bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficiently Converting CO2 into C2H4 using a Porphyrin–Graphene Composite Photocatalyst
Authors: Piao Meihua , Liu Nan , Wang Yanshu , Feng Chunsheng
Published: June 2015

In this work, a photocatalyst consisting of porphyrin and graphene was designed to reduce CO2 to hydrocarbons under visible light. This catalyst can (1) effectively reduce CO2 to hydrocarbons, particularly to C2H4; (2) selectively control the photogenerated electrons transfer path due to the physico-chemical properties of porphyrin and graphene; and (3) reduce the complexity of investigating this photocatalytic process because the photocatalyst has fewer defects, thus preventing the introduction of interference factors.
Satellite tracking of rehabilitated wild Baudin’s cockatoos, Calyptorhynchus baudinii: a feasibility trial to track forest black cockatoos
Authors: Yeap Lian , Shephard Jill M. , Le Souef Anna , Holyoake Carly , Groom Christine , Dawson Rick , Kirkby Tony , Warren Kristin
Published: June 2015

Baudin’s cockatoo, Calyptorhynchus baudinii, is a threatened forest black cockatoo species, endemic to the south-west of Western Australia. In this study we fitted tail-mounted satellite transmitters to two female Baudin’s cockatoos that had undergone treatment and rehabilitation at Perth Zoo and Kaarakin Black Cockatoo Conservation Centre to investigate the feasibility of satellite tracking this species. Both birds were released in Kelmscott, Perth, into an area frequently visited by a flock of wild Baudin’s cockatoos. Both telemetry units provided reliable datasets, with one bird moving ~250 km south from the release site. The success of this trial opens the way to address key objectives in the Forest Black Cockatoo Recovery Plan, including: postrelease survival of rehabilitated birds, flock movement, habitat use, and the identification of critical feeding and breeding habitat. Most importantly, it demonstrates that satellite transmitters can be successfully used to locate and track forest black cockatoo species, which are otherwise difficult to monitor.
Monitoring the use of road-crossing structures by arboreal marsupials: insights gained from motion-triggered cameras and passive integrated transponder (PIT) tags
Authors: Soanes Kylie , Vesk Peter A. , van der Ree Rodney
Published: June 2015

Context Wildlife crossing structures are installed to mitigate the impacts of roads on animal populations, yet little is known about some aspects of their success. Many studies have monitored the use of structures by wildlife, but studies that also incorporate individual identification methods can offer additional insights into their effectiveness. Aims We monitored the use of wildlife crossing structures by arboreal marsupials along the Hume Freeway in south-eastern Australia to (1) determine the species using these structures and their frequency of crossing, (2) determine the number and demographic characteristics of individuals crossing, and (3) use the rate of crossing by individuals to infer the types of movement that occurred. Methods We used motion-triggered cameras to monitor five canopy bridges and 15 glider pole arrays installed at 13 sites along the Hume Freeway. The five canopy bridges were also monitored with passive integrated transponder (PIT)-tag readers to identify the rate of use by individuals. Key results Five species of arboreal marsupial were detected using canopy bridges and glider poles at 11 sites. Our analysis suggested that increasing the number and the distance between poles in a glider pole array reduced the rate of use by squirrel gliders. The PIT tag and camera footage revealed that the structures were used by adult males, adult females and juveniles, suggesting that all demographic groups are capable of using canopy bridges and glider poles. At two canopy bridges, multiple squirrel gliders and common brushtail possums crossed more than once per night. Conclusions Given that previous studies have shown that the freeway is a barrier to movement, and that many of the species detected crossing are subject to road mortality, we conclude that canopy bridges and glider poles benefit arboreal marsupials by providing safe access to resources that would otherwise be inaccessible. Implications Although the factors influencing crossing rate require further study, our analysis suggests that glider pole arrays with fewer poles placed closer together are likely to be more successful for squirrel gliders. The individual identification methods applied here offer insights that are not possible from measuring the rate of use alone and should be adopted in future monitoring studies.
Direct effects of nutrition on behavior: brain-behavior connections.
Authors: Worobey J.
Published: June 2015

This chapter first reviews the structure and development of the central nervous system then provides an overview of the role of nutrients (lipids, fatty acids, macronutrients, micronutrients, polyunsaturated fatty acids, and essential fatty acids) in brain and infant development. It also examines the following associations: polyunsaturated fatty acid supplementation and infant behaviour; cholesterol and adult behaviour; cholesterol and antisocial behaviour; cholesterol and cognitive functioning; and cholesterol-serotonin and brain function.
Bio-behavioral and psychosocial influences on nutrition.
Authors: Tepper B. J.
Published: June 2015

This chapter explores how major biological variables such as sex, age, genetic background and disease influence the nutrition-behaviour paradigm. The major genetic and biological determinants of the nutrition-behavior model are described are discussed together with psychosocial variables. Particular topics discussed include taste perception and preference; genetic taste predispositions; developmental factors and early taste experiences; disease, aging, pregnancy, social interactions and eating attitudes; food availability and cost; and dietary restraint.
Behavioral aspects of overweight and obesity.
Authors: Worobey J.
Published: June 2015

