bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo bioimaging with tissue-specific transcription factor activated luciferase reporters
Authors: Buckley Suzanne M. K. , Delhove Juliette M. K. M. , Perocheau Dany P. , Karda Rajvinder , Rahim Ahad A. , Howe Steven J. , Ward Natalie J. , Birrell Mark A. , Belvisi Maria G. , Arbuthnot Patrick , Johnson Mark R. , Waddington Simon N. , McKay Tristan R. 
Published: July 2015

AbstractThe application of transcription factor activated luciferase reporter cassettes in vitro is widespread but potential for in vivo application has not yet been realized. Bioluminescence imaging enables non-invasive tracking of gene expression in transfected tissues of living rodents. However the mature immune response limits luciferase expression when delivered in adulthood. We present a novel approach of tissue-targeted delivery of transcription factor activated luciferase reporter lentiviruses to neonatal rodents as an alternative to the existing technology of generating germline transgenic light producing rodents. At this age, neonates acquire immune tolerance to the conditionally responsive luciferase reporter. This simple and transferrable procedure permits surrogate quantitation of transcription factor activity over the lifetime of the animal. We show principal efficacy by temporally quantifying NFκB activity in the brain, liver and lungs of somatotransgenic reporter mice subjected to lipopolysaccharide (LPS)-induced inflammation. This response is ablated in Tlr4−/− mice or when co-administered with the anti-inflammatory glucocorticoid analogue dexamethasone. Furthermore, we show the malleability of this technology by quantifying NFκB-mediated luciferase expression in outbred rats. Finally, we use somatotransgenic bioimaging to longitudinally quantify LPS- and ActivinA-induced upregulation of liver specific glucocorticoid receptor and Smad2/3 reporter constructs in somatotransgenic mice, respectively.
Acoustothermal heating of polydimethylsiloxane microfluidic system
Authors: Ha Byung Hang , Lee Kang Soo , Destgeer Ghulam , Park Jinsoo , Choung Jin Seung , Jung Jin Ho , Shin Jennifer Hyunjong , Sung Hyung Jin 
Published: July 2015

AbstractWe report an observation of rapid (exceeding 2,000 K/s) heating of polydimethylsiloxane (PDMS), one of the most popular microchannel materials, under cyclic loadings at high (~MHz) frequencies. A microheater was developed based on the finding. The heating mechanism utilized vibration damping in PDMS induced by sound waves that were generated and precisely controlled using a conventional surface acoustic wave (SAW) microfluidic system. The refraction of SAW into the PDMS microchip, called the leaky SAW, takes a form of bulk wave and rapidly heats the microchannels in a volumetric manner. The penetration depths were measured to range from 210 μm to 1290 μm, enough to cover most sizes of microchannels. The energy conversion efficiency was SAW frequency-dependent and measured to be the highest at around 30 MHz. Independent actuation of each interdigital transducer (IDT) enabled independent manipulation of SAWs, permitting spatiotemporal control of temperature on the microchip. All the advantages of this microheater facilitated a two-step continuous flow polymerase chain reaction (CFPCR) to achieve the billion-fold amplification of a 134 bp DNA amplicon in less than 3 min.
Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants
Authors: Mao Yanping , Graham David W. , Tamaki Hideyuki , Zhang Tong 
Published: July 2015

AbstractHere we employed quantitative real-time PCR (qPCR) assays for polyphosphate kinase 1 (ppk1) and 16S rRNA genes to assess relative abundances of dominant clades of Candidatus Accumulibacter phosphatis (referred to Accumulibacter) in 18 globally distributed full-scale wastewater treatment plants (WWTPs) from six countries. Accumulibacter were not only detected in the 6 WWTPs performing biological phosphorus removal, but also inhabited in the other 11 WWTPs employing conventional activated sludge (AS) with abundances ranging from 0.02% to 7.0%. Among the AS samples, clades IIC and IID were found to be dominant among the five Accumulibacter clades. The relative abundance of each clade in the Accumulibacter lineage significantly correlated (p < 0.05) with the influent total phosphorus and chemical oxygen demand instead of geographical factors (e.g. latitude), which showed that the local wastewater characteristics and WWTPs configurations could be more significant to determine the proliferation of Accumulibacter clades in full-scale WWTPs rather than the geographical location. Moreover, two novel Accumulibacter clades (IIH and II-I) which had not been previously detected were discovered in two enhanced biological phosphorus removal (EBPR) WWTPs. The results deepened our understanding of the Accumulibacter diversity in environmental samples.
Theory of Molecular Collisions
Authors: Balint-Kurti Gabriel G , Palov Alexander 
Published: July 2015

