bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mucoepidermoid carcinoma arising in Warthin’s tumor of the parotid gland: Clinicopathological characteristics and immunophenotypes
Authors: Yu Chunkai , Song Zhigang , Xiao Zhibo , Lin Qiushi , Dong Xiaoqun 
Published: July 2016

AbstractMucoepidermoid carcinoma (MEC), an extremely rare tumor, arises from the epithelial component of preexisting parotid Warthin tumors (WT). Among the 309 cases of surgically resected WTs in Chinese PLA General Hospital and Beijing Shijitan Hospital of Capital Medical University, 5 cases (1.6%) fulfilled the criteria for MECs transformed from WTs. Clinicopathological characteristics of MECs was demonstrated in order to avoid misdiagnosis of this rare type of tumor. All the 5 patients, 3 males and 2 females, presented painless masses in the parotid gland. MECs were located inside or at the edge of WTs, with an obvious transitional zone between WT and MEC. Basal cells of WTs and epidermoid cells of MECs were strongly positive for cytokeratin CK5/6, CK34βE12, and P63; whereas negative for CK7, CK20, and CEA. Mucous cells of MECs were positive for CK7, CEA, as well as periodic acid-Schiff (PAS), whereas negative for CK5/6, CK34βE12, CK20, and P63. MECs patients were followed up for 25–69 months after surgery, presenting no evidence of recurrence or metastasis. Collectively, MECs arising from WT is very rare. The pathological diagnosis was based on histological morphology, especially the transitional zone between WT and MEC.
The Role of Socioeconomic Status in the Narrative Story Retells of School-Aged English Language Learners
Authors: Alt Mary , Arizmendi Genesis D. , DiLallo Jennifer N. 
Published: July 2016

Purpose
We examined the relationship between maternal level of education as an index of socioeconomic status (SES) on the narrative story retells of school-aged children who are English language learners (ELLs) to guide interpretation of results.

Method
Using data available from the Systematic Analysis of Language Transcripts database (Miller & Iglesias, 2012), we were able to compare the language samples of 907 ELL students in kindergarten and 2nd grade whose parents had different levels of education. We used a simple linear regression to see if maternal level of education was predictive of measures of vocabulary, syntax, and narrative structure in Spanish and English narrative story retells.

Results
There were no differences in language measures between children from different SES backgrounds for the Spanish language samples. There were differences with the English language samples in four of the five measures for the kindergarten sample and only three of five measures for the older children, with a smaller percentage of the variance explained.

Conclusion
Despite common knowledge that SES has a negative influence on language, the actual influence on the narrative productions of school-aged ELLs was less than anticipated for English and absent for Spanish. The implications for assessment are discussed and concluded.
Unexpected biases in the distribution of consecutive primes
Authors: Lemke Oliver Robert J. , Soundararajan Kannan 
Published: July 2016

Significance

Prime numbers play a central role in analytic number theory, and are well known to be very well distributed among the reduced residue classes

(

mod

q

)

. Surprisingly, the same does not appear to be true for sequences of consecutive primes, with different patterns occurring with wildly different frequencies. We formulate a precise conjecture, based on the Hardy−Littlewood conjectures, which explains this phenomenon. In particular, we predict that all patterns do occur their fair share of the time in the limit, but that there are secondary terms only very slowly tending to zero that create the observed biases.
Accuracy evaluation of a 3D-printed individual template for needle guidance in head and neck brachytherapy
Authors: Huang Ming-Wei , Zhang Jian-Guo , Zheng Lei , Liu Shu-Ming , Yu Guang-Yan 
Published: July 2016

Abstract
To transfer the preplan for the head and neck brachytherapy to the clinical implantation procedure, a preplan-based 3D-printed individual template for needle insertion guidance had previously been designed and used. The accuracy of needle insertion using this kind template was assessed in vivo. In the study, 25 patients with head and neck tumors were implanted with 125I radioactive seeds under the guidance of the 3D-printed individual template. Patients were divided into four groups based on the site of needle insertion: the parotid and masseter region group (nine patients); the maxillary and paranasal region group (eight patients); the submandibular and upper neck area group (five patients); and the retromandibular region group (six patients). The distance and angular deviations between the preplanned and placed needles were compared, and the complications and time required for needle insertion were assessed. The mean entrance point distance deviation for all 619 needles was 1.18 ± 0.81 mm, varying from 0.857 ± 0.545 to 1.930 ± 0.843 mm at different sites. The mean angular deviation was 2.08 ± 1.07 degrees, varying from 1.85 ± 0.93 to 2.73 ± 1.18 degrees at different sites. All needles were manually inserted to their preplanned positions in a single attempt, and the mean time to insert one needle was 7.5 s. No anatomical complications related to inaccurately placed implants were observed. Using the 3D-printed individual template for the implantation of 125I radioactive seeds in the head and neck region can accurately transfer a CT-based preplan to the brachytherapy needle insertion procedure. Moreover, the addition of individual template guidance can reduce the time required for implantation and minimize the damage to normal tissues.
Consecutive CT-guided core needle tissue biopsy of lung lesions in the same dog at different phases of radiation-induced lung injury
Authors: Yin Zhongyuan , Deng Sisi , Liang Zhiwen , Wang Qiong 
Published: July 2016