This chapter discusses the history, diagnosis, prevalence, sociological aspects, physiological consequences, psychological characteristics, aetiology (including influences related to energy intake and expenditure), treatment (nutritional, pharmacological, surgical and lifestyle modification), and prevention of overweight and obesity.
Introduction.
Authors: Gross S. , Klemmer L.
Published: June 2015

This chapter presents an overview of the conceptual framework used in this book to examine the tourism transport marketplace. Definitions of tourism and transportation are also presented, before further examining tourism transport.
The whirlwind in the Arab nation, 2014–15: from regime change to state collapse
Authors: Dessouki Ali E. Hillal
Published: June 2015

This article is based on the executive summary of a book in the Arabic language, The State of the Arab Nation 2014–2015, edited by Ali E.Hillal Dessouki and published by the Center for Arab Unity Studies. The book analyzes events in the Arab region from 2014 to the first part of 2015. The chapters examine the international order, the Arab regional system, and domestic conditions in the Arab states and neighbouring countries, such as Turkey and Iran. There is also particular focus on the countries of the Arab Spring and the remaining Arab countries, as well as the outlook for the youth in Arab countries and their role in future. Other chapters consider economic developments and their link to political developments and issues relating to science, technology and digital technologies. The final chapters cover the major political hotspots in the region, namely Palestine, Syria, Iraq, Libya and Yemen. The conclusion points to the main challenges facing the Arab nation in 2015.
Globalization of national journals: investigating the growth of international authorship
Authors: GAZNI Ali
Published: June 2015

This study investigated changes in the internationality of national publishers' journals for the period 1990–2013. The patterns of foreign and interregional authorship in papers and references of 4,199 journals from 3,529 publishers were analyzed. The results revealed that foreign authorship increased from 36% to 62% during the period, but interregional authorship only grew from 77% to 82%. The growth in internationality is not the same across disciplines and regions of the world. Agricultural sciences, psychiatry/psychology, and economics and business have the least number of foreign authors, while journals in space science, mathematics, and physics have the most. According to the number of both foreign‐authored papers and foreign‐authored citations, clinical medicine is one of the least international fields. Latin America and Middle East publishers have a greater tendency to publish papers from authors in their countries. In contrast, national publishers in North America have become considerably more international over time. Russia, China, and Brazil publish the least number of foreign authored‐papers in their journals, while Switzerland's journals publish the most.
The ethical issues in instructions for authors of Chinese biomedical journals
Authors: WU Yang , ZOU Qiang
Published: June 2015

229 Chinese‐language biomedical journals from A Guide to The Core Journals of China were investigated for their guidance on 14 ethical issues. The issues of authorship, duplicate submission, privacy and confidentiality, and integrity of the data were mentioned in more than 50% of the journals. Except for the issues of authorship and protection of animals in research, significant differences were found between Chinese Medical Association Publishing House (CMAPH) journals (n = 67) and non‐CMAPH journals (n = 162) (P < 0.05). 66 of the 229 journals did not update their instructions for authors regularly. 196 journal instructions listed authorship criteria, while the other 33 did not. Clinical trial registration policy was required by 26 (11.3%) journals, among which the CONSORT statement for randomized trials was required by 23, and only one journal guided the authors to work in line with the EQUATOR Network. The study concludes that the situation of publishing ethics in the instructions for authors of Chinese biomedical journals is not favorable, and that Chinese biomedical editors should learn more about publishing ethics in order to reduce opportunities for publication problems.
Figuring on fair use
Authors: SMITH Kevin L.
Published: June 2015

How does US copyright law, and especially the doctrine of fair use, impact reusing figures drawn from a previous publication? Does it help if we redraw those figures in an attempt to evade copyright restrictions?
Fair dealing: a concept in UK copyright law
Authors: OWEN Lynette
Published: June 2015

Fair dealing is a concept which provides certain exceptions to UK copyright law; it permits the use of copyright material in certain circumstances without permission from, or payment to, the copyright owner.
Oscillatory exchange bias effect in La0.67Sr0.33MnO3/G-SrMnO3/La0.67Sr0.33MnO3 sandwiches
Authors: Mao H J , Li F , Xiao L R , Wang Y Y , Cui B , Peng J J , Pan F , Song C
Published: June 2015

We investigate the exchange bias effect in La0.67Sr0.33MnO3/G-SrMnO3/ La0.67Sr0.33MnO3 (LSMO/SMO/LSMO) sandwiches, where the spacer is a G-type antiferromagnet. Because of the cycloid bulk spins in the SMO modulated by the top LSMO layer, the sandwich structure exhibits an oscillatory exchange bias behavior as a function of the SMO thickness. This unprecedented phenomenon vanishes in LSMO/SMO bilayers, where the exchange bias saturates as the SMO thickness increases, giving rise to the antiferromagnetic anisotropy constant of SMO, 1.0 –2.0   ×   105 erg cm−3. The results provide a broad opportunity to tailor antiferromagnetic moments by interfacial design for antiferromagnet spintronics.
High power impulse sputtering of chromium: correlation between the energy distribution of chromium ions and spoke formation
Authors: Breilmann W , Eitrich A , Maszl C , Hecimovic A , Layes V , Benedikt J , von Keudell A
Published: June 2015

