalence of the HOXB13 G84E Mutation Among Unaffected Men with a Family History of Prostate Cancer
Authors: Handorf Elizabeth , Crumpler Nicole , Gross Laura , Giri Veda N.
Published: December 2013

HOXB13 (G84E) was reported to significantly increase risk for prostate cancer. The goal of the current analysis was to assess the prevalence of G84E in ethnically‐diverse high‐risk men undergoing prostate cancer screening and place the carrier frequency within the context of prevalence estimates from reported studies to gain insight into the future role of this mutation in genetic counseling. PRAP is a prostate cancer screening program for unaffected men ages 35–69 with a family history of prostate cancer or African descent. HOXB13 G84E was genotyped by pyrosequencing in 649 PRAP participants with available DNA. Prevalence of the mutation was calculated for PRAP and for reported studies and exact binomial confidence intervals were generated. Prevalence of the G84E mutation in non‐African PRAP men was 0.73 %. When placed in context of the literature, this was higher than reported controls. One G84E mutation carrier was notably of Hispanic background. While the HOXB13 G84E mutation may be rare, there may be a future role in genetic testing for this mutation after further studies of clinical utility in assessing prostate cancer risk.
Cultural Consensus Theory for the Ordinal Data Case
Authors: Anders Royce , Batchelder William H.
Published: December 2013

A Cultural Consensus Theory approach for ordinal data is developed, leading to a new model for ordered polytomous data. The model introduces a novel way of measuring response biases and also measures consensus item values, a consensus response scale, item difficulty, and informant knowledge. The model is extended as a finite mixture model to fit both simulated and real multicultural data, in which subgroups of informants have different sets of consensus item values. The extension is thus a form of model-based clustering for ordinal data. The hierarchical Bayesian framework is utilized for inference, and two posterior predictive checks are developed to verify the central assumptions of the model.
Using spectral analysis and fluorescence lifetimes to discriminate between grass and tree pollen for aerobiological applications
Authors: O'Connor David J. , Lovera Pierre , Iacopino Daniela , O'Riordan Alan , Healy David A. , Sodeau John R.
Published: December 2013

A study has been performed that provides the first fluorescence lifetime results on the intrinsic fluorescence monitored for specificin situbiochemical components of individual pollen grains.
Molecular luminogens based on restriction of intramolecular motions through host–guest inclusion for cell imaging
Authors: Liang Guodong , Lam Jacky W. Y. , Qin Wei , Li Jie , Xie Ni , Tang Ben Zhong
Published: December 2013

We developed a new strategy to restrict the motions of AIE molecules through host–guest inclusion, affording new molecular luminogens.
Yellow-light sensitization of a ligand photosubstitution reaction in a ruthenium polypyridyl complex covalently bound to a rhodamine dye
Authors: Bahreman Azadeh , Cuello-Garibo Jordi-Amat , Bonnet Sylvestre
Published: December 2013

A rhodamine dye was covalently attached to a ruthenium complex to enhance the rate of ligand photosubstitution under yellow light irradiation.
Facile one-step solid-phase synthesis of multitopic organic–DNA hybrids via “click” chemistry
Authors: Thaner Ryan V. , Eryazici Ibrahim , Farha Omar K. , Mirkin Chad A. , Nguyen SonBinh T.
Published: December 2013

Small molecule–DNA hybrids can be synthesized in a one-pot fashion and in good yields by coupling multiazide cores to alkyne-modified DNAs on a solid support using click chemistry.
Wide electrochemical window ionic salt for use in electropositive metal electrodeposition and solid state Li-ion batteries
Authors: Murugesan Sankaran , Quintero Oliver A. , Chou Brendan P. , Xiao Penghao , Park Kyusung , Hall Justin W. , Jones Richard A. , Henkelman Graeme , Goodenough John B. , Stevenson Keith J.
Published: December 2013

A stable hydrophobic ionic crystalline solid comprised of the N-propyl-N-methylpiperidinium cation and hexafluorophosphate anion PP13PF6 exhibits a remarkably wide electrochemical window of 7.2 V.
Bioinspired assembly of layered double hydroxide/carboxymethyl chitosan bionanocomposite hydrogel films
Authors: Wang Yi , Zhang Dun
Published: December 2013