Abstract
This project aimed to set up a Beagle dog model of radiation-induced lung injury in order to supply fresh lung tissue samples in the different injury phases for gene and protein research. Three dogs received 18 Gy X-ray irradiation in one fraction, another three dogs received 8 Gy in each of three fractions at weekly intervals, and one control dog was not irradiated. Acute pneumonitis was observed during the first 3 months after radiation, and chronic lung fibrosis was found during the next 4–12 months in all the dogs exposed to radiation. CT-guided core needle lung lesion biopsies were extracted from each dog five times over the course of 1 year. The dogs remained healthy after each biopsy, and 50–100 mg fresh lung lesion tissues were collected in each operation. The incidence of pneumothorax and hemoptysis was 20% and 2.8%, respectively, in the 35 tissue biopsies. A successful and stable radiation-induced lung injury dog model was established. Lung lesion tissue samples from dogs in acute stage, recovery stage and fibrosis stage were found to be sufficient to support cytology, genomics and proteomics research. This model safely supplied fresh tissue samples that would allow future researchers to more easily explore and develop treatments for radiation-induced lung injury.
Morphological and molecular features of astroblastoma, includingBRAFV600Emutations, suggest an ontological relationship to other cortical-based gliomas of children and young adults
Authors: Lehman Norman L. , Hattab Eyas M. , Mobley Bret C. , Usubalieva Aisulu , Schniederjan Matthew J. , McLendon Roger E. , Paulus Werner , Rushing Elisabeth J. , Georgescu Maria-Magdalena , Couce Marta , Dulai Mohanpal S. , Cohen Mark L. , Pierson Christopher R. , Raisanen Jack M. , Martin Sarah E. , Lehman Trang D. , Lipp Eric S. , Bonnin Jose M. , Al-Abbadi Mousa A. , Kenworthy Kara , Zhao Kevin , Mohamed Nehad , Zhang Guojuan , Zhao Weiqiang 
Published: July 2016

AbstractBackground.Astroblastomas (ABs) are rare glial tumors showing overlapping features with astrocytomas, ependymomas, and sometimes other glial neoplasms, and may be challenging to diagnose.Methods.We examined clinical, histopathological, and molecular features in 28 archival formalin-fixed, paraffin-embedded AB cases and performed survival analyses using Cox proportional hazards and Kaplan–Meier methods.Results.Unlike ependymomas and angiocentric gliomas, ABs demonstrate abundant distinctive astroblastic pseudorosettes and are usually Olig2 immunopositive. They also frequently exhibit rhabdoid cells, multinucleated cells, and eosinophilic granular material. They retain immunoreactivity to alpha thalassemia/mental retardation syndrome X-linked, are immunonegative to isocitrate dehydrogenase-1 R132H mutation, and only occasionally show MGMT promoter hypermethylation differentiating them from many diffuse gliomas. Like pleomorphic xanthoastrocytoma, ganglioglioma, supratentorial pilocytic astrocytoma, and other predominantly cortical-based glial tumors, ABs often harbor the BRAFV600E mutation, present in 38% of cases tested (n = 21), further distinguishing those tumors from ependymomas and angiocentric gliomas. Factors correlating with longer patient survival included age less than 30 years, female gender, absent BRAFV600E, and mitotic index less than 5 mitoses/10 high-power fields; however, only the latter was significant by Cox and Kaplan–Meier analyses (n = 24; P = .024 and .012, respectively). This mitotic cutoff is therefore currently the best criterion to stratify tumors into low-grade ABs and higher-grade anaplastic ABs.Conclusions.In addition to their own characteristic histological features, ABs share some molecular and histological findings with other, possibly ontologically related, cortical-based gliomas of mostly children and young adults. Importantly, the presence of BRAFV600E mutations in a subset of ABs suggests potential clinical utility of targeted anti-BRAF therapy.
Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo
Authors: Kapli P. , Lutteropp S. , Zhang J. , Kobert K. , Pavlidis P. , Stamatakis A. , Flouri T. 
Published: July 2016

