bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutant p53 accumulation in human breast cancer is not an intrinsic property or dependent on structural or functional disruption but is regulated by exogenous stress and receptor status
Authors: Bouchalova Pavla , Nenutil Rudolf , Muller Petr , Hrstka Roman , Appleyard M Virginia , Murray Karen , Jordan Lee B , Purdie Colin A , Quinlan Philip , Thompson Alastair M , Vojtesek Borivoj , Coates Philip J 
Published: March 2014

AbstractMany human cancers contain missense TP53 mutations that result in p53 protein accumulation. Although generally considered as a single class of mutations that abrogate wild‐type function, individual TP53 mutations may have specific properties and prognostic effects. Tumours that contain missense TP53 mutations show variable p53 stabilization patterns, which may reflect the specific mutation and/or aspects of tumour biology. We used immunohistochemistry on cell lines and human breast cancers with known TP53 missense mutations and assessed the effects of each mutation with four structure–function prediction methods. Cell lines with missense TP53 mutations show variable percentages of cells with p53 stabilization under normal growth conditions, ranging from approximately 50% to almost 100%. Stabilization is not related to structural or functional disruption, but agents that stabilize wild‐type p53 increase the percentages of cells showing missense mutant p53 accumulation in cell lines with heterogeneous stabilization. The same heterogeneity of p53 stabilization occurs in primary breast cancers, independent of the effect of the mutation on structural properties or functional disruption. Heterogeneous accumulation is more common in steroid receptor‐positive or HER2‐positive breast cancers and cell lines than in triple‐negative samples. Immunohistochemcal staining patterns associate with Mdm2 levels, proliferation, grade and overall survival, whilst the type of mutation reflects downstream target activity. Inhibiting Mdm2 activity increases the extent of p53 stabilization in some, but not all, breast cancer cell lines. The data indicate that missense mutant p53 stabilization is a complex and variable process in human breast cancers that associates with disease characteristics but is unrelated to structural or functional properties. That agents which stabilize wild‐type p53 also stabilize mutant p53 has implications for patients with heterogeneous mutant p53 accumulation, where therapy may activate mutant p53 oncogenic function. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Impacts of vortex intensity and outer winds on tropical cyclone size
Authors: Chan Kelvin T. F. , Chan Johnny C. L. 
Published: March 2014

The present study seeks to understand how the initial vortex intensity and outer winds influence tropical cyclone (TC) size, which is defined as the azimuthally averaged radius of the 10 m 17 m s−1 wind from the TC centre (R17), using a full baroclinic model in a quiescent f‐plane environment. The initial vortex intensity is found to influence the size growth rate in the developing phase of the vortex life cycle. However, when the vortex comes to the mature and/or decaying phase of the vortex life cycle, the initial vortex intensity (ranging between 20 and 40 m s−1 in this study) does not strongly affect TC size. On the other hand, vortex intensification or re‐intensification resulting from inner‐core dynamics is apparently favourable for size growth in most instances. In addition, the lower‐tropospheric outer winds of a vortex (i.e. winds beyond R17; e.g. the environmental flows around the TC) are found to be an important factor governing size change. The outer winds closer to R17 are more effective and can influence the vortex size at an earlier stage, especially if the winds are strong.The impact of the initial lower‐tropospheric outer winds on the TC size evolution appears to be more prominent than that of the initial vortex intensity. The size change is much more sensitive to the outer‐core, rather than inner‐core, dynamics. The higher the angular momentum (AM) beyond R17, the more the AM can be brought towards the centre and hence favour size growth, and vice versa.
Improving manual vacuum aspiration service delivery, introducing misoprostol for cases of incomplete abortion, and strengthening postabortion contraception in Bangladesh
Authors: Begum Ferdousi , Zaidi Shahida , Fatima Parveen , Shamsuddin Latifa , Anowar‐ul‐Azim A.K.M. , Begum Rowshan Ara 
Published: March 2014