High power magnetron sputtering (HiPIMS) discharges generate ions with high kinetic energies in comparison to conventional dc magnetron sputtering. The peculiar shape of the ion energy distribution function (IEDF) is correlated to the formation of localized ionization zones (IZ) in the racetrack of a HiPIMS discharge, so called spokes. This is explained by a local maximum of the electrical potential inside these localized IZ. By using ion energy mass spectrometry, probe experiments and plasma spectroscopy the connection between IZ and IEDFs is evaluated with high temporal resolution. The data of a floating probe next to the target is used to directly monitor the movement of the spokes in the

direction. Chromium is used as target material, because the plasma undergoes a sequence from stochastic spoke formation, to regular spoke pattern rotating in the

direction to a homogeneous plasma torus with increasing plasma power. In particular, the analysis of the transition from the regular spoke pattern to the homogeneous plasma torus at very high plasma powers shows that the high energy part of the IEDF is not affected and only the low energy part is modified. Consequently, one could consider the homogenous plasma torus at very high plasma powers as a a single ionization zone localized over the complete torus, which is formed by merging individual spokes with increasing power. Details and consequences of that model are discussed.
Predicting tumor purity from methylation microarray data
Authors: Zhang Naiqian , Wu Hua-Jun , Zhang Weiwei , Wang Jun , Wu Hao , Zheng Xiaoqi
Published: June 2015

Motivation: In cancer genomics research, one important problem is that the solid tissue sample obtained from clinical settings is always a mixture of cancer and normal cells. The sample mixture brings complication in data analysis and results in biased findings if not correctly accounted for. Estimating tumor purity is of great interest, and a number of methods have been developed using gene expression, copy number variation or point mutation data.

Results: We discover that in cancer samples, the distributions of data from Illumina Infinium 450 k methylation microarray are highly correlated with tumor purities. We develop a simple but effective method to estimate purities from the microarray data. Analyses of the Cancer Genome Atlas lung cancer data demonstrate favorable performance of the proposed method.

Availability and implementation: The method is implemented in InfiniumPurify, which is freely available at https://bitbucket.org/zhengxiaoqi/infiniumpurify.

Contact:  xqzheng@shnu.edu.cn or hao.wu@emory.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets
Authors: Marshall Owen J. , Brand Andrea H.
Published: June 2015

Summary: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalization and background minimization. We describe here damidseq_pipeline, a software pipeline that performs automatic normalization and background reduction on multiple DamID-seq FASTQ datasets.

Availability and implementation: Open-source and freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline is implemented in Perl and is compatible with any Unix-based operating system (e.g. Linux, Mac OSX).

Contact:  o.marshall@gurdon.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The use of acoustic accelerometer tags to determine seasonal changes in activity and catchability of a recreationally caught marine teleost
Authors: Stehfest Kilian M. , Lyle Jeremy M. , Semmens Jayson M.
Published: June 2015

Understanding the way catchability of exploited fish species varies due to changes in individual fish behaviour is a seldom addressed but important requisite for extracting accurate information on fish abundance from catch per unit effort (cpue) data, particularly from baited gears. In this study, cpue data analysis was combined with analysis of movement and activity data from acoustic telemetry tags to determine the nature of seasonal changes in cpue of the recreationally caught sand flathead (Platycephalus bassensis) in a coastal bay and estuary in southeast Tasmania, Australia. Water temperature had a significant influence on cpue of sand flathead with lower catches at lower temperatures. Yet, even at the relatively small scale of this study (10 s of km), the mechanisms in which temperature affects cpue were highly area specific. In the shallow, estuarine part of the study area, changes in cpue were driven by changes in availability, due to seasonal movements of fish in and out of the area. In the deeper bay at the mouth of the estuary, on the other hand, changes in cpue with temperature were most likely driven by temperature-related changes in activity. At lower temperatures, fish were less active, indicating that fish will have a lower probability of encountering bait as well as lower feeding motivation due to lower metabolic debt. This shows the importance of the inclusion of an environmentally influenced catchability parameter in stock assessment models that utilize cpue data from baited gear types, which is often only done implicitly on a coarse temporal scale by accounting for changes in cpue with season. Our study furthermore highlights the usefulness of acoustic telemetry in a fisheries context beyond the basic study of fish movement, allowing the monitoring of activity levels of exploited fish in relation to environmental parameters in the field.
Transcription Analysis of the Beta-Glucosidase Precursor in Wild-Type and
l-
4
i
Mutant
Bombyx mori
(Lepidoptera: Bombycidae)
Authors: Kang Lequn , Huang Fei , Wu Fan , Zhao Qiaoling
Published: June 2015