Almost 100 years have passed since Trautz and Lewis put forward their collision theory of molecular processes. Today, knowledge of molecular collisions forms a key part of predicting and understanding chemical reactions.
This book begins by setting out the classical and quantum theories of atom-atom collisions. Experimentally observable aspects of the scattering processes; their relationship to reaction rate constants and the experimental methods used to determine them are described. The quantum mechanical theory of reactive scattering is presented and related to experimental observables. The role of lasers in the measurement and analysis of reactive molecular collisions is also discussed.
Written with postgraduates and newcomers to the field in mind, mathematics is kept to a minimum, and readers are guided to appendices and further reading to gain a deeper understanding of the mathematics involved.
Textile antenna with EBG structure for body surface wave enhancement
Authors: Tak Jinpil , Hong Youngtaek , Choi Jaehoon 
Published: July 2015

A textile antenna with an electric bandgap (EBG) structure for body surface wave enhancement is proposed. The proposed antenna is composed of a centre‐fed circular patch to generate the TM01 mode and an EBG structure near the patch to guide the TM wave along the horizontal surface (θ = 90°). Considering the wearability, the antenna has been fabricated using only textile materials such as conductive textiles, conductive thread, and a leather substrate, and has an enhanced radiated field along the surface direction in the 5.8 GHz industrial, scientific, and medical (ISM) band for on‐body communication. The proposed antenna has a diameter of 1.98λ0 and a thickness of 0.058λ0 at 5.8 GHz.
The chemical structure of the ZnO/SiC heterointerface as revealed by electron spectroscopies
Authors: Mu Rui , Steigert Alexander , Lin Nanying , Wilks Regan , Bär Marcus , Zhang Yufeng 
Published: July 2015

Abstract
ZnO layers were deposited on 6H-SiC single crystalline wafers by radio frequency magnetron sputtering. The chemical structure of the ZnO/SiC interface was studied by x-ray photoelectron and x-ray excited Auger electron spectroscopy. A complex chemical structure, involving not only silicon–carbon and zinc–oxygen bonds but also silicon–oxygen and zinc–silicon–oxygen bonds was revealed to form at the ZnO/SiC interface. Based on the comparison with the presumably inert (i.e. chemically abrupt) ZnO/Mo interface, it was concluded that a willemite-like zinc silicate (i.e. Zn2SiO4) interface species develops between ZnO and SiC. The presence of this species at the ZnO/SiC interface will affect the electronic structure of the heterojunction and thus needs to be considered for device optimization.
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
Authors: Das Sayoni , Lee David , Sillitoe Ian , Dawson Natalie L. , Lees Jonathan G. , Orengo Christine A. 
Published: July 2015

Abstract
Motivation: Computational approaches that can predict protein functions are essential to bridge the widening function annotation gap especially since &lt;1.0% of all proteins in UniProtKB have been experimentally characterized. We present a domain-based method for protein function classification and prediction of functional sites that exploits functional sub-classification of CATH superfamilies. The superfamilies are sub-classified into functional families (FunFams) using a hierarchical clustering algorithm supervised by a new classification method, FunFHMMer.
Results: FunFHMMer generates more functionally coherent groupings of protein sequences than other domain-based protein classifications. This has been validated using known functional information. The conserved positions predicted by the FunFams are also found to be enriched in known functional residues. Moreover, the functional annotations provided by the FunFams are found to be more precise than other domain-based resources. FunFHMMer currently identifies 110 439 FunFams in 2735 superfamilies which can be used to functionally annotate &gt; 16 million domain sequences.
Availability and implementation: All FunFam annotation data are made available through the CATH webpages (http://www.cathdb.info). The FunFHMMer webserver (http://www.cathdb.info/search/by_funfhmmer) allows users to submit query sequences for assignment to a CATH FunFam.
Contact: sayoni.das.12@ucl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Error filtering, pair assembly and error correction for next-generation sequencing reads
Authors: Edgar Robert C. , Flyvbjerg Henrik 
Published: July 2015