AbstractThe Obstetrical and Gynaecological Society of Bangladesh was an important advocate in mobilizing government authorities to adopt new techniques for postabortion care and provide long‐acting contraceptives post abortion. With the support of the International Federation of Gynecology and Obstetrics (FIGO), the Society provided commodities and training to increase the use of these techniques in 7 private and public hospitals and clinics. Data from two of these institutes for the January 2012 to June 2013 period showed a rapid decrease in the use of dilation and curettage, an increase in the use of manual vacuum aspiration (MVA) and misoprostol, and the progressive adoption of long‐acting reversible contraceptives, permanent contraception, and injectable contraceptives in one of these two hospitals. The Directorates General of Health and Family Planning incorporated training in the use of MVA and misoprostol in their national operation plans. The success in these hospitals shows that the proposed changes have been well accepted by providers and clients.
Changes in the use of manual vacuum aspiration for postabortion care within the public healthcare service network in Honduras
Authors: Chinchilla Ana Ligia , Flores Ivo Flores , Morales Alma Fabiola , de Gil Marina Padilla 
Published: March 2014

AbstractHonduras is one of the 17 priority countries included in the International Federation of Gynecology and Obstetrics (FIGO) Initiative for the Prevention of Unsafe Abortion and its Consequences. The priority category enables the country to request emergency funding to acquire services or commodities that could contribute toward achieving the objectives laid out in its plan of action. These objectives include improving postabortion care by increasing the use of manual vacuum aspiration (MVA) as an outpatient procedure with minimal human and material resources. Since the Ministry of Health lacked funding, use of the emergency fund was approved for the purchase and distribution of MVA kits nationwide to ensure continuity and the hope of increasing MVA use. Eleven hospitals participating in this initiative provided data for analysis of the outcome. These data show no increase in MVA use; however, as discussed in the article, further investigation provided valuable information on the reasons behind these results.
Multiple finger propagation modes in Hele-Shaw channels of variable depth
Authors: Thompson Alice B. , Juel Anne , Hazel Andrew L. 
Published: March 2014

AbstractWe consider the propagation of an air finger into a wide fluid-filled channel with a spatially varying depth profile. Our aim is to understand the origin of the multiple coexisting families of both steady and oscillatory propagating fingers previously observed in experiments in axially uniform channels each containing a centred step-like occlusion. We find that a depth-averaged model can reproduce all the finger propagation modes observed experimentally. In addition, the model reveals new modes for symmetric finger propagation. The inclusion of a spatially variable channel depth in the depth-averaged equations leads to: (i) a variable mobility coefficient within the fluid domain due to variations in viscous resistance of the channel; and (ii) a variable transverse curvature term in the dynamic boundary condition that modifies the pressure jump over the air–liquid interface. We use our model to examine the roles of these two distinct effects and find that both contribute to the steady bifurcation structure, while the transverse curvature term is responsible for the distinctive oscillatory propagation modes.
Speeding up thermocapillary migration of a confined bubble by wall slip
Authors: Liao Ying-Chih , Li Yen-Ching , Chang Yu-Chih , Huang Chih-Yung , Wei Hsien-Hung 
Published: March 2014