Lethal fourth-instar larvae ( l- 4 i ) mutant of Bombyx mori , a recently discovered novel mutant, die from energy depletion due to genetic mutation. Beta-glucosidase is a common digestive enzyme that hydrolyzes cellulose in the diet to provide energy. In this study, the mRNA expression profiles of B. mori beta-glucosidase precursor ( BmpreBG ) were characterized by reverse transcription polymerase chain reaction and quantitative real-time polymerase chain reaction. The transcription level of BmpreBG varied in different tissues and developmental stages, except in the pupa and moth, which are the no-diet period. Remarkably, the mRNA expression level of BmpreBG was sharply reduced in l- 4 i but not in the wild type, which suggested that the digestive function of the mutant was severely damaged. This was consistent with the l- 4 i phenotypic traits of not eating mulberries, lack of energy, and ultimate death. 5′-rapid amplification of cDNA ends showed, for the first time, that BmpreBG has a 160-bp 5′-untranslated region. These findings suggested that B. mori β-glucosidase precursor was involved in the death process of l- 4 i mutant larvae.
The Supraorbital Keyhole Approach
Authors: Tatarli Necati , Ceylan Davut , Şeker Aşkin , Solmaz Bilgehan , Çavdar Safiye , Kiliç Türker
Published: June 2015

Aim:

The major aim of the present anatomical study was to demonstrate the anatomical structures that can be visualized using the supraorbital keyhole approach, both endoscopically and microscopically, from an eyebrow incision to intracranial structures. Furthermore, it defines an optimal craniotomy for surgery.

Methods:

Fine dissection was performed on each side of 5 formalin-fixed adult cadavers according to the surgical procedures of the supraorbital keyhole approach, and each step was documented both endoscopically and microscopically. Furthermore, the distance between the superior temporal line and the supraorbital notch/foramen was measured from the 10 total sides of the 5 cadavers and from the 118 sides of the 59 autopsies.

Results:

Tumors and aneurysms of the anterior cranial fossa can be visualized during the supraorbital keyhole approach. The average distance between the superior temporal line and the supraorbital notch/foramen was measured. The distance obtained from the autopsies on the 25 females was 31.56 ± 4.03 mm on the right side and 31.04 ± 5.40 mm on the left side. The average distance obtained from the autopsies on the 34 males was 34.00 ± 4.59 mm on the right side and 33.59 ± 5.41 mm on the left side. There was no statistically significant difference between right and left in the female and male autopsies or between sexes.

Conclusions:

This anatomical study showed that structures in the anterior and middle cranial fossa can be reached via the supraorbital keyhole craniotomy approach with minimal brain retraction and adequate exposure and with minimal craniotomy size.
Poly-D-L-Lactic Acid Membranes for Bone Regeneration
Authors: Annunziata Marco , Nastri Livia , Borgonovo Andrea , Benigni Marco , Poli Pier Paolo
Published: June 2015

Purpose:

To histologically and histomorphometrically evaluate the biocompatibility and the biological properties of perforated and nonperforated poly-D-L-lactic acid (PDLLA) resorbable membranes, using a model of calvarial monocortical bone defects in domestic pigs.

Methods:

A total of 6 10 × 10 × 10 mm circular calvarial bone defects were prepared in each of the 3 adult female large white domestic pigs and assigned to the following experimental groups: negative control, nonperforated membrane only, perforated membrane only, bone only, bone + nonperforated membrane, and bone + perforated membrane. The PDLLA membranes were fixed by PDLLA pins by means of an ultrasonic device. After 40 days, bone blocks containing the defects were harvested and histologically processed.

Results:

A close contact between the PDLLA devices and the surrounding bone was found, and no trace of inflammatory tissue or signs of infection were detected. Bone regeneration occurred from the preexisting bone with a centripetal pattern. Incomplete bone filling was found in empty defects, whereas all sites filled with bone showed a complete bone formation, irrespectively of the presence and the type of membrane used.

Conclusion:

PDLLA membranes and pins showed to be highly biocompatible toward bone tissue and to do not interfere with the bone healing process of monocortical calvaria defects in domestic pigs. No adjunctive effect of PDLLA membranes, irrespectively of their perforated/nonperforated structure, could be evidenced in terms of bone regeneration under the present experimental conditions. Further studies are needed to investigate the regenerative potential of such devices in other clinically relevant models.
Diagnostic Accuracy of Blood Glucose Measurements in Detecting Venous Compromise in Flaps
Authors: Bashir Muhammad Mustehsan , Tayyab Zahid , Afzal Saira , Khan Farid Ahmad
Published: June 2015

