bluuebunny/crossref_metadata_2025_split huggingface dataset:
An assessment of ecological conditions and threats at the Ethiopian wintering site of the last known eastern colony of Critically Endangered Northern Bald IbisGeronticus eremita
Authors: SERRA G. , BRUSCHINI C. , PESKE L. , KUBSA A. , WONDAFRASH M. , LINDSELL J. A. 
Published: October 2013

SummaryThe long-range, migratory eastern relict population of Northern Bald IbisGeronticus eremitahas been steadily declining since the time of discovery in 2002, despite the protection programme in place at the breeding grounds in Syria. Assessing the ecological conditions and threats along the migration route and at the wintering site, both discovered in 2006, has become a priority for this “Critically Endangered” species. Adult ibises spent the winter at the same site on the central Ethiopian highland plateau, from August until mid-February during five consecutive winters (2006-2011). The wintering site was surveyed during four field visits and assessed through a spatial analysis of 1,067 satellite locations. The site is in an agro-pastoral landscape, inhabited by a settled community of people living in relatively poor and isolated conditions. Home range analysis based on kernel distributions showed that the bald ibises used a core range area of 9.1–19.0 km² (confirmed by direct visual observations in the field) and an extended range area of 61.0–126.1 km². These figures are c.20 and 60 times smaller, respectively, than those calculated for the breeding site in Syria. Eighty-one percent of the core area in Ethiopia was used in all five years confirming the birds’ fidelity to this wintering site. Ibises preferred to forage in wet or dry pastures and in recently cut hayfields, and avoided tall grass, uncut hayfields and cultivation. Despite dependence on human-created habitats, human disturbance observed in the field was minimal. The main short-term threat for the ibises was judged to be the potential raising of attention on the part of the local community specifically towards these few individual ibises. In the medium term, the main threat comes from the conversion of pastures into crops and the potential use of fertilisers and pesticides.
Efficacy of very low-dose prostaglandin E1 in duct-dependent congenital heart disease
Authors: Yucel Ilker K. , Cevik Ayhan , Bulut Mustafa O. , Dedeoğlu Reyhan , Demir İbrahim H. , Erdem Abdullah , Celebi Ahmet 
Published: October 2013

AbstractAimThe present study aims to define the lowest effective prostaglandin E1 dose in patients with inadequacy of pulmonary blood flow and/or intracardiac blood mixing and those with inadequate systemic blood flow.MethodsPatients with inadequacy of both pulmonary blood flow and/or blood mixing (Group 1) and those with inadequate systemic blood flow (Group 2) were retrospectively evaluated in two separate groups with regard to the prostaglandin E1 starting dose given in the referring facility, the lowest and the highest dose administered in our centre, treatment duration, adverse effects, and administered treatment.ResultsNo difference between the groups could be detected with respect to sex or birth weight (p=0.95 and 0.42, respectively). Group 1 and Group 2 were statistically similar in aspect of prostaglandin treatment duration (9.73±0.81 days versus 11.6±1.05 days, p=0.064). When compared with Group 2, the initial, maintenance and lowest efficient doses of prostaglandin E1 treatment were significantly lower and the titrated dose of prostaglandin E1 was significantly higher in Group 1 (p=0.001 for each).ConclusionOur findings indicate that the infusion of prostaglandin at a very low dose (0.003–0.005 mcg/kg/minute) is sufficient to maintain the patency of the ductus arteriosus. A higher dose of prostaglandin E1 may be necessary in patients with inadequate systemic blood flow.
Endothelial function state following repair of cyanotic congenital heart diseases
Authors: Sabri Mohammad Reza , Daryoushi Hooman , Gharipour Mojgan 
Published: October 2013