AbstractIt is usually believed that wall slip contributes small effects to macroscopic flow characteristics. Here we demonstrate that this is not the case for the thermocapillary migration of a long bubble in a slippery tube. We show that a fraction of the wall slip, with the slip length $\lambda $ much smaller than the tube radius $R$, can make the bubble migrate much faster than without wall slip. This speedup effect occurs in the strong-slip regime where the film thickness $b$ is smaller than $\lambda $ when the Marangoni number $S= \tau _{T} R/\sigma _{0}~ (\ll 1)$ is below the critical value $S^* \sim (\lambda /R)^{1/2}$, where $\tau _{T}$ is the driving thermal stress and $\sigma _{0}$ is the surface tension. The resulting bubble migration speed is found to be $U_{b} \sim (\sigma _{0}/\mu )S^{3}(\lambda /R)$, which can be more than a hundred times faster than the no-slip result $U_{b} \sim (\sigma _{0}/\mu )S^{5}$ (Wilson, J. Eng. Math., vol. 29, 1995, pp. 205–217; Mazouchi & Homsy, Phys. Fluids, vol. 12, 2000, pp. 542–549), with $\mu $ being the fluid viscosity. The change from the fifth power law to the cubic one also indicates a transition from the no-slip state to the strong-slip state, albeit the film thickness always scales as $b\sim RS^{2}$. The formal lubrication analysis and numerical results confirm the above findings. Our results in different slip regimes are shown to be equivalent to those for the Bretherton problem (Liao, Li & Wei, Phys. Rev. Lett., vol. 111, 2013, 136001). Extension to polygonal tubes and connection to experiments are also made. It is found that the slight discrepancy between experiment (Lajeunesse & Homsy, Phys. Fluids, vol. 15, 2003, pp. 308–314) and theory (Mazouchi & Homsy, Phys. Fluids, vol. 13, 2001, pp. 1594–1600) can be interpreted by including wall slip effects.
Language effects on the conceptualization of hybrids
Authors: MASHAL NIRA , SHEN YESHAYAHU , JOSPE KARINE , GIL DAVID 
Published: March 2014

abstractThe current study investigates the conceptual hierarchy of humans−animals−plants−non-animate objects by using novel hybrids. Three experiments were conducted. In Experiment 1, twenty-one participants were presented with a grammatically asymmetrical phrase, in which the two components are associated with different linguistic properties, (e.g.,a man with a horse’s head) followed by a visual hybrid, and were asked to judge whether the phrase described the hybrid. In Experiment 2, thirty participants were presented with a visual hybrid and were asked to categorize it according to one of its visually presented components in a forced-choice judgment task. In Experiment 3, twenty-nine participants were presented with a visual hybrid that followed a grammatically symmetrical phrase, in which both components carry similar grammatical properties (e.g.,half-human half-horse), and were asked to judge whether the phrase described the hybrid. A conceptual hierarchy effect was found in Experiment 1 but not in the other two experiments. These findings show that the hierarchy effect occurs only in verbal tasks that involve asymmetrical grammatical constructions. We suggest that the pragmatic tendency to map the hierarchically higher concept onto the higher grammatical function applies to asymmetrical constructions but not to symmetrical constructions.
Comparing parasitological vs serological determination of Schistosoma haematobium infection prevalence in preschool and primary school-aged children: implications for control programmes
Authors: WAMI WELCOME M. , NAUSCH NORMAN , BAUER KATHARINA , MIDZI NICHOLAS , GWISAI REGGIS , SIMMONDS PETER , MDULUZA TAKAFIRA , WOOLHOUSE MARK , MUTAPI FRANCISCA 
Published: March 2014

SUMMARYTo combat schistosomiasis, the World Health Organization (WHO) recommends that infection levels are determined prior to designing and implementing control programmes, as the treatment regimens depend on the population infection prevalence. However, the sensitivity of the parasitological infection diagnostic method is less reliable when infection levels are low. The aim of this study was to compare levels of Schistosoma haematobium infection obtained by the parasitological method vs serological technique. Infection levels in preschool and primary school-aged children and their implications for control programmes were also investigated. Infection prevalence based on serology was significantly higher compared with that based on parasitology for both age groups. The difference between infection levels obtained using the two methods increased with age. Consequentially, in line with the WHO guidelines, the serological method suggested a more frequent treatment regimen for this population compared with that implied by the parasitological method. These findings highlighted the presence of infection in children aged ⩽5 years, further reiterating the need for their inclusion in control programmes. Furthermore, this study demonstrated the importance of using sensitive diagnostic methods as this has implications on the required intervention controls for the population.
Iranian EFL teachers’ perceptions of the difficulties of implementing CALL
Authors: Hedayati Hora (Fatemeh) , Marandi S. Susan 
Published: March 2014