Due to limitations of the current methods for monitoring flap circulation, newer methods with better diagnostic accuracy are needed. A drop in blood glucose levels within flap is a simple method that can be widely used; however, this method has been examined only in small cohorts. The objective of this study was to determine the diagnostic accuracy of blood glucose measurements within flaps in early detection of venous compromise. We sampled 127 pedicled and free flaps, including replants, performed on patients between 12 and 60 years of age. Within flap blood glucose measurements were performed using pinprick and a blood glucose meter at 0, 6, 12, 24 and 48 hours after operation. Daily examination for clinical signs of venous compromise was used to determine flap viability for up to 7th day after operation. Of the 127 flaps, 76 (60%) were performed on men and the mean age ± standard deviation of the patients was 35.8 ± 12.1 years. A cut-off value of 62 mg/dL was determined using a receiver operating characteristic curve. Using this cut-off value, the sensitivity and positive predictive values of within flap blood glucose for determining venous compromise were 90% and 91%, respectively, whereas the specificity and negative predictive values were 78% and 76%, respectively. The overall diagnostic accuracy of within flap blood glucose was 87%. We conclude that blood glucose measurement within flap has acceptable diagnostic accuracy and should be used for early detection of venous compromise.
Impact of Injury Mechanisms on Patterns and Management of Facial Fractures
Authors: Greathouse S. Travis , Adkinson Joshua M. , Garza Ramon , Gilstrap Jarom , Miller Nathan F. , Eid Sherrine M. , Murphy Robert X.
Published: June 2015

Mechanisms causing facial fractures have evolved over time and may be predictive of the types of injuries sustained. The objective of this study is to examine the impact of mechanisms of injury on the type and management of facial fractures at our Level 1 Trauma Center. The authors performed an Institutional Review Board–approved review of our network's trauma registry from 2006 to 2010, documenting age, sex, mechanism, Injury Severity Score, Glasgow Coma Scale, facial fracture patterns (nasal, maxillary/malar, orbital, mandible), and reconstructions. Mechanism rates were compared using a Pearson χ
2 test. The database identified 23,318 patients, including 1686 patients with facial fractures and a subset of 1505 patients sustaining 2094 fractures by motor vehicle collision (MVC), fall, or assault. Nasal fractures were the most common injuries sustained by all mechanisms. MVCs were most likely to cause nasal and malar/maxillary fractures (P < 0.01). Falls were the least likely and assaults the most likely to cause mandible fractures (P < 0.001), the most common injury leading to surgical intervention (P < 0.001). Although not statistically significant, fractures sustained in MVCs were the most likely overall to undergo surgical intervention. Age, number of fractures, and alcohol level were statistically significant variables associated with operative management. Age and number of fractures sustained were associated with operative intervention. Although there is a statistically significant correlation between mechanism of injury and type of facial fracture sustained, none of the mechanisms evaluated herein are statistically associated with surgical intervention.

Clinical Question/Level of Evidence:

Therapeutic, III.
Communications Between the Trigeminal Nerve and the Facial Nerve in the Face
Authors: Hwang Kun , Yang Su Cheol , Song Ju Sung
Published: June 2015

The aim of the article is to elucidate the communications between the trigeminal nerve and facial nerve in the face. In a PubMed search, 328 studies were found using the terms ‘trigeminal nerve, facial nerve, and communication.’ The abstracts were read and 39 full-text articles were reviewed. Among them, 11 articles were analyzed.

In the studies using dissection, the maxillary branch (V2) had the highest frequency (95.0% ± 8.0%) of communication with the facial nerve, followed by the mandibular branch (V3) (76.7% ± 38.5%). The ophthalmic branch (V1) had the lowest frequency of communication (33.8% ± 19.5%). In a Sihler stain, all of the maxillary branches and mandibular branches had communications with the facial nerve and 85.7% (12/14 hemifaces) of the ophthalmic branches had communications. The frequency of communications between the trigeminal nerve and facial nerve were significantly higher (P = 0.00, t-test) in the studies using a Sihler stain (94.7% ± 1.1%) than the studies using dissection (76.9 ± 35.8).

The reason for the significantly higher frequency of trigeminal-facial communication in the studies using a Sihler stain is because of the limitation of the Sihler stain itself. This technique cannot differentiate the motor nerves from sensory nerves at the periphery, and a crossover can be misinterpreted as communication near to nerve terminal.
Assessment of the Facial Soft Tissue Thickness of the Patients Affected by Unilateral Cleft Lip and Palate Using Cone Beam Computed Tomography
Authors: Celikoglu Mevlüt , Buyuk S. Kutalmiş , Sekerci A. Ercan
Published: June 2015

Aim:

The aim of the study was to evaluate the soft tissue thickness of the patients affected by unilateral cleft lip and palate (UCLP) and to compare the findings with a matched control group without cleft using cone beam computed tomography (CBCT).