Layered double hydroxide/carboxymethyl chitosan bionanocomposite hydrogel films with high swelling stability were fabricated by the bioinspired assembly technique.
Glucomannan-poly(N-vinyl pyrrolidinone) bicomponent hydrogels for wound healing
Authors: Shahbuddin Munira , Bullock Anthony J. , MacNeil Sheila , Rimmer Stephen
Published: December 2013

UV initiated and UV plus ceric(iv) initiated polymerisations of N-vinyl pyrrolidinone and poly(ethylene glycol)diacrylate in the presence of konjac glucomannan generated semi-interpenetrating networks or graft conetworks. Both systems were cytocompatible but only the graft conetworks stimulated fibroblast growth and migration.
Two-component organogel for visually detecting nitrite anion
Authors: Xia Qian , Mao Yueyuan , Wu Junchen , Shu Tianmin , Yi Tao
Published: December 2013

A gel state probe for detecting nitrite anions is obtained by complexation of naphthalene diimide undecanoic acid with diaminoanthraquinone.
Design and experimental evaluation tests of a Takagi–Sugeno power system stabiliser
Authors: Nogueira Fabrício G. , Walter Barra , da Costa Carlos T. , de Moraes Anderson R. B. , Gomes Marcus C. M. , de Lana Janio J.
Published: December 2013

In this study, the design, implementation and experimental evaluation tests of a Takagi–Sugeno power system stabiliser (TSPSS) controller is presented. The controller was designed in order to provide a good damping for dominant electromechanical oscillations in power systems for the set of allowed operating conditions. In the proposed TSPSS controller, such requirement was accomplished by implementing a supervision scheme which performs the adaptation of the TSPSS parameters at each sample time, according to the current detected plant operating condition. The TSPSS controller has been implemented as a microcontroller‐based embedded system and its performance was assessed by performing experimental tests in a laboratory scale (10 kVA) power system as well as in field tests performed in a large (350 MVA) generating unit, at Tucuruí Hydroelectric Power Plant. The experimental results also show the good performance of the TSPSS to cope with varying plant operation condition.
AC pollution flashover performance and flashover process of glass insulators at high altitude site
Authors: Jiang Xingliang , Xiang Ze , Zhang Zhijin , Hu Jianlin , Hu Qin , Shu Lichun
Published: December 2013

The ac pollution flashover performance and flashover process of LXHY3‐I6O insulators was investigated at a high altitude site (altitude of 1400m) in this paper. The solid layer method was used, and even‐rising voltage method was adopted. According to the test results, the average pollution flashover voltage (Uav) decreased with the increase of pollution, and there was no obvious relationship between the exponent characterising the influence of pollution and the length of the insulator strings. The relationship between Uav and the length of the insulator strings was nearly linear. Subsequently, the effect of the pollution and the length of insulator strings on the critical flashover arc trajectory were analysed. It concluded that the critical flashover distance (lc) decreased with the increase of pollution, and it was shorter than the leakage distance (L0), whereas there was no significant relationship between lc/L0 and the length of insulator strings. The arc appearance at the high altitude site was very irregular with obvious bending and rocking; the local arcs deviated from the surface of the polluted insulators even more seriously and the diameter was thicker than those obtained in the normal environment. Moreover, the brightness and diameter of local arcs was related to pollution.
Mutually coupled multiple inductive loop system suitable for heterogeneous traffic
Authors: Mohammed Ali S. Sheik , George Boby , Vanajakshi Lelitha
Published: December 2013

A magnetically coupled multiple inductive loop detector system is presented in this study. Automated detection, classification and measurement of speed of vehicles are challenging tasks, in a no‐lane disciplined and heterogeneous traffic. This study proposes an inductive loop sensor wherein multiple numbers of small loops are placed within a large outer loop, for measurement of traffic parameters under such traffic. In the new system the outer loop alone is connected to the measurement unit and all the small loops are coupled inductively to the outer loop. This scheme is simple and effective and can be employed to convert an existing single loop system to a multiple loop system, suitable for heterogeneous traffic. The measurement is based on a synchronous detection method. A special excitation that ensures parallel resonance of the inductive system is employed, which keeps the power consumption minimum. The new system correctly sensed the vehicles, categorised and counted them in undisciplined traffic. The proposed system has been also extended to detect the direction of travel and speed of the vehicles. Results from the prototype developed were found to be accurate proving its practicality in real time traffic monitoring and intelligent transportation system (ITS) applications under a heterogeneous scenario.
Design‐oriented model and critical inductance method for long life isolated power converters
Authors: Pang Hon Man , Pong Bryan Man Hay
Published: December 2013

