bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences in mRNA populations of short and long bovine conceptuses on Day 15 of gestation
Authors: Barnwell Callie V. , Farin Peter W. , Ashwell Christopher M. , Farmer William T. , Galphin Samuel P. , Farin Charlotte E.
Published: March 2016

The majority of pregnancy loss in cattle occurs between Days 8 and 16 of gestation, coincident with the initiation of conceptus elongation and the onset of maternal recognition of pregnancy. Differences in conceptus length on the same day of gestation may be related to an inherent lack of developmental competency or may simply be a consequence of asynchrony with the maternal environment. The objective of this work was to characterize differential patterns of mRNA expression between short and long bovine conceptuses recovered on Day 15 of gestation. Embryos were produced from super‐ovulated Holstein donor cows, and groups of Grade‐1 and Grade‐3 compact morulas were transferred into recipient heifers at Day 6.5 of their cycle. Conceptuses were recovered at Day 15 of gestation, and measured to assess overall length and area. Total RNA was extracted and analyzed on individual GeneChip Bovine Genome Arrays (Affymetrix, Santa Clara, CA). Gene expression was compared between conceptuses derived from the transfer of Grade‐1 versus Grade‐3 embryos; no differences were identified in the profiles of Day‐15 conceptuses of these different embryo grades. When gene expression was compared between conceptuses classified as either short (mean length of 4.2 ± 0.1 mm [standard error]) or long (24.7 ± 1.9 mm) upon recovery at Day 15 of gestation, a total of 348 genes were differentially expressed. Of these, 221 genes were up‐regulated and 127 were down‐regulated in long compared to short conceptuses. In summary, differences in gene expression were identified between conceptuses recovered on Day 15 of gestation, based on their length. These data may be used to identify genes and cellular pathways involved in enhanced conceptus elongation that could serve as markers of successful pregnancy. Mol. Reprod. Dev. 83: 424–441, 2016. © 2016 Wiley Periodicals, Inc.
The Effects of Online and Offline Information Sources on Multiple Store Patronage
Authors: Tagashira Takumi , Minami Chieko
Published: March 2016

The purpose of this study is to examine the relationship between multiple store patronage (MSP) and information source usage both online and offline. In particular, this study investigates the detailed effects of information sources on MSP rather than considering whether consumers choose online or offline sources. In prior studies, MSP has been conceptualized using the consumer cost–benefit framework and relates to consumer multiple store usage. However, even though prior studies have emphasized the importance of information sources in the cost–benefit framework, those that consider MSP have not tested the sources’ effects. This current study conducts empirical count data analysis in the Japanese sports shoes retail market. The results reveal that consumers evaluate information sources using more detailed divisions than simply online and offline. This study contributes to studies on MSP because it is the first to identify the impact of information source usage on MSP.
LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics
Authors: Zuo Guanghong , Zhi Xiaoyang , Xu Zhao , Hao Bailin
Published: March 2016

We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.
Challenges, solutions, and recommendations for Alzheimer's disease combination therapy
Authors: Hendrix James A. , Bateman Randall J. , Brashear H. Robert , Duggan Cynthia , Carrillo Maria C. , Bain Lisa J. , DeMattos Ronald , Katz Russell G. , Ostrowitzki Susanne , Siemers Eric , Sperling Reisa , Vitolo Ottavio V.
Published: March 2016

Given the complex neuropathology Alzheimer's disease (AD), combination therapy may be necessary for effective treatment. However, scientific, pragmatic, regulatory, and business challenges need to be addressed before combination therapy for AD can become a reality. Leaders from academia and industry, along with a former member of the Food and Drug Administration and the Alzheimer's Association, have explored these challenges and here propose a strategy to facilitate proof‐of‐concept combination therapy trials in the near future. First, a more integrated understanding of the complex pathophysiology and progression of AD is needed to identify the appropriate pathways and the disease stage to target. Once drug candidates are identified, novel clinical trial designs and selection of appropriate outcome assessments will be needed to enable definition and evaluation of the appropriate dose and dosing regimen and determination of efficacy. Success in addressing this urgent problem will only be achieved through collaboration among multiple stakeholders.
Epidemiological characterization of ostomized patients attended in referral Center from the city of Maceió, Alagoas, Brazil
Authors: de Freitas Lins Neto Manoel Álvaro , de Araújo Fernandes Danillo Omena , Didoné Eveline Leite
Published: March 2016

Introduction Several clinical conditions imply the realization of a bowel ostomy, as a treatment option. However, the presence of a stoma is an important limitation in the quality of life of the ostomized patient.

Aim To define the epidemiological profile of patients enrolled in the Ostomy Program from two reference services in the city of Maceió, Alagoas, regarding gender, age, classification (as permanent or temporary), type of ostomy with respect to the bowel segment used, and causes.

Method This was a descriptive cross-sectional study whose data were obtained from registration forms of active patients in Ostomy Programs on May 2013.