AbstractBackgroundRepairing cyanotic congenital heart disease may be associated with preserving endothelial function. The present study aimed to evaluate vascular endothelial function in patients with repaired cyanotic congenital heart disease.MethodsIn a case–control study conducted in 2012 in Isfahan, Iran, 42 consecutive patients aged <35 years who had suffered from different types of cyanotic congenital heart disease and had undergone complete repair of their congenital heart defect were assessed in regard to their endothelial function state by measuring flow-mediated dilatation and other cardiac function indices. They were paired with 42 sex- and age-matched healthy controls.ResultsThe mean flow-mediated dilatation was lower in patients with repaired cyanotic congenital heart disease than in the controls [6.14±2.78 versus 8.16±1.49 respectively (p<0.001)]. Significant adverse correlations were found between flow-mediated dilatation, age, and body mass indexes, in those who underwent repair surgery. In addition, flow-mediated dilatation had a positive association with the shortening fraction, ejection fraction, and tricuspid annular plane systolic excursion value, and it was also inversely associated with carotid intima-media thickness and the myocardial performance index. The mean of the flow-mediated dilatation was significantly higher in the group with tetralogy of Fallot along with complete repair before the age of 2.5 years and also in those patients with total anomalous pulmonary venous connection or transposition of the great arteries repaired with an arterial switch operation before 6 months of age, compared with the other two subgroups. This includes patients with a tetralogy of Fallot defect repaired after 4 years of age and those with complex cyanotic congenital heart disease that was repaired after 2.5 years of age (mean age at repair 9±6.1 years).ConclusionEarly repair of a cyanotic defect can result in the protection of vascular endothelial function and prevent the occurrence of vascular accidents at an older age.
Quantitative Annular Dark Field Electron Microscopy Using Single Electron Signals
Authors: Ishikawa Ryo , Lupini Andrew R. , Findlay Scott D. , Pennycook Stephen J. 
Published: October 2013

AbstractOne of the difficulties in analyzing atomic resolution electron microscope images is that the sample thickness is usually unknown or has to be fitted from parameters that are not precisely known. An accurate measure of thickness, ideally on a column-by-column basis, parameter free, and with single atom accuracy, would be of great value for many applications, such as matching to simulations. Here we propose such a quantification method for annular dark field scanning transmission electron microscopy by using the single electron intensity level of the detector. This method has the advantage that we can routinely quantify annular dark field images operating at both low and high beam currents, and under high dynamic range conditions, which is useful for the quantification of ultra-thin or light-element materials. To facilitate atom counting at the atomic scale we use the mean intensity in an annular dark field image averaged over a primitive cell, with no free parameters to be fitted. To illustrate the potential of our method, we demonstrate counting the number of Al (or N) atoms in a wurtzite-type aluminum nitride single crystal at each primitive cell over the range of 3–99 atoms.
Large, high quality single-crystals of the new Topological Kondo Insulator, SmB6
Authors: Hatnean M. Ciomaga , Lees M. R. , Paul D. McK. , Balakrishnan G. 
Published: October 2013

AbstractSmB6 has recently been predicted to be a Topological Kondo Insulator, the first strongly correlated heavy fermion material to exhibit topological surface states. High quality crystals are necessary to investigate the topological properties of this material. Single crystal growth of the rare earth hexaboride, SmB6, has been carried out by the floating zone technique using a high power xenon arc lamp image furnace. Large, high quality single-crystals are obtained by this technique. The crystals produced by the floating zone technique are free of contamination from flux materials and have been characterised by resistivity and magnetisation measurements. These crystals are ideally suited for the investigation of both the surface and bulk properties of SmB6.
Immunosignatures can predict vaccine efficacy
Authors: Legutki Joseph Barten , Johnston Stephen Albert 
Published: October 2013

Significance
Vaccines have been the most important medical intervention developed, yet vaccines for many diseases are still needed. Despite its success, the process to develop a vaccine remains empirical, resting on measuring the number of vaccinees that incur or do not incur an infection. Here we test in the mouse flu model whether the “immunosignature” diagnostic technology could be applied to predict vaccine efficacy. Immunosignatures are produced by profiling the antibody repertoire of an individual on a chip arrayed with nonnatural sequence peptides. It is attractive in that it is a simple but comprehensive measure of the complexity of the humoral response. We found that immunosignatures are a promising approach to predicting whether a vaccine will confer protection.
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
Authors: Schreiber Jacob , Wescoe Zachary L. , Abu-Shumays Robin , Vivian John T. , Baatar Baldandorj , Karplus Kevin , Akeson Mark 
Published: October 2013