Methods:

The study sample consisted of 66 patients (31 women and 35 men) divided into 2 groups as UCLP group (34 patients; 23 men and 11 women; 9 right sided and 25 left sided; mean age: 14.11 ± 3.48 years) and control group (32 patients; 12 men and 20 women; mean age: 15.10 ± 3.13 years) without any cleft. Angular angle between Nasion-A line and Nasion-B line (ANB), angle between Sella-Nasion line and Gonion-Menton line (SN-MP) and linear (glabella, nasion, rhinion, subnasale, labrale superius, stomion, labrale inferius, labiomentale, pogonion, and gnathion) measurements were done using CBCT. Student t test was performed to compare the variables between the groups.

Results:

Soft tissue thickness values for men were higher in both groups, except for rhinion and glabella. Subnasale for women (P = 0.000), men (P = 0.006), and total samples (P = 0.000) and the variable of the labrale superius for men (P = 0.047) and total samples (P = 0.040) were found to be statistically significantly thinner in the UCLP group. SN-MP had significant affect on subnasale thickness (R
2 = 15.8; Beta = −0.397; P = 0.001).

Conclusion:

Thickness of the subnasale and the labrale superius were found to be statistically significantly thinner in the UCLP group compared with the controls.
Adipose-Derived Stem Cells Improve Survival of Random Pattern Cutaneous Flaps in Radiation Damaged Skin
Authors: Hasdemir Mustafa , Agir Hakan , Eren Guler Gamze , Aksu Maksut Gorkem , Alagoz Murat Sahin , Duruksu Gokhan , Saglam Ozlem , Karaöz Erdal
Published: June 2015

Background:

Tissue ischemia and necrosis following surgery after radiotherapy on the skin and subcutaneous tissue are well known to all reconstructive surgeons. Nevertheless, there has been no report so far on local effects of adipose-derived stem cells (ADSCs) on random flap survival elevated in an irradiated rat dorsum. In this experimental study, we aimed to identify the effect of adipose tissue-derived stem cell injection on random flap survival in irradiated tissues.

Methods:

Adipose-derived stem cells were isolated from the groin region of Sprague-Dawley rats and expanded ex vivo for 3 passages. Animals were divided into 2: irradiated and nonirradiated and then again into ADSC injected and noninjected groups altogether 4 groups. After elevation of caudally based dorsal random skin flaps (10 cm long and 3 cm wide), Green fluorescent protein labeled ADSCs were then injected to the base of the pedicle. Radiotherapy was 20 Gy single dose applied during 8 weeks before surgery. At postoperative day 7, flap viability measurement and tissue harvest for histologic and immunocytochemical assessment were performed in all groups.

Results:

We have observed increased flap viability in ADSCs injected irradiated group compared with control radiation group with small but not statistically significantly increase in vessel count per field. Mean survival rate of the flaps in groups A, B, C, and D were 40.46%, 60.07%, 40.90%, and 56.13%, respectively. There was a statistically significant vessel count difference between group B and group A and also with group D (P < 0.001).

Conclusions:

These findings suggest that ADSCs have a potential for enhancing the blood supply of random pattern skin flaps after radiation injury. This mechanism might be both neovascularization and vasodilation along with endothelial repair. Further studies are needed.
Cranial Base and Posterior Cranial Vault Asymmetry After Open and Endoscopic Repair of Isolated Lambdoid Craniosynostosis
Authors: Zubovic Ema , Woo Albert S. , Skolnick Gary B. , Naidoo Sybill D. , Smyth Matthew D. , Patel Kamlesh B.
Published: June 2015

Background:

Previous studies have shown that open cranial vault remodeling does not fully address the endocranial deformity. This study aims to compare endoscopic-assisted suturectomy with postoperative molding helmet therapy to traditional open reconstruction by quantifying changes in cranial base morphology and posterior cranial vault asymmetry.

Methods:

Anthropometric measurements were made on pre- and 1-year postoperative three-dimensionally reconstructed computed tomography scans of 12 patients with unilateral lambdoid synostosis (8 open and 4 endoscopic-assisted). Cranial base asymmetry was analyzed using: posterior fossa deflection angle (PFA), petrous ridge angle (PRA), mastoid cant angle (MCA), and vertical and anterior–posterior (A–P) displacement of external acoustic meatus (EAM). Posterior cranial vault asymmetry was quantified by volumetric analysis.

Results:

Preoperatively, patients in the open and endoscopic groups were statistically equivalent in PFA, PRA, MCA, and A–P EAM displacement. At 1 year postoperatively, open and endoscopic patients were statistically equivalent in all measures. Mean postoperative PFA for the open and endoscopic groups was 6.6 and 6.4 degrees, PRA asymmetry was 6.4 and 7.6%, MCA was 4.0 and 3.2 degrees, vertical EAM displacement was −2.3 and −2.3 millimeters, and A–P EAM displacement was 6.8 and 7.8 millimeters, respectively. Mean volume asymmetry was significantly improved in both open and endoscopic groups, with no difference in postoperative asymmetry between the 2 groups (P = 0.934).