Results Of 216 patients analyzed, 50.5% were female and 49.5% male. The age group with the highest number of cases was that between 60 and 69 years (23.6%) and the average age was 51.3 years. Colostomies accounted for 89.4% of the procedures performed, and 56.9% of procedures were temporary ostomies. As for the cause, the most prevalent was colorectal cancer (40.7%), followed by trauma (18.1%) and acute abdomen (12.0%).

Conclusion The study provides relevant data that can be used as input for prevention and strategies to improve the health of the ostomized population.
Vulvodynia: Assessment and Treatment
Authors: Goldstein Andrew T. , Pukall Caroline F. , Brown Candace , Bergeron Sophie , Stein Amy , Kellogg-Spadt Susan
Published: March 2016

Introduction

Vulvodynia constitutes a highly prevalent form of sexual pain in women, and current information regarding its assessment and treatment is needed.

Aim

To update the scientific evidence published in 2010, from the Third International Consultation on Sexual Medicine, pertaining to the assessment and treatment of women's sexual pain.

Methods

An expert committee, as part of the Fourth International Consultation on Sexual Medicine, was comprised of researchers and clinicians from biological and social science disciplines for the review of the scientific evidence on the assessment and treatment of women's genital pain.

Main Outcome Measures

A review of assessment and treatment strategies involved in vulvodynia.

Results

We recommend the following treatments for the management of vulvodynia: psychological interventions, pelvic floor physical therapy, and vestibulectomy (for provoked vestibulodynia). We also support the use of multidisciplinary treatment approaches for the management of vulvodynia; however, more studies are needed to determine which components are most important. We recommend waiting for more empirical evidence before recommending alternative treatment options, anti-inflammatory agents, hormonal agents, and anticonvulsant medications. Although we do not recommend lidocaine, topical corticosteroids, or antidepressant medication for the management of vulvodynia, we suggest that capsaicin, botulinum toxin, and interferon be considered second-line avenues and that their recommendation be revisited once further research is conducted.

Conclusion

A comprehensive assessment is needed to understand the pain experience of women presenting with vulvodynia. In addition, treatment typically progresses from less invasive to more invasive, and several treatment options are worth pursuing.
Ethical and Sociocultural Aspects of Sexual Function and Dysfunction in Both Sexes
Authors: Atallah Sandrine , Johnson-Agbakwu Crista , Rosenbaum Talli , Abdo Carmita , Byers E. Sandra , Graham Cynthia , Nobre Pedro , Wylie Kevan , Brotto Lori
Published: March 2016

Aims

This study aimed to highlight the salient sociocultural factors contributing to sexual health and dysfunction and to offer recommendations for culturally sensitive clinical management and research as well for an ethically sound sexual health care, counseling and medical decision-making.

Background

There are limited data on the impact of sociocultural factors on male and female sexual function as well as on ethical principles to follow when clinical care falls outside of traditional realms of medically indicated interventions.

Methods

This study reviewed the current literature on sociocultural and ethical considerations with regard to male and female sexual dysfunction as well as cultural and cosmetic female and male genital modification procedures.

Results

It is recommended that clinicians evaluate their patients and their partners in the context of culture and assess distressing sexual symptoms regardless of whether they are a recognized dysfunction. Both clinicians and researchers should develop culturally sensitive assessment skills and instruments. There are a number of practices with complex ethical issues (eg, female genital cutting, female and male cosmetic genital surgery). Future International Committee of Sexual Medicine meetings should seek to develop guidelines and associated recommendations for a separate, broader chapter on ethics.
Effects of Tadalafil Once-Daily or On-Demand vs Placebo on Return to Baseline Erectile Function After Bilateral Nerve-Sparing Radical Prostatectomy – Results from a Randomized Controlled Trial (REACTT)
Authors: Mulhall John P. , Brock Gerald , Oelke Matthias , Fode Mikkel , Probst Kai A. , Henneges Carsten , d'Anzeo Gianluca , Rossi Andrea , Büttner Hartwig
Published: March 2016

Introduction and Aim

The multicenter, randomized, double-blind, double-dummy, placebo-controlled REACTT trial suggested that treatment with tadalafil once daily (OaD) started early after bilateral nerve-sparing radical prostatectomy (nsRP) for prostate cancer may contribute to erectile function (EF)-recovery, which was predefined as achieving an International Index of Erectile Function (IIEF)-EF score ≥22. Here, we report descriptive post-hoc analyses, using the more strict definition for EF-recovery of returning back to the pre-surgery IIEF-EF-level (“back-to-baseline analysis”).

Methods

REACTT included 422 men <68 years with adenocarcinoma of the prostate and preoperative IIEF-EF ≥22 who underwent nsRP at 50 centers from 9 European countries and Canada. Patients were randomized post-nsRP 1:1:1 to 9-month double-blind treatment (DBT) with tadalafil 5 mg OaD (n = 139), tadalafil 20 mg on-demand (pro-re-nata, PRN; n = 142), or placebo (n = 141), followed by 6-week drug-free washout (DFW) and 3-month open-label tadalafil OaD treatment (OLT).

Main Outcome Measures

Proportion of patients returning to their preoperative IIEF-EF category (22–25 or ≥26) at the end of DBT, DFW, and OLT.