AbstractDespite the spread of reliable technological tools and the availability of computers in Iranian universities, as well as the mounting evidence of the effectiveness of blended learning, many Iranian language teachers are still reluctant to incorporate such tools in their English as a foreign language (EFL) classes. This study inspected the status quo of technology integration in Iranian EFL classes and investigated the obstacles, as perceived by the Iranian EFL teachers, toward implementing CALL in Iran. First, 100 EFL teachers completed the Teacher Technology Integration Survey developed by Vannatta and Banister (2009), to help estimate technology use in EFL classes. Then the researchers interviewed twelve teachers, comprising two EFL teacher educators with no CALL experience, four teachers with the experience of integrating technology in their EFL classes, four EFL teachers who had recently finished an online CALL teacher education program, and two EFL teachers with no CALL experience. The semi-structured interview questions were designed by the researchers, one of whom has extensive experience with CALL, and were revised based on the suggestions of a colleague with expertise in teacher education. One of the researchers conducted the interviews, each of which lasted for 30–50 minutes. The researchers used structural content analysis of the interview transcripts to find themes relevant to the research question. The results suggest that on the whole, Iranian EFL teachers do not usually integrate digital technology into their classes; and the obstacles in implementing CALL in language classrooms could be classified into three categories: teacher, facility, and learner constraints. Each of the categories is discussed in detail and suggestions are provided for promoting CALL in the Iranian context.
Very fast germination: additional records and relationship to embryo size and phylogeny
Authors: Parsons Robert F. , Vandelook Filip , Janssens Steven B. 
Published: March 2014

AbstractRecently, a list has been published of angiosperms capable of germinating in less than 24 h (‘very fast germination’). Here, we add three families and 23 species to that list. The main extra families complement ecological groups already recognized – the Cactaceae into the aridity-adapted group and the Tamaricaceae into the floodplain-adapted group. These amended findings on very fast germination (VFG) are integrated into the recent work on the functional ecology of embryo size. They confirm the important connection between germination speed and embryo to seed ratio. Plotting the plant orders containing VFG species on a phylogenetic tree shows that VFG has evolved multiple times throughout angiosperm history, including at least three times within the Caryophyllales. The fact that species with VFG are mainly restricted to advanced clades shows that VFG is a derived trait that evolved as an adaptation to either arid, saline or floodplain habitats.
5-Azacytidine treatment sensitizes tumor cells to T-cell mediated cytotoxicity and modulates NK cells in patients with myeloid malignancies
Authors: Gang A O , Frøsig T M , Brimnes M K , Lyngaa R , Treppendahl M B , Grønbæk K , Dufva I H , Straten P thor , Hadrup S R 
Published: March 2014

AbstractTreatment with the demethylating agent 5-Azacytidine leads to prolonged survival for patients with myelodysplastic syndrome, and the demethylation induces upregulation of cancer-testis antigens. Cancer-testis antigens are well-known targets for immune recognition in cancer, and the immune system may have a role in this treatment regimen. We show here that 5-Azacytidine treatment leads to increased T-cell recognition of tumor cells. T-cell responses against a large panel of cancer-testis antigens were detected before treatment, and these responses were further induced upon initiation of treatment. These characteristics point to an ideal combination of 5-Azacytidine and immune therapy to preferentially boost T-cell responses against cancer-testis antigens. To initiate such combination therapy, essential knowledge is required about the general immune modulatory effect of 5-Azacytidine. We therefore examined potential treatment effects on both immune stimulatory (CD8 and CD4 T cells and Natural Killer (NK) cells) and immune inhibitory cell subsets (myeloid-derived suppressor cells and regulatory T cells). We observed a minor decrease and modulation of NK cells, but for all other populations no effects could be detected. Together, these data support a strategy for combining 5-Azacytidine treatment with immune therapy for potential clinical benefit.
Communication: Resolving the three-body contribution to the lattice energy of crystalline benzene: Benchmark results from coupled-cluster theory
Authors: Kennedy Matthew R. , McDonald Ashley Ringer , DePrince A. Eugene , Marshall Michael S. , Podeszwa Rafal , Sherrill C. David 
Published: March 2014

