bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma
Authors: Bi Mark , Zhao Siming , Said Jonathan W. , Merino Maria J. , Adeniran Adebowale J. , Xie Zuoquan , Nawaf Cayce B. , Choi Jaehyuk , Belldegrun Arie S. , Pantuck Allan J. , Kluger Harriet M. , Bilgüvar Kaya , Lifton Richard P. , Shuch Brian 
Published: February 2016

Significance
Parts of clear cell renal cell carcinomas (ccRCCs) sometimes have histologic features characteristic of a sarcoma. So-called sarcomatoid tumors are more aggressive, difficult to treat, and associated with a poor prognosis. Their pathogenesis has been uncertain. Through separate exome sequencing of carcinomatous and sarcomatoid components, we show that these components share many somatic mutations, including many in genes characteristic of ccRCC. Sarcomatoid elements had significantly more new somatic mutations, particularly in cancer driver genes, than carcinomatous components. In particular, tumor protein p53, AT-rich interaction domain 1A, and BRCA1 associated protein 1 had sarcomatoid-specific homozygous mutation in 10 tumors and were all mutually exclusive, implicating these genes in sarcomatoid degeneration.
Electrical characteristics and rectification performance of wet chemically synthesized vertically aligned n-ZnO nanowire/p-Si heterojunction
Authors: Gayen R N , Bhattacharyya S R 
Published: February 2016

Abstract
Vertically well-aligned n-ZnO nanowire (NW) thin films were deposited onto p-Si substrates by a two-step wet chemical technique to form a p–n heterojunction diode. The morphological and structural characteristics of the ZnO NW performed by scanning electron microscopy (SEM) and x-ray diffraction (XRD) revealed well-aligned h-ZnO NW with a wurtzite structure. A direct optical band gap of 3.30 eV was calculated from the transmittance trace obtained using a UV–VIS–NIR spectrophotometer. The electrical characteristics of the heterojunction diode were studied by capacitance–voltage (C–V) measurement at room temperature, and current–voltage–temperature (I–V–T) measurements performed in the 300–400 K range. The C–V measurements yield a carrier concentration of 1.3  ×  1016 c.c.−1 for the ZnO NW thin film. The ideality factor (n) was found to decrease, while the barrier height (φ
b0) increased with the increase in temperature, when calculated using a thermionic emission model from the non-linear I–V–T plots. The series resistance (R
s) calculated by the Cheung–Cheung method decreased with the increase in temperature. The mean barrier height (0.718 eV) and modified Richardson constant (28.4 A cm−2 K−2) calculated using a Gaussian distribution of barrier heights (considering barrier height inhomogeneity) were closer to the theoretical value than those calculated from the linear approximation of the ln(I
s/T
2) versus 1000/T plot. The variation of the density of interface states with interface state energy was also studied. The n-ZnO NW/p-Si heterojunction diode performed very good half wave rectification in the frequency range 50 Hz–10 kHz, when a sinusoidal ac voltage of amplitude 4.5 V was applied across it.
Civilization and Its Consequences
Authors: Bowden Brett 
Published: February 2016

Abstract
This article outlines the origins and meanings of the concept of civilization in Western political thought. In doing so it necessarily explores the nature of the relationship between civilization and closely related ideas such as progress and modernity. In exploring these concepts, some of their less savory aspects are revealed, including things done in the name of civilization, such as conquest and colonization under the guise of the “burden of civilization.” The article outlines other important aspects, including the relationships between civilization and war and between civilization and the environment. It concludes with a discussion about rethinking and restructuring some of our perspectives on civilization.
Assessment in General Music Education from Early Childhood through High School
Authors: Kastner Julie Derges , Shouldice Heather Nelson 
Published: February 2016

Abstract
This literature review synthesizes and analyzes research on assessment in general music from early childhood through secondary schools. Literature has been analyzed for content being assessed, forms of assessment used, frequency of assessments, teachers’ perceptions and beliefs about assessment, and teachers’ professional development experiences and needs. Findings reveal that the content, forms, and practices of assessment vary according to the amount of autonomy teachers have in assessing their curricula, teachers’ beliefs about assessment, and national and state policies. This is particularly evident when comparing elementary general music teachers in the United States, who have little accountability for conducting assessments, and secondary general music teachers in countries like the United Kingdom and Australia, where they have required composition assessments. This analysis also reveals a need for greater professional development for general music teachers to develop strategies for implementing authentic, valid assessments and using assessment data to support and inform their teaching.
Masculinities, Crime, and Criminal Justice
Authors: Messerschmidt James W. , Tomsen Stephen 
Published: February 2016