Results

Overall, 92.4% of patients had pre-surgery (baseline) IIEF-EF scores ≥26 (tadalafil OaD 94.2%, PRN 91.6%, placebo 91.5%), 7.4% had IIEF-EF 22–25. At the end of DBT, 22.3% of patients on tadalafil OaD had achieved “back-to-baseline” IIEF-EF, compared with 11.3% on tadalafil PRN and 7.8% on placebo. Of all 58 patients “back-to-baseline” at the end of DBT, only 1 PRN-group patient had started from a baseline IIEF-EF <26. The treatment-group difference at the end of DBT was not maintained after DFW. After 3 months of OLT with tadalafil OaD, the proportion of patients with “back-to-baseline” IIEF-EF had almost doubled in all 3 groups.

Conclusion

Changing the definition for EF-recovery from IIEF-EF ≥22 to the more strict definition of “returning back-to-baseline IIEF-EF” had no major impact. Tadalafil OaD started early after nsRP improved drug-assisted EF, but had no effect on unassisted EF following treatment cessation after 9 months.
Erectile Function Recovery After Nerve-Sparing Radical Prostatectomy for Prostate Cancer: Is Back to Baseline Status Enough for Patient Satisfaction?
Authors: Rossi Martina Sofia , Moschini Marco , Bianchi Marco , Gandaglia Giorgio , Fossati Nicola , Dell'Oglio Paolo , Schiavina Riccardo , Brunocilla Eugenio , Farina Elena , Picozzi Marta , Salonia Andrea , Montorsi Francesco , Briganti Alberto
Published: March 2016

Introduction

Several definitions of erectile function (EF) recovery after bilateral nerve-sparing radical prostatectomy (BNSRP) have been proposed based on the results of the International Index of EF (IIEF).

Aim

We aimed at evaluating overall satisfaction (OS) after BNSRP according to the ability to achieve the pretreatment EF.

Methods

We evaluated data of 652 patients treated with BNSRP for clinically localized prostate cancer (PCa). Erectile dysfunction (ED) was classified according to the IIEF-EF domain score. Return to baseline EF was defined as patients who reached the same preoperative ED category during the 3-year follow-up. Cox regression analyses were fitted to predict return to baseline IIEF-EF and to predict OS defined according to the IIEF-OS in the overall population. Logistic regression analyses were performed to analyze OS in men who reached the back to baseline status.

Main Outcome Measures

The outcome of the study was to evaluate back to baseline EF status and to correlate it with postoperative OS.

Results

Preoperative satisfaction was reported by 218 (33.4%) patients. Postoperative satisfaction was achieved by 103 patients. Overall, 383 patients were able to achieve the preoperative IIEF-EF score. However, only 26.9% reported being satisfied. Age and preoperative IIEF-EF score were significantly associated with baseline IIEF-EF recovery (all P ≤ .02). Patients who were able to return to baseline IIEF-EF were more likely to be satisfied (P < .001). Time elapsed between surgery and achievement of baseline IIEF-EF was significantly associated with OS (P < .001). Among patients who were able to achieve the baseline IIEF-EF score, a preoperative IIEF-EF of 22–25 and 26–30 was significantly associated with postoperative satisfaction (all P < .001).

Conclusion

After BNSRP, reaching the baseline IIEF-EF score is not always sufficient to obtain patient satisfaction. Only patients with a preoperative IIEF-EF ≥22 who reached the baseline score after surgery considered themselves satisfied. This should be taken into account in preoperative patient counseling.
2015 ISSVD, ISSWSH, and IPPS Consensus Terminology and Classification of Persistent Vulvar Pain and Vulvodynia
Authors: Bornstein Jacob , Goldstein Andrew T. , Stockdale Colleen K. , Bergeron Sophie , Pukall Caroline , Zolnoun Denniz , Coady Deborah ,   International Society for the Study of Vulvovaginal Disease (ISSVD)
Published: March 2016

Introduction

In 2014, the Executive Council of the International Society for the Study of Vulvovaginal Disease (ISSVD), the Boards of Directors of the International Society for the Study of Women's Sexual Health (ISSWSH), and the International Pelvic Pain Society (IPPS) acknowledged the need to revise the current terminology of vulvar pain, based on the significant increase in high quality etiologic studies published in the last decade.

Methods

The new terminology was achieved in four steps. The first involved a terminology consensus conference with representatives of the three societies, held in April 2015. Then, an analysis of the relevant published studies was used to establish a level of evidence for each factor associated with vulvodynia. The terminology was amended based on feedback from members of the societies. Finally, each society's board accepted the new terminology.