For moderate‐to‐high power converters, electrolytic capacitor is an indispensable component. Life of electrolytic capacitor is critical compared with its semi‐conductor counterparts. This study proposes a new model to analyse the converter life and to design the circuit to lower the current ripple in the electrolytic capacitor in order to reach for longer converter life. Two‐stage power converter (a power factor correction converter followed by a DC–DC converter) is the typical practice for AC–DC converter. Forward converter and Flyback converters are the common choices for the downstream converter for this power range. Comparison between two modes of operation, discontinuous conduction mode and continuous conduction mode (CCM), for the two converter topologies shows a typical CCM Forward converter to have almost 300 times longer life than a CCM Flyback converter. Another focus of the work is to analyse the effect of circuit parameters on the converter life. A critical inductance is established to guide the design for long life converters.
Atomic force microscopy tip characteriser based on the fabrication of nanorod array structures
Authors: Chen Yuqin , Han Guoqiang , He Bingwei
Published: December 2013

An atomic force microscopy (AFM) image is acquired by probe tip scanning on the surface of a sample. It is a distorted representation of the sample because of the finite size of the tip. To modify the distorted image and improve the measurement accuracy of the AFM image, it is important to estimate the tip shape. Tip estimation results mainly rely on the sample‐dimensional uncertainty and AFM image noise. More reliable data of tip morphology can be collected if there is a suitable tip characteriser to reduce the sample‐dimensional uncertainty and improve AFM image accuracy. A new tip characteriser for blind reconstruction of AFM tip morphology has been developed through the fabrication of gold nanorod array structures. Based on template synthesis, the gold film (surface roughness, 162.1 nm) was deposited on porous anodic alumina membrane by magnetron sputtering. The well‐ordered nanorod array structures (100–400 nm height, 60 nm diameter, ∼20 nm at apex and 80 nm pitch) were obtained. In combination with the blind reconstruction algorithm, the prepared nanostructures were used as the tip characteriser to estimate the morphology of the traditional AFM Si3N4 probe, which can effectively reduce the influence of the sample‐dimensional uncertainty and image noise on the result of the tip blind reconstruction.
Osmosensory signaling in
Mycobacterium tuberculosis
mediated by a eukaryotic-like Ser/Thr protein kinase
Authors: Hatzios Stavroula K. , Baer Christina E. , Rustad Tige R. , Siegrist M. Sloan , Pang Jennifer M. , Ortega Corrie , Alber Tom , Grundner Christoph , Sherman David R. , Bertozzi Carolyn R.
Published: December 2013

Significance

Osmotic stress is one of many environmental hazards encountered by bacteria during the course of infection, but our understanding of how bacteria perceive and respond to changes in extracellular osmolarity is still incomplete. We show that
Mycobacterium tuberculosis
, the pathogen that causes tuberculosis in humans, responds, in part, through an osmosensory pathway regulated by the Ser/Thr protein kinase (STPK) PknD. Our work demonstrates that increasing extracellular osmolarity induces expression of a PknD substrate that regulates bacterial transcription, cell wall remodeling, and virulence factor production. Because STPKs are prevalent in bacteria, these proteins may play a broad role in bacterial osmosensing.
Rationality of the Hilbert series of Hopf-invariants of free algebras
Authors: Ferreira Vitor , Murakami Lucia
Published: December 2013

It is shown that the subalgebra of invariants of a free associative algebra of finite rank under a linear action of a semisimple Hopf algebra has a rational Hilbert series with respect to the usual degree function whenever the ground field has zero characteristic.
On vector fields in the plane with the reflection property
Authors: Berhanu S. , Hounie J.
Published: December 2013

We discuss necessary and sufficient conditions for the validity of the analogue of the Schwarz Reflection Principle for homogeneous solutions of complex vector fields in the plane.
Graded Cartan determinants of the symmetric groups
Authors: Tsuchioka Shunsuke
Published: December 2013