Abstract
This essay examines the link between crime and masculinity. It begins with an overview of traditional criminology that either ignored or had a skewed understanding of the nature of the crime–masculinity connection, focusing instead on biology, which often considered crime as a reflection of defective male and female bodies/identities. It then discusses the emergence of new studies on the association between crime and masculinity, informed by social theories of gender, power, and identity. In particular, it reviews Raewyn Connell’s concept of hegemonic masculinity as an explanatory model of different forms of masculinity. It also analyzes the life histories approach to masculinities and criminal justice.
Water Security, Crime and Conflict
Authors: Brisman Avi , McClanahan William , South Nigel 
Published: February 2016

AbstractThis article explores the converging issues of water, crime and security. It begins with an overview of definitions central to the topic and a description of the development of “environmental security” as encompassing energy security, food security, and water security. It then describes “water security”—and its antipode, “water scarcity”—in both historical and contemporary contexts (with a specific focus on the United States) are described. Next, this article considers four linkages between water, scarcity, security, and crime: (a) pollution and violations of laws pertaining to water quality, (b) violations of laws as a result of water scarcity, (c) migration and crime, and (d) water security and terrorism. This article offers a critical reading of “security” and situates securitizing discourses and movements relating to the environment in a political context. It concludes with some thoughts on the potential of future interdisciplinary research and the role of the nation-state in ensuring equitable access to useable water.
Egyptian Law, Saite to Roman Periods
Authors: Lippert Sandra 
Published: February 2016

Abstract
This article treats the development of the Egyptian legal system from the Saite to the Roman period (664 BCE to about 150 CE). It addresses the much-disputed question of whether one can speak about a codification under Darius I and presents the known sources for the Egyptian legal corpus, fragments of which are preserved in demotic and Greek manuscripts, and for its accompanying didactic manual. The formation and activities of judges and notary scribes are described, characteristics of demotic legal documents, the different types that were in use, and their development over time are explained, and the best attested areas of Egyptian law—property transfer by sale, matrimonial property settlements and maintenance obligations, tenancy, credits and indebtedness, and heritage—are outlined through evidence from primary sources.
Hidradenoma Papilliferum: A Clinicopathologic Study of 264 Tumors From 261 Patients, With Emphasis on Mammary-Type Alterations
Authors: Konstantinova Anastasia M. , Michal Michal , Kacerovska Denisa , Spagnolo Dominic V. , Stewart Colin J. , Kutzner Heinz , Zelger Bernhard , Plaza Jose A. , Denisjuk Natalja , Hejda Vaclav , Shelekhova Ksenya , Bisceglia Michele , Danis Dusan , Zamecnik Michal , Kerl Katrin , Guenova Emmanuella , Kazakov Dmitry V. 
Published: February 2016

Abstract:
Hidradenoma papilliferum (HP), also known as papillary hidradenoma, is the most common benign lesion of the female anogenital area derived from anogenital mammary-like glands (AGMLG). HP can be viewed conceptually as the cutaneous counterpart of mammary intraductal papilloma. The authors have studied 264 cases of HP, detailing various changes in the tumor and adjacent AGMLG, with emphasis on mammary-type alterations. In many HP, the authors noticed changes typical for benign breast lesions, such as sclerosing adenosis-like changes, usual, and atypical ductal hyperplasia. Almost in a third of cases, remnants of AGMLG adjacent to the lesion were evident, manifesting columnar changes reminiscent of those seen in breast lesions. This study shows that the histopathological changes in HP run a broad spectrum comparable with that in the mammary counterpart and benign breast disease.
Hybrid Epithelioid Schwannoma/Perineurioma
Authors: Kacerovska Denisa , Michal Michal , Kazakov Dmitry V. 
Published: February 2016

Abstract:
We report a case of a 58-year-old who woman presented with a solitary slowly growing subcutaneous nodule covered by normally appearing skin on her left groin. Microscopically, the lesion was well circumscribed but unencapsulated, and showed biphasic cellular differentiation. One cell population was presented by small rounded (epithelioid) cells arranged singly, in small aggregates or short cords, whereas the second one was composed of cells with slender nuclei and delicate elongated bipolar cytoplasmic processes. On immunohistochemistry, the epithelioid component showed positive reaction for S-100 protein and negative for epithelial membrane antigen (EMA), thus compatible with schwannian differentiation and resembling epithelioid schwannoma. The other component showed a reverse immunophenotype being S-100 protein negative and EMA positive, thus corresponding to perineuriomatous differentiation. The clinicopathologic and immunohistochemical features of the lesion were compatible with hybrid epithelioid schwannoma/perineurioma, a rare morphological variant of peripheral nerve sheath tumors.
Pulmonary functions in children with inflammatory bowel disease
Authors: Gut Guy , Ben-Tov Amir , Lahad Avishai , Soferman Ruth , Cohen Shlomi , Tauman Riva , Sivan Yakov 
Published: February 2016

Objective
To investigate fractional exhaled nitric-oxide (FeNO) levels in children with Crohn’s disease (CD) and ulcerative colitis (UC) and their correlation to disease activity.