Significance
Modification of cytosine bases in DNA can determine when genes are turned on in biological cells. These modifications are important during cell differentiation, embryogenesis, and aberrant cell growth in cancer. Here, we present a nanopore technique that permits direct detection of cytosine, 5-hydroxymethylcytosine, and 5-methylcytosine on individual synthetic DNA strands of known sequence. This technique focuses on three ionic current amplitudes that occur as an enzyme motor pulls the cytosine on a captured DNA strand through the nanopore. For genomic DNA, we predict that a given strand must be read 5–19 times to achieve cytosine methylation calls that are sufficiently accurate for epigenetic studies.
Ctr2 regulates biogenesis of a cleaved form of mammalian Ctr1 metal transporter lacking the copper- and cisplatin-binding ecto-domain
Authors: Öhrvik Helena , Nose Yasuhiro , Wood L. Kent , Kim Byung-Eun , Gleber Sophie-Charlotte , Ralle Martina , Thiele Dennis J. 
Published: October 2013

Significance
Copper is essential for normal growth and development because it serves roles in catalysis, signaling, and structure. Cells acquire copper through the copper transporter 1 (Ctr1) protein, a copper transporter that localizes to the cell membrane and intracellular vesicles. Both copper and the anticancer drug cisplatin are imported by Ctr1 by virtue of an extracellular domain rich in metal-binding amino acids. In this report we demonstrate that a protein structurally related to Ctr1, called Ctr2, plays a role in the generation or stability of a truncated form of Ctr1 lacking a large portion of the extracellular domain. Retention of this domain in mice or cells lacking Ctr2 enhances copper and cisplatin uptake, thereby establishing Ctr2 as a regulator of Ctr1 function.
Keratins as the main component for the mechanical integrity of keratinocytes
Authors: Ramms Lena , Fabris Gloria , Windoffer Reinhard , Schwarz Nicole , Springer Ronald , Zhou Chen , Lazar Jaroslav , Stiefel Simone , Hersch Nils , Schnakenberg Uwe , Magin Thomas M. , Leube Rudolf E. , Merkel Rudolf , Hoffmann Bernd 
Published: October 2013

Significance
For decades, researchers have been trying to unravel one of the key questions in cell biology regarding keratin intermediate filament function in protecting epithelial cells against mechanical stress. For many different reasons, however, this fundamental hypothesis was still unproven. Here we answer this pivotal question by the use of keratin KO cells lacking complete keratin gene clusters to result in total loss of keratin filaments. This lack significantly softens cells, reduces cell viscosity, and elevates plastic cell deformation on force application. Reexpression of single keratin genes facilitates biomechanical complementation of complete cluster loss. Our manuscript therefore makes a very strong case for the crucial contribution of keratins to cell mechanics, with far-reaching implications for epithelial pathophysiology.
Lipoatrophy and severe metabolic disturbance in mice with fat-specific deletion of PPARγ
Authors: Wang Fenfen , Mullican Shannon E. , DiSpirito Joanna R. , Peed Lindsey C. , Lazar Mitchell A. 
Published: October 2013

Significance
Obesity, due to increased adipose (fat) tissue, predisposes to metabolic diseases, including diabetes. Thus, it is important to understand adipose development and function. Peroxisome proliferator-activated receptor gamma (PPARγ) is widely believed to be the master regulator of adipocyte biology. Surprisingly, however, previous studies attempting to delete the PPARγ gene specifically in mouse adipose tissue did not demonstrate a dramatic phenotype. By using newer methods, the present study reports that fat-specific loss of PPARγ causes dramatic loss of adipose tissue, severe insulin resistance and diabetes, fatty liver, and abnormalities of bone, skin, and mammary glands, all of which contain adipose tissue. We show that adipocyte PPARγ is required for normal fat development and metabolic function in vivo.
Designing DNA-grafted particles that self-assemble into desired crystalline structures using the genetic algorithm
Authors: Srinivasan Babji , Vo Thi , Zhang Yugang , Gang Oleg , Kumar Sanat , Venkatasubramanian Venkat 
Published: October 2013