We give the graded Cartan determinants of the symmetric groups. Based on that, we propose a gradation of Hill’s conjecture which is equivalent to Külshammer-Olsson-Robinson’s conjecture on the generalized Cartan invariants of the symmetric groups.
Identification of truncated forms of U1 snRNA reveals a novel RNA degradation pathway during snRNP biogenesis
Authors: Ishikawa Hideaki , Nobe Yuko , Izumikawa Keiichi , Yoshikawa Harunori , Miyazawa Naoki , Terukina Goro , Kurokawa Natsuki , Taoka Masato , Yamauchi Yoshio , Nakayama Hiroshi , Isobe Toshiaki , Takahashi Nobuhiro
Published: December 2013

The U1 small nuclear ribonucleoprotein (snRNP) plays pivotal roles in pre-mRNA splicing and in regulating mRNA length and isoform expression; however, the mechanism of U1 snRNA quality control remains undetermined. Here, we describe a novel surveillance pathway for U1 snRNP biogenesis. Mass spectrometry-based RNA analysis showed that a small population of SMN complexes contains truncated forms of U1 snRNA (U1-tfs) lacking the Sm-binding site and stem loop 4 but containing a 7-monomethylguanosine 5′ cap and a methylated first adenosine base. U1-tfs form a unique SMN complex, are shunted to processing bodies and have a turnover rate faster than that of mature U1 snRNA. U1-tfs are formed partly from the transcripts of U1 genes and partly from those lacking the 3′ box elements or having defective SL4 coding regions. We propose that U1 snRNP biogenesis is under strict quality control: U1 transcripts are surveyed at the 3′-terminal region and U1-tfs are diverted from the normal U1 snRNP biogenesis pathway.
Real-time Detection of Gastric Insufflation Related to Facemask Pressure–controlled Ventilation Using Ultrasonography of the Antrum and Epigastric Auscultation in Nonparalyzed Patients
Authors: Bouvet Lionel , Albert Marie-Laure , Augris Caroline , Boselli Emmanuel , Ecochard René , Rabilloud Muriel , Chassard Dominique , Allaouchiche Bernard
Published: December 2013

Background:

The authors sought to determine the level of inspiratory pressure minimizing the risk of gastric insufflation while providing adequate pulmonary ventilation. The primary endpoint was the increase in incidence of gastric insufflation detected by ultrasonography of the antrum while inspiratory pressure for facemask pressure-controlled ventilation increased from 10 to 25 cm H2O.

Methods:

In this prospective, randomized, double-blind study, patients were allocated to one of the four groups (P10, P15, P20, and P25) defined by the inspiratory pressure applied during controlled-pressure ventilation: 10, 15, 20, and 25 cm H2O. Anesthesia was induced using propofol and remifentanil; no neuromuscular-blocking agent was administered. Once loss of eyelash reflex occurred, facemask ventilation was started for a 2-min period while gastric insufflation was detected by auscultation and by real-time ultrasonography of the antrum. The cross-sectional antral area was measured using ultrasonography before and after facemask ventilation. Respiratory parameters were recorded.

Results:

Sixty-seven patients were analyzed. The authors registered statistically significant increases in incidences of gastric insufflation with inspiratory pressure, from 0% (group P10) to 41% (group P25) according to auscultation, and from 19 to 59% according to ultrasonography. In groups P20 and P25, detection of gastric insufflation by ultrasonography was associated with a statistically significant increase in the antral area. Lung ventilation was insufficient for group P10.