Conclusions:

Patients treated with both open and endoscopic repair of lambdoid synostosis show persistent cranial base and posterior cranial vault asymmetry. The results of endoscopic-assisted suturectomy with postoperative molding helmet therapy are similar to those of open calvarial vault reconstruction.
A novel test for detecting gene-gene interactions in trio studies
Authors: Balliu Brunilda , Zaitlen Noah
Published: June 2015

Epistasis plays a significant role in the genetic architecture of many complex phenotypes in model organisms. To date, there have been very few interactions replicated in human studies due in part to the multiple hypothesis burden implicit in genome-wide tests of epistasis. Therefore, it is of paramount importance to develop the most powerful tests possible for detecting interactions. In this work we develop a new gene-gene interaction test for use in trio studies called the trio correlation (TC) test. The TC test computes the expected joint distribution of marker pairs in offspring conditional on parental genotypes. This distribution is then incorporated into a standard one degree of freedom correlation test of interaction. We show via extensive simulations that our test substantially outperforms existing tests of interaction in trio studies. The gain in power under standard models of phenotype is large, with previous tests requiring more than twice the number of trios to obtain the power of our test. We also demonstrate a bias in a previous trio interaction test and identify its origin. We conclude that the TC test shows improved power to identify interactions in existing, as well as emerging, trio association studies. The method is publicly available atwww.github.com/BrunildaBalliu/TrioEpi.
Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data
Authors: Amenga-Etego Lucas , Li Ruiqi , O’Brien John D.
Published: June 2015

The advent of whole-genome sequencing has generated increased interest in modeling the structure of strain mixture within clinicial infections ofPlasmodium falciparum(Pf). The life cycle of the parasite implies that the mixture of multiple strains within an infected individual is related to the out-crossing rate across populations, making methods for measuring this processin situcentral to understanding the genetic epidemiology of the disease. In this paper, we show how to estimate inbreeding coefficients using genomic data from Pf clinical samples, providing a simple metric for assessing within-sample mixture that connects to an extensive literature in population genetics and conservation ecology. Features of theP. falciparumgenome mean that some standard methods for inbreeding coefficients and related F-statistics cannot be used directly. Here, we review an initial effort to estimate the inbreeding coefficient within clinical isolates ofP. falciparumand provide several generalizations using both frequentist and Bayesian approaches. The Bayesian approach connects these estimates to the Balding-Nichols model, a mainstay within genetic epidemiology. We provide simulation results on the performance of the estimators and show their use on ~ 1500 samples from the PF3K data set. We also compare the results to output from a recent mixture model for within-sample strain mixture, showing that inbreeding coefficients provide a strong proxy for the results of these more complex models. We provide the methods described within an open-sourceRpackagepfmix.
Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers
Authors: Schmidt Søren Fisker , Larsen Bjørk Ditlev , Loft Anne , Nielsen Ronni , Madsen Jesper Grud Skat , Mandrup Susanne
Published: June 2015

The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose tissue inflammation and development of insulin resistance during obesity. In this context, nuclear factor κ-light-chain-enhancer of activated B cells (NFκB) is directly involved and required for the acute activation of the inflammatory gene program. Here, we show that the major transactivating subunit of NFκB, v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), is also required for acute TNF-induced suppression of adipocyte genes. Notably, this repression does not involve RELA binding to the associated enhancers but rather loss of cofactors and enhancer RNA (eRNA) selectively from high-occupancy sites within super-enhancers. Based on these data, we have developed models that, with high accuracy, predict which enhancers and genes are repressed by TNF in adipocytes. We show that these models are applicable to other cell types where TNF represses genes associated with super-enhancers in a highly cell-type–specific manner. Our results propose a novel paradigm for NFκB-mediated repression, whereby NFκB selectively redistributes cofactors from high-occupancy enhancers, thereby specifically repressing super-enhancer-associated cell identity genes.
Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters
Authors: Perduns Renke , Horst-Niessen Ina , Peterhansel Christoph
Published: June 2015

Histone modifications contribute to gene regulation in eukaryotes. We analyzed genome-wide histone H3 Lysine (Lys) 4 trimethylation and histone H3 Lys 9 acetylation (two modifications typically associated with active genes) in meristematic cells at the base and expanded cells in the blade of the maize (Zea mays) leaf. These data were compared with transcript levels of associated genes. For individual genes, regulations (fold changes) of histone modifications and transcript levels were much better correlated than absolute intensities. When focusing on regulated histone modification sites, we identified highly regulated secondary H3 Lys 9 acetylation peaks on upstream promoters (regulated secondary upstream peaks [R-SUPs]) on 10% of all genes. R-SUPs were more often found on genes that were up-regulated toward the blade than on down-regulated genes and specifically, photosynthetic genes. Among those genes, we identified six genes encoding enzymes of the C4 cycle and a significant enrichment of genes associated with the C4 trait derived from transcriptomic studies. On the DNA level, R-SUPs are frequently associated with ethylene-responsive elements. Based on these data, we suggest coevolution of epigenetic promoter elements during the establishment of C4 photosynthesis.
Adhesive–adherent interfaces probed with grazing-incidence small-angle neutron scattering
Authors: Schindler Markus , Moulin Jean-François , Müller-Buschbaum Peter
Published: June 2015