Results and Conclusion

In 2015, the ISSVD, ISSWSH, and IPPS adopted a new vulvar pain and vulvodynia terminology that acknowledges the complexity of the clinical presentation and pathophysiology involved in vulvar pain and vulvodynia, and incorporates new information derived from evidence-based studies conducted since the last terminology published in 2003.
Hitting the Slopes
Authors: Yan Wudan
Published: March 2016

Researchers investigate whether rain droplets alone can cause enough erosion to impact the shapes of hills.
Upcoming Arctic Summit to Include Focus on Climate Change
Authors: Showstack Randy
Published: March 2016

U.S. initiatives aim to protect the marine environment and address climate change in the Arctic, U.S. ambassador says.
Genotoxic effects of X-rays in buccal mucosal cells in children subjected to dental radiographs
Authors: Preethi Naveena , Chikkanarasaiah Nagarathna , Bethur Shakuntala S
Published: March 2016

Objectives/Aims:

Bitewing and digital dental panoramic radiographs have become important adjuvants for successful dental practice in pediatric dentistry. Both methods lead to genetic changes in the oral buccal epithelium that have not yet been satisfactorily explored. The aim of the present study was to evaluate the genotoxic effects induced by X-ray radiation from bitewing and panoramic dental radiography in exfoliated buccal epithelial cells of children, using the Buccal Micronucleus Cytome assay.

Materials and Methods:

Children (n=40) who met the inclusion criteria and provided signed informed consent were included in the study. Children were selected for undergoing bitewing radiographs (group 1; n=20) or digital dental panoramic radiographs (group 2; n=20). Exfoliated buccal mucosal cells were obtained by scraping the right/left buccal mucosa with a wooden spatula immediately before the X-ray exposure and 10±2 days after exposure.

Results:

The frequency of micronuclei increases significantly post exposure to both bitewing and digital dental panoramic radiography in children, but the frequency was higher in bitewing radiographs.

Conclusion:

It was concluded that the frequency of micronuclei increases post exposure to both bitewing and digital panoramic radiographs. Increased radiation exposure results in an increase in micronuclei frequency.
Optically controlled magnetic-field etching on the nano-scale
Authors: Yatsui Takashi , Tsuboi Toshiki , Yamaguchi Maiku , Nobusada Katsuyuki , Tojo Satoshi , Stehlin Fabrice , Soppera Olivier , Bloch Daniel
Published: March 2016

Electric and magnetic fields play an important role in both chemical and physical reactions. However, since the coupling efficiency between magnetic fields and electrons is low in comparison with that between electric fields and electrons in the visible wavelength region, the magnetic field is negligible in photo-induced reactions. Here, we performed photo-etching of ZrO2 nano-stripe structures, and identified an etching-property polarisation dependence. Specifically, the etching rate and etched profiles depend on the structure width. To evaluate this polarisation-dependent etching, we performed numerical calculations using a finite-difference time-domain method. Remarkably, the numerical results revealed that the polarisation-dependent etching properties were determined by the magnetic field distributions, rather than the electric field distributions. As nano-scale structures induce a localised magnetic field, the discovery of this etching dependence on the magnetic field is expected to introduce a new perspective on advanced nano-scale structure fabrication.
Spectral dependence of direct and trap-mediated recombination processes in lead halide perovskites using time resolved microwave conductivity
Authors: Guse Joanna A. , Soufiani Arman M. , Jiang Liangcong , Kim Jincheol , Cheng Yi-Bing , Schmidt Timothy W. , Ho-Baillie Anita , McCamey Dane R.
Published: March 2016

Elucidating the decay mechanisms of photoexcited charge carriers is key to improving the efficiency of solar cells based on organo-lead halide perovskites.
Selective detection of Escherichia coli DNA using fluorescent carbon spindles
Authors: Roy Anurag , Chatterjee Sabyasachi , Pramanik Srikrishna , Devi Parukuttyamma Sujatha , Suresh Kumar Gopinatha
Published: March 2016

We report here the selective and sensitive detection of Escherichia coli (E. coli) DNA using fluorescent carbon spindles leading to the enhancement of fluorescence.
The effect of hypoxia and laminin-rich substrates on the proliferative behavior of human neural stem cells
Authors: Sharee Ghourichaee Sasan , Leach Jennie B.
Published: March 2016

Human neural stem cells cultured on laminin and Matrigel under hypoxia significantly increase both the stem cell density and the percentage of activity proliferating cells.
Interfacial adhesion enhancement of ink-jet printed transparent metallic grid electrodes induced by the coffee-ring effect
Authors: Zhang Zhiliang , Liu Jun
Published: March 2016

An effective strategy was developed to regulate the surface characteristics of silver nanoparticles and enormously enhance interfacial adhesion between transparent metal grids and substrates based on the coffee-ring effect.
An iron-based thin film as a highly efficient catalyst for electrochemical water oxidation in a carbonate electrolyte
Authors: Li Fei , Bai Lichen , Li Hua , Wang Yong , Yu Fengshou , Sun Licheng
Published: March 2016

An iron-based thin film electrodeposited from a CO2 saturated bicarbonate solution showed remarkable activity with a Tafel slope as low as 34 mV dec−1 in a HCO3−/CO32− electrolyte.
An electrochemical peptide cleavage-based biosensor for matrix metalloproteinase-2 detection with exonuclease III-assisted cycling signal amplification
Authors: Wang Ding , Yuan Yali , Zheng Yingning , Chai Yaqin , Yuan Ruo
Published: March 2016