Abstract
Motivation: Next-generation sequencing produces vast amounts of data with errors that are difficult to distinguish from true biological variation when coverage is low.
Results: We demonstrate large reductions in error frequencies, especially for high-error-rate reads, by three independent means: (i) filtering reads according to their expected number of errors, (ii) assembling overlapping read pairs and (iii) for amplicon reads, by exploiting unique sequence abundances to perform error correction. We also show that most published paired read assemblers calculate incorrect posterior quality scores.
Availability and implementation: These methods are implemented in the USEARCH package. Binaries are freely available at http://drive5.com/usearch.
Contact: robert@drive5.com
Supplementary information: Supplementary data are available at Bioinformatics online.
The center for causal discovery of biomedical knowledge from big data
Authors: Cooper Gregory F , Bahar Ivet , Becich Michael J , Benos Panayiotis V , Berg Jeremy , Espino Jessi , Glymour Clark , Jacobson Rebecca Crowley , Kienholz Michelle , Lee Adrian V , Lu Xinghua , Scheines Richard ,   and the Center for Causal Discovery team
Published: July 2015

Abstract
The Big Data to Knowledge (BD2K) Center for Causal Discovery is developing and disseminating an integrated set of open source tools that support causal modeling and discovery of biomedical knowledge from large and complex biomedical datasets. The Center integrates teams of biomedical and data scientists focused on the refinement of existing and the development of new constraint-based and Bayesian algorithms based on causal Bayesian networks, the optimization of software for efficient operation in a supercomputing environment, and the testing of algorithms and software developed using real data from 3 representative driving biomedical projects: cancer driver mutations, lung disease, and the functional connectome of the human brain. Associated training activities provide both biomedical and data scientists with the knowledge and skills needed to apply and extend these tools. Collaborative activities with the BD2K Consortium further advance causal discovery tools and integrate tools and resources developed by other centers.
Stressful Life Events in Children With Functional Defecation Disorders
Authors: Philips Elise M. , Peeters Babette , Teeuw Arianne H. , Leenders Arnold G.E. , Boluyt Nicole , Brilleslijper‐Kater Sonja N. , Benninga Marc A. 
Published: July 2015

ABSTRACTObjectives:The aim of the study was to determine the prevalence of stressful life events including (sexual) abuse in children with functional defecation disorders by performing a systematic review.Methods:We searched MEDLINE, EMBASE, and PsycINFO for cohort, case‐control and cross‐sectional studies investigating the prevalence of stressful life events, including (sexual) abuse in children with functional defecation disorders.Results:The search yielded 946 articles, of which 8 were included with data from 654 children with functional constipation and 1931 children with (constipation‐associated) fecal incontinence (FI). Overall, children with functional defecation disorders had been significantly more exposed to stressful life events than healthy children, with prevalence rates ranging from 1.6% to 90.9%. Being bullied, being a relational victim, interruption of toilet training, punishment by parents during toilet training, and hospitalization were significantly related to FI, whereas separation from the best friend, failure in an examination, severe illness in a close family member, loss of job by a parent, frequent punishment, and living in a war‐affected area were significantly related to constipation. Only 1 study measured the prevalence of child abuse, which reported a significantly higher prevalence of child (sexual) abuse in children with FI compared with controls.Conclusions:The prevalence of stressful life events, including (sexual) abuse is significantly higher in children with functional defecation disorders compared with healthy children. To gain more insight into the true prevalence of child (sexual) abuse in children with functional defecation disorders, more studies are clearly needed.
Baseline Characteristics and Disease Phenotype in Inflammatory Bowel Disease
Authors: Müller Katalin E. , Lakatos Peter L. , Kovacs Judit B. , Arato Andras , Varkonyi Agnes , Nemes Eva , Tarnok Andras , Toth Gergely , Papp Maria , Solyom Eniko , Horvath Agnes , Guthy Ildiko , Kovacs Marta ,   Hungarian Pediatric IBD Registry Group, Veres Gabor 
Published: July 2015