Conclusion:

Inspiratory pressure of 15 cm H2O allowed for reduced occurrence of gastric insufflation with proper lung ventilation during induction of anesthesia with remifentanil and propofol in nonparalyzed and nonobese patients. (Anesthesiology 2014; 120:326-34)
Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
Authors: Wu Yi-Chieh , Rasmussen Matthew D. , Bansal Mukul S. , Kellis Manolis
Published: December 2013

Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.
4-Nitrophenylhydrazinium picrate monohydrate
Authors: Cai Hong-lan , Liu Bing , Qiao Qing-an
Published: December 2013

In the crystal structure of the title compound, C6H8N3O2
+·C6H2N3O7
−·H2O, N—H...O and O—H...O hydrogen bonds link the components into a two-dimensional network parallel to (010). In addition, there are pairs of weak inversion-related C—H...O hydrogen bonds within the two-dimensional network. The three nitro groups are twisted by 1.6 (3), 7.8 (3) and 12.1 (3)° from the ring plane in the anion, while in the cation, the nitro group makes a dihedral angle of 4.6 (2)° with the ring.
4-Formyl-2-nitrophenyl 3-nitro-2-methylbenzoate
Authors: Moreno-Fuquen Rodolfo , Hernández Geraldine , Kennedy Alan R.
Published: December 2013

In the title formyl nitro aryl benzoate derivative, C15H10N2O7, the benzene rings form a dihedral angle of 4.96 (3)°. The mean plane of the central ester group, C—O—C–(=O)—C (r.m.s. deviation = 0.0484 Å), is twisted away from the formyl nitro aryl and benzoate rings by 46.61 (5) and 49.93 (5)°, respectively. In the crystal, the molecules are packed forming C—H...O interactions in chains which propagate along [010]. Edge-fused R
3
3(15) rings are generated along this direction.
1-[2-Hydroxy-4-(prop-2-yn-1-yloxy)phenyl]ethanone
Authors: Selvarani V. , Neelakantan M. A. , Srinivasan T. , Velmurugan D.
Published: December 2013

In the title compound, C11H10O3, there is an intramolecular O—H...O hydrogen bond generating an S(6) ring motif. The O atom of the hydroxy group deviates by 0.0200 (1) Å from the benzene ring to which it is attached. The propyne group is almost linear, the C—C[triple-bond]C angle being 177.83 (15)°, and is almost coplanar with the benzene ring; the C—C—O—C torsion angle being only −1.1 (2)°. In the crystal, molecules are linked via C—H...O hydrogen bonds, forming infinite C(11) chains running parallel to [103]. These chains are linked by a pair of C—H...O hydrogen bonds, enclosing R
2
2(8) inversion dimers, forming a corrugated two-dimensional network lying parallel to (103).
5-(3,5-Difluorophenyl)-1-(4-fluorophenyl)-3-trifluoromethyl-1H-pyrazole
Authors: Manoj Kumar Karikere Ekanna , Suchetan Parameshwar Adimoole , Palakshamurthy Bandrehalli Siddagangaiah , Madan Kumar Shankar , Lokanath Neratur Krishnappagowda , Sreenivasa Swamy
Published: December 2013

In the title compound, C16H8F6N2, the dihedral angle between the pyrazole and difluorobenzene rings is 50.30 (13)°, while those between the pyrazole and fluorobenzene rings and between the difluorobenzene and fluorobenzene rings are 38.56 (13) and 53.50 (11)°, respectively. Aromatic π–π stacking interactions between adjacent difluorobenzene rings [centroid–centroid separation = 3.6082 (11) Å] link the molecules into dimers parallel to [21-2].
1,1′-(Diselanediylbis{[P,P-diphenyl-N-(trimethylsilyl)phosphorimidoyl]methanylylidene})bis[1,1-diphenyl-N-(trimethylsilyl)-λ5-phosphanamine] pentane disolvate
Authors: Thirumoorthi Ramalingam , Chivers Tristram , Laitinen Risto S.
Published: December 2013

The title compound, C62H78N4P4Se2Si4·2C5H12, is made up of two [SeC(PPh2NSiMe3)(PPh2NHSiMe3)] units related by an inversion center situated at the mid-point of the diselenide bond. It crystallized with two disordered molecules of pentane used as solvent of crystallization. It is a rare example of an antiperiplanar diselenide and exhibits a long Se—Se bond of 2.4717 (8) Å. The Se—C bond length of 1.876 (5) Å is short in comparison with the range of values found for other diselenides (1.91–1.97 Å). The molecule exhibits two intramolecular N—H...N hydrogen bonds. In the crystal, there are no significant intermolecular interactions present. One of the Me3Si– groups is disordered over two positions with a refined occupancy ratio of 0.708 (8):0.292 (8). The contribution of the disordered solvent to the scattering was removed with the SQUEEZE option of PLATON [Spek (2009). Acta Cryst. D65, 148–155]. The solvent contribution has been included in the reported molecular weight and density.
3,6-Dichloro-9-(prop-2-yn-1-yl)-9H-carbazole
Authors: Mague Joel T. , Akkurt Mehmet , Mohamed Shaaban K. , Mohamed Asmaa H. , Albayati Mustafa R.
Published: December 2013