An electrochemical peptide biosensor was developed for matrix metalloproteinase-2 detection based on target induced cleavage of a peptide with exonuclease III-assisted cycling signal amplification.
Three orders of magnitude enhancement of proton conductivity of porous coordination polymers by incorporating ion-pairs into a framework
Authors: You Ya-Wen , Xue Chen , Tian Zheng-Fang , Liu Shao-Xian , Ren Xiao-Ming
Published: March 2016

A clathrate NH4Br@HKUST-1 shows three orders of magnitude enhancement of proton conductivity regarding HKUST-1.
Biomimetic synthesis of needle-like fluorescent calcium phosphate/carbon dot hybrid composites for cell labeling and copper ion detection
Authors: Guo Shanshan , Lu Shousi , Xu Pingxiang , Ma Yi , Zhao Liang , Zhao Yuming , Gu Wei , Xue Ming
Published: March 2016

We report a biomimetic method to synthesize needle-like calcium phosphate (CaP) using carbon dots (CDs) and sodium carboxymethylcellulose as dual templates. The CaP/CDs were capable of cell labeling and selective detection of copper ions in drinking water.
A rate equation theory for the pore size distribution of calcined CaCO3 in calcium looping
Authors: Li Z. S. , Liang P. T. , Cai N. S.
Published: March 2016

CaCO3 calcination is an important step in calcium looping, and the formed pore structure of porous CaO is critical for subsequent carbonation towards carbon dioxide. Therefore, it is necessary to investigate the evolution of the pore structure of the sorbent in the calcination step. A mathematical model describing the pore size distribution during the calcination of the CaCO3 particle was developed. CaCO3 calcination is calculated following a shrinking core model at the CaO–CaCO3 interface, and CO2 diffuses through the porous CaO layers. During the decomposition of CaCO3, after the departure of the CO2 molecule from its original lattice, a vacancy will be formed that will diffuse inside the solid, and the collision and coagulation of the vacancy results in pore formation. A rate equation theory was proposed to describe the vacancy coagulation and pore evolution inside the solid, with rate expressions derived for the pore size distribution function with time evolution. To validate the developed model, the evolution of the pore size distribution during CaCO3 calcination was experimentally measured in a high-temperature furnace combined with the nitrogen adsorption method. It was found that there is a characteristic bimodal distribution for the pore structure of calcined CaCO3, with average pore sizes of ∼2.8 nm and ∼50 nm. The calculated results agree well with the experimental data, and the relative importance of growth and coagulation was discussed.
Two-dimensional self-assembly of benzotriazole on an inert substrate
Authors: Grillo F. , Garrido Torres J. A. , Treanor M.-J. , Larrea C. R. , Götze J. P. , Lacovig P. , Früchtl H. A. , Schaub R. , Richardson N. V.
Published: March 2016

Fine tuning of experimental conditions allows dimensional control of benzotriazole species adsorbed on Au(111), revealing a subtle interplay between H-bonding, vdW inter-adsorbate and surface-adsorbate interactions, as highlighted both experimentally and theoretically.
Diastereoselective and regiodivergent oxa-[3 + 2] cycloaddition of Achmatowicz products and cyclic 1,3-dicarbonyl compounds
Authors: Yu Jingxun , Ma Haichen , Yao Hongliang , Cheng Hang , Tong Rongbiao
Published: March 2016

Development of two novel oxa-[3 + 2] cycloaddition reactions of Achmatowicz products with 1,3-dicarbonyl compounds for rapid and highly efficient assembly of polycyclic furopyranones is described. Plausible mechanisms were proposed.
Surface functionalization of polymer substrates with hydroxyapatite using polymer-binding peptides
Authors: Iijima Kazutoshi , Nagahama Hiroumi , Takada Akari , Sawada Toshiki , Serizawa Takeshi , Hashizume Mineo
Published: March 2016

Polymer substrates were modified with hydroxyapatite (HAp) using two bi-functional peptides consists of polymer-binding peptide and triasparate for HAp mineralization in simulated body fluids and HAp-binding peptide for immobilization HAp nanoparticles.
Trace level detection of nitroanilines using a solution processable fluorescent porous organic polymer
Authors: Deshmukh Arundhati , Bandyopadhyay Sujoy , James Anto , Patra Abhijit
Published: March 2016

Sensitive detection of environmentally hazardous nitroanilines, especially p-nitroaniline in solution as well as in contact mode, was achieved employing a solution processable fluorescent porous organic polymer.
Insights into the DNA-binding mechanism of a LytTR-type transcription regulator
Authors: Behr Stefan , Heermann Ralf , Jung Kirsten
Published: March 2016