ABSTRACTObjectives:Predicting short‐term relapses and long‐term prognosis is of utmost importance in paediatric inflammatory bowel disease (IBD). Our aim was to investigate the short‐term disease outcome and medication during the first year in a paediatric incident cohort from Hungary. In addition, association laboratory markers and disease activity indices with short‐term disease outcome and medication were analysed.Methods:From January 1, 2008 to December 31, 2010, demographic data and clinical characteristics of newly diagnosed paediatric patients with IBD <18 years of age were prospectively recorded.Results:A total of 420 patients were identified (Crohn disease [CD] 266 and ulcerative colitis [UC] 124). Initially, 48% (124/256) of the patients with CD had moderate‐to‐severe disease (Pediatric Crohn's Disease Activity Index [PCDAI] >31), and this rate decreased to 2.1% at 1‐year follow‐up. Proportion of patients with UC with moderate‐to‐severe disease (Pediatric Ulcerative Colitis Activity Index >35) at diagnosis declined from 57.5% (69/120) to 6.8% at 1‐year follow‐up. Terminal ileal involvement correlated with higher initial C‐reactive protein (CRP) (P = 0.021) and initial PCDAI (P = 0.026). In UC, elevated CRP (P = 0.002) was associated with disease extension. CRP and PCDAI at diagnosis were associated with the need for immunomodulators at 1 year in children with CD. Initial CRP was also associated with the need for immunomodulators in patients with UC at 1‐year follow‐up.Conclusions:At diagnosis, half of the patients with IBD had moderate‐to‐severe disease, and this rate decreased to <10% after 1 year. Initial CRP and PCDAI were related to the need for aggressive therapy in CD.
Malignant Eccrine Spiradenoma of the Face
Authors: Nyame Theodore T. , Mattos David , Lian Christine G. , Granter Scott R. , Laga Alvaro C. , Caterson E.J. 
Published: July 2015

Abstract
Malignant eccrine spiradenoma, or spiradenocarcinoma, is an exceedingly rare sweat-gland tumor, with only 102 reported cases. Low-grade carcinomas are especially rare with only a few cases reported. Because of the limited number of case reports, the biologic behavior of low-grade malignant eccrine spiradenoma is poorly understood and no evidence-based therapeutic approach is established. Here, the authors report a 29-year-old woman who presented with a history of left-sided facial lesions present since the age of 2 months. Histopathologic examination revealed multiple benign spiradenomas, several of which showed foci of low-grade malignant transformation evidenced by loss of the characteristic 2-cell population seen in the benign tumor component. Included are the clinical presentation, histopathologic description, and surgical decision making in an effort to guide recognition of this rare entity.
Comparison of the Effects of Low-Level Laser Therapy and Ozone Therapy on Bone Healing
Authors: Alan Hilal , Vardi Nigar , Özgür Cem , Hüseyin Ahmet , Yolcu Ümit , Doğan Derya Ozdemir 
Published: July 2015

Abstract
This study aims to compare the effect of low-level laser therapy (LLLT) and ozone therapy on the bone healing. Thirty-six adult male Wistar albino rats were used for this study. Monocortical defects were shaped in right femur of all rats. Defects were filled with nano-hydroxyapatite graft. The animals were divided into 3 groups and each group was than divided into 2 subgroups. Then, LLLT with a diode laser was applied to the first group (G1), ozone therapy was applied to the second group (G2), and no treatment was applied to the third group as a control group (G3). Animals were sacrificed after 4th and 8th weeks and the sections were examined to evaluate the density of the inflammation, the formation of connective tissue, the osteogenic potential, and osteocalcin activity. As a result, there were no significant differences among the groups of 4 weeks in terms of new bone formation. In the immunohistochemical assessment, the number of osteocalcin-positive cells was higher in the laser group compared to the other group of 4 weeks; this difference was statistically significant in the LLLT and ozone groups (P < 0.05). Histomorphometric assessment showed that the new bone areas were higher in the LLLT and ozone groups; furthermore, there was a statistically significant difference in the LLLT in comparison with the control group at 8th week (P < 0.05). At the same time immunohistochemical assessment showed that osteocalcin-positive cells were considerably higher in G2 than G1 at 8th week (P < 0.05). The findings of this study may be the result of differences in the number of treatment sessions. Further studies are therefore needed to determine the optimal treatment modality.
Effect of the Rhinoplasty Technique and Lateral Osteotomy on Periorbital Edema and Ecchymosis
Authors: Kiliç Caner , Tuncel Ümit , Cömert Ela , Şencan Ziya 
Published: July 2015