The inner structure of a pressure-sensitive adhesive (PSA) is investigated at the surface as well as at the buried adhesive–adherent interface. Time-of-flight grazing-incidence small-angle neutron scattering (TOF-GISANS) is used to obtain depth-resolved structural information about the statistical copolymer poly(ethylhexylacrylate-stat-d-methylmethacrylate), which represents a well studied model PSA comprising 80% ethylhexylacrylate and 20% deuterated methylmethacrylate. Small and rare defects of around 40 nm in lateral size are found at the surface, while in the probed film volume a very low concentration of smaller structures of between 25 and 37 nm is found. Acidic and basic cleaning procedures are applied to the silicon adherent to alter the surface chemistry. At the buried interface of the adhesive and adherent no lateral structures are resolvable, irrespective of the surface treatment. The absence of dominant lateral structures shows that the statistical copolymer does not phase separate on a length scale that is of interest for applications. Furthermore, the findings prove the suitability of this kind of sample system for reflectivity measurements and demonstrate the suitability of TOF-GISANS for nondestructive investigations of buried interfaces in adhesion science.
Substrate-stress-induced magnetic and nonmagnetic structural correlations in Fe/Si multilayers
Authors: Paul Amitesh , Teichert Anke , Krist Thomas , Steitz Roland
Published: June 2015

Application of a bias voltage can influence the growth kinetics and thereby the stress in a magnetic multilayer. The inherent structural correlations in turn can influence the magnetic domain structures and thereby the overall device performance. Here, prototypical Fe/Si supermirrors are subjected to stress relaxation during the growth of sequential layers by applying a sufficient substrate bias voltage. A change in the coercivity associated with the grain size variation upon biasing is found. Most interestingly, using polarized neutron scattering, it is possible to identify that the conformal roughness becomes nonconformal with the relaxation of stress within the multilayers. The magnetic domains, on the other hand, always remain nonconformal (independent of the structural change) as they undergo spatial fluctuations around a mean magnetization. This study underscores the importance of the substrate biasing in affecting the structural correlation, which is detrimental to the resultant optical (e.g. supermirror) quality.
Multifit/Polydefix: a framework for the analysis of polycrystal deformation using X-rays
Authors: Merkel Sébastien , Hilairet Nadège
Published: June 2015

Multifit/Polydefix is an open source IDL software package for the efficient processing of diffraction data obtained in deformation apparatuses at synchrotron beamlines. Multifit allows users to decompose two-dimensional diffraction images into azimuthal slices, fit peak positions, shapes and intensities, and propagate the results to other azimuths and images. Polydefix is for analysis of deformation experiments. Starting from output files created in Multifit or other packages, it will extract elastic lattice strains, evaluate sample pressure and differential stress, and prepare input files for further texture analysis. The Multifit/Polydefix package is designed to make the tedious data analysis of synchrotron-based plasticity, rheology or other time-dependent experiments very straightforward and accessible to a wider community.
Low-Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography
Authors: Feld Geoffrey K. , Heymann Michael , Benner W. Henry , Pardini Tommaso , Tsai Ching-Ju , Boutet Sébastien , Coleman Matthew A. , Hunter Mark S. , Li Xiaodan , Messerschmidt Marc , Opathalage Achini , Pedrini Bill , Williams Garth J. , Krantz Bryan A. , Fraden Seth , Hau-Riege Stefan , Evans James E. , Segelke Brent W. , Frank Matthias
Published: June 2015

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introduction via a translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Z plastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Z fixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.
Survey of background scattering from materials found in small-angle neutron scattering
Authors: Barker J. G. , Mildner D. F. R.
Published: June 2015

Measurements and calculations of beam attenuation and background scattering for common materials placed in a neutron beam are presented over the temperature range of 300–700 K. Time-of-flight (TOF) measurements have also been made, to determine the fraction of the background that is either inelastic or quasi-elastic scattering as measured with a 3He detector. Other background sources considered include double Bragg diffraction from windows or samples, scattering from gases, and phonon scattering from solids. Background from the residual air in detector vacuum vessels and scattering from the 3He detector dome are presented. The thickness dependence of the multiple scattering correction for forward scattering from water is calculated. Inelastic phonon background scattering at small angles for crystalline solids is both modeled and compared with measurements. Methods of maximizing the signal-to-noise ratio by material selection, choice of sample thickness and wavelength, removal of inelastic background by TOF or Be filters, and removal of spin-flip scattering with polarized beam analysis are discussed.
Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities
Authors: Vergucht Eva , Brans Toon , Beunis Filip , Garrevoet Jan , Bauters Stephen , De Rijcke Maarten , Deruytter David , Janssen Colin , Riekel Christian , Burghammer Manfred , Vincze Laszlo
Published: June 2015

Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their naturalin vivostate was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitivein vivomulti-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.