Materials and methods
Children with CD and UC (aged 8–18 years) and age-matched healthy controls without respiratory symptoms were recruited. Disease activity was assessed using validated scores. All children performed spirometry and FeNO tests and the association between intestinal disease parameters and pulmonary functions was studied.

Results
Thirty-five children with CD, nine with UC, and 24 healthy controls were enrolled. The mean FeNO level was higher in children with CD compared with the controls. Increased FeNO levels (>23 parts per billion) were more common among CD and UC compared with healthy children (46, 33, and 0%, respectively, P<0.05). Nevertheless, FeNO levels did not correlate with disease activity. There were no significant differences between CD, UC patients, and healthy controls in any of the spirometric variables.

Conclusion
FeNO level, a marker of airway inflammation, is elevated in children with inflammatory bowel diseases irrespective of their intestinal disease activity. Increased FeNO levels are not associated with respiratory symptoms, suggesting a latent pulmonary involvement in the systemic disease.
Cancer Nursing Research Output in Africa 2005 to 2014
Authors: Maree Johanna Elizabeth , Herbert Vivien , Huiskamp Agnes Alice 
Published: February 2016

Background:
This study is the first review of African cancer nursing research as only 1 review focusing on South Africa was conducted in the past decade.

Objective:
The aim of this study was to identify, summarize, and synthesize the findings from previous independent studies conducted by nurses in Africa.

Methods:
The terms cancer nursing and oncology nursing and Africa were used to search PubMed, CINAHL, Web of Science, SA e-publications, and Scopus. Studies reporting research conducted in an African setting, coauthored by a nurse affiliated with an African institution and published between January 1, 2005, and December 31, 2014, in English were included. A data extraction sheet captured the data.

Results:
A potential 536 articles for possible inclusion were identified. Fifty met the inclusion requirements. Cancer in women (78%; n = 39) and prevention and early detection (62%; n = 31) were most commonly investigated. The work was primarily quantitative and collected data on some knowledge aspect from women in the community. Most of the studies (96%; n = 48) did not meet the criteria of high-quality work.

Conclusions:
Africa’s nurses have improved their research output in the field of cancer nursing considerably. Research focusing on the most prevalent cancers, the treatment, the patient living with cancer, the family, extended family, and community is lacking, as is work focusing on pain and other symptoms.

Implications for Nursing Practice:
Nurses in practice should assist nurse researchers to address the identified knowledge gaps to develop cancer nursing science and practice tailored to meet the unique needs of Africa.
IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
Authors: Narayanasamy Shaman , Jarosz Yohan , Muller Emilie E.L. , Laczny Cédric C. , Herold Malte , Kaysen Anne , Heintz-Buschart Anna , Pinel Nicolás , May Patrick , Wilmes Paul 
Published: February 2016

AbstractWe present IMP, an automated pipeline for reproducible integrated analyses of coupled metagenomic and metatranscriptomic data. IMP incorporates preprocessing, iterative co-assembly of metagenomic and metatranscriptomic data, analyses of microbial community structure and function as well as genomic signature-based visualizations. Complementary use of metagenomic and metatranscriptomic data improves assembly quality and enables the estimation of both population abundance and community activity while allowing the recovery and analysis of potentially important components, such as RNA viruses. IMP is containerized using Docker which ensures reproducibility. IMP is available athttp://r3lab.uni.lu/web/imp/.
Integrating regulatory information via combinatorial control of the transcription cycle
Authors: Scholes Clarissa , DePace Angela H. , Sánchez Álvaro 
Published: February 2016

ABSTRACTCombinatorial regulation of gene expression by multiple transcription factors (TFs) enables cells to carry out sophisticated computations that are key to cellular decision-making. How is the information contained in multiple TF binding sites integrated to dictate the rate of transcription? The dominant model is that direct or indirect physical interactions between TFs enable them to combinatorially recruit each other and RNA polymerase to the promoter. Here we develop a quantitative framework to explore an alternative model, where combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle. Our results clarify the null hypotheses for independent action of TFs and show that combinatorial control of the transcription cycle can generate a wide range of analog and Boolean computations without requiring the input regulators to be simultaneously co-localized in the nucleus. This work emphasizes the importance of deciphering TF function beyond activation and repression, highlights the role of the basal promoter in processing regulatory information and suggests qualitative explanations for the flexibility of regulatory evolution.
Analysis of Two-State Folding Using Parabolic Approximation IV: Non-Arrhenius Kinetics of FBP28 WW Part-II
Authors: Sade Robert S. 
Published: February 2016