ABSTRACTMotivationIn recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced “Poisson Tree Processes” (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.ResultsWe introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently, yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.AvailabilitymPTP is implemented in C and is available for download athttp://github.com/Pas-Kapli/mptpunder the GNU Affero 3 license. A web-service is available athttp://mptp.h-its.org.ContactPaschalia.Kapli@h-its.org,Alexandros.Stamatakis@hits.org,Tomas.Flouri@h-its.org
Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort
Authors: Viñuela Ana , Brown Andrew A , Buil Alfonso , Tsai Pei-Chien , Davies Matthew N , Bell Jordana T , Dermitzakis Emmanouil T , Spector Timothy D , Small Kerrin S 
Published: July 2016

AbstractGene expression changes with age have consequences for healthy aging and disease development. Here we investigate age-related changes in gene expression measured by RNA-seq in four tissues and the interplay between genotypes and age-related changes in expression. Using concurrently measured methylation array data from fat we also investigate the relationship between methylation, gene expression and age. We identified age-dependent changes in mean levels of gene expression in 5,631 genes and in splicing of 904 genes. Age related changes were widely shared across tissues, with up to 60% of age-related changes in expression and 47% on splicing in multi-exonic genes shared; amongst these we highlight effects on genes involved in diseases such as Alzheimer and cancer. We identified 137 genes with age-related changes in variance and 42 genes with age-dependent discordance between genetically identical individuals; implying the latter are driven by environmental effects. We also give four examples where genetic control of expression is affected by the aging process. Analysis of methylation observed a widespread and stronger effect of age on methylation than expression; however we did not find a strong relationship between age-related changes in both expression and methylation. In summary, we quantified aging affects in splicing, level and variance of gene expression, and show that these processes can be both environmentally and genetically influenced.
Distance Sampling inR
Authors: Miller David L , Rexstad Eric , Thomas Len , Marshall Laura , Laake Jeffrey L 
Published: July 2016

AbstractEstimating the abundance and spatial distribution of animal and plant populations is essential for conservation and management. We introduce theRpackageDistancethat implements distance sampling methods to estimate abundance. We describe how users can obtain estimates of abundance (and density) using the package as well documenting the links it provides with other more specializedRpackages. We also demonstrate howDistanceprovides a migration pathway from previous software, thereby allowing us to deliver cutting-edge methods to the users more quickly.
The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II
Authors: Laxa Miriam , Müller Kristin , Lange Natalie , Doering Lennart , Pruscha Jan Thomas , Peterhänsel Christoph 
Published: July 2016

AbstractPhotorespiration is essential for the detoxification of glycolate and recycling of carbon to the Calvin Benson Bassham cycle. Enzymes participating in the pathway have been identified, and investigations now focus on the regulation of photorespiration by transporters and metabolites. However, regulation of photorespiration on the gene level has not been intensively studied. Here, we show that maximum transcript abundance of Glu:glyoxylate aminotransferase 1 (GGT1) is regulated by intron-mediated enhancement (IME) of the 5′ leader intron rather than by regulatory elements in the 5′ upstream region. The intron is rich in CT-stretches and contains the motif TGTGATTTG that is highly similar to the IME-related motif TTNGATYTG. The GGT1 intron also confers leaf-specific expression of foreign promoters. Quantitative PCR analysis and GUS activity measurements revealed that IME of the GGT1 5′UTR intron is controlled on the transcriptional level. IME by the GGT1 5′UTR intron was at least 2-fold. Chromatin immunoprecipitation experiments showed that the abundance of RNA polymerase II binding to the intron-less construct is reduced.
Identifying successful strategies for honey value chains in Brazil: a conjoint study
Authors: Figueiredo Junior Hugo Santana de , Meuwissen Miranda P. M. , Van der Lans Ivo A. , Oude Lansink Alfons G. J. M. 
Published: July 2016