The tricyclic aromatic ring system of the title compound, C15H9Cl2N, is essentially planar (r.m.s. deviation = 0.002 Å). The two Cl atoms lie slightly out of the plane of the carbazole ring system, with the C—Cl bonds forming angles of 1.23 (8) and 1.14 (8)° with the plane. The acetylene group has a syn orientation with respect to the ring system. In the crystal, no weak hydrogen bonds nor any π–π stacking interactions are observed.
3-(Adamantan-1-yl)-4-ethyl-1-{[4-(2-methoxyphenyl)piperazin-1-yl]methyl}-1H-1,2,4-triazole-5(4H)-thione
Authors: El-Emam Ali A. , Al-Tuwaijri Hanaa M. , Al-Abdullah Ebtehal S. , Chidan Kumar C. S. , Fun Hoong-Kun
Published: December 2013

In the title compound, C26H37N5OS, the piperazine ring adopts a chair conformation. The triazole ring forms dihedral angles of 67.85 (9) and 59.41 (9)° with the piperazine and benzene rings, respectively, resulting in an approximate V-shaped conformation for the molecule. An intramolecular C—H...O hydrogen bond generates an S(6) ring motif. The crystal structure features C—H...π interactions, producing a two-dimensional supramolecular architecture.
Refinement of macromolecular structures against neutron data withSHELXL2013
Authors: Gruene Tim , Hahn Hinrich W. , Luebben Anna V. , Meilleur Flora , Sheldrick George M.
Published: December 2013

Some of the improvements inSHELX2013makeSHELXLconvenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to useSHELXLfor refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst.(1991), A47, 392–400] restraints to H atoms and discusses several of the features ofSHELXLthat make the program particularly useful for the investigation of H atoms with neutron diffraction.SHELXL2013is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.
Periodic lattices of arbitrary nano-objects: modeling and applications for self-assembled systems
Authors: Yager Kevin G. , Zhang Yugang , Lu Fang , Gang Oleg
Published: December 2013

A formalism is described which enables the simulation or fitting of small-angle scattering data (X-ray or neutron) for periodic heterogeneous lattices of arbitrary nano-objects. Generality is maximized by allowing for particle mixtures, anisotropic nano-objects and definable orientations of nano-objects within the unit cell. The model is elaborated by including a variety of kinds of disorder relevant to self-assembling systems: finite grain size, polydispersity in particle properties, positional and orientation disorder of particles, and substitutional or vacancy defects within the lattice. The applicability of the approach is demonstrated by fitting experimental X-ray scattering data. In particular, the article provides examples of superlattices self-assembled from isotropic and anisotropic nanoparticles which interact through complementary DNA coronas.
Simultaneous diffuse reflection infrared spectroscopy and X-ray pair distribution function measurements
Authors: Beyer Kevin A. , Zhao Haiyan , Borkiewicz Olaf J. , Newton Mark A. , Chupas Peter J. , Chapman Karena W.
Published: December 2013

Combining insights from diffuse reflection infrared Fourier transform spectroscopy and X-ray pair distribution function (PDF) analysis has the potential to deepen our understanding of complex materials systems including heterogeneous catalysts and host–guest systems. This article describes the development of instrumentation and non-ambient reaction cells that enable combined PDF–IR studies without compromise to either measurement. Through careful selection of the IR spectrometer and optics, the IR instrument and reaction cell were adapted to allow angular dispersive X-ray measurements without change to the active IR components. The PDF and diffraction data obtained with this experimental configuration are shown to be of similar quality and resolution to standard capillary-based measurements. Simultaneous combined measurements are demonstrated for desorption of guests from within a Prussian blue analog.
Packing bridges in protein crystal structures
Authors: Carugo Oliviero , Djinović-Carugo Kristina
Published: December 2013