Most bacterial response regulators (RRs) make contact with DNA through a recognition α-helix in their DNA-binding domains. An emerging class of RRs interacts with DNA via a relatively novel type of binding domain, called the LytTR domain, which is mainly composed of β-strands. YpdB belongs to this latter class, is part of a nutrient-sensing network in Escherichia coli and triggers expression of its only target gene, yhjX, in response to extracellular pyruvate. Expression of yhjX mainly occurs in the late exponential growth phase, and in a pulsed manner. Although the DNA-binding sites for YpdB are well defined, exactly how YpdB initiates pulsed gene expression has remained elusive. To address this question, we measured the binding kinetics of wild-type YpdB and the phosphomimetic variant YpdB-D53E to the yhjX promoter region (PyhjX) using surface plasmon resonance (SPR) spectroscopy combined with interaction map® (IM) analysis. Both YpdB and YpdB-D53E bound as monomers to the tandem-repeat sequences in the promoter, with YpdB-D53E displaying a higher maximal binding rate than YpdB. Furthermore, we identified a high-affinity (A-site) and a low-affinity binding site (B-site) within the yhjX promoter. Only YpdB-D53E utilizes an ‘AB-BA’ DNA-binding mechanism, involving sequential and cooperative promoter binding, and rapid, successive promoter clearance. We propose that response regulator phosphorylation, in combination with the cycle of cooperative DNA binding and rapid promoter clearance just described, can account for pulsed gene expression.
A compositional framework for Markov processes
Authors: Baez John C. , Fong Brendan , Pollard Blake S.
Published: March 2016

We define the concept of an “open” Markov process, or more precisely, continuous-time Markov chain, which is one where probability can flow in or out of certain states called “inputs” and “outputs.” One can build up a Markov process from smaller open pieces. This process is formalized by making open Markov processes into the morphisms of a dagger compact category. We show that the behavior of a detailed balanced open Markov process is determined by a principle of minimum dissipation, closely related to Prigogine’s principle of minimum entropy production. Using this fact, we set up a functor mapping open detailed balanced Markov processes to open circuits made of linear resistors. We also describe how to “black box” an open Markov process, obtaining the linear relation between input and output data that holds in any steady state, including nonequilibrium steady states with a nonzero flow of probability through the system. We prove that black boxing gives a symmetric monoidal dagger functor sending open detailed balanced Markov processes to Lagrangian relations between symplectic vector spaces. This allows us to compute the steady state behavior of an open detailed balanced Markov process from the behaviors of smaller pieces from which it is built. We relate this black box functor to a previously constructed black box functor for circuits.
Spatial configurations of charged rod-like particles in external electric field
Authors: Lisina I. , Lisin E. , Vaulina O.
Published: March 2016

Formation of different spatial configurations for system of charged rod-like particles is considered theoretically and numerically, including formation of layered structures in the external electric field. Analytical model for a determination of the angle between the axis of a rod and the symmetry axis of electric trap is presented. New algorithm is proposed here for a dynamical simulation of many interacting non-spherical particles. Conditions for a correct replacement of the interaction between uniformly charged rods by the interaction of “bipoles” (i.e., by two similar point charges) are obtained. Study was performed in a wide range of parameters that are similar to conditions of laboratory experiments in a dusty plasma.
Real-space pseudopotential study of vibrational properties and Raman spectra in Si–Ge core-shell nanocrystals
Authors: Bobbitt N. Scott , Chelikowsky James R.
Published: March 2016

We examine the vibrational properties and Raman spectra of Si–Ge core-shell nanostructures using real-space pseudopotentials constructed within density functional theory. Our method uses no empirical parameters, unlike many popular methods for predicting Raman spectra for nanocrystals. We find the dominant features of the Raman spectrum for the Si–Ge core-shell structure to be a superposition of the Raman spectra of the Ge and Si nanocrystals with optical peaks around 300 and 500 cm−1, respectively. We also find a Si–Ge “interface” peak at 400 cm−1. The Ge shell causes the Si core to expand from the equilibrium structure. This strain induces significant redshift in the Si contribution to the vibrational and Raman spectra, while the Ge shell is largely unstrained and does not exhibit this shift. We find that the ratio of peak heights is strongly related to the relative size of the core and shell regions. This finding suggests that Raman spectroscopy may be used to characterize the size of the core and shell in these structures.
Fluids density functional theory and initializing molecular dynamics simulations of block copolymers
Authors: Brown Jonathan R. , Seo Youngmi , Maula Tiara Ann D. , Hall Lisa M.
Published: March 2016

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.
Automated microwave double resonance spectroscopy: A tool to identify and characterize chemical compounds
Authors: Martin-Drumel Marie-Aline , McCarthy Michael C. , Patterson David , McGuire Brett A. , Crabtree Kyle N.
Published: March 2016

Owing to its unparalleled structural specificity, rotational spectroscopy is a powerful technique to unambiguously identify and characterize volatile, polar molecules. We present here a new experimental approach, automated microwave double resonance (AMDOR) spectroscopy, to rapidly determine the rotational constants of these compounds without a priori knowledge of elemental composition or molecular structure. This task is achieved by rapidly acquiring the classical (frequency vs. intensity) broadband spectrum of a molecule using chirped-pulse Fourier transform microwave (FTMW) spectroscopy and subsequently analyzing it in near real-time using complementary cavity FTMW detection and double resonance. AMDOR measurements provide a unique “barcode” for each compound from which rotational constants can be extracted. To illustrate the power of this approach, AMDOR spectra of three aroma compounds — trans-cinnamaldehyde, α-, and β-ionone — have been recorded and analyzed. The prospects to extend this approach to mixture characterization and purity assessment are described.
Existence of solutions for quasilinear elliptic equations with Hardy potential
Authors: Deng Yinbin , Guo Yuxia , Liu Jiaquan
Published: March 2016