Aim:
The present study aimed to compare edema and ecchymosis in the early and late postoperative periods following the application of different surgical techniques (open and endonasal) and different types of lateral osteotomy (internal and external).

Methods:
The files and photographs of a total of 120 patients whose records were regularly maintained/updated and who underwent septorhinoplasty operation with the same surgeon were retrospectively evaluated. Sixty-nine (57.5%) patients were women and 51 (43.5%) were men. The patients were divided into 4 different groups according to the operations they underwent as follows—Group I: open technique septorhinoplasty + internal/continuous lateral osteotomy; Group II: endonasal rhinoplasty + internal/continuous lateral osteotomy; Group III: open technique septorhinoplasty + external/perforating lateral osteotomy; and Group IV: endonasal rhinoplasty + external/perforating lateral osteotomy. Postoperative edema and ecchymosis, and lateral nasal wall mucosal damage because of osteotomy were evaluated.

Results:
Postoperative second day edema and ecchymosis scores were statistically significantly better in patients in Group II compared with the patients in Group I (P = 0.010 and P = 0.004, respectively). Postoperative first day edema and postoperative seventh day ecchymosis scores were statistically significantly better in the patients in Group IV compared with the patients in Group III (P = 0.025 and P = 0.011, respectively). Intraoperative bleeding was similar in all groups. The nasal tip was more flexible in patients who underwent closed technique rhinoplasty. Unilateral mucosal damage occurred in 3 patients (4%) with internal lateral osteotomy, whereas no mucosal damage was present in patients with external osteotomy.

Conclusions:
The difference in the rate of edema and ecchymosis in the early postoperative period between the closed technique rhinoplasty and the open surgical approach was statistically significant, whereas osteotomy did not cause a significant difference. According to these results, the authors suggest endonasal surgery to prevent the development of edema and ecchymosis, whereas the choice of lateral osteotomy should be dependent on the experience of the surgeon.
Oval Window Temperature Changes in an Endoscopic Stapedectomy
Authors: Dundar Riza , Bulut Hüsamettin , Güler Osman Kadir , Yükkaldiran Ahmet , Demirtaş Yunus , Iynen Ismail , Bozkuş Ferhat , Kulduk Erkan 
Published: July 2015

Objectives:
Following the initial use of endoscopes in otology, the pros and cons of these instruments have been questioned increasingly. These instruments cause an increase in temperature that needs to be investigated. In this study, the authors aimed to investigate the temperature increase caused by endoscopes and light sources in the perilymph by performing a stapedotomy in an animal model under anesthesia.

Study design:
The study was performed in a guinea pig model.

Methods:
In the animal model, a simulated otologic stapes surgery was performed at room temperature. The body temperatures of the guinea pigs were monitored; the temperature increase caused by the 0-degree rigid endoscopes with diameters of 3 and 4 mm as well as the light sources, including halogen, light-emitting diode (LED), and xenon lamps, were monitored following the stapedotomy to measure and document the continuous temperature increase in the perilymph using sensors placed at the oval window.

Results:
Rigid endoscopes cause a temperature increase in the tympanum regardless of their diameter when used with xenon and halogen light sources. The LED light caused a relatively small temperature increase.

Conclusions:
The endoscopic instruments used in the stapes operation caused a temperature increase in the oval window. The authors concluded that this heat could easily be transmitted to the cochlea by the perilymph, which has obstructed contact with the outer environment following stapedomy, resulting in neurosensorial damage.