Significance
The traditional, Edisonian method of research involves taking a system and examining its properties. A preferred alternative is to target a suite of properties and then design the most appropriate system in this context. Here we illustrate such a design approach for the self-assembly of colloids grafted with single-stranded DNA. When two types of colloids grafted with complementary ssDNA sequences are mixed, DNA hybridization can lead to the formation of ordered colloidal crystals. We use the genetic algorithm to design ssDNA-grafted particles that will assemble into a desired structure. Our methodology is easily generalizable, fast and highly selective, and not only accurately reproduces the parameters relevant to four currently realized crystals but also elucidates four currently unobserved structures.
Enhanced fatigue endurance of metallic glasses through a staircase-like fracture mechanism
Authors: Gludovatz Bernd , Demetriou Marios D. , Floyd Michael , Hohenwarter Anton , Johnson William L. , Ritchie Robert O. 
Published: October 2013

SignificanceWe believe this article is of broad interest to the materials science and engineering community. Bulk-metallic glasses (BMGs) are currently considered candidate materials for numerous structural applications. A major limitation in their use as engineering material is the often poor and inconsistent fatigue behavior. Although recently developed BMG composites provide one solution to this problem, fatigue remains a main issue for monolithic metallic glasses. The authors report unexpectedly high fatigue resistance in a monolithic Pd-based glass arising from extensive shear-band plasticity, resulting in a very rough and periodic “staircase” crack trajectory. The research both reveals a unique mechanism in fatigue of a monolithic metallic glass and demonstrates that this mechanism mitigates previous limitations on its use as an engineering material.
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway
Authors: Yang Pengyi , Patrick Ellis , Tan Shi-Xiong , Fazakerley Daniel J. , Burchfield James , Gribben Christopher , Prior Matthew J. , James David E. , Hwa Yang Yee 
Published: October 2013

Abstract
Motivation: With the advancement of high-throughput techniques, large-scale profiling of biological systems with multiple experimental perturbations is becoming more prevalent. Pathway analysis incorporates prior biological knowledge to analyze genes/proteins in groups in a biological context. However, the hypotheses under investigation are often confined to a 1D space (i.e. up, down, either or mixed regulation). Here, we develop direction pathway analysis (DPA), which can be applied to test hypothesis in a high-dimensional space for identifying pathways that display distinct responses across multiple perturbations.
Results: Our DPA approach allows for the identification of pathways that display distinct responses across multiple perturbations. To demonstrate the utility and effectiveness, we evaluated DPA under various simulated scenarios and applied it to study insulin action in adipocytes. A major action of insulin in adipocytes is to regulate the movement of proteins from the interior to the cell surface membrane. Quantitative mass spectrometry-based proteomics was used to study this process on a large-scale. The combined dataset comprises four separate treatments. By applying DPA, we identified that several insulin responsive pathways in the plasma membrane trafficking are only partially dependent on the insulin-regulated kinase Akt. We subsequently validated our findings through targeted analysis of key proteins from these pathways using immunoblotting and live cell microscopy. Our results demonstrate that DPA can be applied to dissect pathway networks testing diverse hypotheses and integrating multiple experimental perturbations.
Availability and implementation: The R package ‘directPA’ is distributed from CRAN under GNU General Public License (GPL)-3 and can be downloaded from: http://cran.r-project.org/web/packages/directPA/index.html
Contact: jean.yang@sydney.edu.au
Supplementary Information: Supplementary data are available at Bioinformatics online.
Governing multicultural populations and family life
Authors: Ali Suki 
Published: October 2013