On the basis of a statistical analysis of the data deposited in the Protein Data Bank [Bermanet al.(2000).Nucleic Acids Res.28, 235–242; Bernsteinet al.(1977).J. Mol. Biol.112, 535–542], it is shown that two symmetry-related protein molecules are frequently bridged by a small molecule/monoatomic ion, which was used in the crystallization medium despite the fact that it is not a physiological ligand of the macromolecule. It is therefore sensible to suppose that some of the solutes used in crystallizations can favour the nucleation process by bridging and opportunely orienting adjacent protein molecules. This would explain why small changes in the composition of the crystallization solution, for example, the presence of a minor amount of a specific additive, can have a dramatic impact on the outcome of a crystallization experiment.
SANS study on self-assembled structures of Pluronic F127 triblock copolymer induced by additives and temperature
Authors: Kim Tae-Hwan , Han Young-Soo , Jang Jong-Dae , Seong Baek-Seok
Published: December 2013

In the temperature range of 303–333 K, the self-assembled structures of a mixture of Pluronic F127 triblock copolymer [PEO106PPO70PEO106; PEO is poly(ethylene oxide) and PPO is poly(propylene oxide)] and an organic derivative, 5-methyl salicylic acid (5mS), in aqueous solution have been investigated using small-angle neutron scattering (SANS). Above a 5mS concentration of 1.93 g l−1, the F127–5mS mixture solution became cloudy with a blue colour arising from the Tyndall effect, indicating that large polymer aggregates had formed in the mixture solution. SANS measurements showed that the self-assembled structure of the F127–5mS mixture transformed from a spherical to a cylindrical micelle with increasing the concentration of 5mS in the temperature range of 303–323 K. When the 5mS concentration was increased to 3.3 g l−1, the self-assembled structure of the F127–5mS mixture at 333 K underwent an additional phase transition from a cylindrical to a spherical micelle of large size at a 5mS concentration of 2.75 g l−1, although its self-assembled structure changed from a spherical to a cylindrical micelle at a 5mS concentration of 1.93 g l−1as well. The phase transitions are explained by the variation of the mass fraction of the hydrophilic part of F127 and the coupled effect of the limited solubility and the strong tendency to bind with amphiphilic molecules of 5mS. Using a simple material balance equation and the structural information obtained from SANS model analyses, the numbers of D2O and of 5mS molecules in the core and corona regions are calculated. This result can provide a simple and easy way to prepare various nanostructures using a Pluronic triblock copolymer in aqueous solution and may be very useful for practical applications of a Pluronic polymer such as various nanobuilding blocks or nanotemplates.
Model-independent structure factors from powder X-ray diffraction: a novel approach
Authors: Straasø Tine , Dippel Ann-Christin , Becker Jacob , Als-Nielsen Jens
Published: December 2013

Under the experimental condition that all Bragg peaks in a powder X-ray diffraction (PXRD) pattern have the same shape, one can readily obtain the Bragg intensities without fitting any parameters. This condition is fulfilled at the P02.1 beamline at PETRA III using the seventh harmonic from a 23 mm-period undulator (60 keV) at a distance of 65 m. For grain sizes of the order of 1 µm, the Bragg peak shape in the PXRD is entirely determined by the diameter of the capillary containing the powder sample and the pixel size of the image plate detector, and consequently it is independent of the scattering angle. As an example, a diamond powder has been chosen and structure factors derived which are in accordance with those calculated from density functional theory methods of theWIEN2kpackage to within an accuracy that allows a detailed electron density analysis.
Numerical reconstruction of an object image using an X-ray dynamical diffraction Fraunhofer hologram
Authors: Balyan Minas K.
Published: December 2013

A numerical method of reconstruction of an object image using an X-ray dynamical diffraction Fraunhofer hologram is presented. Analytical approximation methods and numerical methods of iteration are discussed. An example of a reconstruction of an image of a cylindrical beryllium wire is considered. The results of analytical approximation and zero-order iteration coincide with exact values of the amplitude complex transmission coefficient of the object as predicted by the resolution limit of the scheme, except near the edges of the object. Calculations of the first- and second-order iterations improve the result at the edges of the object. This method can be applied for determination of the complex amplitude transmission coefficient of amplitude as well as phase objects. It can be used in X-ray microscopy.