AbstractA model which treats the denatured and the native conformers as being confined to harmonic Gibbs energy wells has been used to rationalize the physical basis for the non-Arrhenius behaviour of spontaneously-folding fixed two-state systems. It is shown that at constant pressure and solvent conditions: (i) the rate constant for folding will be a maximum when the heat released upon formation of net molecular interactions is exactly compensated by the heat absorbed to desolvate net polar and non-polar solvent accessible surface area (SASA), as the denatured conformers driven by thermal noise bury their SASA and diffuse on the Gibbs energy surface to reach the activated state; (ii) the rate constant for unfolding will be a minimum when the heat absorbed by the native conformers to break various net backbone and sidechain interactions is exactly compensated by the heat of hydration released due to the net increase in SASA, as the native conformers unravel to reach the activated state; (iii) the activation entropy for folding will be zero, and the Gibbs barrier to folding will be a minimum, when the decrease in the backbone and the sidechain mobility is exactly compensated by the increase in entropy due to solvent-release, as the denatured conformers bury their SASA to reach the activated state; (iv) the activation entropy for unfolding will be zero, and the Gibbs barrier to unfolding will be a maximum when the increase in the backbone and sidechain mobility is exactly compensated by the negentropy of solvent-capture on the protein surface, as the native conformers unravel to reach the activated state; (v) while cold denaturation is driven by solvent effects, heat denaturation is primarily due to chain effects; (vi) the speed-limit for the folding is ultimately due to conformational searching; and (vii) Levinthal’s paradox may have little basis if the entropy of solvent-release that accompanies protein folding is taken into consideration.
Detailed temporal structure of communication networks in groups of songbirds
Authors: Stowell Dan , Gill Lisa , Clayton David 
Published: February 2016

AbstractAnimals in groups often exchange calls, in patterns whose temporal structure may be influenced by contextual factors such as physical location and the social network structure of the group. We introduce a model-based analysis for temporal patterns of animal call timing, originally developed for networks of firing neurons. This has advantages over cross-correlation analysis in that it can correctly handle common-cause confounds and provides a generative model of call patterns with explicit parameters for the influences between individuals. It also has advantages over standard Markovian analysis in that it incorporates detailed temporal interactions which affect timing as well as sequencing of calls. Further, a fitted model can be used to generate novel synthetic call sequences. We apply the method to calls recorded from groups of domesticated zebra finch (Taenopyggia guttata) individuals. We find that the communication network in these groups has stable structure that persists from one day to the next, and that “kernels” reflecting the temporal range of influence have a characteristic structure for a calling individual’s effect on itself, its partner, and on others in the group. We further find characteristic patterns of influences by call type as well as by individual.
No evidence for the positive relationship between genetic correlations and heritabilities
Authors: Drobniak Szymon M. , Cichoń Mariusz 
Published: February 2016

AbstractQuantitative genetics predicts, that traits subjected to strong selection should show low heritability and may yield biased estimates of genetic correlations (rg). Similar pattern may also appear if genetic sources of variation are confounded with non-genetic sources. Thus, a positive relationship between genetic correlations and heritabilities (h2) of underlying traits might be observed. Here we test this prediction using a large dataset of published estimates of genetic correlations and employing a powerful meta-analytical approach. We considered both between-traits and cross-sex genetic correlations. We failed to find support for the prediction about a positive rg– h2relationship: our analysis based on nearly 1000 published estimates of genetic parameters indicates that the predicted relationship is weak and statistically non-significant. Thus, low heritability does not preclude the possibility of detecting substantial genetic correlations. Our meta-analysis indicates that published estimates of genetic parameters coming from various experimental designs and obtained using different statistical techniques are not significantly biased in case of weakly-heritable traits.
Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes ofDrosophila melanogaster
Authors: Keightley Peter D. , Campos José L. , Booker Tom R. , Charlesworth Brian 
Published: February 2016

AbstractMany approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derivedversusancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ˜50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength ofNes ≈12.
Inter- and intra-individual differences in fluid reasoning show distinct cortical responses
Authors: Kievit Rogier A. , Scholte H. Steven , Waldorp Lourens J. , Borsboom Denny 
Published: February 2016

AbstractFluid intelligence is a general cognitive ability associated with problem solving in the absence of task-specific knowledge. Neuroscientific studies of fluid intelligence have studied both fluid intelligence tasks of varying difficulty and individual differences in fluid intelligence ability, but have failed to appropriately distinguish the two dimensions. Here we use task-based fMRI (N=34) to show thatwithinandbetweensubject dimensions show both partial overlap and widespread differences. Individuals with higher ability showed widespread increased activity including bilateral frontoparietal systems, whereas more difficult items were associated with more focal activity increases in middle frontal gyri, frontal poles and superior frontal poles. Finally, we show that when difficulty is equated across individuals, those with higher ability tend to show more fronto-parietal activity, whereas low fluid intelligence individuals tend to show greater activity in higher visual areas. The fMRI and behavioural data for our paper are freely available in online repositories.