In this paper, we consider the following quasilinear elliptic equation with Hardy potential and Dirichlet boundary condition: −∑i,j=1NDj(aij(x,u)Diu)+12∑i,j=1NDsai,j(x,u)DiuDju−λ|x|−2u=f(x,u)inΩ, where Ω ⊂ ℝN(N ≥ 3) is a smooth bounded domain, Di=∂∂xi,Dsaij(x,s)=∂∂saij(x,s), and 0≤λ<λ∗:=(N−22)2, and λ|x|−2 is called the Hardy potential. By using the perturbation method, we prove the existence of infinitely many solutions for the above problem.
High precision relative attitude measurement for inner payload of new photoelectric platform
Authors: Wang Y. Y. , Wang L. , Bai X. G. , Ma T. W. , Dai M.
Published: March 2016

A new method for measuring the relative attitude of a load on an airborne photoelectric platform supported by three-axis universal joint structure is proposed. The mathematical model for angle measurement is established, based on which the linear relation between the angle and distance is derived by using the eccentric method. Furthermore, the relative attitude measurement method for a load rotating along the yaw and pitch directions is also proposed based on a unique eccentric structure. Finally, to validate the proposed new method, a comprehensive experiment for measurement angle from −5° to +5° in increments of 0.5° was performed by using the angular capacitive sensor. The experimental results show that the precision of the angular measurement is better than 15″ with maximum 1.24 kHz bandwidth, which meets the relative attitude measurement requirements of the internal load on the airborne photoelectric platform.
Microscopic mechanism of the giant magnetocaloric effect in MnCoGe alloys probed by x-ray magnetic circular dichroism
Authors: Guillou F. , Wilhelm F. , Tegus O. , Rogalev A.
Published: March 2016

One important aspect of the magneto-structural transition in MnCoGe-based materials is the reduction in saturation magnetization from the orthorhombic to the hexagonal phase. Here, by combining an element specific magnetization probe such as x-ray magnetic circular dichroism and band structure calculations, we show that the magnetic moment instability between orthorhombic and hexagonal structures originates from a reduction in the Mn sub-lattice magnetization.
Bifurcation, chaos, and scan instability in dynamic atomic force microscopy
Authors: Cantrell John H. , Cantrell Sean A.
Published: March 2016

The dynamical motion at any point on the cantilever of an atomic force microscope can be expressed quite generally as a superposition of simple harmonic oscillators corresponding to the vibrational modes allowed by the cantilever shape. Central to the dynamical equations is the representation of the cantilever-sample interaction force as a polynomial expansion with coefficients that account for the interaction force “stiffness,” the cantilever-to-sample energy transfer, and the displacement amplitude of cantilever oscillation. Renormalization of the cantilever beam model shows that for a given cantilever drive frequency cantilever dynamics can be accurately represented by a single nonlinear mass-spring model with frequency-dependent stiffness and damping coefficients [S. A. Cantrell and J. H. Cantrell, J. Appl. Phys. 110, 094314 (2011)]. Application of the Melnikov method to the renormalized dynamical equation is shown to predict a cascade of period doubling bifurcations with increasing cantilever drive force that terminates in chaos. The threshold value of the drive force necessary to initiate bifurcation is shown to depend strongly on the cantilever setpoint and drive frequency, effective damping coefficient, nonlinearity of the cantilever-sample interaction force, and the displacement amplitude of cantilever oscillation. The model predicts the experimentally observed interruptions of the bifurcation cascade for cantilevers of sufficiently large stiffness. Operational factors leading to the loss of image quality in dynamic atomic force microscopy are addressed, and guidelines for optimizing scan stability are proposed using a quantitative analysis based on system dynamical parameters and choice of feedback loop parameter.
Thickness-dependent dielectric and energy storage properties of (Pb0.96La0.04)(Zr0.98Ti0.02)O3 antiferroelectric thin films
Authors: Pan Hao , Zeng Yi , Shen Yang , Lin Yuan-Hua , Nan Ce-Wen
Published: March 2016

A series of dense and uniform (Pb0.96La0.04)(Zr0.98Ti0.02)O3 (PLZT) thin films with different thicknesses have been deposited on (La2/3Sr1/3)MnO3/SrTiO3 substrates by a modified chemical solution deposition method. Structural and electrical studies indicate that PLZT thin films show single phase composition and typical antiferroelectric (AFE) characteristics. By increasing the film thickness, the dielectric loss of PLZT thin films is reduced and the hysteresis loops are tailored. The energy storage efficiency increases from 56.8% to 74.1%, while a high energy density of ∼20 J/cm3 is maintained under an electric field of 1200 kV/cm. Additionally, the operating frequencies also have distinct influence on the hysteresis loop shape and the energy storage properties, indicating that energy storage performance of AFE thin films can be enhanced by tuning both film thickness and operating frequencies.
Effective medium based optical analysis with finite element method simulations to study photochromic transitions in Ag-TiO2 nanocomposite films
Authors: Abhilash T. , Balasubrahmaniyam M. , Kasiviswanathan S.
Published: March 2016