AbstractShortly after coming to power in Britain, the Conservative–Liberal Democratic alliance placed family life at the heart of their political agenda, and set out their plans to reform adoption. The paper draws upon debates about the reforms and considers them in articulation with concerns about health of the nation expressed in political pronouncements on ‘broken Britain’ and the failures of ‘state multiculturalism’. The paper considers the debates about domestic (transracial) and intercountry adoption, and uses feminist postcolonial perspectives to argue that we can only understand what are expressed as national issues within a transnational and postcolonial framework which illuminate the processes of state and institutional race‐making. The paper analyses three key instances of biopower and governmentality in the adoption debates: the population, the normalizing family and the individual. The paper argues that we need to understand the reforms as part of a wider concern with the ‘problem’ of multicultural belonging, and that the interlocking discourses of nation, family and identities are crucial to the constitution and regulation of gendered, racialized subjects.
Ultrasonographic evaluation in symptomatic knee osteoarthritis: clinical and radiological correlation
Authors: Malas Fevziye Ünsal , Kara Murat , Kaymak Bayram , Akıncı Ayşen , Özçakar Levent 
Published: October 2013

AbstractAimTo explore the relationship among clinical, radiological and ultrasonographical findings in knee osteoarthritis (OA).MethodSixty‐one patients (122 knees) with knee OA were enrolled. Patients' knees were classified into two groups according to symptom severity. Group I consisted of 61 more symptomatic knees and Group II comprised 61 less symptomatic knees. Subjects were clinically assessed for pain and functional status by using a visual analog scale and the Western Ontario and McMaster Universities Arthritis Index (WOMAC), respectively. Knee radiographs were evaluated by using the Kellgren–Lawrence (K–L) grading system. All knees were also evaluated ultrasonographically for meniscal bulging, distal femoral cartilage thickness, cartilage grading and also for the presence of effusion, Baker's cyst and so on.ResultsBaker's cyst and joint effusion were observed more in Group I when compared with Group II. Positive correlations were found between meniscal bulging and all WOMAC scores (all P < 0.05). K–L grades of the patients were also positively correlated with WOMAC scores (all P < 0.05). Meniscal bulging measurements and K–L grades were positively correlated (P < 0.001). There was a negative correlation between cartilage grades and cartilage thickness measurements (all P < 0.001).ConclusionsWe found that joint space narrowing seemed to be associated with meniscal bulging. Moreover, increased meniscal bulging and presence of Baker's cyst/joint effusion were associated with worse pain or poorer function.
Implantation of Scaffold‐Free Engineered Cartilage Constructs in a Rabbit Model for Chondral Resurfacing
Authors: Brenner Jillian M. , Ventura Nicole M. , Tse M. Yat , Winterborn Andrew , Bardana Davide D. , Pang Stephen C. , Hurtig Mark B. , Waldman Stephen D. 
Published: October 2013

AbstractJoint resurfacing techniques offer an attractive treatment for damaged or diseased cartilage, as this tissue characteristically displays a limited capacity for self‐repair. While tissue‐engineered cartilage constructs have shown efficacy in repairing focal cartilage defects in animal models, a substantial number of cells are required to generate sufficient quantities of tissue for the repair of larger defects. In a previous study, we developed a novel approach to generate large, scaffold‐free cartilaginous constructs from a small number of donor cells (20 000 cells to generate a 3‐cm2 tissue construct). As comparable thicknesses to native cartilage could be achieved, the purpose of the present study was to assess the ability of these constructs to survive implantation as well as their potential for the repair of critical‐sized chondral defects in a rabbit model. Evaluated up to 6 months post‐implantation, allogenic constructs survived weight bearing without a loss of implant fixation. Implanted constructs appeared to integrate near‐seamlessly with the surrounding native cartilage and also to extensively remodel with increasing time in vivo. By 6 months post‐implantation, constructs appeared to adopt both a stratified (zonal) appearance and a biochemical composition similar to native articular cartilage. In addition, constructs that expressed superficial zone markers displayed higher histological scores, suggesting that transcriptional prescreening of constructs prior to implantation may serve as an approach to achieve superior and/or more consistent reparative outcomes. As the results of this initial animal study were encouraging, future studies will be directed toward the repair of chondral defects in more mechanically demanding anatomical locations.