Purpose– Development studies rarely measure the impact of value chain strategies on performance. The purpose of this paper is to quantify the perceived contribution of strategies to the performance of three honey value chains in Brazil.Design/methodology/approach– The value chain structure-conduct-performance (SCP) framework was used to select strategies and two performance indicators, honey production growth and local value-added. In a conjoint study, experts were asked to judge the contribution to the two performance indicators of several hypothetical combinations of value chain strategies.Findings– According to the experts, adoption of specialised technical assistance, sharing resources at the production step, increase in exports, and organic certification were the strategies which contributed the most to performance. Simulations suggested that some honey value chains could have greatly increased their performance with these higher pay-off strategies.Research limitations/implications– Quantifying the perceived impact of individual strategies contributes to improved evaluation of development interventions.Practical implications– Outcomes also show that conjoint analysis is a useful method for policy evaluations in data scarce situations.Originality/value– The paper combines an extended SCP framework for strategy selection and conjoint analysis for strategy evaluation of value chains.
Serving sizes and energy values on the nutrition labels of regular and diet/light processed and ultra-processed dairy products sold in Brazil
Authors: Machado Priscila Pereira , Kraemer Mariana Vieira dos Santos , Kliemann Nathalie , Colussi Cláudia Flemming , Veiros Marcela Boro , Proença Rossana Pacheco da Costa 
Published: July 2016

Purpose– The purpose of this paper is to analyse and compare the serving sizes and energy values reported on the nutrition information of all processed and ultra-processed dairy products in their regular and diet/light versions available for sale in a large supermarket in Brazil.Design/methodology/approach– A check was done for associations between the compliance of reported serving sizes, energy values per serving and energy density for regular foods and foods advertised at “diet/light” (with reduced fat and calories).Findings– The data included information from 451 dairy product labels. Most of the products had serving sizes smaller than the reference set by Brazilian law. A high variability of serving sizes was found for similar products. “Diet/light” foods tend to report serving sizes that are even smaller and more inadequate. Moreover, the energy density of these products was similar to that of the regular foods. Smaller serving sizes may be being presented on “diet/light” foods in order to report lower energy values and on similar foods to show non-existent differences in energy values. These results point to the importance of standardizing serving size information on food labels so that consumers have access to clear and accurate information about food products.Originality/value– This was the first census-type study to analyse the serving size information of dairy products at a supermarket of one of the ten largest supermarket chains in Brazil. This work extends the scope of current food labelling and contributes to the discussion about how nutrition labelling has been presented to Brazilian consumers and its possible consequences for food choices and the guarantee of consumer rights.
Responsible food marketing and standardisation: an exploratory study
Authors: Cairns Georgina , De Andrade Marisa , Landon Jane 
Published: July 2016

Purpose– The purpose of this paper is to explore the feasibility and utility of developing an independently defined and accredited benchmark standard for responsible food marketing. To identify provisional evidence and insights on factors likely to be critical to its successful development and its capacity to strengthen the effectiveness of responsible food marketing policy.Design/methodology/approach– Desk-based cross-policy domain case study.Findings– There is promising evidence that the development and deployment of an evidence-based, independently defined and verified responsible food marketing standard is feasible. Provisional findings on factors critical to the development of an effective standard and strategically significant evidence gaps are presented as insights in support of future food marketing policy and research planning.Research limitations/implications– Further investigation of these preliminary findings is required.Practical implications– The study has provisionally identified an innovative intervention with the potential to strengthen statutory, voluntary and internationally coordinated food marketing control policy approaches.Originality/value– This is the first report of research into the potential for an independent benchmark standard to advance and strengthen responsible food marketing policy goals.
Consumer trust in organic milk of different brands: the role of Chinese organic label
Authors: Yin Shijiu , Chen Mo , Chen Yusheng , Xu Yingjun , Zou Zongsen , Wang Yiqin 
Published: July 2016

Purpose
– Organic certification system became important means to restore consumer confidence in China. The purpose of this paper is to focus on consumer trust in organic milk of different brands and its influencing factors.

Design/methodology/approach
– The data were collected from 876 randomly selected consumers in Shandong Province, China. And an ordered logistic model was established to analyze influencing factors of consumer trust.

Findings
– Chinese consumers generally lack trust in organic milk. Consumer trust for different brands of organic milk was different, and was not high in general. Various factors, namely, age, education years, food safety awareness, evaluation of government regulation policy, evaluation of organic milk price, and purchase convenience, have a significant impact on consumer trust. Factors, such as income, environmental protection consciousness, and risk consciousness, are not significant.

Originality/value
– This research is of academic value and of value to policy makers and suppliers. Government should promote institutional arrangement and strengthening supervision in production, certification, and circulation of organic products. Organic suppliers should implement reliable marketing strategy, such as correct pricing, and build a more extensive and convenient distribution network.