Photochromic transitions in silver nanoparticles (AgNPs) embedded titanium dioxide (TiO2) films under green light illumination are marked by reduction in strength and blue shift in the position of the localized surface plasmon resonance (LSPR) associated with AgNPs. These transitions, which happen in the sub-nanometer length scale, have been analysed using the variations observed in the effective dielectric properties of the Ag-TiO2 nanocomposite films in response to the size reduction of AgNPs and subsequent changes in the surrounding medium due to photo-oxidation. Bergman-Milton formulation based on spectral density approach is used to extract dielectric properties and information about the geometrical distribution of the effective medium. Combined with finite element method simulations, we isolate the effects due to the change in average size of the nanoparticles and those due to the change in the dielectric function of the surrounding medium. By analysing the dynamics of photochromic transitions in the effective medium, we conclude that the observed blue shift in LSPR is mainly because of the change in the dielectric function of surrounding medium, while a shape-preserving effective size reduction of the AgNPs causes decrease in the strength of LSPR.
Very high quantum efficiency in InAs/GaSb superlattice for very long wavelength detection with cutoff of 21 μm
Authors: Jiang Dongwei , Xiang Wei , Guo Fengyun , Hao Hongyue , Han Xi , Li Xiaochao , Wang Guowei , Xu Yingqiang , Yu Qingjiang , Niu Zhichuan
Published: March 2016

The authors report the dependence of the quantum efficiency on beryllium concentration in the active region of type-II InAs/GaSb superlattice infrared detector with a cutoff wavelength around 21 μm. It is found that the quantum efficiency and responsivity show a clear delineation in comparison to the doping concentration. The quantum efficiency is further improved by gradually doping in the absorbing region. At 77 K, the 50% cutoff wavelength of the VLWIR detector is 18 μm, and the R0A is kept at a stable value of 6 Ω cm2. Different beryllium concentration leads to an increase of an average quantum efficiency in the 8–15 μm window from 35% to 55% with a π-region thickness of 3.0 μm, for Ubias = −0.3 V, and no anti-reflection coating. As for a further result, the quantum efficiency reaches at a maximum value of 66% by gradually doping in the absorbing region with the peak detectivity of 3.33 × 1010 cm Hz1/2/W at 15 μm.
Ultrafast terahertz response in photoexcited, vertically grown few-layer graphene
Authors: Fu Maixia , Quan Baogang , He Jingwen , Yao Zehan , Gu Changzhi , Li Junjie , Zhang Yan
Published: March 2016

The terahertz (THz) response from vertically aligned few-layer graphene samples with and without femtosecond optical excitation was investigated. The frequency-dependent optical conductivity of the photoexcited vertically aligned few-layer graphene had a strong free carrier response. Upon photoexcitation, a transient decrease in THz transmission on the subpicosecond timescale was observed. A modulation depth of nearly 16% was demonstrated in the range of the photoexcitation power used. The photoinduced ultrafast response presented here is distinct from previous studies on horizontally grown graphene. The mechanism underlying this photoconductive ultrafast response was investigated by measuring the transmission properties and by calculating the carrier density. The results of these studies are promising for the development of high-performance THz modulators and ultrafast switchable THz photoelectric devices.
Temperature dependent characterization of gallium arsenide X-ray mesa p-i-n photodiodes
Authors: Lioliou G. , Meng X. , Ng J. S. , Barnett A. M.
Published: March 2016

Electrical characterization of two GaAs p+-i-n+ mesa X-ray photodiodes over the temperature range 0 °C to 120 °C together with characterization of one of the diodes as an X-ray detector over the temperature range 0 °C to 60 °C is reported as part of the development of photon counting X-ray spectroscopic systems for harsh environments. The randomly selected diodes were fully etched and unpassivated. The diodes were 200 μm in diameter and had 7 μm thick i layers. The leakage current density was found to increase from (3 ± 1) nA/cm−2 at 0 °C to (24.36 ± 0.05) μA/cm−2 at 120 °C for D1 and from a current density smaller than the uncertainty (0.2 ± 1.2) nA/cm−2 at 0 °C to (9.39 ± 0.02) μA/cm−2 at 120 °C for D2 at the maximum investigated reverse bias (15 V). The best energy resolution (FWHM at 5.9 keV) was achieved at 5 V reverse bias, at each temperature; 730 eV at 0 °C, 750 eV at 20 °C, 770 eV at 40 °C, and 840 eV at 60 °C. It was found that the parallel white noise was the main source of the photopeak broadening only when the detector operated at 60 °C, at 5 V, 10 V, and 15 V reverse bias and at long shaping times (>5 μs), whereas the sum of the dielectric noise and charge trapping noise was the dominant source of noise for all the other spectra.
Thermal motion in proteins: Large effects on the time-averaged interaction energies
Authors: Goethe Martin , Fita Ignacio , Rubi J. Miguel
Published: March 2016

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.