Coupled-cluster theory including single, double, and perturbative triple excitations [CCSD(T)] has been applied to trimers that appear in crystalline benzene in order to resolve discrepancies in the literature about the magnitude of non-additive three-body contributions to the lattice energy. The present results indicate a non-additive three-body contribution of 0.89 kcal mol−1, or 7.2% of the revised lattice energy of −12.3 kcal mol−1. For the trimers for which we were able to compute CCSD(T) energies, we obtain a sizeable difference of 0.63 kcal mol−1 between the CCSD(T) and MP2 three-body contributions to the lattice energy, confirming that three-body dispersion dominates over three-body induction. Taking this difference as an estimate of three-body dispersion for the closer trimers, and adding an Axilrod-Teller-Muto estimate of 0.13 kcal mol−1 for long-range contributions yields an overall value of 0.76 kcal mol−1 for three-body dispersion, a significantly smaller value than in several recent studies.
CAGExploreR: an R package for the analysis and visualization of
promoter dynamics across multiple experiments
Authors: Dimont Emmanuel , Hofmann Oliver , Ho Sui Shannan J , Forrest Alistair R R , Kawaji Hideya , Hide Winston ,   the FANTOM Consortium
Published: March 2014

Summary
Alternate promoter usage is an important molecular mechanism for generating RNA and protein diversity. Cap Analysis Gene Expression (CAGE) is a powerful approach for revealing the multiplicity of transcription start site (TSS) events across experiments and conditions. An understanding of the dynamics of TSS choice across these conditions requires both sensitive quantification and comparative visualization. We have developed CAGExploreR, an R package to detect and visualize changes in the use of specific TSS in wider promoter regions in the context of changes in overall gene expression when comparing different CAGE samples. These changes provide insight into the modification of transcript isoform generation and regulatory network alterations associated with cell types and conditions. CAGExploreR is based on the FANTOM5 and MPromDb promoter set definitions but can also work with user-supplied regions. The package compares multiple CAGE libraries simultaneously. Supplementary Materials describe methods in detail, and a vignette demonstrates a workflow with a real data example.
Availability and implementation: The package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/CAGExploreR).
Contact: edimont@mail.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A Comparison of Peak Callers Used for DNase-seq Data
Authors: Koohy Hashem , Down Thomas A. , Spivakov Mikhail , Hubbard Tim 
Published: March 2014

AbstractGenome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements. A variety of algorithms have been developed to identify regions of open chromatin from raw sequence-tag data, which has motivated us to assess and compare their performance.In this study, four published, publicly available peak calling algorithms used for DNase-seq data analysis (F-seq, Hotspot, MACS and ZINBA) are assessed at a range of signal thresholds on two published DNase-seq datasets for three cell types. The results were benchmarked against an independent dataset of regulatory regions derived from ENCODE in vivo transcription factor binding data for each particular cell type. The level of overlap between peak regions reported by each algorithm and this ENCODE-derived reference set was used to assess sensitivity and specificity of the algorithms.Our study suggests that F-seq has a slightly higher sensitivity than the next best algorithms. Hotspot and the ChIP-seq oriented method, MACS, both perform competitively when used with their default parameters. However the generic peak finder ZINBA appears to be less sensitive than the other three.We also assess accuracy of each algorithm over a range of signal thresholds. In particular, we show that the accuracy of F-Seq can be considerably improved by using a threshold setting that is different from the default value.